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1,826 terms

Exam 1 - Campbell Biology Chapters 1-7

STUDY
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Autotrophs
Are producers of the biosphere
Autotrophs
Produce their own food
Autotrophs
Supply food for global ecosystem
Photoautotrophs
use light energy to produce organic molecules
Photoautotrophs
Plants, algae, and photosynthetic bacteria.
Chloroplast
Double-layered organelle for photosynthesis. Has inner and outer membranes.
Stroma
Fluid enclosed by inner membrane
Thylakoids
Suspended in stroma, interconnected sacs, stacked in grana, contain chlorophylls (green pigments)
Photosynthesis
Makes sugar and O2 from CO2 and H2O
Calvin cycle
Synthesis part
Calvin Cycle
Occurs in stroma of Chloroplasts
Calvin Cycle
Produces sugar molecules from CO2 , ATP and NADPH
Calvin Cycle
Light energy is not necessary
Thylakoid membrane
Where do the Light reactions occur?
Light Reactions
Convert light energy to chemical energy: ATP and NAPH ( high energy intermediate)
red, orange, yellow, green, blue, indigo, violet
ROYGBIV is an abbreviation for what colors.
350-750 NM
Visible light range is?
750 NM
Low energy end = long wave length is what number of wavelength?
350 NM
High energy end = short wave length is what number of wavelength?
Absorption
Light energy can be used.
Transmittance
light penetrates through object=color we see; energy NOT used.
Reflection
Light bounces off object=color we see; energy NOT used.
Pigments
molecules that absorb light
Thylakoids
several pigments are built into _______ membrane?
Chlorophyll a
Reflects green light, absorbs blue-violet and red lights. Participates directly in light reactions
Chlorophyll b
Reflects yellow- green light, absorbs blue and orange lights. Conveys absorbed energy to Chlorophyll a.
Carotenoids
Reflects yellow-orange light, absorb blue-green light. May pass energy to chlorophyll a
Photosystems
When pigment molecule absorbs a photon(solar energy). An electron is raised from ground state to excited state in what systems?
Ground state
an electron that is stable with low energy is at what state?
Excited state
an electron that is unstable with high energy is at what state?
Excited
An ________ electron rapidly drops back to ground state which releases heat
Fluorescent
Some pigments may also emit _______light.
Photosystems
Includes several light harvesting complexes containing: chlorophyll, proteins and carotenoids
reaction
Photosystems include a __________ center that includes the chlorophyll A molecule and the primary electron acceptor
Chlorophyll a
A reaction center always contains what?
Photosystem 2
P680
Pigments
Absorbs photons
Photosystem 1
Delivers the Electron to the NADP+
Photosystem 1
P700
Calvin Cycle
Input is carbon from CO2, NADPH and ATP.
Photosystems
these are used in light reactions
GAL
Most plants produce _____ in Calvin Cycle.
C3 plants
soybean, oats, wheat, rice
C3
When weather is hot and dry, ________plant leaves close their stomata to conserve water. But CO2 entering plants is also decreased (plant yields are decreased).
C4
When its hot and dry in _______ plants, CO2 is made into 4-carbon molecule in one cell type. Stomata are closed to conserve water. Then CO2 is released in another cell for Calvin Cycle to make sugar.
Photosynthesis
Plants make sugar through what process?
Light reactions
NADPH and ATP are produced during the _________
Thylakoid membrane
The location of the light reactions
ATP synthase
H+ flows through the ________ to create ATP
Calvin Cycle
GAL is produced in stroma (the liquid in the middle)
Global Warming
Greenhouse gases-water vapor, CO2, methane has to do with what?
Greenhouse effect
greenhouse gases can trap warm air around Earth more than usual the is called?
Global Warming
CO2 has increased 40% since 1850, causing what
Global Warming
Polar ice melting, extreme weather, rising sea levels, droughts all have to do with what?
Photosynthesis
This can reduce CO2 and global warming.
C6 H12 O6
Glucose's chemical formula
Rubisco
Enzyme vital to the success of the Calvin Cycle
RuBP
Substrate of Rubisco
electrons
The reduction and oxidation of molecules is a way to transport what?
leaf
the organ in which photosynthesis occurs
stoma
CO2 enters, O2 leaves
O2
___ is the bi-product of the light reactions
________ is the first to lose an electron in light reactions
Photosystem 1
hydrogen carrier
NADP
number of PGAL's devoted toward the regeneration of RuBP
Five
organ of photosynthesis
leaf
organelle of photosythesis
chloroplast
smallest unit of life
photon
pigment vital to photosynthesis
chlorophyll A
the only pigment that can "shoot" electrons
chlorophyll A
process in which water is split into hydroge and oxygen
photolysis
stacks of thylakoids
grana
chloroplasts are concentrated in the cells of the ________
palisades or mesophyll
willow tree experiment
Helmont
consume other plants or animals or decompse organic material
heterotrophs
selective permeability
a property of biological membranes, which includes the plasma membrane, that allows some substance to cross them more easily than others
cell membrane
membrane at the boundary of a cell that has a phospholipid bilayer that controls movement of molecules into and out of the cell; proteins are embedded into the phospholipid bilayer
amphipathic molecule
a molecule in which one side is hydrophobic and the other side is hydrophilic, as in phospholipids
fluid mosaic model
the current model of cell membrane structure that states that proteins are attached to/embedded in the fluid matrix of a phospholipid bilayer like a collage
10^7 (times per second)
speed of phospholipids' lateral movement within the membrane; flip-flopping across membrane is rare b/c of hydrophillic/phobic parts (~once per month)
fluid
a membrane in a higher temperature is more ______; a membrane that is unsaturated is also more _______. (vs. colder temperatures/saturation making the membrane more solid)
cholesterol
the steroid that is a "temperature buffer" for the membrane, lowering the temperature needed for it to solidify and making it less fluid at high temperatures
integral protein
membrane protein that penetrates the hydrophobic core of the lipid bilayer
transmembrane protein
integral protein that span the membrane
peripheral protein
membrane protein that are not embedded in the lipid bilayer but are bound to the surface of the membrane
major protein functions (in the plasma membrane)
1. transport 2. enzymatic activity 3. signal transduction 4. cell-cell recognition 5. intercellular joining 6. attachment to the cytoskeleton and extracellular matrix
transport
one of the six major protein functions in the membrane; involves being a hydrophillic channel, a shuttle for substances, or a pump
enzymatic activity
one of the six major protein functions in the membrane; involves being a receptor/having an active site
signal transduction
one of the six major protein functions in the membrane; occurs when an external messenger fits and causes the protein to change shape and relay a message into the inside of the cell
cell-cell recognition
one of the six major protein functions in the membrane; where cells recognize other cells by binding to surface molecules, often carbohydrates (glycoproteins); short-lived
intracellular joining
one of the six major protein functions in the membrane; where proteins of adjacent cells bind together in junctions; long-lasting
attachment (to the cytoskeleton and ECM)
one of the six major protein functions in the membrane; binding to elements of cytoskeleton to maintain cell shape, stabilize locations of certain proteins, and coordinate cellular changes
glycolipids
membrane carbohydrates that are covalently bonded to lipids
glycoproteins
membrane carbohydrates that are covalently bonded to proteins
supramolecule structure
many molecules ordered into a higher level of organization
transport protein
protein that allows passage of hydrophilic substances cross the cell membrane (because they can avoid contact with the lipid bilayer)
channel protein
a type of transport protein that has a hydrophilic channel
aquaporin
the channel protein that facilitates the passage of water through through certain cell membranes
carrier protein
a type of transport protein that binds to molecules in receptors and change shape to shuttle them across the membrane
diffusion
the movement of molecules of any substance so that they spread out evenly into the available space
concentration gradient
diffusing from where it is more concentrated to where it is less concentrated is diffusing down a ______ ______
passive transport
diffusion of a substance across a membrane where the cell does not require energy to do so; because concentration gradient has potential energy
osmosis
the diffusion of water across a selectively permeable membrane
tonicity
the ability of a surrounding solution to cause a cell to gain or lose water, depends on concentration of solutes that cannot cross inside/outside the cell
isotonic solution
a solution with the same rate of diffusion in both directions across a cell membrane; stable
hypertonic solution
a solution in which there more solutes outside the cell, causing the water to rush out the cell, making it shivel; this environment causes problems for organisms
hypotonic solution
a solution in which there are less solutes outside a cell, causing water to enter faster than it leaves, making it lyse (burst); this environment causes problems for organisms
osmoregulation
control of solute concentrations and water balance;
ex/ paramecium with a contractile vacuole
turgid
being very firm, the healthy state for most plant cells, occurs in a hypotonic solution when the cell swells until the cell wall opposes it
flaccid
being limp, occurs when a plant's cell and its surroundings are isotonic
plasmolysis
a phenomenon in a hypertonic environment when plant cells lose water and shrink and the plasma membrane pulls away from the wall
facilitated diffusion
diffusion in which transport proteins (like channel and carrier proteins) help speed the passive movement of molecules across the plasma membrane; no energy needed
ion channels
channel proteins that transport ions
gated channels
ion channels that open or close in response to a stimulus
active transport
the movement of solutes against their concentration gradients (low to high) by carrier proteins; needs energy/ATP; allows cells to maintain concentration different from surroundings
sodium-potassium pump
active transport system. 1) 3 Na+ binds to protein 2) ATP's phosphate for energy 3) Na+ released outside because of new shape 4) 2 K+ binds and releases phosphate from ATP 5) new protein shape 6) K+ is releasted again, ready for Na+
voltage
electrical potential energy, a separation of opposite charges
membrane potential
the voltage difference across a membrane, created by differences in the distribution of positive (outside) and negative (inside) ions; important for nerve cell/organ communication
70 mV
resting membrane potential (inside of cell is negative compared to outside)
electrochemical gradient
the diffusion gradient of an ion driven by a chemical force (the concentration gradient) and an electrical force (effect of membrane potential)
electrogenic pump
transport protein that generates voltage across a membrane
ex/ sodium-potassium pump in animals (net transfer of one positive charge)
proton pump
electrogenic pump of plants, fungi, and bacteria which actively transports hydrogen ions out of the cell; powered by ATP
cotransport
when a single ATP-powered pump that transports a solute indirectly drives the active transport of another solute
ex/ plant cells uses H+ from proton pumps to actively transport sucrose against gradient
exocytosis
a process where transport vesicles migrate to the membrane, fuse with it, and release their contents to the outside of the cell
endocytosis
the process where the cell takes in macromolecules by forming vesicles from the plasma membrane; three types: phagocytosis, pinocytosis, and receptor-mediated
phagocytosis
a type of endocytosis where the cell engulfs a particle with pseudopodia and packages it within a food vacuole
pinocytosis
a type of endocytosis where the cell "gulps" droplets of extracellular fluid into tiny vesicles for the substances dissolved in the droplets
receptor-mediated (endocytosis)
a type of endocytosis where ligands bind to receptors on the membrane and trigger vesicle formation (coated pits → vesicles)
ligands
a term for any molecule that binds specifically to a receptor site on another molecule
ecology
the study of how organisms interact with their environment (Ch. 50)
abiotic
nonliving (Ch. 50)
biotic
pertaining to the living organisms of the environment (Ch. 50)
biosphere
the entire portion of Earth inhabited by life: the sum of all the planet's ecosystems (Ch. 50)
precautionary principle
a guiding principle in making decisions about the environment, cautioning to consider carefully the potential consequences of actions (Ch. 50)
dispersal
the distribution of individuals within geographic population boundaries (Ch. 50)
macroclimate
large-scale variations in climate; the climate of an entire region (Ch. 50)
microclimate
very fine scale variations of climate, such as the specific climatic conditions underneath a log (Ch. 50)
detritus
dead organic matter (Ch. 50)
climograph
a plot of the temperature and precipitation in a particular region (Ch. 50)
canopy
the uppermost layer of vegetation in a terrestrial biome (Ch. 50)
ecotone
the transition from one type of habitat or ecosystem to another, such as the transition from a forest to a grassland (Ch. 50)
imprinting
a type of learned behavior with a significant innate component, acquired during a limited critical period (Ch. 51)
sensitive period
a limited phase in an individual animal's development when learning of particular behavior can take place (Ch. 51)
kinesis
a change in activity or turning rate in response to a stimulus (Ch. 51)
taxis
movement toward or away from a stimulus (Ch. 51)
pheromone
the upper part of the moss capsule (sporangium) often specialized for gradual spore discharge (Ch. 51)
habituation
a very simple type of learning that involves a loss of responsiveness to stimuli that convey little or no information (Ch. 51)
spatial learning
modification of behavior based on experience of the spatial structure of the environment (Ch. 51)
classical conditioning
a type of associative learning; the association of a normally irrelevant stimulus with a fixed behavioral response (Ch. 51)
operant conditioning
a type of associative learning in which an animal learns to associate one of its own behaviors with a reward or punishment and then tends to repeat or avoid that behavior; also called trial-and-error learning (Ch. 51)
foraging
behavior necessary to recognize, search for, capture, and consume food (Ch. 51)
promiscuous
a type of relationship in which mating occurs with no strong pair-bonds or lasting relationships (Ch. 51)
monogamous
a type of relationship in which one male mates with just one female (Ch. 51)
agonistic behavior
a type of behavior involving a contest of some kind that determines which competitor gains access to some resource, such as food or mates (Ch. 51)
altruism
behavior that reduces and individual's fitness while increasing the fitness of another individual (Ch. 51)
population
a localized group of individuals that belong to the same biological species (Ch. 52)
density
the number of individuals per unit area or volume (Ch. 52)
dispersion
the pattern of spacing among individuals withing geographic population boundaries (Ch. 52)
demography
the study of statistics relating to births and deaths in populations (Ch. 52)
big-bang reproduction
a life history in which adults have but a single reproductive opportunity to produce large numbers of offspring, such as the life history of the Pacific salmon; also known as semelparity (Ch. 52)
iteroparity
a life history in which adults produce large numbers of offspring over many years; also known as repeated reproduction (Ch. 52)
carrying capacity
the maximum population size that can be supported by the available resources (Ch. 52)
K-selection
the concept that in certain populations, life history is centered around producing relatively few offspring that have a good chance of survival (Ch. 52)
r-selection
the concept that in certain populations, a high reproductive rate is the chief determinant of life history (Ch. 52)
territoriality
a behavior in which an animal defends a bounded physical space against encroachment by other individuals, usually of its own species - territory defense may involve direct aggression or indirect mechanisms such as scent marking or singing. (Ch. 52)
metapopulation
a subdivided population of a single species (Ch. 52)
community
all the organisms that inhabit a particular area(Ch. 53)
(ecological) niche
the sum total of a species' use of the biotic and abiotic resources in its environment (Ch. 53)
resource partitioning
the division of environmental resources by coexisting species such that the niche of each species differs by one or more significant factor from the niches of all coexisting species (Ch. 53)
character displacement
the tendency for characteristics to be more divergent in sympatric populations of two species than in allopatric populations of the same two species (Ch. 53)
cryptic coloration
camouflage, making potential prey difficult to spot against its background.
aposematic colorization
the bright coloration of animals with effective physical or chemical defenses that acts as a warning to predators (Ch. 53)
parasitism
a symbiotic relationship in which the symbiont (parasite) benefits at the expense of the host (Ch. 53)
mutualism
a symbiotic relationship in which both participants benefit (Ch. 53)
commensalism
a symbiotic relationship in which one organism benefits but the other is neither helped nor harmed (Ch. 53)
species richness
the number of species in a biological community (Ch. 53)
trophic structures
the different feeding relationships in an ecosystem, which determine the route of energy flow and the pattern of chemical cycling (Ch. 53)
invasive species
a species that takes hold outside of its native range; usually introduced by humans
keystone species
a species that is not necessarily abundant in a community yet exerts strong control on community structure by the nature of its ecological role or niche (Ch. 53)
disturbance
a force that changes a biological community and usually removes organisms from it -disturbances, such as fire and storms, play pivotal roles in structuring many biological communities (Ch. 53)
ecosystem
all the organisms in a given area as well as the abiotic factors with which they interact; a community and its physical environment (Ch. 54)
primary producer
an autotroph, usually a photosynthetic organism - collectively, autotrophs make up the trophic level of an ecosystem that ultimately supports all other levels (Ch. 54)
detritivore
a consumer that derives its energy from nonliving organic material; a decomposer (Ch. 54)
gross primary production (GPP)
the total primary production of an ecosystem (Ch. 54)
net primary production (NPP)
the gross primary production of an ecosystem minus the energy used by the producers for respiration (Ch. 54)
critical load
the amount of added nutrient, usually nitrogen or phosphorus, that can be absorbed by plants without damaging ecosystem integrity (Ch. 54)
biological magnification
a trophic process in which retained substances become more concentrated with each link in the food chain (Ch. 54)
endangered species
a species that is in danger of extinction throughout all or a significant portion of its range (Ch. 55)
threatened species
a species that is considered likely to become endangered in the foreseeable future (Ch. 55)
introduced species
a species moved by humans from its native location to a new geographic region; also called an exotic species (Ch. 55)
extinction vortex
a downward population spiral in which positive-feedback loops of inbreeding and genetic drift cause a small population to shrink and, unless reversed, become extinct (Ch. 55)
movement corridor
a series of small clumps or a narrow strip of quality habitat (usable by organisms) that connects otherwise isolated patches of quality habitat (Ch. 55)
biodiversity hot spot
a relatively small area with an exceptional concentration of endemic species and a large number of endangered and threatened species (Ch. 55)
bioremediation
the use of living organisms to detoxify and restore polluted and degraded ecosystems (Ch. 55)
biological augmentation
an approach to restoration ecology that uses organisms to add essential materials to a degraded ecosystem (Ch. 55)
actin
A globular protein that links into chains, two of which twist helically about each other, forming microfilaments (actin filaments) in muscle and other kinds of cells.
basal body
A eukaryotic cell structure consisting of a 9 + 0 arrangement of microtubule triplets. The basal body may organize the microtubule assembly of a cilium or flagellum and is structurally very similar to a centriole.
capsule
(1) A sticky layer that surrounds the cell wall of some prokaryotes, protecting the cell surface and sometimes helping to glue the cell to surfaces. (2) The sporangium of a bryophyte (moss, liverwort, or hornwort).
cell fractionation
The disruption of a cell and separation of its parts by centrifugation.
central vacuole
A membranous sac in a mature plant cell with diverse roles in reproduction, growth, and development.
centriole
A structure in the centrosome of an animal cell composed of a cylinder of microtubule triplets arranged in a 9 + 0 pattern. A centrosome has a pair of centrioles.
centrosome
Structure present in the cytoplasm of animal cells, important during cell division; functions as a microtubule-organizing center. A centrosome has two centrioles.
chloroplast
An organelle found in plants and phot osynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water.
chromatin
The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope.
chromosome
A cellular structure carrying genetic material, found in the nucleus of eukaryotic cells. Each chromosome consists of one very long DNA molecule and associated proteins. (A bacterial chromosome usually consists of a single circular DNA molecule and associated proteins. It is found in the nucleoid region, which is not membrane bounded.) See also chromatin.
cilium
A short cellular appendage containing microtubules. A motile cilium is specialized for locomotion and is formed from a core of nine outer doublet microtubules and two inner single microtubules (the "9 + 2" arrangement) ensheathed in an extension of the plasma membrane. A primary cilium is usually nonmotile and plays a sensory and signaling role; it lacks the two inner microtubules (the "9 + 0" arrangement).
collagen
A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom.
contractile vacuole
A membranous sac that helps move excess water out of certain freshwater protists.
crista
An infolding of the inner membrane of a mitochondrion that houses electron transport chains and molecules of the enzyme catalyzing the synthesis of ATP (ATP synthase).
cytoplasm
The contents of the cell, exclusive of the nucleus and bounded by the plasma membrane.
cytoplasmic streaming
A circular flow of cytoplasm, involving myosin and actin filaments, that speeds the distribution of materials within cells.
cytoskeleton
A network of microtubules, microfilaments, and intermediate filaments that branch throughout the cytoplasm and serve a variety of mechanical, transport, and signaling functions.
cytosol
The semifluid portion of the cytoplasm.
desmosome
A type of intercellular junction in animal cells that functions as a rivet.
dynein
In cilia and flagella, a large contractile protein extending from one microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in dynein shape that lead to bending of cilia and flagella.
electron microscope (EM)
A microscope that uses magnets to focus an electron beam on or through a specimen, resulting in resolving power a thousandfold greater than that of a light microscope. A transmission electron microscope (TEM) is used to study the internal structure of thin sections of cells. A scanning electron microscope (SEM) is used to study the fine details of cell surfaces.
endomembrane system
The collection of membranes inside and around a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles; includes the smooth and rough endoplasmic reticulum, the Golgi apparatus, lysosomes, and vacuoles.
endoplasmic reticulum (ER)
An extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome-studded (rough) and ribosome-free (smooth) regions.
eukaryotic cell
A type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles. Organisms with eukaryotic cells (protists, plants, fungi, and animals) are called eukaryotes.
extracellular matrix (ECM)
The substance in which animal cells are embedded, consisting of protein and polysaccharides synthesized and secreted by cells.
fibronectin
A glycoprotein that helps animal cells attach to the extracellular matrix.
flagellum
A long cellular appendage specialized for locomotion. Like motile cilia, eukaryotic flagella have a core with nine outer doublet microtubules and two inner single microtubules ensheathed in an extension of the plasma membrane. Prokaryotic flagella have a different structure.
food vacuole
A membranous sac formed by phagocytosis of microorganisms or particles to be used as food by the cell.
gap junction
A type of intercellular junction in animals that allows the passage of materials between cells.
glycoprotein
A protein with one or more carbohydrates covalently attached to it.
Golgi apparatus
An organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum and synthesize some products, notably noncellulose carbohydrates.
granum
A stack of membrane-bounded thylakoids in the chloroplast. Grana function in the light reactions of photosynthesis.
integrin
in animal cells, a transmembrane receptor protein that interconnects the extracellular matrix and the cytoskeleton.
intermediate filament
A component of the cytoskeleton that includes filaments intermediate in size between microtubules and microfilaments.
light microscope (LM)
An optical instrument with lenses that refract (bend) visible light to magnify images of specimens.
lysosome
A membrane-enclosed sac of hydrolytic enzymes found in the cytoplasm of animal cells and some protists.
microfilament
A cable composed of actin proteins in the cytoplasm of almost every eukaryotic cell, making up part of the cytoskeleton and acting alone or with myosin to cause cell contraction; also known as an actin filament.
microtubule
A hollow rod composed of tubulin proteins that make up part of the cytoskeleton in all eukaryotic cells and is found in cilia and flagella.
middle lamella
In plants, a thin layer of adhesive extracellular material, primarily pectins, found between the primary walls of adjacent young cells.
mitochondrial matrix
The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the citric acid cycle.
mitochondrion
An organelle in eukaryotic cells that serves as the site of cellular respiration.
motor protein
A protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.
nuclear envelope
The double membrane in a eukaryotic cell that encloses the nucleus, separating it from the cytoplasm.
nuclear lamina
A netlike array of protein filaments lining the inner surface of the nuclear envelope; it helps maintain the shape of the nucleus.
nucleoid
A dense region of DNA in a prokaryotic cell.
nucleolus
A specialized structure in the nucleus, consisting of chromatin regions containing ribosomal RNA genes along with ribosomal proteins imported from the cytoplasmic site of rRNA synthesis and ribosomal subunit assembly. See also ribosome.
nucleus
(1) An atom's central core, containing protons and neutrons. (2) The chromosome-containing organelle of a eukaryotic cell. (3) A cluster of neurons.
organelle
of several membrane-enclosed structures with specialized functions, suspended in the cytosol of eukaryotic cells.
peroxisome
An organelle containing enzymes that transfer hydrogen (H2) from various substrates to oxygen (O2), producing and then degrading hydrogen peroxide (H2O2).
phagocytosis
A type of endocytosis in which large particulate substances are taken up by a cell. It is carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils, and dendritic cells).
plasma membrane
The membrane at the boundary of every cell that acts as a selective barrier, regulating the cell's chemical composition.
plasmodesma
An open channel in the cell wall of a plant through which strands of cytosol connect from an adjacent cell.
plastid
One of a family of closely related organelles that includes chloroplasts, chromoplasts, and amyloplasts (leucoplasts). Plastids are found in cells of photosynthetic organisms.
primary cell wall
In plants, a relatively thin and flexible layer first secreted by a young cell.
prokaryotic cell
A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles.
proteoglycan
A glycoprotein consisting of a small core protein with many carbohydrate chains attached, found in the extracellular matrix of animal cells. A [] may consist of up to 95% carbohydrate.
pseudopodium
A cellular extension of amoeboid cells used in moving and feeding.
ribosomal RNA (rRNA)
The most abundant type of RNA, which together with proteins makes up ribosomes.
ribosome
A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large and a small subunit. In eukaryotic cells, each subunit is assembled in the nucleolus. See also nucleolus.
rough ER
That portion of the endoplasmic reticulum studded with ribosomes.
scanning electron microscope (SEM)
A microscope that uses an electron beam to scan the surface of a sample to study details of its topography.
secondary cell wall
In plants, a strong and durable matrix often deposited in several laminated layers for cell protection and support.
smooth ER
That portion of the endoplasmic reticulum that is free of ribosomes.
stroma
Within the chloroplast, the dense fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water.
thylakoid
A flattened membranous sac inside a chloroplast. Thylakoids exist in an interconnected system in the chloroplast and contain the molecular "machinery" used to convert light energy to chemical energy.
tight junction
A type of intercellular junction in animal cells that prevents the leakage of material between cells.
transmission electron microscope (TEM)
A microscope that passes an electron beam through very thin sections and is primarily used to study the internal ultrastructure of cells.
transport vesicle
A tiny membranous sac in a cell's cytoplasm carrying molecules produced by the cell.
vacuole
A membrane-bounded vesicle whose function varies in different kinds of cells.
vesicle
A sac made of membrane in the cytoplasm.
light microscopy
uses light to permit magnification and viewing of cellular structures up to 1000 times their natural size
scanning electron microscopy
A process that utilizes an electron beam to produce an image of the three-dimensional surface of biological samples
transmission electron microscopy
is used to study internal structures of cells
cell fractionation
technique in which cells are broken into pieces and the different cell parts are separated
cytosol
the aqueous part of the cytoplasm within which various particles and organelles are suspended
nucleoid
A dense region of DNA in a prokaryotic cell.
chromatin
long strands of DNA & proteins found in the eukaryotic cell nucleus; condense to form chromosomes
nucleus
The organelle that contains the DNA and controls the processes of the cell
nucleolus
located in the nucleus, Ribosomal RNA (rRNA) is synthesized from instructions in the DNA
nuclear envelope
double membrane perforated with pores that control the flow of materials in and out of the nucleus, encloses the nucleus, separating it contents from the cytoplasm
ribosomes
organelles made of protein and RNA that direct protein synthesis in the cytoplasm/cytosol & on the outside of the ER or the nuclear envelope
nuclear lamina
A netlike array of protein filaments that maintains the shape of the nucleus.
endoplasmic reticulum
an internal membrane system in which components of cell membrane and some proteins are constructed. 2 distinct regions Smooth ER, Rough ER
rough ER
Secrete proteins, glycoproteins (proteins covalently bonded to carbohydrates, Distributes transport vesicles, proteins surrounded by membranes, is a membrane factory for the cell
smooth ER
Metabolic processes: Synthesis of lipids, Metabolism of carbohydrates, Detoxification of drugs & poisons, Storage of calcium ions
glycoproteins
proteins that have carbohydrates covalently bonded to them
vesicles
small membrane sacs that specialize in moving products into, out of, and within a cell
golgi apparatus
Consist of flattened membranous sac called cisternae. Functions: Modifies products of the ER, Manufactures certain macromolecules, Sorts & packages materials into transport
lysosome
Membranous sac of hydrolytic enzymes that can digest macromolecules. Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides & nucleic acids. Work best in the acidic environment inside the lysosome. Some types can engulf another cell by phagocytosis: this forms a food vacuole
phagocytosis
process in which extensions of cytoplasm surround and engulf large particles and take them into the cell
food vacuole
A membranous sac formed by phagocytosis
contractile vacuole
saclike organelles that expand to collect excess water and contract to squeeze the water out of the cell. found in many freshwater protist
central vacuole
A membranous sac in a mature plant cell. holds organic compunds & water
mitochondria
Powerhouse of the cell, organelle that is the site of cellualr respiration, metabolic process that uses oxygen to generate ATP (energy) production
chloroplast
a structure in the cells of plants and algea, are the site for photosynthesis. structures include thylakoid, stacked to form a granum, stroma
endosymbiont theory
mitochondria and plastids, including chloroplasts, originated as prokaryotic cells engulfed by an ancestral eukaryotic cell. The engulfed cell and its host cell then evolved into a single organism.
mitochondrial matrix
inner membrane of the cristae. some metabolic steps of cellular respiration are catalyzed in this membrane
cristae
repsent a large surface area for enzymes that synthesis of ATP.
thylakoids
A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy.
grana
stacked portion of the thylakoid membrane in the chloroplast. Grana function in the light reactions of photosynthesis
stroma
fluid surrounding the thylakoid membrane. contains the chloroplast DNA & ribosomes as well as many enzymes
plastids
organelles that are surrounded by a double membrane and contain their own DNA
peroxisomes
are oxidative organelles. Contain oxidase enzymes that detoxify alcohol, hydrogen peroxide, and other harmful chemicals. produce hydrogen peroxide and convert it to water
cytoskeleton
a microscopic network of actin filaments and microtubules in the cytoplasm of many living cells that gives the cell shape and coherence
motor proteins
a protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.
microtubules
are hollow rods, thickest of the 3 compnents of the cytoskeleton. functions: shaping the cell (compression-resistance "girders"), cell motility (cilia & flagella), separating chromosomes during cell division, organelle movement
microfilaments
also called actin filaments, are the thinnest components of the cytoskeleton. are solid rods, form 3-D network called CORTEX. main functions: maintenance of cell shape (tension -bearing element) changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility(as in pseudopodia) cell division(cleavage furrow formation
intermediate filaments
are fibers with a diameters in a middle range of the cytoskeleton. are more permanent. Main function: maintenance of cell shape (tension-bearing elements) anchoring of nucleus & certain organelles, formation of nuclear lamina,
centrosome
Structure present in the cytoplasm of animal cells, important during cell division; mictrotubules grow out from a centrosome near the nucleus. A centrosome has two centrioles.
centrioles
One of two tiny structures located in the cytoplasm of animal cells near the nuclear envelope; the centrosome has a pair of centrioles, each with 9 triplets of microtubles arrange in a ring
cilia
short, hair-like structures made of microtubules that enable movement of cells or movement of materials outside a cell
flagella
whiplike tails found in one-celled organisms to aid in movement
cytoplasmic streaming
A circular flow of cytoplasm, involving myosin and actin filaments, that speeds the distribution of materials within cells.
cell wall
strong supporting layer of cellulose or chitin around the cell membrane in plants, algae, and some bacteria
middle lamina
A thin layer of adhesive extracellular material, primarily pectins, found between the primary walls of adjacent young plant cells.
primary cell wall
A relatively thin and flexable cell wall furthest outside that is first secreted by a plant cell
secondary cell wall
Added between the plasma membrane and the primary cell wall, a strong and durable matrix often deposited in several laminated layers for plant cell protection and support
extracellular matrix
The substance in which animal tissue cells are embedded, consisting of protein and polysaccharides.
magnification
the ration of an object's image size to its real size
resolution
the measure of the clarity of the image or the minimum distance of 2 distinguishable points
contrast
accentuates differences in parts of sample
basic features of all cells
plasma membrane, semifluid substance called cytosol/ cytoplasm, chromosomes(carry genes), ribosomes(make proteins)
plasma membrane
selective barrier around the cell (b) allows passage of enough oxygen, nutrients & wastes to service entire cell
Nuclear matrix
a framework of proteins fibers extending throughout the nuclear interior
Endomembrane system
Nuclear envelope, Endoplasmic reticulum, Golgi apparatus, Vrious kinds of vesicles & vacuoles, Plasma membrane
Plasmodesmata
(pores, only found in plant cell) are channels that perforate plant cell walls. passes through water & small solutes(& some proteins & RNA)
cell junctions
Plasmodesmata, tight junctions, desmosomes, gap junctions
tight junctions
membranes of neighboring cells are pressed together, preventing leakage of extra cellular fluid
desmosomes
(anchoring junctions) fastens cells together into strong sheets
gap junctions
(communicating junctions) provide cytoplasmic channels between adjacent cells
extracellular structures
cell walls of plants, the extracellular matrix (ECM) of animals, intercellular junctions
cell walls of plants
is an extracellular structure that distinguishes plant cells from animal cells.
plant cell walls may have multiple layers
primary cell wall, middle lamella, secondary cell wall
basal body
anchors the cilium or flagellum
dynein
drives the bending movement of a cilium or flagellum
actin
A globular protein that links into chains, two of which twist helically about each other, forming microfilaments (actin filaments) in muscle and other kinds of cells.
basal body
A eukaryotic cell structure consisting of a 9 + 0 arrangement of microtubule triplets. The basal body may organize the microtubule assembly of a cilium or flagellum and is structurally very similar to a centriole.
capsule
(1) A sticky layer that surrounds the cell wall of some prokaryotes, protecting the cell surface and sometimes helping to glue the cell to surfaces. (2) The sporangium of a bryophyte (moss, liverwort, or hornwort).
cell fractionation
The disruption of a cell and separation of its parts by centrifugation.
central vacuole
A membranous sac in a mature plant cell with diverse roles in reproduction, growth, and development.
centriole
A structure in the centrosome of an animal cell composed of a cylinder of microtubule triplets arranged in a 9 + 0 pattern. A centrosome has a pair of centrioles.
centrosome
Structure present in the cytoplasm of animal cells, important during cell division; functions as a microtubule-organizing center. A centrosome has two centrioles.
chloroplast
An organelle found in plants and phot osynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water.
chromatin
The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope.
chromosome
A cellular structure carrying genetic material, found in the nucleus of eukaryotic cells. Each chromosome consists of one very long DNA molecule and associated proteins. (A bacterial chromosome usually consists of a single circular DNA molecule and associated proteins. It is found in the nucleoid region, which is not membrane bounded.) See also chromatin.
cilium
A short cellular appendage containing microtubules. A motile cilium is specialized for locomotion and is formed from a core of nine outer doublet microtubules and two inner single microtubules (the "9 + 2" arrangement) ensheathed in an extension of the plasma membrane. A primary cilium is usually nonmotile and plays a sensory and signaling role; it lacks the two inner microtubules (the "9 + 0" arrangement).
collagen
A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom.
contractile vacuole
A membranous sac that helps move excess water out of certain freshwater protists.
crista
An infolding of the inner membrane of a mitochondrion that houses electron transport chains and molecules of the enzyme catalyzing the synthesis of ATP (ATP synthase).
cytoplasm
The contents of the cell, exclusive of the nucleus and bounded by the plasma membrane.
cytoplasmic streaming
A circular flow of cytoplasm, involving myosin and actin filaments, that speeds the distribution of materials within cells.
cytoskeleton
A network of microtubules, microfilaments, and intermediate filaments that branch throughout the cytoplasm and serve a variety of mechanical, transport, and signaling functions.
cytosol
The semifluid portion of the cytoplasm.
desmosome
A type of intercellular junction in animal cells that functions as a rivet.
dynein
In cilia and flagella, a large contractile protein extending from one microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in dynein shape that lead to bending of cilia and flagella.
electron microscope (EM)
A microscope that uses magnets to focus an electron beam on or through a specimen, resulting in resolving power a thousandfold greater than that of a light microscope. A transmission electron microscope (TEM) is used to study the internal structure of thin sections of cells. A scanning electron microscope (SEM) is used to study the fine details of cell surfaces.
endomembrane system
The collection of membranes inside and around a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles; includes the smooth and rough endoplasmic reticulum, the Golgi apparatus, lysosomes, and vacuoles.
endoplasmic reticulum (ER)
An extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome-studded (rough) and ribosome-free (smooth) regions.
eukaryotic cell
A type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles. Organisms with eukaryotic cells (protists, plants, fungi, and animals) are called eukaryotes.
extracellular matrix (ECM)
The substance in which animal cells are embedded, consisting of protein and polysaccharides synthesized and secreted by cells.
fibronectin
A glycoprotein that helps animal cells attach to the extracellular matrix.
flagellum
A long cellular appendage specialized for locomotion. Like motile cilia, eukaryotic flagella have a core with nine outer doublet microtubules and two inner single microtubules ensheathed in an extension of the plasma membrane. Prokaryotic flagella have a different structure.
food vacuole
A membranous sac formed by phagocytosis of microorganisms or particles to be used as food by the cell.
gap junction
A type of intercellular junction in animals that allows the passage of materials between cells.
glycoprotein
A protein with one or more carbohydrates covalently attached to it.
Golgi apparatus
An organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum and synthesize some products, notably noncellulose carbohydrates.
granum
A stack of membrane-bounded thylakoids in the chloroplast. Grana function in the light reactions of photosynthesis.
integrin
in animal cells, a transmembrane receptor protein that interconnects the extracellular matrix and the cytoskeleton.
intermediate filament
A component of the cytoskeleton that includes filaments intermediate in size between microtubules and microfilaments.
light microscope (LM)
An optical instrument with lenses that refract (bend) visible light to magnify images of specimens.
lysosome
A membrane-enclosed sac of hydrolytic enzymes found in the cytoplasm of animal cells and some protists.
microfilament
A cable composed of actin proteins in the cytoplasm of almost every eukaryotic cell, making up part of the cytoskeleton and acting alone or with myosin to cause cell contraction; also known as an actin filament.
microtubule
A hollow rod composed of tubulin proteins that make up part of the cytoskeleton in all eukaryotic cells and is found in cilia and flagella.
middle lamella
In plants, a thin layer of adhesive extracellular material, primarily pectins, found between the primary walls of adjacent young cells.
mitochondrial matrix
The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the citric acid cycle.
mitochondrion
An organelle in eukaryotic cells that serves as the site of cellular respiration.
motor protein
A protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.
nuclear envelope
The double membrane in a eukaryotic cell that encloses the nucleus, separating it from the cytoplasm.
nuclear lamina
A netlike array of protein filaments lining the inner surface of the nuclear envelope; it helps maintain the shape of the nucleus.
nucleoid
A dense region of DNA in a prokaryotic cell.
nucleolus
A specialized structure in the nucleus, consisting of chromatin regions containing ribosomal RNA genes along with ribosomal proteins imported from the cytoplasmic site of rRNA synthesis and ribosomal subunit assembly. See also ribosome.
nucleus
(1) An atom's central core, containing protons and neutrons. (2) The chromosome-containing organelle of a eukaryotic cell. (3) A cluster of neurons.
organelle
of several membrane-enclosed structures with specialized functions, suspended in the cytosol of eukaryotic cells.
peroxisome
An organelle containing enzymes that transfer hydrogen (H2) from various substrates to oxygen (O2), producing and then degrading hydrogen peroxide (H2O2).
phagocytosis
A type of endocytosis in which large particulate substances are taken up by a cell. It is carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils, and dendritic cells).
plasma membrane
The membrane at the boundary of every cell that acts as a selective barrier, regulating the cell's chemical composition.
plasmodesma
An open channel in the cell wall of a plant through which strands of cytosol connect from an adjacent cell.
plastid
One of a family of closely related organelles that includes chloroplasts, chromoplasts, and amyloplasts (leucoplasts). Plastids are found in cells of photosynthetic organisms.
primary cell wall
In plants, a relatively thin and flexible layer first secreted by a young cell.
prokaryotic cell
A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles.
proteoglycan
A glycoprotein consisting of a small core protein with many carbohydrate chains attached, found in the extracellular matrix of animal cells. A [] may consist of up to 95% carbohydrate.
pseudopodium
A cellular extension of amoeboid cells used in moving and feeding.
ribosomal RNA (rRNA)
The most abundant type of RNA, which together with proteins makes up ribosomes.
ribosome
A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large and a small subunit. In eukaryotic cells, each subunit is assembled in the nucleolus. See also nucleolus.
rough ER
That portion of the endoplasmic reticulum studded with ribosomes.
scanning electron microscope (SEM)
A microscope that uses an electron beam to scan the surface of a sample to study details of its topography.
secondary cell wall
In plants, a strong and durable matrix often deposited in several laminated layers for cell protection and support.
smooth ER
That portion of the endoplasmic reticulum that is free of ribosomes.
stroma
Within the chloroplast, the dense fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water.
thylakoid
A flattened membranous sac inside a chloroplast. Thylakoids exist in an interconnected system in the chloroplast and contain the molecular "machinery" used to convert light energy to chemical energy.
tight junction
A type of intercellular junction in animal cells that prevents the leakage of material between cells.
transmission electron microscope (TEM)
A microscope that passes an electron beam through very thin sections and is primarily used to study the internal ultrastructure of cells.
transport vesicle
A tiny membranous sac in a cell's cytoplasm carrying molecules produced by the cell.
vacuole
A membrane-bounded vesicle whose function varies in different kinds of cells.
vesicle
A sac made of membrane in the cytoplasm.
The Molecules of Life
carbohydrates, lipids, proteins, and nucleic acids.
Macromolecules
are the "Molecules of Life" we just talked about. They are: carbohydrates, proteins, and nucleic acids.
These are critically large molecules important for all living things.
Polymer
a long molecule consisting of many similar or identical building blocks linked by covalent bonds.
Monomers
the repeating units that serve as the building
blocks of a polymer.
The Synthesis and Breakdown of Polymers
Although each class of polymer is made up of a different type of monomer, the chemical mechanisms by which cells make and break down polymers are basically the same in all cases.
Enzymes
specialized macromolecules that speed up chemical reactions.
Dehydration Reaction
the loss of a water molecule when two molecules
are covalently bonded to each other.
Hydrolysis
a process that is essentially the reverse of the dehydration reaction.
Carbohydrates
are sugars and polymers of sugars.
Sugars
are monosaccharides. Some monosaccharides are: glucose and fructose.
Monosaccharides
are the simplest carbohydrates, and are generally molecular formulas that are some multiple of the unit CH20.
Disaccharides
consists of two monosaccharides joined
by a glycosidic linkage .
Glycosidic linkage
a covalent bond formed between two monosaccharides by a dehydration reaction.
Polysaccharides
are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages.
Starch
a polymer of glucose monomers, as granules within cellular structures known as plastids, which include chloroplasts.
Glycogen
a polymer of glucose that is like amylopectin but more extensively branched.
Cellulose
is a polysaccharide and a major component of the tough walls that enclose plant cells.
Chitin
the carbohydrate used by arthropods (insects, spiders, crustaceans, and related animals) to build their exoskeletons. (Above is a picture of the exoskeleton of a dragonfly, which is made of Chitin.)
Lipids
are macromolecuels as well. They share one important trait: they mix poorly, if at all, with
water.
Fat
Fats are not polymers, they are large molecules assembled from smaller molecules by dehydration reactions. A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids.
Fatty acid
has a long carbon skeleton, usually 16 or 18 carbo atoms in length. The carbon at one end of the skeleton is part of a carboxyl group, which is the functional group that gives this molecule its name.
Triacylglycerol
a fat that consists of three fatty acids linked to
one glycerol molecule.
Saturated Fatty Acid
a long carbon skeleton that has all possible spots for hydrogen to bond with carbon covalently, used up.
Unsaturated Fatty Acid
a long carbon skeleton that has all possible spots for hydrogen to bond with carbon covalently, not used up. In other words, hydrogen can still bond with carbon covalently.
Trans Fat
are unsaturated fats with "trans" double bonds.
Glycerol Molecule
or

H-C-C-C-H
/ | \
OH OH OH
Main 4 Polysaccharides to know
Cellulose, Starch, Glycogen, Chitin
Phospholipids
make up cell membranes and therefore are essential to all life of cells. Their molecular structure is similar to a fat molecule except, the glycerol has only two fatty acids attached to it rather than 3.
Steroids
lipids characterized by a carbon skeleton consisting of four fused rings.
Cholesterol
a crucial molecule in animals. It is a common component in animal cell membranes.
Catalyst
Chemical agents that selectively speed up chemical reactions without being consumed by the reaction.
Polypeptides
Polymers of amino acids.
Protein
a molecule that consists of one or more polypeptides, each folded and coiled into 3 specific dimensional structures.
Peptide bond
the resulting covalent bond after a dehydration reaction.
Denaturation
the causing of a protein to unravel and lose it native shape, which in turn makes it become biologically inactive.
Chaperonins
Protein molecules that assist in the proper folding of other proteins.
Genes
an amino acid sequence of a polypeptide programmed by a discrete unit of inheritance.
DNA
Deoxyribonucleic Acid
Polynucleotides
a monomer consisting of nucleotides.
Amino acids
there are 20 kinds of these enzymes, which are all unbranched polymers.
Organelles
the membrane enclosed structures within eukaryotic cells.
What are the four main molecules of life?
1) Carbohydrates, 2) Lipids, 3) Nucleic Acids, 4) Proteins
What are the building blocks of lipids?
Lipids are diverse, but the three largest are 1) fats made of glycerol and fatty acids, 2) Phospholipids (fatty acid, phosphate group), 3) steriods - hydrocarbon rings.
Which one is not a huge chain molecule?
Lipids are not really huge chain poymers.
What is a polymer?
Usually via dehydration synthesis, consists of many similar or identical building blocks called monomers. They are linked by covalent bonds.
What is dehydration synthesis?
Creation of polymers One side has a OH, another side has a -COOH. They create a covalent bond, and they byproduct is water. This requires energy.
What helps facilitate dehydration synthesis?
-Catalysts often help.
-reaction is often repeated, chain + polymer to make very long chains.
What is hydrolysis?
-Reverse of dehydration.
-Addition of water causes polymers to break.
-Hydrogen from the water attached to one monomer and hydroxyl attached to another. Polymer is broken.
This releases energy.
Which releases energy? Which requires energy? (Dehydration synthesis, hydrolysis)
-Dehydration synthesis - requires energy
-Hydrolysis - releases energy
Why are polymers very diverse?
-only from 40 - 50 common nomoers
-arrangement and lengths are endless (like an alphabet)
What are the building blocks of carbohydrates?
-carbs are polymers of sugars
What are the three groupings of sugars?
monosaccharides - simple sugars (one sugar)
Disaccharides - double sugars
Polysaccharides - complex sugars, multiple chains
What is a monosaccharide?
-One sugar
-formula of CH2O
-most common: glucose
What is an aldose?
-Monosaccharide made from aldehyde, -C=O at the end
What is a ketone?
-Monosaccharide made from ketone, -C=O in the middle
Is this an aldose or a ketose?
Ketose
Is this an aldose or ketose?
Aldose
What is the naming convention for sugars?
Size of carbon skeleton adds to the name. Three carbons - triose. Six carbons, hexose. 5 carbons - pentose.
-three are the most common
What is also another difference?
Some sugars differ in their spatial arrangement of their parts around an asymmetric carbon.
-Glucose and galactorse differ only in placement of parts around one asymmetric carbon (structural isomer)
In aqueous solutions, glucose forms
Rings
What are the two forms glucose?
Linear and Ring
Why are monosaccharides important?
-used as monomers to add to disaccharides and polysaccharides
-major nutrients for cells. Cellular respiration extract energy that starts with glucose.
What are disaccharides?
Disaccharides are double sugars joined by a covalent bond.
What are two monosaccharides joined by?
-Glycosidic linkages.
-OH ends in sugars, -OH + H creates water, then joins (from dehydration synthesis)
-Usually on the 1-2 carbons
-Or the 1-4 carbons
Sucrose is made from?
Glycosidic linkage between glucose and fructose.
What are polysaccharides
Macromolecules - few hundred to few thousand joined by glycosidic linkages
What are polysaccharides used for?
-Storage - store sugars for later use
-Structural - reinforce's organism structure
What polysaccharide dp plants make for storage?
Starch
-stored in plastids, stockpile of glucose.
-When it needs it, plant then hydrolyzes the bonds between glucose molecules.
-1-4 glycosidic linkages, causes helical polymer
What polysaccharide do animals make?
Glycogen
-lasts only a day in animals, needs to be replenished by food.
-1-4 glycosidic linkages, causes helical polymer
What is a structural polysaccharide in plants?
Cellulose - tough walls that enclose plant cells.
1-4 glycosidic linkages, but CH3OH swaps one on top of the other.
This causes a beta linkage, and structure is LINEAR.
-humans dont have the enzymes to break this down
What is an alpha glucose linkage? A Beta glucose linkage?
Is cellulose ever branched?
No
-They ar elayered one on top of the other by h - bonds.
-layers are called microfibrils
-This is the material that is strong in plants that allows them to hold their shape
What is a structural polysaccharide in animals?
chitin (in arthropods)
What are lipids?
-Diverse group hydrophobic molecules.
-Most of bodies are non polar hydrocarbons
What are the four largest groups of lipids?
1) fat
2) waxes
3) phospholipids
4) steroids
What are fats?
-made from condensation reaction -> glycerol molecule, three fatty acids.
-fatty acid is hydrocarbon skeleton, carboxyl on one end
-skeleton is why fat is hydrophobic.
Creation of fat via dehydration synthesis
-ester linkage beween H in hydroxyl in glycerol + OH in carboxyl in fatty acid
What is saturated fat?
-Saturated with H bonds
-No double bonds in hydrocarbon chain
-No kinks, all molecules pack well
-solid at room temperature.
-animal fat usually saturated
Why is saturated fat bad?
When ingesting, contributes to artherosclerosis
Needs very high temperatures to liquify
What is unsaturated fat?
-have one (unsaturated) or multiple (polyunsaturated) kinks in their hydrocarbon chains
-removal of one or more hydrogen
-kinks are CIS double conds
-liquid at room temperature
-oils
What is a trans double bond
There is a double bond but hydrogens are different sides.
same properties as saturated fat
even harder to break than saturated because harder to break
What is hydrogenization?
Technically break double bond in unsaturated fats by breaking double bond and adding H.
-makes shelf life longer
What happens to melting points with more saturation?
More saturation, higher melting point needed
More unsaturation (more kinks), lower melting point
Put melting points in order lowest to highest?
What are phospholipids?
-Another type of lipid
-head is hydrophilic, tail is hydrophobic
-In aqueous environment, bilayer is formed
What are the parts of a phospholipid?
-head is hydrophilic, alcohol + phosphate group, both polar
-tail is glycerol/hydrocarbon chain
Why are phospholipids important?
Cell membrane
What is a steroid?
Another lipid - made of carbon skeleton with four fused rings.
-components of cellular membranes
-hormone precursors
What are proteins?
Polymers created from same set of 20 amino acids
-also called polypeptides
What are some important examples of proteins?
Enzymes!
help regulate metabolism by acting as catalysts
What two groups are always attached to an amino acid?
-Carboxyl "tail" - c terminus
-amino "head" - n terminus
-Because base and acid, acts as natural buffer
Which part ofthe amino acid gives it its properties?
The R chain
What is the center carbon called?
It is the alpha carbon
What are the four taxonomies of amino acids?
Non polar, polar, electrically charged - acidic, electrically charged - basic
How are amino acids create to form a polypeptide?
When two amino acids are positioned so carboxyl is facing amino, condensation reaction occurs. Peptide bond is created (-COHN)
Why is protein structure important?
Three dminesional shape determines what the protein does.
What is protein confirmation?
folding of polypeptide, sometimes interaction with other polpeptides.
What is the primary level of structure?
-Determined by genetic instruction
-amino head, carboxyl tail
-unique sequence and order of amino acids
-maintained by covalent bonds
What is the secondary structure?
-alpha helix or beta pleated sheet (in certain areas of polypeptide chain, repeated coil or fold)
-Interactions between nonconsecutive amino acids
-are maintained by HYDROGEN BONDS
In secondary structure, where does hydrogen bonding happen?
Hydrogen bonding happens only in amino or carboxyl parts (in -COHN) peptide areas. NOT in side chains.
Which secondary structure is more stretched out?
-beta pleated sheet
-alpha helix is more smooshed together
What is tertiary structure?
Tertiary structure iare pleats and coils to have overall structure.
is it created by the folding of polypeptide chain and is due to interactions of side chains in the polypeptide.
What structures do most proteins stop at?
Tertiary
what causes tertiary structure?
Interaction between side chains in the polypeptide.
What kinds of things reinforce tertiary structure?
-hydrophobic interactions
-vander wals b/w non polar molecules
-ionic bonds between charged ends
0hydrogen bonds
-covalent bonds
-disulfide bonds
What is quarternary structure?
Fourth structure, interaction and structure of two or more polypeptide chains. Example is hemoglobin, made of four polypeptides.
Sickle cell anemia - overview
-One amino acid is replaced by another in primary structure.
-causes hemoglobin to crystallize, form a sickle cell shape
-they are sticky and tend to stick to each other, causing hemoglobin's ability to carry oxygen to be greatly reduced.
Sickle cell anemia - primary and secondary structure
in primary - only one out of long chain of amino acids replaced
secondary structure - causes exposed hydrophobic region
sickle cell anemia - tertiary structure, quarternary structure
tertiary structure - creates hydrophobic region, sticky areas
-stick to each other and create long chains
affects of sickle cell to red blood cell shape
sickle shaped blood cells
What denatures proteins?
change in pH, salt concentration, temperature, other environmental changes.
What helps proteins fold
Chaperonins, assist in keeping nascent protein in folding (keeps other things that would ruin folding away from baby protein).
What are nucleic acids?
-Basic structure of genes (DNA and RNA).
-stores and transmits hereditary information.
What is the subunit of a nucleic acid?
Nucleotides
What is DNA?
-Deoxyribonucleic acid
-double stranded
-made and used inside nucleus
-contains genome
-extremely long (millions of nucleotides)
What is RNA?
-ribonucleic acid
-single stranded
-made in nucleus
-but used outside of nucleus
-contains only a working copy of one or a few genes
-not as long as DNA
Structure difference: DNA vs RNA
Deoxyribose (missing oxygen) vs ribose
Different types of RNA
mRNA - messenger, brings nucleotide to ribosome
rRNA - physically part of ribosome, helps make protein
tRNA - brings each nucleic acid in chain to be attached
What is a nucleotide made up of?
(sugarphosphate backbone)
phosphate group
pentose sugar
nitrogenous base
What are different types of sugars?
Deoxyribose in DNA (lacks oxygen on second carbon in the ring)
ribose in RNA
What is a nucleoside?
Nitrogenous base + sugar
What are the different types of nitrogenous bases? In what order are they in?:
-Pyramidines - 6 ring carbon base - Cytosine, Thymine, Uracil
-Purines - 6 ring fused to 5 ring. Adenine and Guanine.
-DNA: GC AT
-RNA: GC AU
Which nitrogenous base has two rings?
purines
Where is phosphate group attached to?
5' carbon of the sugar.
What links two nucleotides together?
-Phosphodiester bonds
-creates sugar phosphate backbone
What is the interior of DNA/RNA?
stacked nitrogenous base.
In dna, linked by hydrogen bonds between GC/AT groups
Double helix is alwas
complimentary to its h bonded half
Another important nucleotide is
ATP
It is used in photosynthesis and cellular respiration
0main energy carrier in cells
How does ATP work
ATP has adenosine and is attached to three phosphates. It donates one o two phosphate to release energy to become ADP or AMP.
The molecular formula for glucose is C6H12O6. What owuld be the mlecular formula for a polymer made by linking ten glucose molecules together by dehydration synthesis?
C60H102O51 (done forget water molecules - 9 created)
In hydrolysis reaction, __ and in this process water is __
A polymer is brokein up into its consitutent monomers and water is consumed
which of the following is the major energy storage compound of plants seeds?
oils
Rank these molecules in the correct order by size, smallest to greatest
sucrose, water, glucose, protein
protein, sucrose, glucose, water
What is the difference between base pairing in RNA and DNA
base pairing between two strands of DNA can be thousands long, RNA is limited to short stretches of nucleotides.
RNA has urucil. DNA has thymine.
Which two functional groups are always present in a monosaccharide?
-carbonyl c=o
-hydroxyl -oh
Amylase beaks down
Starch
2 DNA strands are connected by what between the hydrogenous bases? Between the sugarphosphate backbones?
-b/w bases, hydrogen bonds in the cneter
-between backbones to form polynucleic acids, phosphodiester bonds
Omega 3 fatty acids are found in
nuts and certain oils
Protein denaturation
heat or other change in environment breaks down the h bonds and other weak bonds in tertiary structure. It causes protein to unravel No shape, no function.
What is a peptide bond?
-COHN, created when carboxyl group and amine group link via dehydration synthesis
fluid mosaic
Membranes are composed of
-a bilayer of phospholipids with
-embedded and attached proteins,
-in a structure biologists call a ________.
phospholipids; unsaturated; liquid
Many ______ are made from _____ fatty acids that have kinks in their tails. These kinks prevent phospholipids from packing tightly together, keeping them in _____ form.
cholesterol; stabilize; fluid
In animal cell membranes, _____ helps
-_____ membranes at warmer temperatures and
-keep the membrane _____ at lower temperatures.
phospholipid
the biological molecule that makes up the bulk of the cell membrane
5 membrane protein functions
transport
receptors
cell adhesion molecules
recognition proteins
communication proteins
What do membrane proteins do?
- maintain cell shape
- coordinate chages inside and outside
- rececptors for chemical messengers
-enzymatic activity
- cell-cell recognition
- intercellular junctions that attach cells to each other
selective permeability
Membranes may exhibit ________, allowing some substances to cross more easily than others.
spontaneously
Phospholipids _____ form a bilayer when mixed with water
Diffusion
______ is the tendency of particles to spread out evenly in an available space.
more; less
In diffusion, particles move from an area of ____ concentrated particles to an area where they are ____ concentrated.
concentration gradient
This moving from more to less concentration means that particles diffuse down their ________.
equilibrium
Eventually, the particles reach ________ where the concentration of particles is the same throughout.
passive transport
Diffusion across a cell membrane does not require energy, so it is called __________.
The concentration gradient itself represents potential energy for diffusion.
water
One of the most important substances that crosses membranes is ____.
osmosis
The diffusion of water across a selectively permeable membrane is called _____.
(5.4)
...
If a membrane permeable to water but not a solute separates two solutions with different concentrations of solute,
-water will cross the membrane,
-moving down its own concentration gradient,
-until the solute concentration on both sides is equal.
hypotonic
the solute concentration is lower outside the cell, water molecules move into the cell, and the cell will expand and may burst
(5.5)
hypertonic
the solute concentration is higher outside the cell, water molecules move out of the cell, and the cell will shrink
(5.5)
isotonic
having the same concentration of solutes, cell volume will not change
Tonicity
______ is a term that describes the ability of a solution to cause a cell to gain or lose water.
______ mostly depends on the concentration of a solute on both sides of the membrane.
osmoregulation
For an animal cell to survive in a hypotonic or hypertonic environment, it must engage in _______, the control of water balance.
...
The cell walls of plant cells, prokaryotes, and fungi make water balance issues somewhat different.
-The cell wall of a plant cell exerts pressure that prevents the cell from taking in too much water and bursting when placed in a hypotonic environment.
-But in a hypertonic environment, plant and animal cells both shrivel.
...
small non-polar molecules such as carbon dioxide, cholesterol, small lipids, sterols and steroid hormones can cross the plasma membrane easily - diffuse across the phospholip bilayer
facilitated diffusion
polar molecules, including water, ions (sodium, chloride, and hydrogen), sugar, amino acids (glucose, proteins, carbohydrates) cannot directly diffuse across the plasma membrane, they need a transport protein in a process called ________.
(5.6)
...
facilitated diffusion:
-does not require energy and
-relies on the concentration gradient.
aquaporin
The very rapid diffusion of water into and out of certain cells is made possible by a protein channel called an _______.
(5.6)
active transport
In _____, a cell
-must expend energy to
-move a solute against its concentration gradient.
(5.8)
Four main stages of active transport
5.8
1. Solute Binding
2. Phosphate Attaching
3. Transport
4. Protein Reversion
Types of Transport
...
Exocytosis (exo, outside)


5.9
_____ is used to export bulky molecules, such as proteins or polysaccharides.
Ex. when we cry, cells in our tear glands use ____ to export a salty solution containing proteins.

(5.9)
Endocytosis (endo, inside)



5.9
_____ is used to import substances useful to the livelihood of the cell.
Phagocytosis

(5.9)
_____ is the engulfment of a particle by wrapping cell membrane around it, forming a vacuole.
"cellular eating"
Pinocytosis

(5.9)
_____ is the same thing except that fluids are taken into small vesicles.
Receptor-mediated endocytosis

(5.9)
_____ uses receptors in a receptor-coated pit to interact with a specific protein, initiating the formation of a vesicle.
Kinetic


(5.10)
_____ energy is the energy of motion (or objects that are moving)
Potential

(5.10)
_____ energy is energy that matter possesses as a result of its location or structure. (ex. ball at top of hill which is not moving, it has a lot of _____ energy. If you then kick the ball and it starts rolling down the hill, the _____ energy gets converted to kinetic energy. We can then put the _____ energy back into the ball if we carry it back up the hill.)
Another example of potential energy

(5.10)
the energy in the chemical bonds that hold atoms together in a molecule. If we take a large molecule and start breaking its covalent bonds apart, we are releasing potental energy. The energy in fuel molecules has a lot of _____ energy in it. It has a combustion engine which will burn gasoline in order for the car to move. Heat is given off as a result of energy and is not useful energy to cells or this vehicle.
Energy example in a living system

(5.10)
in the center is a cell which will take in a fuel molecule (glucose and oxygen on the left). Glucose is the major fuel source for cells and is used to make ATP. Glucose and oxygen are coming together in a metabolic pathway called cellular respiration. The products we get are carbon dioxide and water (right side) (same products from burning gasoline in the vehicle example). The cell will take the potential energy in the covalent bond of the glucose molecule and convert that into the energy stored in ATP molecules. The energy used in ATP molecules can be used to do cellular work. Some energy is given off as heat (red squiggly lines).
Heat

(5.10)
a form of kinetic energy
Energy

(5.10)
the capacity to do work or cause change. It can not be destroyed but can be converted.
Types of kinetic energy


(5.10)
Heat, or thermal energy, is a type of _____ energy associated with the random movement of atoms or molecules.
Light is also a type of _____ energy, and can be harnessed to power photosynthesis.
Chemical


(5.10)
______ energy is the potential energy available for release in a ______ reaction. It is the most important type of energy for living organisms to power the work of the cell.
first law of thermodynamics



(5.10)
__________, energy in the universe is constant, and cannot be created or destoyed. There is a certain amount of energy in the universe. That is all there is or will ever be. One cannot make it or get rid of it. But it can be converted from potential to kinetic and back again.
second law of thermodynamics



(5.10)
__________, energy conversions increase the disorder of the universe. Everytime potential is converted to kinetic (or vice versa) some of it is given off as heat.
Entropy



(5.10)
_____ is the measure of disorder, or randomness. Or increasing disorder. The measurment of the random molecular movement in a system. The more entropy in a system, the more disordered it is. When a substance has a lot of heat, the molecules are moving at a faster rate. (ex. if you have 2 glasses of water and one of them is at room temp and the other is boiling, the boiling has a higher temp and more heat in it. The water molecules are moving around a lot faster. The more molecular motion you have, the more disordered the system becomes.
oxygen; cellular respiration



(5.10)
Cells use ______ in reactions that release energy from fuel molecules.
In ________, the chemical energy stored in organic molecules is converted to a form that the cell can use to perform work.
Exergonic Reaction




5.11
release energy b/c the reactants (left) have more potential energy than the products (right). As the reaction is taken place, the covalent bonds in the reactants are being broken and releasing kinetic energy. Some might be turned back into potential energy in an ATP molecule.
endergonic reaction



5.11
-requires an input of energy and
-yields products rich in potential energy
-begin with reactant molecules that contain relatively little potential energy
-end with products that contain more chemical energy
Photosynthesis; endergonic



5.11
______ is a type of _____ process.
-Energy-poor reactants, carbon dioxide, and water are used.
-Energy is absorbed from sunlight.
-Energy-rich sugar molecules are produced.
metabolism



5.11
A living organism carries out thousands of endergonic and exergonic chemical reactions.
The total of an organism's chemical reactions is called ______.
Energy coupling



5.11
_____ uses the
-energy released from exergonic reactions to drive
-essential endergonic reactions,
-usually using the energy stored in ATP molecules.
adenosine triphosphate



5.12
ATP, _______, high energy molecule, powers (drives) nearly all forms of cellular work.
phosphorylation



5.12
Hydrolysis of ATP releases energy by transferring its third phosphate from ATP to some other molecule in a process called ______.
phosphorylating



5.12
Most cellular work depends on ATP energizing molecules by _____ them.
structure of ATP



5.12
ATP is a nucleotide consists of
-the nitrogenous base adenine,
-center is the the five-carbon sugar ribose,
-three phosphate groups.
adenosine diphosphate; ADP



5.12
when ATP releases some of its potential energy to drive a metabolic reaction in the cell, the 3rd phosphate group is broken off from which releases energy that was stored in that covalent bond. Usually that phosphate group gets attached to a 2nd molecule (often a protein). We call this phosphorylation which is the transfer of that phosphate group from ATP to a substrate molecule. What is left is _______ or ___.
How ATP powers cellular work



5.12
exergonic; glucose



5.12
ATP is a renewable source of energy for the cell.
In the ATP cycle, energy released in an _____ reaction, such as the breakdown of _____,is used in an endergonic reaction to generate ATP.
The ATP cycle



5.12C
activation energy



5.13
We can think of
-as the amount of energy needed for a reactant molecule to move "uphill" to a higher energy but an unstable state
-so that the "downhill" part of the reaction can begin.
activation energy barrier



5.13
the reactant on the left has a lot of potential energy stored in the covalent bond but we have to have an input of energy before the covalent bond is broken. This is represented by the ________. To heat up the reactants is one way to lower the activation energy barrier. Heat can kill living cells.
enzymes



5.13
instead of heat, for living cells, we have biological catalysts called _____ which lower the activation energy barrier
energy profile with and without an enzyme



5.13
activation energy in the presense of an enzyme (red) is much less than with no enzyme (black line). Reduced need for activation energy in the presense of an enzyme.
catalysts; increase; proteins



5.13
Enzymes
-function as biological _____ by lowering the E needed for a reaction to begin,
-_____ the rate of a reaction without being consumed by the reaction (not used up in the process), and
-are usually _____, although some RNA molecules can function as enzymes.
enzymes



5.14
An enzyme
-is very selective in the reaction it catalyzes (usually catalyze only one specific type) and
-has a shape that determines the enzyme's specificity
- Enzymes are specific because their active site fits only specific substrate molecules.
substrate



5.14
The specific reactant that an enzyme acts on is called the enzyme's ______.
active site



5.14
A substrate fits into a region of the enzyme called the _____.
step 1 of the catalytic cycle of an enzyme



5.14
the enzyme sucrase (a lot of enzymes end in -ase)
step 2 of the catalytic cycle of an enzyme; induced fit




5.14
substrate (disaccharide sucrose) binding to the active site of the of the enzyme sucrase. When binding to the active site, the enzyme usually bends a little bit and changes the shape of the substrate. This is called an _______.
step 3 of the catalytic cycle of an enzyme



5.14
sucrase is going to catalyze the hydrolysis of sucrose into its monomers, glucose and fructose.
step 4 of the catalytic cycle of an enzyme



5.14
at the end of the chemical reaction, the products are released so that the glucose and fructose molecules being released from the enzyme and the enzyme is unchanged and ready to catalyze add'l reactions
35-40ºC



5.14
Temperature affects molecular motion.
-An enzyme's optimal temperature produces the highest rate of contact between the reactants and the enzyme's active site.
-Most human enzymes work best at _____
neutrality
The optimal pH for most enzymes is near _____.
cofactors; bind; catalysis
Many enzymes require nonprotein helpers called _____, which
-____ to the active site and
-____ in catalysis.
inorganic; coenzyme
Some cofactors are _____, such as zinc, iron, or copper.
If a cofactor is an organic molecule, such as most vitamins, it is called a _____.
inhibitor; block; reduce



5.15
A chemical that interferes with an enzyme's activity is called an _____.
Competitive inhibitors
-____ substrates from entering the active site and
-____ an enzyme's productivity.
competitive inhibitor



5.15
normal binding of a substrate



5.15
Noncompetitive inhibitors; allosteric; bind; change; prevent



5.15
-____ to the enzyme somewhere other than the active site (also known as an _____ site),
-____ the shape of the active site, and
-____ the substrate from binding.
feedback inhibition



5.15
In some reactions, the product may act as an inhibitor of one of the enzymes in the pathway that produced it. This is called ________.
feedback inhibition



5.15
a lot of metabolic pathways that occur in cells use _____. At the end of a metabolic pathway, a product comes back and acts as an inhibitor in a step earlier in the pathway. The starting molecule is converted by three different enzymes to a final product (green box on right). The product molecules could then come back and inhibit some of the enzymes. When the product does this, it will shut down the metabolic pathway and will stop making product. The product is cutting off its own creation. ex: maybe we are making too much of a certain protein in a cell, _________ will shut down the pathway that makes that protein until the concentration of it has decreased.
enzyme inhibitors



5.16
Many beneficial drugs act as ________, including
-Ibuprofen, inhibiting the production of prostaglandins,
-some blood pressure medicines,
-some antidepressants,
-many antibiotics, and
-protease inhibitors used to fight HIV.
5.16
Enzyme inhibitors have also been developed as pesticides and deadly poisons for chemical warfare.
carbon fixation
The initial incorporation of carbon from CO2 into organic compounds by autotrophic organisms such as photosynthetic plants, algae, or bacteria.
tumor
An abnormal mass of cells that forms within otherwise normal tissue.
ribosomal RMA (rRNA)
The type of ribonucleic acid that, together with proteins, makes up ribosomes; the most abundant type of RNA.
Down syndrome
A human genetic disorder resulting from a condition called trisomy 21, the presence of an extra chromosome 21; characterized by hear and respiratory defects and varying degrees of mental retardation.
molecular biology
The study of the molecular basis of heredity; molecular genetics.
genetic recombination
The production of offspring with gene combinations that differ from that found in either parent.
primary electron acceptor
A molecule in the reaction center of a photosystem that traps the light-excited electron from the reaction-center chlorophyll.
lysogenic cycle
A bacteriophage reproductive cycle in which the viral genome is incorporated into the bacterial host chromosome as a prophage. new phages are not produced, and the host cell is not killed or lysed unless the viral genome leaves the host chromosome.
tail
Extra nucleotides added at the end of an RNA transcript in the nucleus of an eukaryotic cell.
telophase
The fourth and final stage of mitosis, during which daughter nuclei form at the two poles of a cell. Telophase usually occurs together with cytokinesis.
lytic cycle
A viral reproductive cycle resulting in the release of new viruses by lysis (breaking open) of the host cell.
diploid
Containing two sets of chromosomes (pairs of homologous chromosomes) in each cell, one set inherited from each parent; referring to a 2n cell.
mitotic (M) phase
The phase of the cell cycle when mitosis divides the nucleus and distributes its chromosomes to the daughter nuclei and cytokinesis divides the cytoplasm, producing two daughter cells.
chiasma
(plural, chiasmata) The microscopically visible site where crossing over has occurred between chromatids of homologous chromosomes during prophase I of meiosis.
anaphase
The third stage of mitosis, beginning when sister chromatids separate from each other and ending when a complete set of daughters chromosomes has arrived at each of the two poles of the cell.
nucleosome
The bead-like unit of DNA packing in a eukaryotic cell; consists of DNA wound around a protein core made up of eight histone molecules.
Calvin cycle
The second of two stages of photosynthesis; a cyclic series of chemical reaction that occur in the stroma of a chloroplast, using the carbon in CO2 and the ATP and NADPH produced by the light reactions to make the energy-rich sugar molecule G3P, which is later used to produce glucose.
law of segregation
A general rule of inheritance, first proposed by Gregor Mendel, that states that the two alleles in a pair segregate (separate) into different gametes during meiosis.
interphase
The phase in the eukaryotic cell cycle when the cell is not actually dividing. During interphase, cellular metabolic activity is high, chromosomes and organelles are duplicated, and cell size may increase. Interphase accounts for 90% of the cell cycle. See also mitosis
mutation
A change in the nucleotide sequence of DNA; a major source of genetic diversity.
cap
Extra nucleotides added to the beginning of an RNA transcript in the nucleus of a eukaryotic cell.
homozgous
Having two identical alleles for a given gene
pedigree
A family tree representing the occurrence of heritable traits in parents and offspring across a number of generations.
cleavage furrow
The first sign of cytokinesis during cell division in an animal cell; a shallow groove in the cell surface near the old metaphase plate.
polynucleotide
A polymer made up of many nucleotides covalently bonded together
NADPH
An electron carrier (a molecule that carries electrons) involved in photosynthesis. Light drives electrons from chlorophyll to NADP1, forming NADPH, which provides the high-energy electrons for the reduction of carbon dioxide to sugar in the Calvin cycle.
trait
A variant of a character found within a population, such as purple flowers in pea plants.
heterozygous
Having two different alleles for a given gene
genetic code
The set of rules giving the correspondence between nucleotide triplets (codons) in mRNA and amino acids in protein.
metaphase
The second stage of mitosis. During metaphase, the centromeres of all the cell's duplicated chromosomes are lined up on an imaginary plate equidistant between the poles of the mitotic spindle.
stop codon
In mRNA, one of three triplets (UAG, UAA, UGA) that signal gene translation to stop.
Huntington's disease
A human genetic disease caused by a dominant allele; characterized by uncontrollable body movements and degeneration of the nervous system; usually fatal 10-20 years after the onset of symptoms.
life cycle
The entire sequence of states in the life of an organism, from the adults of one generation to the adults of the next
hypothesis
(plural, hypotheses) A tentative explanation that a scientist proposes for a specific phenomenon that has been observed.
somatic cell
Any cell in a multicellular organism except a sperm or sperm or egg cell or a cell that develops into a sperm or egg; a body cell.
testcross
The mating between an individual of unknown genotype for a particular character and an individual that is homozgous recessive for that same character.
dihybrid cross
A mating of individuals differing at two genetic loci.
mitosis
The division of a single nucleus into two genetically identical daughter nuclei. Mitosis and cytokinesis make up the mitotic (M) phase of the cell cycle.
hypothesis
(plural, hypothesis) A tentative explanation that a scientist proposes for a specific phenomenon that has been observed.
locus
(plural, loci) The particular site where a gene is found on a chromosome. Homologous chromosomes have corresponding gene loci.
chromatin
The combination of DNA and proteins that constitutes chromosomes; often used to refer to the diffuse, very extended form taken by the chromosome when a eukaryotic cell is not dividing.
fetilization
The union of a haploid sperm cell with a haploid egg cell, producing a zygote.
mitotic spindle
A spindle-shaped structure formed of microtubules and associated proteins that is involved in the movement of chromosomes during mitosis and meiosis. (A spindle is shaped roughly like a football.)
Punnett square
A diagram used in the study of inheritance to show the results of random fertilization.
malignant tumor
An abnormal tissue mass that spreads into neighboring tissue and to other parts of the body; a cancerous tumor.
cross
The cross-fertilization of two different varieties of an organism or of two different species; also called hybridization.
recombination frequency
With respect to two given genes, the number of recombinant progeny from a mating divided by the total number of progeny carry combinations of alleles different from that seen in either of the parents as a result of independent assortment of chromosomes and crossing over
photosystem
A light-harvesting unit of a chloroplast's thylakoid membrane; consists of several hundred
molecules, a reaction center chlorophyll, and a primary election acceptor
monohybrid cross
A mating of individuals differing at one genetic locus.
P generation
The parent individuals from which offspring are derived in studies of inheritance. P stands for parental.
DNA
Deoxyribonucleic acid The genetic material that organisms inherit from their parents; a double-stranded helical macromolecule consisting of nucleotide monomers with deoxyribose sugar, a phosphate group, and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and thymine (T). See also gene.
nondisjunction
An accident of meiosis or mitosis in which a pair of homologous chromosomes or a pair of sister chromatids fail to separate at anaphase.
zygote
The fertilized egg, which is diploid, that results from the union of haploid gametes (sperm and egg) during fertilization.
karyotype
A display of micrographs of the metaphase chromosomes of a cell, arranged by size and centromere position
linked genes
Genes located close enough together on a chromosome that they are usually inherited together.
Linkage
A map of a chromosome showing the relative position of genes.
transcription
The synthesis of RNA on a DNA template.
crossing over
The exchange of segments between chromatids of homologous chromosomes during prophase I of meiosis
ABO
Genetically determined classes of human blood that are based on the presence or absence of carbohydrates A and B on the surface of red blood cells. The ABO blood group phenotypes, also called types, ate A, B, AB, and O.
hyphthesis
(plural, hypotheses) A tentative explanation that a scientist proposes for a specific phenomenon that has been observed.
cell cycle control system
A cyclically operating set of proteins that triggers and coordinates events in the eukaryotic cell cycle.
retrovirus
An RNA virus that reproduces by means of a DNA molecule. It reverse-transcribes its RNA into DNA, inserts the DNA into a cellular chromosomes, and then transcribes more copies of the RNA from the viral DNA. HIV and a number of cancer-causing viruses are retroviruses.
prophage
Phage DNA that has inserted into the DNA of a prokaryotic chromosome.
virus
A microscopic particle capable of infecting cells of living organisms and inserting its genetic material. Viruses have a very simple structure and are generally not considered to be alive because they do not display all the characteristics associated with life.
terminator
A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene.
polygenic inheritance
The additive effect of two or more genes on a single phenotypic characteristic.
dominant allele
In a heterozgote, the allele that determines the phenotype with respect to a particular gene.
cytosine (C)
A single-ring nitrogenous base found in DNA and RNA.
genotype
The genetic makeup of an organism.
sugar-phosphate backbone
The alternating chain of sugar and phosphate to which DNA and RNA nitrogenous bases are attached
start codon
On mRNA, the specific three-nucleotide sequence (AUG) to which an initiator tRNA molecule binds, starting translation of genetic information.
provirus
Viral DNA that inserts into a host genome.
law of independent assortment
A general rule of inheritance, first proposed by Gregor Mendel, that states that when gametes form during meiosis, each pair of alleles for a particular character segregate (separate) independently of each other pair.
phenotype
The expressed traits of an organism.
prophase
The first stage of mitosis. During prophase, duplicated chromosomes condense to form structures visible with a light microscope, and the mitotic spindle forms and begins moving the chromosomes toward the center of the cell.
AIDS
Acquired immunodeficiency syndrome; the late stages of HIV infection, characterized by a reduced number of T cells; usually results in death caused by opportunistic infection.
translation
The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of language from nucleotides to amino acids
character
A heritable feature that varies among individuals within a population, such as flower color in pea plants.
hypercholesterolemia
An inherited human disease characterized by an excessively high level of cholesterol in the blood.
achonddroplasia
A form of human dwarfism caused by a single dominant allele. The homozygous condition is lethal.
cytokinesis
The division of the cytoplasm to form two separate daughter cells. Cytokinesis usually occurs during thelophase of mitosis, and the two processes (mitosis and cytokinesis) make up mitotic (M) phase of the cell cycle.
haploid
Containing a single set of chromosomes; referring to an n cell.
sex-linked gene
A gene located on a sex chromosome.
trisomy 21
See Down syndrome
centromere
The region of a chromosome where two sister chromatids are joined and where spindle microtubules attach during mitosis and meiosis. The centromere divides at the onset of anaphase during mitosis and anaphase II meiosis.
RNA polymerase
An enzyme that links together the growing chain of RNA nucleotides during transcription, using a DNA strand as a template.
F2 generation
The offspring of the F1 generation. F2 stands for second filial.
recessive allele
In heterozygotes, the allele that has no noticeable effect on the phenotype
rule of multiplaction
A rule stating that the probability of a compound event is the product of the separate probabilities of the independent events.
incomplete dominance
A type of inheritance in which the phenotype of a heterozygote (Aa) is intermediate between the phenotypes of the two types of homozgotes (AA and aa)
stroma
A thick fluid enclosed by the inner membrane of a chloroplast. Sugars are made in the stoma by the enzymes of the Calvin cycle.
chromosome theory of inheritance
A basic principle in biology stating that genes are located on chromosomes and that the behavior of chromosomes during meiosis accounts for inheritance patterns.
codominant
Expressing two different alleles of a gene in a heterozygote.
electromagnetic spectrum
The full range of radiation, from the very short wavelengths of gamma rays to the very long wavelengths of radio signals.
wavelength
The distance between crests of adjacent waves, such as those go the electromagnetic spectrum
cancer
A malignant growth or tumor caused by abnormal and uncontrolled cell division
uracil (U)
A single-ring nitrogenous base found in RNA.
chlorophyII
A light-absorbing pigment in chloroplasts that plays a central role in converting solar energy to chemical energy.
cell plate
A membranous disk that forms across the midline of a dividing plant cell. During cytokinesis, the cell plant grows outward, accumulating more cell wall material and eventually fusing into a new cell wall.
reverse transcriptase
An enxyme that catalyzes the synthesis of DNA on an RNA template.
HIV
Human immunodeficiency virus; the retrovirus that attack the human immune system and cause AIDS.
radiation therapy
Treatment for cancer in which parts of the body that have cancerous tumors are exposed to high-energy radiation to disrupt cell division of the cancer cells.
double helix
The form assumed by DNA in living cells, referring to its two adjacent polynucleotide strands wound into a spiral shape
anticodon
On a tRNA molecule, a specific sequence of three nucleotides that is complementary to a codon triplet on mRNA.
reaction center
In a photosystem in a chloroplast, the chlorophyll a molecule and primary electron acceptor that trigger the light reaction of photosynethesis. The cholorphyll donates an electron excited by light energy to the primary electron transport chain.
guanine (G)
A double-ring nitrogenous base found in DNA and RNA.
pleiotrophy
The control of more than one phenotypic character by a single gene.
light reaction
The first of two stages in photosynthesis, the steps in which solar energy is absorbed and converted to chemical energy in the form of ATP and NADPH. The light reaction power the sugar-producing Calvin cycle but produce no sugar themselves.
asexual reproduction
The creation of genetically identical offspring by a single parent, without the participation of gametes (sperm and egg)
metastasis
The spread of cancer cells beyond their original site.
photon
A fixed quantity of light energy. The shorter the wavelength of light, the greater the energy of a photon.
antibiotics
drugs that disable or kill infectious bacteria
light microscope (LM)
an optical instrument with lenses that refract/bend visible light to magnify images and project them into a viewer's eye or onto photographic film
magnification
an increase in the apparent size of an object
resolving power
a measure of the clarity of an image; the ability of an optical instrument to show two objects as separate
cell theory
the theory that all living things are composed of cells and hat all cells come from other cells
electron microscope
an instrument that focuses an electron beam through or onto the surface of a specimen, achieves a thousandfold greater resolving power than a light microscope
scanning electron microscope (SEM)
a microscope that uses an electron beam to study the surface architecture of a cell or other specimen
transmission electron microscope (TEM)
a microscope that uses an electron beam to study the internal structure of thinly sectioned specimens
prokaryotic cells
a type of cell lacking a nucleus and other organelles, found only in the domains bacteria and archaea
eukaryotic cells
a type of cell that has a membrane-enclosed nucleus and other membrane-enclosed organelles
plasma membrane
a thin layer of lipids and proteins that sets a cell off from its surrounding and acts as a selective barrier to the passage of ions and molecules into and out of a cell
ribosomes
a cellular structure consisting of RNA and protein organized into two subunits and functioning as the site of protein synthesis in the cytoplasm
organelles
a membrane-enclosed structure with a specialized functi0n within a eukaryotic cell
nucleus - an atom's central core, containing protons and neutrons, the genetic control center of a eukaryotic cell
cytoplasm
everything inside a eukaryotic cell between the plasma membrane and the nucleus, consists of a semifluid medium and organelles, can also refer to the interior of a prokaryotic cell
phospholipids
made up of glycerol joined to two fatty acids and a phosphate group; hydrophobic tail and a hydrophilic head
phospholipid bilayer
a double layer of phospholipid molecules that is the primary component of all cellular membranes
fluid mosaic
a description of membrane structure, depicting a cellular membrane as a mosaic of diverse protein molecules embedded in a fluid bilayer made of phospholipid molecules
extracellular matrix
a substance in which the cells of an animal tissue are embedded, consists of protein and polysaccharides.
cell junctions
a structure that connects animal cells to one another in a tissue.
nuclear envelope
a double membrane, perforated with pores, that encloses the nucleus and separates it from the rest of the eukaryotic cell
chromatin
the combination of dna and proteins that constitutes chromosomes, often used to refer to the diffuse, very extended form taken by the chromosomes when a eukaryotic cell is not dividing.
chromosome
a gene-carrying structure found in the nucleus of a eukaryotic cell and most visible during mitosis and meiosis, also, the main gene-carrying structure of a prokaryotic cell, consists of one very long thread-like dna molecule
nucleolus
a structure within the nucleus of a eukaryotic cell where ribosomal RNA is made and assembled with proteins to make ribosomal subunits, consists of parts of the chromatin DNA, RNA transcribed from the DNA, and proteins imported from the cytoplasm.
endomembrane system
a network of organelles that partitions the cytoplasm of eukaryotic cells into functional compartments. some of the organelles are structurally connected to each other, whereas others are structurally seperate but functionally connected by the traffic of vesicles between them.
endoplasmic reticulum
an extensive membranous network in a eukaryotic cell, continuous with the other nuclear membrane and coposed of ribosome-studded and ribosome-free regions.
rough ER
a network of interconnected membranous sacs in a eukaryotic cell's cytoplasm, studded with ribosomes that make membrane proteins and secretory proteins.
transport vesicles
a tiny membranous sphere in a cell's cytoplasm carrying molecules produced by the cell, buds from the endoplasmic reticulum or golgi apparatus.
smooth ER
a network of interconnected membranous tubules in a eukaryotic cell's cytoplasm; lacks ribosomes.
golgi apparatus
an organelle in eukaryotic cells consisting of stacks of membranous sacs that modify, store, and ship products of the endoplasmic reticulum.
food vacuoles
a tiny sac in the eukaryotic cell's cytoplasm that engulfs nutrients, the simplest of digestive compartment.
central vacuole
a membrane-enclosed sac occupying most of the interior of a mature plant cell, have diverse roles in reproduction, growth, and development.
chloroplasts
an organelle found in plants and photosynthetic protists. enclosed by two concentric membranes, a chloroplast absorbs sunlight and uses it to power the synthesis of organic food molecules aka sugar.
stroma
a thick fluid enclosed by the inner membrane of a chloroplast, sugars are made here by the enzymes of the calvin cycle.
grana
a stack of hollow disks formed of thlakoid membranes in a chloroplast, the sites where light energy is tapped by chlorophyll and converted to chemical energy during the light reactions of photosynthesis.
mitochondria
an organelle in eukaryotic cells where celluar respiration occurs. enclosed by two concentric membranes, where most of the cell's ATP is made.
matrix
the thick fluid contained within the inner membrane of the mitochondrion.
cristae
infoldings of the inner membrane of a mitochondrion that houses the electon transport chain and the enzyme catalyzing the synthesis of ATP.
cytoskeleton
network of protein filaments within some cells that helps the cell maintain its shape and is involved in many forms of cell movement.
microtubules
straight, hollow tubes of proteins that give rigidity, shape, and organization to a cell
activation energy
the amount of energy that reactants must absorb before a chemical reaction will start.
active site
the part of an enzyme molecule where a substrate molecule attaches (by means of weak chemical bonds); typically, a pocket or groove on the enzyme's surface
active transport
the movement of a substance across a biological membrane against its concentration gradient, aided by specific transport proteins and requiring input of energy (often as ATP)
ADP
(adenosine diphosphate) a molecule composed of adenosine and two phosphate groups, combing a third phosphate with ADP in an energy-consuming reaction results in the molecule ATP.
calorie
the amount of energy that raises the temperature of 1g of water by 1 degree C.
chemical energy
energy stored in the chemical bonds of molecules; a form of potential energy.
concentration gradient
an increase or decrease in the density of a chemical substance within a given region. cells often maintain concentration gradients of hydrogen ions across their membranes. when a gradient exists, the ions or other chemical substances involved tend to move from where they are more concentrated to where they are less concentrated.
conservation of energy
the principle that energy cannot be created nor destroyed.
diffusion
the spontaneous movement of particles of any kind down a concentration gradient; that is, movement of particles from where they are more concentrated to where they are less concentrated.
endocytosis
the movement of material into the cytoplasm of a cell via cell membranes or vesicles.
energy
the capacity to perform work, or to move mater in a direction it would not move if left alone.
entropy
a measure of disorder, or randomness. one form of disorder is heat, which is random molecular motion.
enzymes
a protein that serves a biological catalyst, changing the rate of a chemical reaction without itself being changed in the process.
enzyme inhibitor
a chemical that interferes with an enzyme's activity by changing the enzyme's shape, either by plugging up the active site or binding to another site on the enzyme.
exocytosis
the movement of materials out of the cytoplasm of a cell via membranous vesicles or vacuoles.
facilitated diffusion
the passage of a substance across a biological membrane down its concentration gradient, aided by specific transport proteins.
feedback regulation
a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.
hypertonic
in comparing two solutions, referring to the one with the higher concentration of the solutes.
hypotonic
in comparing two solutions, referring to the one with the lower concentration of the solutes.
induced fit
the interaction between a substrate molecule and the active site of an enzyme, which changes shape slightly to embrace the substrate and catalyze the reaction.
isotonic
having the same solute concentration as another solution
kinectic energy
energy of motion. moving matter performs wok by transferring its motion to other matter, such as leg muscles pushing bicycle pedals.
metabolism
the total of all the chemical reactions in an organism.
osmoregulation
the control of the gain or loss of water and dissolves solutes in an organism.
osmosis
the diffusion of water across a selectively permeable membrane.
passive transport
the diffusion of a substance across a biological membrane without any input of energy.
phagocytosis
type of endocytosis in which a cell engulfs macromolecules, other cells or particles into its cytoplasm.
pinocytosis
cellular "drinking"; a type of endocytosis in which the cell takes fluid and dissolved solutes into small membranous vesicles.
plasmolysis
a phenomenon that occurs in plant cells in a hypertonic environment. the cell loses water and shrivels, and its plasma membrane pulls away from the cell wall, usually killing the cell.
potential energy
stored energy; the energy that an object has due to its location and/or arrangement. water behind a dam and chemical bonds both possess potential energy.
receptor-mediated endocytosis
the movement of specific molecules into a cell by the inward budding of vesicles. the vesicles contain proteins with receptor sites specific to the molecules being taken in.
signal transduction pathway
a series of molecular changes that converts a signal on a target cell's surface to a specific response inside the cell.
substrate
(1) a specific substance [reactants] on which an enzyme acts. (2) a surface in or on which an organism lives.
transport protein
a membrane protein that helps move substances across the cell membrane
Evolution
Accounts for the unity and diversity of life; Organism's adaptations to its environment; Process of change that transformed life on Earth

Ex: Ghost plant is adapted to conserving water which helps it survive in crevices of rock walls
Order
Structure of an organism
Regulation
Regulation of blood through a jackrabbit's ears helps it maintain a constant body temperature by adjusting heat exchange with the surrounding air
Energy Processing
Hummingbird gets nectar from flowers, uses the chemical energy to fly and other shiet
Growth and Development
Inherited information carried by genes controls the pattern of growth & development of organisms
Reproduction
(Living) organisms produce their own kind
Response to Environment
Venus fly trap plant capturing a prey that landed on its trap
Evolutionary Adaptation
Giraffes' long necks to reach leaves from trees and their long legs require them to have a long neck to bend down to drink water from lakes
Levels of Biological Organization
Biospheres, Ecosystems, Communities, Populations, Organisms, Organs and Organ Systems, Organelles, Molecules, Tissues, and Cells
Emergent Properties
Result from the arrangement and interaction of parts within a system

Ex: An injury to the human head might damage the brain, disabling proper function - even though all the brain tissues are still intact.
Reductionism
Reduction of complex systems to simpler components that are more manageable to study

Ex: Studying molecular structure of DNA helps us to understand chemical basis of inheritance
Systems Biology
Constructs models for dynamic behavior of whole biological systems; Enables biologists to pose new kinds of large-scale questions
Organism Interaction
Plants take up nutrients from the soil and the chemicals from the airs and use energy from the sun. Interactions between plants and other organisms result in cycling of chemical nutrients within an ecosystem.

*One harmful outcome of human interactions with the environment: Global climate change aka global warming, due to fossil fuel burning further resulting in higher levels of CO2
Structure and Function
Correlated at all levels of biological organization

Ex: A leaf's thin and flat shape maximizes the amount of sunlight that can be captured by its chloroplasts
Cell
Lowest level of organization that can perform all activities required for life; Basic unit of structure and function
Eukaryotic Cell
Membrane-enclosed organelles; Largest organelle in this type of cell is the nucleus
Prokaryotic Cell
Simpler and smaller; DNA isn't separated from the rest of the cell by enclosure in a membrane-bounded nucleus; no enclosed membrane organelles
DNA
Aka deoxyribonucleic acid; the substance of genes
Genes
The units of inheritance that transmit information from parents to offspring; Encode info. for building molecules in the cells, most notably proteins
Nucleotides
Monomers that make up nucleic acids, are abbreviated A, T, C, G
RNA
Ribonucleic acid; Genes control protein production indirectly using this as an intermediary; DNA is transcribed to this
Gene Expression
The process by which the information in a gene directs the production of a cellular product
Genomics
"Library" of genetic instructions that an organism inherits; Large scale analysis of DNA sequences
Genomics Approach
Depends on....

"High throughput" technology, which yields huge amounts of data

"Bioinformatics": the use of computational tools to process a large volume of data

Interdisciplinary research terms
Negative Feedback
As more of a product accumulates, the process that creates slows down and less of the product is produced
Positive Feedback
When an end product speeds up its own production

Ex: When a blood vessel is damaged, structures in the blood called platelets begin to come together
Theodosius Dobzhansky
"Nothing in biology makes sense except in the light of evolution."
Taxonomy
Branch of biology that names and classifies species and formalizes the ordering of species
into groups of increasing range, based on the level of similar characteristics
Three Domains of Life
Bacteria, Eukarya, and Archaea
Bacteria
Most diverse and well-known prokaryotes; classified into multiple kingdoms
Archaea
Live in Earth's extreme environments (ex: salty lakes, hot springs), Single-celled, no nucleus, oldest organisms on earth
Domain Eukarya: Kingdom Plantae
Terrestrial multicellular eukaryotes and plants that carry out photosynthesis
Domain Eukarya: Kingdom Fungi
Defined in part by the nutritional mode of its members; Absorbs nutrients from outside their bodies
Domain Eukarya: Kingdom Animalia
Consists of multicellular eukaryotes that ingest other organisms
Protists
Domain Eukarya type; Unicellular or simple multicellular eukaryotic organisms that generally do not fit in any other kingdom

Ex: Organisms inhabiting in pond water
Cilia
Extensions of cells that function in locomotion; 9 + 2 configuration/arrangement

There are "signatures" in the cells, which are arranged microtubules
The Origin of Species
Charles Darwin's theory that:

Species showed evidence of "descent with modification" from common ancestors

Natural selection is the mechanism behind "decent with modification"
Natural Selection
The environment "selects" for the propagation of beneficial traits in organisms
Three Observations from Nature
Individuals in a population vary in their traits (mainly heritable traits), A population can produce far more offspring of their own, Species generally suit the environments they're adapted to
Inquiry
Search for information and explanation
Data
Recorded information
Qualitative Data
Data in form of recorded and written descriptions
Quantitative Data
Data in form of numerical measurements
Inductive Reasoning
Brings out generalizations from specific observations
Questions that can't be addressed by science
A hypothesis since it is testable/falsifiable; Supernatural and religious explanations that are outside the bounds of science
Theory
General enough to create many new specific hypotheses that can be tested; provides more evidence than a hypothesis
Model Organism
A species that is easy to grow in the lab and lends itself particularly well to the questions being investigated
Matter
Anything that takes up space and has mass
Element
Substance that cannot be broken down to other substances by chemical reactions simplest form in which a substance occurs
Compound
Substance consisting of two or more elements in a fixed ratio; has characteristics different from those of its elements
Trace elements
Elements required by an organism in minute quantities
Elements that make up 96% of the living matter
Carbon, Hydrogen, Oxygen, Nitrogen
Remaining 4% of living matter
Calcium, Phosphorus, Potassium, Sulfur
Atom
Smallest unit of matter that still retains the properties of an element
Subatomic particles
Atoms are composed of this; Includes neutrons, protons, and electrons
Atomic Mass
Atomic Number (Protons) + Neutrons

Total mass of the protons and neutrons in an atom, measured in atomic mass units
Atomic Nucleus
An atom's central core, containing protons and neutrons. Electrons are too microscopic to be included in this.
Daltons
The unit of measurement used to measure the neutron and proton mass
Isotopes
Two atoms of an element that differ in number of neutrons
Radioactive Isotopes
Isotopes that decay spontaneously from within, giving off particles and unstable energy

Can be used in bio. research for: Dating fossils, Tracing atoms through metabolic processes, and diagnosing medical disorders
Energy
Capacity to cause change
Potential energy
The energy that matter has because of its location or structure; The electrons of an atom differ in their amount of this type of energy
Electron shell
An energy level representing the distance of an electron from the nucleus of an atom.
Valence electrons
The electrons in the outermost shell (main energy level) of an atom; chemical behavior is mostly determined by these
Full valence shells
Inert (unable to move, resists motion)
Chemical bonds
An interaction between electrons of two different atoms resulting from the sharing of outer-shell electrons or the presence of opposite charges
Covalent bonds
Form when electrons are shared between atoms; S and P orbitals may hybridize, creating molecular shapes
Single Covalent bond
Sharing of one pair of valence electrons
Double Covalent bond
Sharing of two pairs of valence electrons
Electronegativity
An atom's attraction for the electrons in a covalent bond. The more ________________ an atom, the more strongly it pulls shared electrons towards itself
Nonpolar Covalent bond
The atoms share the electrons equally
Polar Covalent bond
One atom is more electronegative, and the atoms do not share the electron equally
Ionic bonds
Formed when one or more electrons are transferred from one atom to another

Ex: The transfer of an electron from Sodium to Chlorine
Ion
A charged atom (molecule)
Cation
Positively charged ion (they lose electrons)
Anion
Negatively charged ion (they gain electrons)
Ionic Compounds
Compounds formed by ionic bonds
Hydrogen bond
Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

Ex: Electronegative partners in living cells are oxygen and nitrogen atoms
Van der Waals interactions
Attractions between molecules that are close together as a result of these charges
Molecule's shape
Important to its function; Determined by the positions of its atoms' valence orbitals
Chemical reactions
Making and breaking of chemical bonds, leads to change in composition of matter; Most _____________ are reversible
Photosynthesis
Important chemical reaction: Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen
Chemical equilibrium
Is reached when the forward and reverse reaction rates are equal
Water
About 2/3 of our bodies is this; Biological medium on Earth; Cells are about 70 - 95% of this; Main reason why Earth is habitable; Has a high specific heat

*Less dense as a solid than a liquid because there are molecules straightened out so there's spaces in between which causes it to be lighter
Four of Water's Properties that facilitate environment for life
Cohesive behavior, Ability to moderate temperature, Expansion upon freezing, Versatility as a solvent
Cohesion of Water Molecules
Helps pull water upward in the microscopic water-conducting cells of plants
Hydrogen bonding
Keeps water molecules close to each other, also responsible for water's surface tension
Evaporative cooling
Based on water's high heat of vaporization; The property of a liquid whereby the surface becomes cooler during evaporation, owing to a loss of highly kinetic molecules to the gaseous state.
Solvent
Ex: Water is a versatile ___________, because its polar molecules are attracted to charged and polar substances capable of forming hydrogen bonds
Hydrophilic
Have an affinity for water
Hydrophobic
Have a phobia for water
Molarity
The number of moles of solute per liter of solution is used as a measure of solute concentration in solutions
Molecular Mass
The sum of the masses of all the atoms in a molecule; sometimes called molecular weight.
Heat
A measure of the total amount of kinetic energy due to molecular motion

Absorbed when hydrogen bonds break; Released when hydrogen bonds form
Specific Heat
The amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1 degrees Celcius
Heat of vaporization
Heat of a liquid must absorb for 1 gram to be converted to gas
Solution
A liquid that is a homogeneous mixture of substances
Solvent
The dissolving agent of a solution
Solute
The substance that is dissolved
Aqueous solution
One in which water is the solvent
Hydrogen Shell
When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules
Buffers
Resists changes in pH in biological fluids; Consists of an acid-base pair that combines reversibly with hydrogen ions
Ocean Acidification
Decreasing pH of ocean waters due to absorption of excess atmospheric CO2 from the burning of fossil fuels
Hydrocarbons
Consist of only carbon and hydrogens
Isomers
Compounds with the same molecular formula but different structures and properties. Three types: Structural, Cis-trans, and Enantiomers
Vitalism
The idea that organic compounds arise only in organisms, was disproved when chemists synthesized these compounds
Mechanism
The view that all natural phenomena are governed by the physical and chemical
Structural isomers
Have different covalent arrangements of their atoms
Cis-trans isomers
Have the same covalent bonds but differ in spatial arrangements
Enantiomers
Isomers that are mirror images of each other; Important to the pharmaceutical industry
Functional groups
The components of organic molecules that are most commonly involved in chemical reactions
Seven functional groups
Hydroxyl, Carbonyl, Carboxyl, Amino, Sulfhydryl, Phosphate, Methyl
ATP
The "currency for life"; Adenosine Triphosphate; The primary energy-transferring molecule in a cell
Deductive reasoning
Generally used after the hypothesis has been developed; Involves logic that flows in the opposite direction (general to specific)
Orbital
The 3-D space where an electron is found 90% of the time
Ion
A charged atom (or molecule)
Polarity
Allow water molecules to form hydrogen bonds with each other
Cohesion
An attraction between molecules of the same substance; holds the hydrogen bonds together
Surface tension
A measure of how hard it is to break the surface of a liquid
Adhesion
A attraction between molecules of different substances
Joule
Another unit of energy where 1 J = 0.239 cal, 1 cal = 4.184 J
Celsius scale
Measure of temperature using Celcius degrees
Colloid
A stable suspension of fine particles in a liquid
Acid
Any substance that increases the H+ concentration of a solution
Base
Any substance that decreases the H+ concentration of a solution
Buffer
Substances that minimize changes in concentrations of H+ and OH- in a solution; Most of these consist of an acid-base pair that reversibly combines with H+
pH scale
Describes how acidic or basic a solution is
basal body
A eukaryotic cell organelle consisting of a 9 + 0 arrangement of microtubule triplets; may organize the microtubule assembly of a cilium or flagellum; structurally identical to a centriole.
cell theory
(biology) the theory that cells form the fundamental structural and functional units of all living organisms
cell wall
a thin membrane around the cytoplasm of a cell
cellular metabolism
chemical activities of a cell
central vacuole
A membranous sac in a mature plant cell with diverse roles in reproduction, growth, and development.
centriole
one of two small cylindrical cell organelles composes of 9 triplet microtubules
chloroplast
plastid containing chlorophyll and other pigments
chromatin
the readily stainable substance of a cell nucleus consisting of DNA and RNA and various proteins
chromosome
a threadlike body in the cell nucleus that carries the genes in a linear order
cilia
short structures projecting from a cell and containing bundles of microtubules that move a cell through its surroundings or move fluid over the cell's surface
crista
the infoldings of th mitochondrial inner membrane
cytoplasm
a jellylike fluid inside the cell in which the organelles are suspended
cytoskeleton
a microscopic network of actin filaments and microtubules in the cytoplasm of many living cells that gives the cell shape and coherence
electron microscope (EM)
__
endomembrane system
The collection of membranes inside and around a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles.
endoplasmic reticulum (ER)
Extensive network of membranous tubules that extend from the nuclear membrane to the cell membrane
endosymbiosis
Process through which early prokaryotic cells are thought to have engulfed other, smaller cells and eventually incorporated them as organelles; these cells evolved into modern-day eukaryotes.
eukaryotic cell
cell with a nucleus (surrounded by its own membrane) and other internal organelles
extracellular matrix (ECM)
--
flagellum
a lash-like appendage used for locomotion (e.g., in sperm cells and some bacteria and protozoa)
glycoprotein
a conjugated protein having a carbohydrate component
Golgi apparatus
a net-like structure in the cytoplasm of animal cells (especially in those cells that produce secretions)
Granum
a stack of thylakoids
Integrin
A receptor protein built into the plasma membrane that interconnects the extracellular matrix and the cytoskeleton.
intermediate filament
A component of the cytoskeleton that includes all filaments intermediate in size between microtubules and microfilaments.
intermembrane space
the region between the inner membrane and the outer membrane of a mitochondrion or a chloroplast. The main function of the intermembrane space is nucleotide phosphorylation.
light microscope (LM)
--
lysosome
an organelle found in the cytoplasm of most cells (especially in leukocytes and liver and kidney cells)
microfilament
solid rod of protein, thinner than a microtubule, that enables a cell to move or change shape
micrograph
photograph of the view through a microscope
microtubule
A hollow rod of tubulin protein in the cytoplasm of all eukaryotic cells and in cilia, flagella, and the cytoskeleton.
mitochondrial matrix
The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the Krebs cycle.
mitochondrion
in eukaryotic cells, the cell organelle that is surrounded by two membranes and that is the site of cellular respiration, which produces ATP
nuclear envelope
layer of two membranes that surrounds the nucleus of a cell
nucleoid
A dense region of DNA in a prokaryotic cell.
nucleolus
The organelle where ribosomes are made, synthesized and partially assembled, located in the nucleus
nucleus
a part of the cell containing DNA and RNA and responsible for growth and reproduction
organelle
specialized structure that performs important cellular functions within a eukaryotic cell
peroxisome
A microbody containing enzymes that transfer hydrogen from various substrates to oxygen, producing and then degrading hydrogen peroxide.
plasma membrane
a thin membrane around the cytoplasm of a cell
plasmodesma
An open channel in the cell wall of a plant through which strands of cytosol connect from an adjacent cell.
prokaryotic cell
cell lacking a nucleus and most other organelles
ribosome
an organelle in the cytoplasm of a living cell
rough ER
A network of interconnected membranous sacs in a eukaryotic cell's cytoplasm; covered with ribosomes that make membrane proteins and secretory proteins.
scanning electron microscope (SEM)
electrons bounce off of surface object, passes a beam of electrons over surface and provide and 3-D surface
smooth ER
That portion of the endoplasmic reticulum that is free of ribosomes.
stroma
the supporting tissue of an organ (as opposed to parenchyma)
thylakoid
A flattened membrane sac inside the chloroplast, used to convert light energy into chemical energy.
transmission electron microscope (TEM)
electrons pass through very thin sections
transport vesicle
A tiny membranous sac in a cell's cytoplasm carrying molecules produced by the cell.
vacuole
a tiny cavity filled with fluid in the cytoplasm of a cell
vesicle
A membrane bound sac that contains materials involved in transport of the cell.
What are living organisms on Earth mainly made up of?
Carbon
How does carbon enter the biosphere?
Via plants. They use solar energy to transfer atmospheric CO2 into the molecules of life
What is organic chemistry? How did it come about?
Organic chemistry is the study of carbon compounds, regardless of origin.
-In the early 1800s, Berzelius made distinction between compounds from living things and not. He called it organic (he was heavily influenced by vitalism).
-Eventually, chemists began to synthesize organic compounds. urea was the first one.
In the 1950s Miller tested whether complex organimc molecules could arise abiotically and spontaneously in early Earth conditions. They did.
What is vitalism? What is mechanism?
Vitalism was the belief that a life force existed outside the jurisdiction of physical and chemical laws. This is why only organic molecules were from organisms only. Mechanism is the opposite - it is the belief that physical and chemical laws govern all natural phenomena, including the process of life. In the 1950s, this helped to push the idea that organic molecules could spontaneously and abiotically be created from inorganic molecules.
Why is carbon very verstile?
Carbon creates inexhaustible variety because:
1) it can form 4 bonds, hence able to form large and complex molecules. It's valence shell has 4 atoms in different orbitals, so it can covalently bond with four other atoms Each carbon acts as an intersection point from which a molecle can branch off. This is why biological molecule sare so diverse.
2) There are actually only 5 main major elements of life, C,H,O,N,S,P - but carbon is the key for diversity.
What is tetravalence?
Tetravalence is when a molecule like carbon has the ability to create four covalent bonds with other atoms and can therefore branch off in as many as four directions.
what shape does carbon universally have?
A carbon with a group of four has a tetrahderal shape.
What are hydrocarbons? Why are they important?
The hydrocarbons are long chains of hydrogens covalently bonded to carbon skeleton. They are the major components of fossil fuels. In living being, organic molecules have regions of hydrocarbons, like fatty acids. When in reactions, they release a TON of energy.
What is the forumula for hydrocarbon?
CnH2n+2
What are carbon isomers?
compounds that have the same number of atoms of the same elements but different structures.
What are the three types of isomers we learned about in class?
Structural - same molecular formula, different structure of bonding
geometric - different arrangement about a double bond
enantiomers - mirror images
What happens to the possibility of structural isomers as carbon skeletons increase in size?
Possible isomers increase tremendously.
Geometric isomers
Single bonds allow atoms they join to rotate freely. With double bonds, it is more rigid.
Enantiomers
Four groups arranged in space around asymmetric carbon in two different ways. They are mirror images of each other. One is viologically acive and the other is in active.
What is the chiral carbon?
It is the middle carbon atached to four different atoms or group of atoms.
Example of geometric isomers
Example of enantiomers
What type of isomers are these?
1) structural
2) structural
3) same molecule
4) enantiomer
5) geometric
6) structural
What type of isomers are these?
7) not isomers, different formula
8) enantiomers
9) geometric
10) structural
11) not isomers, different formula
12) not isomers, same
What are functional groups?
Functional groups are chemical groups attached to the carbon atom and gives the molecule specific properties.
They are CASHCaMP.
What are they? (CASHCaMP)
Carboxyl - COOH
Amino - NH2
Sulfhydryl - SH
Hydroxyl - OH
CArbonyl - CO
methyl - CH3
Phosphate - -PO4
What does a carboxyl often dissociate to?
H+ + O-C=O-
What are carboxyls called?
Carboxylic acids
Which functional group is a weak acid?
Carboxyls. The H tends to dissociate from the OH.
Is carboxyl polar or non polar?
Polar!
Where are carboxyls in?
Fatty acids AND amino acids.
what are molecules with amino group called?
Amines
Which functional group imparts basic properties to molecule?
Amines, -NH2. They can absorb an H to become NH3.
Where are amines found?
Amino acids, nucleic acid, proteins.
What is the building block of protines?
Amino acids.
What does an amino acid look like?
Amino acids have amino on one side and a carboxyl on the other. there is an R attached to the chiral carbon.
What imparts the properties in an amino acid?
The R group.
Why are amino acids natural buffers?
One side can accept a proton (NH2) but the other side can donate (COOH).
Amino acids always have which isomer?
They always have enantiomers. Living organisms only make the L enantiomer amino acids. If not living, the process creates equal amounts of L and R.
What are molecules with sulfhydryls called?
"thiols"
where are they?
They are in proteins. Two of them create a disulfide bridge. They stabilize protein's tertiary structure. It actually exists cisteines.
Are sulfhydryls polar or non polar?
Polar
What are hydroxyls called?
alcohols
are hydroxyls polar or non polar
polar
where are hydroxyls found?
Sugars and alcohols
Sugars always have which two functional groups?
carbonyl and hydroxyl
Carbonyl groups are
C=O
If the carbonyl group is in the middle of a hydrocarbon chain, it is called
a ketone
if the carbonyl group is at the end of a hydrocarbon chain, it is called an
aldehyde
What is a popular aldehyde?
glucose
Fully ringed form of glucose does not have a free carbonyl group
ketones and aldehydes may be
Structural isomers. They have differen tproperties because they have different structures.
What is an aldose?
Sugars that have the aldehyde groups.
What is a ketose?
Sugars that have ketone groups.
Is carbonyl polar?
yes
Which group is the only non polar molecule?
Methyl group. It is the only hydrophobic group.
Which group is the only hydrophobic funtional group?
Methyl group.
what are methyls called?
Methylated compounds.
Where are methyl groups located?
They are non reactive and change shape They are everywhere that needs to be hydrophobic.
What group is ionized 2+?
phosphate
Which group is a strong acidic?
Phosphate group
Which group can donate two protons?
Phosphate group
Where is the phosphate group located?
In ATP, RNA, DNA
Point out the functional groups
This functional group is polar because the electronegative oxygen has a strong attraction for electrons. Water is attracted to this group, and therefore molecules that have this group (such as sugars) tend to dissolve in water. Alcohols are characterized by this functional group. What is this?
Hydroxyl groups "-OH"
This group is polar because oxygen has a strong attraction for electrons. If this group is at the end of a carbon skeleton, the molecule is called an aldehyde; otherwise it is called a ketone.
Carbonyl group "-CO"
The two electronegative oxygens of this group pull electrons away from the hydrogen atom. This weakens the bond between oxygen and hydrogen, and the hydrogen atom tends to dissociate from the molecule as a hydrogen (H+) ion. Because it donates hydrogen ions, this group is acidic, and molecules that contain these groups are known as carboxylic acids.
carboxyl group "-COOH"
The slightly electronegative nitrogen atom in this group tends to pick up hydrogen ions from the surrounding solution, and thus this functional group acts as a base. Because of the added hydrogen ion, this group usually has a +1 charge in the cell. This group is characteristic of organic molecules called amines.
amino group "-NH2"
Molecules termed thiols are characterized by this group, which resembles a hydroxyl group. These groups interact to help stabilize the structure of many proteins.
sulfhydryl "-SH"
The electronegative oxygens of this functional group draw electrons, and as a result the group acts as an acid, losing hydrogen ions to the surrounding solution. This dissociation leaves the group with a negative charge. This group is important in ATP and the transfer of energy between organic molecules.
phosphate group "-OPO3^2-"
Which group is most likely for an organic molecule behaving as a base?
amino group
The first organic molecule to be synthesized from in organic susbstances is
Acetic acid.
A straight chain carbon compound constructed from ___ must contain at least one arbon carbon double bond.
six hydrogen, three carbon. (draw it out)
what are properties of hydrocarbons?
-hydrophobic
-nonpolar
-good source of stored energy
Glucose and hexanoic acid each contains six cabon atoms but they have completely different properties. Glucose is a nutrient found in food; hexanoic gas is poinsonous. Their differences must be due to
Different functional groups
Although the structures of the functional groups that are most important to life vary, they all share one thing in common. They:
are all hydrophilic and increase the organic compounds water solubility. The only exception to this is the methyl group.
Which group's OH tends to dissociate?
carboxyl
Is an -SH alone a thiol?
no. It needs an R group attached
What is ATP's importance in the cell?
ATP stores the potential to react with water, thereby removing a phosphate group and releasing energy for cellular processes.
The two compounds are related to each other by:
-isomers
-organic compounds
-double-bonded compounds
-hydrocarbons
-All of the listed responses are correct.
all of the above
polar molecule
a molecule (such as water) with an uneven distribution of charges in different regions of the molecule
cohesion
the linking together of like molecules, often by hydrogen bonds
adhesion
cling of one substance to another, such as water to plant cell walls by means of hydrogen bonds
surface tension
a measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules
kinetic energy
the energy associated with the relative motion of objects. Moving matter can perform work by imparting motion to other matter.
heat
the total amount of kinetic energy due to the random motion of atoms or molecules in a body of matter; also called thermal energy. Heat is energy in its most random form.
temperature
a measure of the intensity of heat in degrees, reflecting the average kinetic energy of the molecules
Celsius scale
a temperature scale equal to 5/9 (F-32) that measures the freezing point of water at ) degrees Celsius and the boiling point of water at 100 degrees celsius
calorie (cal)
the amount of heat energy required to raise the temperature of 1 g of water by 1 degree Celsius; also the amount of heat energy that 1 g of water releases when it cools by 1 degree Celsius. The Calorie (with a capital C), usually used to indicate the energy content of food, is a kilocalorie.
kilocalorie (kcal)
a thousand calories; the amount of heat energy required to raise the temperature of 1 kg of water by 1 degree Celsius
joule (J)
a unit of energy; 1 J = 0.239 cal; 1 cal = 4.184 J
specific heat
the amount of heat that must be absorbed of lost for 1 g of a substance to change its temperature by 1 degree Celsius
heat of vaporization
the quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state
evaporative cooling
the process in which the surface of an object becomes cooler during evaporation, a result of the molecules with the greatest kinetic energy changing from the liquid to the gaseous state.
solution
a liquid that is a homogenous mixture of two or more substances
solvent
the dissolving agent of a solution. Water is the most versatile solvent known
solute
a substance that is dissolved in a solution
aqueous solution
a solution in which water is the solvent
hydration shell
the sphere of the water molecules around a dissolved ion
hydrophilic
having an affinity for water
colloid
a mixture made up of a liquid and particles that (because of their large size) remain suspended rather than dissolved in that liquid
hydrophobic
having no affinity for water; tending to coalesce and form droplets of water
molecular mass
the sum of the masses of all the atoms in a molecule; sometimes called molecular weight
mole (mol)
the number of grams of a substance that equals its molecular weight in daltons and contains Avogadro's number of molecules
molarity
a common measure of solute concentration, referring to the number of moles of solute per liter of solution
hydrogen ion
a single proton with a charge of 1+. The dissociation of a water molecule (H2O) leads to the generation of a hydroxide ion (OH-) and a hydrogen ion (H+); in water, H+ is not found alone but associates with a water molecules to form a hydronium ion
hydroxide ion
a water molecule that has lost a proton; OH-
hydronium ion
a water molecule that has an extra proton bound to it; H3O+, commonly represented as H+
acid
a substance that increases the hydrogen ion concentration of a solution
base
a substance that reduces the hydrogen ion concentration of a solution
pH
a measure of hydrogen ion concentration equal to -log [H+] and ranging in value from 0 to 14
buffer
a solution that contains a weak acid and its corresponding base. A buffer minimizes changes in pH when acids or bases are added to the solution
ocean acidification
decreasing pH of ocean waters due to absorption of excess atmospheric CO2 from the burning of fossil fuels
acid precipitation
rain, snow, or fog that is more acidic than pH 5.2
What is the devil's garden?
A bunch of Duroia hirsuta trees that are located in the South American Rainforest, and they live in a patch of land where no other trees grow. The devil's garden is basically an area protected by a colony of ants.
What protects the Duroia hirsuta trees?
Ants that live in the hollow stems of the tree. They do not plant the trees, but instead give them room to grow.

They inject intruder with poisonous chemical called formic acid. In this way, the ants create space for the growth of the Duroia trees that serve as their home
Where did Formic Acid get its name from?
It in fact got its name from the Latin word for ant, Formica.
What is formic acid used for by most ants?
The formic acid probably serves as a disinfectant the protects the ants against microbial parasites. The devil's garden ant is the first ant who uses it as a herbicide.
What are organisms composed of?
Matter
What is matter?
Matter is anything that takes up space and has a mass.
What is matter made up of?
Elements
What are elements?
An element is a substance that cannot be broken down to other substances by chemical reactions.
How many elements are currently recognized as being found in nature?
92 (e.i gold, copper, carbon and oxygen)
What is a compound?
A compound is a substance consisting of two or more elements combined in a fixed ratio.
Of the 92 natural elements, what percent are essential elements?
20-25%
What are essential elements?
They are elements that an organism needs to live a healthy life and reproduce.
What elements make up 96% of living matter?
oxygen, nitrogen, carbon and hydrogen.
What are trace elements?
Trace elements are required by an organism in only minute quantities.
What trace element is needed by all sources of life?
Iron
What happens when a human doesn't get an efficient amount of iodine?
Iodine is an essential ingredient of a hormone produced by the thyroid gland. An iodine deficiency in the diet causes the thyroid to grow to abnormal size, a condition called goiter.
What are the Essential Elements in the human body, symbol and percentage of body mass (including water)?
Oxygen (O) 65.0%
Carbon (C) 18.5%
Hydrogen (H) 9.5%
Nitrogen (N) 3.3%
Calcium (Ca) 1.5%
Phosphorus (P) 1.0%
Potassium (K) 0.4%
Sulfur (S) 0.3%
Sodium (Na) 0.2%
Chlorine (Cl) 0.2%
Magnesium (Mg) 0.1%
What is an atom?
An atom is the smallest unit of matter that still remains the properties of an element.
What are the smaller parts of matter of an atom called?
subatomic particles.
How many subatomic particles have been found but what are the main ones?
hundreds but the main ones are neutrons, electrons and protons.
Are protons and electrons charged?
Yes, they are charged.
What is the charge of a proton?
It has one positively charged unit.
What is the charge of an electron?
It has one negatively charged unit.
What is the charge of neutron?
It doesn't have a charge, it is neutral.
What is an atomic nucleus?
An atom's dense central core at the center ot it, containing neutrons and protons.
What do the electrons do?
The electrons form a sort of cloud of negative charge around the nucleus, and it is the attraction between opposite charges that keeps the electrons in the vicinity of the nucleus.
What is about the mass of neutrons and protons?
1.7 x 10^24 grams or almost 1 dalton.
What form of measurement is used with atoms, molecules and subatomic particles?
Daltons. In honor of John Dalton, the British scientist who helped develop atomic theory around 1800. (The dalton is the same as the atomic mass unit, or amu).
What is the mass of electrons compared to neutrons and protons?
1/2,000 of a proton of neutron's mass.
What is the Atomic Number?
The number of protons and electrons in an element used to classify elements
Where is the Atomic number written?
It is written as a subscript to the left of the symbol.
Is an atom neutral in electrical charge and if so, what does it mean or why not?
Unless otherwise indicated, yes. It means that for every proton there is an equal number of electrons.
What is the mass number?
It is the sum of protons plus neutrons in the nucleus of an atom.
Where do you write the mass number?
You write it on the left side of the symbol above the Atomic number, so that the mass number is like the numerator in a fraction.
How do you find out how many neutrons are in an element?
You minus the mass number from the atomic number.
What are Isotopes?
Atoms of the same element that have different numbers of neutrons, and therefore have a greater mass.
What is a Radioactive Isotope?
Isotope in which the nucleus decays (breaks down) over time, giving off radiation in the form of matter and energy
What are atoms mostly?
Empty space. For example, let's say that the atom helium was the size of a football stadium. The nucleus would be a tiny erase in the middle of the stadium and the electrons would be two tiny gnats flying around the stadium.
What subatomic particles are involved in chemical reactions?
Only the electrons, since the nuclei don't get close enough to interact.
What is energy?
The capacity to cause change, especially to do work (to move matter against an opposing force).
What is potential energy?
It is the energy that matter possesses because of its location or structure.
What causes potential energy?
The electrons of an atom have potential energy because of how they are arranged in relation to the nucleus. The negatively charged electrons are attracted to the positively charged nucleus. It takes work to move a given electron father away from the nucleus, so the more distant an electron is from the nucleus, the greater its potential energy.
What are electron shells?
An energy level of electrons at a characteristic average distance from the nucleus of an atom.
How many electrons can the first shell hold?
2 electrons
How many electrons does the second shell hold?
8 electrons
What are valence electrons?
An electron in the outermost shell.
What are valence shells?
The outermost energy shell of an atom contain the valence electrons involved in the chemical reactions of that atom.
What is an orbital?
The 3 dimensional space where an electron can be found 90% of the time.
Do atoms with the same number of electrons in their valence have similar chemical behavior?
Yes. For example, fluoride and chlorine both have 7 valence, and both form a compound when combined with sodium.
What is an unreactive atom?
An atom that has a completed valence shell, that is, it will not interact readily with other atoms.
how many electrons do each orbital contain?
2
What are chemical bonds?
An attraction between to atoms, resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atom. The bonded atom gain complete outer electron shells.
What are two strongest type of chemical bonds?
Covalent and ionic bonds.
What are covalent bonds?
Are atoms that are sharing a pair of valence electrons.
What is a molecule?
Two or more atoms held together by a covalent bond.
What is electronegativity?
The attraction of a given atom for the electrons of a covalent bond.
What is a nonpolar covalent bond?
A type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity.
What is a polar covalent bond?
A covalent bond between two atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.
What is a single bond?
A single covalent bond; the sharing of a pair of valence electrons by two atoms.
What is a double bond?
A double covalent bond' the sharing of two pairs of valence electrons by two atoms.
Name the types of ways to model molecules.
Electron Distribution Diagram (shows the electrons and shells)

Lewis Dot Structure ( H:H) and Structural Formula (H-H)

Space filling model (shows space, but nothing else)
What is a valence?
the bonding capacity of a given atom; usually equals the number of unpaired electrons required to complete the atom's outermost (valence) shell.
The more electronegative an atom is...?
The more strongly it pulls shared electrons toward itself.
Why are the electrons in a nonpolar bond equal?
Because they have the same amount of electronegativity. The atoms are at a a tug-a-war stand-off.
What is the most electronegative element?
Oxygen.
What is an Ionic bond?
They are two atoms that are so unequal in their attraction for valence that the more electronegative atom strips an electron completely away from its partner.
What is an ion?
An atom or group of atoms that has gained or lost one of more electrons, thus acquiring a change. A charged atom? Ask Miss Andrea...
What is a cation?
A positively charged ion
What is an anion?
A negatively charged ion
What are ionic compounds?
A compound resulting from formation of an ionic bond; Also called a salt.
What are salts?
An ionic compound.
What is a hydrogen bond?
A weak type of chemical bond that is formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule or in another region of the same molecule.
What are van der Waals interactions?
Weak attractions between molecules or parts of molecules that result from transient local partial charges.
What are chemical reactions?
The making and breaking of chemical bonds.
What are reactants?
The starting materials in a chemical reaction
What are products?
The end result of a chemical reaction.
What do two opposite-headed arrows mean?
That the reaction is reversible.
What are one of the factors affecting the rate of a reaction?
The concentration of reactants. The greater the concentration of reactant molecules, the more frequently they collide with one another and have an opportunity to react and form products. Same is true for products.
chemical equilibrium
A state of balance in which the rate of a forward reaction equals the rate of the reverse reaction and the concentrations of products and reactants remain unchanged.
element
any substance that cannot be broken down to any other substance by chemical reactions
compound
a substance consisting of two or more different elements combined in a fixed ratio
trace element
an element indispensable for life but required in extremely minute amounts
atom
smallest unit of matter that retains the properties of an element, made up of three subatomic components
electron
a subatomic particle with a single negative electrical charge which moves around the nucleus of an atom
neutron
a subatomic particle having no electrical charge found in the nucleus of atom
proton
a subatomic particle with a single positive charge found in the nucleus of an atom
atomic nucleus
an atom's dense central core, containing protons and neutrons
atomic mass
the total mass of an atom, which is the mass in grams of 1 mole of the atom
atomic number
the number of protons in the nucleus of the atom, unique for each element and designated by a subscript to the left of the elemental symbol
anion
a negatively charged ion
cation
a positively charged ion
covalent bond
a type of strong chemical bond in which two atoms share one or more pairs of valence electrons
dalton
a measure of mass for atoms and subatomic particles; the same as the atomic mass unit or amu
double bond
the sharing of two pairs of valence electrons by two atoms
electronegativity
the attraction of a given atom for the electrons of a covalent bond
electron shell
an energy level of electrons at a characteristic average distance from the nucleus of an atom
energy
the capacity to cause change, especially to do work (to move matter against an opposing force)
chemical equilibrium
in a chemical reaction, the state in which the rate of the forward reaction equals the rate of the reverse reaction, so that the relative concentrations of the reactants and products do not change with time.
hydrogen bond
a type of weak chemical bond that is formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.
ion
an atom or group of atoms that has gained or lost one or more electrons, thus acquiring a charge
ionic bond
a chemical bond resulting from the attraction of oppositely charged ions
ionic compound or salt
a compound resulting from the formation of an ionic bond
isotope
one of several atomic forms of an element, each with the same number of protons but different number of neutrons thus differing the atomic mass
mass number
the sum of the number of protons and neutrons in an atom's nucleus
molecular formula
a type of molecular notation representing the quantity of constituent atoms, but not the nature of the bonds that join them
nonpolar covalent bond
a type of covalent bond in which electrons are shared equally between two atoms of similar elecronegativity
orbital
the three dimensional space where an electron is found 90% of the time
polar covalent bond
a covalent bond between atoms that differ in electronegativity. the shared electrons are pulled closer to the more elecronegative atom, making it slightly negative and the other atom slightly positive.
potential energy
the energy that matter possesses as a result of its location or structure
product
a material resulting from a chemical reaction
radioactive isotope
an isotope that is unstable; the nucleus decays spontaneously giving off detectable particles and energy
reactant
a starting material in a chemical reaction
single bond
a single covalent bond; the sharing of a pair valence electron by two atoms
structural formula
a type of molecular notation in which the constituent atoms are joined by lines representing covalent bonds
valence
the bonding capacity of a given atom; usually equals the number of unpaired electrons required to complete the atom's outermost (valence) shell
valence electron
an electron in the outermost electron shell
valence shell
the outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom.
van der Waals interactions
weak attractions between molecules or parts of molecules the result from localized charged fluctuations
70-95%
cells are ___-___% water
hydrogen bonding
bonding that is a result of the polarity of water molecules
polar molecule
A molecule (such as water) with opposite charges on opposite sides.
4
maximum number of hydrogen bonds for a water molecule
the cohesion of water molecules
organisms depend on
cohesion
The binding together of like molecules, often by hydrogen bonds.
cohesion due to hydrogen bonding
contributes to the transport of water against gravity in plants
adhesion
The attraction between different kinds of molecules.
surface tension
A measure of how difficult it is to stretch or break the surface of a liquid. Water has a high one because of the hydrogen bonding of surface molecules.
moderates temperatures
function of water on earth for temperatures
absorbing heat from warmer air, releasing stored heat to colder air (acts as an effective heat bank)
how water stabilizes air temperatures
kinetic energy
The energy of motion, which is directly related to the speed of that motion. Moving matter does work by imparting motion to other matter.
heat
The total amount of kinetic energy due to molecular motion in a body of matter. Energy in its most random form.
temperature
A measure of the intensity of heat in degrees, reflecting the average kinetic energy of the molecules.
celsius scale
A temperature scale (°C) equal to 5/9 (°F 232) that measures the freezing point of water at 0°C and the boiling point of water at 100°C.
calorie (cal)
The amount of heat energy required to raise the temperature of 1 g of water by 1°C
kilocalories (kcal or C)
A thousand calories; the amount of heat energy required to raise the temperature of 1 kg of water by 1°C.
joule
A unit of energy: 1 J=50.239 cal; 1 cal
specific heat
The amount of heat that must be absorbed or lost for 1 gram of a substance to change its temperature by 1°C.
high
the specific heat of water is relatively
heat is released
when hydrogen bonds form
heat must be absorbed to
break hydrogen bonds
heat of vaporization
The quantity of heat a liquid must absorb for 1 gram of it to be converted from the liquid to the gaseous state.
evaporative cooling
the surface becomes cooler during evaporation because highly kinetic molecules become gaseous
less
ice is less or more dense than water
solution
A homogeneous mixture of two or more substances.
solvent
the substance in which the solute dissolves
solute
the substance dissolved
aqueous solution
solution in which water is the solvent
hydration shell
sphere of water molecules around each dissolved ion
water
the solvent of life
hydrophilic
Having an affinity for water; readily absorbing or dissolving in water.
hydrophobic
Repelling, tending not to combine with, or incapable of dissolving in water.
-phobic
ionic and nonpolar substances are hydro (-philic or -phobic)
mole (mol)
the molecular weight of a substance expressed in grams
molecular weight
the sum of all the atomic weights of the atoms in a given molecule
Avogadro's Number
number of molecules in a mole, 6.02x10^23
molarity
number of moles of solute per liter of solution
hydrogen ion
single proton with a charge of +1
hydroxide ion
OH-, charge of -1
acid
a substance that increases the hydrogen ion concentration of a solution
base
a substance that reduces the hydrogen ion concentration of a solution
neutral
a solution in which the H+ and OH- concentrations are equal is
strong acid
an acid that ionizes completely in aqueous solution
strong base
A base that dissociates completely into ions in solution.
7
neutral pH
the more basic you get
the higher you go on the pH scale
each pH unit
represents a tenfold difference in H+ and OH- concentrations (i.e. pH 3 is 10^3 times more acidic than pH 6)
buffers
substances that cause a solution to resist changes in pH
acid-base pairs
most buffers are
acid precipitation
Rain, snow, or fog that is more acidic than pH 5.6.
presence of sulfur oxides and nitrogen oxides in the air
causes acid precipitation
bonds broken when water vaporizes
bonds between water molecules
equal in their number of molecules
a mole of table sugar and a mole of vitamin C are
10^-4 M
Acid rain made the pH of a lake 4.0. What is the hydrogen ion concentration of the lake?
How does a hydrogen bond form?
When the oxygen of one water molecule is electrically attracted to the hydrogen of a nearby molecule.
____ is the basis for water's unusual properties
"Hydrogen bonding between water molecules..."
Polar molecule definition
The opposite ends of the molecule have opposite charges
Polar molecule example
the water molecule, which is shaped like a wide V.
A slightly positive/negative hydrogen of one molecule is attracted to the slightly positive/negative oxygen of a nearby molecule.
positive/negative
Cohesion definition
a phenomenon where hydrogen bonds hold the substance together
Cohesion due to hydrogen bonding contributes to the ________
transport of water against gravity in plants.
Adhesion definition
the clinging of one substance to another.
Adhesion of water to the walls of vessels helps ________
"counter the downward pull of gravity"
Water that evaporates from a leaf is replaced by ___________
"water from the vessels in the veins of the leaf.
kinetic energy defn
energy of motion. the faster it moves, the more KE it has
heat defn
total quantity of kinetic energy due to molecular motion in body of mater
temperature defn
measures intensity of heat due to the 'average' KE of molecules
A swimmer crossing the English channel has a higher temperature/heat than the water, ut the ocean contains far more temperaure/heat because of its volume
temperature, heat
Whenever two objects of different temperature are brought together, heat passes from the warmer/cooler to the cooler/warmer body until the two are the same temperature
warmer, cooler
Molecules in the cooler object speed up/slow down at the expense of the kinetic energy of the warmer object
speed up
Celsius scale Defn
Indication of temp. At sea level, water freezes at 0 C and boils at 100 C. The temp of the human body avgs 37 deg, and comfortable room temp at 20-25 C.
Calorie Defn
The amount of heat energy it takes to raise the temp of 1 g of water by 1 degree C. Also the amount of hea t that1 g of water releases when it cools by 1 degree C.
kilocalorie Defn
1,000 cal, The quantity of heat required to raise the temp of 1 kg of water by 1 C.
Specific Heat Defn
___ of a substance is defined as the amount of heat that must be absorbed or lost for 1 g of that substance to change its temp by 1 C.
The specific heat of water?
1 calorie per gram per degree Celsius, 1 cal/g/C.
Water has an unusually high/low specific heat?
high
Because of this high specific heat of water relative to other materials, water will change its temperature "more/less" when it absorbs or loses a given amount of heat
less
Specific heat can be thought of as a measure of....
how well a substance resists changing its temperature when it absorbs or releases heat.
Specific heat in relation to hydrogen bonding?
Heat must be absorbed in order to break hydrogen bonds, and heat is released when hydrogen bonds form. A calorie of heat causes a relatively small change in the temp of water because much of the heat energy i used to disrupt hydrogen bonds before the wtr molecules can begin moving faster. And when the temp of wtr drops slightly, many additional hydrogen bonds form, releasing a considerable amount of enrgy int he form of heat.
Relevance of water's high specific heat to life on earth??
A large body of water can absorb and store a huge amt of heat from the sun in the day time and during summer, while warming up only a few degrees. Because of the high specific heat, the water that covers most of Earth keeps temp fluctuations on land an din water within limits that permit life. Also, because organisms are made primarily of water, they are more able to resist changes in their own temp than if they were made of a liquid with a lower specific heat.
Why don't oceans and lakes freeze solid?
Becaues ice floats. Ice is less dense than liquid water because its more organized hydrogen bonding causes causes expansion into a crystal formation. Floating ice allows life to exist under the frozen surface of lakes and polar seas.
Heat of vaporization defn
the quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state.
What is evaporative cooling and why does it occur
As liquid evaporates, the surface of the liquid that remains behind cools down. This occurs becuaes the hottest molecules, those with the greatest kinetic energy, are the most likely to leave as gas.
Evaporation of water from the leaves of a plant helps keep the tissues of the leaves....
from becoming too warm int he sunlight.
Solution defn
a liquid that is a completely homogeneous mixture of two or more subsntaces
Solvent defn
The dissolving agent of a solution
Solute defn
The substance that is dissolved.
Aqueous solution defn
one in which water is the solvent.
If a cube of sugar was placed in water, which is the solvent and the other the solute?
Water is the solvent and sugar is the solute.
Water is/is not a universal solvent
is not!
Hydration shell defn
The sphere of water molecules around each dissolved ion.
When NaCl is placed in Water, which regions electrically attracted? how does this result in the dissloving of NaCl?
The oxygen regions of the water moelcules are negatively charged and cling to sodium cations. The hydrogen regions of the water molecules are positively charged and are attracted to chloride anions. As a result, water surrounds the individual sodium and chloride ions, separating and shielding them from one another.
What plant compounds are dissolved water?
the sap of plants
hydrophyllic defn
any substance, ionic or polar, that have affinity for water. Also applied to substances that do not dissolve, such as Cotton.
hydrophobic defn
substance without affinity for water. non-ionic and nonpolar, repel water, such as Vegetable oil. Also, the cell membrane, which has molecules related to oils.
Mole defn
equal to the number of the molecular weight of a substance, but upscaled from daltons to units of grams.
Molecular weight defn
the sum of the weights of all the atoms in a molecule
Avogadro's number
6.02 x 10 to the 23, the number of molecules in a mole.
Molarity defn
The number of moles of solute per liter of solution, the unit of concentration most often used by biologists for aqueous solutions.
How would we make a liter (L) of solution consisting of 1 mol of sucrose dissolved in water?
We would weight out 1 mol of sucrose, 341 g, and gradually add water, while stirring, until the sugar was completely dissolved. Then add enough water to bring the total volume of the solution up to 1 L. At this point, we would have 1-molar (1 M) solution of sucrose.
Hydrogen ion defn
a single proton with a charge of + 1.
Hydroxide ion defn
(OH-), a water molecule that has lost a proton, now a charge of -1.
Why is the dissociation of water, which is reversible and statisticaly rare, impt in the chemsistry of life?
Hydrogen and hydroxide ions are very reactive. Changes in their concentrations can drastically affect a cell's proteins and other complex molecules. Concentrations of H and OH- are equal in pure water, but add in solutes (acids and bases), and this disrupts the balance, or pH.
Acid defn
a substance that increases the hydrogen ion concentration of a solution.
Base defn
A substance that reduces the hydrogen ion concentration of a solution.
When hydrochloric acid (HCl) is added to water, hydrogen ions dissociate from chloride ions. This additional source of H+ results int he solution having more H than OH-. such a solution is known as a "acidic/basic" solution
"acidic"
A solution with a higher concentration of OH- than H is said to be acidic or basic?
basic
A solution in which the H and OH concentrations are equal is said to be:
neutral
pH defn
of a solution is defined as the negative logarithm (base 10) of the hydrogen ion concentration.
pH rises/declines as H + increases
declines
pH of 3 compared to pH of 6 means
there is a thousand times difference... 3 is a thousand times more acidic than 6.
Buffers defn
substances that minimize changes in the concentrations of H+ and OH- in a solution.
pH of human blood?
7.4
A person cannot survive for more than few minutes if the blood pH drops to ____ or rises to ____
7, 7.8
A buffer works by:
accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to the solution when they have been depleted.
What contribues to pH stability in human blood?
Carbonic acid (H2CO3), dissociates to yield a bicarbonate ion (HCO3-) and a hydrogen ion(H+)
Acid precipitation defn
refers to rain, snow or fog that is more acidic than 5.6.
Causes of acid precipitation
causes primarily by the prescence in the atomosphere of sulfur oxides and nitrogen oxides, gaseous compounds that react with water in the air to form strong acids, which fall to the earth with rain or snow.
Major source of sulfur and nitrogen oxides?
Burning of fossil fuels (coal, oil, and gas) in factories and automobiles.
Strong acidity can alter the structure of biological molecule and prevent them from...
carrying the essential chemical processes of life.
Element
A subsctance that cannot be broken down to other substance by ordinary chemcial means.
Matter
Anything that occupies space and has mass.
Compound
a substance consisting of two or more different elements combined in a fixed ratio.
Trace elements
an element that is essential for life but required in extremely minute amounts.
Atom
The smallest unit of matter that retains the properties of an element.
Proton
A subatomic particle with a single positive electrical charge, found in the nucleus of an atom.
Electron
A subatomic particle with a single negative electrical charge. One or more electrons move around the nuclues of an atom.
Neutron
A subatomic particle having no electrical charge, found in the nucleus of an atom.
Nucleus
An atom's central core, containing protons and neutrons.
Mass Number
The sum of the number of protons and neutrons in an atom's nucleus.
Atomic Mass
The total mass of an atom; also called atomic weight. Given as a whole number, the atomic mass approximately equals the mass number.
Isotopes
One of several atomic forms of an element, each with teh same number of protons but different number of neutrons.
Radioactive Isotope
An isotope whose nucleus decays spontaneously, giving off particles and energy.
Atomic Number
The number of protons in each atom of a particular element.
Electron Shells
An energy level representing the distance of an electron from the nucleus of an atom.
Chemical Bonds
An attraction between two atoms resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atoms. The bonded atoms gain complete outer electron shells.
Covalent Bond
A strong chemical bond in which two atoms share one or more pairs of outer-shell electrons.
Molecule
Two or more atoms held together by covalent bonds.
Electronegativity
The attraction of a given atom for the electrons of a covalent bond.
Nonpolar Covalent Bonds
A covalent bond in which electrons are shared equally between two atoms of similar electronegativity.
Polar Covalent Bond
A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electornegative atom, making it slightly negative and the other atom slightly positive.
Polar Molecule
A molecule containing polar covalent bonds and having an unequal distribution of charges.
Ion
An atom or group of atoms that has gained or lost one or more electrongs, thus acquiring a charge.
Ionic Bond
A chemical bond resulting from the attraction between oppositely charged ions.
Salt
A compound resulting from the formation of ionic bonds; also called an ionic compound.
Hydrogen Bonds
A type of weak chemical bond formed when the partially positive hydrogen atom participating in a polar covalent bond in one molecule is attracted to the partially negative atom participating in a polar covalent bond in another molecule (or in another region of the same molecule).
Chemical Reaction
The making and breaking of chemical bonds, leading to changes in the composition of matter.
Reactants
A starting material in a chemical reaction.
Product
An ending material in a chemical reaction.
Cohesion
The sticking together of molecules of the same kind, often by hydrogen bonds.
Adhesion
The attraction between different kinds of molecules.
Surface Tension
A measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules.
Heat
The amount of energy associated with the movement of atoms and molecules in a body of matter.
Temperature
Measures the intensity of heat.
Evaporative Cooling
occurs because the molecules with the greates energy leave.
Solution
A liquid that is a homogeneous mixture of two or more substances.
Solvent
The dissolving agent of a solution. Water is the most versatile solvent known.
Solute
A substance that is dissolved in a solution.
Aqueous Solution
A solution in which water is the solvent.
Acid
A substance that increases the hydrogen ion concentration in a solution. 0 on pH scale is a strong acid.
Base
A substance that decreases the hydrogen ion concentration in a solution. 14 is a strong base on the pH scale.
pH Scale
A scale we used to describe how acidic or basic a solution is. The scale ranges from 0-14, 0 being the most acidic and 14 being the most basic. 7 is neutral (pure water)
Buffers
A chemical substance that resists changes in pH by accepting hydrogen ions from or donating hydrogen ions to solutions.

substance that minimize changes in pH.
Acid Precipitation
Rain, snow or fog that is more acidic than pH 5.2.
Ocean Acidification
Decreasing pH of ocean waters due to absoprtion of excess atmospheric CO2 from the burning of fossil fuels.
What 4 elements make up about 96% of living matter?
Oxygen, carbon, hydrogen, and nitrogen.
The nucleus of an atom contains...??
Neutrons and protons.
First shell of an atom can contain how many electrons?
2
Second shell of an atom can contain how many electrons?
8
Third shell of an atom can contain how many electrons?
8
Fourth shell of an atom can contain how many electrons?
18
Ammonia
A small, very toxic molecule (NH3) produced by nitrogen fixation or as a metabolic waste product of protein and nucleic acid metabolism.
Anion
a negatively charged ion
Atom
smallest unit of matter that retains the properties of an element
Atomic Mass
the total mass of an atom, which is the mass in grams of 1 mole of the atom
Atomic nucleus
an atom's dense central core, containing protons and neutrons
Atomic number
number of protons in the nucleus of an atom
Cation
a positively charged ion
Chemical bond
an attraction between two atoms, resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atom. The bonded atoms gain complete out electron shells
Chemical equilibrium
in a chemical reaction, the state in which the rate of the forward reaction equals the rate of the reverse reaction, so thate the relative concentrations of the reactants and product don not change with time
Chemical reaction
the making and creaking of chemical bonds, leading to changes in the composition of matter
compound
a substance consisting of two or more different elements combined in a fixed ratio
covalent bond
a type of strong chemic bond in which two atoms share one or more pairs of valence electrons
dalton
a measure of mass for atoms and subatomic particles, the same as the atomic mass unit ( or amu)
double bond
a double covalent bond; the sharing of two pairs of valence electrons by two atoms
electron
subatomic particle with a single negative electrical charge and a mass about 1/2,000 that of a neutron or proton. One or more neutrons move around the nucleus of an atom
Electron shell
an energy level of electrons at a characteristic average distance from the nucleus of an atom
electronegativity
the attraction of a given atom for the electrons of a covalent bond
Element
any substance that cannot be broken down to any other substance by chemical reactions
energy
the capacity to cause change, especially to do work (to move matter against an opposite force)
hydrogen bond
any type of weak chemical bond that is formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule
ion
an atom or group of atoms that has gained or lost one or more electrons, thus acquiring a charge
ionic bond
a chemical bond resulting from the attraction between oppositely charged ions
ionic compound
a compound resulting from the formation of an ionic bond, also called a salt
isotope
one of several atomic forms of an element, each with the same number of protons but a different number of neutrons, thus differing in atomic mass
mass number
the sum of the number of protons and neutrons in an atom's nucleus
matter
anything that takes up space and has mass
molecular formula
a type of molecular notation representing the quantity of constituent atoms, but not the nature of the bonds that join them
molecule
two or more atoms held together by covalent bonds
neutron
a subatomic particle having no electrical charge, with a mass of about 1.7 x 10-24, found in the nucleus of an atom
nonpolar covalent bond
a type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity
nucleus
an atom's central core, containing protons and neutrons
orbital
the three-dimensional space where an electron is found 90% of the time
polar covalent bond
a covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly postive
potential energy
the energy that matter possesses as a result of its location or spatial arrangement (structure)
product
a material resulting from a chemical reaction
proton
a subatomic particle is a single positive electrical charge, found in the nucleus of an atom
radioactive isotope
an isotope that is unstable; the nucleus decays spontaneously, giving off detectable particles and energy
reactant
a starting material in a chemical reaction
salt
a compound resulting from the formation of an ionic bond, also called an ionic compound
single bond
a single covalent bond; the sharing of a pair of valence electrons by two atoms
structural formula
a type of molecular notation in which constituent atoms are joined by lines representing covalent bonds
Theory
an explanation that is broad in scope generates new hypotheses, and is supported by a large body of evidence
Trace element
an element indispensable for life but required in extremely minute amounts
valence
a bonding capacity of a given atom; usually equals the number of paired electrons required to complete the atom's outermost (valence) shell
valence electron
an electron in the outermost electron shell
valence shell
The outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom.
van der Waals interactions
Weak attractions between molecules or parts of molecules that result from localized charge fluctuations.
matter
anything that takes up space and has mass
element
any substance that cannot be broken down to any other substance by chemical reactions
compound
a substance consisting of two or more different elements combined in a fixed ratio
essential elements
a chemical element required for an organism to survive, grow, and reproduce
trace elements
an element indispensable for life but required in extremely minute amounts
atom
the smallest unit of matter that retains the properties of an element
neutrons
a subatomic particle having no electrical charge (electrically neutral), with a mass of about 1.7 x 10^-24 g, found in the nucleus of an atom
protons
a subatomic particle with a single positive electrical charge, with a mass of about 1.7 x 10^-24 g, found in the nucleus of an atom
electrons
a subatomic particle with a single negative electrical charge and a mass about 1/2000 that of a neutron or proton. One or more electrons move around the nucleus of an atom
atomic nucleus
an atom's dense central core, containing protons and neutrons
dalton
a measure of mass for atoms and subatomic particles; the same as the atomic mass unit, or amu
atomic number
the number of protons in the nucleus of an atom, unique for each element and designated by a subscript to the left of the elemental symbol
mass number
the sum of the number of protons and neutrons in an atom's nucleus
atomic mass
the total mass of an atom, which is the mass in grams of 1 mole of the atom
isotope
one of several atomic forms of an element, each with the same number of protons but a different number of neutrons, thus differing in atomic mass
radioactive isotope
an isotope (an atomic from a chemical equation) that is unstable; the nucleus decays spontaneously, giving off detectable particles and energy
energy
the capacity to cause change, especially to do work (to move matter against an opposing force)
potential energy
the energy that matter possesses as a result of its location or spatial arrangement (structure)
electron shells
an energy level of electrons at a characteristic average distance from the nucleus of an atom
valence electrons
an electron in the outermost electron shell
valence shell
the outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom
orbital
the three-dimensional space where an electron is found 90% of the time
chemical bonds
an attraction between two atoms, resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atoms. The bonded atoms gain complete outer electron shells
covalent bond
a type of strong chemical bond in which two atoms share one or more pairs of valence electrons
molecule
two or more atoms held together by covalent bonds
single bond
a single covalent bond; the sharing of a pair of valence electrons by two atoms
double bond
a double covalent bond; the sharing of two pairs of valence electrons by two atoms
valence
the bonding capacity of a given atom; usually equals the number of unpaired electrons required to complete the atom's outermost (valence) shell
electronegativity
the attraction of a given atom for the electrons of a covalent bond
nonpolar covalent bond
a type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity
polar covalent bond
a covalent bond between atoms that differ in electronegativity. the shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive
ion
an atom or group of atoms that has gained or lost one or more electrons, thus acquiring a charge
cation
a positively charged ion
anion
a negatively charged ion
ionic bond
a chemical bond resulting from the attraction between oppositely charged ions
ionic compounds
a compound resulting from the formation of an ionic bond; also called a salt
hydrogen bond
a type of weak chemical bond that is formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule or in another region of the same molecule
van der Waals interactions
weak attractions between molecules or parts of molecules that result from transient local partial charges
reactants
a starting material in a chemical reaction
products
a material resulting from a chemical reaction
chemical equilibrium
in a chemical reaction, the state in which the rate of the forward reaction equals the rate of the reverse reaction, so that the relative concentrations of the reactants and products do not change with time.
polar molecule
a molecule (such as water) with an uneven distribution of charges in different regions of the molecule
cohesion
the linking together of like molecules, often by hydrogen bonds
adhesion
cling of one substance to another, such as water to plant cell walls by means of hydrogen bonds
surface tension
a measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules
kinetic energy
the energy associated with the relative motion of objects. Moving matter can perform work by imparting motion to other matter.
heat
the total amount of kinetic energy due to the random motion of atoms or molecules in a body of matter; also called thermal energy. Heat is energy in its most random form.
temperature
a measure of the intensity of heat in degrees, reflecting the average kinetic energy of the molecules
Celsius scale
a temperature scale equal to 5/9 (F-32) that measures the freezing point of water at ) degrees Celsius and the boiling point of water at 100 degrees celsius
calorie (cal)
the amount of heat energy required to raise the temperature of 1 g of water by 1 degree Celsius; also the amount of heat energy that 1 g of water releases when it cools by 1 degree Celsius. The Calorie (with a capital C), usually used to indicate the energy content of food, is a kilocalorie.
kilocalorie (kcal)
a thousand calories; the amount of heat energy required to raise the temperature of 1 kg of water by 1 degree Celsius
joule (J)
a unit of energy; 1 J = 0.239 cal; 1 cal = 4.184 J
specific heat
the amount of heat that must be absorbed of lost for 1 g of a substance to change its temperature by 1 degree Celsius
heat of vaporization
the quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state
evaporative cooling
the process in which the surface of an object becomes cooler during evaporation, a result of the molecules with the greatest kinetic energy changing from the liquid to the gaseous state.
solution
a liquid that is a homogenous mixture of two or more substances
solvent
the dissolving agent of a solution. Water is the most versatile solvent known
solute
a substance that is dissolved in a solution
aqueous solution
a solution in which water is the solvent
hydration shell
the sphere of the water molecules around a dissolved ion
hydrophilic
having an affinity for water
colloid
a mixture made up of a liquid and particles that (because of their large size) remain suspended rather than dissolved in that liquid
hydrophobic
having no affinity for water; tending to coalesce and form droplets of water
molecular mass
the sum of the masses of all the atoms in a molecule; sometimes called molecular weight
mole (mol)
the number of grams of a substance that equals its molecular weight in daltons and contains Avogadro's number of molecules
molarity
a common measure of solute concentration, referring to the number of moles of solute per liter of solution
hydrogen ion
a single proton with a charge of 1+. The dissociation of a water molecule (H2O) leads to the generation of a hydroxide ion (OH-) and a hydrogen ion (H+); in water, H+ is not found alone but associates with a water molecules to form a hydronium ion
hydroxide ion
a water molecule that has lost a proton; OH-
hydronium ion
a water molecule that has an extra proton bound to it; H3O+, commonly represented as H+
acid
a substance that increases the hydrogen ion concentration of a solution
base
a substance that reduces the hydrogen ion concentration of a solution
pH
a measure of hydrogen ion concentration equal to -log [H+] and ranging in value from 0 to 14
buffer
a solution that contains a weak acid and its corresponding base. A buffer minimizes changes in pH when acids or bases are added to the solution
ocean acidification
decreasing pH of ocean waters due to absorption of excess atmospheric CO2 from the burning of fossil fuels
acid precipitation
rain, snow, or fog that is more acidic than pH 5.2
polar covalent bond
a covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive
Primary Structure
linear sequence of amino acids.
Secondary Structure
Alpha helix and beta pleated sheet formed by hydrogen bonds between atoms of the polypeptide backbone.
Tertiary Structure
Three-dimensional shape formed by interactions between R groups.
Quaternary Structure
Association of multiple polypeptides.
alpha (α) helix
The spiral shape resulting from the coiling of a polypeptide in a protein's secondary structure.
amino acid
An organic molecule containing a carboxyl group and an amino group; serves as the monomer of proteins.
amino group
In an organic molecule, a functional group consisting of a nitrogen atom bonded to two hydrogen atoms.
anabolic steroid
A synthetic variant of the male hormone testosterone that mimics some of its effects.
carbohydrate
Member of the class of biological molecules consisting of simple single-monomer sugars (monosaccharides), two-monomer sugars (disaccharides), and other multiunit sugars (polysaccharides).
carbon skeleton
The chain of carbon atoms that forms the structural backbone of an organic molecule.
carbonyl group
In an organic molecule, a functional group consisting of a carbon atom linked by a double bond to an oxygen atom.
carboxyl group
In an organic molecule, a functional group consisting of an oxygen atom double-bonded to a carbon atom that is also bonded to a hydroxyl group.
cellulose
A large polysaccharide composed of many glucose monomers linked into cable-like fibrils that provide structural support in plant cell walls.
chitin
A structural polysaccharide found in many fungal cell walls and in the exoskeletons of arthropods.
cholesterol
A steroid that is an important component of animal cell membranes and that acts as a precursor molecule for the synthesis of other steroids such as hormones.
dehydration reaction
A chemical process in which two molecules become covalently bonded to each other with the removal of a water molecule. Also called condensation.
denaturation
A process in which a protein unravels, losing its specific structure and hence function; can be caused by changes in pH or salt concentration or by high temperature. Also refers to the separation of the two strands of the DNA double helix, caused by similar factors.
deoxyribonucleic acid (DNA)
A double-stranded helical nucleic acid molecule consisting of nucleotide monomers with deoxyribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and thymine (T). Capable of replicating, is an organism's genetic material.
disaccharide
A sugar molecule consisting of two monosaccharides linked by a dehydration reaction.
double helix
The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.
enzyme
A protein (or RNA molecule) that serves as a biological catalyst, changing the rate of a chemical reaction without itself being changed into a different molecule in the process.
fat
A large lipid molecule made from an alcohol called glycerol and three fatty acids; a triglyceride. Most fats function as energy-storage molecules.
functional group
An assemblage of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.
gene
A discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses). Most of the genes of a eukaryote are located in its chromosomal DNA; a few are carried by the DNA of mitochondria and chloroplasts.
glycogen
An extensively branched polysaccharide of many glucose monomers; serves as an energy-storage molecule in liver and muscle cells; the animal equivalent of starch.
hydrocarbon
A chemical compound composed only of the elements carbon and hydrogen.
hydrolysis
A chemical process in which polymers are broken down by the chemical addition of water molecules to the bonds linking their monomers; an essential part of digestion.
hydrophilic
"Water-loving"; pertaining to polar, or charged, molecules (or parts of molecules) that are soluble in water.
hydrophobic
"Water-fearing"; pertaining to nonpolar molecules (or parts of molecules) that do not dissolve in water.
hydroxyl group
In an organic molecule, a functional group consisting of a hydrogen atom bonded to an oxygen atom.
isomer
Organic compounds with the same molecular formula but different structures and, therefore, different properties.
lipid
An organic compound consisting mainly of carbon and hydrogen atoms linked by nonpolar convalent bonds, making the compound mostly hydrophobic. Lipids include fats, phospholipids, and steroids and are insoluble in water.
methyl group
In an organic molecule, a carbon bonded to three hydrogens.
monomer
A chemical subunit that serves as a building block of a polymer.
monosaccharide
The simplest carbohydrate; a simple sugar with a molecular formula that is generally some multiple of CH2O. Monosaccharides are the building blocks of disaccharides and polysaccharides.
nucleic acid
A polymer consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular structures and activities. The two types of nucleic acids are DNA and RNA.
nucleotide
An organic monomer consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group. Nucleotides are the building blocks of nucleic acids.
organic compound
A chemical compound containing the element carbon and usually synthesized by cells.
peptide bond
The covalent linkage between two amino acid units in a polypeptide; formed by a dehydration reaction.
phosphate group
A functional group consisting of a phosphorus atom covalently bonded to four oxygen atoms.
phospholipid
A lipid made up of glycerol joined to two fatty acids and a phosphate group, giving the molecule a nonpolar hydrophobic tail and a polar hydrophilic head. Phospholipids form bilayers that function as biological membranes.
polymer
A large molecule consisting of many identical or similar molecular units, called monomers, covalently joined together in a chain.
polypeptide
A polymer (chain) of amino acids linked by peptide bonds.
polysaccharide
A carbohydrate polymer consisting of hundreds to thousands of monosaccharides (sugars) linked by dehydration synthesis.
primary structure
The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.
protein
A functional biological molecule consisting of one or more polypeptides folded into a specific three-dimensional structure.
quaternary structure
The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.
ribonucleic acid (RNA)
A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis and as the genome of some viruses.
saturated
Pertaining to fats and fatty acids whose hydrocarbon chains contain the maximum number of hydrogens and therefore have no double covalent bonds. Saturated fats and fatty acids solidify at room temperature.
secondary structure
The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.
starch
A storage polysaccharide found in the roots of plants and certain other cells; a polymer of glucose.
steroid
A type of lipid whose carbon skeleton is in the form of four fused rings with various chemical groups attached; examples are cholesterol, testosterone, and estrogen.
tertiary structure
The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.
unsaturated
Pertaining to fats and fatty acids whose hydrocarbon chains lack the maximum number of hydrogen atoms and therefore have one or more double covalent bonds. Unsaturated fats and fatty acids do not solidify at room temperature.
Amino Group Identify
--NH2
Carboxyl Group Identify
--COOH
polar covalent bonds
bonds in which electrons are not shared equally between atoms of different elements in a compound
polar molecule
molecule with an unequal distribution of charge, resulting in the molecule having a positive end and a negative end
cohesion
the binding together of like molecules, often by hydrogen bonds
adhesion
attraction between molecules of different substances
surface tension
a measure of how difficult it is to stretch or break the surface of a liquid
calorie
unit of heat defined as the quantity of heat required to raise the temperature of 1 gram of water by 1 degree centigrade at atmospheric pressure
joule
SI unit of energy, used to measure work
specific heat
the heat required to raise the temperature of one gram of a substance one degree centigrade
heat of vaporization
the amount of energy required for the liquid at its boiling point to become a gas
evaporative cooling
the property of a liquid whereby the surface becomes cooler during evaporation, owing to a loss of highly kinetic molecules to the gaseous state.
hydration shell
sphere of water molecules around each dissolved ion
colloid
a mixture consisting of tiny particles that are intermediate in size between those in solutions and those in suspensions and that are suspended in a liquid, solid, or gas
molecular mass
the sum of the masses of all atoms in a molecule
mole
the molecular weight of a substance expressed in grams
molarity
concentration measured by the number of moles of solute per liter of solvent
hydronium ion
H3O+
hydroxide ion
OH-
hydrogen ion
H+
buffer
an ionic compound that resists changes in its pH
pH
a value that indicated the acidity or alkalinity of a solution on a scale of 0-14, based on the proportion of H+ ions.
ocean acidification
decreasing pH of ocean waters due to absorption of excess atmospheric CO2 from the burning of fossil fuels
acid precipitation
rain containing acids that form in the atmosphere when industrial gas emissions (especially sulfur dioxide and nitrogen oxides) combine with water
Kinetic Energy
Energy of motion.
Celsius Scale
Water freezes 0c and boils at 100c.
Temperature
Is a measure of heat intensity that represents average kinetic energy of molecule.
Solution
A liquid that is a completely homogeneous mixture of two or more substance.
Solvent
A liquid substance capable of dissolving other substances.
Solute
Substance that is being dissolve.
Aqueous solution
a solution in which water is the solvent
Base
A substance that reduces the hydrogen ion concentration of a solution
selective permeability
a property of biological membranes that allows them to regulate the passage of substances across them
amphipathic
having both a hydrophilic region and a hydrophobic region
fluid mosaic model
the currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of protein molecules drifting laterally in a fluid bilayer of phospholipids.
integral protein
a transmembrane protein with hydrophobic regions that extend into and often completely span the hydrophobic interior of the membrane and with hydrophilic regions in contact with the aqueous solution on one or both sides of the membrane (or lining the channel in the case of a channel protein).
peripheral protein
a protein loosely bound to surface of a membrane or to part of an integral protein and not embedded in the lipid bilayer
glycolipid
a lipid with one or more covalently attached carbohydrates
glycoprotein
a protein with one or more covalently attached carbohydrates
transport protein
a transmembrane protein that helps a certain substance or class of closely related substances to cross the membrane
aquaporin
a channel protein in the plasma membrane of a plant, animal or microorganism cell that specifically facilitates osmosis, the diffusion of free water across the membrane
diffusion
the spontaneous movement of a substance down its concentration or electrochemical gradient, from a region where it is more concentrated to a region where it is less concentrated.
concentration gradient
a region along which the density of a chemical substance increases or decreases.
passive transport
the diffusion of a substance across a biological membrane with no expenditure of energy
osmosis
the diffusion of free water across a selectively permeable membrane
tonicity
the ability of a solution surrounding a cell to cause that cell to gain or loose water.
isotonic
referring to a soultion that, when surrounding a cell, causes no net movement of water into or out of a cell
hypertonic
referring to a solution that, when surrounding a cell, will cause the cell to lose water
hypotonic
referring to a solution that, when surrounding a cell, will cause the cell to take up water.
osmoregulation
regulation of solute concentrations and water balance by a cell or organism
turgid
swollen or distended, as in plant cells. (A walled cell becomes turgid if it has a lower water potential then its surroundings, resulting in entry of water.
flaccid
lacking turgor (stiffness or firmness), as in the plant cell in surroundings where there is a tendency for water to leave the cell. ( A wall cell becomes flaccid if it has a higher water potential than its surroundings, resulting in the loss of water.)
plasmolysis
a phenomenon in walled cells in which the cytoplasm shrivels and the plasma membrane pulls away from the cell wall; occurs when the cell loses water to a hypertonic environment
facilitated diffusion
the passage of molecules or ions down their electrochemical gradient across a biological membrane with the assistance of specific transmembrane transport proteins, requiring no energy expenditure.
ion channels
a transmembrane protein channel that allows a specific ion to diffuse across the membrane down its concentration or electrochemical gradient.
gated channels
a transmembrane protein channel that opens or closes in response to a particular stimulus
active transport
the movement of a substance across a cell membrane against its concentration gradient, mediated by specific transport proteins and requiring an expenditure of energy
sodium-potassium pump
a transport protein in the plasma membrane of animal cells that actively transports sodium out of the cell an potassium into the cell
membrane potential
the difference in electrical charge (voltage) across a cell's plasma membrane due to the differential distribution of ions. Membrane potential affects the activity of excitable cells and the transmembrane movement of all charged substances.
electrochemical gradient
the diffusion gradient of an ion, which is affected by both the concentration difference of an ion across a membrane (a chemical force) and the ion's tendency to move relative to the membrane potential (an electrical force).
electrogenic pump
an active transport protein that generates voltage across a membrane while pumping ions.
proton pump
an active transport protein in a cell membrane that uses ATP to transport hydrogen ions out of a cell against their concentration gradient, generating a membrane potential in the process
cotransport
the coupling of the "downhill" diffusion of one substance to the "uphill" transport of another against its own concentration gradient
exocytosis
the cellular secretion of biological molecules by the fusion of vesicles containing them with the plasma membrane.
endocytosis
cellular uptake of biological molecules and particulate matter via formation of vesicles from the plasma membrane.
ligands
molecule that binds specifically to another molecule, usually a larger one.
phagocytosis
a type of endocytosis in which large particulate substances or small organisms are taken up by a cell. It's carried out by some protists and by certain immune cells of animals.
pinocytosis
a type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes
receptor-mediated endocytosis
the movement of specific molecules into a cell by the inward budding of vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances
Light Microscope
Simple and compound, uses magnification and light to view the subject. First used in 1665. Resolution limitation is 0.2 micro meters (um)
Magnification
Ratio of object's image to real size.
Resolution
Minimum distance between two points at which they can still be distinguished as separate points.
Electron microscope
Introduced in 1950. Uses electrons, not light. has better resolution, 0.2 nano meters. can resolve proteins, viruses and small molecules. Excellent for cytology
Transmission Electron Microscope (TEM)
Aims a beam at a thin cross section (slice) of specimen which has been stained with metal particles. Viewed as a 2D image on a screen.
Scanning Electron Microscope (SEM)
Aims a beam at the surface of a specimen stained with metal particles. Provides 3D image of the surface of a specimin on a screen
Cell fractionation
separates major organelles to study the function of each cell
Homogenate
Blend, disrupt the cell walls
Centrifugation
Spinning very fast
Supernatant
The liquid left separate from the pellet after spinning
Decant
removing the supernatant
Pellet
The organelles that settle at the bottom during spinning.
Prokaryotic cells
Bacteria and Archaea. No true nucleus, no membrane bound organelles. Still has DNA contained in a nucleoid.
Nucleus
Information center of the cell
Cytoplasm
Everything between the the plasma membrane and the nucleus
Cytosol
the aqueous part of the cytoplasm within which various particles and organelles are suspended
Exclusive to Plant cells
Cell wall, chloroplasts, central vacuole, Plasmadesmata
Exclusive to animal cells
Lysosomes, centrioles, flagella (some plant sperm have them)
Plasma membrane
Made of phopholipids, regulates passage of materials into and out of the cell.
Chromatin
DNA and proteins which make up chromosomes
Chromosomes
long segments of chromatin, only visible during cell division.
Nucleolus
Area of the nucleus where ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm.
Endomembrane system
Nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vacuoles.
Endoplasmic reticulum (ER)
Membranous network of tubules and sacs (cisternae) that separate its internal lumen (cisternal space) from the cytosol. Connected to the nuclear envolope
Rough Endoplasmic reticulum (ER)
Rough because of ribosomes. Makes secretory proteins. Proteins may have carbohydrates added to them. Packaged in vesicles. Also makes membranes for other organelles.
Ribosomes
Organelles that are sites for proteins assembly. Can be free (suspended in cytoplasm) or bound (attached to ER).
Golgi apparatus
Made of stacked, flattened sacs (cisternae) that manufacture, store, sort and ship products from the ER. Vesicles transport proteins between the golgi and other cell structures. Cis and trans are shipping and receiving side.
Lysosomes
Membrane enclosed bag of hydrolytic enzymes that digest macromolecules. 4 digestive enzymes: carbohydrases, proteases, lipases, and nucleases. Made in the R-ER and processed int he golgi. Keeps destructive enzymes from the cytosol.
Phagocytosis
Digestion of external organic matter that is captured by the cell.
Autophagy
digestion of the cells own organic matter (recycling)
Smooth ER
No ribosomes. Synthesizes lipids, phospholipids and steroids. Carbohydrate metabolism. Detox of drugs and poisons. Stores calcium ions.
Mirochondria
Sites for cellular respiration to make ATP. has its own DNA. Only in eukaryotes.
Cytoskeleton
Support structure for the cell.
Chloroplasts
Chlorophyll containing sites of photosynthesis. Only found in plants and algae.
Stroma
in plants, the solution that surrounds the thylakoids in a chloroplast
Thylakoids
Flattened sacks stacked into grana that are critical for converting light into chemical energy
Cell wall
Cellulose fibers. Plants only. Protection, rigidity, rpevent excess H2O uptake.
Extracellular matrix
Outside of the cell. Support, cushioning, communication.
All forms of life share common properties.
Order, Reproduction, Growth & Development, Energy Processing, Response to Environment, Regulation, and Evolutionary Adaptation.
Order
Life has a highly ordered structure. Living cells are the basis of this complex organization.
Reproduction
Organisms reproduce their own kind.
Growth and Development
DNA dictates the pattern of growth and development in a given organism.
Energy Processing
When we eat food, we utilize that as energy for daily functioning, growth, and development.
Response to Environment
All organisms respond to environmental stimuli.
Regulation
There are many methods different organisms do to maintain a safe homeostasis.
Evolutionary Adaptation
Organisms adapt over time to better suit their environment, as the successful members of a species pass down their DNA onto following generations.
Life's Hierarchy of Oganization
Biosphere
Ecosystem
Community
Population
Organism
Organ System
Organ
Tissue
Cell
Organelle
Molecule
Why are cells considered the basic units of life?
They are the lowest level on life's hierarchy of organization that can carry out all the activities required for life. All organisms are composed of cells.
Prokaryotic Cell
A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles; found only in the domains Bacteria and Archaea. First to evolve.
Eukaryotic Cell
A type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles. Protists, plants, fungi, and animals.
Systems Biology
An approach to studying biology that aims to model the dynamic behavior of whole biological systems based on the study of the interactions among the system's parts.
Explain how photosynthesis functions in both the cycling of chemical nutrients and the flow of energy in an ecosystem.
Photosynthesis uses light to convert CO2 and water into energy-rich food. This is how most organisms get their nutrients and chemical energy.
DNA
The chemical substance of genes.
Genes
The units of inheritance that transmit information from parents to offspring. Genes are grouped into longer molecules called chromosomes and control the activities of the cell.
3 Domains of Lfie
Domain Bacteria, Domain Archaea, and Domain Eukarya.
Domain Bacteria
Prokaryotic.
Domain Archaea
Prokaryotic. Live in Earth's extreme environments.
Producers
Provide food for a particular ecosystem.
Consumers
Eat plants and other animals.
Decomposers
Small animals, fungi, and bacteria that decompose waste and remains of dead organisms; act as recyclers
Energy
An ecosystem gains and loses energy constantly.
Chemical energy
passed through a series of consumers, eventually decomposes.
Water
Life first evolved in water.All living organisms require water. Universal solvent.
Matter
Anything that occupies space and has mass. Matter is composed of chemical elements.
Element
A substance that cannot be broken down into other substances. There are 92 elements in nature.
Elements in the Humans
65% Oxygen, 18.5% Carbon, 9.5% Hydrogen, 3.3% Nitrogen; 3.7% calcium, phosphorous, potassium, sulfur, sodium, chlorine, and magnesium. >.01% other trace elements.
Compound
A substance containing 2 or more elements in a fixed ratio. More common than pure elements.
Atom
Smallest unit of matter that still retains the properties of an element. Consist of 3 subatomic particles: proton, neutron, and electron.
Atomic #
= #of protons. Atoms of the same element will always have the same atomic number. Isotopes will have a different mass #.
Mass #
The sum of protons and neutrons in the nucleus.
Isotope
Atoms that vary in their # of neutrons but have the same # of protons.
Noble Gases
[Group 8] non-reactive; already have 8 electrons.
Covalent Bond
Join atoms into molecules via electron sharing. It is the strongest type of chemical bond.
Ionic Bond
Attraction between ions of opposite charge. i.e. NaCl
Nonpolar Covalent Bond
In molecules of only 1 element, the pull between them is equal.
Polar Covalent Bond
Water has atoms with different electronegativities. Oxygen attracts more shared electrons than hydrogen. Water is a polar molecule.
Hydrogen Bond
Weak bonds important in chemistry (and life).
Cohesion
The tendency of molecules to stick to others of the same kind. Much stronger for H2O than other liquids. Related to surface tension.
Adhesion
The tendency of 2 kinds of molecules to stick together.b
Surface Tension
A measure of how difficult it is to break the surface of a liquid. Hydrogen bonds give water a strong surface tension.
Heat
The energy associated with movement of atoms and molecules in matter. Heat is released when hydrogen bonds form.
Temperature
Measures the intensity of heat.
Acid
A compound that releases H2 into a solution.
Base
A compound that accepts H2.
pH Scale
Describes how acidic or basic a solution is. Ranges from 0-14; 0=most acidic, 14= most basic.
light microscopy
uses light to permit magnification and viewing of cellular structures up to 1000 times their natural size
scanning electron microscopy
A process that utilizes an electron beam to produce an image of the three-dimensional surface of biological samples; the sample is coated with a thin layer of a heavy metal such as gold or palladium and then exposed to an electron beam
transmission electron microscopy
electrons penetrate an ultrathin section of tissue to strike a photographic plate
cell fractionation
technique in which cells are broken into pieces and the different cell parts are separated
cytosol
the aqueous part of the cytoplasm within which various particles and organelles are suspended
nucleoid
A dense region of DNA in a prokaryotic cell.
chromatin
long strands of DNA found in the eukaryotic cell nucleus; condense to form chromosomes
nucleus
The organelle that contains the DNA and controls the processes of the cell
nucleolus
The organelle where ribosomes are made, synthesized and partially assembled, located in the nucleus
nuclear envelope
double membrane perforated with pores that control the flow of materials in and out of the nucleus
ribosomes
organelles made of protein and RNA that direct protein synthesis in the cytoplasm
nuclear lamina
A netlike array of protein filaments that maintains the shape of the nucleus.
endoplasmic reticulum
an internal membrane system in which components of cell membrane and some proteins are constructed
rough ER
That portion of the endoplasmic reticulum studded with ribosomes, attached to nuclear membrane and synthesizes phospholipids for cell membrane
smooth ER
synthesis of lipids, phospholipids and steroid sex hormones-help detoxify drugs and poisons (liver cells) involves adding hydroxyl groups to drugs to make soluble and easier to flush from body
glycoproteins
proteins that have carbohydrates covalently bonded to them
vesicles
small membrane sacs that specialize in moving products into, out of, and within a cell
golgi apparatus
stack of membranes in the cell that modifies, sorts, and packages proteins from the endoplasmic reticulum
lysosome
organelle filled with enzymes needed to break down certain materials in the cell
phagocytosis
process in which extensions of cytoplasm surround and engulf large particles and take them into the cell
food vacuole
A membranous sac formed by phagocytosis of microorganisms or particles to be used as food by the cell.
contractile vacuole
saclike organelles that expand to collect excess water and contract to squeeze the water out of the cell
central vacuole
A membranous sac in a mature plant cell with diverse roles in reproduction, growth, and development.
mitochondria
Powerhouse of the cell, organelle that is the site of ATP (energy) production
chloroplast
a structure in the cells of plants and some other organisms that captures energy from sunlight and uses it to produce food
endosymbiont theory
mitochondria and plastids, including chloroplasts, originated as prokaryotic cells engulfed by an ancestral eukaryotic cell. The engulfed cell and its host cell then evolved into a single organism.
mitochondrial matrix
The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the Krebs cycle.
cristae
Infoldings of the inner membrane of a mitochondrion that houses the electon transport chain and the enzyme catalyzing the synthesis of ATP.
thylakoids
A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy.
grana
stacked portion of the thylakoid membrane in the chloroplast. Grana function in the light reactions of photosynthesis
stroma
The fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water.
plastids
organelles that are surrounded by a double membrane and contain their own DNA
peroxisomes
Contain oxidase enzymes that detoxify alcohol, hydrogen peroxide, and other harmful chemicals
cytoskeleton
a microscopic network of actin filaments and microtubules in the cytoplasm of many living cells that gives the cell shape and coherence
motor proteins
a protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.
microtubules
hollow tubes of protein about 25 nanometers in diameter, support the cell and moves organelles within the cell, composed of tubulin polymers
microfilaments
thinner, solid rods of protein that enable the cell to move or change shape when protein subunits slide past one another, composed of actin subunits
intermediate filaments
range from 7-11nm in diameter, and strengthen the cell and help maintain its shape, stabilize the positions of organelles, and stabilize the position of the cell with respect to surrounding cells through specialized attachment to the cell membrane, composed of keratin subunits
keratin
hard protein material found in the epidermis, hair, and nails
actin
A globular protein that links into chains, two of which twist helically about each other, forming microfilaments in muscle and other contractile elements in cells.
tubulin
globular protein subunit forming the hollow cylinder of microtubules
centrosome
Structure present in the cytoplasm of animal cells, important during cell division; functions as a microtubule-organizing center. A centrosome has two centrioles.
centrioles
One of two tiny structures located in the cytoplasm of animal cells near the nuclear envelope; play a role in cell division.
cilia
short, hair-like structures made of microtubules that enable movement of cells or movement of materials outside a cell
flagella
whiplike tails found in one-celled organisms to aid in movement
basel body
a structure resembling a centriole that produces a cilium or flagellum and anchors this structure within the plasma membrane
dynein
A contractile protein connecting microtubules in the '9+2- arrangement of cilia and eukaryotic flagella. The contraction of dynein produces the characteristic movement of these structures.
cortex
(1) The outer region of cytoplasm in a eukaryotic cell, lying just under the plasma membrane, that has a more gel-like consistency than the inner regions, due to the presence of multiple microfilaments. (2) In plants, ground tissue that is between the vascular tissue and dermal tissue in a root or eudicot stem.
myosin
A protein present in muscle fibers that aids in contraction and makes up the majority of muscle fiber, thick filaments
pseudopodia
A cellular extension of amoeboid cells used in moving and feeding
cytoplasmic streaming
A circular flow of cytoplasm, involving myosin and actin filaments, that speeds the distribution of materials within cells.
cell wall
strong supporting layer of cellulose or chitin around the cell membrane in plants, algae, and some bacteria
middle lamina
A thin layer of adhesive extracellular material, primarily pectins, found between the primary walls of adjacent young plant cells.
primary cell wall
A relatively thin and flexable cell wall furthest outside that is first secreted by a plant cell
secondary cell wall
Added between the plasma membrane and the primary cell wall, a strong and durable matrix often deposited in several laminated layers for plant cell protection and support
extracellular matrix
The substance in which animal tissue cells are embedded, consisting of protein and polysaccharides.
proteoglycans
a glycoprotein consisting of a small core protein with many carbohydrate chains attached, found in the extracellular matrix of animal cells.
fibronectin
a glycoprotein that helps animal cells attach to the extracellular matrix.
integrins
in animal cells, a transmembrane receptor protein that interconnects the extracellular matrix and the cytoskeleton.
plasmodesmata
An open channel in the cell wall of plants through which strands of cytosol connect from adjacent cells
gap junctions
provide cytoplasmic channels between adjacent animal cells
tight junctions
Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
desmosomes
specialized junctions that hold adjacent cell together, consist of dense plate at point of adhesion plus extracellular cementing material
All forms of life share common properties.
Order, Reproduction, Growth & Development, Energy Processing, Response to Environment, Regulation, and Evolutionary Adaptation.
Order
Life has a highly ordered structure. Living cells are the basis of this complex organization.
Reproduction
Organisms reproduce their own kind.
Growth and Development
DNA dictates the pattern of growth and development in a given organism.
Energy Processing
When we eat food, we utilize that as energy for daily functioning, growth, and development.
Response to Environment
All organisms respond to environmental stimuli.
Regulation
There are many methods different organisms do to maintain a safe homeostasis.
Evolutionary Adaptation
Organisms adapt over time to better suit their environment, as the successful members of a species pass down their DNA onto following generations.
Life's Hierarchy of Oganization
Biosphere
Ecosystem
Community
Population
O