308 terms

Animal Biology- Exam 1

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Biology
the scientific study of life on Earth
Life (physics)
a process that can retain complexity and replicate (matter is not replicated, information is)
Life (biology)
a characteristic that distinguishes entities that contain and sustain certain properties versus entities which lack or have ceased to maintain these properties (such as order, energy processing, homeostasis, response, reproduction, and adaptation)
Properties of Life
1. Living things are organized
2. Living things process materials and energy
3. Living things maintain homeostasis
4. Living things respond to stimuli
5. Living things reproduce
6. Living things can adapt
Order
-all living things exhibit complex patterns of matter
-hierarchical, each new level can be described by interactions of smaller parts at the levels below it
-The functions of living things emerges from this
Order of living things
atom-> molecule-> organelle-> cell-> tissue-> organ-> organ system -> organism
Energy Processing
living organisms take in energy to maintain organization and to produce the other emergent phenomena associated with life
Two most abundant Energy processing in living organism on Earth
Cellular respiration and photosynthesis
Metabolism
transformation of energy by converting chemicals and energy into biological components (anabolism) and decomposing organic matter (catabolism)
Anabolism
set of metabolic pathways that construct larger molecules from smaller ones (endergonic = requires energy)
Example of Anabolism
plants using sunlight to grow
Catabolism
set of metabolic pathways that deconstruct larger molecules into smaller ones (exergonic = releases energy)
Example of Catabolism
eating a cheese burger
homeostasis
-property of a system in which variables are regulated so that internal conditions remain stable
-maintain an internal balance
-Complex chemical reactions work to maintain optimal internal conditions
Urinary and Endocrine system
organ systems that work to maintain homeostasis in animals (e.g. regulation of body temp, blood sugar, and pH)
3 features of homeostasis
sensor, control, effector
Sensor
sensing component that monitors and responds to changes in the environment
Control
receives info from sensors, initiates response to info so as to bring conditions within an optimal range
Effector
the target acted on by the control to bring about the change back to the normal state
Behavior
(response to stimuli) the responses of living organisms to internal and/or external stimuli
(ex: plants responding to sunlight by growing)
Reproduction
-the biological process by which new individual organisms are produced from their "parents"

-In actuality, the information from the parent(s) is what is being reproduced, not the matter itself (The order of nuclei in your DNA is information that is being reproduced)
Adaptation
-the ability of a population change, over generational time, in response to the environment
-must happen at the level of information (DNA)
-tend to gain or lose physical traits that are beneficial or not beneficial to survive
-evolve overtime to be beneficial for reproduction
Science
-(Latin, "to know") - a process that builds and organizes knowledge about the universe
-A means by which to collect and analyze information
-
Information
what is conveyed or represented by a particular arrangement or sequence of things
Limits
what science can't do
-cannot draw conclusions about the supernatural
-does not tell you how to use scientific knowledge (can't tell you what to do with it
or can't point towards right or wrong answer)
-cannot produce true information regarding subjective experiences (opinions are not facts)
Supernatural
attributed to some force beyond scientific understanding or the laws of nature
Discovery science
process of scientific inquiry that focuses on using observations to describe nature
Steps:
Step 1: Find/observe new things/phenomena
Step 2: Describe, in detail, what you've found
Verifiable observation
observation whose truth/accuracy can be demonstrated
Examples of Discovery Science
ocean floor (submarine) or rover on mars
Scientific modeling
process of scientific inquiry that aims to make a particular process or feature of the world easier to understand by using existing knowledge to create a simplified model
(usually done if something is too expensive/complicated to study in real life)
Hypothesis-driven science
process of scientific inquiry that uses the steps of the scientific method to answer scientific questions
Hypothesis
a preliminary explanation for a phenomenon that has been observed
Scientific method
a body of scientific techniques used to investigate and understand phenomena observed in the universe
1. Observations
2. Question
3. Hypothesis
4. Prediction
5. Experiment
6. Analyze and Intepret
In science, the result of the experiment does what?
either supports or does not support the hypothesis
Is knowledge gained even when you are wrong?
yes
Can multiple hypothesis explain a single observation?
yes it is possible
Rigorous scrutiny
-new ideas and discoveries are scrutinized, questioned, and evaluated until all evidence supports them
-Never assume anything, always be critical
Openness and collaboration
scientific knowledge is often shared publicly and can therefore be further built upon by others
Physics
scientific study of the motion and behavior of matter and energy through time and space (All living organisms are bound by the physical properties of the universe)
Matter
-anything that has mass and occupies space
-can exist in several different states within the universe (solid, liquid, gas, plasma)
Energy
the ability to do work or bring about change
Plasma
the most abundant matter in the universe due to stars
atom
smallest unit of matter that still retains the properties of an element
proton
positively charged, 1 amu
electron
negatively charged, 0 amu
neutron
no charge, 1 amu
elements
-a substance that cannot be broken down into other substances by chemical means
-distinguished by the # of protons they contain
-92 naturally existing ones in the universe
Why isn't helium found in living organisms?
Helium is a noble gas and doesn't like to form bonds because already satisfied
Atomic symbol
code for a chemical element, depicted by letters of alphabet
Atomic number
# of protons of an atoms, determines which element it is
Mass number
the sum of the # of protons and neutrons in the nucleus of an atom
Electrically neutral atom
the overall charge of the atom is zero (positive and negative forces are equal)
Weight and Charge
the properties of the element can vary in what two important ways
Weight
by altering neutron number, the weight of an atom can increase or decrease
Charge
adding or removing electrons from an electrically neutral atom gives the atom a positive or negative charge
Isotope
variant of a chemical element which differs in neutron number
Chemistry
the scientific study of matter, its properties, and interactions with other matter
Electron shells
electrons orbit the nucleus of an atom in specific energy configurations
- shells closest to the nucleus are lower in energy and more stable
-electrons fill each shell from the inside (closest to the nucleus) out
Valence shell
the outermost shell of an atom, determines how an atom will behave in chemical reactions
Chemistry rule of thumb
atoms tend to bond in such a way that each atom fills its valence shell
-Most energetically stable form for elements
-Elements that already contain a full valence shell rarely form chemical bonds
Electronegativity
the measure of the tendency to an atom to attract electrons
General rules for when atoms combine
#1 - if there is a difference in electronegativity between two elements, an ionic or polar covalent bond forms
#2 - if electronegativity charges are equal, a non-polar covalent bond forms
Ionic bond
a type of chemical bond that involves the attraction between oppositely charged ions
-occurs between metal and nonmetal
-rarely found in living organisms because bonds form non-living matter
Ion
an atom in which the total number of electrons is not equal to the total number of protons
anion
negative ion, has more electrons than protons
cation
positive ion, has more protons than electrons
Covalent bond
chemical bond that involves the sharing of electron pairs between atoms
Nonpolar covalent bond
electrons are shared equally among the atoms in the molecule due to equal electronegativity
Polar covalent bond
although shared, electrons spend a greater amount of time around the atom with the highest electronegativity
-shared electrons form the bond
-this creates a partial charge difference
Molecule
a group of two or more atoms held together by chemical bonds
-formed by ionic or covalent bonds
(hydrogen bonds don't)
Hydrogen bond
attractive force between the hydrogen attached to an electronegative atom of one molecule, and an electronegative atom of a different molecule
-bonds form between molecules, not atoms
-always involves a hydrogen atom
-weakest of three bonds
-not limited just to water (think F & DNA)
Properties of Water
1. Water is a solvent
2. Water is neutral
3. Water has a high heat capacity
4. Ice is less dense than water
5. Water Molecules are cohesive and adhesive
Solvent
-can dissolve more types of substances than any other compound in the known universe
-Incredibly important because chemical reactions depend on direct, physical contact between atoms/molecules
In order for water to be a good solvent, and allow for a plethora of chemical reactions to occur...
it must be in liquid form
(liquid is a rare form of water in the universe because temperature has to be just right)
Solution
a liquid consisting of a mixture of 2 or more substances; a solvent and a solute
Solvent
the dissolving agent in a solution (water is the most versatile)
Solute
a substance that is dissolved in a liquid to form a solution (ex: salt)
How do relatively weak hydrogen bonds break apart stronger ionic and covalent bonds?
Because there are trillions more hydrogen bonds, than ionic or polar, in solution
How water functions as a solvent?
Water pulls on the electronegative ends of ionic or polar covalent compounds which, in turn, breaks those bonds
Hydrophilic
water 'loving' molecules, dissolve in water (salt, sugar, etc.)
Hydrophobic
water 'fearing' molecules, do not dissolve in water (fat, oil, wax, etc.)
Base
a compound that acquires hydrogen ions and removes them from a solution (e.g. OH- hydroxide ion)
Acid
a compound that releases hydrogen ions (H+) to a solution
Why is water neutral?
Because the two ions (H+ and OH-) occur in equal proportions
pH
the measure of hydrogen ions (positive charges) in a solution
heat capacity
the ratio of heat absorbed by a material to the change in temperature
Water
has the 2nd highest heat capacity of any compound in the universe (ammonia being #1)
Heat
amount of energy associated with the movement of atoms in a body of matter
Temperature
the average speed of molecules in a body of matter
Where is the heat (energy) stored in water? (i.e. what allows water to store more heat than other compounds?)
-The energy from heat is first transferred into the hydrogen bonds before going into the H2O molecules
-Because there are so many hydrogen bonds in water, and energy is first used to break these bonds, it takes a lot of energy to raise water's temperature!
Why coastal areas have a generally milder climate than inland areas?
-Releases heat to warm the atmosphere, absorbs heat to cool it
-Regulates the global climate keeping it consistent (no large fluctuations)
Cohesion
the property of like molecules sticking together
-water sticks to itself
-hydrogen bonds hold water molecules together
-water's property is much stronger than other liquids
Adhesion
the property of unlike molecules sticking together
Importance of Cohesion and adhesion
important for such biological properties as how plants supply water to their cells and how sweating regulates body temperature
When is water most dense?
4 degree C
why does ice floats?
due to hydrogen bonds
(Molecules of liquid water break and make new hydrogen bonds constantly, allowing them to pack tight. In ice, all molecules are bond permanently to their neighbors at exact distances)
Inorganic molecules
molecules synthesized by geologic or cosmic means (i.e. formed in planets or stars)
- Contain very little carbon
- Small molecules
Example of Inorganic molecules
ammonia, water, carbon dioxide, hydrogen sulfide
Water
-accumulates throughout the two hundred million years
- brought by meteors and asteroids (no protective atmosphere exists yet)
-acts as a solvent in which inorganic solutes dissolve
-allows otherwise separated molecules to come in contact and form chemical bonds
Chemical evolution
-formation of more complex molecules from simple, inorganic molecules
-Formation of complex molecules (greater order) requires the input of energy
- Inorganic molecules form, at random, throughout the universe w/o the need for much (if any) energy input
"Primordial soup" hypothesis
energy from solar radiation and electrical discharges in the atmosphere catalyzed the formation of complex molecules from simple inorganic molecules
Ingredients needed to form more complex molecules:
1. Inorganic molecules
2. Liquid water
3. energy (geothermal, electrical, kinetic)
Miller-Urey experiment
chemical experiment that stimulated early Earth to test chemical evolution hypothesis
Results of Miller-Urey Experiment
Complex molecules were created in abundance, including many of the types utilized by living organisms today
Iron-sulfur world hypothesis
- dissolved inorganic molecules, emitted from thermal vents in the oceans, pass over iron/nickel sulfide minerals which act as a catalyst that drives chemical evolution
-Inorganic molecules + water + geothermal energy + iron/nickel sulfide
catalytic transition metals
Iron and nickel sulfides; they make it easier (require less energy) for inorganic compounds to bond together
Cosmic Seeding
-theory that complex molecules were brought, in abundance, to early earth by extraterrestrial objects
-Purposes that complex molecules did not originate on Earth but were instead brought to earth
- Carried by meteorites, asteroids, and comets
Organic Molecules
-chemical compounds containing carbon synthesized by living organisms
-Formed by covalent bonds between atoms
-Often quite large (contain many bonded atoms
Four categories of living organisms
-Nucleic Acids
-Lipids
-Carbohydrates
-proteins
Why is carbon so important?
-4 valence electrons and therefore can form up to 4 covalent bonds with other atoms
-Can form an endless diversity of molecular structures
-Each covalent bond formed between atoms stores energy
Carbon Skeleton
a series of carbons bonded with hydrogen atoms that form a foundation (skeleton) for many organic molecules
- May be linear or ring structured
Functional Group
-a specific combination of bonded atoms that always react in the same way, regardless of the particular carbon skeleton
-define how organic molecules react with other chemicals in reactions
Amino Acid (aa)
small organic molecules consisting of a central carbon atom bonded to 4 covalent partners:
-Multiple amino acids combine together to make a protein
4 parts of a Protein
1. Side Group (R) (varies in all aa)
2. Amino Group (-NH2)
3. Hydrogen (-H)
4. Carboxyl Group (COOH)
(2-4 are identical in all aa)
Amino acids with non-polar side groups
hydrophobic and rarely participate in hydrogen bonding
Amino acids with polar and ionic side groups
are hydrophilic and readily participate in chemical reactions
How do amino acids link together to form proteins?
Living organisms must expend energy to create macromolecules from molecules.
polymerization
The linkage of small organic molecules into larger macromolecules
-Living organisms must expend energy to synthesize macromolecules
Monomer
general term for a small organic molecule, "building block"
Polymer
molecule composed of multiple monomers
Dehydration synthesis
-a class of chemical reactions that links monomers to create polymers
-the reaction results in the creation and loss of water (hence dehydration)
-requires energy input
Hydrolysis
- a class of chemical reactions that uses water to breakdown organic polymers into monomers
-water is consumed in reaction
-releases energy
Protein (polypeptide)
- a large organic macromolecule consisting of one or more long chains of amino acids
-a polymer of amino acid monomers
Peptide bond
covalent linkage between the carboxyl group of one amino acid to the amine group of another
-Condensation reaction releases water as a byproduct
primary structure
- unique sequence of amino acids in a protein
-dictates overall structure
-differs from protein to protein
-how amino acids react with one another determines shape
Secondary Structure
hydrogen bonds formed between amino acids that form unique local patterns (substructures)
e.g. alpha helices & beta sheets
-form due to hydrogen bonding between the carboxyl group of one amino acid and the hydrogen atom of another amino acid
Tertiary structure
-overall 3-D shape of the protein
- Completely folded protein comprised of 1 amino acid chain
Quaternary structure
- proteins with 2 or more amino acid chains bonded together
-form due to bonding between the side groups of amino acids
Hydrophobic interactions
clumping of hydrophobic side chains away from water
Disulfide linkage
covalent bonding between sulfur containing side groups
Enzymes
any class of small molecules that speed up chemical reactions
Functions of Proteins
1. Structural- provides support
2. Storage- provide amino acids for growth
3. Contractile- aid in movement
4. Transport - help transport substances
5. Enzymatic- speed up chemical reactions
Carbohydrates ("carbs")
- bio molecules consisting of simple sugars and polymers of sugars
-are sugars
Functions of Carbs
Energy source - metabolized by most consumers
Energy storage
Structural components - in plants
Monosaccharide
- basic building block of carbohydrates (monomer), the simplest form of carbs
(EX: 6-carbon sugars = glucose and fructose or 5-carbon sugars = ribose and deoxyribose)
Disaccharide
- dehydration reaction results in two linked sugars
(EX: surcose)
Why do we love sugar so much?
-Digestible sugars are rare in the natural environment
-Humans evolved to acquire nutrients when available, sweetness indicated high calorie
Polysaccharide
(complex carbs) long chains of sugars = polymers of monosaccharides
-used by living organisms to store energy and to create structures
Starch
- a long, linear polymer of glucose
(energy storage molecule of plants)
Glycogen
- multi-branched polymer of glucose (energy storage molecule of animals and fungi)
Cellulose
-consists of a linear chain of several hundred to several thousand glucose units
-link to form cell walls in plants and algae
-cannot be metabolized by most animals
Chitin
-consists of a linear chain of several hundred to several thousand glucosamine units
-Utilized extensively in exoskeletons of insects and crustaceans
Nucleic acids
macromolecules comprised of chains of nucleotides
Functions of Nucleic acids
1. Storing Information
2. Structural unit
3. Enzymatic (speed up chemical reactions)
Nucleotides
- the monomer unit of nucleic acids
3 parts of Nucelotides
1. Phosphate Group (same all in)
2. 5 carbon sugar (ribose or deoxyribose)
3. Nitrogenous base (cytosine, thymine, uracil, adenine, or guanine)
Pyrimidine
single-ringed nitrogenous bases (cytosine, thymine, uracil)
Purines
double-ringed nitrogenous bases
(adenine, guanine)
Phosphodiester bond
the linkage between the phosphate group of one nucleotide and the sugar of another nucleotide

-condensation reaction
- Always joins the 5' carbon of one nucleotide to the 3' carbon of another (Gives every nucleic acid chain an orientation (5' end and 3' end))
Sugar-phosphate backbone
linkage between the phosphate group of one nucleotide and the sugar of another nucleotide
-Backbone holds nucleotides together and allows for nucleotide bases to interact
-very strong chains
DNA (deoxyribonucleic acid)
- a nucleic acid polymer which utilizes the 5-carbon sugar deoxyribose ("D")
-has four base configurations: A, G, T, C,
-sole function, in living organisms, is to store information
(double helix shape when two combine)
RNA (ribonucleic acid)
a nucleic acid polymer which utilizes the 5-carbon sugar ribose ("R")
-has four base configurations: A, G, U, C
-Many different types of RNA macromolecules exist in living organisms encompassing a plethora of roles (tRNA, rRNA, mRNA, siRNA, ...)
Function of RNA
store information, act as a structural unit, act as an enzyme
Lipids
-a broad group of organic molecules characterized by their hydrophobic and amphiphilic properties
(Individual onesmay cluster together to form macromolecules but do not chemically bond like monomers)
-no monomers means no polymers
Amphiphilic
-a molecule having both hydrophilic and hydrophobic parts
(EX: Lipid molecules have both polar and non-polar ends)
Fats
-consist of a glycerol (polar molecule) joined with three long fatty acid chains
-2 types of fats found in nature; saturated and unsaturated
Fatty Acid
-long chain of hydrogen-carbon bonds (carbon skeleton) with a carboxylic functional group (COOH-)
(more bonds it forms-> more energy you store)
Saturated Fat
-fatty acid tails are completely "saturated" with carbon-hydrogen bonds
-High energy due to maximum hydrogen covalent bonds (bonds = energy)
(Examples: cream, cheese, lard, butter, meat)
Unsaturated Fat
-a fat in which there is at least one double bond within the fatty acid chain
- Lower calorie due to fewer bonds
(examples: avocados, nuts, oils)
Why are saturated fats solids and unsaturated fats liquids?
-Saturated fatty acid tails are linear and allow saturated fat molecules to stack on each other.
-Kinked fatty acid tails of unsaturated fats do not allow for stacking
Trans fat (hydrogenated oil)
-a type of unsaturated fat not found in nature but produced by the food industry to allow foods to have a longer shelf life
-Found in margarine, snack foods, and fried fast food
-Linked to coronary heat disease
Phospholipids
-consist of a glycerol and phosphate "head" and 2 fatty acid "tails"
-One of the fatty acid tails is saturated, the other is unsaturated
-Polar head (hydrophilic), nonpolar tail (hydrophobic)
-not a type of fat
(cluster together, in aqueous solutions, forming macromolecule structures)
Steroids
-group of ringed organic molecules comprised of 17 carbon atoms arranged in a four-ring structure
-Different from fats & phospholipids in structure and often function as signaling molecules but can also be structural
Cholesterol
-organic molecule found in all animals
- Important component of animal cell membranes (structural)
- "Base steroid" from which your body produces other steroids (e.g. estrogen and testosterone) (signaling)
Three stages of Origin of Life
1. Synthesis of organic monomers
2. a. synthesis of protocells
b. synthesis of organic marcomolecules
3. abiogensis
phospholipids and ribonucleotides
Two organic molecules likely formed the earliest organic macromolecules
Phospholipids
cluster and form larger structures w/o energy needed to form chemical bonds
Ribonucleotides
can link and self-replicate
Protocells
-a self organized spherical collection of lipids
-cell- like vessel; barrier allows for contained chemical reactions
RNA-world hypothesis
-proposes that RNA led to life on Earth b/c it is the only macromolecule known to self-replicate (reproduction)
Abiogenesis
-the process of life arising from non-living matter

(RNA became enclosed in a lipid protocell forming the first cell precursors -> DNA, proteins, and polysaccharides formed within these precursors)

-sustained chemical processes in replicating vessels, could be classified as "alive" = a cell
Cell Theory
1. Cell is the most basic unit of life
2. All living organisms are composed of one or more cells
3. All cells arise form pre-existing cells
Last universal common ancestor (LUCA)
-the most recent common ancestor of all life on Earth

(thus, All living things, past and present, are related to one another)
-Arose, following chemical evolution, ~3,500,000,000 years ago
-Would be classified as a prokaryotic cell today
Prokaryotic cells
cells lacking a nucleus and other organelles
-Bacteria and Archaea
-Very small, ~1/10 the size of eukaryotic cells
-are all unicellular and reproduce asexually
-Largest, most biologically successful group of organisms to ever exist on Earth
Plasma membrane
-a phospholipid bilayer that forms the boundary between the cell and its environment
-regulates molecules in and out of the cell
-part of response and homeostasis feature of cell
-descendant of early protocell lipid bilayers
Cell wall
rigid structure that provides protection to prokaryotic cells and prevents water loss
peptidoglycan
a sugar-protein hybrid polymer, usually prokaryotic cell walls are comprised of this
Capsule
-outermost layer of prokaryotes, comprised of sugars
-sticky, helps cell attach to surfaces
ribosomes
- an ancient molecular machine that functions as a factory for building proteins

-Believed to have originated in the RNA world as a self-replicating complex that later evolved to synthesize proteins
-Link amino acids together by catalyzing the formation of peptide bonds
-made up of a combination of RNA and proteins
(rRNA forms this)
Cytosol/cytoplasm
-thick, jelly-like fluid on the inside of a cell in which everything else is suspended
-Mostly water (70%), but also dissolved salts and proteins
Chromosomes
- information-carrying structure of all living cells
-Recipe book for all cellular functions
-Made up of DNA and protein, circular structure in prokaryotes
Nucleoid
area of prokaryotic cell where chromosome is localized
-Chromosome is condensed into this small area but not separate from the cytosol
Plasmid
-small, circular extrachromosomal piece of DNA
-May carry information but not information necessary for the function of the cell
-Can be used to pass information between two prokaryotic cells
Flagella
-ash-like appendage that protrudes from the cell body of some, but not all, prokaryotic cells
-allows prokaryotic cells to move towards and away from things
Eukaryotic cells
-any organism whose cells contain a nucleus and other membrane-bound organelles
-can be unicellular or multicellular
-arose 1.7-2 bya
Found only in Prokaryotic Cells
Plasmid
Cell wall
Nucleoid
Capsule
Circular DNA
Found in only Eurkaryotic Cells
Nucleus
Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vacuoles
Mitochondria
Chloroplasts
Cytoskeleton
Linear DNA
Found in both Eurkaryotic and Prokaryotic Cells
Plasma membrane, Cytosol/Cytoplasm, Chromosomes, Ribosomes
Organelle
a membrane-enclosed compartment with a specialized function within a eukaryotic cell ("a cell within a cell)
Nucleus
-the genetic control center of a eukaryotic cell
-Contains the chromosomes, RNA, and the nucleolus
(- chromosomes in eukaryotes are linear instead of circular)
Nucleolus
-dense spot within the nucleus where ribosomes are assembled
-ribosomes are shipped out of the nucleus where they attach to the ER
Nuclear Envelope
-phospholipid membrane that defines the nuclear compartment
-Protects/stores the DNA chromosomes
Nuclear Pores
-protein channels in the nuclear envelope
-Regulates transportation of molecules between the nucleus and cell cytoplasm
[Executive boardroom doorway (authorized personal only!)]
ER (endoplasmic reticulum)
-extensive membranous network, acts as the main site for protein and lipid synthesis within the cell
-Continuous with the nuclear membrane
-2 types: Rough & Smooth
Rough ER
-has ribosomes attached to it, site of protein synthesis
-
Smooth ER
-site of lipid synthesis, does not contain ribosomes
-produces phospholipids and steroids
-protein enzymes catalyze reactions that form lipids in here
Transport Vesicles
-sacs of membrane that bud off from the cell's organelles
-Move molecules from organelle to organelle as well as into and out of the cell
- Used and produced by multiple organelles
Golgi Apparatus
-receives, refines, stores, and distributes the chemical products of the cell
-works in close partnership with the ER
-acts like a distribution center by sending materials to their appropriate destinations
How does the Golgi Apparatus work?
1. One side of a Golgi stack serves as a receiving dock for vesicles from the ER
2. As proteins and lipids move from one side of the Golgi to the other, they are modified
3. Shipping side of Golgi: finished products are carried via vesicles to other organelles or to the plasma membrane
Lysosomes
-an organelle filled with digestive enzymes for breaking down macromolecules
-(enzymes break down large molecules like proteins, polysaccharides, fats, nucleic acids, and even other entire organelles)
-acidic (4.5)
Cytoskeleton
-a series of intercellular proteins that help a cell with shape, support, and movement
Functions of Cytoskeleton
-support plasma membrane (act as skeleton)
-some form internal cell network for vesicles to move upon
-involved in cell movement
-important for cell division
Cilia & Flagella
-hair-like projections that function either to move a cell or to move things across a cell
In single-celled eukaryotes, ________- propel the cell through its environment
flagella
In multicellular organisms, ___________ move liquids and molecules across the cell surface
cilia
What cells are the only cells in humans that have a flagellum?
sperm
Mitochondria
-organelle where energy is generated by the breakdown of chemical compounds (catabolism)
- Energy transfer process = cellular respiration
- Harvest energy from organic molecules consumed by organism
- Have their own ribosomes, membrane, and DNA
- Asexually reproduce within cell
Chloroplast
- organelle, found only in plants and algal cells, converts sunlight to chemical energy (anabolism)
-energy transfer process = photosynthesis
-have their own ribosomes, membrane, and DNA
-asexually reproduce within cell
How are eukaryotic cell power plants are unique from other organelles?
-contain their own circular chromosome separate from the chromosomes of the host cell
-have own ribosomes
-reproduce on their own within the host cell
-both have a double membrane
Symbiosis
a close, long-term physical interaction between organisms of different species
Endosymbiosis
-occurs when an organism of one species lives inside an organism of another species
Endosymbiotic theory
-states that the energy organelles of eukaryotes originated as a symbiosis between separate single-celled organisms
(ex: mitochondria and chloroplasts were once free-living prokaryotic cells that were engulfed by a larger cell and formed a symbiotic relationship)
-Explains origin of eukaryotic cells from prokaryotic cells
Abiogenesis
-the process of life arising from non-living matter
(ex: RNA became enclosed in a lipid protocell forming the first cell precursors -> DNA, proteins, and polysaccharides formed within these precursors)
Plasma Membrane
-separates the living world from the non-living world
-"skin" of all organisms
(fundamentally one of the most important steps in the formation of life on this planet)
Plasma membrane
-a phospholipid bilayer inclosing the cell cytoplasm
-present in both prokaryotes and eukaryotes
-Regulates the entrance and exit of molecules from the cell
- Allows for homeostasis, response, metabolism, and greater order
Amphiphilic
-a molecule having both hydrophilic and hydrophobic parts
Hydrophobic interactions
- interactions between the nonpolar molecules placed in a polar solution
-require no energy input
micelle
-phospholipids may form a droplet with the hydrophobic tails clustering away from the water and the hydrophilic heads facing the water.
Permeable
the property of a material that allows matter to pass through it
(ex: cells with plasma membrane exchange materials and energy with the environment)
Selective permeability
-membranes allow some substances across much more readily than others
-dependent on electric charge, polarity, and mass of the molecule(s)
-dependent on temperature of the environment (high temperature = higher permeability)
What molecules can pass through cell membrane?
Small hydrophobic, nonpolar molecules and small uncharged polar molecules
What molecules can't pass through cell membrane?
Large, uncharged polar molecules and ions
Kink in fatty acids for plasma membrane
(phospholipids, in a bilayer, are constantly moving, rotating, and even flipping between layers)
-Kink in fatty acid tails keeps them from clustering too closely
-Kink also creates space for other, small molecules to permeate between the layers
How can the plasma membrane regulate its permeability?
Cholestrol
Cholesterol
-a polar steroid that intercalates between phospholipid molecules in the plasma membrane
-Regulates the permeability, fluidity, and flexibility of the membrane
-more of this, then the less permeable/fluid/flexible the plasma membrane
heat
-the amount of energy associated with the movement of atoms in a body of matter
-more of this, more energy and more movement of molecules
Brownian motion
-the random motion of solutes, suspended in a fluid, resulting from their collision with fast moving molecules of the fluid (solvent)
-Responsible for diffusion
(ex: matter, in a liquid state, is in constant motion)
Diffusion
the movement of molecules down a concentration gradient
-factors: Temperature, pressure, electrical currents, and molecular size
Concentration gradient
-an increase or decrease in the density of a molecule within a given region
Equilibrium
-when the net movement of molecules stops
-molecule concentration is uniform- no concentration gradient
-all molecules are still moving, but they are equally spread out in solution
osmosis
-the diffusion of water down its concentration gradient
-From high to low concentration
-Equilibrium extends not only to the solute but also to the water molecules
Passive Transport
-requires no energy input to move molecules from one side of the membrane to the other
-do not require any energy input to move across the plasma membrane
(ex: Molecules simply move from high to low concentration)
isotonic solution
there is no net movement of water b/c solute concentrations are the both in cell and outside so water moves equally in both directions
hypotonic solution
-there is a higher concentration of water outside the cell than inside
-water mainly diffuses into the cell (cell has more solutes so water rushes in to dilute them) via osmosis
-water rushes into cell and may cause it to burst
hypertonic soluntion
-there is a higher concentration of water inside the cell than outside
-water mainly diffuses out of the cell to dilute the solutes in the hypertonic solution
-water leaves the main cell, causing it to shrivel up
crenation
when water leaves the cell, causing it to shrivel up
Large polar molecules and charged molecules (ions
require protein channels to get them through the membrane
membrane proteins
-involved in many jobs including regulating the traffic of molecules into and out of the cell
Besides phospholipids and cholesterol, what are found extensively in cell membranes?
proteins
Integral Proteins
-span lipid bilayer
- Include channel, carrier, and pump proteins
Peripheral proteins
-reside on one side or the other of the lipid bilayer
-Include enzymatic and cytoskeleton proteins
Facilitated Diffusion
-diffusion of molecules into or out of a cell through a channel or carrier protein
- Help contribute to selective permeability of the membrane
- Do not require energy to power molecule movement (diffusion)
Channel Protein
-integral protein that allows particular molecules to cross the membrane freely
-channel open at both ends
-only very small molecules like H2O (not proteins/carbs/nucleotides)
Aquaporins
-channel proteins that allow water to cross the membrane quickly
-As opposed to squeezing through the phospholipids
(most abundant)
carrier proteins
-interact with specific molecules to transport them across the membrane
-only one side is open at a time, when the correct molecule enters, it is recognized and transported

(Example: Glut-1 allows only glucose molecules across the plasma membrane)
Electrochemical gradient
-combined effect of a concentration gradient and an electrical gradient
Ion channel proteins
-allow certain ions to diffuse across the plasma membrane passively
(B/c membrane is nonpolar, small charged molecules can't slip between the phospholipids bilayer)
Active transport
requires energy input from the cell to move molecules against their concentration gradient
Pump Transport
-an integral carrier protein that utilizes chemical energy to "pump" molecules from a region of lower concentration to one of higher concentration
-B/c this process opposes equilibrium, it requires energy input
-energy comes from ATP
Bulk Transport
-large molecules, such as proteins and complex carbohydrates, are too large to fit through integral proteins, they instead are transported by vesicles
-Requires transport vesicle and energy (vesicle creation, movement)
- Concentration gradient somewhat irrelevant
Two Types of Bulk Transport
Endocytosis and Exocytosis
Endocytosis
process by which large molecules are moved into the cell from the environment via transport vesicles
(ex: amoeba ingests bacterial cell )
Exocytosis
transport vesicle carrying large molecules fuses with the plasma membrane releasing molecules outside of the cell
(ex: stomach cells dump enzymes into stomach)
Cell Recognition Proteins
-fingerprint for the cell, important for immune system responses and cell to cell interactions
Glycoproteins
-membrane proteins with carbohydrate chains attached to them
-type of cell recognition protein
Enzymatic proteins
-catalyze specific chemical reactions necessary for membrane and cell function
(ex: catalyze formation of ATP which, in turn, powers active transport pumps)
Junction Proteins
-integral proteins that join to their counterparts in adjacent cells to link cells together
-occur in multicellular organisms (essential)
-linkage forms tissues (higher order)
Fluid Mosaic Model
-describes the cell membrane as a 2-D liquid in which phospholipids, cholesterol, and proteins move throughout
-membrane is dynamic, not static
Surface-area-to-volume ratio
-ratio of a cells outside area to its internal volume
(ex: higher surface-area-to-volume ratio increases the efficiency of transporting materials into and out of the cell)
What do cells need in order to exchange materials across membrane ?
a large surface area
Life
- a process that can retain complexity and replicate
(requires energy input to maintain order)
Energy
the property that must be transferred to an object in order to perform work on, or to heat, the object
-Allows living things to grow, develop, metabolize, and reproduce
Kinetic Energy
the energy of motion (work)
Potential Energy
the energy posses by an object
(ex: glucose stored in tree leaves)
1st Law of Thermodynamics
states that energy cannot be created or destroyed, but can be changed from one form to another
-"Law of Conservation of Energy"
-The amount of energy in the universe remains constant
2nd Law of Thermodynamics
-energy cannot be changed from one form to another without a loss of usable energy
-Describes how matter behaves in the universe
-"law of entropy"
-Usable energy is constantly decreasing
Entropy
-measure of the unavailable energy in a system
-always increasing (disorder is always increasing)
Exergy
-measure of available energy in a system
-always decreasing
Thermodynamic equilibrium
-state at which all energy in the universe is equal
-No movement from high to low energy (No "heat" at all)

(Why clocks move forwards not backwards (concentration gradient of the universe))
If order in the universe is constantly diminishing, how is life possible?
Energy must be consumed to maintain complexity
-Life does not oppose the 2nd Law. Living organisms dissipate higher level energy and create entropy
-Require constant energy input to maintain order
Energy processing
-living organisms take in energy to maintain organization and the other emergent phenomena associated with life
(most abundant in universe: cellular respiration, photosynthesis)
Metabolism
the sum of the chemical reactions that occur in a living cell
Anabolism
set of metabolic pathways that construct larger molecules from smaller ones (endergonic = requires energy)
Catabolism
set of metabolic pathways that deconstruct larger molecules into smaller ones (exergonic = releases energy)
Endergonic reaction
-chemical reaction that requires the input of energy to occur
-increasing order and creates potential energy
(ex: polymerization)
Exergonic reaction
-spontaneous chemical reactions that release energy
-reduces order and releases potential or kinetic energy
(ex: hydrolysis)
Metabolic pathway
-series of linked reactions, beginning with a particular reactant and terminating with an end product
-reactions usually occur in a sequence
-can be endergonic or exergonic
-requires energy at most steps
-involves creation and consumption of ATP
ATP (adenosine triphosphate)
-organic molecule universally used by cells to store and transfer energy
-nucleotide composed of adenine (nitrogen containing base), ribose (sugar), and three (tri) phosphate groups
-"Molecular unit of currency"
Where is PE stored in ATP?
-stored in the chemical bond holding the 3rd phosphate group to the molecule
Chemical Energy
-energy stored in chemical bonds of molecules
-a form of potential energy
The higher the potential energy if...
more bonds or the more unstable the bond
Endergonic Reaction
-creation of ATP from ADP and P requires input of energy from other sources
(ex: energy from solar radiation or chemical reactions)
Exergonic reaction
-the breakdown of ATP releases potential energy (and a phosphate)
-allows free energy to do work and drive other processes (ex: metabolism)
Cellular respiration
aerobic metabolic pathway for the production of ATP in most eukaryotic organisms
-Involves the transfer of electrons (e-) from compounds with high potential energy (food) to an e- transport chain and eventually to an electron acceptor (O2)
Aerobic
requires the presence of oxygen to occur
Mitochondria
organelle in which the majority of ATP molecules are produced during the process of cellular respiration
Internal parts of Mitochondria
Cristae and Matrix
Cristae
short, finger-like projections formed by the folding of the inner membrane of mitochondria
-recall, double membrane
Matrix
liquid within inner membrane of mitochondria
-similar to cytosol
redox reaction
chemical reaction in which electrons are lost from one substance (oxidation) and added to another (reduction)
-always occur together
-H+ always follows the e-
Glycolysis
chemical breakdown of a glucose (C6) into two molecules of pyruvate (C3)
-occurs in cytoplasm
-Products: 2 ATP, 2 NADH, and two energy rich pyruvate molecules
NADH
electron carrier, transports e- to electron transport chain
-transport e- to the electron transport chain
Prep Reaction
-intermediary step in which the 2 pyruvate molecules lose a carbon atom and attach to a molecule known as coenzyme A (CoA)
-Occurs in the mitochondrial inner membrane
-Carbons released as CO₂ (waste product)
-Loss of carbon atoms causes pyruvates to become acetic acids (C2)
-Products: 2 NADH, 2 CO2, and two acetic acids
Citric Acid Cycle
finishes extracting the energy from glucose by dismantling acetic acid and transferring energy into ATP and e-
-occurs in mitochondrial matrix
- Final oxidized carbons are released as CO2 (waste)
-Products: 2 ATP, 6 NADH, 2 CO2, and 2 FADH2
FADH2
-electron carrier, transports e- to the electron transport chain
-similar to NADH
Electron Transport
electrons, held by NADH and FADH2, are used to power a series of reactions which ultimately form the majority of ATP during cellular respiration
-occurs in the inner mitochondrial membrane
-O₂ combines with "spent" electrons to form H₂O (waste)
-Products: 34 ATP and H2O
Are sugars the only organic molecules that can lead to ATP production?
NO! can be carbohydrates, proteins, fats
-Organic molecules, other than carbohydrates, enter cellular respiration at different steps
What bonds does cellular respiration breaks to release their potential energy?
covalent bonds of organic molecules
Where are energy from electrons transferred?
to ATP or stored on NADH or FADH2
What happens to carbon and oxygen in cellular respiration?
carbon is lost as CO2
Oxygen is consumed to make H2O
Heterotroph (consumer)
an organism that cannot synthesize its own organic molecules from inorganic ingredients

-Must obtain organic monomer units and energy by consuming other organisms or their organic products
-can synthesize proteins, polysaccharides, lipids, and nucleic acids but only from the monomer units they consume
-Undergo cellular respiration
Autograph (producer)
an organism that synthesizes organic molecules from inorganic ingredients
-Sustain themselves w/o eating other organisms or their molecules
-Undergo cellular respiration and photosynthesis
-examples: plants/algae
Autograph Energy Processing
Solar energy (kinetic) converted into potential energy (carbohydrates)
Heteograph Energy Processing
Carbohydrate (potential energy) converted into kinetic energy (muscle contraction)
Autographs
create order
-more organized, more potential energy, less stable
Heterographs
breakdown order
-less organized, less potential energy, more stable
Photosynthesis
process by which certain autotrophic organisms transform light energy into chemical energy
-Potential energy stored in the covalent bonds of sugars (glucose)
-Anabolic reaction
-Mass is gained
What is opposite of photosynthesis reaction?
cellular respiration