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715 terms

Biology 1406 Final Exam

McGraw-Hill 2nd Ed.
STUDY
PLAY
What is homeostasis
the process whereby living organisms regulate their cells and bodies to maintain relatively stable internal conditions
What are the characteristics of living things
1. Cells and Organization
2. Energy use and metabolism
3. Response to environmental changes
4. Regulation and homeostasis
5. Growth and Development
6. Reproduction
7. Biological Evolution
atom
the smallest component of an element having the chemical properties of the element
molecule
Two or more atoms held together by covalent bonds.
macromolecule
many molecules bonded together to form a polymer such a polypeptide (carbohydrates, proteins and nucleic acids are examples)
cell
the simplest unit of a living organism, composed of molecules and macromolecules, form larger structures such as membranes
tissue
association of many cells of the same type
organ
two or more types of body tissues combined to perform a common function
organism
a living thing that maintains an internal order that is separated from the environment
population
group of individuals of the same species that occupy the same environment and can interbreed with one another
community
an assemblage of populations of different species that live in the same place at the same time
ecosystem
the biotic community of organisms in an area as well as the abiotic environment affecting the community
biosphere
the regions on the surface of the earth and in the atmosphere where living organisms exist
What are the two mechanisms of evolutionary change
Vertical descent and horizontal gene transfer
vertical descent
Progression of changes in lineage (a series of ancestors). Occurs from generation to generation. New species evolve from pre-existing species by accumulation of mutations (natural selection)
horizontal gene transfer
A process in which an organism incorporates genetic material from another organism without being the offspring of that organism
What are the three domains
Bacteria, Archaea, and Eukarya
What are the four kingdoms
animalia, fungi, plantae, and protista
bacteria
single-celled organisms that lack a nucleus; prokaryotes
archaea
Single-celled, no nucleus, Live in harsh conditions
eukarya
Domain of all organisms whose cells have nuclei, including protists, plants, fungi, and animals
protista
single-celled organism with nuclei (algae, protozoans)
plantae
A classification kingdom made up of eukaryotic, multicellular organisms that have cell walls made mostly of cellulose, that have pigments that absorb light, and that supply energy and oxygen to themselves and to other life-forms through photosynthesis
animalia
Kingdom of the most complex organisms; multi-cellular, heterotrophic, lack rigid cell walls, mobile, tissues in internal organs, sensory organs, nervous system
taxonomy
the science of naming and classifying organisms
binomial nomenclature
a system for giving each organism a two-word scientific name that consists of the genus name followed by the species name
genomes
the complete instructions for making an organism, consisting of all the genetic material in that organism's chromosomes
proteomes
the complete complement of proteins that a cell or organism can make
scientific method
a general approach to gathering information and answering questions so that errors and biases are minimized
Five Stages of Scientific Method
Observations, Hypothesis, Experimentation, Data & Analysis, Accept/Reject Hypothesis
metabolism
All of the chemical reactions that occur within an organism
biological evolution
Changes in the genetic composition of a population through successive generations.
theory
a broad explanation of some aspect of the natural world that is substantiated by a large body of evidence; makes valid predictions
hypothesis
a proposed explanation for a natural phenomenon based on previous observations or experimental studies
discovery-based science
the collection and analysis of data without the need for a preconceived hypothesis
subatomic particles
protons, neutrons, and electrons
where are subatomic particles located
Protons and neutrons are found in the nucleus and electrons are found in the electron shell
protons
positive- found in nucleus- same number as electrons
neutrons
neutral- found in nucleus- number can vary
electrons
negative- found in orbitals- same number as protons
why are atoms electrically neutral
they have an equal # of protons and electrons
orbitals
Regions within electron shells where electrons orbit the nucleus
s orbitals
sphere shaped; hold 2 electrons
p orbitals
3 dumbbell/propeller shaped orbitals (2p); can hold 4 pairs of electrons
1st shell
holds a max of 2 electrons; 1 spherical orbital (1s)
2nd shell
1 spherical orbital (2s) & 3 dumbbell shaped orbitals (2p) can hold up to 8 electrons
What is the atomic number of an atom
The number of protons in the nucleus of the atom
atomic mass
total mass of the protons and neutrons in an atom, measured in atomic mass units
molecules
Groups of two or more atoms held together by chemical bonds
ions
electrically charged atoms that have gained or lost electrons
ionic bonds
bond formed when one or more electrons are transferred from one atom to another
covalent bonds
A type of strong chemical bond in which two atoms share one pair of valence electrons
polar covalent bond
when two atoms with different electronegativites form a covalent bond; the shared electrons are more likely to be in the outer shell of the atom of higher electronegativity rather than the atom of lower electronegativity
nonpolar covalent bond
a covalent bond in which the bonding electrons are shared equally by the bonded atoms, resulting in a balanced distribution of electrical charge
hydrogen bond
A type of weak chemical bond 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.
which is the strongest chemical bond
covalent bond
occurs between atoms whose outer electron shells are not full; can share up to three pairs of electrons
covalent bonds
occur because the distribution of electrons around the atoms creates a polarity, or difference in electric charge, across the molecule
polar covalent bond
bonds between atoms with similar electronegativities
nonpolar covalent bonds
cations
net positively charged ions
anions
ions with a negative charge
occur when a cation binds to an anion
ionic bonds
what type of bonding is likely to occur between two water molecules or strands of DNA-
hydrogen bond
isotope
multiple forms of an element, differ in the number of neutrons
make up about 95% of the atoms in living organisms
hydrogen, oxygen, carbon, and nitrogen
octet rule
States that atoms lose, gain or share electrons in order to acquire a full set of eight valence electrons in their outer shell
chemical reaction
a change in which one or more reactants change into one or more products; characterized by the breaking of bonds in reactants and the formation of bonds in products
chemical properties
a property or characteristic of a substance that is observed during a reaction in which the chemical composition or identity of the substance is changed
properties of water
1-Universal Solvent (Dissolves all hydrophillic molecules)
2-Cohesion (sticks to itself)
3-Adhesion (sticks to other substances)
4-Heat capacity (water can absorb a lot of heat and remove heat when evaporating due to breaking H-bonds)
5-Surface tension (Water striders can float on water surface)
cell theory
idea that all living things are composed of cells, cells are the basic units of structure and function in living things, and new cells are produced from existing cells
response to environmental changes
to survive living organisms must be able to respond to changes
mutations
Random errors in gene replication that lead to a change in the sequence of nucleotides; the source of all genetic diversity
natural selection
the principle that, among the range of inherited trait variations, those that lead to increased reproduction and survival will most likely be passed on to succeeding generations
bioluminescence
Produce and emit light by means of a chemical reaction in which chemical energy is converted to light energy
reductionism
reducing complex systems to simpler components that are more manageable to study
molecular biology
study of the molecular basis of genes and gene expression; molecular genetics
anatomy and physiology
structures and functions of plants and animals
control group
in an experiment, the group that is not exposed to the treatment; contrasts with the experimental group and serves as a comparison for evaluating the effect of the treatment
experimental group
A subject or group of subjects in an experiment that is exposed to the factor or condition being tested.
element
a pure substance made of only one kind of atom
atomic nucleus
An atom's central core, containing protons and neutrons.
energy shells
An energy level representing the distance of an electron from the nucleus of an atom.
energy
the ability to do work or cause change
valence electrons
an electron that is found in the outermost shell of an atom and that determines the atom's chemical properties
daltons
what atomic mass is measured in, also known as amu
mole
the amount of a substance that contains as many particles as there are atoms in exactly 12 g of carbon-12
avogadro's number
6.022 x 10^23. The number of particles in exactly one mole of a pure substance
radioisotope
unstable isotope; lose energy by emitting subatomic particles and/or radiation
trace elements
present in extremely small quantities but still are essential for normal growth and function
molecular formula
shows the types and numbers of atoms combined in a single molecule of a molecular compound
compound
refers to a molecule composed of two or more different elements
example: h20
double bond
when atoms share two pairs of electrons
electronegativity
measure of its ability to attract electrons in a bond with another atom
polar molecules
molecules composed predominantly of nonpolar bonds
enzymes
molecules found in all cells that facilitate or catalyze many biologically important chemical reactions
van der waals forces
a slight attraction that develops between the oppositely charged regions of nearby molecules
if an atom or molecules gains or loses one or more electrons, it acquires a net electric charge and becomes-
ion
free radical
atoms or molecules with one or more unpaired valence electrons
reactants
the elements or compounds that enter into a chemical reaction
products
the elements or compounds produced by a chemical reaction
chemical equilibrium
in a reversible chemical reaction, the point at which the rate of the forward reaction equals the rate of the reverse reaction
solute
substances dissolved in liquid
solvent
the liquid in which solutes are dissolved
the solvent for chemical reactions
water
solution
solvents dissolve in a solvent to form a
aqueous solutions
solutions in which water is the solvent
hydrophillic
water loving, polar, dissolve in water, form hydrogen bonds
hydrophobic
"Water-fearing"; pertaining to nonpolar molecules (or parts of molecules) that do not dissolve in water
amphipathic
molecule that has both a hydrophilic region and a hydrophobic region such as a phosopholipid
micelles
formed when amphipathic molecules are mixed with water, polar regions on outside, non polar regions on inside
concentration
a measure of the amount of solute dissolved in a solvent
molecular mass
The sum of the masses of all the atoms in a molecule
molarity
A common measure of solute concentration, referring to the number of moles of solute per liter of solution.
What are the three states of water-
1. solid (ice)
2. liquid (water)
3. gas (water vapor)
heat of vaporization
the quantity of heat a liquid must absorb for 1 gram/mole of it to be converted from the liquid to the gaseous state; this is caused by hydrogen bonds
heat of fusion
the amount of heat energy that must be withdrawn or released from a substance to cause it to change from the liquid to the solid state
colligative properties
properties that depend strictly on the total number of dissolved solutes, not on the specific type of solute
hydrolysis
Breaking down complex molecules by the chemical addition of water
condensation reaction
Two or more molecules combining to form one larger molecule with the loss of a small molecule
dehydration reaction
a molecule of water is lost during the reaction; a specific kind of condensation reaction
evaporation
water vaporizes at extraordinary temperatures; it still requires the same energy to change water from a liquid to a gas
specific heat
the amount of heat required to raise the temperature of 1g of a substance 1 degree Celsius (it takes considerable heat to raise the temperature of water)
cohesion
water molecules attracting to each other; due to hydrogen bonding
adhesion
the ability of water to be attracted to/adhere to, a surface that is not electrically neutral
surface tension
measure of the attraction between molecules at the surface of a liquid (allows insects to walk on water)
hydroxide ions
Negatively charged particles (OH) composed of oxygen and hydrogen atoms released from a base when dissolved in water
acids
substances that release hydrogen ions when dissolved in water
strong acid
An acid that ionizes completely in aqueous solution
ex:hydrochloric acid
weak acid
an acid that does not completely ionize in water
ex: carbonic acid
base
compound that absorbs hydrogen ions in a solution
ex: sodium hydroxide; NaOH---> Na+ + OH-
pH
the negative logarithm to the base 10 of the H+ concentration
neutral in pH because the concentration of hydroxide ions and hydrogen ions are equal
pure water
The pH of a solution can affect...
1. The shapes and functions of molecules
2. The rates of many chemical reactions
3. The ability of two molecules to bind to each other
4. The ability of ions or molecules to dissolve in water
Buffers
composed of a weak acid and its related baseorg;a compound that accepts or releases H+ in response to pH change; help to keep a constant pH
As acidity increases the pH...
decreases
Acidic
pH 0-6
human stomach fluid- pH1
lemon juice-pH2
grapefruit juice-pH3
beer-pH4
tomato juice-pH4
urine-pH5 & 6
Neutral
pH 7
milk, pure water, human blood
Alkaline
pH 8-14
seawater-pH 8
baking soda-pH 9
milk of magnesia-pH 10
household ammonia-pH 11
bleach-pH 12-14
what is the OH- concentration at pH 8?
10-8M
organic molecules
Contain carbon-hydrogen bonds. Found in living things carbohydrates, lipids, proteins, nucleic acids
organic chemistry
the study of carbon-containing molecules
Carbon forms _____ covalent bonds with other atoms.
4; because Carbon has 4 electrons in its outer shell and needs 4 more
hydrocarbons
An organic molecule consisting only of carbon and hydrogen; poorly soluble in water
functional groups
groups of atoms with characteristic chemical features and properties
isomers
Two structures with an identical molecular formula but different structures and characteristics
structural isomers
contain the same atoms but in different bonding relationships
stereoisomers
Identical bonding relationships but the spatial positioning of the atoms differs in the two isomers
cis-trans isomers
Carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds
enantiomer
pair of molecules that are mirror images
monomers
(meaning one part) small molecules that link together to form polymers
polymers
(meaning many parts) formed by linking together many smaller molecules called monomers
condensation reaction
process by which two or more molecules combine to form polymers through a chemical reaction
dehydration reaction
results in removal of a water molecule;essential to the formation of polymers
dehydration reaction
essential for the formation of glycogen from glucose monomers; essential for the formation of triglycerides (fat) from glycerol and fatty acids
hydrolysis reaction
Breaking down polymers into monomers using water
carbohydrates
Organic compounds made of carbon, hydrogen, and oxygen atoms in the proportion of 1:2:1; carbon containing compounds that are hydrated (contain water)
monosaccharides
simple sugars (glucose, galactose (from milk), fructose (from fruit)); very water soluable
disaccharides
two sugars; carbohydrates composed of two monosaccharides
starch
polysaccharides found in plant cells
glycogen
polysaccharides found in animal cells
cellulose
A polysaccharide that provides structural support for plant cell walls
chitin
A polysaccharide; plays a structural role in the cell walls of fungi and in the exoskeletons of insects
glycosaminoglycans
large polysaccharides that play a structural role in animals
lipids
hydrophobic molecules composed mainly of hydrogen and carbon atoms; nonpolar; insoluble in water
ex: fats, phopholipids, steroids, waxes and oils
The source of variation in fat molecules is ____.
fatty acid composition
Fatty acids can vary in number and ______.
location of C-C double bonds
Fatty acids vary in ____.
length
Can be liquid or solid in room temperature, depending on fatty acid composition-
fats
triglycerides
long term energy storage molecules formed during condensation synthesis between 3 fatty acids and one molecule of glycerol
saturated fatty acid
when all the carbons in a fatty acid are linked by single covalent bonds; all the carbons are saturated with covalently bound hydrogen
unsaturated fatty acid
a fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail
What is the main difference between a fat (triglyceride) and a phospholipid?
A phospholipid has 2 fatty acids attached to a glycerol; a fat has 3
The tertiary structure of a protein is dependent on-
the side chain composition of each amino acid within the protein
Saturated fats have _____ melting points and tend to be _____ at room temperature.
high;solid
ex: animal fats (cooking a hamburger)
Unsaturated fats are _____ at room temperature.
liquid
ex: olive oil
steroids
lipids characterized by a carbon skeleton consisting of four fused carbon rings
phospholipids
a lipid that is a structural component in cell membranes;with hydrophobic head and hydrophillic tail
proteins
polymers composed of carbon, hydrogen, oxygen and nitrogen and sometimes sulfur
amino acids
the building blocks of proteins
cell
simplest structure shared among all living organisms
proteins involved in gene expression and regulation
make mRNA from a DNA template; synthesize polypeptides from mRNA; regulate genes
ex: RNA polymerase synthesizing RNA from DNA, transcription factor proteins involved in gene regulation
motor proteins
initiate movement
metabolic enzymes
increase the rate of chemical reactions
cell signaling proteins
enable cells to communicate with each other and with the environment
ex: taste receptors in the tongue
structural proteins
support and strengthen structures
ex: actin provides shape to the cytoplasm of plant and animal cells; collagen gives strength to tendons
transporter proteins
promote movement of solids across plasma membranes
ex: glucose transporters move glucose from outside cells to inside cells where it can be used for energy
peptide bond
the covalent bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
polypeptide
A polymer (chain) of many amino acids linked together by peptide bonds.
primary structure of a polypeptide
The amino acid sequence, determined by genes
secondary structure of a polypeptide
helix & pleated sheet; flexible and can fold into a number of shapes
helix
a polypeptide backbone forms a repeating helical structure stabilized by hydrogen bonds along the backbone
pleated sheet
regions of the polypeptide backbone that lie parallel to each other; repeating zig zag
quaternary structure of a polypeptide
proteins consist of more than one polypeptide chain
protein subunits
individual polypeptides; may be identical polypeptides or different
multimeric proteins
(meaning multiple parts)
ex: hemoglobin
Which factor is critical for the folding of proteins?
-ionic bonds
-hydrogen bonds
-van del Waals forces
-disulfide bridges
Comparing solutions with a pH of 6 and and pH of 8
The solution with a pH of 8 has 100 times lower concentration of hydrogen ions than a solution with a pH of 6
a nucleotide is composed of-
-phosphate group
-nitrogenouse base
-carbon sugar
Protein structure is influenced by several factors:
-hydrogen bonds
-ionic bonds and other polar interactions
-hydrophobic effect
-van der Waals forces
-disulfide bridges
nucleic acids
responsible for the storage, expression, and transmission of genetic information
deoxyribonucleic acid
found in DNA
ribonucleic acid
found in RNA
DNA strands are covalently held together by _____.
phosphodiester linkages between adjacent phosphate and sugar molecules, with the bases protruding from the side of the phosphate-sugar backbone
Purine bases
adenine, guanine
Pyrimidine bases
cytosine, thymine
DNA is composed of-
purines and pyrimidines
A pairs with-
G pairs with-
T
C
RNA
consists of a single strand of nucleotides
DNA
consists of a double strand of nucleotides
Ribose
the sugar in RNA
Thymine is replaced with Uracil in-
RNA
cell biology
the study of cells
cell theory
1. All living organisms are composed of one or more cells
2. Cell are the smallest units of life
3. New cells only come from pre-existing cells by cell division
microscopy
enables researchers to study the structure and function of cells
resolution
a measure of the clarity of an image; ability to observe to adjacent objects as distinct from one another
contrast
the ability to visualize a particular cell structure may depend on how different it looks from an adjacent structure
ex: using color dye
magnification
the ratio between the size of an image produced by a microscope and its actual size
light microscope
utilizes light for illumination; 1mm-1um
measures: fish egg, plant and animal cells, nucleus, some bacteria, mitochondria
electron microscope
uses electrons for illumination; 100um-0.1nm
measures: small bacteria, viruses, ribosomes, proteins, lipids, small molecules, atoms
transmission electron microscope
an electron microscope that transmits a beam through a specimen, detecting its electrons and forming a highly magnified image on a screen
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
cell structure is determined by 4 factors-
1. matter
2. energy
3. orgainzation
4. information
protein-protein interactions
the specific interactions between proteins; critical to cell structure and function
genes
contain the genetic material to create cells with particular structures and functions
plasma membrane
double layer of phospholipids and embedded proteins, forms an important barrier between the cell and its external environment
cytoplasm
region of the cell contained within the plasma membrane
nucleoid region
where the genetic material (DNA) is located
ribosomes
involved in polypeptide synthesis
cell wall
supports and protects the plasma membrane and the cytoplasm in plants, algae, and some bacteria (prokaryotic cells only)
glycocalyx
an outer vicous-covering surrounding the bacteria; traps water and keeps bacteria from drying out (prokaryotic cells only)
capsule
a sticky, gelatinous substance around the cell wall; allows cells to stick together or to the host cell (prokaryotic cells only)
pili
allow prokaryotes to attach to surfaces and to each other and allows them to transfer DNA (prokaryotic cells only)
flagella
long, thin, whip-like structures, with a core of microtubules, that enable some cells to move (Prokaryotic cells only)
organelle
A membrane-enclosed structure with a specialized function within a cell (eukaryotic cells only)
compartmentalization
they have many membrane-bound organelles that separate the cell into different regions (eukaryotic cells only)
cilia and flagella
-involved in cell motility
-require ATP to work
-require motor proteins to work
-composed of an internal structure call the axoneme
metabolism
sum of all chemical reactions by cells
enzyme
protein that accelerates the rate of a chemical reaction
catabolism
breakdown of a molecule into small components
anabolism
Process of building up complex materials (proteins) from simple materials
cytoskeleton
forms a network of protein fibers within the cytoplasm; provides cell shape, organization and movement
microtubules
hollow tubes of protein about 25 nanometers in diameter, support the cell and moves organelles within the cell, composed of tubulin polymers
centrosome
area of the cytoplasm near the nucleus that coordinates the building and breaking of microtubules in the cell
centrioles
Structure: Small, cylindrical parts of the cytoskeleton.
Function: Aid in cell division
intermediate filaments
are composed of several different proteins and they are thicker than microfilaments; found in parts of the cell subject to mechanical stress, they help stabilize positions of organelles such as the nucleus and help attach cells to one another
actin filaments
a thin type of protein filament composed of actin proteins that forms part of the cytoskeleton and supports the plasma membrane and plays a key role in cell strength, shape and movement
motor proteins
use ATP as a source of energy to promote various types of movement; consists of a head, hinge, and tail
ex: muscle contraction
Composed of microtubules, Intermediate filaments, and actin filaments-
cytoskeleton
nucleus
The organelle that contains the DNA and controls the processes of the cell
endomembrane system
A network of membranes inside and around a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles.
vesicles
small membrane sacs that specialize in moving products into, out of, and within a cell
nuclear envelope
double membrane perforated with pores that control the flow of materials in and out of the nucleus
nuclear pores
pores which allows materials to move in and out of the cell nucleus
chromosome
in a eukaryotic cell, one of the structures in the nucleus that are made up of DNA and protein
chromatin
combination of DNA and protein molecules, in the form of long, thin fibers, making up the genetic material in the nucleus of a eukaryotic cell
nuclear matrix
the nuclear skeleton, a shape-maintaining protein; serves to organize the chromosomes within the nucleus
nucleolus
small, dense region within most nuclei in which the assembly of ribosomes begins
endoplasmic reticulum
a system of membranes that is found in a cell's cytoplasm and that assists in the production, processing, and transport of proteins and in the production of lipids
cisternae
A space containing fluid, such as those occurring between the membranes of flattened sacs of the Golgi apparatus and the endoplasmic reticulum, also between the two membranes of the nuclear envelope
lumen
The internal space of an organelle
ER lumen
the space inside the ER where proteins are folded, modified and prepared for transport to other locations in the cell or are tagged for export from the cell
rough endoplasmic reticulum
-covered with ribosomes
Structure: A network of interconnected membranes forming channels within the cell
Function: sorting & synthesis of proteins; transportation system; attachment of carbohydrate to proteins and lipids
glycosylation
the attachment of carbohydrates to a protein or lipid, producing a glycoprotein or glycolipid
smooth endoplasmic reticulum
-lacks ribosomes
-Function: synthesis, modification of lipids, calcium balance, detoxification, carbohydrate metabolism
-the liver contains a lot of smooth er
ex: alcoholics have an abundancy of smooth ER
golgi apparatus
stack of membranes in the cell that modifies, sorts, and packages proteins from the endoplasmic reticulum
proteolysis
the hydrolysis of proteins into peptides and amino acids by cleavage of their peptide bonds
proteases
an enzyme that cuts proteins into smaller polypeptides
secretory vessicles
Secrete substances outside the cell by exocytosis
secretory pathway
cellular pathway for synthesizing and sorting soluble and membrane proteins localized to the ER, Golgi and lysosomes; plasma membrane proteins; and proteins eventually secreted from the cell
exocytosis
the process by which a substance is released from the cell through a vesicle that transports the substance to the cell surface and then fuses with the membrane to let the substance out
endocytosis
process by which a cell takes material into the cell by infolding of the cell membrane
lysosomes
Small organelles found in animals cells filled with enzymes; one function is to break down lipids, carbohydrates, and proteins from food particles; may also break down old cell parts
acid hydrolases
Enzymes that degrade various macromolecules and that require an acidic pH to function properly. Acid hydrolases are found within the lysosomes of cells
vacuole
A fluid filled organelle that stores enzymes or water
central vacuole
in some protists and in most plant cells, a large, fluid-filled organelle that stores water, enzymes, metabolic wastes, and other materials
tonoplast
membrane enclosing the central vacuole
contractile vacuoles
saclike organelles that expand to collect excess water and contract to squeeze the water out of the cell
phagocytic vacuoles
a vacuole that functions in the degradation of food particles or bacteria
peroxisomes
Contain oxidase enzymes that detoxify alcohol, hydrogen peroxide, and other harmful chemicals
catalase
Enzyme responsible for breaking down hydrogen peroxide into water and oxygen
glyoxysomes
specialized peroxisomes found in fat-storing tissues of plant seeds that have enzymes which convert fatty acids to sugars; used for energy until photosynthesis occurs to produce its own sugar
membrane transport
The movement of ions and molecules across biological membranes
cell signaling
the molecular mechanisms by which cells detect and respond to external stimuli and send messages to other cells
cell adhesion
A role of the plasma membrane, critical for animal cells to properly interact to form a multicellular organism; allows cells to recognize each other
mitochondrian
organelle where cellular respiration occurs and most ATP is generated
cristae
an infolding of the inner membrane of a mitochondrian that house the electron transport chain and the enzyme catalyzing the synthesis of ATP
chloroplasts
organelles that capture the energy from sunlight and convert it into chemical energy in a process called photosynthesis
Similarities between mitochondria and chloroplasts-
-both are surrounded by a double membrane
-both make ATP
-both have their own DNA and ribosomes
-similar in size
semiautonomous organelles
Organelles that can grow and divide to reproduce themselves, but they are not completely autonomous because they depend on other parts of the cell for their internal components
ex: Mitochondria and chloroplasts
A eukaryotic cell is a system with four interacting parts-
1. nucleus
2. endomembrane system
3. cytosol
4. semiautonomous organelles
Endomembrane system is composed of-
1. network of membranes enclosing the nucleus
2. endoplasmic reticulum
3. golgi apparatus
4. lysosomes
5. vacuoles
6. plasma membrane
plasma membrane
function: membrane transport in and out of the cell
-selectively permeable
-cell signaling using receptors
-cell adhesion
Increase in number via binary fission, or splitting in two-
mitochondria & chloroplasts
endosymbiosis
a mutually beneficial relationship in which one organism lives within another
plastids
a family of closely related plant organelles (includes chloroplasts)
Pathways for protein sorting in a Eukaryotic cell-
Rough ER-->Golgi Apparatus-->vesicles-->plasma membrane
cytosol
central coordinating region for many metabolic activities of Eukaryotic cells
What is 9 +2 arrangement?
In the cillia and flagella of most Eukaryotic organisms, the microtubules form-
Microtubules and motor proteins facilitate movement involving cell appendages called-
flagella and cillia
Biological membranes
a mosaic of lipids, proteins and carbohydrates
phospholipid bilayer
-framework of the biological membrane
Composed of: plasma membrane layers composed of phospholipid molecules arranged with polar heads facing the outside and nonpolar tails facing the inside
fluid-mosaic model
exhibits properties that resemble a fluid because lipids and proteins can move relative to each other within the membrane
Approximately ______ of all genes encode membrane proteins.
25%
What kind of proteins bound to membranes?
integral membrane proteins bound to membranes (transmembrane proteins, lipid-anchored proteins)
Glycosylation
the process of covalently attaching a carbohydrate to a lipid or protein
glycosylation
Functions: protect cells from chemical and mechanical damage, keep other cells at a distance, prevent undesirable cell-cell interactions, keeps lysosome from digesting itself, cell to cell recognition (EX: sperm/egg interactions, blood clotting, inflammatory responses)
integral membrane protein
-A protein embedded in the lipid bilayer of a cell. -These are typically cell surface receptors, channels, or pumps. (also called transmembrane protein)
-Cannot be released from the membrane unless the membrane is dissolved with an organic solvent
NOT ALL CAN MOVE!!!!
transmembrane protein
a protein that has one or more regions that are physically embedded in the hydrophobic region of a cell membrane's phospholipid bilayer
lipid-anchored protein
Has a lipid molecule that is covalently attached to an amino acid side chain within the protein
peripheral membrane proteins
don't interact with hydrophobic interior of phospholipid bilayer, noncovalently bound to regions of integral membrane proteins that project out from membrane, or they're bound to polar head groups of phospholipids; typically bound to membrane by hydrogen/ionic bonds
Membranes are Semifluid
most lipids can rotate freely around their long axes and move laterally within the membrane leaflet
Flipflop of lipids
requires ATP and Flippase
fluidity
individual molecules remain in close association yet have the ability to readily move within the membrane
factors affecting fluidity
1) Temperature
2) length of fatty acid chains
3) presence of double bond in the acyl tails
4) cholesterol (more cholesterol increases membrane fluidity), length of fatty acyl tails
glycolipid
A lipid covalently attached to a carbohydrate
glycoprotein
A protein covalently attached to a carbohydrate
Where is the synthesis of membrane components?
-in eukaryotes, cytosol and endomembrane system work together to synthesize most lipids.
-process occurs at cytosolic leaflet of smooth ER.
How are lipids transferred to other membranes?
-transferred via vesicles to Golgi, lysosomes, vacuoles, or plasma membrane.
-Lipids in ER membrane can diffuse laterally to nuclear envelope.
Membrane transport
The movement of ions and molecules across biological membranes (in and out of the cell)
passive membrane transport
No energy is required, moves from higher to lower concentrations, and goes down the concentration gradient
passive membrane diffusion
diffusion of a solute through a membrane without transport protein; does not require energy or ATP
facilitated diffusion
diffusion of a solute with the aid of transport protein, spontaneous passage of molecules and ions across a biological membrane down their concentration gradients
active transport
movement of a solute across a membrane against its gradient from a region of low concentration to higher concentration
Which molecules can passively diffuse across a membrane?
Gases like CO2, N2, O2 and few small uncharged molecules like ethanol
Tonicity
The ability of a solution surrounding a cell to cause that cell to gain or lose water
isotonic
describes a solution whose solute concentration is equal to the solute concentration inside a cell
hypotonic
describes a solution whose solute concentration is lower than the solute concentration inside a cell (the cell swells and bursts)
hypertonic
describes a solution whose solute concentration is higher than the solute concentration inside a cell (the cell shrinks)
osmosis
diffusion of molecules through a semipermeable membrane from a place of higher concentration to a place of lower concentration until the concentration on both sides is equal
turgor pressure
the pressure that is exerted on the inside of cell walls and that is caused by the movement of water into the cell
plasmolysis
a phenomenon in walled cells in which the cytoplasm shrivels and the plasma membrane pulls away from the cell wall when the cell loses water to a hypertonic environment
Transmembrane proteins
provide a passageway for the movement of ions and hydrophillic molecules across membranes
channels
form an open passageway for the facilitated diffusion of ions, water or molecules across the membrane
crenation
shrinkage of a cell caused by contact with a hypertonic solution
transport protein
a protein located in the cell membrane that provides a passageway for the movement of ions and hydrophillic molecules across membranes
2 types of transport proteins
1. channels
2. transporters
gated
a property of many channels that allows them to open and close to control the diffusion of solutes through a membrane
transporters
(carriers) membrane protein that binds a solute and undergoes a confrontational change to allow movement of the solute across a membrane
differences between channels and transporters-
Transporters tend to be much slower than channels.
Transporters
-allow cells to take up certain hormones and neurotransmitters
-play a key role in export
-provide the principle pathway for the uptake of organic molecules
-play an important role in regulating pH and controlling cell volume
3 types of transporters (carriers)-
1. uniporters
2. symporters
3. antiporters
uniporters
bind a single ion or molecule and transport it across the membrane
symporters (cotransporters)
bind two or more ions or molecules and transport them in the same direction
antiporters
bind two or more ions or molecules and transport them in opposite directions
Active Transport
-energetically unfavorable and requires the import of energy
Primary Active Transport
uses a pump; a type of transporter that directly uses energy to transport a solute against a gradient
Secondary Active Transport
use of a pre-existing gradient to drive the active transport of another solute
What is Na+/K+-ATpase
this pump can actively transport Na+ and K+ against their gradients by using the energy from ATP hydrolysis
-produces an electrical gradient across the membrane
- it is considered a electrogenic pump
electrogenic pump
generates an electrical gradient
Endocytosis/Exocytosis
transport large molecules such as proteins and polysaccharides, and even very large particles
Exocytosis
material inside the cell packaged into vesicles and excreted into the extracellular matrix
Endocytosis
plasma membrane invaginates, or folds inward, to form a vesicle that brings substances into the cell
receptor-mediated endocytosis
a receptor in the plasma membrane is specific for a given cargo
Pinocytosis
involves the formation of membrane vesicles from the plasma membrane as a way for cells to internalize the extracellular fluid
-allows cells to sample the extracellular solutes
Phagocytosis
involves the formation of an enormous membrane vesicle called a phagosome, or phagocytic vacuole, that engulfs a large particle such as bacterium
energy
the ability to do work or cause change
potential energy
Stored energy
kinetic energy
energy of motion
First law of Thermodynamics
Law of conservation of energy. Energy can be transferred and transformed, but it cannot be created or destroyed.
Second law of thermodynamics
Law states every energy transfer or transformation increases the entropy of the universe. Ordered forms of energy are at least partly converted to heat, and in spontaneous reactions, the free energy of the system also decreases.
entrophy
degree of disorder of a system
enthalpy (H)
the total energy of a system
Free Energy (G)
the energy available to promote change or do work
Spontaneous reactions
reactions that occur naturally and that favor the formation of products at the specified conditions
Exergonic
reaction that releases energy
Endergonic
A chemical reaction that requires the input of energy in order to proceed
Exergonic
-negative free energy change
-spontaneous
-free energy is released during product formation
Endergonic
-positive free energy change
-requires addition of free energy
-not spontaneous
^G <0
reaction favors the formation of products
^G>0
reaction favors the formation of reactants
An endergonic reaction can/cannot be coupled to an exergoinic reaction
can
Ribozymes
an RNA molecule that functions as an enzyme, catalyzing reactions during RNA splicing
Catalyst
an agent that speeds up the rate of a chemical reaction without being permanently changed or consumed
Activation energy
an initial input of energy
Active site
the location in an enzyme where the chemical reaction takes place
Substrate
the reactant molecules that bind to an enzyme at the active site and participates in the chemical reaction
allosteric site
A site on an enzyme other than the active site, to which a specific substance binds, thereby changing the shape and activity of the enzyme
What are the steps of an enzyme-catalyzed reaction?
1. ATP and glucose bind to the enzyme
2. Enzyme undergoes conformational change that binds the substrates more tightly. This induced fit strains the chemical bonds within the substrates and/or brings them closer together.
3. Substrates are converted to products.
4. Products are released. Enzyme is reused.
A key feature of nearly all enzymes is they bind to their substrates with a high degree of _______.
specificity
substrate
the right-sized key
active site
key hole
enzyme
the lock
competitive inhibition
molecules that bind to the active site of an enzyme and inhibit the ability of the substrate to bind
induced fit
conformational changes cause the substrates to bind more tightly to the enzyme
Noncompetitive inhibition
binds noncovalently to an enzyme at a location outsides the active site, called the allosteric sit, and inhibits the enzymes function
Additional factors Influence Enzyme Function
Prosthetic groups
cofactors
coenzymes
the environment
prosthetic groups
small molecules that are permanently attached to the surface of an enzyme and aid in catalysis
cofactors
usually inorganic ions, such as Fe3+ or Zn2+, that temporarily bind to the surface of an enzyme and promote a chemical reaction
coenzyme
organic molecules that temporarily bind to an enzyme and participate in the chemical reaction but are left unchanged after the reaction is completed
ex: B vitamins
Catabolic reaction
result in the breakdown of molecules into smaller molecules
-EXERGONIC
anabolic reaction
involve the synthesis of larger molecules from smaller precursor molecules
-ENDERGONIC
-must be coupled to an exergonic reaction
2 ways to make ATP
1. substrate level phosphorylation
2. chemiosmosis
Substrate level phosphorylation
enzyme directly transfers phosphate from one molecule to another molecule
chemiosmosis
energy stored in an electrochemical gradient is used to make ATP from ADP and Pi
Redox
(reduction-oxidation reaction) electron removed from one molecule is added to another
oxidation
removal of electrons
reduction
addition of electrons
feedback inhibition
the product of a metabolic pathway inhibits an enzyme that acts early in the pathway, thus preventing an over accumulation of the product
Why is mRNA degradation important?
function: a cell conserves energy by degrading mRNAs ; mRNAs may be faulty
How do mRNA degradate?
exonucleases and and exosomes
exonucleases
enzyme cleaves off nucleotides from end
exosome
multiprotein complex uses exonucleases
____________ contain hydrolases to break down proteins, carbohydrates, nucleic acids, and lipids.
Lysosomes
Lysosomes
digest substances taken in by endocytosis
Autophagy
Recycling of worn-out organelles through endocytosis
Autophagosome
a vesicle formed around a worn-out organelle; this vesicle then fuses with a lysosome which digests the organelle.
Steps of protein degradation in eukaryotic cells
1) string of ubiquitins are attached to a target proteins
2) protein with attached ubiquitins is directed to the proteasome
3) protein I unfolded by enzymes in the cap and injected into the core proteasome. Ubiqutin is released back into the cytosol
4) protein is degraded to small peptides and amino acids
5) small peptides and amino acids are recycled back to the cytosol
What is C6H12O6 + 6O2 6CO2 + 6H2O (ATP + Heat)?
cellular respiration
Is cellular respiration an endergonic or exergonic reaction?
exergonic
What is the final products of glucose oxidation during aerobic cell respiration?
ATP, Heat, and CO2
Location of glycolysis
Occurs in the cytosol of a cell
Anaerobic
process that does not require oxygen
Aerobic
process that requires oxygen
reactants of glycolysis
glucose, 2 ATP, 2NAD+
products of glycolysis
2 ATP, 2 NADH, 2 pyruvate
How many stages are there in aerobic respiration?
4
Stages in Aerobic Respiration
1. Glycolysis (cytosol)
2. Acetly CoA formation (mitochondria matrix)
3. Kerbs Cycle (mitchondria matrix)
4. Oxidative phosphorylation (mitochondria inner membrane)
Where do the ETC and ATP synthase occur?
mitochondria inner membrane
Fermentation
breakdown of organic molecules without net oxidation
ethanol fermentation
A form of fermentation occurring in yeast which NADH passes its hydrogen atoms to acetaldehyde, generating carbon dioxide, ethanol, and NAD +
lactate fermentation
The process in animal cells by which pyruvic acid accepts electrons from NADH to form Lactic Acid
Reactants of Citric Acid Cycle
Acetyl CoA, Oxaloacetate.
Products of Citric Acid Cycle
6 NADH, 2 FADH2, 2 ATP, 4 CO2
What is formed when acetyl attaches to oxaloacetate?
citric acid
Energy released by the electron transport chain is used to pump H+ ions into which location?
mitochondrial intermembrane space
Can proteins and fats be used as energy sources to drive aerobic respiration?
yes
cellular respiration
the metabolic reactions that a cell uses to get energy from food molecules and release waste products
Electron Transport Chain
consists of a group of protein complexes and small organic molecules embedded in the inner mitochondrial membrane
autotroph
an organism that can make its own food
heterotroph
organism that obtains food by consuming other living things
6CO2 + 6H2O C6H12O6+6O2 is what?
-photosynthesis
-anabolic
-endergonic
Where does photosynthesis take place?
chloroplasts
Chloroplasts
organelles found in plant cells that carry out photosythesis
Chlorophyll
pigment that gives plants their green color
stomata
Pore-like openings in leaves that allow gases (CO2 and O2) and water to diffuse in and out of the leaves.
thylakoid membrane
structure: a membrane within the chloroplast that forms many flattened, fluid-filled tubules that enclose a single, convoluted compartment.
Function: It contains pigment molecules and is the site where the light-dependent reactions of photosynthesis occurs
thylakoids
flattened saclike membranes that are arranged in stacks
thylakoid lumen
A fluid-filled interior space enclosed by the thylakoid membrane
granum
a stack of thylakoids
stroma
structure: The fluid of the chloroplast surrounding the thylakoid membrane
function: involved in the synthesis of organic molecules from carbon dioxide and water
light reactions
-produce ATP and NADPH
-chemical reactions that convert the sun's energy to chemical energy;
-take place in the thylakoid membrane in the chloroplast
Main role of pigment molecules within light- harvesting complex
directly absorb photons of light
Path of electron flow that occurs during photosynthesis-
H20--->Photo System 2--->P680--->Final Electron Acceptor--->Electron Transport Chain--->Photo System 1--->P700
Chlorophyll A
A type of blue-green photosynthetic pigment that participates directly in the light reactions.
Chlorophyll B
A type of yellow-green accessory photosynthetic pigment that transfers energy to chlorophyll A
carotenoids
The yellow and orange and sometimes red pigment that gives color to leaves in the fall
Photosystem 1
Function: Reaction Center is P700(far red)
-Uses Light to excite electrons and converts NADP to NAPDH
-It has light dependent reactions
-also splits water to make Oxygen
(comes 2nd)
Photosystem 2
a light reaction in which ATP and NADPH are produced (comes 1st)
Locations of-
Light reaction- grana
splitting of water- thylakoid space
ETC- thylakoid membrane
ATP synthase- intermembrane space
Calvin Cycle- stroma
Stages of Calvin Cycle (light dependent reaction)
-Uses CO2 from atmosphere to produce carbohydrate.
-Carbon dioxide fixation
-Carbon dioxide reduction
-Ribulose-1,5-bisphosphate (RuBP) regeneration
Reactants for Calvin Cycle
carbon dioxide, NADPH, and ATP
Products for Calvin Cycle
ATP, NADPH
During the light reaction, water is oxidized to form oxygen, where do electrons go from this process?
transferred to P680+ molecules
The 2 stages of Photosynthesis-
1. Light Reactions (thylakoid membrane)
2. Calvin cycle (light dependent reactions-stroma)
Light reactions produce-
ATP, NADPH, and O2
photorespiration
a metabolic pathway in plants that consumes oxygen, produces carbon dioxide, generates no ATP, and reduces photosynthesis
What are C3 plants
-90% of the plant species
-Use enzyme rubisco to make 3-carbon compound during carbon fixation
-no bundle sheet cell
examples: wheat, rice, potatos, oak trees
What are C4 plants
-predominate in hot, dry weather
-minimize photorespiration
-bundle sheet cell
examples: sugarcane, corn, Bermuda grass
CAM plants
-Store the organic acids made at night in vacuoles and use them for photosynthesis during the day when stomata are closed
-no bundle sheet cel
examples: cacti, pineapple
What is ECM?
(extracellular matrix) network of material secreted from the cells forming a complex meshwork outside of cells
-major component of certain parts of plants and animals
Bone & cartiliage: animals
woody parts: plants
Animal cells secrete ________ that helps to support and organize cells.
ECM
Extracellular Matrix
Components: major macromolecules are proteins and polysaccharides,
proteins: form large fibers
polysaccharides: give gel-like chracter
Functions: strength, structural support, organization, and cell signaling
Major components of the ECM of animals-
adhesive and structural proteins
Adhesive proteins in the ECM of animals-
Fibronectin & Laminin
Structural proteins in the ECM of animals-
Collagen & Elastin
Fibronectin
connects cells to the ECM and to the cell surface and helps to organize components in the ECM
Laminin
connects cell to the ECM and to the cell surface and helps to organize components in the basal lamina, a specialized ECM found next to epithelial cells
Collagen
provides tensile strength; main protein found in bone, cartilage, tendon, and skin
Elastin
provides elasticity; expands and returns to its original shape
What are the major polysaccharides found in animal ECM?
In vertebrates, glycosaminoglycans
Glycosaminoglycans
long unbranched polysaccharides with a repeating disaccharide unit; highly negative charge attracts positive ions and water
Chondroitin sulfate
example of GAG's, cartilage
Hyaluronic acid
example of GAG's; found in skin, eyes, and joint fluid
Chitin
(exoskeleton) important ECM in invertebrates; forms hard protective outer covering in insects and shell fish
plant cell walls
composition: cellulose and pectin
function: provides strength and resistance to compression
primary cell wall
very flexible; allows to new cells to increase in size
cellulose
polysaccharide consisting of glucose monomers that reinforces plant-cell walls
cell junctions
connections between cells that hold the cells together as a unit
Cell Junctions in Animals
-Anchoring junctions
-Tight junctions
-Gap junctions
Anchoring junctions
cell junctions that hold adjacent cells together or bond cells to the ECM; mechanically strong
Type: animal cell junction
ex: the layer of cells that lines the intestines
Tight junctions
junctions between adjacent cells in a layer that prevent the leakage of material between cells
type: animal cell junction
Gap junctions
channels that permit the direct exchange of ions and small molecules between the cytosol of adjacent cells
type: animal cell junction
middle lamella
a polysaccharide layer that cements together the cell walls of adjacent cells
type: plant cell junction
plasmodesmata
passageways between the cell walls of adjacent cells that can be opened or closed. When open, they permit the direct diffusion of ions and molecules between cells
type: plant cell junction
integral membrane proteins
cell adhesion molecules or CAMs
two types of CAM's
1. cadherins
2. integrins
adherens junctions
connect cells to each other via cadherins
bind to cytoskeletal filaments called actin filaments
desmosomes
connect cells to each other via cadherins
connected to cytoskeletal filaments called intermediate filaments
hemidesmosomes
connect cells to extracellular matrix via integrins
interact with intermediate filaments
focal adhesions
connect cells to the extracellular matrix via integrins
bind to actin filments
cadherins
create cell-to-cell junctions
promote cell-to-cell adhesion
binding requires the presence of calcium ions (Ca2+ dependent adhering molecule)
integrins
creates connections between cells and the extracellular matrix
integrin is bound to fibronectin
cell adhesion molecules (CAM's)
critical for keeping cells in their correct locations
abnormalities often associated with cancer
tight junctions (occluding junctions)
(in animals) forms a tight seal between adjacent cells and thereby prevents ECM from leaking between cells
tight junctions
made by occludin and claudin
bind to each to form tight seal
not mechanically strong, not bound to cytoskeleton
gap junctions
(in animals) connects small gap between plasma membranes of cells
gap junctions
six connexin proteins in one cell align with six connexin proteins in an adjacent cell to form a connexon
Connexon
allows passage of ions and small molecules
allows cells to directly share metabolites and directly signal each other
apoptosis
cell death
What was the Griffith Experiment on streptococcus pnemoniae?
experiment where dead cells were transformed into live cells by a virulent strain. they used pnemonnucous and mice and the they hypothesized that the material in the dead bacterial cells could genetically transform living bacterial cells and concluded that a chemical substance from one cell is capable of genetically transforming another cell.
transformation
process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria
Hershey and Chase
concluded that the genetic material of the bacteriophage was DNA, not protein
nucleotides
building blocks of DNA
RNA vs DNA
RNA - ribose sugar, contains uracil, single strand
DNA - deoxyribose sugar, contains thymine, double strand
Chargoff Rule
A=T C=G
The mechanism of DNA replication is-
semiconservative
DNA helicase
An enzyme that unwinds the DNA double helix during DNA replication;, enzyme that breaks the hydrogen bonds between bases during DNA replication
DNA ligase
-Joins the Okazaki fragments;
-A linking enzyme essential for DNA replication -Catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain
DNA polymerase
enzyme that "proofreads" new DNA strands, helping to ensure that each molecule is a nearly perfect copy of the original DNA; covalently links nucleotides together to form DNA
DNA primase
synthesizes short RNA primers
single-stranded binding proteins
a class of proteins that attach to separated strands of DNA during replication or transcription, preventing them from re-forming a double helix
topoisomerase
a protein that breaks, swivels, and rejoins DNA strands
okazaki fragments
Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
During the replication process, the two complementary strands of DNA separate and serve as _______ for the synthesis of new daughter strands of DNA.
template strands (also called parental strands)
telomerase
an enzyme that catalyzes the lengthening of telomeres. The enzyme includes a molecule of RNA that serves as a template for new telomere segments
telomeres
Repeated DNA sequences at the ends of eukaryotic chromosomes
transcription
DNA is copied into a complementary sequence in RNA; does not permanently alter the structure of DNA; results in a functional product
gene expression
conversion of the information encoded in a gene first into messenger RNA and then to a protein
promoter
A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA
promoter region
A regulatory region a short distance upstream from the 5' end of a transcription start site that acts as the binding site for RNA polymerase. A region of DNA to which RNA polymerase binds in order to initiate transcription
RNA polymerase II
in eukaryotes, this type of polymerase transcribes the mRNAs
introns
noncoding regions; transcribed but not translated
exons
expressed sequence of DNA; codes for a protein
RNA processing
Modification of RNA transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends
alternative splicing
different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns
Capping
the enzyme addition of a 7-methyl guanosine to the 5' end of mRNA
function: needed for proper exit of mRNA from nucleus and binding to ribosome
poly A tail
A sequence of 50 to 250 adenine nucleotides added onto the 3' end of a pre-mRNA molecule
function: increases stability and lifespan in cytosol
codon
three-nucleotide sequence on messenger RNA that codes for a single amino acid
degenerate
more than one codon can specify the same amino acid
start codon
AUG
tRNA
type of RNA that binds to specific amino acids and transports them to the ribosome during protein synthesis
anticodon
three nucleotides on the RNA that are complementary to the sequence of a codon in mRNA
aminoacyl-tRNA synthetases
catalyzes attachment of amino acids to their particular tRNAs, produces charged tRNA (translation)
How many destinct aminoacyl-tRNA synthetases does each cell make?
one for each of 20 different amino acids
release factors
recognize stop codon and cleaves polypeptide from tRNA
location of the eukaryotic ribosome for translation
cytosol
translation
the process of synthisizing a specific polypeptide on a ribosome in the cytoplasm
Initiation
In translation-DNA replication is initiated when helicase enzyme breaks the hydrogen bonds holding the base pairs together and the DNA uncoils; mRNA, a tRNA with the first amino acid, and the two ribosomal subunits assemble
Elongation
In translation-protein synthesis in which a polypeptide increases in length one amino acid at a time from start codon to stop codon
Termination
In translation-complex disassembles at stop codon releasing completed polypeptide
Which bonds hold the amino acids of a growing polypeptide in elongation?
peptide bond
One Gene-One Enzyme Hypothesis
proposed by Beadle and Tatum
one gene-one enzyme hypothesis
a single gene controlled the synthesis of a single enzyme
polypeptide
a linear sequence of amino acids
functional protein
composed of two or more different polypeptides
ex: Hemoglobin
transcription
produces an RNA copy of a gene
structural genes
(most genes) produce an RNA molecule that contains the information to specify a polypeptide with a particular amino acid sequence
mRNA
carry information from the DNA to cellular components called ribosomes
central dogma
proposed by Francis Crick; During transcription, DNA codes for mRNA, which codes for polypeptides during translation
DNA--->RNA--->Protein
gene
an organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product
tRNA
type of RNA that carries amino acids to the ribosome
provides the site where translation occurs
ribosome
regulatory sequences
site for the binding of regulatory proteins
RNA polymerase
synthesizes strands of RNA, an enzyme that pries the 2 strands of DNA apart and hooks together the RNA nucleotides as they base pair along the DNA template
open complex
the stage of initiation of transcription when RNA polymerase causes the two strands of DNA to separate to form the "transcription bubble"
template strand
the strand of DNA that the RNA polymerase uses as a guide to build complementary mRNA
coding strand
the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine
pre-mRNA
contains both introns and exons
mature mRNA
The final product that results when the pre-mRNA in eukaryotes undergoes processing events before it exits the nucleus
splicing
The process by which introns are removed from primary RNA transcripts and the remaining exons are connected together
spliceosome
the combination of snRNPs and introns that are removed during transcription from the mRNA
genetic code
sequence of nucleotides that specifies the amino acid sequence of a protein
coding sequence
a region that specifies the amino acid sequence of a polypeptide
termination codons/nonsense codons
UAA
UAG
UGA
n-terminus
amino terminus
c-terminus
carboxyl terminus
peptidyl site
P site-amino acid are released and peptide bond forms
aminoacyl site
A site- on the ribosome where a charged tRNA initially binds
exit site
E site- the RNA that has lost its amino acid exits from here
Initiation stage
translation-
1. mRNa binds to the small ribosomal subunit
2. Initiator tRNA binds to the start codon in mRNA
3. Large ribosomal subunit binds
-requires the help of initiation factors
-requires an input of energy
Elongation stage
translation-
1. tRNA entry: a charges tRNA binds to the A site
2. Peptidyl transfer reaction: a bond forms between the polypeptide chain and the amino acid in the A site. The polypeptide is transferred to the A site
3. Translocation of ribosome and release of tRNA
-occurs at a fast rate
Termination
translation-
1. A release factor binds to the stop codon at the A site
2. The polypeptide is released from the tRNA in the P site. The tRNA is then released
3. The mRNA, ribosomal subunits, and release factor dissassociate
gene expression
transcription and translation of genes into proteins
gene regulation
ability of an organism to control which genes are transcribed in response to the environment
What affects the regulation of gene expression in Eukaryotes?
1. transcriptional regulation
2. RNA processing
3. Translation
4. post-translation
small effector molecules
exerts its effects by binding to a regulatory transcriptional factor and causing a conformational change in the protein
regulatory transcription factors
-proteins that bind to DNA in the vicinity of a promoter
-affect the rate of transcription of one or more nearby genes
-can either decrease or increase the rate of transcription
cell differentiation
the process by which a cell becomes specialized for a specific structure or function
activators
Transcription factors that bind to DNA and increase the rate of transcription
-positive control
repressors
Transcription factors that bind to DNA and inhibit transcription
-negative control
polycistronic mRNA
mRNA that contains the information for more than one gene
lac O site
regulatory site- sequence of nucleotides that provides a binding site for a repressor protein
lac operon
inducible operon- gene system with a promoter, an operator gene, and three structural genes that control lactose metabolism
allolactose
-acts as a small effector molecule to regulate the lac operon
-inducer molecule that prevents transcription repression in the lac operon
-when levels increase/decrease in E.coli, increases the rate of transcription
inducer
A small molecule that increases the rate of transcription of a specific gene, often by binding to and inactivating a repressor protein
CAP site
DNA sequence that acts as a regulator switch -example of positive control
-located just upstream of the lac promoter
lac repressor
acts as a negative regulator by turning off transcription when attached to the operator site
What is the relationship between glucose and cAMP in lac operon?
glucose inhibits production of cAMP and so prevents binding of CAP to DNA
Where does the cAMP-CAP complex bind?
CAP site near the lac promoter
cAMP site
cyclic AMP- entices RNA polymerase to bind to the promoter which increases transcription
Different globin peptides are expressed at _____ levels during the embryonic, fetal stages, and adult stages of mammalian development.
different
Where does RNA polymerase bind and start transcription?
promoter region
mutation
heritable changes in genetic material
gene mutation
a change in the base sequence of a gene
point mutation
gene mutation in which a single base pair in DNA has been changed
silent mutation
alters a base but does not change the amino acid
missense mutation
changes a single amino acid in a polypeptide; may not alter function if substituted amino acid is similar in chemistry to original
ex: sickle cell disease
nonsense mutation
a mutation that changes an amino acid codon to one of the three stop codons, resulting in a truncated polypeptide
somatic cell mutation
-affect a limited area of the body
-are not transmitted to offspring
-affect skin cells & muscle cells
ex: white patch of hair
germ line mutation
-mutation that occurs in reproductive cells and ends up being carried by gametes (eggs and sperm)
-heritable
UV light
produces thymine dimer mutations
-involves covalent binding between adjacent pyrimidines (C or T)
cancer
a disease of multicellular organisms characterized by uncontrolled cell division
spontaneous mutations
result from abnormalities in biological processes
ex: transposons, errors in DNA replication, changes in nucleotide structure
induced mutation
caused by environmental agents that enter the cell and alter the structure of DNA
ex: chemical agents, physical agents (x-ray, uv)
x-rays
cause base deletions, single nicks in DNA, cross linking, and chromosomal breaks
direct repair
a repair enzyme recognizes an incorrect structure in the DNA and directly converts it back to a correct structure
base excision and nucleotide excision repair
an abnormal base or nucleotide is recognized, and a portion of the strand containing the abnormality is removed. The complementary DNA strand is then used as a normal DNA strand
methyl-directed mismatch repair
similar to excision repair except that the DNA defect is a base pair mismatch in the DNa, not an abnormal nucleotide. The mismatch is recognized, and a strand of DNA in the region is removed. The complementary strand is used to synthesize a normal strand of DNA.
nucleotide excision repair (NER)
removes segements of damaged DNA
Human genetic disorders
occur when a component of the NER system is missing
metastic
Cancer that has spread from one place to another within the body is called ______________.
oncogenes
cause the overactivity of proteins that that promote cell division
gene amplification
increase in the number of copies of a proto-oncogene
mutations in____ convert them to oncogenes.
proto-oncogenes
cytogenic
a field of genetics that involves the microscopic examination of chromosomes and cell division
How many checkpoints are there in cell cycles?
3; G1,G2, and M
karyotype
reveals the number, size and form of chromosomes found within an actively dividing cell
How many pairs of chromosomes do humans have?
23 pairs; 46 total chromosomes
How many autosomes do humans have?
22 pairs
How many sex chromosomes do humans have?
1 pair (xx-female, xy-male)
diploid
an organism or cell having two sets of chromosomes or twice the haploid number
haploid
an organism or cell having only one complete set of chromosomes
cell cycle
series of events in which a cell grows, prepares for division, and divides to form two daughter cells
order of mitosis
Interphase-->Prophase-->Anaphase-->Telophase-->Cytokinesis
G1 phase
The first gap, or growth phase, of the cell cycle, consisting of the portion of interphase before DNA synthesis begins
S phase
The synthesis phase of the cell cycle; the portion of interphase during which DNA is replicated
G2 phase
The second gap, or growth phase, of the cell cycle, consisting of the portion of interphase after DNA synthesis occurs
M phase
the phase in the cell cycle where mitosis and cytokinesis occur resulting in cell division
The cell cycle is controlled by _______.
check point proteins
mitotic cell division
a cell divides to produce two daughter cells that are genetically identical to the original cell (mother cell)
mitotic spindle
responsible for organizing and sorting the chromosomes during cell division
centrosomes
Microtubule-organizing centers that help to form and organize the mitotic spindle during mitosis
Interphase
Prior to mitosis- the chromosomes are decondensed and found in the nucleus
Prophase
In mitosis- sister chromatids condense, and the mitotic spindle starts to form. The nuclear envelope begins to disassociate into vesicles
Prometaphase
In mitosis- The nuclear envelope has completely disassociated into vesicles, and the mitotic spindle is fully formed. Sister chromatids attach to the spindle via kinetochore microtubules.
Metaphase
In mitosis- sister chromatids align along the metaphase plate
Anaphase
In mitosis- sister chromatids separate, and the individual chromosomes move toward the poles as the kinetochore microtubules shorten. Polar microtubules lengthen and push the poles apart
Telophase and Cytokinesis
In mitosis- chromosomes decondense and the nuclear envelope reforms. Cytokinesis separates the mother cell into two daughter cells, which begins with a cleavage furrow in animal cells.
meiosis
a process in cell division during which the number of chromosomes decreases to half the original number by two divisions of the nucleus, which results in the production of sex cells
bivalent
Homologous pairs of sister chromatids associated with each other, lying side by side
synapsis
process of forming a bivalent
function of bivalent
contributes to the genetic diversity of a species
Meiosis 1
separates homologous chromosomes-
results in 2 haploid daughter cells with half the number of chromosomes as the original cell, the daughter cells have a set of chromosomes and alleles that are different from each other an from the original diploid cell
Meiosis 2
produces 4 haploid daughter cells, separates sister chromatids
Meiosis 1 vs Meiosis 2 vs Mitosis
-mitosis begins with 12 chromatids that are joined together as 6 pairs of sister chromatids
-meiosis 2 begins with 6 chromatids that are joined together as 3 pairs of sister chromatids
-mitosis ends with two daughter cells that are diploid
-meiosis 2 ends with four daughter cells that are haploid
Steps in Meiosis 1
1. Prophase 1
2. Metaphase 1
3. Anaphase 1
4. Telophase 1 and cytokinesis
Steps in Meiosis 2
1. Prophase 2
2. Prometaphase 2
3. Metaphase 2
4. Anaphase 2
5. Telophase 2 and cytokinesis
euploid
normal chromosome number
polyploid
a condition in which a cell contains three or more sets of homologous chromosomes
aneuploidy
an organism in which the chromosome number is not an exact multiple of the haploid number
monosomic
A chromosomal condition in which a particular cell has only one copy of a chromosome, instead of the normal two
trisomic
referring to a diploid cell that has three copies of a particular chromosome instead of the normal two
nondisjunction
error in meiosis in which homologous chromosomes don't separate; gametes end up with wrong number of chromosomes
alloploid
Contains at least one set of chromosomes from two or more different species
triple X syndrome
A genetic abnormality in which a female has an extra X sex chromosome; characterized by decreased fertility, some genital abnormality, and slight mental retardation.
down syndrome
an autosomal condition of intellectual disability and associated physical disorders caused by an extra copy of chromosome 21
edward syndrome
an autosomal disorder in which there is an extra 18th chromosome; characterized by mental and physical impairment, facial abnormalities, extreme muscle tone, early death
turner syndrome
(XO) A sex chromosomal disorder in which affected women have only one X chromosome, causing sexual underdevelopment, short stature, and webbed neck
klinefelter syndrome
(XXY) sex chromosomal disorder in males that is characterized by small testes, enlarged breasts and reduced sperm production and mental retardation
cytokinesis in plant cells
Cell Plate
cytokinesis in animal cells
cleavage furrow
Step 1 for producing a kareotype
a sample of blood is collected and treated with drugs that stimulate cell division. The sample is then subjected to centerfugation
Step 2 for producing a kareotype
The supernatant is discarded, and the cell pellet is suspended in a hypotonic solution. This causes the cells to swell and the chromosomes to spread out from each other.
Step 3 for producing a kareotype
the sample is subjected to centerfugation a second time to concentrate the cells. The cells are suspended in a fixative, stained, and placed on a slide
Step 4 for producing a kareotype
The slide is viewed by a light microscope equipped with a camera; the sample is seen on a computer screen. The chromosomes can be photographed and arranged electronically on the screen
Step 5 for producing a kareotype
For a diploid human cell, 2 complete sets of chromosomes from a single cell constitute a kareotype of that cell
synaptonemal complexes
connect homologous chromosomes, not required for pairing of homologous chromosomes; form at the beginning of meiosis
Why did Mendel use pea plants
-fast growing
-self pollinating
-lots of traits to study
-ease of making crosses
P generation
True-breeding parents
F1 generation
offspring of the p generation
F2 generation
the offspring of the F1 generation
trait
identifiable characteristic of an organism, usually refers to a variant
example: seed color
characteristics
a distinguishing feature or quality
ex: height
hybridization
breeders cross two genetically different individuals
self-fertilization
In plants, the fusion of two gametes from the same individual to form a diploid offspring
cross-fertilization
The fusion of sperm and egg derived from two different individuals
single factor crosses
support the observation that the two alleles for a given gene are distributed randomly among an individuals gametes
two factor crosses
support the observation that alleles for a given trait are distributed randomly among an individuals gametes-- independent of the alleles for other traits
test cross
the crossing of an individual of unknown genotype with a homozygous recessive individual to determine the unknown genotype
chromosome theory of inheritance
1. genes are carried from parents to offspring on chromosomes
2. somatic cells contain a maternal and paternal set of chromosomes
3. the paternal and maternal chromosomes assort randomly during meiosis
4. gametes are haploid and somatic cells are diploid
genotype
The genetic makeup of an organism
ex: TT-homozygous dominant
tt- homozygous recessive
Tt- heterozygous
dominant
the displayed trait
recessive
masked by the presence of the dominant trait
phenotype
observable traits of an organism that are the result of gene expression
ex: tall, dwarf
dihybrid
Crosses between individuals that differ in two traits
What features of meiosis allow for independent assortment of chromosomes?
random alignment of homologous sister chromatids on the metaphase plate
pedigree
a diagram that shows the occurrence of a genetic trait in several generations of a family
autosomes
any chromosome that is not a sex chromosome
sex chromosomes
one of the 23 pairs of chromosomes in the human, contains genes that will determine the sex of the individual
X-linked genes
Genes that are considered recessive and located only on the X Chromosome
Sex determination
X-Y system: mammals
X-O system: insects
Z-W system: birds
sex linked
genes that are on one sex chromosome but not on the other
hemizygous
The term used to describe the single copy of an X-linked gene in a male
mendelian inheritance
the inheritance patterns of genes that segregate and assort independently
X-linked inheritance
A pattern of inheritance in which a recessive gene is carried on the X chromosome, so that males are more likely to be affected
ex: hemophilia A
Incomplete dominance
one allele is not completely dominant over another
ex: pink four o'clocks
codominance
situation in which both alleles of a gene contribute to the phenotype of the organism equally
ex: AB blood type
pleiotrophy
the ability of a single gene to have multiple effects
ex: sickle cell anemia
The blood types of a couple are AB and B. Can this couple have a baby with blood type O?
no
gene interaction
a single character is controlled by two or more genes, each of which has two or more alleles
epistasis
when one gene masks the affect of another gene the ratio is modified
ex: 2 genes involved in flower color in sweet peas
linkage
when two genes tend to be transmitted as a unit
nonrecombinants (parental types)
offspring's traits have not changes from parental generations
recombinants (nonparental types)
different combination of traits from parental generation
genetic mapping
the study of the arrangement of genes in a species' genome
-shows a linear arrangement of genes
-allows us to estimate the relative distances between linked genes based on the likelihood that crossover will occur between them
extranuclear inheritance
also called cytoplasmic inheritance- transmission of genes located outside the cell nucleus
Mitochondria and Chloroplasts contain there own ______.
geonomes
Organelle genomes smaller than nuclear genome but more important to _______.
phenotypes
Genes transmitted outside of the nucleus occur through-
extranuclear inheritance and cytoplasmic inheritance
chloroplasts and mitochondrial genomes
does not obey Mendel's law of segregation, often maternally inherited, some species do exhibit biparental or paternal inheritance
X inactivation
in female mammals, the inactivation of one X chromosome in each somatic cell
ex: calico cat coat pattern
barr body
Inactivated X chromosome
ex: calico cat coat pattern
epigenetic inheritance
inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
biparental inheritance
inheritance of organelles from both parents. Occurs in single-celled yeast and some plants
paternal inheritance
only the pollen contributes chloroplasts