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98% of the mass of every living organism is composed of oxygen, carbon,

hydrogen, phosphorus, nitrogen, sulfur

orbital: A region in space surrounding the atomic nucleus in which an
electron is most likely to be found.
only two electrons in each orbital
first shell only contains one s orbital, second shell contains four
orbitals (one s orbital and 3 p orbitals)
octet rule: atoms with unpaired electrons (unfilled orbitals) will gain or
lose electrons with other atoms so that they have eight electrons in their
outermost shell
covalent bond: Chemical bond based on the sharing of electrons between
two atoms.
very strong and stable
electronegativity: The tendency of an atom to attract electrons
when it occurs as part of a compound.
o depends on how many protons the atom has and the distance
between the nucleus and the electrons in the valence shell
o if two atoms are close in electronegativity they share
electrons equally in a nonpolar covalent bond, when electrons
are drawn to one nucleus (higher electronegativity) more than
another the bond is polar covalent
when one interacting atom is much more electronegative than the
other, a complete transfer of one or more electrons may take place
ion: An electrically charged particle that forms when an atom gains
or loses one or more electrons.
o cation is (+), anion is (-)
hydrogen bond: A weak electrostatic bond which arises from the
attraction between the slight positive charge on a hydrogen atom and a
slight negative charge on a nearby oxygen or nitrogen atom.
van der waals forces: Weak attractions between atoms resulting from the
interaction of the electrons of one atom with the nucleus of another. This
type of attraction is about one-fourth as strong as a hydrogen bond.
buffer: A substance that can transiently accept or release hydrogen ions
and thereby resist changes in pH.
essential to homeostasis, if biological molecules lost or gain h+ ions
then their properties change
weak acid and corresponding base

polymer: A large molecule made up of similar or identical subunits called


functional group: A characteristic combination of atoms that contributes

specific properties (such as charge or polarity) when attached to larger
molecules (e.g., carboxyl group; amino group).

isomer: Molecules consisting of the same numbers and kinds of atoms,

but differing in the bonding patterns by which the atoms are held
structural isomers differ in how their atoms are joined together
cis-trans isomer: In molecules with a double bond (typically
between two carbon atoms), identifies on which side of the double
bond similar atoms or functional groups are found. If they are on
the same side, the molecule is a cis isomer; in a trans isomer,
similar atoms are on opposite sides of the double bond.
optical isomers: Two molecular isomers that are mirror images of
each other.
o asymmetric carbon
condensation reaction: A chemical reaction in which two molecules
become connected by a covalent bond and a molecule of water is released
(AH + BOH AB + H2O.) (Contrast with hydrolysis reaction.)
result in formation of covalent bonds between monomers
hydrolysis reactions break polymers into monomers by adding

protein: Long-chain polymer of amino acids with twenty different common

side chains. Occurs with its polymer chain extended in fibrous proteins, or
coiled into a compact macromolecule in enzymes and other globular
proteins. The component amino acids are encoded in the triplets of
messenger RNA, and proteins are the products of genes.

polypeptide: A large molecule made up of many amino acids joined by

peptide linkages. Large polypeptides are called proteins.

proteins consist of one or more polypeptide chains which are

unbranched polymers of covalently linked amino acids
amino acid: An organic compound containing both NH2 and COOH groups.
Proteins are polymers of amino acids.
carboxyl and amino functional group attached to same carbon
(called alpha carbon), also attached to alpha carbon is a hydrogen
atom and an r group
o r group: The distinguishing group of atoms of a particular
amino acid; also known as a side chain.
o the alpha carbon is asymmetrical so amino acids exist as
optical isomers called d and l amino acids, l are commonly
found in proteins
o both carboxyl and amino groups are ionized, so amino acids
are simultaneously acids and bases
o five amino acids have ionized hydrophilic side chains, five
have polar side chains and are hydrophilic, seven have
hydrophobic nonpolar side chains, cysteine has terminal sh
group and can form a covalent bond with another cysteine
called a disulfide bridge, glycine side chain only has single
hydrogen, proline forms covalent bonds with hydrocarbon side
chains forming a ring
peptide linkage: The bond between amino acids in a protein; formed
between a carboxyl group and amino group (CONH) with the loss of
water molecules.
in the c-n linkage, the adjacent alpha carbons are not free to rotate
fully, limiting the folding of the polypeptide chain
the oxygen bound to the carbon in the carboxyl group carries a
slight negative charge whereas the hydrogen bound to the
nitrogen in the amino group is slightly positive, this asymmetry of
charge favors hydrogen bonding within the protein molecule itself
and between molecules
primary structure (joined amino acid monomers) secondary structure
(alpha helices or beta pleated sheets) tertiary structure (polypeptide
folds are stabilized by bonds which form specific shapes) quaternary
structure (two or more polypeptides assemble to form larger proteins)
alpha helix is a right handed coil, r groups extend outward from
peptide backbone, hydrogen bonds form between the hydrogen of
the n-h of one amino acid and the oxygen of the c=o of another
beta pleated sheet formed from two or more polypeptide chains
that are extended and aligned

in the tertiary structure the proteins exposed outer r groups can

interact with other molecules in the cell, tertiary structure defined
by interactions between r groups
o covalent disulfide bridges, hydrogen bonds, hydrophobic side
chains aggregate together in interior of the protein and are
stabilized by van der waals forces, ionic attractions form
between positively and negatively charged side chains
forming salt bridges
denaturation: Loss of activity of an enzyme or nucleic acid molecule as a
result of structural changes induced by heat or other means.
chaperone: A protein that guards other proteins by counteracting
molecular interactions that threaten their three-dimensional structure.
carbohydrates: Organic compounds containing carbon, hydrogen, and
oxygen in the ratio 1:2:1 (i.e., with the general formula CnH2nOn).
Common examples are sugars, starch, and cellulose.
source of stored energy, used to transport stored energy, serve as carbon
skeletons that can be rearranged to form new molecules
monosaccharides (simple sugars, monomers) disaccharides (two
monosaccharides bonded covalently) oligosaccharides (3-20
monosaccharides) polysaccharides (hundreds of thousands of
glucose: The most common monosaccharide; the monomer of the
polysaccharides starch, glycogen, and cellulose.
exists in straight chains and rings (alpha d glucose and beta d)
glycosidic linkage: Bond between carbohydrate (sugar) molecules through
an intervening oxygen atom (O).
polysaccharides are not necessarily linear chains of monomers, each
monomer unit has several sites that are capable of forming glycosidic
linkages and thus branched molecules are possible
starches are polysaccharides of glucose, different starches can be
distinguished by the amount of branching on the 1 and 6 carbon
energy storage compound of plants
glycogen is highly branched polymer of glucose, energy storage
compound for animals
cellulose is structural material of plant cell walls, stable because of beta
glycosidic linkages
lipid: Nonpolar, hydrophobic molecules that include fats, oils, waxes,
steroids, and the phospholipids that make up biological membranes.

fats and oils store energy, phospholipids play an important structural role

in cell membranes, steroids are hormones and vitamins

triglyceride: A simple lipid in which three fatty acids are combined with
one molecule of glycerol.
fats are solid at room temperate, oils are liquid
glycerol: A three-carbon alcohol with three hydroxyl groups; a
component of phospholipids and triglycerides.
fatty acid: A molecule made up of a long nonpolar hydrocarbon
chain and a polar carboxyl group. Found in many lipids.
esther linkage: A condensation (water-releasing) reaction in which
the carboxyl group of a fatty acid reacts with the hydroxyl group of
an alcohol. Lipids, including most membrane lipids, are formed in
this way.
saturated fatty acid: A fatty acid in which all the bonds between
carbon atoms in the hydrocarbon chain are single bondsthat is, all
the bonds are saturated with hydrogen atoms.
unsaturated fatty acid: A fatty acid whose hydrocarbon chain
contains one or more double bonds.
phospholipid: A lipid containing a phosphate group; an important
constituent of cellular membranes.
phosphate functional group has negative charge making it
hydrophilic and attracts polar water molecules, two fatty acids are
hydrophobic and aggregate together, form a bilayer
carotenoid: A yellow, orange, or red lipid pigment commonly found as an
accessory pigment in photosynthesis; also found in fungi.
steroid: Any of a family of lipids whose multiple rings share carbons. The
steroid cholesterol is an important constituent of membranes and is the
base of steroid hormones such as testosterone.
nucleoid: The region that harbors the chromosomes of a prokaryotic cell.
Unlike the eukaryotic nucleus, it is not bounded by a membrane.
cytoplasm: The contents of the cell, excluding the nucleus.
cytosol: The fluid portion of the cytoplasm, excluding organelles and
other solids.
ribosome: A small particle in the cell that is the site of protein synthesis.
cell wall: A relatively rigid structure that encloses cells of plants, fungi,
many protists, and most prokaryotes, and which gives these cells their
shape and limits their expansion in hypotonic media
cell walls of most bacteria (but not archaea) contain peptidoglycan
some bacteria have outer membrane that encloses peptidoglycan
some bacteria have slimy polysaccharide layer called capsule
enclosing cell wall, not essential to prokaryotic life

photosynthetic bacteria have internal membrane system that contains

molecules necessary for photosynthesis
flagellum: Long, whiplike appendage that propels cells. Prokaryotic
flagella differ sharply from those found in eukaryotes.
complex ring structure motor proteins spin flagellum
pili: hairlike protein structures used for adherence that project from
surface of some types of bacteria
nuclear envelope: two membranes surrounding nucleus which separate
gene transcription (in nucleus) from gene translation (in cytoplasm)
chromatin: The nucleic acid-protein complex that makes up eukaryotic
chromosomes: In bacteria and viruses, the DNA molecule that contains
most or all of the genetic information of the cell or virus. In eukaryotes, a
structure composed of DNA and proteins that bears part of the genetic
information of the cell.
nuclear lamina: protein meshwork, maintains shape of nucleus by being
attached to both chromatin and nuclear envelope
endomembrane system: A system of intracellular membranes that
exchange material with one another, consisting of the Golgi apparatus,
endoplasmic reticulum, plasma membrane, nuclear envelope, and
lysosomes when present.
endoplasmic reticulum: A system of membranous tubes and flattened
sacs found in the cytoplasm of eukaryotes. Exists in two forms: rough ER,
studded with ribosomes; and smooth ER, lacking ribosomes.
rough er receives newly synthesized proteins and transports these
proteins to other locations within the cell, while inside rough er
proteins can be chemically modified and tagged for delivery to
specific locations, proteins shipped to other destinations enclosed
within vesicles that pinch off
smooth er chemically modifies small molecules taken in by the cell
that may be toxic to make them more easily removed, site for
glycogen degradation in animal cells, synthesizes lipids and
steroids, stores calcium ions
golgi apparatus: A system of concentrically folded membranes found in
the cytoplasm of eukaryotic cells; functions in secretion from the cell by
flattened membranous sacs called cisternae that are piled up and
small membrane enclosed vesicles
o cisternae has cis region closest to rough er, medial region,
and trans region closest to plasma membrane

o protein containing vesicles from rough er fuse with cis region

release cargo into lumen of golgi vesicles bud off from
trans region
receives protein containing vesicles from rough er,
modifies/concentrates/packages/sorts proteins, adds and modifies
carbohydrates added to proteins in the rough er, synthesizes some
polysaccharides for plant cell walls
primary lysosome: A membrane-enclosed organelle originating from the
Golgi apparatus and containing hydrolytic enzymes.
contain digestive enzymes and hydrolyze macromolecules
(proteins, polysaccharides, nucleic acids, lipids) into monomers
small vesicle called phagosome (through phagocytosis) containing
food or materials breaks free from plasma membrane and moves
into cytoplasm phagosome fuses with primary lysosome to form
secondary lysosome particles digested products pass through
membrane of lysosome, used secondary lysosome fuses with
plasma membrane and releases undigested particles
autophagy: The programmed destruction of a cells components.
mitochondria: Energy-generating organelles in eukaryotic cells that
contain the enzymes of the citric acid cycle, the respiratory chain, and
oxidative phosphorylation.
production of atp through cellular respiration
smooth and protective outer membrane and inner membrane which
folds inward and has shelflike structures called cristae which contain
molecules for atp generation
space enclosed by inner membrane called mitochondrial matrix,
contains enzymes/ribosomes/dna
plastids are only present in plant cells and certain protists
chloroplasts: An organelle bounded by a double membrane
containing the enzymes and pigments that perform photosynthesis.
Chloroplasts occur only in eukaryotes.
o thylakoid: A flattened sac within a chloroplast. Thylakoid
membranes contain all of the chlorophyll in a plant, in
addition to the electron carriers of photophosphorylation.
Thylakoids stack to form grana.
o grana suspended in stroma fluid, contains ribosomes and dna
peroxisome: An organelle that houses reactions in which toxic peroxides
are formed and then converted to water.
glyoxysomes: An organelle found in plants, in which stored lipids are
converted to carbohydrates.

vacuole: Membrane-enclosed organelle in plant cells that can function for

storage, water concentration for turgor, or hydrolysis of stored

plant vacuoles store toxic byproducts and waste, swell like balloons
and stiffen from water pressure (turgor) which supports the plant,
contain some pigments of flowers, hydrolyze stored proteins in
contractile vacuoles found in many freshwater protists, enlarge as
water enters then rapidly contracts to force water out
cytoskeleton: The network of microtubules and microfilaments that gives
a eukaryotic cell its shape and its capacity to arrange its organelles and to
supports cell and maintains its shape, holds organelles and other
particles in position, moves around organelles and particles,
movement of cytoplasm (cytoplasmic streaming), interacts with
extracellular structures and anchors cell in place
microfilaments: In eukaryotic cells, a fibrous structure made up of
actin monomers. Microfilaments play roles in the cytoskeleton, in
cell movement, and in muscle contraction
o each monomer has a positive and negative end which allows
long double helical chains to form
o actin filaments interact with myosin (motor protein) and allow
muscle contraction in animal cells
intermediate filaments are tough, ropelike proteins with 50 different
types, more permanent than other types of filaments
o anchor cell structures in place, resist tension and stretch
through cytoplasm
microtubules: Tubular structures found in centrioles, spindle
apparatus, cilia, flagella, and cytoskeleton of eukaryotic cells. These
tubules play roles in the motion and maintenance of shape of
eukaryotic cells.
o assembled from dimers (two monomers) of tubulin protein
(alpha-tubulin and beta-tubulin), positive and negative end
o serve as tracks for motor proteins: Specialized proteins that
use energy to change shape and move cells or structures
within cells.
kinesin binds to microtubule and walks along it by
changing shape from the negative to the positive end,
cytoplasmic dynein moves toward negative end
o form cilia and flagella in eukaryotes, each cilia has nine fused
doublets of microtubule chains and two unlinked microtubule
chains in the center

doublets slide past each other with motor protein

dynein, and nexin allows bending
endosymbiosis theory: The theory that the eukaryotic cell evolved via the
engulfing of one prokaryotic cell by another.

fluid mosaic model: A molecular model for the structure of biological

membranes consisting of a fluid phospholipid bilayer in which suspended
proteins are free to move in the plane of the bilayer.
the proteins are noncovalently embedded in the phospholipid
bilayer by their hydrophobic regions but their hydrophilic domains
are exposed to the watery conditions on either side of the bilayer
cholesterol embedded in the membrane

a membrane with shorter chain fatty acids, unsaturated fatty acids, or

less cholesterol is less fluid, cholesterol and long chain saturated fatty
peripheral membrane proteins: Proteins associated with but not
embedded within the plasma membrane.
integral membrane proteins: Proteins that are at least partially embedded
in the plasma membrane.
hydrophilic r groups interact with water and stick out into the
aqueous environment inside or outside the cell
hydrophobic side chains interact with fatty acids on the interior of
the bilayer
membrane proteins and lipids interact generally only noncovalently

transmembrane protein: An integral membrane protein that spans the

phospholipid bilayer.

some proteins can move freely in the bilayer

carbohydrates located on outer surface of plasma membrane serve as

recognition sites for other cells and molecules

glycolipid: a carbohydrate covalently bonded to a lipid, recognition
signal for other cells
glycoprotein: one or more short carbohydrate chains covalently
bonded to a protein
proteoglycan: A glycoprotein containing a protein core with attached long,
linear carbohydrate chains.
two kinds of carbohydrates, one small one that keeps the
proteoglycan attached to the cell, large sulfated polysaccharide is
responsible for specific recognition and adhesion
homotypic: Pertaining to adhesion of cells of the same type.
heterotypic binding of between different molecules on different cells
cell junction: Specialized structures associated with the plasma
membranes of epithelial cells. Some contribute to cell adhesion, others to
intercellular communication.
epithelial tissue lines body cavities and body surfaces
tight junction: A junction between epithelial cells in which there is
no gap between adjacent cells.
gap junction: A 2.7-nanometer gap between plasma membranes of
two animal cells, spanned by protein channels. Gap junctions allow
chemical substances or electrical signals to pass from cell to cell.
desmosomes: hold neighboring cells firmly together, but materials
can still move around in the extracellular matrix
integrin: In animals, a transmembrane protein that mediates the
attachment of epithelial cells to the extracellular matrix.

passive transport across cell membrane doesnt require the input of
chemical energy, happens due to concentration gradient
smaller molecules diffuse faster, higher temperatures lead to faster
diffusion, bigger concentration gradient leads to faster diffusion
simple diffusion: Diffusion that does not involve a direct input of energy
or assistance by carrier proteins. (usually hydrophobic molecules pass
osmosis: Movement of water across a differentially permeable membrane,
from one region to another region where the water potential is more
hypertonic: higher solute concentrate, isotonic: equal solute
concentration, hypotonic: lower solute concentration

facilitated diffusion: polar or charged substances do not readily diffuse

across membranes without a protein helper

channel protein: An integral membrane protein that forms an
aqueous passageway across the membrane in which it is inserted
and through which specific solutes may pass.
carrier: In facilitated diffusion, a membrane protein that binds a
specific molecule and transports it through the membrane.
ion channel: An integral membrane protein that allows ions to diffuse
across the membrane in which it is embedded, hydrophilic pore
gated channel: A membrane protein that changes its three-dimensional
shape, and therefore its ion conductance, in response to a stimulus. When
open, it allows specific ions to move across the membrane.
voltage or ligand (stimulus molecule) gated
uniporter: membrane transport protein that carries a single substance in
one direction.
symporter: A membrane transport protein that carries two substances in
the same direction.
antiporter: A membrane transport protein that moves one substance in
one direction and another in the opposite direction.
primary active transport: Active transport in which ATP is hydrolyzed,
yielding the energy required to transport an ion or molecule against its
concentration gradient.
secondary active transport: A form of active transport that does not use
ATP as an energy source; rather, transport is coupled to ion diffusion
down a concentration gradient established by primary active transport.

endocytosis: A process by which liquids or solid particles are taken up by

a cell through invagination of the plasma membrane.
plasma membrane folds inward forming a small pocket around
materials from the environment, pocket deepens forming a vesicle,
vesicle separates from plasma membrane and moves into cell
phagocytosis: part of plasma membrane engulfs large particles
pinocytosis: Endocytosis by a cell of liquid containing dissolved
receptor mediated endocytosis: Endocytosis initiated by macromolecular
binding to a specific membrane receptor.

receptors are integral membrane proteins, cytoplasmic surface is

coated with other proteins such as clathrin so called coated pits,
once inside vesicle loses its clathrin coat and may fuse with a
lysosome to have its contents digested
exocytosis: A process by which a vesicle within a cell fuses with the
plasma membrane and releases its contents to the outside.

signal transduction pathway: The series of biochemical steps whereby a

stimulus to a cell (such as a hormone or neurotransmitter binding to a

receptor) is translated into a response of the cell.
hormone: A chemical signal produced in minute amounts at one site in a
multicellular organism and transported to another site where it acts on
target cells.
autocrine: A chemical signal that binds to and affects the cell that
makes it.
juxtacrine: signal only affects cells adjacent to the cell that
produced the signal
paracrine: Pertaining to a chemical signal, such as a hormone, that
acts locally, near the site of its secretion.
ligand: Any molecule that binds to a receptor site of another (usually
larger) molecule.
dissociation constant (Kd): measure of the affinity of the receptor
for its ligand
o Kd = ([R][L])/[RL]
o lower Kd means higher binding ability, the cell is more
sensitive to the receptors ligand
membrane receptors: large or polar ligands cant cross lipid bilayer, have
to bind to transmembrane protein with extracellular binding domain
gated ion channels
protein kinase receptor: protein kinase is an enzyme that catalyzes
the addition of a phosphate group from ATP to a target protein
g protein linked receptor: A class of receptors that change
configuration upon ligand binding such that a G protein binding site
is exposed on the cytoplasmic domain of the receptor, initiating a
signal transduction pathway.
o g proteins can bind the receptor, gtp/gdp, effector protein (a
protein responsible for the cellular response to a signal
transduction pathway)
o g protein is partially inserted into lipid bilayer and partially
exposed to cytoplasm, is mobile
intracellular receptors: small or nonpolar ligands can diffuse across lipid
bilayer and enter the cell, bind to receptors inside cell

many are transcription factors that to move to dna after binding

ligand and alter expression of certain genes
others are always in nucleus and require ligand to enter nucleus
second messenger: A compound, such as cAMP, that is released within a
target cell after a hormone (the first messenger) has bound to a surface
receptor on a cell; the second messenger triggers further reactions within
the cell.
cyclic amp (cAMP): A compound formed from ATP that acts as a
second messenger, rapidly amplify and distribute signal
lipid derives second messengers, certain phospholipids hydrolyzed
into component parts by enzymes
calcium ions, nitric oxide, cyclic gmp,
protein kinase cascade: A series of reactions in response to a molecular
signal, in which a series of protein kinases activate one another in
sequence, amplifying the signal at each step.
at each stage signal is amplified because each newly activated
protein kinase can catalyze phosphorylation of many target proteins
signal that originally arrived at plasma membrane is communicated
to nucleus
gap junction: A 2.7-nanometer gap between plasma membranes of two
animal cells, spanned by protein channels. Gap junctions allow chemical
substances or electrical signals to pass from cell to cell.
connexon: a protein channel linking adjacent animal cells.
plasmodesmata: Cytoplasmic strands connecting two adjacent plant cells.
desmotubule: A membrane extension connecting the endoplasmic
reticulum of two plant cells that traverses the plasmodesma.

metabolism: The sum total of the chemical reactions that occur in an

organism, or some subset of that total (as in respiratory metabolism).
potential energy: Energy not doing work but with the potential to do so,
such as the energy stored in chemical bonds.

anabolic reactions: A synthetic reaction in which simple molecules are

linked to form more complex ones; requires an input of energy and

captures it in the chemical bonds that are formed.
endergonic: A chemical reaction in which the products have higher
free energy than the reactants, thereby requiring free energy input
to occur.
catabolic reaction: A synthetic reaction in which complex molecules are
broken down into simpler ones and energy is released.
exergonic: A chemical reaction in which the products of the reaction
have lower free energy than the reactants, resulting in a release of
free energy.
enthalpy (h): The total energy of a system.

free energy (g): Energy that is available for doing useful work, after

allowance has been made for the increase or decrease of disorder.

G = H TS
o t = temperature, s = entropy
o if G is negative, free energy is released
o if G is positive, free energy is consumed
every chemical reaction proceeds to a certain extent but not necessarily
to completion, each reaction has specific equilibrium point which is
related to the free energy released by the reaction under specified
ATP releases a relatively large amount of energy when hydrolyzed to ADP
and Pi (inorganic phosphate), can phosphorylate (donate a phosphate
group to) molecules which gain some of the energy stored in the atp
consists of nitrogenous base adenine bonded to ribose (a sugar), which is
attached to a sequence of three phosphate groups
ATP + H2O ADP + Pi + free energy
under standard laboratory conditions G is about 7.3 kcal/mol
under cellular conditions G can be as much as 14 kcal/mol
phosphate groups are negatively charged and so they repel each other, it
takes energy to get two phosphates near enough to each other to make
the covalent bond that links them together.
some of this energy is stored as potential energy in the p-o bonds
between the phosphates in ATP

enzyme: A catalytic protein that speeds up a biochemical reaction.

ribozyme: An RNA molecule with catalytic activity.
transition state: In an enzyme-catalyzed reaction, the reactive condition

of the substrate after there has been sufficient input of energy (activation
energy) to initiate the reaction.
enzymes do this by orienting substrates, straining substrates, or
adding charges
activation energy (Ea): The energy barrier that blocks the tendency for a
chemical reaction to occur.
the activation energy is the energy needed to change the reactants
into unstable molecular forms called transition-state intermediates
o higher free energy than the reactants or the products
substrate: The molecule or molecules on which an enzyme exerts
catalytic action.
active site: The region on the surface of an enzyme or ribozyme where
the substrate binds, and where catalysis occurs.
enzyme substrate complex: An intermediate in an enzyme-catalyzed
reaction; consists of the enzyme bound to its substrate(s).
enzymes lower the energy barrier for a reaction
acid-base catalysis: the acidic or basic side chains of the amino
acids in the active site transfer H+ to or from
the substrate, destabilizing a covalent bond in the substrate, and
permitting it to break.
covalent catalysis: a functional group in a side chain forms a
temporary covalent bond with a portion of the substrate.
metal ion catalysis: metal ions such as copper, iron, and
manganese, which are often firmly bound to side chains
of enzymes, can lose or gain electrons without detaching from
the enzymes.
induced fit: A change in the shape of an enzyme caused by binding to its
substrate that exposes the active site of the enzyme.
prosthetic groups are distinct non-amino acid atoms or molecular
groupings that are permanently bound to enzymes, inorganic cofactors
include ions such as copper/zinc/iron that are bound, a coenzyme is a
non-protein carbon containing molecule that is required for the action of
one or more enzymes
if an inhibitor covalently binds to certain side chains at the active site of
an enzyme, it will permanently inactivate the enzyme by destroying its
ability to interact with its normal substrate

competitive inhibitor: A non-substrate that binds to the active site of an

enzyme and thereby inhibits binding of its substrate.

this inhibition is reversible ie. if the concentration of substrate
surpasses the concentration of inhibitor
uncompetitive inhibitor: binds to the enzyme-substrate
complex, preventing the complex from releasing products
noncompetitive inhibitor: binds to an enzyme at a site distinct from
the active site. This binding causes a change in the shape of the enzyme
that alters its activity
allosteric regulation: Regulation of the activity of a protein (usually
an enzyme) by the binding of an effector molecule to a site other
than the active site.
allosteric enzymes have multiple active sites, binding of a substrate to
one active site causes a slight change in the protein structure that
influences the adjacent subunit and makes it more likely to bind its
end product inhibition: when an end product is in high concentration
some of it binds to an allosteric site on the enzyme, causing it to become
each enzyme is most active at a particular ph, if ph changes then the
ionization of carboxyl groups and amino groups changes and the folding
of the proteins can be altered
isozymes: Enzymes of an organism that have somewhat different amino
acid sequences but catalyze the same reaction.

the glucose catabolism pathway extracts the energy stored in the

covalent bonds of glucose and stores it instead in atp molecules via

phosphorylation reaction
ADP + Pi + free energy ATP

glycolysis: The enzymatic breakdown of glucose to pyruvic acid.

one glucose converted to two molecules of the three carbon product

pyruvate, anaerobic process because doesnt require o2
cellular respiration uses o2 and is aerobic, each pyruvate molecule is
completely converted into three molecules of CO2 through a set of
catabolic pathways including pyruvate oxidation, the citric acid cycle, and
an electron transport system. in the process, a great deal of the energy
stored in the covalent bonds of pyruvate is captured to form ATP.
fermentation: The anaerobic degradation of a substance such as glucose
to smaller molecules such as lactic acid or alcohol with the extraction of
redox reaction: A chemical reaction in which one reactant is oxidized
(loses electrons) and the other is reduced (gains electrons). Short for
reduction-oxidation reaction.
the more reduced a molecule is, the more energy is stored in its
covalent bonds
coenzyme nad+ acts as an electron carrier, its reduced form
accepts two electrons and becomes nadh
glucose use 2 atp fructose 1,6 bisphosphate glyceraldehyde 3phosphate two nad+ reduced, 4 atp made two pyruvate
takes place in cytosol and has 10 enzyme catalyzed reactions

net production is two atp, two nadh, two pyruvate per glucose
next step is oxidation of pyruvate to a two carbon acetate molecule and

co2, the acetate is then bound to coenzyme a to form acetyl coenzyme a

acetyl coa donates its acetyl group to the four carbon compound
oxaloacetate, forming citrate

citric acid cycle: acetyl coa citrate 2 nadh formed and 2 co2 gtp and

fadh2 formed nadh formed oxaloacetate regenerated

respiratory chain occurs in inner mitochondrial membrane, electrons from
nadh and fadh2 are passed along the chain which is a series of protein
complexes in the inner mitochondrial membrane
containing electron carriers and enzymes. The carriers gain free energy
when they become reduced and release free energy when they
are oxidized
during electron transport, protons are actively transferred from the
matrix to the intermembrane space
The concentration of H+ in the intermembrane space is higher than
in the matrix, and this gradient represents a source of potential
energy. The diffusion of those protons across the membrane is
coupled with the formation of ATP
o proton motive force: Force generated across a membrane
having two components: a chemical potential (difference in
proton concentration) plus an electrical potential due to the
electrostatic charge on the proton.
chemiosmosis: Formation of ATP in mitochondria and chloroplasts,
resulting from a pumping of protons across a membrane (against a
gradient of electrical charge and of pH), followed by the return of the
protons through a protein channel with ATP synthase activity.
atp synthase acts as a channel allowing h+ to diffuse back into the
matrix and uses the energy of the diffusion to make atp from adp
and pi
atp synthase has f0 unit which is trans membrane region that is h+
channel and f1 unit which has active sites for atp synthesis
when h+ diffuses through the channel the potential energy is
converted to kinetic energy which causes central polypeptide to
fermentation: The anaerobic degradation of a substance such as glucose
to smaller molecules such as lactic acid or alcohol with the extraction of
lactic acid fermentation lactate is product
alcoholic fermentation takes place in certain yeasts, ethanol product
glycolysis and fermentation form 2 atp, glycolysis and cellular respiration
form 32 atp
polysaccharides are hydrolyzed to glucose, lipids broken down into
glycerol and fatty acids (glycerol is converted to intermediate in
glycolysis, fatty acids converted to acetyl coa), proteins hydrolyzed into
amino acids

allosteric regulation: Regulation of the activity of a protein (usually an

enzyme) by the binding of an effector molecule to a site other than the

active site.
in a metabolic pathway, a high concentration of the final product
can inhibit the action of an enzyme that catalyzes an earlier

meiosis: Division of a diploid nucleus to produce four haploid daughter

cells. The process consists of two successive nuclear divisions with only
one cycle of chromosome replication. In meiosis I, homologous
chromosomes separate but retain their chromatids. The second
division meiosis II, is similar to mitosis, in which chromatids separate.
to reduce the chromosome number from diploid to haploid
to ensure that each of the haploid products has a complete set of

1. early prophase: the chromatin begins to condense following interphase
2. mid prophase I: synapsis aligns homologs, chromosomes condense
3. late prophase I/prometaphase: chromosomes continue to coil and
shorten, crossing over genetic material in a homologous pair, nuclear
envelops begins to break down
4. metaphase I: homologous pairs line up on metaphase plate
5. anaphase I: homologous chromosomes move to opposite ends of the
6. telophase I: chromosomes gather into nuclei, original cell divides
7. prophase II: chromosomes condense again following brief interphase
8. metaphase II: the centromeres of paired chromatids line up along he
metaphase plate of each cell
9. anaphase II: the chromatids separate becoming their own
chromosomes and move to opposite poles
10.telophase II: chromosomes gather into nuclei, cells divide

synapsis: The highly specific parallel alignment (pairing) of homologous

chromosomes during the first division of meiosis

chiasma: An X-shaped connection between paired homologous
chromosomes in prophase I of meiosis. A chiasma is the visible
manifestation of crossing over between homologous chromosomes.
aneuploidy: A condition in which one or more chromosomes or pieces of
chromosomes are either lacking or present in excess.
caused by nondisjunction
tumor: A disorganized mass of cells. Malignant tumors spread to other
parts of the body.
malignant: Pertaining to a tumor that can grow indefinitely and/or
spread from the original site of growth to other locations in the
metastasis: malignant cells can become lodged in a distant other part of
the body, establishing tumors at the new site
oncogene: A gene that codes for a protein product that stimulates cell
proliferation. Mutations in oncogenes that result in excessive cell
proliferation can give rise to cancer.
mutated positive regulators in cancer cells that are overly active or
present in excess
tumor suppressor: A gene that codes for a protein product that inhibits
cell proliferation; inactive in cancer cells.
mutant tumor suppressor alleles are recessive, mutant oncogene alleles
are dominant
somatic mutation: Permanent genetic change in a somatic cell (as
opposed to a germ cell, the egg or sperm). These mutations affect the
individual only; they are not passed on to offspring.
germ line mutation: Mutation in a cell that produces gametes (i.e., a
germ line cell)
character: In genetics, an observable feature, such as eye color.

trait: In genetics, a specific form of a character: eye color is a character;

brown eyes and blue eyes are traits.

true breeding: A genetic cross in which the same result occurs every time
with respect to the trait(s) under consideration, due to homozygous
parental (p) generation: The individuals that mate in a genetic cross.
Their offspring are the first filial (F1) generation.

second filial (F2) generation: The second filial generation; the immediate

progeny of a mating between members of the F1 generation.

monohybrid cross: A mating in which the parents differ with respect to
the alleles of only one locus of interest.
particulate theory: In genetics, the theory that genes are physical entities
that retain their identities after fertilization.
recessive: In genetics, an allele that does not determine phenotype in the
presence of a dominant allele. (Contrast with dominance.)
gamete: The mature sexual reproductive cell: the egg or the sperm.

diploid: Having a chromosome complement consisting of two copies

(homologs) of each chromosome. Designated 2n.

haploid: Having a chromosome complement consisting of just one copy of
each chromosome; designated 1n or n.
allele: The alternate form of a genetic character found at a given locus on
a chromosome.
homozygous: In diploid organisms, having identical alleles of a given
gene on both homologous chromosomes.
heterozygous: In diploid organisms, having different alleles of a given
gene on the pair of homologs carrying that gene.
phenotype: The observable properties of an individual resulting from both
genetic and environmental factors.
genotype: An exact description of the genetic constitution of an
individual, either with respect to a single trait or with respect to a larger
set of traits.
alleles of different genes sort independently of one another during
gamete formation
wild type: Geneticists term for standard or reference type. Deviants from
this standard, even if the deviants are found in the wild, are usually
referred to as mutant. (Note that this terminology is not usually applied
to human genes.)
incomplete dominance: Condition in which the heterozygous phenotype is
intermediate between the two homozygous phenotypes.
codominance: A condition in which two alleles at a locus produce different
phenotypic effects and both effects appear in heterozygotes.
pleiotropy: The determination of more than one character by a single
epistasis: Interaction between genes in which the presence of a particular
allele of one gene determines whether another gene will be expressed.

heterosis: The superior fitness of heterozygous offspring as compared

with that of their dissimilar homozygous parents. Also called hybrid vigor.
two parameters describe the effects of genes and environment on the
penetrance: The proportion of individuals with a particular genotype
that show the expected phenotype.
expressivity: The degree to which a genotype is expressed in the
phenotype; may be affected by the environment.
quantitative variation is when phenotype varies continuously over a
quantitative trait loci: A set of genes determining a complex
character (trait) that exhibits quantitative variation (variation in
amount rather than in kind).
recombination accounts for why linked alleles are not always inherited
together, alleles at different loci on the same chromosome can be
recombined by crossing over, and separating from one another
recombinant frequency: The proportion of offspring of a genetic
cross that have phenotypes different from the parental phenotypes
due to crossing over between linked genes during gamete
monoecious: Pertaining to organisms in which both sexes are housed in
a single individual that produces both eggs and sperm.
dioecious: Pertaining to organisms in which the two sexes are housed in
two different individuals, so that eggs and sperm are not produced in the
same individuals.
sex linked inheritance: Pattern of inheritance characteristic of genes
located on the sex chromosomes of organisms having a chromosomal
mechanism for sex determination.

transfection: Insertion of recombinant DNA into animal cells.

genetic marker: (1) In gene cloning, a gene of identifiable phenotype that
indicates the presence of another gene, DNA segment, or chromosome
fragment. (2) In general, a DNA sequence such as a single nucleotide
polymorphism whose presence is correlated with the presence of other
linked genes on that chromosome.
purine bases: adenine/guanine, pyrimidine bases: cytosine/thymine
a-t and g-c through h bonding
van der waals forces between adjacent bases on the same strand
dna is double stranded right handed helix with sugar phosphate backbone
and base pairs lined up on the inside, antiparallel, major and minor
grooves in which the outer edges of the nitrogenous bases are exposed

phosphate groups connected to 3 carbon of one deoxyribose molecule

and the 5 carbon of the next, linking them together

5 end: The end of a DNA or RNA strand that has a free phosphate
group at the 5 carbon of the sugar (deoxyribose or ribose).
3 end: The end of a DNA or RNA strand that has a free hydroxyl
group at the 3 carbon of the sugar (deoxyribose or ribose).
semiconservative replication: The way in which DNA is synthesized. Each
of the two partner strands in a double helix acts as a template for a new
partner strand. Hence, after replication, each double helix consists of one
old and one new strand.
deoxyribonucleoside triphosphates are free monomers brought together
to form dna by having their three phosphate groups attached to 5 carbon
on the deoxyribose sugar (datp, dttp, dgtp, dctp)
origin of replication: DNA sequence at which helicase unwinds the DNA
double helix and DNA polymerase binds to initiate DNA replication.
dna polymerase: Any of a group of enzymes that catalyze the formation
of DNA strands from a DNA template.
primer: Strand of nucleic acid, usually RNA, that is the necessary starting
material for the synthesis of a new DNA strand, which is synthesized from
the 3 end of the primer.
primase: An enzyme that catalyzes the synthesis of a primer for
DNA replication.

single strand binding protein: In DNA replication, a protein that binds to

single strands of DNA after they have been separated from each other,
keeping the two strands separate for replication.
leading strand: In DNA replication, the daughter strand that is
synthesized continuously.
can grow continuously at its 3 end as the fork opens
lagging strand: In DNA replication, the daughter strand that is
synthesized in discontinuous stretches.
synthesis of this new strand moves in direction opposite to that in
which the replication fork is opening
okazaki fragments: Newly formed DNA making up the lagging
strand in DNA replication. DNA ligase links Okazaki fragments
together to give a continuous strand.
each okazaki fragment requires its own primer
sliding dna clamp: Protein complex that keeps DNA polymerase bound to
DNA during replication
doughnut shape that binds to dna polymerase-dna complex
telomeres: Repeated DNA sequences at the ends of eukaryotic
these repeats bind special proteins that prevents the dna repair
system from recognizing the chromosome ends as breaks
since lagging strand terminal rna primer is removed, no dna can be
synthesized to replace it because there is no 3 end, each
chromosome becomes slightly shorter with each cell division as
telomeric dna is lost, when full genes are lost the cell dies
telomerase: An enzyme that catalyzes the addition of telomeric
sequences lost from chromosomes during DNA replication.

dna proofreading: during replication, an incorrect nucleotide may be

added, the proteins of the replication complex immediately recognize and
excise the incorrect nucleotide, polymerase adds correct nucleotide
mismatch repair: A mechanism that scans DNA after it has been
replicated and corrects any base-pairing mismatches.
excision repair: DNA repair mechanism that removes damaged DNA and
replaces it with the appropriate nucleotide.
polymerase chain reaction (pcr): An enzymatic technique for the rapid
production of millions of copies of a particular stretch of DNA where only
a small amount of the parent molecule is available.

dna amplification, contains sample of double stranded dna from

biological sample as a template, two short artificially synthesized
primers that are complementary to the ends of the sequence, the
four dntps, dna polymerase, salts and a buffer to maintain near
neutral ph
heating mixture to denature dna reaction cooled to allow primers
to bind to template strands reaction is warmed so dna
polymerase can make complementary strands
mutagen: Any agent (e.g., a chemical, radiation) that increases the
mutation rate.
the function of a gene is to prescribe the production of a single,
specific polypeptide
transcription: The synthesis of RNA using one strand of DNA as a
messenger rna (mrna): Transcript of a region of one of the strands
of DNA; carries information (as a sequence of codons) for the
synthesis of one or more proteins.
mrna travels from nucleus to cytoplasm where it is translated
ribosomal rna (rrna): Several species of RNA that are incorporated into
the ribosome. Involved in peptide bond formation.
transfer rna (trna): A family of folded RNA molecules. Each tRNA carries a
specific amino acid and anticodon that will pair with the complementary
codon in mRNA during translation.
requires dna template for complementary base pairing, four
ribonucleoside triphosphates (atp, gtp, ctp, utp), rna polymerase enzyme

1. initiation: rna polymerase binds to special sequence of dna called

promoter which tells polymerase where to start transcription and which
strand of dna to transcribe
a. transcription factors: Proteins that assemble on a eukaryotic
chromosome, allowing RNA polymerase II to perform transcription.
2. elongation: In molecular biology, the addition of monomers to make a
longer RNA or protein during transcription or translation.
a. polymerase unwinds dna about 10 base pairs at a time and reads
template strand in the 3 to 5 direction
3. termination: particular base sequences specify termination
genetic code: The set of instructions, in the form of nucleotide triplets,
that translate a linear sequence of nucleotides in mRNA into a linear
sequence of amino acids in a protein.
codon: Three nucleotides in messenger RNA that direct the
placement of a particular amino acid into a polypeptide chain.
start codon: The mRNA triplet (AUG) that acts as a signal for the
beginning of translation at the ribosome.
stop codons: Any of the three mRNA codons that signal the end of
protein translation at the ribosome: UAG, UGA, UAA.
pre mrna: Initial gene transcript before it is modified to produce
functional mRNA. Also known as the primary transcript
intron: Portion of a gene within the coding region that is transcribed
into pre-mRNA but is spliced out prior to translation.
exon: A portion of a DNA molecule, in eukaryotes, that codes for
part of a polypeptide.
a 5 cap is added to the 5 end of pre mrna, chemically modified
molecule of gtp and facilitates the binding of mRNA to the ribosome
for translation, and it protects the mRNA from being digested by
ribonucleases that break down RNAs
poly a tail: A long sequence of adenine nucleotides (50250) added
after transcription to the 3 end of most eukaryotic mRNAs
rna splicing: The last stage of RNA processing in eukaryotes, in
which the transcripts of introns are excised through the action of
small nuclear ribonucleoprotein particles (snRNP).
spliceosome: RNA-protein complex that splices out introns from
eukaryotic pre-mRNAs
translation: The synthesis of a protein (polypeptide). Takes place on
ribosomes, using the information encoded in messenger RNA.

trnas bind to specific amino acids, trnas bind to mrnas with anti codons,

trnas interact with ribosomes

trna charging with correct amino acid is achieved by aminoacyl trna
synthase enzymes, each enzyme specific for one amino acid and its
corresponding amino acid, uses atp to make bond
ribosome: A small particle in the cell that is the site of protein synthesis.
large and small subunit, large subunit has APE sites
o A site is where charged trna anti codon binds to mrna codon
o P site is where trna adds amino acid to polypeptide chain
o E site is where trna, having given up its amino acid, stays
before being released from the ribosome
1. initiation: formation of initiation complex, anti codon of methionine
charged trna binds to aug start codon
a. initiation complex: In protein translation, a combination of a
small ribosomal subunit, an mRNA molecule, and the tRNA
charged with the first amino acid coded for by the mRNA;
formed at the onset of translation.
2. elongation: A charged tRNA whose anticodon is complementary to the
second codon of the mRNA now enters the open A site, large subunit
breaks bond between trna and amino acid in p site, catalyzes
formation of peptide bond between that amino acid and the one in the
a site
3. termination: elongation stops when stop codon enters a site

signal sequence: The sequence within a protein that directs the protein to
a particular organelle.
proteolysis: cutting of a polypeptide chain catalyzed by proteases

glycosylation: addition of sugars to proteins to form glycoproteins

phosphorylation: addition of phosphate groups, change folding

prokaryotic cells shut off supply of unneeded protein by: down regulating
the transcription of mrna for the protein, hydrolyzing mrna after it is
made and preventing translation, hydrolyzing protein after it is made,
inhibiting the function of the protein
negative regulation: A type of gene regulation in which a gene is normally
transcribed, and the binding of a repressor protein to the promoter
prevents transcription.
positive regulation: A form of gene regulation in which a regulatory
macromolecule is needed to turn on the transcription of a structural gene;
in its absence, transcription will not occur.

inducer: A compound that stimulates the synthesis of a protein

constitutive proteins: Proteins that an organism produces all the time,

and at a relatively constant rate.

structural gene: A gene that encodes the primary structure of a protein
not involved in the regulation of gene expression.
operon: A genetic unit of transcription, typically consisting of
several structural genes that are transcribed together; the operon
contains at least two control regions: the promoter and the
operator: The region of an operon that acts as the binding site for
the repressor.
inducible system: substrate of the metabolic pathway (the inducer)
interacts with regulatory protein (the repressor), rendering the repressor
incapable of binding to the operator and thus allowing transcription
generally controls catabolic pathways which are turned on only
when the substrate is available
repressible system: the product of a metabolic pathway (the corepressor)
binds to a regulatory protein, which is then able to bind to the operator
and block transcription
generally control anabolic pathways which are turned on until the
concentration of the product becomes excessive
catabolite repression: In the presence of abundant glucose, the
diminished synthesis of catabolic enzymes for other energy sources.
not all promoters are identical but they share consensus sequences that
allow them to be recognized by rna polymerase and other proteins,
consensus sequence is a short stretch of dna that appears with little
variation in many different genes
sigma factor: In prokaryotes, a protein that binds to RNA polymerase,
allowing the complex to bind to and stimulate the transcription of a
specific class of genes

tata box: An eight-base-pair sequence, found about 25 base pairs before
the starting point for transcription in many eukaryotic promoters, that
binds a transcription factor and thus helps initiate transcription.
where dna begins to denature so template strand is exposed
general transcription factors: In eukaryotes, transcription factors that
bind to the promoters of most protein-coding genes and are required for
their expression. Distinct from transcription factors that have specific
regulatory effects only at certain promoters or classes of promoters.

helix-turn-helix motif: two alpha helices are connected via a non helical
turn, interior facing recognition helix interacts with bases inside dna,
exterior facing helix sits on sugar phosphate backbone

viral genome contains promoter that binds host rna polymerase and these
viral genes are transcribed, viral genes encode proteins that shut down
host transcription and stimulate viral genome replication
lysogeny: A form of viral replication in which the virus becomes
incorporated into the host chromosome and remains inactive. Also called
a lysogenic cycle. (Contrast with lytic cycle.)
prophage: The noninfectious units that are linked with the chromosomes
of the host bacteria and multiply with them but do not cause dissolution
of the cell. Prophage can later enter into the lytic phase to complete the
virus life cycle.
prophage knows when to switch to lytic cycle because viral genome
includes genes that code for regulatory proteins ci and cro which
compete for specific promoters on viral dna, ci represses the
expression of genes in lytic cycle and promotes lysogeny and cro
has opposite effect
under favorable bacterial growth conditions, ci accumulates and
outcompetes cro for dna binding, bacteriophage enters lysogenic

epigenetics: The scientific study of changes in the expression of a gene or

set of genes that occur without change in the DNA sequence.

cpg islands: DNA regions rich in C residues adjacent to G residues.
Especially abundant in promoters, these regions are where methylation of
cytosine usually occurs.
maintenance methylase: An enzyme that catalyzes the methylation of the
new DNA strand when DNA is replicated.
extra methyl groups in a promoter attract proteins that bind methylated
dna, these proteins are generally involved in the repression of gene
transcription so heavily methylated genes are usually inactive
chromatin remodeling: strong attraction between positively charged
histone tails and dna, enzyme adds acetyl groups to histone tails reducing
their affinity for dna, opens up dna for transcription
genomic imprinting: The form of a genes expression is determined by
parental source (i.e., whether the gene is inherited from the male or
female parent).
sperm and egg have different methylation patterns in genes

euchromatin: Diffuse, uncondensed chromatin. Contains active genes that

will be transcribed into mRNA.

heterochromatin: Densely packed, dark-staining chromatin; any genes it
contains are usually not transcribed.
alternative splicing: A process for generating different mature mRNAs
from a single gene by splicing together different sets of exons during RNA
microrna: A small, noncoding RNA molecule, typically about 21 bases
long, that binds to mRNA to inhibit its translation.
small interfering rnas bind to target rna and degrade it
regulation of translation: modification of guanosine triphosphate cap on 5
end of mrna prevents translation
translational repressor: A protein that blocks translation by binding
to mRNAs and preventing their attachment to the ribosome.
regulation of protein longevity
ubiquitin: A small protein that is covalently linked to other cellular
proteins identified for breakdown by the proteosome.
genome sequencing: Determination of the nucleotide base sequence of
the entire genome of an organism.
high throughput sequencing: Rapid DNA sequencing on a micro scale in
which many fragments of DNA are sequenced in parallel.
1. large molecule of dna cut up into small fragments of about 100 bps,
can be done using mechanical forces or enzymes
2. dna denatured by heat
3. short synthetic oligonucleotides added to the end of each fragment
and then attached to a solid support
4. dna amplified by pcr using primers complementary to the synthetic
oligonucleotides, multiple copies of dna allow for easy detection of
added nucleotides during sequencing
5. solution with universal primer, dna polymerase, the four dntps
added to dna, each of four dntps is tagged with different colored
fluorescent dye
6. synthesis reaction set up so that only one nucleotide is added to the
new dna strand in the sequencing cycle, after each addition the
unincorporated dntps are removed
7. the fluorescence of the new nucleotide at each location is detected
with a camera, color indicated which base was added
8. fluorescent tag removed from the nucleotide that is already
attached and dna synthesis cycle repeated, images captured after
each cycle

9. set of partial sequences called reads are overlapping, computer

assembles the reads into overlapping fragments, overlaps removed
to produce single assembled sequence
functional genomics: The assignment of functional roles to the proteins
encoded by genes identified by sequencing entire genomes.
open reading frames: coding regions of genes, recognized by start
and stop codons and by consensus sequences that indicate
locations of introns
determine amino acid sequences, regulatory sequences (ie
promoters/terminators), rna genes, other noncoding sequences (ie
telomeres, repetitive sequence)
comparative genomics: Computer-aided comparison of DNA sequences
between different organisms to reveal genes with related functions.
prokaryotic genomes
relatively small and organized into one chromosome, compact with
more than 85% of dna in protein coding sequences and rna genes,
usually dont have introns, may have plasmids
metagenomics: The practice of analyzing DNA from environmental
samples without isolating intact organisms.
composite transposon: Two transposable elements located near one
another that transpose together and carry the intervening DNA
sequence with them.
eukaryotic genomes
larger than prokaryotic genome, more regulatory sequences,
repeated sequences, lots of noncoding dna, multiple chromosomes
gene family: A set of similar genes derived from a single parent
gene; need not be on the same chromosomes. The vertebrate
globin genes constitute a classic example of a gene family.
pseudogene: A DNA segment that is homologous to a functional
gene but is not expressed because of changes to its sequence or
changes to its location in the genome.
highly repetitive sequences: Short (less than 100 bp),
nontranscribed DNA sequences, repeated thousands of times in
tandem arrangements.
moderately repetitive sequences: DNA sequences repeated 10
1,000 times in the eukaryotic genome. They include the genes that
code for rRNAs and tRNAs, as well as the DNA in telomeres.
retrotransposons (LTRs, SINEs, LINEs) are transcribed onto rna
which acts as a template for new dna, new dna becomes inserted at
a new location in the genome, copy and paste method
o dna transposons are cut and pasted to new locations

o insertion of a transposon into a coding region results in

haplotype: Linked nucleotide sequences that are usually inherited as a
unit (as a sentence rather than as individual words).
pharmacogenomics: The study of how an individuals genetic makeup
affects his or her response to drugs or other agents, with the goal of
predicting the effectiveness of different treatment options.
proteome: The complete set of proteins that can be made by an
organism. Because of alternative splicing of pre-mRNA, the number of
proteins that can be made is usually much larger than the number of
protein-coding genes present in the organisms genome.
determined by gel electrophoresis which separates proteins by
electric charge and size, mass spectrometry
metabolome: The quantitative description of all the small molecules in a
cell or organism.
recombinant dna: A DNA molecule made in the laboratory that is derived
from two or more genetic sources.
restriction enzyme: Any of a type of enzyme that cleaves double-stranded
DNA at specific sites; extensively used in recombinant DNA technology.
Also called a restriction endonuclease.
sticky ends: On a piece of two-stranded DNA, short, complementary, onestranded regions produced by the action of a restriction endonuclease.
Sticky ends facilitate the joining of segments of DNA from different
transformation (bacteria)/transfection (animals): Insertion of recombinant
DNA into a host cell.
transgenic: Containing recombinant DNA incorporated into the
genetic material.
selectable marker: A gene, such as one encoding resistance to an
antibiotic, that can be used to identify (select) cells that contain
recombinant DNA from among a large population of untransformed cells.
methods for inserting dna into host cells: cells may be chemically treated
to make outer membrane more permeable then mixed with dna so it can
diffuse into the cell, (electroporation) short electric shock used to create
temporary pores in membrane through which dna can center, viruses and
bacteria can insert dna into host cells, transgenic animals can be
produced by injecting recombinant dna into nuclei of fertilized eggs
replicon: A region of DNA replicated from a single origin of replication.
newly introduced dna can become part of a replicon by insertion
into the host chromosome or by entering the host cell as part of a

vector: A plasmid or virus that carries an inserted piece of DNA into a

bacterium for cloning purposes in recombinant DNA technology.

plasmid: A DNA molecule distinct from the chromosome(s); that is,
an extrachromosomal element; found in many bacteria. May
replicate independently of the chromosome.
o relatively small and easy to manipulate in a lab, restriction
enzyme recognition sequences only occur once in the plasmid
sequence, contain genes that confer antibiotic resistance
which serve as selectable markers, have bacterial origin of
replication and can replicate independently of host
viruses can accommodate larger dna and are used as vectors for
eukaryotes, infect cells naturally
reporter gene: A genetic marker included in recombinant DNA to indicate
the presence of the recombinant DNA in a host cell.
antibiotic resistance genes, lac z gene in e coli, green fluorescent
genomic library: All of the cloned DNA fragments generated by the
breakdown of genomic DNA into smaller segments.
complementary dna (cDNA): DNA formed by reverse transcriptase acting
with an RNA template; essential intermediate in the reproduction of
retroviruses; used as a tool in recombinant DNA technology; lacks
cDNA library: A collection of complementary DNAs derived from
mRNAs of a particular tissue at a particular time in the life cycle of
an organism.
knockout: A molecular genetic method in which a single gene of an
organism is permanently inactivated.
homologous recombination: Exchange of segments between two
DNA molecules based on sequence similarity between the two
molecules. The similar sequences align and crossover. Used to
create knockout mutants in mice and other organisms.
antisense rna: A single-stranded RNA molecule complementary to, and
thus targeted against, an mRNA of interest to block its translation.
rna interference (RNAi): A mechanism for reducing mRNA translation
whereby a double-stranded RNA, made by the cell or synthetically, is
processed into a small, single-stranded RNA, whose binding to a target
mRNA results in the latters breakdown.
dna microarray: A small glass or plastic square onto which thousands of
single-stranded DNA sequences are fixed so that hybridization of cellderived RNA or DNA to the target sequences can be performed.

expression vector: A DNA vector, such as a plasmid, that carries a DNA

sequence for the expression of an inserted gene into mRNA and protein in
a host cell.
inducible promoter which responds to specific signals that can be
used to express transgene at high levels, tissue specific promoter
expressed only in certain tissues at certain times, signal sequence
pharming: The use of genetically modified animals to produce medically
useful products in their milk.
totipotent: Possessing all the genetic information and other capacities
necessary to form an entire individual. (ie. zygote)
genomic equivalence: no information is lost from the nuclei of cells as
they pass through the early stages of embryonic development
cytoplasmic environment around nucleus can determine cells fate
stem cell: In animals, an undifferentiated cell that is capable of
continuous proliferation. A stem cell generates more stem cells and a
large clone of differentiated progeny cells.
meristem: Plant tissue made up of undifferentiated actively dividing cells.

adult animal stem cells are multipotent

multipotent: Having the ability to differentiate into a limited number

of cell types.
bone marrow stem cells have two types, one becomes red and
white blood cells, other makes bone and connective tissues like
blastocyst: An early embryo formed by the first divisions of the fertilized
egg (zygote). In mammals, a hollow ball of cells.
pluripotent: Having the ability to form all of the cells in the body
but not a complete organism.
embryonic stem cells
induced pluripotent stem cells: Multipotent or pluripotent animal stem
cells produced from differentiated cells in vitro by the addition of several
genes that are expressed.
molecular evolution: The scientific study of the mechanisms and
consequences of the evolution of macromolecules.
homology: A similarity between two or more features that is due to
inheritance from a common ancestor. The structures are said to be
homologous, and each is a homolog of the others.
sequence alignment: A method of identifying homologous positions in
DNA or amino acid sequences by pinpointing the locations of deletions
and insertions that have occurred since two (or more) organisms diverged
from a common ancestor.

similarity matrix: A matrix used to compare the degree of divergence

among pairs of objects. For molecular sequences, constructed by

summing the number or percentage of nucleotides or amino acids that
are identical in each pair of sequences.
multiple substitutions: more than one change has occurred at given
position between ancestor and observed sequence, coincident
substitutions: at a given position each observed sequence is different
from ancestor, parallel substitutions: same substitution has occurred
between two observed sequences and ancestor, back
substitution/reversion: after a change in given position a subsequent
substitution changes it back to ancestral state
synonymous (silent) substitution: A change of one nucleotide in a
sequence to another when that change does not affect the amino acid
specified (i.e., UUA UUG, both specifying leucine).
nonsynonymous (missense) substitution: A change in a gene from one
nucleotide to another that changes the amino acid specified by the
corresponding codon (i.e., AGC AGA, or serine arginine).
neutral theory: A view of molecular evolution that postulates that most
mutations do not affect the amino acid being coded for, and that such
mutations accumulate in a population at rates driven by genetic drift and
mutation rates.
positive selection: Natural selection that acts to establish a trait that
enhances survival in a population.
observed rate of nonsynonymous substitutions exceeds rate of
synonymous substitutions
purifying selection: The elimination by natural selection of detrimental
characters from a population.
observed rate of synonymous substitutions exceeds rate of
nonsynonymous substitutions
lateral gene transfer: The transfer of genes from one species to another,
common among bacteria and archaea.
reticulations: depictions of lateral gene transfer events on the
underlying species tree
gene duplication: The generation of extra copies of a gene in a genome
over evolutionary time. A mechanism by which genomes can acquire new
both copies of the gene retain original function, can result in a
change in the amount of gene product produced
both copies may retain the ability to produce the original product,
expression of genes may diverge in different tissues or in different
times in development

one copy becomes incapacitated by the accumulation of deleterious

substitutions and become a nonfunctional pseudogene, or become
eliminated from the genome
one copy of the gene retains original function, second copy
accumulates enough substitutions to perform a different function
gene tree: A graphic representation of the evolutionary relationships of a
single gene in different species or of the members of a gene family.
concerted evolution: The common evolution of a family of repeated
genes, such that changes in one copy of the gene family are replicated in
other copies of the gene family, and thus evolve in concert.
unequal crossing over: When a highly repeated gene sequence
becomes displaced in alignment during meiotic crossing over, so
that one chromosome receives many copies of the sequence while
the second chromosome receives fewer copies.
biased gene conversion: A mechanism of concerted evolution in
which a DNA repair system appears biased in favor of using
particular nucleotide sequences as templates for repair, resulting in
the rapid spread of the favored sequence across all copies of the
orthologs: Homologous genes whose divergence can be traced to
speciation events.
paralogs: Homologous genes whose divergence can be traced to gene
duplication events.
in vitro evolution: A method based on natural molecular evolution that
uses artificial selection in the laboratory to rapidly produce molecules with
novel enzymatic and binding functions.
single stranded negative sense rna virus: virus whos genome is rna that
is the complement of the mrna needed for protein translation
gene for rna polymerase to make complementary mrna from their
single stranded positive sense rna virus: positive sense genomes already
set for translation, no replication to form a complement strand is needed
before translation can take place, most abundant and diverse viruses
rna retroviruses: An RNA virus that contains reverse transcriptase. Its
RNA serves as a template for cDNA production, and the cDNA is
integrated into a chromosome of the host cell.
double stranded rna viruses, double stranded dna viruses

adaptive defenses: One of the two general types of defenses against

pathogens. Involves antibody proteins and other proteins that recognize,

bind to, and aid in the destruction of specific viruses and bacteria. Present
only in vertebrate animals.
plasma: The liquid portion of blood, in which blood cells and other
particulates are suspended.
lymph: A fluid derived from blood and other tissues that accumulates in
intercellular spaces throughout the body and is returned to the blood by
the lymphatic system.
lymph node: A specialized structure in the vessels of the lymphatic
system. Lymph nodes contain lymphocytes, which encounter and
respond to foreign cells and molecules in the lymph as it passes
through the vessels.
lymphocyte: One of the two major classes of white blood cells;
includes T cells, B cells, and other cell types important in the
immune system.
white blood cells: Cells in the blood plasma that play defensive roles in
the immune system. Also called leukocytes.
lymphocytes, phagocytes: One of two major classes of white blood
cells; one of the nonspecific defenses of animals; ingests invading
microorganisms by phagocytosis.
antibody: One of the myriad proteins produced by the immune system
that specifically binds to a foreign substance in blood or other tissue fluids
and initiates its removal from the body.
antigen: Any substance that stimulates the production of an
antibody or antibodies in the body of a vertebrate.
antibodies bind specifically to antigens that are recognized by the
body as nonself
major histocompatibility complex (mhc): A complex of linked genes, with
multiple alleles, that control a number of cell surface antigens that
identify self and can lead to graft rejection.
t cell receptor: A protein on the surface of a T cell that recognizes the
antigenic determinant for which the cell is specific.
cytokine: A regulatory protein made by immune system cells that affects
other target cells in the immune system.

innate defenses: In animals, one of two general types of defenses against
pathogens. Nonspecific and present in most animals.
o act very rapidly, include barriers such as skin, phagocytic cells that
ingest invaders, molecules that are toxic to invaders

bacteria rarely penetrate intact skin, saltiness/dryness of skin is

inhospitable for bacteria growth, presence of normal flora compete with
pathogens for space and nutrients
barriers in nose/internal organs
o mucus: A viscous substance secreted by mucous membranes (e.g.,
mucosal epithelium). A barrier defense against pathogens in innate
immunity in animals and a protective coating in many animal organ
o lysozyme: An enzyme in saliva, tears, and nasal secretions that
hydrolyzes bacterial cell walls.
o defensin: A type of protein made by phagocytes that kills bacteria
and enveloped viruses by insertion into their plasma membranes.
pattern recognition receptors (prrs) distinguish self from nonself,
recognize pathogen associated molecular patterns (pamps)
toll like receptors active signal transduction pathways involved in
adaptive/innate defenses, binding of pamp to receptors activates
transcription factors that enter nucleus and activate transcription of
genes encoding defensive proteins
complement system: A group of eleven proteins that play a role in some
reactions of the immune system.
protein binds to antibody on microbe or microbe itself, help
phagocytes recognize it, activate inflammatory response, lyse
invading cells
interferons: Glycoproteins produced by virus-infected animal cells;
interferons increase the resistance of neighboring cells to the virus.
natural killer cells: A type of lymphocyte that attacks virus-infected cells
and some tumor cells as well as antibody-labeled target cells.
dendritic cells are phagocytes that act as messengers between the innate
and adaptive systems, endocyte pathogens, secrete signals that activate
adaptive defenses
inflammation: A nonspecific defense against pathogens; characterized by
redness, swelling, pain, and increased temperature.
mast cells: Cells, typically found in connective tissue, that release
histamine in response to tissue damage.
tumor necrosis factor: A family of cytokines (growth factors) that
causes cell death and is involved in inflammation.
prostaglandin: Any one of a group of specialized lipids with
hormone-like functions.
histamine: A substance released by damaged tissue, or by mast
cells in response to allergens. Histamine increases vascular
permeability, leading to edema (swelling).

phagocytes produces cytokines that signal the brain to produce a

fever, rise in body temperature accelerates lymphocyte production
and phagocytosis

antigenic determinant: The specific region of an antigen that is
recognized and bound by a specific antibody. Also called an epitope.
immunological memory: The capacity to more rapidly and massively
respond to a second exposure to an antigen than occurred on first
antigen presenting cell: In cellular immunity, a cell that ingests and
digests an antigen, and then exposes fragments of that antigen to the
outside of the cell, bound to proteins in the cells plasma membrane.
clonal selection: Mechanism by which exposure to antigen results in the
activation of selected T- or B-cell clones, resulting in an immune
o clonal deletion: Inactivation or destruction of lymphocyte clones
that would produce immune reactions against the animals own
effector cells: In cellular immunity, B cells and T cells that attack an
antigen, either by secreting antibodies that bind to the antigen or by
releasing molecules that destroy any cell bearing the antigen.
memory cells: Long-lived lymphocytes produced after exposure to
antigen. They persist in the body and are able to mount a rapid response
to subsequent exposures to the antigen.
primary immune response: The first response of the immune system to
an antigen, involving recognition by lymphocytes and the production of
effector cells and memory cells.
secondary immune response: A rapid and intense response to a
second or subsequent exposure to an antigen, initiated by memory
humoral immune response: The response of the immune system
mediated by B cells that produces circulating antibodies active against
extracellular bacterial and viral infections.
immunoglobins: A class of proteins containing a tetramer consisting of
four polypeptide chainstwo identical light chains and two identical heavy
chainsheld together by disulfide bonds; active as receptors and
effectors in the immune system.

constant region: The portion of an immunoglobulin molecule whose

amino acid composition determines its class and does not vary
among immunoglobulins in that class.
variable region: The portion of an immunoglobulin molecule or T
cell receptor that includes the antigen-binding site and is
responsible for its specificity.
two antigen binding sites on each antibody
during b cell development genes encoding immunoglobin chains are
cut out, rearranged, and joined together, enormous diversity of
class switching: Occurs when a B cell changes the immunoglobulin class it
synthesizes (e.g., a B cell making IgM switches to making IgG).
induced by helper t cells that send cytokine signals that bind to
receptors on target b cells resulting in recombination and altered
expression of immunoglobin genes
cellular immune response: Immune system response mediated by T cells
and directed against parasites, fungi, intracellular viruses, and foreign
tissues (grafts).
t cell receptors bind only to antigens displayed by mhc proteins on the
surface of an antigen presenting or target cells
cytotoxic t cells: Cells of the cellular immune system that recognize and
directly eliminate virus-infected cells.
helper t cell: Type of T cell that stimulates events in both the cellular and
humoral immune responses by binding to the antigen on an antigenpresenting cell.
class I mhc molecules: Cell surface proteins that participate in the cellular
immune response directed against virus-infected cells.
class II mhc molecules: Cell surface proteins that participate in the cellcell interactions (of T-helper cells, macrophages, and B cells) of the
humoral immune response.
regulatory t cells: The class of T cells that mediates tolerance to self

allergic reaction: An overreaction of the immune system to amounts of an

antigen that do not affect most people; often involves IgE antibodies.
immediate hypersensitivity: A rapid, extensive overreaction of the
immune system against an allergen, resulting in the release of large
amounts of histamine, contrast with delayed hypersensitivity
autoimmunity: An immune response by an organism to its own molecules
or cells.

failure of negative selection, a clone of lymphocytes making

antibodies against self antigens wasnt destroyed by clonal deletion
t cells that recognize a nonself antigen also recognize something on a self
antigen with a similar structure

neuron: A nervous system cell that can generate and conduct action

potentials along an axon to a synapse with another cell.

cell body contains nucleus and most organelles
dendrites: Branching fibers (processes) of a neuron. Dendrites are
usually relatively short compared with the axon, and commonly
carry information to the neuronal cell body.
axon: The process (branching structure) of a neuron that conducts
action potentials away from the cell body.
o carry information away form the originating cell body
(presynaptic cell) to receiving target cell (postsynaptic cell)
axon terminal: The end portion of an axon, which passes action
potentials to another cell. Axon terminals can form synapses and
release neurotransmitter.
synapse: A specialized type of junction where a neuron meets its target
cell (which can be another neuron or some other type of cell) and
information in the form of neurotransmitter molecules is exchanged
across a synaptic cleft.
oligodendrocyte: A type of glial cell that myelinates axons in the central
nervous system.
schwann cell: A type of glial cell that myelinates axons in the peripheral
nervous system.
myelin: Concentric layers of plasma membrane that form a sheath
around some axons; myelin provides the axon with electrical insulation
and increases the rate of transmission of action potentials.
astrocyte: A type of glial cell that contributes to the blood-brain barrier
by surrounding the smallest, most permeable blood vessels in the brain.
blood brain barrier: The selective impermeability of blood vessels in
the brain that prevents most chemicals from diffusing from the
blood into the brain.
can take up neurotransmitters that have been released so control
the communication between pre and post synaptic cells, store
glycogen and provide neurons with nutrients, can release
neurotransmitters and have signaling properties, aid in repair and
regeneration of neurons, can signal changes in blood composition

tripartite synapse: The idea that a synapse includes not only the
pre- and postsynaptic neurons involved but also encompasses many
connections with glial cells called astrocytes.
microglia: Glial cells that act as macrophages and mediators of
inflammatory responses in the central nervous system.
membrane potential: The difference in electrical charge between the
inside and the outside of a cell, caused by a difference in the distribution
of ions.
na+ concentration higher outside cell and k+ concentration higher
inside, k+ diffuses out of the cell and leaves unbalanced negative
charge inside
resting potential: The membrane potential of a living cell at rest. In cells
at rest, the interior is negative to the exterior.
sodium potassium pump: Antiporter responsible for primary active
transport; it pumps sodium ions out of the cell and potassium ions into
the cell, both against their concentration gradients. Also called a sodiumpotassium ATPase.
electrochemical gradient: The concentration gradient of an ion across a
membrane plus the voltage difference across that membrane.
equilibrium potential: The membrane potential at which an ion is at
electrochemical equilibrium, i.e., there is no net flux of the ion across the
patch clamping: Technique for isolating a tiny patch of membrane to allow
the study of ion movement through a particular channel.
voltage gated channel: A type of gated channel that opens or closes when
a certain voltage exists across the membrane in which it is inserted.
chemically gated channel: A type of membrane channel that opens or
closes depending on the presence or absence of a specific molecule that
binds either to the channel protein itself or to a separate receptor that
alters the three-dimensional shape of the channel protein.
mechanically gated channel: A molecular channel that opens or closes in
response to mechanical force applied to the plasma membrane in which it
is inserted.
graded membrane potential: Small local change in membrane potential
caused by opening or closing of ion channels.
action potentials: Generated by neurons, these are electrical signals that
transmit information via waves of depolarization or hyperpolarization of
the cell membrane.
axon hillock: The junction between an axon and the neurons cell
body; where action potentials are generated.

voltage gated na+ channels concentrated at axon hillock open

briefly, na+ rushes into cell and depolarizes the membrane causing
more na+ channels to open, threshold reached, large number of
na+ channels open, then voltage gated na+ channels close and k+
channels open returning membrane back to negative potential
threshold: The level of depolarization that causes an electrically
excitable membrane to fire an action potential.
voltage gated na+ channels have refractory period of one to two
milliseconds in which they cant open again
two gates, activation and inactivation, activation gate responds
faster than inactivation gate
dip in membrane potential following an action potential is afterhyperpolarization/undershoot
action potentials are all or none, spreads by local current flow to adjacent
parts of the membrane as it travels down the axon
action potentials travel faster in large diameter axons and myelinated
axons because they jump from node to node
node of ranvier: A gap in the myelin sheath covering an axon; the
point where the axonal membrane can fire action potentials.
salutatory conduction: The rapid conduction of action potentials in
myelinated axons; so called because action potentials appear to
jump between nodes of Ranvier along the axon.
electrical synapse: A type of synapse at which action potentials spread
directly from presynaptic cell to postsynaptic cell.
numerous gap junctions, connexins form pores that connect the two
cells, very fast and can proceed in either direction, cannot be
chemical synapse: Neural junction at which neurotransmitter molecules
released from a presynaptic cell induce changes in a postsynaptic cell.
neurotransmitter: A substance produced in and released by a neuron (the
presynaptic cell) that diffuses across a synapse and excites or inhibits
another cell (the postsynaptic cell).
synaptic cleft: The space between the presynaptic cell and the
postsynaptic cell in a chemical synapse.
neuromuscular junction: Synapse (point of contact) where a motor
neuron axon stimulates a muscle fiber cell.
acetylcholine (ach): A neurotransmitter that carries information
across vertebrate neuromuscular junctions and some other
synapses. It is then broken down by the enzyme
acetylcholinesterase (AChE).

motor end plate: The depression in the postsynaptic membrane of

the neuromuscular junction where the terminals of the motor
neuron sit.
spatial summation: In the production or inhibition of action potentials in a
postsynaptic cell, the interaction of depolarizations and hyperpolarizations
produced at different sites on the postsynaptic cell.
temporal summation: In the production or inhibition of action potentials
in a postsynaptic cell, the interaction of depolarizations or
hyperpolarizations produced by rapidly repeated stimulation of a single
point on the postsynaptic cell.
ionotropic receptors: A receptor that directly alters membrane
permeability to a type of ion when it combines with its ligand.
metabotropic receptors: A receptor that that indirectly alters membrane
permeability to a type of ion when it combines with its ligand.
neurotransmitter action needs to be terminated, can be destroyed by
enzyme, diffuse away from cleft, taken up by active transport by nearly
cell membranes
agonist: A chemical substance (e.g., a neurotransmitter) that elicits a
specific response in a cell or tissue.
antagonist: A biochemical (e.g., a drug) that blocks the normal
action of another biochemical substance.
neural network: An organized group of neurons that contains three
functional categories of neuronsafferent neurons, interneurons, and
efferent neuronsand is capable of processing information.
afferent neurons: neurons that carry sensory information and
impulses to the central nervous system
efferent neurons: neurons that carry commands and impulses
outward from the central to the peripheral nervous system
interneurons: A neuron that communicates information between
two other neurons.
ganglion: A cluster of neurons that have similar characteristics or
central nervous system: That portion of the nervous system that is the
site of most information processing, storage, and retrieval; in vertebrates,
the brain and spinal cord.
peripheral nervous system: The portion of the nervous system that
transmits information to and from the central nervous system, consisting
of neurons that extend or reside outside the brain or spinal cord and their
supporting cells.
gray matter: In the nervous system, tissue that is rich in neuronal cell

white matter: In the central nervous system, tissue that is rich in

spinal reflex: The conversion of afferent to efferent information in the
spinal cord without participation of the brain.