Biochemistry (Lehninger 5E 1-14)

Front 1

The amount of energy (in joules) required to convert all the molecules in 1 mole of a reacting substance from the ground state to the transition state

Back 1

Activation energy, delta G double dagger

Front 2

The phase of intermediary metabolism concerned with the energy-requiring biosynthesis of cell components from smaller precursors

Back 2

Anabolism

Front 3

One of the five kingdoms of living organisms; includes many species that thrive in extreme environments of high ionic strength, high temperature, or low pH

Back 3

Archaebacteria

Front 4

One of the five kingdoms of living organisms. Eubacteria have a plasma membrane but no internal organelles or nucleus

Back 4

Eubacteria

Front 5

The phase of intermediary metabolism concerned with the energy-yielding degradation of nutrient molecules

Back 5

Catabolism

Front 6

An atom with substituents arranged so that the molecule is not superimposable on its mirror image

Back 6

Chiral center

Front 7

The spatial arrangement of an organic molecule that is conferred by the presence of either (1) double bonds, about which there is no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged in a specific sequence. Configurational isomers cannot be interconverted without breaking one or more covalent bonds

Back 7

Configuration

Front 8

The spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation

Back 8

Conformation

Front 9

The filamentous network providing structure and organization to the cytoplasm; includes actin filaments, microtubules, and intermediate filaments

Back 9

Cytoskeleton

Front 10

A chemical reaction that consumes energy (that is, for which delta G is positive)

Back 10

Endergonic reaction

Front 11

The heat content of a system

Back 11

Enthalpy, H

Front 12

The extent of randomness or disorder in a system

Back 12

Entropy, S

Front 13

The state of a system in which no further net change is occurring; the free energy is at a minimum

Back 13

Equilibrium

Front 14

A unicellular or multicellular organism with cells having a membrane-bounded nucleus, multiple chromosomes, and internal organelles

Back 14

Eukaryote

Front 15

A chemical reaction that proceeds with the release of free energy (that is, for which delta G is negative)

Back 15

Exergonic reaction

Front 16

The component of the total energy of a system that can do work at constant temperature and pressure

Back 16

Free-energy change, delta G

Front 17

All the genetic information encoded in a cell or virus

Back 17

Genome

Front 18

The entire set of enzyme-catalyzed transformations of organic molecules in living cells; the sum of anabolism and catabolism

Back 18

Metabolism

Front 19

A chemical intermediate in the enzyme-catalyzed reactions of metabolism

Back 19

Metabolite

Front 20

An inheritable change in the nucleotide sequence of a chromosome

Back 20

Mutation

Front 21

In eukaryotes, a membrane-bounded organelle that contains chromosomes

Back 21

Nucleus

Front 22

A bacterium; a unicellular organism with a single chromosome, no nuclear envelope, and no membrane-bounded organelles

Back 22

Prokaryote

Front 23

The free-energy change for a reaction occuring under a set of standard conditions: temperature, 298K, pressure 1 atm, and all solutes at 1M concentration

Back 23

Standard free-energy change, delta G degree

Front 24

Compounds that have the same composition and the same order of atomic connections, but different molecular arrangements

Back 24

Stereoisomers

Front 25

Biology-based inter-disciplinary study field that focuses on the systematic study of complex interactionsin biological systems, thus using a new perspective (holism versus reductionism) to study them.

Back 25

Systems biology

Front 26

Containing both polar and nonpolar domains

Back 26

amphipathic

Front 27

The energy required to break a bond

Back 27

bond energy

Front 28

A system capable of resisting changes in pH, consisting of a conjugate acid-base pair in which the ratio of proton acceptor to proton donor is near unity

Back 28

buffer

Front 29

Formation of a bond accompanied by the release of the elements of water from the joining atoms

Back 29

condensation

Front 30

A proton donor and its corresponding deprotonated species; for example, acetic acid (donor) and acetate (acceptor)

Back 30

conjugate acid-base pair

Front 31

(1) An equilibrium constant (K{d}) for the dissociation of a complex of two or more biomolecules into its comjponents; for example, dissociation of a substrate from an enzyme. (2) The dissociation constant (K{a}) of an acid, describing its dissociation into its conjugate base and a proton

Back 31

dissociation constant (K{a})

Front 32

A constant, characteristic for each chemical reaction; relates the specific concentrations of all reactants and products at equilibrium at a given temperature and pressure

Back 32

equilibrium constant (K{eq})

Front 33

An equation relating the pH, the pK(a), and the ratio of the concenrations of the proton-acceptor (A<->) and proton-donor (HA) species in a solution

Back 33

Henderson-Hasselbalch equation

Front 34

A weak electrostatic attraction between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom

Back 34

hydrogen bond

Front 35

Cleavage of a bond, such as an anhydride or peptide bond, by the addition of the elements of water, yielding two or more products

Back 35

hydrolysis

Front 36

Polar or charged; describing molecules or groups that associate with (dissolve easily in) water

Back 36

hydrophilic

Front 37

Nonpolar; describing molecules or groups that are insoluble in water

Back 37

hydrophobic

Front 38

The association of nonpolar groups, or compounds, with each other in aqueous systems, driven by the tendency of the surrounding water molecules to seek their most stable (disordered) state

Back 38

hydrophobic interactions

Front 39

Describes a solution of higher osmolarity than that from which it is separated by a semipermeable membrane

Back 39

hypertonic

Front 40

Describes a solution of lower osmolarity than that from which it is separated by a semipermeable membrane

Back 40

hypotonic

Front 41

The product of the concentrations of H<+> and OH<-> in pure water: K{W} = [H<+>][OH<->] = 1 x 10<-14> at 25 degrees C

Back 41

ion product of water (K{W})

Front 42

Describes a solution of the same osmolarity as that from which it is separated by a semipermeable membrane

Back 42

isotonic

Front 43

London Dispersion Forces, named after the German-American physicist Fritz London, are weak intermolecular forces that arise from the interactive forces between temporary multipoles in molecules without permanent multipole moments. London dispersion forces are also known as dispersion forces, London forces, or induced dipole–dipole forces

Back 43

London forces

Front 44

An aggregate of amphipathic molecules in water, with the nonpolar portions in the interior and the polar portions at the exterior surface, exposed to water

Back 44

micelle

Front 45

Osmolarity is the measure of solute concentration, defined as the number of osmoles of solute per liter of solution (osmol/L). The osmolarity of a solution is usually expressed as Osm (pronounced "osmolar"), in the same way that the molarity of a solution is expressed as "M" (pronounced "molar"). Whereas molarity measures the number of moles of solute per unit volume of solution, osmolarity measures the number of moles of solute particles per unit volume of solution

Back 45

osmolarity

Front 46

Bulk flow of water through a semipermeable membrane into another aqueous compartment containing solute at a higher concentration

Back 46

osmosis

Front 47

The negative logarithm of the hydrogen ion concentration of an aqueous solution

Back 47

pH

Front 48

The negative logarithm of an equilibrium constant

Back 48

pK(a)

Front 49

A plot of the pH versus the equivalents of base added during titration of an acid

Back 49

titration curve

Front 50

The attractive or repulsive force between molecules (or between parts of the same molecule) other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral molecules

Back 50

van der Waals interactions

Front 51

(1) Formally, an abbreviation denoting any alkyl group (2) Occasionally, used in a more general sense to denote virtually any organic substituent (the R groups of amino acids, for example)

Back 51

R group

Front 52

A dipolar ion, with spatially separated positive and negative charges

Back 52

zwitterion

Front 53

A few amino acids joined by peptide bonds

Back 53

oligopeptide

Front 54

A general term describing any repeated unit of one or more stably associated protein subunits within a larger protein structure. If a protomer has multiple subunits, the subunits may be identical or different

Back 54

protomer

Front 55

A lipid-protein aggregate that serves to carry water-insoluble lipids in the blood. The protein component alone is an apolipoprotein

Back 55

lipoprotein

Front 56

A long chain of amino acids linked by peptide bonds; the molecular weight is generally less than 10,000

Back 56

polypeptide

Front 57

A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds

Back 57

protein

Front 58

A metal ion or an organic compound (other than an amino acid) that is covalently bound to a protein and is essential to its activity

Back 58

prosthetic group

Front 59

A multisubunit protein having two or more identical polypeptide chains

Back 59

oligomeric protein

Front 60

A protein containing a carbohydrate group

Back 60

glycoprotein

Front 61

A protein containing one or more prosthetic groups

Back 61

conjugated protein

Front 62

A substance that can act as either a base or an acid

Back 62

ampholyte

Front 63

A substituted amide linkage between the alpha-amino group of one amino acid and the alpha-carboxyl group of another, with the elimination of the elements of water

Back 63

peptide bonds

Front 64

alpha-substituted carboxylic acids, the building blocks of proteins

Back 64

amino acids

Front 65

An atom with substituents arranged so that the molecule is not superimposable on its mirror image

Back 65

chiral center

Front 66

Capable of donating and accepting protons, thus able to serve as an acid or a base

Back 66

amphoteric

Front 67

The capacity of a substance to rotate the plane of plane-polarized light

Back 67

optical activity

Front 68

The configuration of four different substituent groups around an asymmetric carbon atom, in relation to D- and L-glyceraldehyde

Back 68

absolute configuration

Front 69

The nonuniform distribution of electrons in a molecule; polar molecules are usually soluble in water

Back 69

polarity

Front 70

The only amino acid residue in a polypeptide chain with a free alpha-amino group; defines the amino terminus of the polypeptide

Back 70

amino-terminal (N-terminal) residue

Front 71

The only amino acid residue in a polypeptide chain with a free alpha-carboxyl group; defines the carboxyl terminus of the polypeptide

Back 71

carboxyl-terminal (C-terminal) residue

Front 72

The pH at which a solute has no net electric charge and thus does not move in an electric field; also called isoelectric pH

Back 72

isoelectric point (pl)

Front 73

The residue-by-residue conformation of the backbone of a polymer

Back 73

secondary structure

Front 74

The three-dimensional conformation of a polymer in its native folded state

Back 74

tertiary structure

Front 75

The three-dimensional structure of a multisubunit protein; particularly the manner in which the subunits fit together

Back 75

quaternary structure

Front 76

Two or more amino acids covalently joined by peptide bonds

Back 76

peptide

Front 77

List the 7 non-polar, aliphatic R group amino acids

Back 77

GAPVLIM

Front 78

List the 3 aromatic R group amino acids

Back 78

FYW

Front 79

List the 5 polar, uncharged R group amino acids

Back 79

STCNQ

Front 80

List the 3 positively charged R group amino acids

Back 80

KHR

Front 81

List the 2 negatively charged R group amino acids

Back 81

DE

Front 82

Gly; G non-polar, aliphatic R group

Back 82

Glycine

Front 83

Ala; A; non-polar, aliphatic R group

Back 83

Alanine

Front 84

Pro; P; non-polar, aliphatic R group

Back 84

Proline

Front 85

Val; V; non-polar, aliphatic R group

Back 85

Valine

Front 86

Leu; L; non-polar, aliphatic R group

Back 86

Leucine

Front 87

Ile; I; non-polar, aliphatic R group

Back 87

Isoleucine

Front 88

Met; M; non-polar, aliphatic R group

Back 88

Methionine

Front 89

Phe; F; aromatic R group

Back 89

Phenylalanine

Front 90

Tyr; Y; aromatic R group

Back 90

Tyrosine

Front 91

Trp; W; aromatic R group

Back 91

Tryptophan

Front 92

Ser; S; polar, uncharged R group

Back 92

Serine

Front 93

Thr; T; polar, uncharged R group

Back 93

Threonine

Front 94

Cys; C; polar, uncharged R group

Back 94

Cysteine

Front 95

Asn; N; polar, uncharged R group

Back 95

Asparagine

Front 96

Gln; Q; polar, uncharged R group

Back 96

Glutamine

Front 97

Lys; K; positively charged R group

Back 97

Lysine

Front 98

His; H; positively charged R group

Back 98

Histidine

Front 99

Arg; R; positively charged R group

Back 99

Arginine

Front 100

Asp; D; negatively charged R group

Back 100

Aspartate

Front 101

Glu; E; negatively charged R group

Back 101

Glutamate

Front 102

Cleaves Lys, Arg @ C (-K, -R)

Back 102

Trypsin

Front 103

Cleaves Arg @ C (-R)

Back 103

Submaxillarus protease

Front 104

Cleaves Phe, Trp, Tyr @ C (-F, -W, -Y)

Back 104

Chymotrypsin

Front 105

Cleaves Asp, Glu @ C (-D, -E)

Back 105

S. aureus V8 protease

Front 106

Cleaves Asp, Glu @ N (D-, E-)

Back 106

Asp-N-protease

Front 107

Cleaves Leu, Phe, Trp, Tyr @ N (L-, F-, W-, Y-)

Back 107

Pepsin

Front 108

Cleaves Lys @ C (-K)

Back 108

Endoproteinase Lys C

Front 109

Cleaves Met @ C (-M)

Back 109

Cyanogen bromide

Front 110

Five types of constraints to alpha helix stability

Back 110

1. A residue's intrinsic helical propensity; 2. Interactions between R groups, especially 3-4 residues apart; 3. bulkiness of adjacent R groups; 4. Occurrence of P & G residues; 5. The helical dipole and interactions with residues at the ends

Front 111

A helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding; one of the most common secondary structures in proteins

Back 111

alpha helix

Front 112

Found only in mammals, these proteins constitute almost the entire dry weight of hair, wool, nails, claws, quils, horns, hooves, and much of the outer layer of skin. Evolved for strength

Back 112

alpha-keratin

Front 113

Insoluble fibrous protein aggregate

Back 113

amyloid

Front 114

Disease resulting from an unhealthy buildup of insoluble fibrous protein aggregates

Back 114

amyloidoses

Front 115

An extended, zigzag arrangement of a polypeptide chain; a common secondary structure in proteins

Back 115

beta conformation

Front 116

A zigzag of polypeptide chains arranged side by side to form a structure resembling a series of pleats

Back 116

beta sheet

Front 117

A type of secondary structure in polypeptides consisting of four amino acid residues arranged in a tight turn so that the polypeptide turns back on itself

Back 117

beta turn

Front 118

Connecting elements linking successive runs of alpha helix or beta conformations -- particularly common are b___ t_____ that connect the ends of two adjacent segments of an antiparallel bets sheet. 180 degree turn involving 4 residues with carbonyl oxygen hydrogen of first residue bonding with amino hydrogen of the fourth residue

Back 118

beta turn

Front 119

"disorder maker" - a substance which denatures macromolecules by interfering with stabilizing intramolecular forces for macromolecules

Back 119

chaotropic agent

Front 120

Elaborate protein complexes required for the folding of some cellular proteins that do not fold spontaneously

Back 120

chaperonin

Front 121

light-absorbing entity as in circular dichroism spectroscopy

Back 121

chromophore

Front 122

Structureal asymmetry in a molecule gives rist to differences in absorption of left-handed versus right-handed plane-polarized light. Measurement of this difference is called c_______ d_________ spectroscopy

Back 122

circular dichroism (CD) spectroscopy

Front 123

One of the top 2 levels of protein structural classification organization; C____ is purely structural. Below the fold level, categorization is based on evolutionary relationships

Back 123

class

Front 124

Like alpha-keratins, this has evolved to provide strength. It is found in connective tissue such as tendons, cartilage, the organic matrix of bone, and the cornea of the eye.

Back 124

collagen

Front 125

The spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation

Back 125

conformation

Front 126

The simplest type of rotational symmetry, involving rotation about a fixed axis

Back 126

cyclic symmetry

Front 127

Partial or complete unfolding of the specific native conformation of a polypeptide chain, protein, or nucleic acid

Back 127

denaturation

Front 128

A somewhat more complicated rotational symmetry in which a two-fold rotational axis intersects an n-fold axis at right angles; this symmetry is defined as Dn

Back 128

dihedral symmetry

Front 129

A distinct structural unit of a polypeptide; d______ may have separate functions and may fold as independent, compact units

Back 129

domain

Front 130

Insoluble proteins that serve in a protective or structural role; contain polypeptide chains that generally share a common secondary structure

Back 130

fibrous proteins

Front 131

A distinct folding pattern for elements of secondary structure, observed in one or more proteins; also called a motif or supersecondary structure

Back 131

fold

Front 132

One of the top two levels of protein structural classification organization; F___ is purely structural. Below this level, categorization is based on evolutionary relatinships

Back 132

fold

Front 133

Soluble proteins with a globular (somewhat rounded) shape

Back 133

globular proteins

Front 134

Oligomers can have either rotational symmetry or h______ s_______; individual subunits can be superimposed on others by rotation about one or more rotational axes or by helical rotation.

Back 134

helical symmetry

Front 135

A family of proteins which generally have a molecular weight near 70k, and are more abundant in cells stressed by elevated temperatures; heat shock proteins 70,000

Back 135

Hsp70

Front 136

The association of nonpolar groups, or compounds, with each other in aqueous systems, driven by the tendency of the surrounding water molecules to seek their most stable (disordered) state

Back 136

hydrophobic interactions

Front 137

A more complex rotational symmetry regularly encountered in proteins. Based on a regular 12-cornered polyhedron with 20 equilateral triangular faces. Each face can be brought to coincidence with another face by rotation about one or more of three axes.

Back 137

icosahedral symmetry

Front 138

Proteins that interact with partially folded or improperly folded polypeptides, facilitating correct folding pathways or providing microenvironments in which folding can occur.

Back 138

molecular chapereone

Front 139

The state in the protein folding process resulting from a "hydrophobic collapse"; a collapsed state with many residue side chains not completely fixed

Back 139

molten globule

Front 140

A distinct folding pattern for elements of secondary structure, observed in one or more proteins; also called a fold or supersecondary structure

Back 140

motif

Front 141

A multi-subunit protein

Back 141

multimer

Front 142

The biologically active conformation of a macromolecule

Back 142

native conformation

Front 143

A short polymer, usually of amino acids, sugars, or nucleotides; the definition of "short" is somewhat arbitrary, but usually less than 50 subunits

Back 143

oligomer

Front 144

Two or more amino acids covalently joined by peptide bonds

Back 144

peptide group

Front 145

Catalyzes the interconversion of the cis and trans isomers of Pro residue peptide bonds, which can be a slow step in the folding of proteins that contain some Pro peptide bonds in the cis conformation.

Back 145

peptide prolyl cis-trans isomerase (PPI)

Front 146

Proteinaceous infections only protein

Back 146

prion

Front 147

Of the peptide bonds between amino acid residues other than Pro, > 99.95% are trans. However, for peptide bonds involving the P imino nitrogen, about 6% are cis- many occurring at beta-turns

Back 147

Proline isomers (6% cis)

Front 148

Hydroxylates specific Pro residues in procollagen. This enzyme, (Mr 240,000) is an alpha2beta2 tetramer in all vertebrate sources

Back 148

Prolyl 4-hydroxylase

Front 149

One of the most important resources available to biochemists; the P______ D___ B___

Back 149

Protein Data Bank (PDB)

Front 150

A widely distributed enzyme that catalyzes the interchange, or shuffling, of disulfide bonds until the bonds of the native conformation are formed. Among its functions, it catalyzes the elimination of folding intermediates with inappropriate cross-links

Back 150

protein disulfide isomerase (PDI)

Front 151

Proteins with significant similarity in primary structure and / or with similar tertiary structure and function are said to be in the same p______ f_____

Back 151

protein family

Front 152

A general term describing any repeated unit of one or more stably associated protein subunits within a larger protein structure. If a p_______ has multiple subunits, the subunits may be identical or different

Back 152

protomer

Front 153

The three-dimensional structure of a multisubunit protein; particularly the manner in which the subunits fit together

Back 153

quaternary structure

Front 154

Displays allowed values for phi and psi

Back 154

Ramachandran plot

Front 155

Certain globular proeins will regain their native structure and their biological activity if returned to conditions in which the native conformation is stable. This process is called r___________

Back 155

renaturation

Front 156

Oligomers can have either r_________ s_______ or helical symmetry; individual subunits can be superimposed on others by rotation about one or more rotational axes or by helical rotation.

Back 156

rotational symmetry

Front 157

The residue-by-residue conformation of the backbone of a polymer

Back 157

secondary structure

Front 158

spider silk

Back 158

silk fibroin

Front 159

When water surrounds a hydrophobic molecule, the optimal arrangement of hydrogen bonds results in a a highly structured shell of water around the molecule. What's the shell called?

Back 159

solvation layer

Front 160

In the context of protein structure, the tendency to maintain a native conformation

Back 160

stability

Front 161

Grouped as s____________, these are two or more families with little similarity in amino acid sequence that sometimes make use of the same major structural motif and have structural similarities.

Back 161

superfamilies

Front 162

A distinct folding pattern for elements of secondary structure, observed in one or more proteins; also called a motif or fold

Back 162

supersecondary structure

Front 163

The three-dimensional conformation of a polymer in its native folded state

Back 163

tertiary structure

Front 164

(1) An equilibrium constant (K{d}) for the dissociation of a complex of two or more biomolecules into its components; for example, dissociation of a substrate from an enzyme (2) The dissociation constant (K{a}) of an acid, describing its dissociation into its conjugate base and a proton

Back 164

dissociation constant (K{d})

Front 165

A change in the conformation of an enzyme in response to substrate binding that renders the enzyme catalytically active; also used to denote changes in the conformation of any macromolecule in response to ligand binding such that the binding site of the macromolecule better conforms to the shape of the ligand

Back 165

induced fit

Front 166

A contractile protein; the major component of the thick filaments of muscle and other actin-m_____ systems

Back 166

myosin

Front 167

A defense protein synthesized by the immune system of vertebrates

Back 167

antibody

Front 168

A functional and structural unit of the muscle contractile system

Back 168

sarcomere

Front 169

A heterogenous pool of antibodies produced in an animal by a number of different B lymphocytes in response to an antigen. Different antibodies in the pool recognize different parts of the antigen

Back 169

polyclonal antibodies

Front 170

A molecule capable of eliciting the synthesis of a specific antibody in vertebrates

Back 170

antigen

Front 171

A protein (generally with multiple subunits) with multiple ligand-binding sites, such that ligand binding at one site affects ligand binding at another

Back 171

allosteric protein

Front 172

A protein making up the thin filaments of muscle; also an important component of the cytoskeleton of many eukaryotic cells

Back 172

actin

Front 173

A small molecule that binds specifically to a larger one; for example, a hormone is the ligand for its specific protein receptor

Back 173

ligand

Front 174

A small molecule which, when linked to a larger molecule, elicits an immune response

Back 174

hapten

Front 175

A subclass of leukocytes involved in the immune response. B lymphocytes synthesize and secrete antibodies; T lymphocytes either play a regulatory role in immunity or kill foreign and virus-infected cells

Back 175

lymphocytes

Front 176

A system of flat membranous vesicles that surrounds each myofibril

Back 176

sarcoplasmic reticulum

Front 177

aka active site; the ligand-binding site

Back 177

catalytic site

Front 178

aka antigenic determinant; The particular molecular structure within the antigen to which an individual antibody or T-cell receptor binds

Back 178

epitope

Front 179

aka catalytic site; the ligand-binding site

Back 179

active site

Front 180

aka concerted model; may be viewed as the "all-or-none" limiting case of the sequential model of cooperative binding

Back 180

MWC model

Front 181

aka epitope; The particular molecular structure within the antigen to which an individual antibody or T-cell receptor binds

Back 181

antigenic determinant

Front 182

aka MWC (Monod, Wyman, Changeux) model; may be viewed as the "all-or-none" limiting case of the sequential model of cooperative binding

Back 182

concerted model

Front 183

An antibody protein generated against, and capable of binding specifically to, an antigen

Back 183

immunoglobulin

Front 184

An antigenic determinant; the particular chemical group or groups within a macromolecule (antigen) to which a given antibody binds

Back 184

epitope

Front 185

An enzyme particularly abundant in erythrocytes which catalyzes the reaction between CO2 and water to make bicarbonate

Back 185

carbonic anhydrase

Front 186

Antibodies produced by a cloned hybridoma cell, which therefore are identical and directed against the same epitope of the antigen

Back 186

monoclonal antibodies

Front 187

antigen binding fragments of IgG

Back 187

Fab

Front 188

basal fragment of IgG which readily crystallizes

Back 188

Fc

Front 189

Complex nitrogenous compound containing four substituted pyrroles covalently joined into a ring; often complexed with a central metal atom

Back 189

porphyrin

Front 190

component of muscle fibers, about 1000 per fiber, these are 2 micrometers in diameter and each consist of a vast number of regularly arrayed thick and thin filaments comploexed to other proteins

Back 190

myofibrils

Front 191

Cooperative binding model in which ligand binding can induce a change of conformation in an individual subunit; a conformational change in one subunit makes a similar change in an adjacent subunit, as well as the binding of a second ligand molecule, more likely

Back 191

sequential model

Front 192

destroys host cells infected by viruses and also destroys some parasites and foreign tissues

Back 192

cellular immune system

Front 193

Function is to produce soluble signaling proteins called cytokines, which include the interleukins; these cells interact with macrophages, and participate only indirectly in the destruction of infected cells and pathogens, stimulating the selective proliferation of killer T and B cells that can bind to a particular antigen

Back 193

helper T cells

Front 194

hemoglobin without oxygen

Back 194

deoxyhemoglobin

Front 195

Immunoglobulin that occurs either in a monomereic, membrane-bound form or in a secreted form that is cross-linked pentamere of this basic structure; has charicteristic mu heavy chain

Back 195

IgM

Front 196

Immunoglobulin with characteristic alpha heavy chain; found principally in secretions such as saliva, tears, and milk, can be a monomer, dimer, or trimer

Back 196

IgA

Front 197

Immunoglobulin with characteristic delta heavy chain

Back 197

IgD

Front 198

Immunoglobulin with characteristic eta heavy chain

Back 198

IgE

Front 199

In immune system context, identical B cells that synnthesize monoclonal antibodies

Back 199

clone

Front 200

In muscles, aggregates of myosin molecules

Back 200

thin filament

Front 201

In this procedure, proteins that have been separated by gel electrophoresis are transferred electrophoretically to a nitrocellulose membrane; the membrane is blocked, then treated successively with primary antibody, secondary antibody linked to enzyme, and substrate. A colored precipitate forms only along the band containing the protein of interest; allows the detection of a minor component in a sample and provides an approximation of its molecular weight

Back 201

immunoblot assay

Front 202

Killer T cells

Back 202

cytotoxic T cells

Front 203

Latin <humor> "fluid"; directed at bacterial infections and extracellular viruses (those found in bodily fluids)

Back 203

humoral immune system

Front 204

Lowered oxygenation of peripheral tissues to to inadequate functioning of the lungs or circulatory system

Back 204

hypoxia

Front 205

One of a class of blood cells (lymphocytes) of thymic origin, involved in cell-mediated immune reactions

Back 205

T lymphocyte (T cell)

Front 206

One of a class of blood cells (lymphocytes), responsible for the production of circulating antibodies

Back 206

B lymphocyte (B cell)

Front 207

Plot of the log(theta divided by (1 - theta)) to describe the cooperativity of ligand binding sites quantitatively

Back 207

Hill plot

Front 208

Precursor stem cells of erythrocytes

Back 208

hemocytoblasts

Front 209

relaxed state of hemoglobin -- has a higher affinity for O2 than the T state

Back 209

R state

Front 210

Skeletal muscle consists of parallel bundles of m_____ f_____, each fiber a single, very large, multinucleated cell, 20 to 100 micrometers in diameter

Back 210

muscle fibers

Front 211

tense state of hemoglobin -- has a lowere affinity for O2 than the R state

Back 211

T state

Front 212

The complex organic ring structure in heme, to which is bound a single iron atom in its ferrous (divalent iron) state; porphyrins are four pyrrole rings linked by methene bridges with substitutions at one or more of the corners

Back 212

protoporphyrin

Front 213

The crevice or pocket on a protein in which a ligand binds

Back 213

binding site

Front 214

The interaction between actin and myosin must be regulated so that contraction occurs only in response to the appropriate signals from the nervous system; the regulation is mediated by a complex of two proteins t__________, and troponin

Back 214

tropomyosin

Front 215

The interaction between actin and myosin must be regulated so that contraction occurs only in response to the appropriate signals from the nervous system; the regulation is mediated by a complex of two proteins tropomyosin, and t_______

Back 215

troponin

Front 216

The iron-porphyrin prosthetic group of heme proteins

Back 216

heme

Front 217

the largest single polypeptide chains discovered thus far (in human cardiac muscle, it has 26,926 amino acid residues); links the thick filaments to the Z disk, providing additional organization to the overall structure

Back 217

titins

Front 218

The M line organizes thick filaments of muscle fibers; it contains the proteins p_________, C-protein, and M-protein.

Back 218

paramyosin

Front 219

The M line organizes thick filaments of muscle fibers; it contains the proteins paramyosin, C-_______, and M-protein.

Back 219

C-protein

Front 220

The M line organizes thick filaments of muscle fibers; it contains the proteins paramyosin, C-protein, and M-_______.

Back 220

M-protein

Front 221

The major class of antibody molecule and one of the most abundant proteins in the blood serum; has four polypeptide chains: two large heavy chains, and two light chains linked by noncovalent and disulfide bonds into a complex of Mr 150k.

Back 221

immunoglobulin G (IgG)

Front 222

The molecules acted upon by enzymes

Back 222

substrates

Front 223

The process that increases the number of immune system cells that can respond to a particular pathogen

Back 223

clonal selection

Front 224

The slope of the Hill plot, denoted n-sub-H, which is a measure of the degree of cooperativity of ligand binding sites; the measured value of n-sub-H is always less than the actual number of ligand-binding sites in the protein

Back 224

Hill coefficient

Front 225

These receptors are on the surface of killer T cells; Receptors are proteins usually found on the outer surface of cells and extending through the plasma membrane; they recognize and bind extracellular ligands, triggering changes inside the cell;

Back 225

T-cell receptors

Front 226

Thin actin filaments are attached at one end to the Z disk in a regular pattern. The assembly includes the minor muscle proteins a____-a______, desmin, and vimentin

Back 226

alpha-actinin

Front 227

Thin actin filaments are attached at one end to the Z disk in a regular pattern. The assembly includes the minor muscle proteins alpha-actinin, d_____, and vimentin

Back 227

desmin

Front 228

Thin actin filaments are attached at one end to the Z disk in a regular pattern. The assembly includes the minor muscle proteins alpha-actinin, desmin, and v_______

Back 228

vimentin

Front 229

Thin filaments in muscle fibers also contain a large protein called n_______ of about 7000 amino acid residues, thought to be structured as an alpha helix long enough to span the length of the filament

Back 229

nebulin

Front 230

This thin structure bisects the A band; it is a region of high electron density in the middle of the thick filaments

Back 230

M line

Front 231

This thin structure bisects the I band in muscle fibers

Back 231

Z disk

Front 232

Type of leukocyte; ingests large particles and cells by phagocytosis

Back 232

macrophages

Front 233

When examined under an electron microscope, muscle fibers reveal alternating regions of high and low electron density; this is the darker band which stretches the length of the thick filament and includes the region where parallel thick and thin filaments overlap

Back 233

A bands

Front 234

When examined under an electron microscope, muscle fibers reveal alternating regions of high and low electron density; this is the region of the bundle that in cross section would contain only thin filaments

Back 234

I bands

Front 235

When the normal ligand and modulator for a protein are identical, the interaction is termed h_________

Back 235

homotropic

Front 236

When the normal ligand and the modulator for a protein are different molecules, the interaction is termed h___________

Back 236

heterotropic

Front 237

White blood cells

Back 237

leukocytes

Front 238

not to be confused with acid dissociation constant; describes the equilibrium between the complex and the unbound components of the complex; provides a measure of the affinity of the ligand L for the protein; units of inverse molar; a higher value is a higher affinity

Back 238

association constant, Ka

Front 239

the effect of pH and CO2 concentratino on the binding and release of oxygen by hemoglobin (named after Niels Bohr's father Christian)

Back 239

Bohr effect

Front 240

enzyme-linked immunosorbent assay, which can be used to rapidly screen for and quantify an antigen in a sample

Back 240

ELISA

Front 241

The reversible binding of a proetin to a ligand can be described by a simple e_________ e_________

Back 241

equlibrium expression

Front 242

Quantitative description of the degree of cooperativity among lignd binding sites: the H___ e_______

Back 242

Hill equation

Front 243

The constant domains of immunoglobulins has a characteristic structure known as the i_____________ f___, which is a well-conserved structural motif in the all-beta class of proteins

Back 243

immunoglobulin fold

Front 244

The amount of energy (in joules) required to convert all the molecules in 1 mole of a reacting substance from the ground state to the transition state.

Back 244

activation energy

Front 245

The region of an enzyme surface that binds the substrate molecule and catalytically transforms it; also known as the catalytic site.

Back 245

active site

Front 246

A regulatory enzyme, with catalytic activity modulated by the noncovalent binding of a specific metabolite at a site other than the active site.

Back 246

allosteric enzyme

Front 247

The protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity.

Back 247

apoenzyme

Front 248

The protein portion of a protein, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for activity.

Back 248

apoprotein

Front 249

The energy derived from noncovalent interactions between enzyme and substrate or recteptor and ligand.

Back 249

binding energy (delta G b)

Front 250

An organic cofactor required for the action of certain enzymes; often contains a vitamin as a component.

Back 250

coenzyme

Front 251

An inorganic ion or a coenzyme required for enzyme activity.

Back 251

cofactor

Front 252

A type of enzyme inhibition reversed by increasing the substrate concentration; a competitive inhibitor generally competes with the normal substrate or ligand for a protein's binding site.

Back 252

competitive inhibition

Front 253

(1) An equilibrium constant (K{d}) for the dissociation of a complex of two or more biomolecules into its components; for example, dissociation of a substrate from an anzyme. (2) The dissociation constant (K{a}) of an acid, describing its dissociation into its conjugate base and a proton.

Back 253

dissociation constant (K{d})

Front 254

A biomolecule, either protein or RNA, that catalyzes a specific chemical reaction. It does not affect the equilibrium of the catalyzed reaction; it enhances the rate of a reaction by providing a reaction path with a lower activation energy.

Back 254

enzyme

Front 255

A constant, characteristic for each chmical reaction; relates the specific concentrations of all reactants and products at equilibrium at a given temperature and pressure.

Back 255

equilibrium constant (Keq)

Front 256

Inhibition of an allosteric enzyme at the beginning of a metabolic sequence by the end product of the sequence; also known as end-product inhibition.

Back 256

feedback inhibition

Front 257

Catalysis involving proton transfer(s) to or from a molecule other than water.

Back 257

general acid-base catalysis

Front 258

The normal, stable form of an atom or molecule; as distinct from the excited state.

Back 258

ground state

Front 259

A catalytically active enzyme including all necessary subunits, prosthetic groups, and cofactors

Back 259

holoenzyme

Front 260

A change in the conformation of an enzyme in response to substrate binding that renders the enzyme catalytically active; also used to denote changes in the conformation of any macromolecule in response to ligand binding such that the binding site of the macromolecule better conforms to the shape of the ligand.

Back 260

induced fit

Front 261

An algebraic transform of the Michaelis-Menten equation, allowing determination of V{max} and K{m} by extrapolation of [S] to infinity.

Back 261

Lineweaver-Burk equation

Front 262

The substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half its maximum velocity.

Back 262

Michaelis constant (K{m})

Front 263

The equation describing the hyperbolic dependence of the initial reaction velocity, V{0}, on substrate concentration, [S], in many enzyme-catalyzed reactions: V{0} = V{max}[S] / K{m} + [S]

Back 263

Michaelis-Menten equation

Front 264

The reversible inhibition pattern resulting when an inhibitor molecule can bind to either the free enzyme or to the enzyme-substrate complex (not necessarily with the same affinity)

Back 264

mixed inhibition

Front 265

A metal ion or an organic compound (other than an amino acid) that is covalently bound to a protein and is essential to its activity.

Back 265

prosthetic group

Front 266

Enzymes that transfer the terminal phosphoryl group of ATP or another nucleoside triphosphate to a Ser, Thr, Tyr, Asp, or His side chain in a target protein, thereby regulating the activity or other properties of that protein.

Back 266

protein kinases

Front 267

The proportionality constant that relates the velocity of a chemical reaction to the concentration(s) of the reactant(s)

Back 267

rate constant

Front 268

(1) Generally, the step in an enzymatic reaction with the greatest activation energy or the transition state of highest free energy. (2) The slowest step in a metabolic pathway.

Back 268

rate-limiting step

Front 269

Any chemical species in a reaction pathway that has a finite chemical lifetime

Back 269

reaction intermediate

Front 270

An enzyme having a regulatory function through its capacity to undergo a change in catalytic activity by allosteric mechanisms or by covalent modification.

Back 270

regulatory enzyme

Front 271

Inhibition by a molecule that binds reversibly to the enzyme, such that the enzyme activity returns when the inhibitor is no longer present.

Back 271

reversible inhibition

Front 272

Acid or base catalysis involving the constituents of water (hydroxide or hydronium ions).

Back 272

specific acid-base catalysis

Front 273

The ability of an enzyme or receptor to discriminate among competing substrates or ligands

Back 273

specificity

Front 274

The free-energy change for a reaction occurring under a set of standard conditions: temperature, 298K; pressure 1 atm or 101.3 kPa; and all solutes at 1M concentration

Back 274

standard free-energy change

Front 275

A nonequilibrium state of a system through which matter is flowing and in which all components remain at a constant concentration

Back 275

steady state

Front 276

The specific compound acted upon by an enzyme

Back 276

substrate

Front 277

A relatively inert molecule that is transformed by an enzyme, at its active site, into a reactive substance that irreversibly inactivates the enzyme.

Back 277

suicide inhibitor

Front 278

An activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate

Back 278

transition state

Front 279

The number of times an enzyme molecule transforms a substrate molecule per unit time, under conditions giving maximal activity at substrate concentrations that are saturating.

Back 279

turnover number

Front 280

The reversible inhibition pattern resulting when an inhibitor molecule can bind to the enzyme-substrate complex but not to the free enzyme.

Back 280

uncompetitive inhibition

Front 281

The maximum velocity of an enzymatic reaction when the binding site is saturated with substrate.

Back 281

V{max}

Front 282

An inactive precursor of an enzyme; for example, pepsinogen, the precursor of pepsin.

Back 282

zymogen

Front 283

Transient covalent bonds are formed between the enzyme and the substrate

Back 283

covalent catalysis

Front 284

The oldest approach to understanding enzyme mechanisms; determine the rate of a reaction and how it changes in response to changes in experimental parameters

Back 284

enzyme kinetics

Front 285

A simplifying approach in kinetics experiments, measuring the first 60 seconds or less of the reaction

Back 285

initial rate V0 (initial velocity)

Front 286

When the enzyme is first mixed with a large excess of substrate, this is the initial period during which the concentration of ES builds up.

Back 286

pre-steady state

Front 287

State of enzymatic reactions in which ES and the concentrations of any other intermediates remains approximately constant over time

Back 287

steady-state kinetics

Front 288

rate constant of catalysis; turnover number

Back 288

kcat

Front 289

Includes competitive, uncompetitive, and mixed inhibition

Back 289

reversible inhibition

Front 290

V=k[S]

Back 290

rate equation

Front 291

A large restriction in the relative motions of two substrates that are to react; one of the obvious benefits of binding substrates to an enzyme

Back 291

entropy reduction

Front 292

formation of weak bonds between substrate and enzyme results in d__________ of the substrate

Back 292

desolvation

Front 293

Nearly one third of all known enzymes require one or more metal ions for catalytic activity; the metals can contribute ionic interactions to orient a substrate, stabilize charged reaction states or mediate oxidation reduction reactions by reversible changes in the metal ion's oxidation state

Back 293

metal ion catalysis

Front 294

Enzymes that exhibit a hyperebolic dependence of initial velocity on substrate concentration are said to follow M________-M_____ k_______;

Back 294

Michaelis-Menten kinetics

Front 295

Line with 1/initial velocity and negative Michaelis constant as Y- and X-intercepts, respectively; uses the Lineweaver-Burk equation

Back 295

double-reciprocal plot

Front 296

turnover number divided by Michaelis constant (kcat divided by Km)

Back 296

specificity constant

Front 297

These compounds hijack the normal enzyme reaction mechanism to inactivate the enzyme

Back 297

mechanism-based inactivators

Front 298

In chymotrypsin, Ser195 is linked to His57 and Asp102 in a hydrogen-bonding network referred to as the c_________ t____

Back 298

catalytic triad

Front 299

These viruses possess an RNA genome and an enzyme, reverse transcriptase, capable of using RNA to direct the synthesis of a complementary DNA

Back 299

retrovirus

Front 300

Allosteric enzymes function through reversible, noncovalent binding of regulatory compounds called a_________ e________, or allosteric modulators, which are generally small metabolites or cofactors

Back 300

allosteric effecters

Front 301

Some enzymes are regulated by reversible c_______ m____________

Back 301

covalent modification

Front 302

Catalyzes removal of phophoryl groups

Back 302

protein phosphatases

Front 303

Protein precursors

Back 303

proprototeins

Front 304

Enzyme precursors

Back 304

proenzymes

Front 305

By convention, these are red

Back 305

"galacto" sugars

Front 306

By convention, these are blue

Back 306

"gluco" sugars

Front 307

By convention, these are green

Back 307

"manno" sugars

Front 308

The end of a nucleic acid that lacks a nucleotide bound at the 3' position of the terminal residue

Back 308

3' end

Front 309

The end of a nucleic acid that lacks a nucleotide bound at the 5' position of the terminal residue

Back 309

5' end

Front 310

Abe

Back 310

Abequose

Front 311

A second messenger within cells; its formation by adenylyl cyclase is stimulated by certain hormones or other molecular signals.

Back 311

adenosine 3',5'-cyclic monophosphate (cyclic AMP, cAMP)

Front 312

A right-handed helical structure of DNA usually observed under nonaqueous conditions; the most stable structure of double-stranded RNA in aqueous solution under physiological conditions

Back 312

A-form DNA

Front 313

A mixture of sulfated heteropolysaccharides made up of D-galactose and an L-galactose derivative ether-linked between C-3 and C-6. It is a complex mixture of polysaccharides, all with the same backbone structure, but substituted to varying degrees with sulfate and pyruvate.

Back 313

agar

Front 314

Repeating units of D-Gal(beta 1->4)3,6-anhydro-L-Gas2S(alpha 1 repeating units)

Back 314

agarose

Front 315

The agar component with the fewest charged groups (sulfates, pyruvates); useful in the biochemistry lab due to its remarkable gel-forming property

Back 315

agarose

Front 316

The most well studied proteoglycan aggregate

Back 316

aggrecan

Front 317

Acids generated by the oxidation of the carbonyl carbons of aldoses; hexose derivatives

Back 317

aldonic acid

Front 318

A simple sugar in which the carbonyl carbon atom is an aldehyde; that is, the carbonyl carbon is at one end of the carbon chain.

Back 318

aldose

Front 319

Branched glucose homopolysaccharide; (alpha1->4) links and (alpha 1->6) branches @ every 24-30 residues

Back 319

amylopectin

Front 320

Unbranched glucose homopolysaccharide; (alpha 1->4) links

Back 320

amylose

Front 321

Spontaneous rewinding. Etymology of the word indicates heating, for a process that heats then cools in order to separate strands and then induce combination at milder conditions

Back 321

anneal

Front 322

The carbon atom bearing the aldehyde or ketone function that is involved in cyclization of a sugar

Back 322

anomeric carbon

Front 323

Two stereoisomers of a given sugar that differ only in the configuration about the carbonyl (anomeric) carbon atom.

Back 323

anomers

Front 324

3',5' phosphodiester bonds that run in opposite directions would be a___________

Back 324

antiparallel

Front 325

Ara

Back 325

Arabinose

Front 326

Plasmids designed for the cloning of very long segments of DNA.

Back 326

bacterial artificial chromosomes

Front 327

Virus that attacks bacteria

Back 327

bacteriophages

Front 328

Two nucleotides in nucleic acid chains that are paired by hydrogen bonding of their bases; for example, A with T or U, and G with C.

Back 328

base pair

Front 329

The stable structure of most DNA in aqueous solution under physiological conditions.

Back 329

B-form DNA

Front 330

Some restriction endonucleases cleave both strands of DNA at the opposing phosphodiester bonds, leaving no unpaired bases on the ends, often called b____ e____

Back 330

blunt ends

Front 331

Glucosamine, galactosamine, and mannoseamine typically have an acetylated amino group on carbon number __

Back 331

C-2

Front 332

Any newly synthesized protein in the endoplasimic reticulum already has a complex oligosaccharide attached, which can be bound by either of two ER lectins that are also chaperones -- this one is membrane-bound

Back 332

calnexin

Front 333

Any newly synthesized protein in the endoplasimic reticulum already has a complex oligosaccharide attached, which can be bound by either of two ER lectins that are also chaperones -- this one is soluble

Back 333

calreticulin

Front 334

A DNA library consisting of sequences derived from mRNAs, and thus from the expressed genes of a cell.

Back 334

cDNA library

Front 335

One of four types of protein interactions with NS domains of heparin sulfate; the high density of negative charges in heparan sulfate attracts positively charged lipoprotein lipase molecules and holds them by elecrostatic and sequence-specific interactions with NS domains

Back 335

cell surface localization / concentration

Front 336

Protein functioncan be described on three levels. This level describes the network of interactions engaged in by the protein.

Back 336

cellular function

Front 337

Enzyme capable of hydrolyzing the beta 1->4 glycosidic bond

Back 337

cellulase

Front 338

Branched glucose homopolysaccharide; (beta 1->4) links of D-glucose

Back 338

cellulose

Front 339

Most abundant polysaccharide in nature; cotton is composed almost entirely of this; hydrogen bonds between the monomers, and between the chains makes the structure tough and water-insoluble

Back 339

cellulose

Front 340

Linear homopolysaccharide of N-acetylglucosamine; (beta 1->4) linked chains results in alternating acetylated amino groups for a tough but flexible water-insoluble structure; think exoskeletons

Back 340

chitin

Front 341

Linear homopolysaccharide composed of N-acetylglucosamine residues in (beta1->4) linkage; the only difference from cellulose is the replacement of the hydroxyl group at C-2 with an acetylated amino group.

Back 341

chitin

Front 342

Greek "chondros" <cartilage>; this substance contributes to the tensile strength of cartilage, tendons, ligaments, and the walls of the aorta.

Back 342

chondroitin sulfate

Front 343

The production of large numbers of identical DNA molecules, cells, or organisms, from a single ancestral DNA molecule, cell, or organism.

Back 343

cloning

Front 344

Small molecule of DNA capable of self-replication. Typically plasmids or viral DNAs

Back 344

cloning vectors

Front 345

Genome comparisons

Back 345

comparative genomics

Front 346

The two antiparallel polynucleotide chains of double-helical DNA are not identical in either base sequence or composition. Instead, they are c____________ to each other.

Back 346

complementary

Front 347

A DNA used in DNA cloning, usually made by reverse transcriptase; complementary to a given mRNA.

Back 347

complementary DNA (cDNA)

Front 348

Prepared from RNA in a multistep reaction catalyzed by the enzyme reverse transcriptase

Back 348

complementary DNAs

Front 349

One of four types of protein interactions with NS domains of heparin sulfate; a conformation change induced in the protein on binding a specific polysaccharide NS domain allows its interaction with a cofactor

Back 349

conformational activation

Front 350

A series of overlapping clones or continuous sequence defining an uninterrupted section of a chromosome.

Back 350

contig

Front 351

One of four types of protein interactions with NS domains of heparin sulfate; NS domains interact with both the cofactor and the receptor, bringing the oligomeric complex together and increasing the effectiveness of a low concentration of the cofactor

Back 351

coreceptor for extracellular ligands

Front 352

A structure in which hairpins form in each of two complementary strands of nucleic acid at the same location.

Back 352

cruciform

Front 353

Mannose 6-phosphate

Back 353

death warrant (tag for lysosomal destination)

Front 354

Nucleotides containing 2-deoxy-D-ribose as the pentose component

Back 354

deoxyribonucleotides

Front 355

Bacterial and yeast polysaccharides made up of (alpha1->6)-linked poly-D-glucose; dental placque, formed by bacteria on the surface of teeth, is rich in this.

Back 355

dextrans

Front 356

A carbohydrate consisting of two covalently joined monosaccharide units.

Back 356

disaccharide

Front 357

DNA microarray

Back 357

DNA chips

Front 358

Involves separating a specific gene or DNA segment from a larger chromosome, attaching it to a small molecule of carrier DNA, and then replicating this modified DNA thousands or millions of times through both the increase in host cell number and the creation of multiple copies of the cloned DNA in each cell.

Back 358

DNA cloning

Front 359

aka DNA typing or DNA profiling

Back 359

DNA fingerprinting

Front 360

An enzyme that creates a phosphodiester bond between the 3' end of one DNA segment and the 5' end of another.

Back 360

DNA ligase

Front 361

A collection of DNA sequences immobilized on a solid surface, with individual sequences laid out in patterned arrays that can be probed by hybridization.

Back 361

DNA microarray

Front 362

Material outside the cell

Back 362

ECM, extracellular matrix

Front 363

An approach to insert DNA segments by using a high-voltage pulse to transiently render the bacterial membrane permeable to large molecules.

Back 363

electroporation

Front 364

One of four types of protein interactions with NS domains of heparin sulfate; binding of a protein and another on adjacent NS domains brings the two proteins into close proximity, favoring their interaction

Back 364

enhanced protein-protein interaction

Front 365

Two stereoisomers differing in configuration at one asymmetric center, in a compound having two or more asymmetric centers

Back 365

epimers

Front 366

A protein sequence or domain bound by some well-characterized antibody.

Back 366

epitope tag

Front 367

A specific type of sequence-tagged site representing a gene that is expressed.

Back 367

expressed sequence tag (EST)

Front 368

Cloning vectors with the transcription and translation signals needed for the regulated expression of a cloned gene

Back 368

expression vectors

Front 369

Gel-like material filling the extracellular space in the tissues of multicellular animals; also called ground substance, which holds the cells together and provides a porous pathway for the diffusion of nutrients and oxygen to individual cells

Back 369

extracellular matrix (ECM)

Front 370

A method for representing molecules to show the configuraiton of groups around chiral centers. Also known as projection formulas.

Back 370

Fischer projection formulas

Front 371

Fru

Back 371

Fructose

Front 372

Red triangle

Back 372

Fucose; Fuc

Front 373

A simple sugar containing the five-membered furan ring

Back 373

furanose

Front 374

The protein product of a gene created by the fusion of two distinct genes or portions of genes.

Back 374

fusion protein

Front 375

A four-stranded DNA structure formed in nucleic acid sequences rich in G residues

Back 375

G tetraplex

Front 376

Yellow and white square

Back 376

Galactosamine; GalN

Front 377

Yellow circle

Back 377

Galactose; Gal

Front 378

Membrane lipids of eukaryotic cells in which the polar head group, the part of the lipid that forms the outer surface of the membrane, is a complex oligosaccharide containing a sialic acid and other monosaccharide residues

Back 378

gangliosides

Front 379

A chromosomal segment that codes for a single functional polypeptide chain or RNA molecule.

Back 379

gene

Front 380

aka recombinant DNA technology

Back 380

genetic engineering

Front 381

A DNA library containing DNA segments representing all (or most) of the sequences in an organism's genome.

Back 381

genomic library

Front 382

A science devoted broadly to the understanding of cellular and organism genomes

Back 382

genomics

Front 383

Blue-white diamond and blue square

Back 383

GlcA and GlcNAc aka hyaluronic acid

Front 384

Blue and whie square

Back 384

Glucosamine; GlcN

Front 385

Blue circle

Back 385

Glucose; Glc

Front 386

Blue and white diamond

Back 386

Glucuronic acid; GlcA

Front 387

Another term for polysaccharide; a polymer of monosaccharide units joined by glycosidic bonds

Back 387

glycan

Front 388

A compound containing a carbohydrate component bound covalently to a protein or lipid, forming a glycoprotein or glycolipids.

Back 388

glycoconjugate

Front 389

Branched glucose homopolysaccharide; (alpha 1->4) links and (alpha 1->6) branches @ every 8-12 residues

Back 389

glycogen

Front 390

The main storage homopolysaccharide in animals

Back 390

glycogen

Front 391

The main storage polysaccharide of animal cells.

Back 391

glycogen

Front 392

A lipid containing a carbohydrate group.

Back 392

glycolipid

Front 393

The systematic characterization of all of the carbohydrate components of a given cell or tissue, including those attached to proteins and to lipids

Back 393

glycomics

Front 394

A protein containing a carbohydrate group.

Back 394

glycoprotein

Front 395

A heteropolysaccharide of two alternating units: one is either N-acetylglucosamine or N-acetylgalactosamine; the other is a uronic acid (usually glucuronic acid). Formerly called mucopolysaccharide

Back 395

glycosaminoglycan

Front 396

Heteropolysaccharides of the extracellular matrix

Back 396

glycosaminoglycans

Front 397

Bonds between a sugar and another molecule (typically an alcohol, purine, pyrimidine, or sugar) through an intervening oxygen.

Back 397

glycosidic bonds

Front 398

One of two major families of membrane heparin sulfate proteoglycans; these are attached to the membrane by a lipid anchor, a derivative of the membrane lipid phosphatidylinositol

Back 398

glypicans

Front 399

A protein that lights up.

Back 399

green fluorexcent protein (GFP)

Front 400

A structure in which a single strand of nucleic acid folds back and pairs with itself due to the presence of complementary sequences arranged palindromically.

Back 400

hairpin

Front 401

A method for representing cyclic chemical structures so as to define the configuration of each substituent group; the method commonly used for representing sugars.

Back 401

Haworth perspective formulas

Front 402

Product of the condensation of an aldehyde and an alcohol

Back 402

hemiacetal

Front 403

Product of the condensation of a ketone and an alcohol.

Back 403

hemiketal

Front 404

Named to distinguish it from glycosylation, which is the *enzymatic* transfer of glucose to a protein, the extent of this phenomena is measured clinically by extracting hemoglobin from a small sample of blood and separating GHB from unmodified hemoglobin electrophoretically, taking advantage of the charge difference resulting from modification of the amino groups.

Back 404

hemoglobin glycation

Front 405

Heparin is a fractionated form of this sulfate, derived mostly from mast cells (a type of leukocyte).

Back 405

heparan sulfate

Front 406

Some tumor cells secrete this enzyme which degrades the ECM

Back 406

heparinase

Front 407

Polysaccharides that contain two or more different kinds of monomeric species

Back 407

heteropolysaccharides

Front 408

By convention, these are squares divided diagonally

Back 408

hexosamine

Front 409

By convention, these are circles

Back 409

hexoses

Front 410

A simple sequence of six or more residues of a specific amino acid which binds tightly and specifically to nickel ions.

Back 410

His tags

Front 411

Polysaccharides that contain only a single monomeric species

Back 411

homopolysaccharides

Front 412

Unusual hydrogen bonding involving N-7, O6 and N6 atoms of purines in non-Watson-Crick DNA structures, such as triplex DNA.

Back 412

Hoogsteen pairing

Front 413

N-7, O6 and N6 of purines can participate in the hydrogen bonding of triplex DNA, which is unusual. The positions of these atoms are called H________ positions.

Back 413

Hoogsteen positions

Front 414

Altenating residues of D-glucuronic acid and N-Acetylglucoseamine

Back 414

hyaluran (hyaluronic acid)

Front 415

Provides the jellylike consistency of the vitreous humor of the vertebrate eye

Back 415

hyaluran (hyaluronic acid)

Front 416

aka hyaluronic acid, the glycosaminoglycan that contains alternating residues of D-glucuronic acid and N-acetylglucosamine; forms clear, highly viscous solutions that serve as lubricants in the synovial fluid of joints and give the vitreous humor of the vertbrate eye its jellylike consistency; (Greek "hyalos" <glass> due to its glassy or transluscent appearance.

Back 416

hyaluronan

Front 417

A high molecular weight, acidic polysaccharide typically composed of the alternating disaccharide GlcUA(beta>3)GlcNAc. Hyaluronic acid is a major component of the extracellular matrix, and forms larger complexes (proteoglycans) with proteins and other acidic polysaccharides.

Back 417

hyaluronic acid

Front 418

Strand of DNA composed of segments of two different species

Back 418

hybrid duplexes

Front 419

Gold and white diamond

Back 419

Iduronic acid; IdoA

Front 420

Once bateriophase lambda fragments are ligated to foreign DNA, the resultant recombinant DNAs can be packaged into phage particles by adding them to crude bacterial cell extracts that contain all the proteins needd to assemble a comploete phage. This is called i_ v____ packaging

Back 420

in vitro packaging

Front 421

A membrane protein that mediates the interaction between cells and the ECM

Back 421

integrin

Front 422

Palindrome. Regions of DNA of base sequence having twofold symmetry over two strands of DNA

Back 422

inverted repeats

Front 423

A simple monosaccharide in which the carbonyl group is a ketone

Back 423

ketose

Front 424

Gal(beta1->4)Glc

Back 424

lactose

Front 425

A protein that binds a carbohydrate, commonly an oligosaccharide, with very high affinity and specificity, mediating cell-cell interactions.

Back 425

lectin

Front 426

Synthetic DNA fragments insereted between the ends that are being ligated; used by researchers to create new DNA sequences.

Back 426

linkers

Front 427

The dominant surface feature of the outer membrane of gram-negative bacteria, such as E coli and S typhimurium; these molecules are the prime targets of the antibodies produced by the vertebrate immune system in response to bacterial infections

Back 427

lipopolysaccharides

Front 428

The wider of the two helical grooves on the surface of a DNA molecule.

Back 428

major groove

Front 429

Green circle

Back 429

Mannose; Man

Front 430

A class of RNA molecules, each of which is complementary to one strand of DNA; carries the genetic message from the chromosome to the ribosomes.

Back 430

messenger RNA (mRNA)

Front 431

The injection of DNA directly into a nucleus using a very fine needle

Back 431

microinjection

Front 432

The less prominent of the two helical grooves on the surface of a DNA molecule

Back 432

minor groove

Front 433

When an inverted repeat occurs within an individual strand of the DNA, the sequence is called a m_____ r_____

Back 433

mirror repeats

Front 434

Protein functioncan be described on three levels. This level describes the biochemical activity of a protein, including details such as the reaction san enzyme catalyzes or the ligands a receptor binds.

Back 434

molecular function

Front 435

An RNA with the information encoding a single polypeptide

Back 435

monocistronic mRNA

Front 436

A carbohydrate consisting of a single sugar unit.

Back 436

monosaccharide

Front 437

Secreted or membrane glycoproteins that can contain large numbers of O-linked oligosaccharide chains. Present in most secretions, the give mucus its characteristic slipperiness

Back 437

mucins

Front 438

Mur

Back 438

Muramic acid

Front 439

The change in specific rotation of a pyranose or furanose sugar or glycoside accompanying the equilibration of its alpha- and beta- anomeric forms

Back 439

mutarotation

Front 440

An inheritable change in the nucleotide sequence of a chromosome.

Back 440

mutation

Front 441

N-Acetylated domain in a proteoglycan

Back 441

NA

Front 442

Yellow square

Back 442

N-Acetylgalactosamine; GalNAc

Front 443

Blue square

Back 443

N-Acetylglucosamine; GlcNAc

Front 444

By convention, these are squares

Back 444

N-acetylhexoses

Front 445

Mur2Ac

Back 445

N-Acetylmuramic acid

Front 446

Purple diamond

Back 446

N-Acetylneuraminic acid (sialic acid); New5Ac

Front 447

Highly sulfated domain in a proteoglycan

Back 447

NS

Front 448

A compound consisting of a purine or pyrimidine base covalently liked to a pentose.

Back 448

nucleoside

Front 449

A nucleoside phosphorylated at one of its pentose hydroxyl groups.

Back 449

nucleotide

Front 450

A single protein domain that binds adenosine, it can be used in different enzymes

Back 450

nucleotide-binding fold

Front 451

Covalent bond joining two monosaccharides; formed when the hydroxyl group of one sugar reacts with the anomeric carbon of the other.

Back 451

O-glycosidic bond

Front 452

A short polymer of nucleotides (usually less than 50)

Back 452

oligonucleotide

Front 453

When suitably located restriction sites are not present, this approach can create a specific DNA sequence change.

Back 453

oligonucleotide-directed mutagenesis

Front 454

Several monosaccharide groups joined by glycosidic bonds

Back 454

oligosaccharide

Front 455

Genes in different organisms that possess a clear sequence and functional relationship to each other

Back 455

orthologs

Front 456

A segment of duplex DNA in which the base sequences of the two strands exhibit twofold rotational symmetry about an axis

Back 456

palindrome

Front 457

3',5' phosphodiester bonds that run in the same direction would be p_______

Back 457

parallel

Front 458

Genes similarly related to each other within a single species

Back 458

paralogs

Front 459

Protein function can be described on three levels. This level describes the effects on the entire organism.

Back 459

phenotypic function

Front 460

A chemical grouping that contains two alcohols esterified to one molecule of phosphoric acid, which thus serves as a bridge between them.

Back 460

phosphodiester linkage

Front 461

An extrachromosomal, independently replicating, small circular DNA molecule; commonly employed in genetic engineering.

Back 461

plasmid

Front 462

An RNA with the information encoding two or more polypeptides

Back 462

polycistronic mRNA

Front 463

Inserted DNA fragments with multiple recognition sequences

Back 463

polylinkers

Front 464

A repetitive procedure that results in a geometric amplification of a specific DNA sequence.

Back 464

polymerase chain reaction (PCR)

Front 465

A covalently linked sequence of nucleotides in which the 3' hydroxyl of the pentose of one nucleotide residue is joined by a phophodiester bond to the 5' hydroxyl fo the pentose of the next residue.

Back 465

polynucleotide

Front 466

A linear or branched polymer of monosaccharide units linked by glycosidic bonds

Back 466

polysaccharide

Front 467

A labeled DNA or RNA fragment, complementary to the DNA being sought

Back 467

probe

Front 468

A hybrid macromolecule consisting of a heteropolysaccharide joined to a polypeptide; the polysaccharide is the major component

Back 468

proteoglycan

Front 469

Some proteoglycans can form these entities, enormous supramolecular assemblies of many core proteins all bound to a single molecule of hyaluronan

Back 469

proteoglycan aggregates

Front 470

A sulfated glycosaminoglycan can be attached to extracellular proteins to form p____________

Back 470

proteoglycans

Front 471

The basic unit consists of a "core protein" with covalently attached glycosaminoglycans; typically attached to a Ser residue in a S-G-X-G sequence via tetrasaccharide bridge

Back 471

proteoglycans

Front 472

The full complement of proteins expressed in a given cell, or the complete complement of proteins that can be expressed by a given genome.

Back 472

proteome

Front 473

Broadly, the study of the protein complement of a cell or organism.

Back 473

proteomics

Front 474

A variation of gel electrophoresis that allows the separation of very large DNA segments.

Back 474

pulsed field gel electrophoresis

Front 475

A nitrogenous heterocyclic base found in nucleotides and nucleic acids; containing fused pyrimidine and imidazole rings.

Back 475

purine

Front 476

A simple sugar containing the six-membered pyran ring.

Back 476

pyranose

Front 477

A nitrogenous base found in nucleotides and nucleic acids

Back 477

pyrimidine

Front 478

DNA formed by the joining of genes into new combinations.

Back 478

recombinant DNA

Front 479

Methods used to accomplish cloning and recombination. Aka genetic engineering

Back 479

recombinant DNA technology

Front 480

The end of a polysaccharide having a terminal sugar with a free anomeric carbon; the terminal residue can act as a reducing sugar

Back 480

reducing end

Front 481

A sugar in which the carbonyl (anomeric) carbon is not involved in a glycosidic bond and can therefore undergo oxidation

Back 481

reducing sugar

Front 482

Site-specific endodeoxyribonucleases causing cleavage of both strands of DNA at points within or near the specific site recognized by the enzyme; important tools in genetic engineering.

Back 482

restriction endonucleases

Front 483

Variations, among individuals in a population, in the length of certain restriction framgments within which certain genomic sequences occur. These variations result from rare sequence changes that create or destroy restriction sites in the genome.

Back 483

restriction fragment length polymorphisms (RFLPs)

Front 484

A restriction endonuclease and the corresponding methylase are sometimes referred to as a r__________-m___________ system

Back 484

restriction-modification system

Front 485

Rha

Back 485

Rhamnose

Front 486

Cells also contain nucleotides with phosphate groups other than on the 5' carbon. This one is a cyclic monophosphate at the 2' and 3' carbons that is an end product of hydrolysis of RNA by certain ribonucleases. Others include adenosine 3',5'-cyclic monophosphate (cAMP) and cGMP.

Back 486

ribonucleoside 2',3'-cyclic monophosphates

Front 487

Cells also contain nucleotides with phosphate groups other than on the 5' carbon. This one is a monophosphate at the 3' carbon that is an end product of hydrolysis of RNA by certain ribonucleases. Others include ribonucleoside 2',3'-cyclic monophosphates, adenosine 3',5'-cyclic monophosphate (cAMP) and cGMP.

Back 487

ribonucleoside 3'-monophosphates

Front 488

Ribonucleoside 5'-monophosphate. A nucleotide containing D-ribose as its pentose component.

Back 488

ribonucleotide

Front 489

Rib

Back 489

Ribose

Front 490

A class of RNA molecules serving as components of ribosomes.

Back 490

ribosomal RNA (rRNA)

Front 491

An effector molecule synthesized within a cell in response to an external signal (first messenger) such as a hormone.

Back 491

second messenger

Front 492

A large family of membrane proteins, lectins that bind oligosaccharides on other cells tightly and specifically, and serve to carry signals across the plasma membrane

Back 492

selectins

Front 493

DNA fingerprinting is based on these, which are slight sequence differences between individuals, 1 bp in every 1,000 bp on average.

Back 493

sequence polymorphisms

Front 494

Any known sequence that has been mapped within a chromosome and / or clones derived from it.

Back 494

sequence-tagged site (STS)

Front 495

A type of sequence variation, different from RFLPs now used most commonly in DNA typing.

Back 495

short tandem repeats (STRs)

Front 496

Plasmids that can be propagated in cells of two or more different species.

Back 496

shuttle vectors

Front 497

Another term for siglec

Back 497

sialoadhesins

Front 498

sialic acid-recognizing Ig-superfamily lectins

Back 498

siglec

Front 499

Single genomic base pair changes that distinguish one individual from another within a given species

Back 499

single nucleotide polymorphisms (SNPs)

Front 500

A set of methods used to create specific alterations in the sequence of a gene.

Back 500

site-directed mutagenesis

Front 501

A DNA hybridization procedure in which one or more specific DNA fragments are detected in a larger population by means of hybridization to a complementary, labeled nucleic acid probe.

Back 501

Southern blot

Front 502

A mix of amylose and amylopectin, this is the main storage homopolysaccharide in plants

Back 502

starch

Front 503

Contains two types of glucose polymer, amylose and amylopectin

Back 503

starch

Front 504

Some restriction endonucleases make staggered cuts on the two DNA strands, leaving two to four nucleotides on one strand unpaired at each resulting end. These unpaired strands are referred to as s_____ e___

Back 504

sticky ends

Front 505

Fru(2beta<->alpha1)Glc

Back 505

sucrose

Front 506

One of two major families of membrane heparin sulfate proteoglycans; has a single transmembrane domain and an extracellular domain with three to five heparin sulfate chains and sometimes chondroitin sulfate

Back 506

syndecans

Front 507

This proteoglycan has a single transmembrane domain and an extracellular domain bearing three to five chains of heparan sulfate and in some cases chondroitin sulfate

Back 507

syndecans

Front 508

Conserved gene order along the chromosomes of different species

Back 508

synteny

Front 509

This developing field studies the multitude of biochemical changes in a cell, including the changes in the cellular protein populations, as a function of environmental or genetic stresses.

Back 509

systems biology

Front 510

A peptide or protein that binds to a known ligand with high affinity and specificity; fusion proteins enable us to use affinity chromatography to purify almost any protein because the target protein can be fused with this protein, which may be attached to either the carboxyl or amino terminus.

Back 510

tag

Front 511

The cloning vector from Agrobacterium tumefaciens, a plant parasite, which can aid in cloning plants.

Back 511

Ti plasmid

Front 512

Cells derived from a particular animal tissue and grown under appropriate conditions can maintain their differentiated properties; these cells are grown in a t_____ c______

Back 512

tissue culture

Front 513

The process of forming mRNA on a DNA template

Back 513

transcription

Front 514

A class of RNA molecules (Mr 25,000 to 30,000), each of which combines covalently with a specific amino acid as the first step in protein synthesis

Back 514

transfer RNA (tRNA)

Front 515

The process of introducing vectors into bacteria cells.

Back 515

transformation

Front 516

Describing an organism that has genes from another organism incorporated within its genome as a result of recombinant DNA procedures.

Back 516

transgenic

Front 517

Glc(alpha1<->1alpha)Glc

Back 517

trehalose

Front 518

aka hemolymph

Back 518

trehalose

Front 519

A DNA structure with three strands

Back 519

triplex DNA

Front 520

This technique allos the separation and display of up to 1,000 different proteins on a single gel. Mass spectrometry can then be used to partially sequence individual protein spots and assign each to a gene.

Back 520

two-dimensional gel electrophoresis

Front 521

First isolated by Hamilton Smith in 1970, these are simpler, require no ATP, and cleave DNA within the recognition sequence itself, distinguishing it from Type I and Type III.

Back 521

Type II restriction endonucleases

Front 522

Acids generated by oxidation of the carbons at the other ends of the carbon chain from the carboxyl carbon; hexose derivatives (e.g. glucuronic, galacturonic, or mannuronic acids

Back 522

uronic acid

Front 523

A DNA molecule known to replicate sutonomously in a host cell, to which a segment of DNA may be spliced to allow its replication; for example, a plasmid or an artificial chromosome.

Back 523

vector

Front 524

Very efficient means to deliver DNA.

Back 524

viral vectors

Front 525

Gold star

Back 525

Xyl

Front 526

Xyl

Back 526

Xylose

Front 527

These vectors contain all the elements needed to maintain a eukaryotic chromosome in the yeast nucleus.

Back 527

yeast artificial chromosomes

Front 528

A left-handed DNA structure, usually restricted to certain repetitive sequences.

Back 528

Z-form DNA

Front 529

Free energy change for electroneutral active transport

Back 529

ΔGt = RT ln(C2/C1) where R is 8.315 J/molK and T is in Kelvin

Front 530

Free energy change for electrogenic active transport

Back 530

ΔGt = RT ln(C2/C1) + ZFΔψ where R is 8.315 J/molK, T is in Kelvin, Z is charge of the ion, F is the Faraday constant 96,500 J/Vmol, and Δψ is the transmembrane potential in volts -- typically .05V inside to outside and -.05V outside to inside

Front 531

Indirectly activate (through GTP-binding proteins, or G proteins) enzymes that generate intracellular second messengers. This type of receptor is illustrated by the beta-adrenergic receptor system that detects epinephrine (adrenaline)

Back 531

GPCR

Front 532

Plasma membrane receptors that are also enzymes. when one of these receptors is activated by its extracellular ligand, it catalyzes the phosphorylation of several sytosolic or plasma membrane proteins. the insulin receptor is one example; the receptor for epidermal growth factor (EGF-R) is another

Back 532

Receptor tyrosine kinases

Front 533

Also plasma membrane receptors with an enzymatic cytoplasmic domain. The intracellular second messenger for these receptors, cyclic guanosine monophosphate (cGMP), activates a cytosolic protein kinase that phosphorylates cellular proteins and thereby changes their activities

Back 533

Receptor guanylyl cyclases

Front 534

Channels of the plasma membrane that open and close in response to the binding of chemical ligands or changes in transmembrane potential. These are the simplest signal transducers. The acetylcholine receptor ion channel is an example of this mechanism

Back 534

Gated ion channels

Front 535

Receptors that interact with macromolecular components of the extracellular matrix (such as collagen) and convey instructions to the cytoskeletal system about cell migration or adherence to the matrix. Integrins illustrate this general type of transduction mechanism

Back 535

Adhesion receptors

Front 536

Receptors that bind specific ligands (such as the hormone estrogen) and altere the rate at which specific genes are transcribed and translated into cellular proteins. Because steroid hormones function through mechanisms intimately related to the regulation of gene expression, we considere them here only briefly and defere a detailed ddiscussion of their action until Chapter 28

Back 536

Nuclear receptors (steroid receptors)

Front 537

FA

Back 537

fatty acids

Front 538

GL

Back 538

glycerolipids

Front 539

GP

Back 539

glycerophospholipids

Front 540

SP

Back 540

sphingolipids

Front 541

ST

Back 541

sterol lipids

Front 542

PR

Back 542

prenol lipids

Front 543

SL

Back 543

saccharolipids

Front 544

PK

Back 544

polyketides

Front 545

Integral membrane protein with a single transmembrane helix with amino-terminal domain outside the cell

Back 545

Integral membrane Type I

Front 546

Integral membrane protein with a single transmembrane helix with carboxyl-terminal domain outside the cell

Back 546

Integral membrane Type II

Front 547

Integral membrane protein with multiple transmembrane helices in a single polypeptide

Back 547

Integral membrane Type III

Front 548

Integral membrane protein with multiple transmembrane helices in multiple polypeptides assembled to form a channel through th emembrane

Back 548

Integral membrane Type IV

Front 549

Integral membrane protein held to the bilayer primarily by covalently linked lipids

Back 549

Integral membrane Type V

Front 550

Integral membrane protein held to the bilayer by both transmembrane helices and GPI (lipid) anchors

Back 550

Integral membrane Type VI

Front 551

Isoprenoid alcohols with 11 to 24 isoprene units

Back 551

dolichols

Front 552

Forms of vitamin E

Back 552

tocopherols

Front 553

Vitamin D3

Back 553

cholecalciferol

Front 554

An organic substance required in small quantities in the diet of some species; generally functions as a component of a coenzyme

Back 554

vitamin

Front 555

A family of molecules derived from arachidonate; muscle contractants that constrict air passages in the lungs and are involved in asthma

Back 555

leukotrienes

Front 556

A class of molecules derived from arachidonate and involved in platelet aggregation during blood clotting

Back 556

thromboxanes

Front 557

A class of lipid-soluble, hormonelike regulatory molecules derived from arachidonate and other polyunsaturated fatty acids

Back 557

prostaglandins

Front 558

A class of lipids containing the steroid nucleus

Back 558

sterols

Front 559

Sphingolipids, containing complex oligosaccharides as head groups; especially common in nervous tissue

Back 559

gangliosides

Front 560

Cerebrosides and globosides, carrying no charge at neutral pH

Back 560

neutral glycolipids

Front 561

Neutral glycosphingolipids with two or more sugars at the head group

Back 561

globosides

Front 562

Sphingolipid containing one sugar residue as a head group.

Back 562

cerebroside

Front 563

Sphingolipids with one or more sugars linked directly to the hydroxyl at C-1 of ceramide

Back 563

glycosphingolipids

Front 564

Lipids composed of ceramide, a fatty acid in amide linkage, and a phosphorylcholine or phosphoethanolamine head group.

Back 564

sphingomyelins

Front 565

An amphipathic lipid with a sphingosine backbone to which are attached a long-chain fatty acid and a polar alcohol.

Back 565

sphingolipid

Front 566

A phospholipid with an alkenyl ether substituent on the C-1 of glycerol

Back 566

plasmalogen

Front 567

An amphipathic lipid with a glycerol backbone; fatty acids are ester-linked to C-1 and C-2 of glycerol, and a polar alcohol is attached through a phosphodiester linkage to C-3

Back 567

glycerophospholipid

Front 568

A lipid containing a carbohydrate group

Back 568

glycolipid

Front 569

A lipid containing one or more phosphate groups

Back 569

phospholipid

Front 570

Enzymes that catalyze the hydrolysis of triacylglycerols

Back 570

lipases

Front 571

An ester of glycerol with three molecules of fatty acid; also called a triglyceride or neutral fat

Back 571

triacylglycerol

Front 572

A long-chain aliphatic carboxylic acid found in natural fats and oils; also a component of membrane phospholipids and glycolipids

Back 572

fatty acid

Front 573

The family of fatty acids with a double bond between the third and fourth carbon from the methyl end of the chain.

Back 573

polyunsaturated fatty acids (PUFAs)

Front 574

PUFAs with a double bond three away from the methyl end

Back 574

omega-3 fatty acids

Front 575

PUFAs with a double bond six away from the methyl end

Back 575

omega-6 fatty acids

Front 576

Lipids in which one of the two acyl chains is attached to glycereol in ether, rather thatn ester, linkage.

Back 576

ether lipids

Front 577

The aliphatic ether analog of phosphatidylcholine. An ether lipid consisting of an ether-linked alkane, an acetyl ester, and choline.

Back 577

platelet-activating factor

Front 578

A group of membrane lipids that predominates in plant cells. One or two galactose residues are connected by a glycosidic linkage to C-3 of a 1,2-diacylglycerol. Probably the most abundant membrane lipids in the biosphere.

Back 578

galactolipids

Front 579

Sphingosine with H as the head group. The structural foundation of sphingolipids; Sphingosine is made from serine and palmitic acid; when a fatty acid is attached in amide linkage to C-2 of sphingosine, the result is a ceramide.

Back 579

ceramide

Front 580

The major sterol in animal tissues; amphipathic, with a polar head group (OH) and a nonpolar hydrocarbon body (the steroid nucleus and the hudrocarbon side chain).

Back 580

cholesterol

Front 581

Polar derivatives of cholesterol that act as detergents n the intestine, emulsifying dietary fats to make them more readily accessible to digestive lipases.

Back 581

bile acids

Front 582

cholecalciferol

Back 582

vitamin D3

Front 583

In its various forms, functions as a hormone and as the visual pigment of the vertebrate eye.

Back 583

viatmin A (retinol)

Front 584

The collective name for a group of closely related lipids called tocopherols, all of which contain a substituted aromatic ring and a long ispernoid side chain.

Back 584

vitamin E

Front 585

The aromatic ring of this viatmin undergoes a cycle of oxidation and reduction during the formation of active prothrombin, a blood plasma protein essential in blood clotting.

Back 585

vitamin K

Front 586

All the lipids present in a specific cell type.

Back 586

lipidome

Front 587

An integral protein that provides for the regulated transport of a specific ion, or ions, across a membrane

Back 587

ion channel

Front 588

Membrane proteins that selectively allow transmembrane diffusion of water molecules

Back 588

aquaporins (AQPs)

Front 589

A compound that binds one or more metal ions and is capable of diffusing across a membrane, carrying the bound ion

Back 589

ionophore

Front 590

Family of ATP-driven transporters that remove drugs and other hydrophobic compounds from cells.

Back 590

multidrug transporters

Front 591

A member of a large family of membrane transporters that have sequences that make up ATP-binding cassettes. These trtansporters move a large variety of substrates, including inorganic ions, lipids, and nonpolar drugs, outward across the plasma membrane, using ATP as the energy source.

Back 591

ABC transporter

Front 592

Ion (usually proton) pumps typically found in intracellular membrane compartments including vacuoles

Back 592

V-type ATPases

Front 593

An enzyme complex that forms ATP from ADP and phosphate during oxidative phosphorylation in the inner mitochondrial membrane or the bacterial plasma membrane, and during photophosphorylation in chloroplasts

Back 593

ATP synthase

Front 594

Ion (usually proton) pumps related to the ATP synthase of mitochondria and chloroplasts

Back 594

F-type ATPases

Front 595

Ion pumps that are reversibly phosphorylated as part of the transport cycle.

Back 595

P-type ATPases

Front 596

Contributing to an electrical potential across a membrane

Back 596

electrogenic

Front 597

Energy-requiring transport of a solute across a membrane in the direction of increasing concentration

Back 597

active transport

Front 598

A transport system that carries only one solute, as distinct from cotransport

Back 598

uniport

Front 599

Cotransport of solutes across a membrane in the same direction

Back 599

symport

Front 600

Cotransport of two solutes across a membrane in opposite directions.

Back 600

antiport

Front 601

The simultaneous transport, by a single transporter, of two solutes across a membrane

Back 601

cotransport systems

Front 602

Proteins that span a membrane and transport specific nutrients, metabolites, ions, or proteins across the membrane; sometimes called permeases.

Back 602

transporters

Front 603

Diffusion of a polar substance across a biological membrane through a protein transporter, also called passive diffusion or passive transport.

Back 603

facilitated diffusion

Front 604

The energy required to maintain a separation of charge and of concentration across a membrane

Back 604

electrochemical potential

Front 605

The sum of the gradients of concentration and of electric charge of an ion across a membrane; the driving force for oxidative phosphorylation and phtotophosphorylation.

Back 605

electrochemical gradient

Front 606

The difference in electrical potential across a biological membrane, commonly measured by the insertion of a microelectrode. Typical membrane potentials vary from -25 mV (by convention, the negative sign indicates that the inside is negative relative to the outside) to greater than -100 mV across some plant vacuole membranes.

Back 606

membrane potential (V{m})

Front 607

The movement of solute molecules across a membrane to a region of lower concentration, unassisted by a protein transporter.

Back 607

simple diffusion

Front 608

(1) A family of proteins that facilitate membrane fusion. (2) The protein product of a gene created by the fusion of two distinct genes or portions of genes.

Back 608

fusion proteins

Front 609

A technique used to quantify the diffusion of membrane components (lipids or proteins) in the plane of the bilayer.

Back 609

FRAP (Fluorescence return after photobleaching)

Front 610

Membrane proteins that catalyze the movement of lipids from one leaf of a membrane bilayer to the other. Catalyzes the translocation of aminophospholipids (phosphatidylethanolamine and phosphatidylserine) from the extracellular to the cytosolic leaflet of the plasma membrane, contributing to the asymmetric distribution of phospholipids: phosphatidylethanolamine and phosphatidylserine primarily in the cytosolic leaflet, and the sphingolipids and phosphatidylcholine in the outer leaflet.

Back 610

flippases

Front 611

A scale that expresses the relative hydrophobic and hydrophilic tendencies of a chemical group.

Back 611

hydropathy index

Front 612

Proteins that are lossely or reversibly bound to a membrane by hydrogen bonds or electrostatic forces; generally water-soluble once released from the membrane. Also called extrinsic proteins.

Back 612

peripheral proteins

Front 613

Proteins firmly bound to a membrane by hydrophobic interactions; as distinct from peripheral proteins. Also called intrinsic proteins.

Back 613

integral proteins

Front 614

A double layer of oriented amphipathic lipid molecules, forming the basic structure of biological membranes. The hydrocarbon tails face inward to form a continuous nonpolar phase.

Back 614

bilayer

Front 615

An aggregate of amphipathic molecules in water, with the nonpolar portions in the interior and the polar portions at the exterior surface, exposed to water.

Back 615

micelle

Front 616

A model describing biological membranes as a fluid lipid bilayer with embedded proteins; the bilayer exhibits both structural and functional asymmetry.

Back 616

fluid mosaic model

Front 617

A hollow sphere, formed because the bilayer sheet is relatively unstable and spontaneously folds back on itself

Back 617

vesicle

Front 618

These proteins are found both in the cytosol and in association with membranes. Their affinity for membranes results in some cased from the protein's noncovalent interaction with a membrane protein or lipid, and in other cases from the presence of one or more lipids. This reversible association is generally regulated.

Back 618

amphitropic proteins

Front 619

Glycoprotein in erythrocyte that spans the plasma membrane. The amino terminus is outside the membrane. The carboxyl terminus is inside the membrane. There is a hydrophobic segment in the center of about 18 residues long inside the membrane.

Back 619

glycophorin

Front 620

Phospholipid molecules lying on membrane proteim surfaces. Their head groups interacting with polar amino acid residues at the intter and outer membrane-water interfaces, and their side chains associated with non-polar residues. These lipids form a shell around the protein.

Back 620

annular lipids

Front 621

The positively charged Lys, His, and Arg residues of membrane proteins occur more commonly on th ecytoplasmic face of membranes

Back 621

positive-inside rule

Front 622

A structural motif, in addition to alpha helix common in bacterial membrane proteins, in which 20 or more transmembrane segments form sheets that line a cylinder.

Back 622

beta barrel

Front 623

Proteins that allow certain polar solutes to cross the outer membrane of gram-negative bacteria such as E. coli; they have many-stranded beta barrels lining the polar transmembrane passage

Back 623

porins

Front 624

A semisolid state of a lipid bilayer below physiological temperatures in which all types of motion of individual lipid molecules are strongly constrained. Paracrystalline bilayer.

Back 624

gel phase

Front 625

A fluid state of a lipid bilayer above physiological temperatures in which individual hydrocarbon chains of fatty acides are in constant motion produced by rotation about the carbon-carbon bonds of the long acyl chains

Back 625

liquid-disordered state

Front 626

At intermediate (physiological) temperatures, the lipid bilayer exists in this state; there is less thermal motion in the acyl chains, but lateral movement in the plane of the bilayer still occurs

Back 626

liquid-ordered state

Front 627

These enzymes move plasma membrane phospholipids from the cytosolic to the extracellular leaflet, and are ATP-dependent. Members of the ABC transporter family which actively transport hydrophobic substrates outward across the plasma membrane.

Back 627

floppases

Front 628

Proteins that move any membrane phospholipid across the bilayer down its concentration gradient (from the leaflet where it has higher concentration to the leaflet where is has a lower concenration); not dependent on ATP.

Back 628

scramblases

Front 629

Cholesterol-sphingolipid structures in the outer monolayer of the plasma membrane, visible with atomic force microscopy, are slightly thicker and more ordered (less fluid) than neighboring membrane rafts

Back 629

microdomains

Front 630

aka microdomains; liquid-ordered sphingolipid microdomains adift on an ocean of liquid-disordered phospholipids

Back 630

rafts

Front 631

An integral membrane protein with two globular domains connecgted by a hairpin-shaped hydrophobic domain, which binds the protein to the cytoplasmic leaflet of the plasma membrane. Three palmitoyl groups attached to the carboyl-terminal globular domain further anchor it to the membrane. This protein binds cholesterol in the membrane, and its presence forces the associated lipid bilayer to curve inward, forming 'little caves' in the surface of the cell

Back 631

caveolin

Front 632

Little caves; unusual rafts: they involve both leaflets of the bilayer

Back 632

caveolae

Front 633

Family of proteins involved in membrane fusion occurring at synapses, when intracellular vesicles loaded with neurotransmitter fuse with the plasma membrane

Back 633

SNAREs

Front 634

SNAREs in the target membrane with which the vesicle fuses during membrane fusion occurring at synapses.

Back 634

t-SNAREs

Front 635

Surface adhesion proteins that mediate a cell's interaction with the etracellular matrix and with other cells, including some pathogens.

Back 635

integrins

Front 636

Another plasma membrane protein involved in surface adhesion, which undergoes homophilic interactions with molecules identical to this one in an adjacent cell

Back 636

cadherins

Front 637

Posseses extgracellular domains that, in the presence of Ca<2+>, bind specific polysaccharides on the surface of an adjacent cell

Back 637

selectins

Front 638

aka facilitated diffusion

Back 638

passive transport

Front 639

aka transporters

Back 639

permeases

Front 640

Transporters that bind their substrates with high stereospecificity, catalyze transport at rates well below the limits of free diffusion, and are saturable in the same sense as are enzymes: there is some substrate concentration above which further increases will not produce a greater rate of transport

Back 640

carriers

Front 641

Transporters that generally allow transmembrane movement at rates orders of magnitude greater than those typical of carriers, rates approaching the limit of unhindered diffusion.

Back 641

channels

Front 642

Carriers that simply facilitate diffusion down a concentration gradient

Back 642

passive transporter

Front 643

These transporters can drive substrates across the membrane against a concentration gradient, some using energy provided directly by a chemical reaction (primary active transporters) and some coupling uphill transport of one substrqate with downhill transport of another (secondary transporters)

Back 643

active transporter

Front 644

Catalyzes electroneutral cotransport of anions across the plasma membrane; aka anion exchange (AE) protein

Back 644

chloride-bicarbonate exchanger

Front 645

aka chloride-bicarbonate exchanger

Back 645

anion exchange (AE) protein

Front 646

An exchange with no net transfer of charge

Back 646

electroneutral

Front 647

In this form of active transport, solute accumulation is coupled directly to an exergonic chemical reaction, such as conversion of ATP to ADP + P

Back 647

primary active transport

Front 648

This form of active transport occurs when endergonic (uphill) transport of one solute is coupled to the exergonic (downhill) flow of a different solute that was originally pumped uphill by primary active transport

Back 648

secondary active transport

Front 649

Phosphate analog

Back 649

vanadate

Front 650

Moves calcium ions out of the cell

Back 650

plasma membrane Ca2+ pump

Front 651

P-type ATPases closely related in structure and mechanism; Contains three cytosolic domains formed by long loops connectin transmembrane helices: the N domain, the P domain, and the A domain

Back 651

sarcoplasmic and endoplasmic reticulum calcium (SERCA) pumps

Front 652

Cotransporter that couples phosphorylation-dephosphorylation of the critical Asp residue to the simultaneous movement of both Na+ and K+ against their electrochemical gradients. Responsible for maintaining low Na+ and high K+ concentrations in the cell relative to the extracellular fluid

Back 652

Na+K+ATPase

Front 653

Responsible for the striking resistance of certain tumors to some generally effective antitumor drugs.

Back 653

multi-drug transporter (MDR1)

Front 654

Well-studied prototype for proton-driven cotransporters; this E coli protein consists of a single polypeptide chain of 417 residues that function s as a monomer to transport one proton and one lactose molecule into the cell, with the net accumulation of lactose

Back 654

lactose transporter (lactose permease)

Front 655

The lactose transporter is one membere of this family of transporters, which comprises 28 families. almost all the members of this superfamily have 12 transmembrane domains (the few exceptions have 14)

Back 655

major facilitator superfamily (MFS)

Front 656

These transporters in the apical plasma membrane of the intestinal epithelial cell take up glucose from the intestine in a process driven by the downhill flow of Na+

Back 656

Na+-glucose symporters

Front 657

In these channels, which are generally oligomeric, binding of an extracellular or intracellular small molecule forces an allosteric transition in the protein, which opens or closes the channel

Back 657

ligand-gated channels

Front 658

In these channels, a change in transmembrane electrical potential (V{m}) causes a charged protein domain to move relative to the membrane, opening or closing the channel

Back 658

voltage-gated ion channels

Front 659

glycosylated derivatives of phosphatidylinositol

Back 659

GPI

Front 660

Programmed cell death, in which a cell brings about its own death and lysis, signaled from outside or programmed in its genes, by systematically degrading its own macromolecules

Back 660

apoptosis

Front 661

Defective regulatory genes that can lead to cancer. They encode proteins the normal function of which is to restraini cell division.

Back 661

tumor suppressor genes

Front 662

A cancer-causing gene; any of several mutant genest that cause cells to exhibit rapid, uncontrolled proliferation.

Back 662

oncogene

Front 663

One of a family of small secreted proteins (such as interleukins or interferons) that activate cell division or differntiation by binding to plasma membrane receptors in sensitive cells.

Back 663

cytokine

Front 664

Proteins or other molecules that act from outside a cell to stimulate cell growth and division

Back 664

growth factors

Front 665

Supramolecular assembly of enzymatic complexes that function in the degradation of damaged or unneeded cellular proteins.

Back 665

proteasome

Front 666

A small, highly conserved protein that targets an intracellular protein for degradation by proteasomes. Several ubiquitin molecules are covalently attached in tandem to a Lys residue in the target protein by a specific ubiquitinating enzyme.

Back 666

ubiquitin

Front 667

One of a family of proteins that activate cyclin-dependent protein kiinases and thereby regulate the cell cycle.

Back 667

cyclin

Front 668

A short (12 to 20 bp) DNA sequence to which receptors for steroid, retinoid, thyroid, and vitamin D hormones bind, altering the expression of the contiguous genes. For each hormone, there is a concsensus sequence preferred by the cognate receptor.

Back 668

hormone response element (HRE)

Front 669

Signal-transducing systems found in prokaryotes and plants, composed of a receptro His kinase that phosphorylates an internal His residue when occupied by its ligand. It then catalyzes phosphoryl transfer to a second component, the response regulator, which, when phosphorylated, alters the output of the signaling system.

Back 669

two-component signaling systems

Front 670

One of a family of Ca<2+>-binding proteins; in its Ca<2+>-bound state, calmoduling associates with and modulates the activities of a variety of proteins.

Back 670

calmodulin (CaM)

Front 671

A trimeric GTPbinding protein that, when activated by an associated plasma membrane receptor, acts to inhibit a neighboring membrane enzyme such as adenylyl cyclase. G{i} has effects opposite those of G{s}.

Back 671

inhibitory G protein (G{i})

Front 672

A trimeric regulatory GTP-binding protein that, when activated by an associated plasma membrane receptor, stimulates a neighboring membrane enzyme such as adenylyl cyclase. G{s} has effects opposite those of G{i}

Back 672

stimulatory G protein (G{s})

Front 673

Serpentine receptors

Back 673

7 transmembrane segment (7tm) receptors

Front 674

Serpentine receptors

Back 674

G protein-coupled receptors (GPCR)

Front 675

A large family of membrane receptor proteins with seven transmembrane helical segments. These receptors often associate with G proteins to transduce an extracellular signal into a change in cellular metabolism.

Back 675

serpentine receptors

Front 676

A family of heterotrimeric GTP-binding proteins that act in intracellular signaling pathways. Commonly, ligand binding to a serpentine receptor induces the exchange of GTP for bound GDP, enabling the G protein to activate a downstream enzyme in a signaling pathway. G proteins have intrinsic GTPase activity, and therefore self-inactivate.

Back 676

G proteins

Front 677

A protein domain that binds tightly to a phosphotyrosine residue in certain proteins such as the receptor tyrosine kinases, initiating the formation of a multiprotein complex that acts in a signaling pathway.

Back 677

SH2 domain

Front 678

Strictly, the phosphorylation of an amino acid residue in a protein, catalyzed by the same molecule. Often extended to include phosphorylation of one subunit of a homodimer by the other subunit.

Back 678

autophosphorylation

Front 679

An effector molecule synthesized within a cell in response to an external signal (first messenger) such as a hormone.

Back 679

second messenger

Front 680

Time-dependent loss of sensitivity to a ligand during its continued presence.

Back 680

desensitization

Front 681

A series of reactions, often involved in regulatory events, in which one enzyme activates another (often by phosphorylation), which activates a third, and so on. The effect of a catalyst activating a catalyst is a large amplification of the signal that initiated the cascade.

Back 681

enzyme cascade

Front 682

The process by which an extracellular signal (chemical, mechanical, or electrical) is amplified and converted to a cellular response.

Back 682

signal transduction

Front 683

In biosignaling, this is achieved by the precise molecular complementarity between the signal and receptor molecules

Back 683

specificity

Front 684

This relationship between signal (ligand) and receptor can be expressed as the dissociation constant K{d}, usually 10<-10> M or less -- meaning that the receptor detects picomolar concentrations of a signal molecule.

Back 684

affinity

Front 685

This characteristic of receptor-ligand interactions results in large changes in receptor activation with small changes in ligand concentration

Back 685

cooperativity

Front 686

Results when an enzyme associated with a signal receptor is activated and, in turn, catalyzes the activation of many molecules of a second enzyme, each of which activates many molecules of a third enzxyme, and son on. The result of enzyme cascades

Back 686

amplification

Front 687

Refers to the ability of the system to receive multiple signals and produce a unified response appropriate to the needs of the cell or organism.

Back 687

integration

Front 688

This analysis of receptor-ligand binding allows us to estimate the number or feceptor-binding sites in a given preparation and the dissociation constant.

Back 688

Scothard analysis

Front 689

Structural analogs that bind to a receptor and mimic the effects of its natural ligand

Back 689

agonists

Front 690

Analogs that bind the receptor without triggering the normal effect and thereby block the effects of agonists, including the biological ligand.

Back 690

antagonists

Front 691

Receptors found in different target tissues, such as muscle, liver, and adipose tissue, that mediate different responses to epinephrine. An integral protein with seven hydrophobic regions of 20-28 amino acid residues that "snake" back and forth across the plasma membrane seven times.

Back 691

beta-andrenergic receptors

Front 692

aka GPCRs, aka heptahelical receptors. G protein-coupled receptors

Back 692

serpentine receptors

Front 693

aka GPCRs, aka serpentine receptors. G protein-coupled receptors

Back 693

heptahelical receptors

Front 694

In the GTP-bound conformation, the G protein exposes reviously buried regions called S_____ _ and S_____ II that interact with proteins downstream in the signaling pathway, until the G protein inactivates itself by hydrolyzing its bound GTP to GDP.

Back 694

switch I

Front 695

In the GTP-bound conformation, the G protein exposes reviously buried regions called S_____ I and S_____ II that interact with proteins downstream in the signaling pathway, until the G protein inactivates itself by hydrolyzing its bound GTP to GDP.

Back 695

switch II

Front 696

aka regulators of G protein signaling (RGSs), these proteins increase the intrinsic GTPase activity of G proteins up to 100,000-fold

Back 696

GTPase activator proteins (GAPs)

Front 697

aka GTPase activator proteins (GAPs), these proteins increase the intrinsic GTPase activity of G proteins up to 100,000-fold

Back 697

regulators of G protein signaling (RGSs)

Front 698

Associated with G protein, these molecules catalyze the process of replacing bound GDP with GTP -- switching the protein on.

Back 698

guanosine nucleotide-exchange factors

Front 699

Secreted by Vibrio cholerae in the intestine of the infected person, this is a heterodimeric protein that triggers continuous activation of the adnylyl cyclase of intestinal epithelial cells, chronically high cAMP, and chronically active PKA, which causes massive water loss as the cells respond to the ensuing osmotic imbalance.

Back 699

cholera toxin

Front 700

An integral protein of the plasma membrane with its active site on the cytoplasmic face. When activated, catalyzes cAMP synthesis from ATP

Back 700

adenylyl cyclase

Front 701

Produced by Bordetella perttussis, catalyzes ADP-ribosylation of the alpha subunit of G{i}. The result is destruction of the ciliated epithelial cells of the lung that normally sweep away mucus, which triggers "whooping cough"

Back 701

pertussin toxin

Front 702

aka protein kinase A (PKA), which is allosterically activated by cAMP to catalyze the phosphorylation of other proteins, including glycogen phophorylase b kinase to begin the process of mobilizing glycogen stores in liver and muscle tissue.

Back 702

cAMP-dependent protein kinase

Front 703

aka cAMP-dependent protein kinase A, which is allosterically activated by cAMP to catalyze the phosphorylation of other proteins, including glycogen phophorylase b kinase to begin the process of mobilizing glycogen stores in liver and muscle tissue.

Back 703

protein kinase A (PKA)

Front 704

Sequence of redidues most commonly occuring at each position in a set of similar sequences; in this case, the sequence surrounds a Ser or Thr residue that gets phosphorylated, marking it for regulation by PKA

Back 704

consensus sequence

Front 705

Involved in one of several mechanisms to cause termination of the beta-andrenergic response by removing the second messenger: hydrolysis of cAMP to 5'-AMP, which is not active as a second messenger

Back 705

cyclic nucleotide phosphodiesterase

Front 706

aka GRK2 for G protein-coupled receptor kinases (GRKs) number 2; phosphorylates several Ser residues near the carboxyl terminus of the receptor, which is on the cytoplasmic side of the plasma membrane. Receptor phosphorylation creates a binding site for beta-arrestin (or arrestin 2)

Back 706

beta-andrenergic receptor kinase beta ARK

Front 707

Receptor phosphorylation by beta-andrenergic receptor kinase creates a binding site for this protein, which, when this protein binds, effectively prevents further interaction between the receptor and the G protein.

Back 707

beta-arrestin

Front 708

beta-ARK is a member of this family of these kinases, all of which phosphorylate GPCRs on their carboxyl-terminal cytoplasmic domains and play roles similar to that of beta-ARK in desensitization and resensitization of their receptors.

Back 708

G protein-coupled receptor kinases (GRKs)

Front 709

In many cell types, the catalytic subunit of PKA can also move into the nucleus, where it phosphorylates this protein, which alters the expression of specific genes regulated by cAMP.

Back 709

cAMP response element binding protein (CREB)

Front 710

A factor that explains how so many types of signals can be mediated by a single second messenger, such as cAMP, is the confinement of the signaling process to a specific region of the cell by these proteins, which are noncatalytic proteins that hold together other protein molecules that function in concert.

Back 710

adaptor proteins

Front 711

These are multivalent adaptor proteins; one part binds to the R subunits of PKA and another to a specific structure in the cell, confining the PKA to the vicinity of that structure.

Back 711

AKAP (A kinase anchoring proteins)

Front 712

A broad class of GPCRs are coupled to this lipase in the plasma membrane that is specific for phosphatidylinositol 4,5-bisphosphate (or PIP2); this one cuts the first O-P bond in the phosphodiester bond of the head group, splitting it into diacylglycerol and IP3 -- two powerful second messengers

Back 712

phospolipase C (PLC)

Front 713

One of the powerful second messengers made by phospholipase C (PLC) (not IP3 or inisitol 1,4,5-triphosphate) when phosphotidylinositol 4,5-bisphosphate is cleaved.

Back 713

diacylglycerol

Front 714

One of the powerful second messengers made by phospholipase C (PLC) (not not diacylglycerol) when phosphotidylinositol 4,5-bisphosphate is cleaved.

Back 714

inositol 1,4,5-triphosphate, IP3

Front 715

Activated by the elevated [Ca<2+>] triggered by IP3, as well as diacylglycerol, this enzyme phosphorylates cellular proteins to produce some of the cellular responses to a given hormone signal

Back 715

protein kinase (PKC)

Front 716

From Aequorea victoria, this proton emits a photon in the green region when excited by absorption of a photon of light

Back 716

green fluorescent protein (GFP)

Front 717

The energy of the donor molecule passes directly to a nearby molecule (the acceptor) without emission of a photon, exciting the acceptor, which can then fluoresce.

Back 717

fluorescence resonance energy tranfer (FRET)

Front 718

The action of this group of compounds is attributable to their effects on PKC. They apparently mimic cellular diacylglycerol as second messengers, but do not metabolize; therefore they continuously activate PKC, and end-up promoting the formation of tumors

Back 718

tumor promoters

Front 719

Calmodulin is an integral subunit of these kinases. When intracellular [Ca<2+>] increases, calmodulin binds Ca<2+> and undergoes a change in conformation that activates this kinase.

Back 719

calmodulin-dependent protein kinases (CaM kinases)

Front 720

These kinases are a large family of plasma membrane receptors with intrinsic protein kinase activity, which transduce extracellular signals by a mechanism fundamentally different from that of GPCRs

Back 720

receptor tyrosine kinases (RTKs)

Front 721

In RTK signalling, the phosphorylation of three critical Tyr residues by INS-R

Back 721

autophosphorylation

Front 722

Ras is the prototype of this family of proteins that mediates a wide variety of signal transductions

Back 722

small G proteins

Front 723

Mitogen-activated protein kinases; mitogens are extracellular signal that induces mitosis and cell division

Back 723

MAPK

Front 724

These cascades mediate signaling initiated by a variety of growth factors, such as platelet-derived growth factor (PDGF) and epidermal growth factor (EGF)

Back 724

MAPK cascades

Front 725

The second messenger to which GTP is converted when guanylyl cyclases are activated

Back 725

guanosine 3',5'-cyclic monophosphate (cyclic GMP)

Front 726

aka protein kinase G; many of the actions of cGMP in animals are mediated by this enzyme, which is activated by cGMP to phosphorylate Ser and Thr residues in target proteins

Back 726

cGMP-dependent protein kinase (PKG)

Front 727

Guanylyl cyclase in the kidney is activated by this peptide hormone, which is released by cells in the cardiac atrium when the heart is stretched by increased blood volume. Carried in the blood to the kidney, this molecule activates guanylyl cyclase in cells of the collecting ducts, resulting in a rise in [cGMP] that triggers increased renal excretion of Na+ and consequently of water, driven by the change in osmotic pressure.

Back 727

atrial natriuretic factor (ANF)

Front 728

This peptide regulates Cl<-> secretion in the intestine; it activates a guanylyl cyclase in the plasma membrane of epithelial cells lining the intestine

Back 728

guanylin

Front 729

Ca<2+> enzyme that produces nitric oxide from arginine

Back 729

NO synthase

Front 730

The pain caused by contraction of a heart deprived of O2 because of blocked coronary arteries

Back 730

angina pectoris

Front 731

Phosphotyrosine-binding domains -- another binding partner for P-Tyr proteins

Back 731

PTB domains

Front 732

Three types of these channels are essential to the signaling mechanism for neuronal action potentials

Back 732

voltage-gated ion channels

Front 733

Runs the entire length of an axon; closed when the membrane is at rest at V{m} of -60 mV, but opens briefly in response to acetylcholine

Back 733

voltage-gated Na+ channels

Front 734

Runs the entire length of an axon; closed when the membrane is at rest at V{m} of -60 mV, but opens a split second after Na+ channels in response to the depolarization caused by the flow of Na+ into the axon

Back 734

voltage-gated K+ channels

Front 735

At the distal end of the axon, this channel opens after the influx of Na+ and efflux of K+, triggering a release of acetylcholine to signal either a neuron to fire or a muscle to contract

Back 735

voltage-gated Ca2+ channels

Front 736

Mediates the passage of an electrical signal at some types of synapses and at a neuromuscular junction (between the motor neuron and muscle fiber) signaling the muscle to contract

Back 736

nicotinic acetylcholine receptor

Front 737

Proteins of the plasma membrane that mediate the adhesion of cells to each other and to the extracellular matrix, and carry signals in both directions across the membrane.

Back 737

integrins

Front 738

Breast cancer drug that exploits the specificity of the steroid-receptor interaction; this drug is an estrogen antagonist, competing with estrogen for binding to the estrogen receptor, but with little or no effect on gene expression, stopping the growth of remaining cancer cells after cancer surgery or chemotherapy.

Back 738

tamoxifen

Front 739

Binds to the progesterone receptor and blocks hormone actions essential to implantation of the fertilized ovum in the uterus

Back 739

mifepristone (RU 486)

Front 740

e.g., sugars, and amino acids to which bacteria swim

Back 740

attractants

Front 741

First component of the two-component system for bacterial signaling; this kinase catalyzes transfer of the phosphoryl group from the His residue to an Asp residue on a second, soluble protein, called the response regulator

Back 741

receptor histidine kinase

Front 742

The second protein in the two-component system for bacterial signaling

Back 742

response regulator

Front 743

A common motif in plant signaling involves these kinases, which have a single helical segment in the plasma membrane that connects a receptor domain on the outside with a protein Ser/Thr kinase on the cytoplasmic side.

Back 743

receptorlike kinases

Front 744

An integral protein with the seven membrane-spanning alpha-helices characteristic of GPCRs

Back 744

Rhodopsin

Front 745

Light-absorbing pigment (chromophore) that is covalently bonded to opsin, the protein component of rhodopsin, through a Schiff base to a Lys residue.

Back 745

11-cis-retinal

Front 746

When a photon is absorbed by the retinal component of rhodopsin, the energy causes a photochemical change in which 11-cis-retinal is converted to this molecule

Back 746

all-trans-retinal

Front 747

In its excited conformation, rhodopsin interacts with this second protein, which hovers nearby on the cytoplasmic face of the disk membrane. Shares many functional features with G{s} and G{i}. It can bind to either GDP or GTP

Back 747

transducin

Front 748

Prolonged illumination causes rhodopsin to expose several Thr and Ser residues which must be quickly phosphorylated by this kinase

Back 748

rhodopsin kinase

Front 749

This Ca<2+> -binding protein inhibits hrodopsin kinase at high [Ca2+]

Back 749

recoverin

Front 750

the phosphorylated carboxyl-terminal domain of rhodopsin is bound by this protein, preventing further interaction between activated rhodopsin and transducin

Back 750

arrestin 1

Front 751

See only blue and green (two primary colors)

Back 751

red-dichromats

Front 752

See only red and blue (two primary colors)

Back 752

green-dichromats

Front 753

See three primary colors, but with altered red

Back 753

red-analogous trichromats

Front 754

See three primary colors but with altered green

Back 754

green-anomalous trichromats

Front 755

If a sufficient number of odorant molecules encounter receptors, this potential is strong enough to cause the neuron to fire an action potential that ultimately registers in the brain as a specific smell

Back 755

receptor potential

Front 756

Like transducin but for taste

Back 756

gustducin

Front 757

Protein kinases that orchestrate the metabolic activities of the cell to produce orderly cell division are heterodimers with a regulatory unit called cyclin and this catalytic subunit

Back 757

cyclin dependent protein kinase (CDK)

Front 758

A very important CDK substrate; when DNA damage is detected, this protein participates in a mechanism that arrests cell division in G1; named for the tumor cell line in which it was discovered

Back 758

retinoblastoma protein pRb

Front 759

Oncogenes are derived from these genes in animal host cells, which encode growth-regulating proteins.

Back 759

proto-oncogenes

Front 760

An RTK (receptor Tyr kinase) that must be activated for the formation of new blood vessels (angiogenesis) to provide a solid tumor with its own food supply; inhibition of this growth factor might starve a tumor of essential nutrients

Back 760

vascular endothelial growth factor receptor (VEGF-R)

Front 761

Covalent attachment of the adenylyl group (AMP) to some protein or small molecule.

Back 761

adenylylation

Front 762

The phase of intermediary metabolism concerned with the energy requiring biosynthesis of cell components from smaller precursors.

Back 762

anabolism

Front 763

An organism that can synthesize its own complex molecules from very simple carbon and nitrogen sources, such as carbon dioxide and ammonia.

Back 763

autotroph

Front 764

The phase of intermediary matabolism concerned with the energy yielding degradation of nutrient molecules.

Back 764

catabolism

Front 765

An electron donor and its corresponding electron acceptor form; for example, Cu<+> (donor) and Cu<2+> (acceptor), or NADH (donor) and NAD<+> (acceptor)

Back 765

conjugate redox pair

Front 766

Enzymes catalyzing the removal of pairs of hydrogen atoms from their substrates.

Back 766

dehydrogenases

Front 767

Nucleotide coenzymes (FMN and FAD) containing riboflavin

Back 767

flavin nucleotides

Front 768

An enzyme containing a flavin nucleotide as a tightly bound prosthetic group.

Back 768

flavoprotein

Front 769

An organism that requires complex nutrient molecules, such as glucose, as a source of energy and carbon.

Back 769

heterotroph

Front 770

An enzyme that hydrolizes a molecule of inorganic pyrophosphate to yield two molecules of (ortho) phosphate; also known as pyrophosphatase

Back 770

inorganic pyrophosphatase

Front 771

In cells, the enzyme-catalyzed reactions that extract chemical energy from nutrient molecules and utilize it to synthesize and assemble cell coponents.

Back 771

intermediary metabolism

Front 772

The entire set of enzyme-catalyzed transformations of organic molecules in living cells; the sum of anabolism and catabolism.

Back 772

metabolism

Front 773

A chemical intermediate in the enzyme-catalyzed reactions of metabolism

Back 773

metabolite

Front 774

An enzyme that catalyzes the transfer of the terminal phosphate of a nucleoside 5'-triphosphate to a nucleoside 5'-diphosphate

Back 774

nucleoside diphosphate kinase

Front 775

An enzyme that catalyzes an oxidation-reduction reaction

Back 775

oxidoreductase

Front 776

The actual free-energy change of ATP hydrolysis under the nonstandard conditions prevailing within a cell.

Back 776

phosphorylation potential

Front 777

A nucleotide coenzyme containing the pyridine derivative nicotinamide; NAD or NADP

Back 777

pyridine nucleotide

Front 778

A general or neutral term for an electron or an electron equivalent in the form of a hydrogen atom or a hydride ion.

Back 778

reducing equivalent

Front 779

The electromotive force exhibited at an electrode by 1 M concentrations of a reducing agent and its oxidized form at 25 degrees C and pH 7.0; a measure of the relative tendency of the reducing agent to lose electrons.

Back 779

standard reduction potential

Front 780

An ester of carboxylic acid with a thiol or mercaptan

Back 780

thioester

Front 781

Generally convergent metabolic pathways

Back 781

catabolic pathways

Front 782

Generally divergent metabolic pathways

Back 782

anabolic pathways

Front 783

When K'{eq} is greater than 1.0, then standard Gibb's free energy is positive or negative?

Back 783

negative

Front 784

When Gibb's standard free energy is negative, which direction does the reaction proceed?

Back 784

forward

Front 785

When K'{eq} is less than 1.0, then standard Gibb's free energy is positive or negative?

Back 785

positive

Front 786

When Gibb's standard free energy is positive, which direction does the reaction proceed?

Back 786

reverse

Front 787

When K'{eq} is equal to 1.0, then standard Gibb's free energy is positive or negative?

Back 787

neither -- it's zero

Front 788

When Gibb's standard free energy is zero, which direction does the reaction proceed?

Back 788

neither -- it's in equilibrium

Front 789

Bioenergetics is the quantitative study of e_____ t____________ - changes of one form of energy into another - that occur in living cells, and of the nature and function of the chemical processes underlying these transductions.

Back 789

energy transduction

Front 790

An expression of the amount of energy capable of doing work during a reaction at constant temperature and pressure.

Back 790

Gibbs free energy G

Front 791

The heat content of the reacting system. It reflects the number and kinds of chemical bonds in the reactants and products.

Back 791

Enthalpy H

Front 792

A quantitative expression for the randomness or disorder in a system.

Back 792

Entropy S

Front 793

aka standard transformed constants, and written with a prime symbol (') to indicate a biochemical standard state of [H+] of 10<-7> M (pH 7), [H2O] 55.5 M, Mg<2+> of 1mM.

Back 793

Standard free-energy change

Front 794

Ratio of the concentrations of the products to the reactants; aka "Q"

Back 794

Mass-action ratio Q

Front 795

aka Nicotinic acid, which is synthesized from tryptophan; precursor to pyridine-like rings of NAD and NADP;

Back 795

niacin

Front 796

aka Phosphogluconate pathway

Back 796

hexose monophosphate pathway

Front 797

An oxidative pathway beginning with glucose 6-phosphate and leading, via 6-phosphogluconate, to pentose phosphates and yielding NADPH. Also called the pentose phosphate pathway.

Back 797

phosphogluconate pathway

Front 798

A pathway that serves to interconvert hexoses and pentoses and is a source of reducing equivalents and pentoses for biosynthetive processes; present in most organisms. Also called the phosphogluconate pathway.

Back 798

pentose phosphate pathway

Front 799

A vitamin; an enzymatic cofactor involved in carboxylation reactions

Back 799

biotin

Front 800

The biosynthesis of a carbohydrate from simpler, noncarbohydrate precursors such as oxaloacetate or pyruvate.

Back 800

gluconeogenesis

Front 801

The active coenzyme form of vitamin B(1); involved in aldehyde transfer reactions.

Back 801

thiamine pyrophosphate (TPP)

Front 802

Inherited disease in which galactose cannot be converted into glucose

Back 802

galactosemia

Front 803

Common condition in adults, in which lack of intestinal lactase results in inability to digest milk products.

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lactose intolerance

Front 804

Enzymes that catalyze the transformation of compounds into their positional isomers

Back 804

isomerases

Front 805

Enzymes that catalyze the transposition of functional groups

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mutases

Front 806

ATP formation from ADP and P{i}, driven by electron flow through a series of membranebound carriers, with a proton gradient as the direct source of energy driving rotational catalysis by ATP synthase.

Back 806

respiration-linked phosphorylation

Front 807

Phosphorylation of ADP or some other nucleoside 5'-diphosphate couple to the dehydrogenation of an organic substrate; independent of the electron-transfer chain.

Back 807

substrate-level phosphorylation

Front 808

Any molecule with the general chemical form R-C-OPO{2-3}

Back 808

acyl phosphate

Front 809

Multiple forms of an enzyme that catalyze the same reaction but differ from each other in their amino acid sequence, substrate affinity, V{max}, and/or regulatory properties; also called isoenzymes

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isozymes

Front 810

The anaerobic conversion of glucose to ethanol via glycolysis

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ethanol (alcohol) fermentation

Front 811

The metabolic condition in which the supply of oxygen is severely limited.

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hypoxia

Front 812

Energy-yielding anaerobic breakdown of a nutrient molecule, such as glucose, without net oxidation; yields lactate, ethanol, or some other simple product.

Back 812

fermentation

Front 813

The catabolic pathway by which a molecule of glucose is broken down into two molecules of pyruvate.

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glycolysis

Front 814

In step 2 of glycolysis, the enzyme phosphohexose isomerase (aka phosphoglucose isomerase) catalyzes the reversible isomerization of this aldose to the ketose fructose 6-phosphate

Back 814

glucose 6-phosphate

Front 815

In step 1 of glycolysis, the phosphorylation of glucose to yield glucose 6-phosphate, with ATP as phosphoryl donor, and is irreversible under intracellular conditions, is catalyzed by this enzyme

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hexokinase

Front 816

In step 3 of glycolysis, PFK-1 (phosphofructokinase-1) catalyzes the transfer of a phosphoryl group from ATP to fructose 6-phosphate to yield this product

Back 816

fructose 1,6-bisphosphate

Front 817

In step 4 of glycolysis, this enzyme is often simply called aldolase. It catalyzes a reversible aldol condensation in which fructose 1,6-bisphosphate is cleaved into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate.

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fructose 1,6-bisphosphate aldolase

Front 818

In step 4 of glycolysis, this enzyme is aka fructose 1,6-bisphosphate aldolase. It catalyzes a reversible aldol condensation in which fructose 1,6-bisphosphate is cleaved into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate.

Back 818

aldolase

Front 819

In step 4 of glycolysis, this is the aldose product of the cleavage of fructose 1,6-bisphosphate by fructose 1,6-bisphosphate aldolase

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glyceraldehyde 3-phosphate

Front 820

In step 4 of glycolysis, this is the ketose product of the cleavage of fructose 1,6-bisphosphate by fructose 1,6-bisphosphate aldolase

Back 820

dihydroxyacetone phosphate

Front 821

In step 5 of glycolysis, this enzyme catalyzes the reversible conversion of dihydroxyacetone phosphate to glyceraldehyde 3-phosphate

Back 821

triose phosphate isomerase

Front 822

Step 6 of glycolysis is the oxidation of glyceraldehyde 3-phosphate to this salt, catalyzed by glyceraldehyde 3-phosphate dehydrogenase

Back 822

1,3-bisphosphoglycerate

Front 823

In step 6 of glycolysis, the oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate, this enzyme catalyzes the first step in the payoff phase of glycolysis.

Back 823

glyceraldehyde 3-phosphate dehydrogenase

Front 824

In step 7 of glycolysis, this enzyme transfers the high-energy phosphoryl group from the carboxyl group of 1,3-bisphosphoglycerate to ADP, to form ATP and 3-phosphoglycerate

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phosphoglycerate kinase

Front 825

In step 8 of glycolysis, this enzyme catalyzes the reversible shift of the phosphoryl group between C-2 and C-3 of glycerate; Mg<2+> is essential for this reaction.

Back 825

phosphoglycerate mutase

Front 826

In step 9 of glycolysis, this enzyme promotes the reversible removal of a molecule of water from 2-phosphoglycerate to yield PEP

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enolase

Front 827

In step 10 of glycolysis, this enzyme catalyzes the transfer of the phosphoryl group from phosphoenolpyruvate to ADP; this reaction also requires K<+> and either Mg<2+> or Mn<2+>

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pyruvate kinase

Front 828

Final product of glycolysis

Back 828

pyruvate

Front 829

A life-threatening condition produced by the lowering of blood pH due to accumulation of acetoacetate and beta-hydroxybutyrate

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ketoacidosis

Front 830

A protein that acts at the level of mRNA synthesis to stimulate the production of at least eight glycolytic enzymes and the glucose transporters when oxygen supply is limited

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hypoxia-inducible transcription factor (HIF-1)

Front 831

This salivary enzyme hydrolyzes the internal (alpha1->4) glycosidic linkages of starch, to begin digestion in the mouth

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alpha-amylase

Front 832

starch phosphorylase is the homolog in plants; this enzyme catalyzes the phosphorylitic reactionat the nonreducing end of storage polysaccharides

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glycogen phosphorylase

Front 833

glycogen phosphorylase is the homolog in animals; this enzyme catalyzes the phosphorylitic reactionat the nonreducing end of storage polysaccharides

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starch phosporylase

Front 834

This enzyme removes branches from storage polysaccharides to enable continued enzyme action by glycogen phosphorylase in animals or starch phosphorylase in plants

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debranching enzyme

Front 835

A liver enzyme that catalyzes the phosphorylation of fructose at C-2 rather than C-6, enabling a major pathway of fructose entry into glycolysis in muscles and kidney.

Back 835

fructokinase

Front 836

This enzyme cleaves fructose 1-phosphate into glyceraldehyde and dihydroxyacetone phosphate

Back 836

fructose 1-phosphate aldolase

Front 837

Catalyzes the phosphorylation of glyceraldehyde by ATP to form glyceraldehyde 3-phosphate

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triose kinase

Front 838

Catalyzes the production of galactose 1-phosphate from D-galactose (the phosphorylation of galactose)

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galactokinase

Front 839

abbreviated UDP, this molecule serves as a coenzyme-like carrier of hexose groups during the epimerization of galactose 1-phosphate to glucose 1-phosphate

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uridine diphosphate

Front 840

Catalyzes the isomerization of mannose 6-phosphate to fructose 6-phosphate, an intermediate of glycolysis

Back 840

phosphomannose isomerase

Front 841

When animal tissues cannot be supplied with enough oxygen to oxidize the pyruvate and NADH produced in glycolysis, then NAD+ is regenerated from NADH by the reduction of pyruvate to this molecule

Back 841

lactate

Front 842

This enzyme catalyzes the reduction of pyruvate in the fermentation pathway to L-lactate

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lactate dehydrogenase

Front 843

The general term for processes that extract energy as ATP but do not consume oxygen or change the concentrations of NAD+ or NADH

Back 843

fermentation

Front 844

Catalyzes the first step of the 2-step alcohol fermentation process, decarboxylating pyruvate to yield acetaldehyde

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pyruvate decarboxylase

Front 845

Catalyzes the first step of the 2-step alcohol fermentation process, reducing acetaldehyde to ethanol

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alcohol dehydrogenase

Front 846

A mitochondrial enzyme that requires the coenzyme biotin, and functions to convert pyruvate to oxaloacetate

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pyruvate carboxylase

Front 847

This mitochondrial enzyme reduces the oxaloaetate formed from pyruvate to malate at the expense of NADH

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malate dehydrogenase

Front 848

This enzyme converts oxaloacetate to PEP in a Mg<2+>-dependent reation that requires GTP as the phosphoryl group donor, and which is reversible under intracellular conditions

Back 848

phosphorenolpyruvate carboxykinase

Front 849

In gluconeogenesis this Mg<2+>-dependent enzyme promotes the essentially irreveresible hydrolysis of the C-1 phosphate to convert fructose 1,6-bisphosphate to fructose 6-phosphate

Back 849

fructose 1,6-bisphosphatase (FBPase-1)

Front 850

In gluconeogenesis, the production of glucose from glucose 6-phosphate is catalyzed by this enzyme

Back 850

glucose 6-phosphatase

Front 851

Amino acids that can undergo net conversion to glucose are said to be g_________

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glucogenic

Front 852

Adipocytes carry out a truncated version of gluconeogenesis, known as g________________, the conversion of pyruvate to dihydroxyacetone phosphate via the early reactions of gluconeogenesis, followed by reduction of the dihydroxyacetone phosphate to glycerol phosphate.

Back 852

glyceroneogenesis

Front 853

The first reaction of the pentose phosphate pathway is the oxidation of glucose 6-phosphate to form 6-phosphoglucono-delta-lactone by this enzyme

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glucose 6-phosphate dehydrogenase (G6PD)

Front 854

The lactone produced by G6PD in the pentose phosphate pathway is hydrolyzed to the free acid 6-phosphogluconate by a l________

Back 854

lactonase

Front 855

This enzyme oxidates and decaroxylizes 6-phosphogluconate to form the ketopentose ribulose 5-phosphate

Back 855

6-phosphogluconate dehydrogenase

Front 856

In the pentose phosphate pathway, this enzyme converets ribulose 5-phosphate to its aldose isomer, ribose 5-phosphate.

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phosphopentose isomerase

Front 857

This enzyme catalyzes the transfer of a two-carbon fragment from a ketose donor to an aldose acceptor in the pentose phosphate pathway

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transketolase

Front 858

This enzyme catalyzes the reaction similar to the aldolase reaction of glycolysis: a three-carbon fragment is removed from sedoheptolose 7-phosphate and condensed with glyceraldehyde 3- phosphate, forming fructose 6-phosphate and erythrose 4-phosphate.

Back 858

transaldolase

Front 859

The reactions in the pathway whose end products are ribose 5-phosphate, CO2, and NADPH are oxidative, so that the name of the pathway is the o________ p______ p_______ p______

Back 859

oxidative pentose phosphate pathway

Front 860

A process that converts hexose phosphates to pentose phosphates is crucial to photosynthetic assimilation of CO2 by plants is reductive, so that the name of the pathway is the r________ p______ p_______ p______

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reductive pentose phosphate pathway

Front 861

Glycolysis, step 1

Back 861

Phosphorylation of glucose

Front 862

Glycolysis, step 2

Back 862

Conversion of glucose 6-phosphate to fructose 6-phosphate

Front 863

Glycolysis, step 3

Back 863

Phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate

Front 864

Glycolysis, step 4

Back 864

Cleavage of fructose 1,6-bisphosphate (into glyceraldehyde 3- phosphate, and dihydroxyacetone phosphate)

Front 865

Glycolysis, step 5

Back 865

Interconversion of the triose phosphates (dihydroxyacetone phosphate to glyceraldehyde 3-phosphate)

Front 866

Glycolysis, step 6

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Oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate

Front 867

Glycolysis, step 7

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Phosphoryl transfer from 1,3-bisphosphoglycerate to ADP

Front 868

Glycolysis, step 8

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Conversion of 3-phosphoglycerate to 2-phosphoglycerate

Front 869

Glycolysis, step 9

Back 869

Dehydration of 2-phosphoglycerate to phosphoenolpyruvate (PEP)

Front 870

Glycolysis, step 10

Back 870

Transfer of the phosphoryl group from phosphoenolpyruvate to ADP (PEP to pyruvate)