Kapitel 3

Question 1

Region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction. (Figure 1–7)

Answer 1

active site

Question 2

Protein in which allosteric changes in conformation alter the activity of the protein and enable it to serve as a general switch allowing one molecule in a cell to affect the fate of another.

Answer 2

allosteric protein

Question 3

Change in a protein’s conformation brought about by the binding of a regulatory ligand (at a site other than the protein’s catalytic site) - or by covalent modification. The change in conformation alters the activity of the protein and can form the basis of directed movement. (Figures 3–57 and 16–29)

Answer 3

allostery (adjective allosteric)

Question 4

Common folding pattern in proteins - in which a linear sequence of amino acids folds into a right-handed helix stabilized by internal hydrogen-bonding between backbone atoms. (Figure 3–7)

Answer 4

alpha helix (α helix)

Question 5

Self-propagating - stable β-sheet aggregates built from hundreds of identical polypeptide chains that become layered one over the other to create a continuous stack of β sheets. The unbranched fibrous structure can contribute to human diseases when not controlled.

Answer 5

amyloid fibrils

Question 6

Protein secreted by activated B cells in response to a pathogen or foreign molecule. Binds tightly to the pathogen or foreign molecule - inactivating it or marking it for destruction by phagocytosis or complement-induced lysis. (Figure 24–23)

Answer 6

antibody

Question 7

Protein produced by B cells in response to a foreign molecule or invading microorganism. Binds tightly to the foreign molecule or cell - inactivating it or marking it for destruction by phagocytosis or complement-induced lysis.

Answer 7

antibody (immunoglobulin - Ig)

Question 8

Any molecule that can induce an adaptive immune response or that can bind to an antibody or T cell receptor.

Answer 8

antigen

Question 9

Common structural motif in proteins in which different sections of the polypeptide chain run alongside each other - joined together by hydrogen-bonding between atoms of the polypeptide backbone. Also known as a β pleated sheet. (Figure 3–7)

Answer 9

beta sheet (β sheet)

Question 10

Region on the surface of one molecule (usually a protein or nucleic acid) that can interact with another molecule through noncovalent bonding.

Answer 10

binding site

Question 11

Small molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes - often by forming a covalent bond to the substrate. Examples include biotin - NAD+ - and coenzyme A.

Answer 11

coenzyme

Question 12

Especially stable rodlike protein structure formed by two or more α helices coiled around each other. (Figure 3–9)

Answer 12

coiled-coil

Question 13

The folded - three-dimensional structure of a polypeptide chain.

Answer 13

conformation

Question 14

Portion of a protein that has a tertiary structure of its own. Larger proteins are generally composed of several domains - each connected to the next by short flexible regions of polypeptide chain. Homologous domains are recognized in many different proteins.

Answer 14

domain (protein domain)

Question 15

Ratio of forward and reverse rate constants for a reaction. Equal to the association or affinity constant (Ka) for a simple binding reaction (A + B ⇌ AB). (Figure 3–44)

Answer 15

equilibrium constant (K)

Question 16

The process in which a product of a reaction feeds back to inhibit a previous reaction in the same pathway. (Figures 3–55 and 3–56)

Answer 16

feedback inhibition

Question 17

Also called GTPase; an enzyme that converts GTP to GDP.

Answer 17

GTP-binding protein

Question 18

An enzyme that converts GTP to GDP. GTPases fall into two large families. Large trimeric Gproteins are composed of three different subunits and mainly couple GPCRs to enzymes or ion channels in the plasma membrane. Small monomeric GTP-binding proteins (also called monomeric GTPases) consist of a single subunit and help relay signals from many types of cell-surface receptors and have roles in intracellular signaling pathways - regulating intracellular vesicle trafficking - and signaling to the cytoskeleton. Both trimeric G proteins and monomeric GTPases cycle between an active GTP-bound form and an inactive GDP-bound form and frequently act as molecular switches in intracellular signaling pathways. See page 820.

Answer 18

GTPase

Question 19

Any molecule that binds to a specific site on a protein or other molecule. From Latin ligare - to bind.

Answer 19

ligand

Question 20

In ligand binding - the conformational coupling between two separate ligand-binding sites on a protein - such that a conformational change in the protein induced by binding of one ligand affects the binding of a second ligand.

Answer 20

linkage

Question 21

Enzyme that catalyzes the cutting of polysaccharide chains in the cell walls of bacteria.

Answer 21

lysozyme

Question 22

Repeating sequence of atoms along the core of the polypeptide chain.

Answer 22

polypeptide backbone

Question 23

Linear sequence of monomer units in a polymer - such as the amino acid sequence of a protein.

Answer 23

primary structure

Question 24

Transmissible spongiform encephalopathy—such as Kuru and Creutzfeldt–Jakob disease (CJD) in humans - scrapie in sheep - and bovine spongiform encephalopathy (BSE - or “mad cow disease”) in cows—that is caused and transmitted by an infectious - abnormally folded protein (prion). (Figure 3–33)

Answer 24

prion disease

Question 25

See domain

Answer 25

protein domain

Question 26

Enzyme that transfers the terminal phosphate group of ATP to one or more specific amino acids (serine - threonine - or tyrosine) of a target protein.

Answer 26

protein kinase

Question 27

An individual protein chain in a protein composed of more than one chain.

Answer 27

protein subunit

Question 28

Study of all the proteins - including all the covalently modified forms of each - produced by a cell - tissue - or organism. Proteomics often investigates changes in this larger set of proteins—in “the proteome”—caused by changes in the environment or by extracellular signals.

Answer 28

proteomics

Question 29

Three-dimensional relationship of the different polypeptide chains in a multisubunit protein or protein complex.

Answer 29

quaternary structure

Question 30

Region of an enzyme surface to which a regulatory molecule binds and thereby influences the catalytic events at the separate active site.

Answer 30

regulatory site

Question 31

Protein that binds groups of intracellular signaling proteins into a signaling complex - often anchoring the complex at a specific location in the cell. (Figure 15–10)

Answer 31

scaffold protein

Question 32

Regular local folding pattern of a polymeric molecule; in proteins - α helices and

Answer 32

secondary structure

Question 33

The part of an amino acid that differs between amino acid types. The side chains give each type of amino acid its unique physical and chemical properties. (Panel 3–1 - pp. 112–113)

Answer 33

side chain

Question 34

Complex three-dimensional form of a folded polymer chain - especially a protein or RNA molecule.

Answer 34

tertiary structure

Question 35

Structure that forms transiently in the course of a chemical reaction and has the highest free energy of any reaction intermediate. Its formation is a rate-limiting step in the reaction. (Figure 3–47)

Answer 35

transition state

Question 36

Small - highly conserved protein present in all eukaryotic cells that becomes covalently attached to lysines of other proteins. Attachment of a short chain of ubiquitins to such a lysine can tag a protein for intracellular proteolytic destruction by a proteasome. (Figure 3–69)

Answer 36

ubiquitin

Question 37

Any one of a large number of enzymes that attach ubiquitin to a protein - often marking it for destruction in a proteasome. The process catalyzed by a ubiquitin ligase is called ubiquitylation. (Figure 3–71)

Answer 37

ubiquitin ligase