Ch 4 - Protein Structure and Function

Question 1

active site

Answer 1

region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation

Question 2

allosteric

Answer 2

describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site; such changes from one conformation to another often alter the protein’s activity or ligand affinity

Question 3

α helix (alpha helix)

Answer 3

folding pattern, common in many proteins, in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid

Question 4

amino acid sequence

Answer 4

the order of the amino acid subunits in a protein chain. sometimes called the primary structure of a protein

Question 5

antibody

Answer 5

protein produced by B lymphocytes in response to a foreign molecule or invading organism. binds to the foreign molecule or cell extremely tightly, thereby inactivating it or marking it for destruction

Question 6

antigen

Answer 6

molecule or fragment of a molecule that is recognized by an antibody

Question 7

β sheet (beta sheet)

Answer 7

folding pattern found in many proteins in which neighbouring regions of the polypeptide chain associate side-by-side with each other through hydrogen bonds to give a rigid flattened structure

Question 8

binding site

Answer 8

region on the surface of a protein, typically a cavity or groove, that interacts with another molecule (a ligand) through the formation of multiple noncovalent bonds

Question 9

C-terminus

Answer 9

the end of a polypeptide chain that carries a free carboxyl group (-COOH)

Question 10

chromatography

Answer 10

technique used to separate the individual molecules in a complex mixture on the basis of their size, charge, or their ability to bind to a particular chemical group. in a common form of the technique, the mixture is run through a column filled with a material that binds the desired molecule, and it is then eluted from the column with a solvent gradient.

Question 11

coenzyme

Answer 11

small molecule that binds tightly to an enzyme and helps it to catalyze a reaction

Question 12

coiled-coil

Answer 12

stable, rodlike protein structure formed when two or more α helices twist repeatedly around each other

Question 13

conformation

Answer 13

precise, three-dimensional shape of a protein or other macromolecule based on the spatial location of its atoms in relation to one another

Question 14

cryoelectron microscopy (cryo-EM)

Answer 14

technique for observing the detailed structure of a macromolecule at very low temperatures after freezing native structures in ice

Question 15

disulfide bond

Answer 15

covalent cross-link formed between the sulfhydryl groups on two cysteine side chains; often used to reinforce a secreted protein’s structure or to join two different proteins together

Question 16

electrophoresis

Answer 16

technique for separating a mixture of proteins or DNA fragments by placing them on a polymer gel and subjecting them to an electric field. the molecules migrate through the gel at different speeds depending on their size and net charge

Question 17

enzyme

Answer 17

a protein that catalyzes a specific chemical reaction

Question 18

feedback inhibition

Answer 18

a form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway

Question 19

fibrous protein

Answer 19

a protein with an elongated, rodlike shape, such as collagen or a keratin filament

Question 20

globular protein

Answer 20

any protein in which the polypeptide folds into a compact, rounded shape. includes most enzymes

Question 21

GTP -binding protein

Answer 21

intracellular signaling protein whose activity is determined by its association with either GTP or GDP. includes both trimeric G proteins and monomeric GTPases, such as Ras

Question 22

helix

Answer 22

an elongated structure whose subunits twist in a regular fashion around a central axis, like a spiral staircase

Question 23

intracellular condensate

Answer 23

a large aggregate of phase-separated macromolecules that creates a region with a special biochemistry without the use of an encapsulating membrane

Question 24

intrinsically disordered-sequence

Answer 24

region in a polypeptide chain that lacks a definite structure

Question 25

ligand

Answer 25

general term for a small molecule that binds to a specific site on a macromolecule

Question 26

lysozyme

Answer 26

enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears, where it serves as an antibiotic

Question 27

mass spectrometry

Answer 27

sensitive technique that enables the determination of the exact mass of all the molecules in a complex mixture

Question 28

Michaelis constant (Km)

Answer 28

the concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound

Question 29

motor protein

Answer 29

protein such as myosin or kinesin that uses energy derived from the hydrolysis of a tightly bound ATP molecule to propel itself along a protein filament or polymeric molecule

Question 30

nuclear magnetic resonance (NMR) spectroscopy

Answer 30

technique used for determining the three-dimensional structure of a protein in solution

Question 31

N-terminus

Answer 31

the end of a polypeptide chain that carries a free α-amino group

Question 32

peptide bond

Answer 32

covalent chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid.

Question 33

polypeptide, polypeptide chain

Answer 33

linear polymer composed of multiple amino acids. proteins are composed of one or more polypeptide chains.

Question 34

primary structure

Answer 34

the amino acid sequence of a protein

Question 35

protein domain

Answer 35

segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function.

Question 36

protein family

Answer 36

a group of polypeptides that share a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins

Question 36

protein

Answer 36

macromolecule built from amino acids, that provides cells with their shape and structure and performance most of their activities

Question 37

protein machine

Answer 37

assembly of protein molecules that operates as a cooperative unit to perform a complex series of biological activities, such as replicating DNA

Question 38

protein kinase

Answer 38

enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein

Question 39

protein phosphatase

Answer 39

enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site

Question 40

protein phosphorylation

Answer 40

the covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alter the activity or properties of the target protein

Question 41

quaternary structure

Answer 41

complete structure formed by multiple, interacting polypeptide chains that form a larger protein molecule

Question 42

scaffold protein

Answer 42

protein with multiple binding sites for other macromolecules, holding them in a way that speeds up their functional interactions

Question 43

secondary structure

Answer 43

regular local folding pattern of a polymeric molecule. in proteins, it refers to α helices and β sheets

Question 44

side chain

Answer 44

portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid unique properties

Question 45

substrate

Answer 45

a molecule on which an enzyme acts to catalyze a chemical reaction

Question 46

subunit

Answer 46

a monomer that forms part of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid. can also refer to a complete molecule that forms part of a larger molecule. many proteins, for example, as composed of multiple polypeptide chains, each of which is called a protein subunit

Question 47

tertiary structure

Answer 47

complete three-dimensional structure of a fully folded protein

Question 48

transition state

Answer 48

transient structure that forms during the course of a chemical reaction; in this configuration, a molecule has the highest free energy; it is no longer the substrate, but it is not yet the product

Question 49

turnover number

Answer 49

the maximum number of substrate molecules that an enzyme can convert into product per second

Question 50

Vmax

Answer 50

the maximum rate of an enzymatic reaction, reached when the active sites of all of the enzyme molecules in a sample are fully occupied by substrate

Question 51

x-ray crystallography

Answer 51

technique used to determine the three-dimensional structure of a protein molecule by analyzing the diffraction pattern produced when a beam of x-rays is passed through an ordered array of the protein