KH 05

Question 1

Proteins perform an extraordinarily diverse array of activities both inside and outside cells, yet most of these diverse functions are based on the ability of proteins to engage in a common activity, which is?

Answer 1

Binding. Proteins bind to one another, to other macromolecules, to small molecules, and to ions.

Question 2

How do we call the molecule to which a protein binds?

Answer 2

Its ligand

Question 3

In some cases, ligand-binding changes the _____ of the protein.

Answer 3

conformation. This ligand-induced conformational change is integral to the mechanism of action of many proteins.

Question 4

What are the 2 properties that are of primary importance in ligand-binding?

Answer 4

Specificity and affinity

Question 5

What is specificity?

Answer 5

The ability of a protein to bind only one particular ligand, even in the presence of a vast excess of irrelevant molecules.

Question 6

What is affinity?

Answer 6

The tightness, or strength of binding, expressed as dissociation constant (Kd). The stronger the interaction, the lower the Kd.

Question 7

What is binding?

Answer 7

An interaction between complementary molecular surfaces.

Question 8

Protein binding specificity arises from numerous interactions which are individually _____, but, if numerous, collectively _____.

Answer 8

weak, strong

Question 9

What are antibodies?

Answer 9

Antibodies are proteins that circulate in the blood and are made by the immune system in response to antigens, which are usually macromolecules present in infectious agents. They bind to the antigen’s epitope.

Question 10

How are antibodies shaped?

Answer 10

Antibodies are Y-shaped molecules, often formed from two identical longer, or heavy, chains and two identical shorter, or light, chains. Near the end of each arm are six highly variable loops, called complementarity-determining regions (CDRs), which form the antigen-binding sites. The sequences of these six loops are highly variable in amino acid sequence among antibodies, generating unique complementary ligand-binding sites that make them specific for different epitopes.

Question 11

What are enzymes?

Answer 11

Enzymes are an extremely diverse class of catalytically active proteins whose ligands include the substrates of the reactions they catalyze .

Question 12

Where does substrate binding and reaction catalysis occcur?

Answer 12

At the enzyme’s active site.

Question 13

What does substrate specificity arise from?

Answer 13

The substrate binding site

Question 14

The substrate, and the substrate binding site interact at _____ molecular surfaces.

Answer 14

complementary

Question 15

An active site consists of two functionally important regions: the _____ site, which recognizes and binds the substrate or substrates, and the _____ site, which carries out the chemical reaction once the substrate has bound.

Answer 15

substrate-binding, catalytic

Question 16

What is the Vmax (maximal velocity)?

Answer 16

The maximal rate of catalysis given saturating amounts of substrate. Depends on the amount of enzyme and how fast it can work – the turnover number.

Question 17

What is the Km (Michaelis constant)?

Answer 17

The substrate concentration that supports a rate of catalysis equal to one-half of the Vmax. Depends on, and is a measure of, the affinity of enzyme-substrate
binding.

Question 18

What is the turnover number?

Answer 18

Enzymatic cycles per second at top speed.

Question 19

What is an example of enzyme substrate-binding and catalytic site details?

Answer 19

The serine protease trypsin

Question 20

What do proteases do in polypeptides?

Answer 20

They hydrolyze peptide bonds.

Question 21

What is the family of proteases whose catalytic mechanism involves a serine residue in the catalytic site?

Answer 21

The serine proteases

Question 22

What are proteases?

Answer 22

Enzymes that perform proteolysis (break down proteins into smaller polypeptides or single amino acids).

Question 23

Protein folding brings “distant” amino acids into _____.

Answer 23

proximity

Question 24

What is an enzyme that has a 2-step catalytic mechanism involving 3 amino acid side chains
Asp-102, His-57, and Ser-195 (N.B., not closely positioned in linear protein sequence)?

Answer 24

Trypsin

Question 25

What 2 things can enzyme pH optima reflect?

Answer 25

1. Active site acid-base chemistry
2. Sensitivity of overall protein conformation to charge distribution

Question 26

How many different active sites does the mammalian fatty acid synthase polypeptide have?

Answer 26

It has 7 active sites that catalyze sequential steps in fatty acid synthesis.

Question 27

What is the allosteric effect?

Answer 27

The binding of a ligand at one site on a protein can lead to conformational changes that affect the binding of another ligand molecule at a different site.

Question 28

What is an example of the allosteric effect?

Answer 28

The nature of the ligand bound to the nucleotide-binding domain of the molecular chaperone Hsp70, i.e., ATP versus ADP, affects the conformation of the substrate-binding domain, which changes its interactions with the misfolded “client” protein.

Question 29

A major manifestation of allosteric effects is in _____ _____ in regulatory proteins in response to ligand binding or post-translational modification.

Answer 29

conformational switches

Question 30

What does “allostery” refer to?

Answer 30

It refers to any change in a protein’s tertiary or quaternary structure, or in both, induced by the noncovalent binding of a ligand.

Question 31

Non-covalent binding of ___ and ___ are widely used as allosteric switches to control protein activity
(important in cellular signal transduction pathways)

Answer 31

Ca++, GTP

Question 32

What do allosteric switches do?

Answer 32

Allosteric switches turn the activity of many different proteins on or off by binding to them non-covalently.

Question 33

What is phosphorylation?

Answer 33

The addition of a phosphate group to a molecule.

Question 34

What is dephosphorylation?

Answer 34

The removal of a phosphate group to a molecule.

Question 35

Phosphorylation is catalyzed by enzymes called _____ _____.

Answer 35

protein kinases

Question 36

Dephosphorylation is catalyzed by enzymes called _____ _____.

Answer 36

protein phosphatases

Question 37

Phosphorylation of amino acid side chains,
a rapidly reversible _____ modification of protein structure.

Answer 37

covalent!

Question 38

What is an example of post-translational modification?

Answer 38

Modification of protein conformation and activity through
phosphorylation and dephosphorylation

Question 39

What is frequently used in cellular signal transduction pathways?

Answer 39

Phosphorylation and dephosphorylation

Question 40

How many different protein kinases does the human genome encode?

Answer 40

More than 500. Many are specific for just one, or a few, specific target proteins.

Question 41

Frequently the target of a kinase or a phosphatase is another kinase or phosphatase, creating a “_____” effect.

Answer 41

cascade. Such kinase cascades permit amplification of a signal and many levels of fine-tuning.

Question 42

The Nobel Prize in Physiology or Medicine 1992 was awarded jointly to Edmond H. Fischer and Edwin G. Krebs. What was their discovery?

Answer 42

They were awarded the Nobel Prize for their discoveries concerning reversible protein phosphorylation as a
biological regulatory mechanism.