Ch 4: Protein Structure and Function

Question 1

Allosteric proteins

Answer 1

Most enzymes are allosteric proteins, which means they can exixt in two conformations that differ in catalytic activity. The enzyme activity can be turned on or off by ligands that bind to a distinct region to either stabilize the active or inactive conformation of the protein

Question 2

What is feedback inhibition?

Answer 2

One of the most common ways to regulate enzyme activity where an enzyme early in a metabolic pathway is inhibited by the binding of one of the pathway’s end products

Question 3

Phosphorylation and dephosphorylation

Answer 3

How many proteins are regulated in eukaryotic cells. Catalyzed by a protein kinase (phosphorylation), or a protein phosphatase (dephosphorylation)

Regulates the protein by altering the activity or properties of the target protein

Question 4

Primary structure of a protein

Answer 4

The amino acid sequence

Question 5

Secondary structure of a protein

Answer 5

Regular folding patterns in a polymer (aka a helixes and beta sheets)

Question 6

Tertiary structure of a protein

Answer 6

Complete three dimensional structure of a fully folded protein

Question 7

Quaternary structure of a protein

Answer 7

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

Question 8

Antibody

Answer 8

protein produced by b lymphocytes in response to a foreign molecule or invading organism. Binds to that organism, inactivating it or marking it for destruction

Question 9

Antigen

Answer 9

something that is recognized by an antibody

Question 10

Binding site

Answer 10

region on the surface of a protein (usually a cavity or groove) that interacts with another molecule (a ligand) through the formation of multiple non covalent bonds

Question 11

disulfide bond

Answer 11

covalent cross-link between two sulfhydryl groups on teh ocystein side chains that are often used to reinforce a proteins structure or join two proteins together

Question 12

C terminus

Answer 12

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

Question 13

lysosyme

Answer 13

enzyme that severs the polysaccharide chains that form the cell walls of bacteria

Found in many secretions such as saliva and tears, so it acts as an antibiotic

Question 14

N terminus

Answer 14

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

Question 15

peptide bond

Answer 15

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

Question 16

Polypeptide backbone

Answer 16

repeating sequence of the atoms -N-C-C that forms the core of a protein molecule and to which the amino acid side chains are attached

Question 17

protein domain

Answer 17

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

Question 18

protein kinase

Answer 18

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

Question 19

protein phosphatase

Answer 19

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

Question 20

transition state

Answer 20

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

Question 21

Protein molecules that have a quaternary structure will always have two or more of which of the following?

Answer 21

Protein domains: they will contain multiple polypeptide chains or subunits, each of which will be formed from one or more protein domains

Question 22

What does the primary structure of a protein refer to?

Answer 22

The linear amino acid sequence of a protein

Question 23

Indicate whether the following is true or false and why:
Chaperone proteins provide the energy needed for a protein to fold into the correct conformation

Answer 23

False, because protein folding is an energetically favorable process and so does not require in input of outside energy. Chaperon proteins assist with folding, but not by providing energy.

Question 24

Enzymes alter teh speed of a reaction without affecting the overall energy (thermodynamics) of its reactants or produces. Enzymes accomplish this by doing what?

Answer 24

Reducing the activation energy of a reaction.

Question 25

What is true and what is false about enzymes?

Answer 25

True: they can bring reactants together in the proper orientation for chemistry to occur.
False: They usually require an input of energy from ATP for activation
True: They can form covalent bond with their substrates
True: They can change the shape of substrates to increase the rate of a particular reaction

Question 26

What determines the specificity an antibody has for it antigen?

Answer 26

Polypeptide loops in its variable domains

Question 27

How do most motor proteins ensure that their movements are unidirectional?

Answer 27

They couple a conformational change to the hydrolysis of an ATP molecule, which makes the reaction very difficult to reverse.

Question 28

What correctly describes phosphorylation of a protein?

Answer 28

It can increase or decrease a protein’s activity, depending on the site of the phosphorylation and the structure of the protein.

Question 29

How does phosphorylation control protein activity?

Answer 29

The phosphate group induces a change in the the proteins conformation. This is one way to regulate protein activity.