Kaplan Biochemistry: Chapter 3 Protein Functions

Question 1

What is Kd

Answer 1

Kd is the dissociation constant. It tells you how well a specific substrate will bind to the enzyme.

E + S ES -> E + P

Kd= [E][S]/[ES]

The smaller the Kd, the stronger the Substrate is bound to the Enzyme.

Question 2

What is Kcat

Answer 2

Kcat is the rate of reaction of the enzyme; turnover of substrate to product / unit time.

Vmax = Kcat [Enzyme]

Question 3

what is a hydrolase

Answer 3

an enzyme that catalyzes the hydrolysis of a particular substrate.

Question 4

a hydroxylase is a type of enzyme within a broader category of enzymes called:

Answer 4

oxidoreductases.

Question 5

The protein channel Na+/K+ ATPase exchanges ___ Na+ for ___ K+

Answer 5

3 Na+ out; 2 K+ in

• maintains an overall negative charge inside the cell.

Question 6

what is the primary structure of a protein

Answer 6

peptide bonds. the amino acid sequence

Question 7

what forces stabilize the secondary structure of a protein

Answer 7

stabilized by H bonding between backbone molecules in the alpha helix of beta pleated sheet conformation

Question 8

what forces stabilize the tertiary and quarternary structure of a protein

Answer 8

stabilized by the side chain interactions: H bonding, disulfide bonds, dipole dipole bonds.

Question 9

a competitive inhibitor graph looks like:
What state does the comp inhibitor bind to?
what kinetic parameters are constant? Which varies?

Answer 9

-looks like a cross over at the y axis
binds to ENZYME ONLY
Km increases, Vmax is constant

Question 10

an UNcompetitive inhibitor graph looks like:
What state does the UNcomp inhibitor bind to?
what kinetic parameters are constant? Which varies?

Answer 10

-looks like two parallel lines
binds to E-S
Km decreases, Vmax decreases

Question 11

a NONcompetitive inhibitor graph looks like:
What state does the NONcomp inhibitor bind to?
what kinetic parameters are constant? Which varies?

Answer 11

a non comp inhibitor crosses over at the x axis.
binds to ES or E
Km stays the same, Vmax decreases.

Question 12

What is suicide inhibition

Answer 12

irreversible enzyme inhibition. Usually inhibits via covalent bond-hard to break.

Question 13

kinesin brings vesicles towards the ___ end of the microtubule

Answer 13

POSITIVE end. Ex/ to the synaptic terminal— positive end is the end where the microtubules DIDN’T originate from.

Question 14

Dyneins bring vesicles towards the ___ end

Answer 14

NEGATIVE ends. Ex/ towards the SOMA.

Question 15

homotropic regulation

Answer 15

when a molecule serves as a substrate for its target enzyme, as well as a regulatory molecule of the enzyme’s activity.

Question 16

3 possible outcomes when an antibody binds to its antigen

Answer 16

1) neutralizing the antigen: making the pathogen unable to exerts its effects
2) opsonization: marking the pathogen for immediate destruction by WBCs
3) agglutinating: clumping together the antigen and antibody into large INSOLUBLE protein complexes that can be phagocytized by macrophages.

Question 17

____ are Ca2+ mediated glycoproteins that hold similar types of cells together.

Answer 17

Cadherin

Question 18

in G proteins, when____ is replaced with ___-, the alpha subunit is able to dissociate from the beta and gamma subunits.

Answer 18

when GDP is replaced with GTP.

Question 19

in Native PAGE, the negative charge proteins will migrate:

Answer 19

towars the positive charge electode. therefore, native page varies with mass-to-charge ratio and mass-to-size ratio.

Question 20

SDS PAGE separates proteins on the basis of ___

Answer 20

mass. SDS page coats the entire protein so it is all negative. charge doesn’t matter, they will all migrate to the same pole. but the larger proteins will not migrate as fast on the gel.

Question 21

what is isoelectric focusing

Answer 21

protein separation based on isoelectric point. when the protein is neutral.

Question 22

in isoelectric focusing, what acts as the anode? as the cathode?

Answer 22

acidic gel is at the POSITIvE anode (its electrochemical cell), and basic gel is at the NEGATIVE cathode. it is neutral in the middle of the gel.

proteins that are + charged will begin to migrate to the cathode where the basic gel is. the proteins that are negatively charged will begin migrating toward the anode, where the acidic gel is.

Question 23

in anion exhange chromatography, the column is ____ charged. What charge elutes faster?

Answer 23

column is POSITIVELY charged. attracts the negative proteins. POSTIVE charged particles will elute faster.

therefore, in anion exchange chromatography, you exchange anions for positive ions.

Question 24

in size exclusion chromatography, which sized proteins elut faster?

Answer 24

larger proteins elute faster.

Question 25

what type of protein would be best seen under UV spec?

Answer 25

aromatic proteins. UV light excites the conjugated systems of double bonds.