Module 2: Protein Structure and Function

Question 1

What are the three possibilities that can happen to a protein when it is trying to fold?

Answer 1

1. Fold into their correct configuration -i.e. it won’t make a mistake in the first place.
2. Incompletely folded proteins are correctly folded with help of a molecular chaperone protein.
3. If still failed to be corrected, misfolded proteins are recognized for degradation and are digested in proteasome.

Question 2

General principle of chaperones

Answer 2

to prevent inappropriate interactions between amino acid residues and increase the efficiency of protein folding

Question 3

two classes of chaperones

Answer 3

monomeric molecular chaperones and multimeric chaperonin complex

Question 4

Molecular chaperones

Answer 4

monomeric proteins that bind to hydrophobic amino acid residues on a polypeptide and prevent the protein from forming incorrect folds due to hydrophobic interactions in aqueous environment within a protein or with other proteins

Question 5

List three examples of molecular chaperones

Answer 5

Hsp70 in cyotsol and mitochondria
BiP in endoplasmic reticulum
DnaK in bacteria

Question 6

Chaperonins

Answer 6

large, macromolecular complexes containing a collection of proteins that act like a barrel in which an unfolded protein may move into and fold in isolation

Question 7

List three examples of chaperonins

Answer 7

TCiP in cytosol
GroEL in bacteria or chloroplast
Hsp60 in mitochondria

Question 8

three domains of Hsp60

Answer 8

apical domain, intermediate domain and equatorial domain

Question 9

Two steps of protein degradation

Answer 9

1. Tagging proteins by attachement of ubiquitin molecules

2. Degradation of the tagged protein into short peptide sequences by the proteasome

Question 10

Ubiquitinylation

Answer 10

covalent attachement of ubiquitin to the proteins targeted for degradation

Question 11

Three enzymes required for ubiquitinylation

Answer 11

E1: Ubiquitin activating enzyme, E2: Ubiquitin conjugating enzyme, and E3: Ubiquitin ligase

Question 12

What is function of proteins dependent on?

Answer 12

function is dependent on their ability to bind with other molecules - i.e. their structure determines their function

Question 13

Ligand

Answer 13

molecule that is bound by protein

Question 14

two things ligand binding must demonstrate

Answer 14

high affinity and specificity

Question 15

Affinity

Answer 15

strength of binding between protein and ligand, where strength is determined by the amount of time molecules remain binded

Question 16

Specificity

Answer 16

ability of a protein to preferentially bind to one or small number of molecules

Question 17

What does affinity and specificity of an interaction depend upon?

Answer 17

molecular complementary

Question 18

Molecular Complementary

Answer 18

dependent upon non covalent interactions between facing surfaces

Question 19

Shape Complementary

Answer 19

dependent upon whether the shapes of facing surfaces of different molecules fit together

Question 20

cAMP

Answer 20

important regulatory molecule that can module protein function

Question 21

Binding Affinity

Answer 21

• free energy of interaction between a protein (P) and its ligand (L) can vary greatly
• measured by the association constant for the binding equilibrium (Keq)

Question 22

Enzymes

Answer 22

• proteins that catalyze molecular reactions

- reduces free energy at transition state

Question 23

How do enzymes increase rate of reaction?

Answer 23

by lowering activation energy

Question 24

Two functional regions of the active site

Answer 24

Binding site/pocket (determines specificity) and Catalytic site (promotes reaction)

Question 25

Vmax

Answer 25

maximal velocity of a reaction at saturating substrate concentrations

Question 26

What happens to Vmax when two different substrates - one with high affinity interaction with enzyme and another with low affinity interaction, have the same enzyme concentration (constant)?

Answer 26

They will have the same Vmax because regardless of the amount of substrate this is the point at which enzyme-substrate binding pockets are saturated.

Question 27

Michaelis Constant (Km)

Answer 27

• concentration of substrate at which reaction velocity is half maximal
• is a measure of the affinity of an enzyme for the substrate

Question 28

What is the relationship between Km and affinity?

Answer 28

Km has a reciprocal relationship with affinity

Question 29

PKA has two substrates

Answer 29

target protein and nucleotide ATP

Question 30

What is the binding domains in PKA called?

Answer 30

kinase core

Question 31

Six general mechanisms for regulating protein function

Answer 31

Allosteric regulation, covalent modification, proteolytic cleavage, signal-induced regulation of protein levels, compartmentalization, and enzyme complexes formation

Question 32

Allosteric Regulation

Answer 32

modification of protein function by the binding of an effector molecule at a site other than the proteins active site

Question 33

Allosteric modulators

Answer 33

small molecules that bind to sites other than the active site of a protein to modify function

Question 34

Allosteric activators

Answer 34

exerts a positive effect on protein function (i.e. positive modulators)

Question 35

Allosteric Inhibitors

Answer 35

exerts a negative effect on protein function (i.e. negative modulators)

Question 36

The two confirmations that PKA switches in between

Answer 36

Active monomer and inactive tetramer

Question 37

Cooperative Allostery

Answer 37

• specialized form of allosteric modulation
• this is the binding of a ligand to one subunit in a multimeric complex that changes the affinity of all of the subunits for that ligand

Question 38

Haemoglobin

Answer 38

• protein that shows cooperative allostery
• oxygen binding protein found in RBCs
• must have high affinity for oxygen in lungs where it picks up oxygen, and low affinity for oxygen in tissues where it must release oxygen

Question 39

2,3 BPG

Answer 39

• is the allosteric inhibitor of haemoglobin
• is found in high concentrations in the target tissue where it decreases the affinity of haemoglobin for oxygen, further increasing efficiency of oxygen delivery

Question 40

Phosphoregulation

Answer 40

an “on-off” switch for enzymes via the addition or removal of chemical groups

Question 41

Phosphorylation

Answer 41

is an activating event which results in addition of two negative charges

Question 42

Proteolytic cleavage

Answer 42

irreversible mechanism in which mechanism allows a cell to make a lot of protein in an inactive form and then rapidly cleave it at specific points to activate it

Question 43

Two efficient ways for enzyme complex formation

Answer 43

1. All three enzymes may bind to form multimeric complex.

2. Addition of scaffold protein to which the three enzymes can bind to.