Lecture 6 (Protein Function)

Question 1

Ligand Binding Sites

Answer 1

Accepts, interacts, and reacts with another molecule through the formation of multiple non-covalent bonds.

Question 2

An enzyme that does have two adjacent amino acids in the active site is ______

Answer 2

The enzyme binding cyclic AMP

Question 3

Lysozyme Mechanism

Answer 3

Cleaves the glycosidic bond between NAM and NAG sugars. The sugars are attached in a Beta 1-4 conformation. The amino acids that participate in the cleavage reaction are Asp 52 and Glu 38. Glu donates a proton to the glycosydic bond oxygen and causes a carbocation species to be created

Question 4

True or False. Lysozyme can catalyze glycosidic cleavage of gram negative bacteria.

Answer 4

FALSE. Gram negative bacteria do not have the peptidoglycan membrane exposed like gram positive bacteria. In gram negative bacteria, the thin peptidoglycan layer is sandwiched between inner and outer membranes. it’s hard for lysozyme to get in there.

Question 5

Hemoglobin

Answer 5

Conformational change when ligand binding occurs. Exhibits cooperative binding to oxygen.

Question 6

Allostery

Answer 6

Process by which biological molecules transmit the effect of binding at one site to another, often distal, functional site, allowing for regulation of activity. The binding of effectors to allosteric sites results in a conformational change.

Question 7

Give an example of allosteric regulation

Answer 7

Product inhibition. This would be negative regulation

Question 8

What molecule acts as a negative regulator in aspartate carbamoyltransferase?

Answer 8

CTP. A direct product inhibition. Aspartate carbamoyltransferase acts in pyrimidine base synthesis. Bound CTO causes conformational change that hides the active site

Question 9

Phosphorylation and dephosphorylation

Answer 9

Control protein function by reversible phosphorylation. Default is dephosphorylation.

Question 10

True or false. Phosphorylation can only activate proteins, not deactivate them.

Answer 10

FALSE. Phosphorylation can both activate or deactivate a protein.

Question 11

Elongation Factor Tu

Answer 11

Found in prokaryotes. A GTPase switch protein. Escorts amino acyl tRNA to the A site of the ribosome. when correct codon anticodon binding occurs, GTP is hydrolized and EF-Tu releases the tRNA

Question 12

Cyclin Dependent Protein Kinase

Answer 12

Some proteins integrate signals through subunit interactions. One phosphate is an inhibitor while another is an activator. The cyclin, the activator phosphate must be attached in order to turn on activity. The inactivating Pi must be off.

Question 13

Src gene

Answer 13

Encodes a mutant tyrosine kinase that attaches phosphate groups to the amino acid tyrosine in host cell proteins

Question 14

SH3 Domains

Answer 14

Found on RSV. Binds to proline rich sequences.

Question 15

SH2 domain

Answer 15

Binds to phospho-tyrosine residues

Question 16

What are all the domains in the Reus Sarcoma Virus?

Answer 16

There are four total domains. The SH3 domain. The SH2 domain. Large Kinase Domain and Small kinase domain

Question 17

Besides 4 domains, what other molecules are found in the Reus Sarcoma Virus

Answer 17

An ATP

Question 18

Describe the sequence of events in Src activity.

Answer 18

1) The phoshate leaves Phospho-tyrosine bound to SH2 causing a loosening of the structure.
2) Activator with proline rich sequences binds to SH3, along with another phospho-tyrosine in SH2.
3) Freed activating site is opened and phosphorylation of the activating loop occurs

Question 19

Heat Shock proteins

Answer 19

Family of proteins that are produced by cells in response to exposure to stressful conditions. Many members of this family perform chaperone function by stabilizing new proteins to endure correct folding.

Question 20

HSP and damaged proteins

Answer 20

Heat shock proteins help guide proteins that have been damaged by heat shock back to their proper conformation