3D Protein Structure

Question 1

Describe peptide bond formation

Answer 1

OH from carboxyl group leaves and binds with H from amine group of neighboring amino acid to form water will amide bond forms between remaining C and N

Question 2

Secondary structure

Answer 2

Think local folds

alpha helix, beta sheets, beta turns

Question 3

Important about peptide bond in protein structure

Answer 3

resonance form puts 6 atoms in a plane

Question 4

Phi and psi

Answer 4

Rotation angles around alpha carbons

Favors trans configuration

Question 5

3 forms of secondary structures

Answer 5

Alpha helix - densely packed, R groups are sticking out & are not involved so can be formed regardless of sequence, can be amphipathic to interact with different molecules

Beta sheet - loosely packed, antiparallel, R groups alternate & are not involved so can be formed regardless of sequence, can be amphipathic to interact with different molecules

Beta turn - held by H-bonds, 4 carbons make the turn, R-groups not very involved so can be formed regardless of sequence

Question 6

What secondary structures are amphipathic

Answer 6

Beta sheet & alpha helix

Question 7

Name the biggest force holding together the proteins in an aqueous solution. Where could this present as an example?

Answer 7

Hydrophobic, makes sense since it is aqueous

In the cytoplasm of a cell because it is watery

Question 8

Name all forces at work in protein structure

Answer 8

Hydrophobic interactions
Electrostatic interactions
H-bonds
Disulfide bonds

Question 9

What are some common parallel beta-sheet folds?

Answer 9

Saddle sheets - twisted, saddle shape
Barrel sheets - fold and twist into a round barrel shape

These are common folds in different major types of proteins and are not indicative of protein chemical make-up per se

Question 10

What are lipid proteins primarily driven by when folding?

Answer 10

Hydrophobic interaction (ex. bacteriorhodopsin)

Question 11

EXAMPLE OF LIPID PROTEIN:

Describe porin

Answer 11

Lipid protein that acts as a pore by having a hydrophobic exterior and a hydrophilic pore on the interior

Question 12

EXAMPLE OF LIPID PROTEIN:

How can an alpha helix be inserted into a hydrophobic lipid membrane?

Answer 12

By its hydrophobic amino acid side chains (ex. prostaglandin H2 synthase)

Question 13

Where do membrane anchors come from?

Give examples

Answer 13

Post-translational modifications
Phosphorylation
Glycosylation
Acetylation
Methylation

Question 14

What is significant about post-translational modifications in lipids?

Answer 14

They provide anchoring for the protein into the lipid membrane

Question 15

What is an important characteristic of proteins? Explain

Answer 15

They are dynamic:

Polypeptide flexibility
Alternative conformations (Hb)
Intrinsically unstructured - disordered to some extent

Question 16

Describe the folding pathway

Classes of helpers

Answer 16

There are a variety of enzymes and other mechanisms to assist in correct folding

disuflide isomerases, peptidyl isomerases chaperonins, chaperones

Question 17

Describe the protein problem in patients with cystic fibrosis

Answer 17

Disease of protein folding kinetics: folding happens too slowly and so checkpoint enzymes think that these proteins are messed up and begin to degrade them

Question 18

Describe the protein problem in patients with sickle cell disease

Answer 18

Disease of protein aggregation: One mutation causes lack of O2 binding and thus a hydrophobic patch to be exposed. Protein consequently wants to get out of aqueous environment. It panics and quickly binds to another protein. When many do this a sickle-cell forms

Question 19

Describe the protein problem with Hungtington’s disease

Answer 19

Disease of abnormal protein-protein interaction: protein that encodes has a lot of glutamines in a row, but when the run of glutamines gets above 39 (normal is 6-39), Huntington’s start to set in

Question 20

What other disease is thought to develop from abnormal protein-protein interactions?

Answer 20

Alzheimer’s

Question 21

What are examples of quaternary proteins?

Answer 21

Hemoglobin and myoglobin

Question 22

What is heme?

Answer 22

A tightly-bound (prosthetic group) cofactor in hemoglobin and in myoglobin that binds O2