Intro to Protein Structure

Question 1

define protein

Answer 1

group of organic compounds composed of 1 or more A.A chains and form essential part of all living life

Question 2

what is the simplest A.A and what is its R group?

Answer 2

glycine-R group is H

Question 3

What are lysine and arginine at physiological pH?

Answer 3

protonated and basic

Question 4

When is histidine protonated?

Answer 4

below pH 6

Question 5

What are glutamic acid and aspartic acid at physiological pH?

Answer 5

negatively charged

Question 6

What chiral form are all A.A in?

Answer 6

L-form

Question 7

Peptide bond characteristics

Answer 7

no rotation round bond, C=O and N-H in same plane, other 2 bonds can rotate, side chains can’t clash with main chain (steric hindrance)

Question 8

What is the strongest bond in a protein?

Answer 8

covalent

Question 9

What type of bond is disulphide bridges?

Answer 9

covalent

Question 10

What are ionic interactions?

Answer 10

electrostatic attractions between charged side chains

Question 11

When are ionic interactions especially strong?

Answer 11

when ion pairs are in protein interior and excluded from water

Question 12

Where are the majority of charged groups on a protein and what happens to them?

Answer 12

surface of protein and they get neutralised

Question 13

What are hydrophobic interactions?

Answer 13

hydrophobic core and hydrophilic surface as hydrophobic side chains packed into centre of protein

Question 14

Why do Van der Waals still have an effect on protein conformation if they’re so weak?

Answer 14

large number of them

Question 15

What is the alpha helix stabilised by?

Answer 15

H bonds between C=O and N-H

Question 16

Which handed helices are favoured and why?

Answer 16

Right handed because A.A are L-form.

Question 17

How many A.A along the helix stabilise the structure?

Answer 17

4

Question 18

What bond hold 2 or more beta stands together to form a beta pleated sheet?

Answer 18

hydrogen between N-H and C=O

Question 19

What are the 2 forms of beta pleated sheet and what do they allow for?

Answer 19

parallel and antiparallel and allow for best h bond group alignment

Question 20

Which A.A is know as the “kinky” A.A and why?

Answer 20

Proline - loses NH group when joins polypeptide chain, no h bond with C=O of another residue, distorts helix

Question 21

What conformation are proteins folded into?

Answer 21

single of lowest energy

Question 22

What are the 2 ways folding can occur?

Answer 22

spontaneous or with chaperones

Question 23

What do chaperones do?

Answer 23

Bind to partly folded polypeptide, ensuring folding goes along most energetically favourable route

Question 24

Name 2 common denaturants and what they break

Answer 24

urea (H bonds) and 2-mercaptoethanol (breaks disulphide)

Question 25

Define secondary structure, give examples

Answer 25

local structural motifs within a protein, alpha helix or beta pleated sheet

Question 26

Define tertiary structure

Answer 26

arrangement of secondary structure motifs into compact globular structures called domains

Question 27

Define quaternary structure

Answer 27

3 dimensional structure of a multimeric protein composed of several sub units

Question 28

What does post-translational modifications allow?

Answer 28

A.A to be modified to novel A.A to enhance capabilities of protein