Protein structure and function

Question 1

What are the 2 ends of a polypeptide?

Answer 1

-First amino acid has NH3+ group (N terminal end)
-Last amino acid has COO- group (C terminal end)

Question 2

Definition of amino acid

Answer 2

-Amino acid has a carboxylic group and amino group attached to the same carbon (alpha carbon)
-When these combine a peptide bond is formed

Question 3

2 examples of post translational covalent modifications

Answer 3

-Disulphide (S-S) bridges between 2 cysteines
=>join subunits together (e.g. insulin)

-Glycosylation (addition of sugars)
=> O linked -OH of threonine and serine
=> N linked -NH2 of asparagine

Question 4

Primary structure of proteins

Answer 4

-sequence of amino acids in peptide chain

Question 5

Secondary structure of proteins

Answer 5

-folding/coiling of peptide chain (alpha helix or beta pleated sheet)

Question 6

Tertiary structure of proteins

Answer 6

-peptide chain folds upon itself
-how the whole polypeptide subunit is folded in 3D

Question 7

Quaternary structure of proteins

Answer 7

-folded peptide chains join together
-how the whole functional protein is formed in 3D

Question 8

Alpha helix features

Answer 8

-Stabilised by hydrogen bonds within the same polypeptide chain (backbone not sidechains)
-H bonds formed between peptide bond carbonyl-O and H of N-H every 4th peptide
-Regular right handed helix
-3.6 residues/turn stabilised by H bonds
-R groups on the outside
-Rigid cylinder shape, acts as ‘architectural’ support for protein

Question 9

Beta pleated sheets features

Answer 9

-Stabilised by hydrogen bonds between peptide strands
-Linear peptide strands

Question 10

2 types of beta sheet structures

Answer 10

A) -Antiparallel beta sheet
-Beta hairpin bend

B) -Parallel beta sheet
-(arrow points to C terminus)

Question 11

What is collagen triple helix?

Answer 11

-3 chains
-Found in collagen
-Hydrogen bonds between chains
-3 residues/turn
-Left handed helix

Question 12

Proteins with high % of alpha helix and beta pleated sheet

Answer 12

-Hb is made up of 60% alpha helix
-Fibrillar proteins (e.g. silk fibres - fibroin) have high % beta pleated sheet
=> Gives them high tensile strength, but no elasticity

Question 13

What forces stabilise protein structure?

Answer 13

Covalent
-Disulphide bridges

Non-covalent bonds
-Hydrogen bonds
-Electrostatic interactions
-Van der Waals forces
-Hydrophobic effects

Question 14

What is a hydrogen bond?

Answer 14

-2 electro negative atoms compete for the same hydrogen atom
H bond donors:
-O e.g. O-H
-N e.g. N-H

H bond acceptors:
-O e.g. C–O

Question 15

What are electrostatic interactions?

Answer 15

-Exist between charged side chains
At physiological pH:
-Aspartate and Glutamate carboxyl groups (COO-) are ionised
-Lysine and Arginine amino groups (NH3+) are ionised

Question 16

What are Van der Waals forces?

Answer 16

-The sum of the attractive or repulsive forces between molecules
=>Excluding those due to covalent, hydrogen, electrostatic
-Dependent on dipole effect caused by unequal distribution of electrons
=>Partial negative and partial positive charge across a covalent bond

Question 17

What are hydrophobic effects?

Answer 17

-Hydrophobic regions of a protein fold in such a way to minimise the contact with aqueous environment
-Hydrophilic outside, hydrophobic inside
-Hydrophobic regions are unable to form hydrogen bonds

Question 18

Why are proteins sensitive to denaturation?

Answer 18

-Amount of stabilisation energy in a protein is quite small
-Proteins have thousands of possible structures only one of which is functional
-Amino acid sequence encodes the final structure but also the pathway that leads to that structure

Question 19

What factors can denature protein?

Answer 19

-Temperature
-pH
-Ionic strength

Question 20

How many amino acids make up the proteins in humans?

Answer 20

20
-Each AA has a different R group attached to the alpha carbon
-R group defines properties and function

Question 21

What are essential amino acids?

Answer 21

9 of the 20 amino acids cannot be synthesised in the body
-They are supplemented through diet

Question 22

3 amino acids that are not universally encoded in DNA

Answer 22

Hydroxyproline (hydroxylation of proline) - component of collagen that forms triple helix structure

Selenocysteine -encoded by STOP codons and has reduced pKa

Homocysteine - contains extra methyl group needed to synthesis cysteine

Question 23

Features of peptide bond

Answer 23

-Forms between alpha amino and alpha carboxylic groups of adjacent AAs.
-Very strong bond which is short, has no rotation, with R groups in the trans configuration
-Partial negative charge on oxygen atom and partial positive charge on nitrogen atom help form H bonds

Question 24

Defects in AA metabolism leading to disease

Answer 24

-One form of albinism due to defective tyrosinase (tyrosine -> melanin)

-Phenylketonuria (PKU)
-Defective phenylalanine hydroxylase (phenylalanine->tyrosine)
-Causes reduced tyrosine production and hormones which are derived from it (dopamine and melanin)

Question 25

Recognise structures of 20 amino acids

Answer 25