SFP2: Protein Structure

Question 1

Name three functional roles of proteins

Answer 1

• enzymes and catalytic
• structural elements
• carriers
• hormones and effectors
• receptors
• movement
• defence
• transcription factors
• chaperones
• storage

Question 2

What is the human proteome

Answer 2

The total number of different proteins (estimated >100,000)

Question 3

What is protein molecular weight commonly expressed in?

Answer 3

Daltons (1Da=1amu)

This is absolute molecular weight - mass (in g) of 1 mole

Question 4

What does amphoteric mean?

Answer 4

Having the characteristics of an acid and a base

Question 5

What does zwitteronic mean?

Answer 5

A molecule carrying both a positive and negative charge

Question 6

Is the D or L isoform of an amino acid found in proteins?

Answer 6

L-isomers

Question 7

Which amino acid is the only one with no chiral centre?

Answer 7

Glycine (because the R group is a hydrogen)

Question 8

What does the peptide bond form between?

Answer 8

Between alpha-carbonyl and alpha-amino group of amino acids

Question 9

What is a residue?

Answer 9

An amino acid in a polypeptide

Question 10

What is the molecular weight of an amino acid in daltons?

Answer 10

120Da

Question 11

What does the rigid planar nature of peptide bond influence?

Answer 11

Protein folding

Question 12

What bonds along the backbone are the only bonds that can rotate?

Answer 12

The bonds around the C-N- this allows the polypeptide to fold into regular structures

Question 13

Is trans or cis conformation favoured?

Answer 13

Trans as there is less repulsion between atoms connected to Calpha

Question 14

What is primary structure of an amino acid?

Answer 14

Amino acid sequence, results from covalent bonds

Question 15

How does a circular protein occur?

Answer 15

When N terminus of a protein is condensed with the C terminus

Question 16

What is the secondary structure of a protein?

Answer 16

Local conformation of a polypeptide chain

Question 17

What are the three basic common units of secondary structure in globular proteins?

Answer 17

Alpha-helix
Beta sheets
Turns

Question 18

What is tertiary structure?

Answer 18

Overall folding of a polypeptide chain (spatial arrangement of amino acids which are far apart in the linear sequence)

Question 19

What bonds is tertiary structure stabilised by?

Answer 19

Hydrophobic
Van der walls
Hydrogen bonds
Electrostatic bonds

Question 20

What is Quarternary structure

Answer 20

Non-covalent association of more than one polypeptide unit (or subunit)

Question 21

What is alpha helix

Answer 21

hydrogen bonds between main chain residues (1-5, 2-6 etc.)
3.6 AA residues / turn
Side chains on outside of helix
Right handed ‘screw-thread’

Question 22

What is a beta sheet

Answer 22

Can be ‘parallel’ or ‘anti-parallel’

Hydrogen bonds between C double bond P and N-H from main chain

Question 23

Do polar or non-polar amino side chains position to the inside of an amino acid?

Answer 23

Non-polar on the inside -> hydrophobic core

Question 24

What are turns?

Answer 24

Connect regions of helix/beta sheet - hydrogen bonds

Beta turns have hairpin structure where amino acid (n) hydrogen bonded to amino acid (n+3)

Question 25

What is a domain?

Answer 25

A super secondary structure

Subsections of larger proteins, fold independently often encoded by a single exon