Proteins

Question 1

What direction does a protein have and what do polypeptides consist of?

Answer 1

N to C
Polypeptides are linear heteropolymers consisting of L-amino acids (mostly) linked by trans peptide bonds.

Question 2

What is the double bond character of a peptide bond?

Answer 2

peptide bonds have a partial double bond character and
free rotation of the peptide bonds are not possible
Theu have a resonance structure and the actual structure is somewhere in between.

Question 3

What is the most common peptide bond (cis/trans)?

Answer 3

Trans is more common

Question 4

What are the different structures of a protein?

Answer 4

primary structure=amino acid sequence
secondary structure=structural elements with more than one amino acid e.g alpha helix and beta sheet
tertiary structure=overall conformation (shape) elements of secondary structure linked by loops and turns and protein fold
quaternary structure=multiple polypeptides (subunits)

Question 5

Give an example of a positively charged protein?

Answer 5

Cytochrome c

Question 6

Give the amino acids that form the the structure of collagen and fibroin?
X=other amino acids
What is elastin rich in?

Answer 6

Collagen (connective tissue)
Gly-X-Pro or Gly-X-Hyp

fibroin (silk)
Gly-Ala-Gly-Ala plus 10% Ser
elastin (connective tissue)
rich in glycine, proline and alanine

Question 7

Important things to note about the Secondary structure: helix

Answer 7

It is right-handed clockwise helix
0.54 nm
3.6 amino acids per turn
weak hydrogen bonds holding helix together

Question 8

Dermcidin protein?

Answer 8

An antimicrobial peptide and has an amphipathic helix
One side is hydrophilic and the other half (semicircle) is hydrophobic
This secondary structure allows it to stick to the membranes of bacteria disrupt them and then cause the bacteria to die.

Question 9

How are sheets drawn in proteins?

Answer 9

Drawn with an arow so we can see its direction

Question 10

What helps proteins fold in the right way?

Answer 10

Chaperone proteins

Question 11

Globular proteins and its hydrophobic interactions

Answer 11

hydrophobic core (amino acid residues with hydrophobic side chains) and stacking interactions between aromatic side chains possible (hydrophilic surface amino acid residues with hydrophilic side chains)

Question 12

The globin fold: an alpha helical fold

Answer 12

Myoglobin is a globular protein
compact
hydrophobic core
highly conserved tertiary structure

Question 13

The TIM barrel: an alpha/beta fold

Answer 13

TIM: triose phosphate isomerase
toroid shape
interior lined by beta sheet
exterior composed of alpha helix

Question 14

Within a protein they may have different domains (folds).

Answer 14

e.g. the enzyme pyruvate kinase has three distinct domains
separate regions of tertiary structure
may arise from gene fusion

Question 15

Hemoglobin – 4o structure

Answer 15

four subunits
haem prosthetic group in each
2 alpha and 2 beta subunits each with a globin fold
cooperative binding of oxygen

Question 15

Hemoglobin – 4o structure

Answer 15

four subunits
haem prosthetic group in each
2 alpha and 2 beta subunits each with a globin fold
cooperative binding of oxygen

Question 16

What is pH?

Answer 16

A measure of the concentration of H+
catalysis may be dependent on the ionisation state of acid/base groups which in turn depends on pH