Lecture 3 - Protein strucure and function

Question 1

Functional products of the genome (5)

Answer 1

o Carrier functions – trafficking oxygen
o Metabolic functions - Enzymes producing and utilising energy
o Form parts of the Cellular machinery – splicesomes, ribosomes
o Make up structural scaffold – microtubules, nucleosomes
o Sensing molecules – receptors and their ligands

Question 2

Zwitterions (4)

Answer 2

At a intermediate pH/ neutral isolelectric point
Carboxyl group - deprotonated - ve charge
Amine group - protonated +ve charge
R group may possess a group with a charge

Question 3

Zwitterions (4)

Answer 3

At a intermediate pH/ neutral isolelectric point
Carboxyl group - deprotonated - ve charge
Amine group - protonated +ve charge
R group may possess a group with a charge

Question 4

High pH (3)

Answer 4

Carbonyl group - Already deprotonated
Amine group - Deprotonated
Overall charge = -ve charge

Question 4

Low pH

Answer 4

Acucuc

Question 5

Side chains - amino acids

Answer 5

Hydrophilic = Polar (Acidic/Basic/Neutral)
Hydrophobic = Non-polar
20 amino acids
9 essential amino acids

Question 6

Amino acid residues (4)

Answer 6

AA resides make up a polypeptide chain.
The sequence of AA residues is the primary structure.
The variable side chain R is usually arranged in a trans formation. 0.1% peptide bonds have a less energetically favourable cis arrangement.

Question 7

Primary structure (2)

Answer 7

Strong covalent bonds

Sequence of Amino acids

Question 8

Secondary structure (4)

Answer 8

Alpha helixes
Beta sheets
Beta turns
By intra chain hydrogen bonding

Question 9

Beta sheet (3)

Answer 9

Continuously folded polypeptide chain forms sheets
Parallel or anti
Anti is stronger e.g. silk fibroin

Question 10

Alpha helix (6)

Answer 10

Spiral structure
Occurs between hydrogen of amine group and carbonyl group
Right handed helix is stabilised by H bonds
4 resides along the chain
3.6 resides per turn
Residues can be hydrophobic/philic

Question 11

Tertiary structure (6)

Answer 11

Intra molecular bonding 
Disulphide bonds (S=S in cystine aa)
Ionic - charged R groups
Hydrophobic/philic interactions - depending on environment e.g. aqueous or in a membrane 
Van der Waals
Hydrogen bonding

Question 12

Tertiary example

Answer 12

Thyroid stimulating hormone combines seven transmembrane domains

Question 13

Quaternary and example (2)

Answer 13

Folding to final protein

Haemoglobin

Question 14

Myoglobin vs Haemoglobin vs Fetal H (7)

Answer 14

Tertiary structure is myoglobin (found in muscles)
Quaternary is haemoglobin
M has multiple alpha helixes bound to a haem group which are similar to the tertiary structure on H (2 a and 2 b)
M has a higher binding affinity than H
FH has a binding affinity than H
All have different primary structures
H undergoes conformational change to give higher or lower affinity depending if its in lungs / muscles.

Question 15

Cofactors define + 4 examples

Answer 15

Non-protein components necessary for the effective functioning of an enzyme 
Haem of Haemoglobin 
Ions (Zn 2+ or Mg2+) 
NAD
FAD

Question 16

Coenzymes

Answer 16

Small non-organic protein molecules that bind temporarily to the active site of enzyme molecule, either just before or after the same time the substrate binds.

Question 17

Determining shape or size

Answer 17

X Ray crystallography

NMR (nuclear magnetic resonance) spectroscopy

Question 19

3 types of proteins + examples

Answer 19

Globular - spherical, water-soluble proteins e.g. insulin

Conjugated- globular portion with a prosthetic group e.g. haemoglobin and catalase

Fibrous proteins - Long, insoluble , structural proteins e.g. keratin, elastin, myosin and collagen.
Collagen has a triple not alpha helix.