Protein Structure

Question 1

Definition of primary

Answer 1

Sequence of AA in peptide chain

Question 2

Definition of secondary

Answer 2

Folding of chain into a helix/b pleated sheets

Question 3

Definition of tertiary

Answer 3

Peptide chain folds upon itself

Question 4

Definition of quaternary

Answer 4

Folded peptide chains joined together

Question 5

Functional groups on amino acids

Answer 5

Amino

Carboxyl

Question 6

Reactions between amino acids and dipeptides

Answer 6

Dehydration/synthesis

Acid hydrolysis

Question 7

Properties of peptide bonds

Answer 7

Has characteristics of C=C
However, C-N bond length shorter than expected, no rotation, trans groups
Partial -ve on O
Partial +ve on N
HB can form between 2 polar AA

Question 8

Direction of polypetides

Answer 8

NH3+ = N terminal
COO- = C terminal

Question 9

Covalent linkages, post translation modification

Answer 9

Disulphide bridges Cys-Cys
Glycosylation
Phosphorylation
Methylation via NH2 groups

Question 10

How does glycosylation work

Answer 10

Sugars bind to OH of Thr, Her

Sugars bind tp NH2 of Asn

Question 11

How does phosphorylation affect proteins

Answer 11

Cell signal transduction

Change in enzyme activity

Question 12

How does methylation via NH2 groups affect proteins

Answer 12

Histones and gene expression

Question 13

Properties of a helices

Answer 13

HB in same PP chain, not between side chains
HB formed between COOH, NH2 of every 4th peptide
RH helix
Turn stabilized by HB
R groups on outside
Rigid cylinder, support for protein

Question 14

Properties of b pleated sheets

Answer 14

Linear peptide chains
HB between chains holds strands in B sheet
Side chains in each strand alternately lie above and below sheet plane

Question 15

Properties of collagen triple helix

Answer 15

3 chains with HB between chains
LH helix
Gly, Pro, hydroxypro, repeated sections

Question 16

Forces that stabilize protein structure

Answer 16

Covalent (disulphide bridges)
HB
IB
LF
Hydrophobic effects

Question 17

How do HB work

Answer 17

2 delta -ve atoms compete for the same H atom

Between H and lone electron pair on O, N

Question 18

How do IB work

Answer 18

Between charged side chains
Asp, Glu COO-
Arg, Lys NH3+

Question 19

How do LF work

Answer 19

Sum of attractive/repulsive forces between molecules

Unequal distribution of electrons results in instantaneous dipoles

Question 20

How do hydrophobic effects work

Answer 20

Fold in a way to minimize contact with water

Cannot form HB due to hydrophobic R groups

Question 21

How to disrupt protein structure and function

Answer 21

pH
Temperature
Ionic strength

Question 22

How are proteins folded

Answer 22

All proteins have different structures but only 1 is functional
Primary structure encodes pathway that leads to final structure which is most stable

Question 23

What can misfiled proteins result in

Answer 23

Mutations can cause a protein to fold incorrectly

If not folded properly, stable protein aggregates can form

Question 24

Neurological symptoms in Creutzfeldt Jakob disease

Answer 24

Walking difficulties
Slurred speech
Numbness
Dizziness
Visual problems

Question 25

Psychological symptoms of Creutzfeldt Jakob disease

Answer 25

Severe depression
Withdrawal
Anxiety
Irritability
Insomnia

Question 26

What happens to the normal prion proteins

Answer 26

Normal cellular prion proteins become pathogenic prion proteins

Pathogenic prions can form fibril aggregates

Question 27

Compare the structures of prion proteins

Answer 27

PrPc
a helix, no b sheets
Susceptible to proteolysis

PrPsc
less a helix, b sheet present
Protease resistant

Both have the same AA sequence