Amino Acids And Proteins

Question 1

What’s a hydrogen bond?

Answer 1

Electromagnetic attraction that occurs between a H atom and an electronegative atom (N,F or O)

Question 2

Positives of being hydrophobic

Answer 2

Can pass through lipid bilayers

Good for anhydrous storage

Question 3

Characteristics of the peptide bond

Answer 3

No rotation due to double bond characteristics
Planar
Carbonyl oxygen and amide hydrogen in trans orientation
Stronger than most other bonds

Question 4

What is the pI?

Answer 4

The pH at which the protein has no net overall charge

Question 5

How do pI and pH interact

Answer 5

pH>pI then protein is deprotonated, loses H+ therefore becomes more negative

pH<pI then protein is pronated, gains H+ therefore becomes more positive

Question 6

What is the primary structure of a protein ?

Answer 6

The unique sequence of amino acids in a protein

Question 7

Bonds involved I primary structure…

Answer 7

Covalent bonds

Question 8

What is the secondary structure of proteins?

Answer 8

Local spatial arrangement of polypeptide backbone

Question 9

Bonds in secondary structure…

Answer 9

Hydrogen bonds

Question 10

Features of an a-helix

Answer 10

Right handed
3.6 AAs per turn
0.54 nm pitch
All amide hydrogens point up and all carbonyl oxygens down

Question 11

What are helix formers?

Answer 11

Small hydrophobic residues such as ala and leu

Question 12

What helix breakers?

Answer 12

Pro = as rotation around N-C (centre C)bond  is impossible
Gly = tiny R groups support other conformations

Question 13

Features of a B sheet

Answer 13

Fully extended conformation
0.35 nm between adjacent AAs
R groups alternate between opposite sides of the chain

Question 14

Why are bonds in parallel sheets weaker than anti parallel ?

Answer 14

In parallel bonds are at angles so weaker, while in parallel they are straight

Question 15

Bonds in tertiary and quarternary structures?

Answer 15

Hydrogen bonds
Van der waals
Hydrophobic interactions 
Covalent bonds
Ionic interactions

Question 16

What does tertiary structure do?

Answer 16

Produce an overall 3D structure

Involves folding of secondary structure which can bring AAs further away in primary structure closer together

Question 17

What is quarternary structure?

Answer 17

Interactions between and arrangement of different polypeptides chains within the same protein

Question 18

Differences between globular and fibrous proteins

Answer 18

Globular have roles of catalyst, regulation and have a compact shape, fibrous involved in support, protection, shape and have many long starbdsc
Globular have several types of secondary and fibrous single type of secondary structure
Globular are usually soluble and fibrous insoluble
Globular have complex tertiary structure and fibrous have little or no tertiary structure.

Question 19

How are amyloid fibrils formed?

Answer 19

From proteins that contain B-sheets as part of their normal structure. In disease states fibrils form because Bsheets from 1 protein molecule associate with the same region on another molecule. This continues resulting in formation of large insoluble aggregates –> fibrils

Question 20

How do aromatic compounds stop the formation of amyloid fibrils?

Answer 20

Aromatic AAs are important I’m stabilising interaction of Bsheets between adjacent proteins. Therefore aromatic compounds have been found to interfere with amyloid fibril formation by blocking the interaction of aromatic side chains.