Q/A Session 1

Question 1

How does and aa look as a zwitterion?

Answer 1

• Amine side is protonated

- CA is deprotonated (becoming a carboxylate)

Question 2

Characteristics of a Non-Polar side chain

Answer 2

• Mainly composed of hydrocarbons
• Found in the core of the protein
• Hydrophibobic

Question 3

Characteristics of Polar Groups

Answer 3

• Can either be charged or uncharged
• If the pH changes, can become charged/uncharged
• Surface of protein. Polar groups make the protein soluble

Question 4

Characteristics of polar uncharged

Answer 4

-Polar groups in the side chains but uncharged at neutral pH

Question 5

Characteristics of polar charged

Answer 5

• An O by itself indicates negative charge

- Positive charge on the N atom indicated a negative charge

Question 6

What is produced when a peptide bond forms?

Answer 6

Water

-Condendsation reaction

Question 7

Whats the configuration of an aa

Answer 7

Trans, minimises steric hinderance

Question 8

Is there rotation around a peptide bond?

Answer 8

No

Question 9

Characteristics of peptide bond

Answer 9

• Planar
• Rigid
• Linear
• Cannot rotate

Question 10

Psi bond (trident shaped)

Answer 10

Goes between Calpha-C

Question 11

Phi bond (O with slash)

Answer 11

Goes between C-N

Question 12

Formation of secondary structure is called

Answer 12

Nucleation

Question 13

What are secondary structures stabilised by

Answer 13

What hold them together which is hydrogen bonds

Question 14

Where do amino acid side chains point

Answer 14

Outwards from the helix

Question 15

What are the 2 unfavourable amino acids in the alpha helix formation?

Answer 15

• Glycine (too flexible)

- Proline (too bulky)

Question 16

Explain the n+4 stabilising the alpha helix

Answer 16

Hydrogen bond goes between the Oxygen of Amino acid n ——– Hydrogen of amino acid n+4
O(n)—-hydrogen bond—-H(n+4)

Question 17

How many strand in a beta sheet

Answer 17

2-10

Question 18

What aa are used in turns on the beta sheets?

Answer 18

• Glycine due to flexibility

- Proline due to naturally occurring bend

Question 19

What direction do antiparallel bond patterns tend to be (beta sheets)

Answer 19

vertical

Question 20

What direction do parallel bond patterns tend to be (beta sheets)

Answer 20

diagonal

Question 21

How are beta sheets pleated?

Answer 21

With a right hand twist

Turning clockwise

Question 22

What are tertiary structures?

Answer 22

Collection of secondary structures making a 3D sturcute

Question 23

Tertiary structures stabilised by:

Answer 23

1. Metal ion coordination
2. Hydrophobic interactions
3. electrostatic interaction
4. Hydrogen bonds
5. Disulfide bond

Question 24

What are quaternary structures made from

Answer 24

-Made up of 2+ tertiary structures

Question 25

What are quaternary structrues held together by?

Answer 25

Weak/non covalent bonds

Question 26

What are supersecondary structures?

Answer 26

Combinations of secondary structures that form recognisable patterns

Question 27

What are domains?

Answer 27

Combinations of super secondary structures that form independently folded regions -Have hydrophobic cores

Question 28

What is a chaperone?

Answer 28

helps to assist with correct folding by passively preventing incorrect folding - >no ATP required - >hydrophobic molecules

Question 29

What is a chaperonin?

Answer 29

Larger proteins that require ATP to function

Question 30

What is protein folding driven by?

Answer 30

Hydrophobic interactions

Question 31

What is the order of protein folding?

Answer 31

1. Formation of secondary structures 2. Several secondary structures come together and form super-secondary structures->domains 3. Several domains come together and form almost tertiary 4. Small conformational changes give final tertiary structure

Question 32

What is pka?

Answer 32

pH at which an ionisable group is 50% ionised

Question 33

Is pka for an amino group high or low?

Answer 33

High

Question 34

Is pka for a carboxyl group high or low?

Answer 34

Low