4 - Protein Structure

Question 1

What are some of the roles of proteins?

Answer 1

• Ligands
• Receptors
• Membrane transport
• Catalysts
• Muscle contraction
• Structural support
• Immune protection

Question 2

What are the 1,2,3,4 structures of proteins?

Answer 2

1 - Covalently bound linear amino acid sequence coded for by a gene

2 - Local arrangement of polypeptide backbone. Hydrogen bonds so alpha helix or beta pleated sheets

3 - 3D spatial arrangement of amino acids, electrostatic attractions, disulphide bonds, VDW

4 - Association of different polypeptides to form a multisubunit protein, all of the above forces

Question 3

What is the structure of an amino acid?

Answer 3

Question 4

What deermines the properties of an amino acid?

Answer 4

The R group

Question 5

What is an amino acid residue?

Answer 5

Question 6

What can amino acids be classified as?

Answer 6

Question 7

What is pK?

Answer 7

• Measure of acid strength worked out from K_a
• Smaller pK means greater acid strength

Question 8

What will happen if:

1. pH < pK?
2. pH > pK?

Answer 8

1. Amino acid will be protonated
2. Amino acid will be deprotonated

Question 9

What is a conjugate protein?

Answer 9

Polypeptide containing a covalent attachment of a non-polypeptide e.g lipoprotein

Question 10

How is a peptide bond formed and draw a peptide bond?

Answer 10

Question 11

What are the characterisitcs of a peptide bond?

Answer 11

- Rigid (N-C has partial double bond characteristics)

- Planar (C_a-CO-NH-C_a all in same plane)

- Trans (C_a‘S on opposite sides)

Question 12

Why are peptide bonds not cis?

Answer 12

Would be steric clashes between R groups as they are too close

Question 13

What is pI?

Answer 13

The isoelectric point of a protein, where there is no overall net charge on the protein

Question 14

What is the pI of a basic and acidic amino acid?

Answer 14

Basic- pI > 7

Acidic - pI < 7

pH > pI deprotonated

pH < pI protonated

Question 15

What are the differences in structure between alpha helix and beta pleated sheet?

Answer 15

Question 16

What structure of beta pleated sheets isn’t as stable?

Answer 16

• Parallel

Question 17

What are the differences between fibrous and globular proteins?

Answer 17

Globular have motifs and domains

Question 18

What is a motif and a domain?

Answer 18

• In globular proteins

Motif: Folding patterned containing multiple secondary structures

Domain: Part of a polpeptide that folds into a distinct shap for a function

Question 19

How do water soluble proteins and membrane proteins fold? fold?

Answer 19

Water soluble: Hydrophilic outside, hydrophobic inside

Membrane protein: Reverse

Question 20

What is the main difference between a secretory protein and an intrinsic protein?

Answer 20

Secretory protein has disulphide bonds

Question 21

What are all the types of bonds in each protein structure

Answer 21

Question 22

How do proteins fold?

Answer 22

• In a semi-ordered process according to the primary sequence
• Driven by localised folding to find the most stable conformation

Question 23

What are amyloid fibres?

Answer 23

Misfolded beta pleated sheet proteins so proteins that were normally soluble are now insoluble

e.g CJD, BSE, dementia

Question 24

How do you work out the ratio of protonated to deprotonated forms of amino acid at a certain pH?

Answer 24

Henderson-Hasselbalch