Lecture 6

Question 1

Why are proteins important?

Answer 1

• mediate nearly all of the processes in a cell
• they have diverse structure and function
• all proteins use the same set of 20 amino acids

Question 2

Name few different types of protein

Answer 2

• enzymes
• motor proteins
• signal proteins
• transport proteins
• structural proteins

Question 3

Describe the primary structure of protein

Answer 3

• amino acid sequence

Question 4

What are amino acids

Answer 4

• amino acids are building blocks of protein
• all 20 amino acids have similar structure, differing in their side chain (R) which dictates their behaviour

Question 5

Amino acids can be grouped into 4 categories which are

Answer 5

1. non polar
2. polar (uncharged)
3. acidic
4. basic

Question 6

what are the basic amino acids

Answer 6

• Arginine
• Lysine

Question 7

what are the acidic amino acids

Answer 7

• aspartic acid
• glutamic acid

Question 8

Name an uncharged polar amino acid

Answer 8

• serine

Question 9

Name a non polar amino acid

Answer 9

• valine

Question 10

What are peptides

Answer 10

2+ amino acids joined by peptide bonds which were formed as a result of a condensation reaction

Question 11

What is each side of a peptide labelled as?

Answer 11

• peptides have directionality with an amino acid terminus (N-terminus) on one side and a carboxyl terminus (C-terminus) in the other
• it is written from left to right
• N terminus to C terminus

Question 12

peptides bonds are found between what

Answer 12

• peptides bonds are found between carbonyl carbon and nitrogen

Question 13

What dictates the shape of a protein

Answer 13

• the specific amino acid sequence

Question 14

what dictates how the protein folds

Answer 14

• the side chain

Question 15

What is the secondary structure of a protein

Answer 15

• stable arrangements of amino acids

Question 16

Name 2 stable secondary structures

Answer 16

• the a helix
• the b sheet

Question 17

The a helix

Answer 17

• peptide backbone wraps around imaginary axis
• 3.6 residues/turn
• r-group face outwards
• stabilized by hydrogen bonds

Question 18

how are a helices stabilized by H-bonds

Answer 18

• stabilized by intrachain hydrogen bonds between C double bond O group of each residue with N-H group of amino acids 4 residues away on the polypeptide chain backbone

Question 19

what affects the stability of a helices

Answer 19

1. electrostatic or steric interactions between adjacent side chains can affect the stability of an a-helix
2. electrostatic or steric interactions between amino acids 3-4 residues away can affect the stability of an a-helix
3. proline and glycine are usually not found in helices
   - the nitrogen of proline is in a rigid ring which interferes statically with the backbone
   - proline in a peptide bond is missing an amide hydrogen to form hydrogen bonds
   - glycine is very flexible and allows for conformations that aren’t suitable for a helices
   - glycine is so small so it can’t protect the backbone hydrogen bonds from the aqueous environment

Question 20

side chains affect protein _________

Answer 20

localization

Question 21

amphipathic helices

Answer 21

• one side is hydrophobic residues and the other side is hydrophilic residues. Allowing for membrane separation
• helices with a region of hydrophobic residues flanked by hydrophilic residues can allow for membrane spanning

Question 22

what is a protein with a helices

Answer 22

• a keratin
• forms coiled coils which gives it strength

Question 23

what are B sheets

Answer 23

• composed of B strands
• stabilized by intrachain hydrogen bonds
• B sheets can be parallel or anti parallel depending on orientation of strands

Question 24

Parallel B-sheets

Answer 24

• strands run zig zag in the same direction
• hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand

Question 25

anti-parallel B sheets

Answer 25

• strands run zig zagged in opposite direction
• hydrogen bonds connect each amino acid on one strand to one different amino acid on the adjacent strand

Question 26

what are some B sheet properties

Answer 26

• B sheets can be twisted
• R groups are perpendicular from the plane of the sheet

Question 27

Give an example of a B sheet

Answer 27

• silk fibroin

Question 28

When can B sheet be found in transmembrane

Answer 28

• only if they are a part of the B barrel structure
• hydrophobic side chains line the outer surface of the b barrel