Biochemistry intro 4 - Proteins

Question 1

What is primary protein structure?

Answer 1

The sequence of amino acid residues. The amino acids can rotate so polypeptides are not straight

Question 2

What is secondary protein structure?

Answer 2

This is the hydrogen-bonded three dimensional arrangement of a polypeptide chain but only considers the backbone of the polypeptide and falls into 3 types:

1. Alpha (α) helix
2. Beta (β) pleated sheet
3. Triple helix

Question 3

True or false: Each amino acid in a chain is referred to as a residue

Answer 3

True

Question 4

True or False: Only one type of secondary structure can occur within one protein

Answer 4

False - Different types of secondary structure can occur within one protein (so one protein can contain both α helix and β sheet)

Question 5

Describe the secondary structure - Alpha (α) helix

Answer 5

The α-helix is a rod-like structure with the peptide chain tightly coiled and the side chains of amino acid residues extending outward from the axis of the spiral.
Each amide carbonyl group is hydrogen-bonded to the amide hydrogen of a peptide bond that is four residues away along the same chain.
There are on average 3.6 amino acid residues per turn of the helix, and the helix winds in a right-handed (clockwise) manner in almost all natural proteins. Proline residues break α-helices because it disrupts the sequence of hydrogen bonds by producing kinks

Question 6

Describe the secondary structure - Beta (β) pleated sheet

Answer 6

Beta (β) pleated sheet is formed by the carboxy to amide hydrogen bonds which form between peptide chains. If the polypeptide chain runs in the same direction it forms a parallel β sheet but if the chain runs in opposite directions it form an anti-parallel structure. The sheet is pleated because the carbon-carbon bonds are tetrahedral and cannot exist in a planar form. Proline (Pro) and Glycine (Gly) residues can create turns to form a zig-zag structure

Question 7

Describe how the repeating tripeptide unit structure of collagen is formed (collagen triple helix)

Answer 7

• Collagens are major components of bone and connective tissue (e.g cartilage, tendons)
• This repeating sequence is adopts a left-handed helical structure with 3 residues per turn.
• Three of these helices twist around each other to form a right-handed superhelix known as tropocollagen
• Hydrogen bonds involving hydroxylysine and hydroxyproline hold chains together

Question 8

Explain why collagen is important

Answer 8

1. Collagen influences the strength of connective tissue
2. Weakened collagen can result in bleeding gums
3. Covalent cross-linking between collagen molecules increase with age - meaning the meat from older animals is tougher
4. Weakened collagen can result in SCURVY - this is because the enzyme which hydroxylates proline residues requires ascorbic acid (Vitamin C) so dietary deficiency of vitamin C results in reduction of hydroxyproline which results in weakened collagen, hence scurvy can occur
5. Collagen contains a high proportion of hydroxylated proline residues

Question 9

Are collagen fibres water soluble?

Answer 9

Collagen fibres are water INSOLUBLE however lowering the pH of a solution can increase water solubility

Question 10

What is tertiary protein structure?

Answer 10

This is the 3D structure of an entire polypeptide, including all side chains. It is determined by interactions between side chain functional groups, including disulfide bonds, hydrogen bonds, salt bridges, and hydrophobic interactions.

Question 11

What is quaternary protein structure?

Answer 11

This is when proteins contain more than one polypeptide chain held together by mainly noncovalent bonds but sometimes covalent interactions hold them together. These structures may also contain prosthetic groups (e.g iron in haem) which are non-protein components. E.g Haemoglobin is composed of 4 subunits and contains prosthetic group iron in haem - binding of one oxygen changes affinity of other subunits

Question 12

What are the two types of tertiary structure?

Answer 12

1. Fibrous proteins - Contain polypeptide chains organised parallel along a single axis. Tend to be insoluble. Consist of long fibres/sheets that are strong (e.g keratin of hair, collagen of connective tissue of skin and bones)
2. Globular proteins - Proteins folded to more or less a spherical shape. Tend to be soluble. Non-polar side chains are buried inside (e.g Myoglobin and haemoglobin)

Question 13

Name 5 interactions which stabilise tertiary structure

Answer 13

1. Covalent disulphide bonds
2. Salt bridges
3. Hydrogen bonds
4. Hydrophobic interactions
5. Ionic bonds

Question 14

Name 3 things which can effect protein structure

Answer 14

1. Mutations can have a major effect on protein structure and function (e.g sickle cell anaemia due to single nucleotide sequence change)
2. Protein folding can go wrongs and so incorrect folding can result in problems such as Creutzfeldt-jakob disease (effects brain)
3. Denaturing caused by: Too much heat, extremes of pH, detergents, urea, thiol agents and reducing agents (both disrupt disulphide bonds)

Question 15

What is a protein domain?

Answer 15

A discrete region of polypeptide chain that has folded into a self-contained 3D structure (independently into a stable tertiary structure)