B.1.2 Molecules - PROTEINS

Question 1

Describe the reason and type diversity within protein structure and function.

Answer 1

Chemical diversity R groups of amino acids monomers is the basis for immense variety and diversity in protein structure and function.

R groups:
1. 20 different types
2. Infinite variety of polypeptides
3. Can be hydrophobic (alanine) or hydrophilic (serine)

Hydrophilic r groups:
1. Acidic (Additional carboxyl group): aspartic acid
2. Basic (Additional amino groups): lysine
3. Polar (serine)

Question 2

Draw the generalised structure of an amino acid

Answer 2

The drawing should include:
1. Amino group (NH2)
2. R group (H,C,r group)
3. carboxyl group (OCOH)

Question 3

Outline the impact of primary structure.

Answer 3

STRUCTURE:
1. Sequence of amino acid
2. number of amino acids
3. Type – 20
4. peptide bonds via condensation reactions

FUNCTION:
Primary structure determines the folding of the protein

Question 4

Outline the aspects of secondary structure with examples.

Answer 4

STRUCTURE:
1. Based upon hydrogen bonding within the strand -> forms an alpha helix or beta pleated sheet
2. Regular and repeated interactions between amino acids within the same strand with h-bonding
3. Resistant to heat and damage

EXAMPLES:
Beta pleated sheet: spider silk
Alpha helix: structural proteins like collagen, keratin, tendons, ligaments

Hydrogen bonding occurs between the hydrogen of an amino group and carboxyl group of another amino acid

Question 5

Describe the aspects of tertiary structure.

Answer 5

The tertiary structure is the interactions among R-Groups within a polypeptide that determines its folding.

1. Based on r-group interactions:
   - ionic bonding (+ and -)
   - hydrogen bonding (H and O/N between different amino acids)
   - hydrophobic interactions (R group may associate towards the interior of the protein)
   - disulfide bridges/bonding between cysteine residues (S-S type of covalent bond between cysteine amino acids)
2. Irregular folding

Question 5

Draw the generalised structure of an amino acid

Answer 5

This should include:
1. amino group
2. carboxyl group
3. R-group

BE LABELED!!

Question 5

Describe the aspects of the quaternary structure

Answer 5

The quaternary structure is the interactions of two or more polypeptides to form a protein

(Polypeptides can fold to become a protein)

Quaternary structures only refer to when MULTIPLE CHAINS join together to form a protein that consists of more than 1 polypeptide

Ex: Hemolobin, immunoglobin

Question 6

Describe the dietary requirements for amino acids.

Answer 6

ESSENTIAL AMINO ACIDS: amino acids that cannot be synthesised that must be obtained from food/diet - 10 of them

NON-ESSENTIAL AMINO ACIDS: amino acids that can be synthesises and are not required in hte diet - 10 of them

Question 6

Outline the effect of pH on protein structure

Answer 6

1. Enzymes have optimal pH – below/above it lowers enzyme activity
2. Too acidic/basic pH changes protein structure of enzyme -> denatures it -> changes shape of active site (or teriary structure)
3. R-group interactions are alered - hydrogen bonds/ionic bonds in the enzyme are altered
4. The substrate can’t bind to the active site and the enzyme-substrate complex can’t form

Question 6

Draw the reaction between amino acid monomers forming dipeptides (and longer chains of amino acid/polypeptides:

Answer 6

This should include:

1. amino acid monomers
2. dipeptide/polypeptide is formed
3. OH (carboxylic acid) and H (amino group) reacts together
4. Water is formed
5. Peptide bond is formed

Question 6

How do you find the number of possible amino acid combinations with a polypeptide? What about the number of peptide bonds?

Answer 6

Let n = the number of amino acids monomers in the chain

Possible combinations = 20^ n
Peptide bonds = n-1

Proteome: all of the proteins produced in a cell/organisms

Question 6

Describe the effect of temperature on protein structure

Answer 6

1. Enzymes have an optimal temperature -> in which the reaction rate is highest -> temperatures above/highest leads to lower rates of reaction
2. High temperature -> denaturation -> change of shape of the protein and active site
3. This is due to the intermolecular bonds and interactions being broken (hydrogen bonds/ R-group interactions)

Question 6

Recall the effect of polar and non-polar amino acids on tertiary structure of proteins

Answer 6

POLAR:
1. causes protein to fold -> tertiary structure so they are on the OUTSIDE
2. Hydrophilic amino acids will associate with water
3. Polar amino acids will form hydrogen bonds with water

NON POLAR
1. cause protein to fold -> tertiary structure so they are on the INSIDE
2. Hydrophobic amino acids will not associate with water

Integral proteins have regions with hydrophobic amino acids which associate with the lipid bilayer/non-polar region/inside

Question 6

Outline conjugated proteins

Answer 6

A conjugated protein is one that has a quaternary structure and a non-polypeptide group attached.

For example, hemoglobin has Fe 2+ in its heme that binds to oxygen.

Question 7

Outline the diffence in shape/form and function of globular and fibrous proteins in with insulin and collagen.

Answer 7

GLOBULAR/INSULIN:
2. rounded/spherical
2. Funcitonal (catalytic, transport)
3. Generally soluble in water
4. Irregular amino acid sequence
5. more sensitive to changes in heat/pH, etc.
Ex: catalase, aemoglobin, insulin, immunoglobulin

FIBROUS/COLLAGEN
1. long and narrow
2. structural (strength and support)
3. generally insoluble in water
4. repetitive amino acid sequence
5. less sensitive to changes in heat and pH
EX: collagen, myosin, fibrin, actin, keratin, elastin

Question 8

Outline the location and structure of hemoglobin

Answer 8

1. Found in red blood cells (280 million molecules of hemoglobin)
2. Has 4 subunits that interlock to form the compact molecule
3. Each subunit is a conjugated protein that consists of the following:
   - A PROTEIN CHAIN (globin)
   - PROSTHETIC GROUP (haem)
4. Globin consists of 150 amino acid residues in the form of a helix that is folded 5-7 times
5. Has a Fe2+ in heme that may combine loosely and reversibly with a molecule of oxygen

A prosthetic group is a helper molecule that enables other molecules to be biologically active.

Haem is a flat molecule of 4 pyrrole groups, held by = C – groups: at the centre is an atom of iron (II)

Question 9

Outline the quarternary structure of non-conjugated proteins

Answer 9

Non-conjugated proteins don’t have a chemical group attached. They include insulin and collagen.

INSULIN:
1. A hormone (from the pancreas) that promotes the synthesis and storage of glycogen in muscle and liver cells
2. A short chain of 21 amino acids folds to form a globular protein
3. disulfide bridges form between 2 cysteine residues/amino acid

COLLAGEN:
1. 3 polypeptide coils together to form a t riple helix
2. Repeated units of amino acids – Every third amino acid is glycine (smallest), with the other 2 mostly being proline and hydroxyproline
3. Covalent and hydrogen bonds between the chain provides the strength