Protein Structure

Question 1

What is a peptide bond and how is it formed?

Answer 1

C=O - N-H
Formed by condensation reaction between carboxyl group and amino group

Question 2

Properties of peptide bonds:

Answer 2

• Very stable
• Cleaved by proteolytic enzymes - proteases or peptidases

Question 3

What is a protein? What structures does it have?

Answer 3

• A protein is a large polypeptide, usually from 10s to 1000s amino acids
• Function is dependent on structure

Question 3

What is a protein? What structures does it have?

Answer 3

• A protein is a large polypeptide, usually from 10s to 1000s amino acids
• Function is dependent on structure

Question 4

Difference between proteins and peptides:

Answer 4

• Protein - functional, synthesised by a cell w/50+ amino acids
• Peptide - piece of a protein w/ less than 50 amino acids

Question 5

What is the primary structure?

Answer 5

Linear sequence of amino acids, held by covalent bonds. Sequence of amino acids in protein determine where bonds will form thus structure and thus function

Question 6

What is the secondary structure?

Answer 6

• Alpha Helix - H-bonds between each carbonyl group and the H of the N, side chain looks outwards
• Beta Pleated Sheets - H bonds between linear
  regions of polypeptide chains, chains from 2 proteins or same protein
• Hairpin Loop/ Beta Turn - If the chain is folding back, structure is usually a 4 amino acid turn, due to hydrogen bonds between amino acids - determined by the local interactions between the side chains and sequence of amino acids.

Question 7

What is the super secondary structure?

Answer 7

Combination of secondary alpha and beta structures.

Question 8

What is the tertiary structure?

Answer 8

3D conformation of a protein.
Folding of the secondary structure into a globular structure due to bonds such as ionic bonds, disulphide bridges and Van Der Waal forces.
Can change with temperature or pH.

Question 9

What is the quaternary structure?

Answer 9

3D structure of protein with multiple subunits.
2 or more tertiary structures joined together to form a protein e.g. haemoglobin or collagen

Question 10

What are the forces between proteins?
Explain them:

Answer 10

• Van Der Waals forces: Weak attractive/repulsive force between atoms due to fluctuating electrical charge
• Hydrogen bonds: Between polar groups. In amino acid side chains, oxygen and nitrogen in main chain and water.
• Hydrophobic forces: as uncharged and non-polar side chain are repelled by water, these hydrophobic side chains tend to form tightly packed cores in the interior of proteins, excluding water molecules.
• Ionic bonds: Between fully/partially charged groups. Weakened in aqueous systems by shielding by water molecules and other ions in solution.
• Disulphide bonds: Very strong covalent bonds between sulphur atoms

Question 11

What factors influence rate of reaction?

Answer 11

• Temperature
• pH
• Concentration of reactants
• Catalysts
• Surface area of a solid reactant
• Pressure of gaseous reactants or products.

Question 12

What are enzymes?

Answer 12

Enzymes are proteins that work as biological catalysts

Question 13

How do enzymes work?

Answer 13

Provide an alternative reaction pathway with a lower activation energy.
Bind to substrates and convert them to products, they then release the products and return to their original form.

Question 14

What else can enzymes be used for?

Answer 14

Can be used for diagnostic purposes since they control metabolism, can be used as disease markers e.g when released in bloodstream, when they should be present. A lot of drugs work by inhibiting the actions of enzymes

Question 15

How can enzymes be regulated?

Answer 15

Can be regulated by altering the concentration of substrates, products, inhibitors or activators
They can also be regulated by modifying the enzyme itself by phosphorylation.

Question 16

What is an isoenzyme?

Answer 16

Enzymes that have a different structure and sequence but catalyse the same reaction

Question 17

How does temperature affect enzymes?

Answer 17

As T increases, the stability of the enzyme structure decreases - bonds weaken, eventually leading to denaturation and thus lower reaction speed.

Question 17

How does temperature affect enzymes?

Answer 17

As T increases, the stability of the enzyme structure decreases - bonds weaken, eventually leading to denaturation and thus lower reaction speed.

Question 18

What are coenzymes? How do they work?

Answer 18

Complex organic structures which help to maximise the repertoire of enzymes.
They can’t themselves catalyse a reaction but can help enzymes to do so. They bind with the enzyme protein molecule to form the active enzyme.

Question 19

Give examples of coenzymes:

Answer 19

Can be metal ions (Fe 2+, Mg 2+, Zn 2+) or organic usually derived from vitamins or both (e.g. Fe 2+ and heme)

Question 20

How many types of coenzymes are there and what are they?

Answer 20

2.
Activation-transfer coenzymes
Oxidation-reduction coenzymes

Question 21

What is an activation transfer coenzyme?

Answer 21

Form a covalent bond and are regenerated at the end of the reaction

Question 22

What is an oxidation reduction coenzyme?

Answer 22

Involved in reactions where electrons are transferred from one compound to the other. E.g. NAD + transfers electrons with hydrogen and is important in energy processes including the generation of ATP.

Question 23

Where is haemoglobin and myoglobin found?

Answer 23

• Haemoglobin - found in erythrocytes, oxygen carrier in the blood
• Myoglobin - found in the muscle, serves as a reserve supply of oxygen and also facilitates the movement of O2 in muscles.

Question 24

Similarities between haemoglobin and myoglobin:

Answer 24

Both have Porphyrin ring in the core which holds an iron atom, this is called a heme. Iron atom is the site of oxygen binding

Question 25

Does myoglobin and haemoglobin both have quaternary structure?

Answer 25

Haemoglobin - Yes. Has 2 alpha subunits, 2 beta subunits
Myoglobin - No. only 3rd 1 polypeptide chain

Question 26

How does pp of O2 affect haemoglobin saturation:

Answer 26

As it increases so does haemoglobin saturation

Question 27

How does temp. H+ and pp CO2 affect haemoglobin saturation?

Answer 27

Modify structure of haemoglobin and alter its affinity for O2
Increase - haemoglobin decreased affinity for O2 and increased unloading of O2 from blood. Decrease acts in opposite manner.

Question 28

What is the genetic disorder that is characterised by the formation of hard, sticky, sickle-shaped red blood cells - caused by a mutation in haemoglobin

Answer 28

Sickle cell anaemia

Question 29

What is produced to bind to antigens on toxins or proteins?

Answer 29

Antibodies, immunoglobins

Question 30

What are the types of antibodies?

Answer 30

IgG, IgM, IgA etc

Question 31

What causes variability in antibodies?

Answer 31

Variable region
Amino acid in variable region, varies to produce a potentially infinite variety of 3D shapes to recognise an infinite variety of foreign antigens

Question 32

What is the structure of the variable region?

Answer 32

Made of 2 light chains and 2 heavy chains
VL and VH