Protein Structure

Question 1

What is the basic structure of amino acids?

Answer 1

Central CH bonded to COOH (carboxyl group, C double bonded to O and single to OH), variable R group and H2N (amine group)

Question 2

How do amino acids join together?

Answer 2

In a condensation reaction between the carboxyl group of one amino acid and the amino group of another, forming a peptide bond + a water molecule

Question 3

What molecules bond in the reaction between two amino acids?

Answer 3

CO from carboxyl group and NH from amine group; OH and H form water

Question 4

Describe the primary structure in proteins

Answer 4

Specific order of amino acids in a polypeptide chain; helps determine the final 3D shape of the protein and determined by DNA sequence of the gene that codes for it

Question 5

Describe the secondary structure of proteins

Answer 5

Chain begins to fold, as the positively-charged H attracted to negatively charged O, forming a hydrogen bond across polypeptide chain
- can be either alpha helix or beta pleated sheet

Question 6

Describe the tertiary structure of proteins

Answer 6

Overall final folded 3D shape of polypeptide; critical for how protein functions

Question 7

Describe quaternary structure of proteins

Answer 7

When proteins are made up of several polypeptide chains called sub-units; may also contain non-protein molecules called prosthetic groups which help proteins carry out their function (those with are called conjugated proteins)

Question 8

Give an example of a conjugated protein

Answer 8

Haemoglobin, has 4 prosthetic groups called haem made of iron, which is where oxygen attaches

Question 9

Which bonds are involved in primary, secondary, tertiary and quatenary structure?

Answer 9

primary = peptide
secondary = hydrogen
tertiary = side chains, ionic, disulphide bridges (if R groups have sulfur), hydrophobic/philic reactions, hydrogen
quaternary = all of the above

Question 10

What are the properties of globular proteins?

Answer 10

Have compact, spherical shape, soluble due to hydrophilic amino acids being on the surface and hydrophobic in the centre

Question 11

Describe an example of a globular protein

Answer 11

Haemoglobin; has 4 polypeptide chains and carries oxygen around the body so must be soluble; has iron containing haem groups which bind to oxygen

Question 12

Describe properties of fibrous proteins

Answer 12

• Made up of long polypeptide chains tightly coiled to form rope-like shape
• Insoluble due to many hydrophobic amino acids
• Often have structural roles due to strength from many bonds, e.g tendons, bones, arteries

Question 13

Describe an example of a fibrous protein

Answer 13

Collagen is found in skin, ligaments and tendons; made up of 3 polypeptide chains twisted into a triple-helix
- Every 3rd amino acid is glycine a/ R group hydrogen, allowing polypeptide chains to wrap tightly with hydrogen bonds
- Staggered molecules to avoid weak spots

Question 14

What are enzymes?

Answer 14

“Biological catalysts” which speed up the rate of reaction without being used up, by reducing activation energy

Question 15

What type of molecule are enzymes?

Answer 15

Globular proteins

Question 16

What are intracellular and extra cellular enzymes?

Answer 16

• Intracellular = produced and function inside the cell
• Extracellular = secreted by cells and catalyse reactions outside cells

Question 17

Give examples of intracellular and extracellular enzymes

Answer 17

Intracellular - Catalase; converts harmful hydrogen peroxide to water and oxygen
Extracellular - Amylase; involved in carbohydrate digestion as it hydrolyses starch into simple sugars, secreted by salivary glands + pancreas

Question 18

What is activation energy and how do enzymes lower it?

Answer 18

Minimum amount of energy needed by the substrate to become unstable enough for a reaction to occur; enzymes offer an alternate reaction pathway and reduce stability of bonds in reactant

Question 19

What is the lock and key model?

Answer 19

States shape of active site is exactly complimentary to the substrate

Question 20

What is the induced-fit model?

Answer 20

States the active site changes shape slightly to fit around the substrate

Question 21

How does changing temperature affect enzymes?

Answer 21

• as temperature increases, rate of reaction increases as kinetic energy is higher so more collisions and E-S complexes formed
• however once an enzymes optimum temperature is reached, increasing temperature further decreases rate of reaction as bonds holding tertiary structure in place break and active site may change shape and become denatured

Question 22

Describe how changing pH affects enzyme concentration

Answer 22

Rate of reaction is optimum at each enzymes optimum pH (usually pH7), going above or below this means H and OH ions disrupt the ionic and hydrogen bonds in its tertiary structure

Question 23

What are competitive inhibitors?

Answer 23

Molecules other than the substrate which bind to the active site; lower rate of reaction by preventing substrate from binding

Question 24

What are non-competitive inhibitors?

Answer 24

Molecules which bind to the allosteric site, changing the shape of the active site of the enzyme permanently and stopping rate of reaction