Proteins & enzymes

What are some functions of proteins?

• Structural (e.g. collagen)

• Enzymes (e.g. amylase)

• Transport (e.g. haemoglobin)

• Hormones (e.g. insulin, glucagon)

What are proteins made of?

Amino acids:

• a hydrogen atom

• a basic amino group

• an acidic carboxyl group

• a variable “R group”

How are polypeptides formed?

When multiple amino acids are joined together by peptide bonds in a condensation reaction, resulting in molecules of water being formed as well

What is the primary structure of a protein?

The specific sequence of amino acids in the polypeptide chain

What is the secondary structure of a protein?

The folding of the primary structure into an alpha-helix or beta-pleated sheet due to the formation of hydrogen bonds

What is meant by alpha-helix?

• The polypeptide chain is wound round to form a helix & is held together by hydrogen bonds running parallel with the long helical axis

• There are many hydrogen bonds → very stable & strong structure

What is meant by beta-pleated sheet?

The polypeptide chain zig-zags backwards & forwards, forming a sheet of anti-parallel strands & is held together by hydrogen bonds

What is the tertiary structure of a protein?

• The 3D folding of a protein, held together by hydrogen bonds, ionic bonds or disulphide bonds between R groups

• Polar amino acids on outside & non-polar on inside

What is the quaternary structure of a protein?

The folding of more than one polypeptide chain

What are globular proteins & give an example?

• Have a tertiary & quaternary structure, held together by hydrogen/ionic bonds & disulphide bridges → hydrophilic on the outside & hydrophobic on the inside

• Haemoglobin is composed of four globular (2 alpha & 2 beta) polypeptide chains (globins). Each chain contains a prosthetic haem group, with Fe²⁺ in the centre

What are fibrous proteins & give an example?

Long, thin insoluble polypeptide chains that form structural components:

• e.g. collagen → 3 polypeptide chains that form a triple helix, held together by hydrogen bonds (many triple helices joined together)

What is denaturation?

• If the hydrogen bonds break in the secondary, tertiary & quaternary structure, then the protein loses its 3D structure

• The polypeptide chain just folds into a random coil & the protein loses its function (happens at very high temperatures or at very low/high pH)

  • covalent bonds aren’t broken however, so the primary structure remains intact

What are intracellular & extracellular enzymes?

• Intracellular enzymes: catalyse all metabolic reactions inside cells & organelles (e.g. respiration & protein synthesis)

• Extracellular enzymes: synthesised inside cells but then are exported & catalyse reactions outside the cell (e.g. digestive enzymes)

What is the lock-and-key model?

• The shape of an enzyme’s active site is complementary to the shape of the substrate molecule

• So, the substrate molecule binds to the active site & the product is released

What is the induced-fit model?

• The active site’s shape is not directly complementary, so changes shape slightly to accommodate the substrate to form an ES complex → puts strain on substrate bonds, lowering activation energy

• When products have been made & leave, the active site returns to its original shape

How does temperature affect the rate of enzyme reactions?

• Up to optimum temperature, rate of reaction increases as enzyme & substrate molecules have more kinetic energy → collide more often & also have energy to overcome activation energy

• Above optimum temperature, hydrogen bonds holding secondary, tertiary & quaternary structures of enzyme together are broken → enzyme loses its specific shape, becoming a random coil → substrate can no longer bind

How does pH affect the rate of enzyme reactions?

• The pH affects the charge of the R-groups of the amino acids at the active site

• The enzyme & substrate could adopt the same positive (low pH: too many H⁺ ions) or negative (high pH: too many OH^- ions) electrical charge, causing electrostatic repulsion, so ES complexes cannot form

How does enzyme concentration affect the rate of enzyme reactions?

• As enzyme concentration increases, the rate of reaction also increases as there are more enzyme molecules available to catalyse the reaction

• At very high enzyme concentrations, the substrate concentration becomes the limiting factor → rate of reaction plateaus

How does substrate concentration affect the rate of enzyme reactions?

• As substrate concentration increases, the rate of reaction also increases as more substrate molecules can collide with enzyme molecules → more ES complexes formed

• At higher substrate concentrations, the enzyme active sites become saturated with substrates, so enzyme concentration becomes the limiting factor → graph plateaus

What are competitive inhibitors?

• Molecules with a similar structure to the normal substrate molecule & can fit into the active site of the enzyme

• They compete with the substrate for the active site, so the reaction is slower

• However, if the substrate concentration is increased high enough, it will out-compete the competitive inhibitor & the rate can approach a normal rate

What are non-competitive inhibitors?

• Molecules with a different structure from the substrate molecule & do not fit into the active site

• They bind to the allosteric site on the enzyme & change the active site, so that the substrate molecules can no longer bind

• Increasing the substrate concentration has no effect because the amount of active enzymes are reduced

Outline the process of end-product inhibition

• When the final product of a metabolic pathway reaches a high concentration, it binds to the first enzyme in the pathway at an allosteric site

• This causes a conformational change in the enzyme, altering the 3D shape of the active site

• This means the substrate is unable to bind effectively, reducing the rate of ES complex formation & slowing the pathway

What is the biochemical test for proteins?

Biuret test:

• Add few drops of sodium/potassium hydroxide & then add copper sulphate

• If proteins are present, solution will change from blue to purple