proteins 2

What are amino acids?

Monomers of proteins.

What three groups make up the general structure of an amino acid?

Amine group, carboxyl group, R group.

What does NH₂ represent in an amino acid?

The amine group.

What does COOH represent in an amino acid?

The carboxyl group.

What does the R group represent?

Variable side group determining amino acid identity.

Why do the 20 common amino acids differ from one another?

Differences in their R groups.

What reaction joins amino acids together?

Condensation reactions.

What bond forms between two amino acids?

Peptide bonds.

What molecule is released during peptide bond formation?

Water.

What is a dipeptide?

Two amino acids joined by a peptide bond.

formed by a condensation reaction

What is a polypeptide?

Polymer chain of many amino acids linked by peptide bonds.

via condensation reactions

What determines the sequence of amino acids in a polypeptide?

The gene encoding the polypeptide.

How is the primary structure of a protein defined?

The linear sequence of amino acids.

Why is the primary structure crucial for protein function?

Determines folding and higher structure.

What interactions produce the secondary structure of proteins?

Hydrogen bonding along the chain.

What are the two main forms of secondary structure?

α-helix and β-pleated sheet.

How are hydrogen bonds involved in an α-helix?

Regular hydrogen bonding holds the coil.

How are hydrogen bonds involved in β-pleated sheets?

Hydrogen bonds form between parallel strands.

What determines the tertiary structure of a protein?

Interactions between R groups.

What three key bonds stabilise tertiary structure?

Hydrogen bonds, ionic bonds, disulfide bridges.

Which tertiary bond is strongest?

Disulfide bridges.

Which tertiary bond is weakest?

Hydrogen bonds.

What is an ionic bond in protein structure?

Bonds between oppositely charged R groups.

What are disulfide bridges?

Covalent bonds between sulfur-containing R groups.

Which amino acid typically forms disulfide bridges?

Cysteine.

Why are disulfide bridges important for protein stability?

Strong covalent stability reinforces folded structure.

What is quaternary structure?

More than one polypeptide chain e.g. haemoglobin

Formed by interactions between polypeptides

(hydrogen bonds, ionic bonds, disulfide bridges)

Why may a protein consist of more than one polypeptide chain?

Some proteins require multi-subunit assembly to function.

Give an example of a quaternary protein.

Haemoglobin.

How do hydrogen, ionic and disulfide bonds contribute to quaternary structure?

They stabilise and maintain the multi-subunit arrangement.

Why can proteins have such varied functions?

Structural variation produces diverse shapes.

How does structure relate to protein function?

Function depends entirely on precise 3D conformation.

What reagent is used in the biuret test?

Biuret reagent (NaOH + Cu²⁺ solution).

What colour change indicates a positive biuret test?

Blue → lilac.

Why does biuret reagent detect proteins?

Copper ions complex with peptide bonds.

What initial step is needed before adding the copper sulfate solution in the biuret test?

Make the solution alkaline with NaOH.

Why is the biuret test qualitative?

It only shows presence, not amount.

What would a negative biuret test look like?

The solution stays blue.

How can reliability of the biuret test be improved?

Replicate tests, use controls, standardise volumes.

What experimental technique can separate amino acids?

Chromatography.

Why must known amino acid standards be run alongside chromatography samples?

To compare Rf values for identification.

What feature allows amino acids to separate on chromatography paper?

Different solubilities in the mobile vs stationary phases.

What is an enzyme?

A protein catalyst.

How do enzymes affect activation energy?

They lower activation energy.

Why is lowering activation energy important in living systems?

Allows reactions to occur rapidly at biological temperatures.

What is the induced-fit model?

The active site is not initially complementary to the substrate

Active site moulds around substrate on binding.

How does the induced-fit model differ from the lock-and-key model?

Lock-and-key suggests fixed shape; induced-fit allows active site flexibility.

What happens to the enzyme’s active site when substrate binds?

It changes shape slightly to fit substrate more closely.

Why is enzyme specificity determined by tertiary structure?

Tertiary structure determines active-site shape.

What is an enzyme–substrate complex?

The temporary binding of enzyme and substrate.

Why do enzymes catalyse both intracellular and extracellular reactions?

Their catalytic roles occur both inside and outside cells.

How does temperature affect enzyme activity?

Rate rises with temperature until optimum is reached.

What happens to enzymes at very high temperatures?

Enzymes denature as bonds break and active site changes shape.

How does pH affect enzyme function?

pH affects ionisation of R groups and active-site shape.

What is the effect of pH

on enzyme-controlled

reaction?

Too high or too low a pH will interfere with the charges in the amino acids in the active site.

This breaks the ionic and hydrogen bonds holding the tertiary structure in place

therefore the active site changes shape and the enzyme denatures

Different enzymes have a different optimal pH

How does enzyme concentration affect rate of reaction?

At low enzyme concentrations, there will be fewer collisions between the enzyme and substrate.

At high enzyme concentrations, the rate plateaus because there are more enzymes than the substrate, so there are empty active sites.

How does substrate concentration affect rate of reaction?

At low substrate concentrations, there will be fewer collisions

between the enzyme and substrate.

At high substrate concentrations, the rate plateaus because all the enzyme active sites are saturated

What is a competitive inhibitor?

A molecule that is similar shape to substrate binds to the active site.

How do competitive inhibitors reduce reaction rate?

It reduces availability of active sites.

How can the effect of a competitive inhibitor be overcome?

By adding excess substrate.

What is a non-competitive inhibitor?

A molecule that binds to an enzyme at the allosteric site

causing the active site to change shape

Why can non-competitive inhibition not be overcome by adding more substrate?

It changes active-site shape permanently for some fraction of enzymes.

How does inhibitor concentration affect enzyme rate?

Higher inhibitor concentration decreases rate by reducing functioning enzymes.

Inhibitor Graphs

With a high enough substrate concentration, the competitive inhibitors are knocked out of the active site and the rate of reaction will return to the same as with no

inhibitor.

The rate of reaction with a non-competitive inhibitor will be lower at all substrate concentrations.

Why do different enzymes have different optimals?

Their structures suit different cellular environments.

Why does enzyme activity eventually fall in a closed system even without denaturation?

Substrate is used up, decreasing reaction rate.

What evidence shows models of enzyme action changed over time?

Experimental evidence showed active sites change shape on binding.

Why was the induced-fit model accepted over lock-and-key?

It better explained observed changes in enzyme–substrate binding.

How do enzymes contribute to whole-organism function?

They catalyse essential metabolic reactions across tissues and systems.

What variable must be controlled when investigating enzyme rate experimentally?

Temperature, pH, enzyme concentration, substrate concentration, inhibitor concentration.

Why must initial rate be measured in enzyme experiments?

Because substrate concentration changes during the reaction.

How can initial rate be determined from a graph?

By drawing a tangent at t = 0.

Why is uncertainty calculated in rate measurements?

To assess precision of rate measurements.

What key practical allows investigation of enzyme variables?

Required Practical 1: effect of a named variable on enzyme-controlled rate.