1- Proteins, RP1

Biological molecules

Describe/ draw the general structure of an amino acid

• COOH= carboxyl group

• R= variable group

• H2N= amine group

How many amino acids are common in all organisms? How do they vary?

• 20 amino acids are common in all organisms

• differ only in their side/ variable group

Describe how amino acids join together

• condensation reaction

• removing a water molecule

• between carboxyl group of one and amine group of another

• forming a peptide bond

What are dipeptides and polypeptides?

• dipeptide= 2 amino acids joined together

• polypeptide= many amino acids joined together

  > a functional protein may contain one or more polypeptides

Describe the primary structure of a protein

sequence of amino acids in a polypeptide chain, joined by peptide chain

Describe the secondary structure of a protein

• folding (repeating patterns) of polypeptide chain e.g. alpha helix/ beta pleated sheet

• due to hydrogen bonding between amino acids

• between amine group and carboxyl group of different amino acids

Describe the tertiary structure of a protein

• 3D folding of polypeptide chain

• due to interactions between amino acid R groups (dependent on sequence of amino acids)

• forming hydrogen, ionic bonds and disulphide bonds

Describe the quaternary structure of a protein

• more than one polypeptide chain

• formed by interactions between polypeptides (hydrogen, ionic bonds, disulphide bridges)

Describe the test for proteins

1. add biuret reagent (sodium hydroxide + copper II sulphate)

2. positive result= purple/lilac colour (negative stays blue)—> indicates presence of peptide bonds

How do enzymes act as biological catalysts?

• each enzyme lowers activation energy of reaction it catalyses

• to speed up rate of reaction

Enzymes catalyse a wide range of intracellular and extracellular reactions that determine structures and functions from cellular to whole-organism level

Describe the induced-fit model of enzyme action

1. Substrate binds to (not completely complementary) active site of enzyme

2. causing active site to change shape (slightly) so it is complementary to substrate

3. so enzyme- substrate complex forms

4. causing bonds in substrate to bend/ distort, lowering activation energy

Describe how models of enzyme action have changed over time

• initially lock and key model- active site a fixed shape, complementary to one substrate

• now induced-fit model

Explain the specificity of enzymes

• specific tertiary structure determines shape of active site- dependent on sequence of amino acids (primary structure)

• active site is complementary to a specific substrate

• only this substrate can bind to active site, inducing fit and forming an E-S complex

Describe and explain the effect of enzyme concentration on the rate of enzyme-controlled reactions

• As enzyme conc increases, rate of reaction increases

  > enzyme conc= limiting factor (excess substrate)

  > more enzymes so more available active sites

  > so more E-S complexes form

• At a certain point, rate of reaction stops increasing/ levels off

  > substrate conc.= limiting factor (all substrates in use)

Describe and explain the effect of substrate concentration on the rate of enzyme-controlled reactions

• As substrate conc increases, rate of reaction increases

  > substrate conc= limiting factor (too few enzymes molecules to occupy all active sites)

  > more E-S complexes form

• At a certain point, rate of reaction stop increasing/ levels off

  > enzyme conc= limiting factor

  > as all active sites saturated/ occupied (at a given time)

Describe and explain the effect of temperature on the rate of enzyme-controlled reactions

• As temp increases, rate of reaction increases

  > more kinetic energy

  > so more E-S complexes form

• As temp increases above optimum, rate of reaction decreases

  > enzymes denature- tertiary structure and active sites change shape

  > as hydrogen/ ionic bonds break

  > so active site no longer complementary

  > so fewer E-S complexes form

Describe and explain the effect of pH on the rate of enzyme-controlled reactions

• As pH increases/ decreases above/ below optimum, rate of reaction decreases

  > enzymes denature- tertiary structure and active site change shape

  > as hydrogen/ ionic bonds break

  > so active site no longer complementary

  > so fewer E-S complexes form

Describe and explain the effect of competitive inhibitors on the rate of enzyme-controlled reactions

• As conc of competitive inhibitor increases, rate of reaction decreases

  > similar shape to substrate

  > competes for/ binds to/ blocks active site

  > so substrates can’t bind and fewer E-S complexes form

• Increasing substrate conc reduces effect of inhibitors (dependent on relative concs of substrate and inhibitor)

Describe and explain the effect of non-competitive inhibitors on the rate of enzyme-controlled reactions

• As conc of non-competitiove inhibitors increases, rate of reaction decreases

  > binds to site other than the active site (allosteric site)

  > changes enzyme tertiary structure/ active site shape

  > so active site no longer complementary to substrate

  > so substrates can’t bind so fewer E-S complexes form

• Increasing substrate conc has no effect on rate of reaction as change to active site is permanent

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Give examples of variables that could affect the rate of an enzyme-controlled reaction

• enzyme conc/ vol

• substrate conc/ vol

• temperature of solution

• pH of solution

• inhibitor conc

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Describe how temperature can be controlled

• use a thermostatically controlled water bath

• monitor using a thermometer at regular intervals and add hot/ cold water if temperature fluctuates

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Describe how pH can be controlled

• use a buffer solution

• monitor using a pH meter at regular intervals

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Why were the enzyme + substrate solutions left in the water bath for 10 mins before mixing?

so solutions equilibrate/ reach the temperature of the water bath

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Describe a control experiment

• use denatured enzymes (e.g. by boiling)

• everything else same as experiment, e.g. same conc/ vol of substrate (at start) and enzyme, same type/ vol of buffer solution, same temperature

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Describe how the rate of an enzyme- controlled reaction can be measured

• Measure time taken for reaction to reach a set point, e.g. conc/ vol/ mass/ colour of substrate or product

  > rate of reaction= 1/time= S^-1

• Measure conc/ vol/ mass/ colour of substrate or product at regular intervals (or using a continuous data logger) throughout reaction

  > plot on a graph with time on the x axis and whatever is being measured on the y axis

  > draw a langent at t=0 (or any other time for rate at a particular point)

• initial rate of reaction= change in y/ change in x = cm³ s^-1

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Suggest a safety risk and explain how to reduce this risk

• handling enzymes may cause an allergic reaction

• avoid contact with skin by wearing gloves and eye protection

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Explain why using a colourimeter to measure colour change is better than comparison to colour standards

• not subjective

• more accurate

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Explain a procedure that could be used to stop each reaction

• boil/ add strong acid/ alkali= denature enzyme

• put in ice= lower kinetic energy so no E-S complexes form

• add high conc of inhibitor= no E-S complexes form

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Describe how processed data can be presented in a graph

• independent variable on x axis, rate of reaction on y axis including units

• linear number sequence on axis, appropriate scale

• plot coordinates accurately as crosses

• join point to point with straight lines if cannot be certain of intermediate values OR draw a smooth curve

RP1: Effect of a named variable on the rate of an enzyme-controlled reaction

Explain why the rate of reaction decreases over time throughout each experiment

• initial rate is highest as substrate conc not limiting/ many E-S complexes form

• reaction slows as substrate used up and often stops as there is no substrate left