Biological Molecules (A)

Examples of reactions enzymes catalyse

-Respiration

-Digestion

-Production of collagen

Where does enzyme action occur

-Intracellular

-Extracellular

Intracellular

Within cells

Extracellular

Outside cells

What biological molecule are enzymes

Proteins

Activation energy

The amount of energy that needs to be supplied to the chemicals before the reaction will start

What usually provides the activation energy for reactions

Heat

How do enzymes catalyse reactions

They lower the activation energy of a reaction, speeding up the rate of reaction

Explain how enzyme-substrate complexes lower the activation energy for synthesising molecules

Being attached to the enzyme holds the two substrate molecules close together, reducing any repulsion between the molecules so that they bond easier

Explain how enzyme-substrate complexes lower the activation energy for the breakdown of molecules

Fitting into the active site puts strain on the bonds in the substrate, so the substrate molecule breaks up more easily

What are the models for enzyme action

-Lock and Key

-Induced Fit

Lock and key model

The substrate fits into the enzyme the same way a key fits into a lock

Induced fit model

After an enzyme-substrate complex is formed, the active site changes shape slightly fit the substrate

Explain why enzymes are highly specific

The shape of their active site is determined by their tertiary structure which is determined by their primary structure. Each different enzyme has a different tertiary structure and so a different shaped active site, which only one complementary substrate will fit in so only this reaction is catalysed

What happens if the enzyme’s tertiary structure is altered

The active site will change shape so the substrate will no longer fit

What is the primary structure of a protein controlled by

A gene

What happens if a mutation occurs in the gene controlling the primary structure of an enzyme

The tertiary structure changes

Explain how increasing temperature affects enzyme activity

-At first, it increases as molecules have more kinetic energy so the enzymes are more likely to collide with the substrate molecules and with more energy

-If temperature too high, denatures

Explain how a high temperature can cause an enzyme to denature

The vibrations break some of the bonds holding an enzyme in shape, changing the shape of the active site so that the substrate no longer fits

Optimum temperature for most human enzymes

37°C

Explain how pH can affect an enzyme

A pH too low or too high means that the H⁺ and OH^- ions can mess up the ionic and hydrogen bonds that hold the enzymes tertiary structure in place, changing the active site’s shape

Explain how increasing enzyme concentration affects rate of reaction

-The more enzyme molecules, the more likely substrate molecules are to collide and form an enzyme-substrate complex, increasing rate of reaction.

-Rate eventually plateaus when substrate concentration is limiting rate of reaction

Explain how increasing substrate concentration affects rate of reaction

-More substrate molecules means collisions between enzymes and substrates are more likely, increasing rate of reaction until saturation point

-Increasing beyond saturation point has no effect

Saturation point

The point at which all active sites are full

Explain why rate of reaction will not continue to increase as more substrate is added at saturation point

There are no free active sites, so adding them makes no difference

Explain what happens to the rate of reaction of an enzyme-controlled reaction if no variables are changed

Substrates are being used up so the substrate concentration decreases with time, decreasing the rate of reaction

Enzyme inhibitors

Prevent enzyme activity by binding to the enzyme

Competitive inhibition

Inhibitor molecules have a similar shape to the substrate molecules so compete with the substrate to bind with the active site, blocking it

Explain how increasing competitive inhibitor concentration affects rate of reaction

Decreases rate of reaction as the inhibitors fill up the active sites, stopping enzyme-substrate complexes from forming

Non-competitive inhibition

Inhibitor molecules bind to the enzyme away from its active site, causing it to change shape so that substrate molecules will no longer fit in it

Explain what happens if substrate concentration of an competitively inhibited reaction is increased

The substrates have a greater chance of binding to the active site before an inhibitor, increasing the rate of reaction

Explain what happens if substrate concentration of an non-competitively inhibited reaction is increased

The enzymes will still be inhibited, so there is barely any change to reaction rate

Experiment to investigate the effect of temperature on an enzyme-controlled reaction by measuring the speed at which a product is made

1- Set up boiling tubes containing equal volumes and concentrations of hydrogen peroxide. Add an equal volume of buffer solution to each.

2- Place each boiling tube into a water bath of a different temperature. Wait for the tubes to reach the temperature.

3- Add catalase to the boiling tube

4- Attach a delivery tube from the bung of the boiling tube into a trough of water containing an upturned measuring cylinder.

5- Record volume the water rose by in a set length of time.

6- Repeat 3 times for each temperature at different temperatures

7- Calculate an average rate of reaction for each temperature

Explain the use of hydrogen peroxide in the enzyme experiment

Catalase catalyses the breakdown of hydrogen peroxide into water and oxygen. Oxygen displaces water, so the volume risen an upturned measuring cylinder is equal to the volume of oxygen added

What variables should be controlled in the enzyme temperature experiment

-Volume and concentration of hydrogen peroxide

-Volume of buffer (to control pH)

-Volume and concentration of catalase

What is the volume of oxygen produced in the enzyme temperature experiment

The volume the upturned cylinder increased by

What does catalase catalyse the break down of

Hydrogen peroxide

What does catalase catalyse the breakdown of hydrogen peroxide into

Oxygen and water

What does amylase catalyse the breakdown of

Starch

What does amylase catalyse the breakdown of starch into

Maltose

Experiment to investigate the effect of enzyme concentration on the rate if reaction

1- Add a drop of iodine into each well of a spotting tile

2- Mix together a known concentration of amylase and starch in a test tube.

3- Use a pipette to add the mixture into a well at regular intervals

4- Wells remain browny-orange when all starch is broken down

5- Repeat with different amylase concentrations

How to alter the enzyme experiments to measure the effect of pH on enzyme-controlled reactions

Change the independent variable to the pH of the buffer added to each test tube

How to calculate the initial rate of reaction

Draw a tangent to the graph at t=0 and calculate its gradient

Triglycerides

A molecule of glycerol with three fatty acids attached

Describe the structure of a fatty acid

A carboxylic acid group attached to a structurally variable long tail of hydrocarbons

Explain the solubility of lipids in water

Insoluble because the tails of fatty acids are hydrophobic

Hydrophobic

Repel water molecules

What molecule is this?

Fatty acid

What molecule is this?

Glycerol

Explain how triglycerides form

A condensation reaction between three fatty acids and a glycerol molecule

Ester bond

Chemical bond between a glycerol and fatty acid molecule

Types of fatty acids

-Saturated fatty acid

-Unsaturated fatty acid

Saturated fatty acid

No double bonds between carbon atoms

Unsaturated fatty acid

At least one double bond between carbon atoms

What is the structural difference between a saturated and unsaturated fatty acid (caused by double bonds)

An unsaturated fatty acid has a kink in the chain where a double bond is

Types of lipids

-Triglycerides

-Phospholipids

Type of lipid in cell membranes

Phospholipids

Phospholipid

Two fatty acids and a phosphate group joined to a glycerol

Property of the phosphate group of a phospholipid

Hydrophilic

Hydrophilic

Attracts water

Function of triglycerides

Energy storage molecules

Why are triglycerides good energy storage molecules

They have a long hydrocarbon tail containing lots of chemical energy

Explain whether triglycerides cause the cell to swell up or not

Triglycerides are insoluble in water so do not affect the water potential of the cell so do not cause water to enter by osmosis so do not cause the cell to swell up

What do many triglycerides in a cell form

They clump together as insoluble droplets

Explain why triglycerides clump together as droplets

The fatty acid tails are hydrophobic

Explain the structure of a triglycerides droplet

Hydrocarbon tails face inwards so are furthest from water, glycerol heads face outwards to shield tails from water

Phospholipid function

Make up the bilayer of cell membranes

Explain the structure of the bilayer of cell membranes

Form a double layer of phospholipids with the heads facing outwards and the tails facing inwards

Explain how the cell membrane acts as a barrier to water-soluble substances

The centre of the bilayer is hydrophobic so water-soluble substances can’t easily pass through it

What is the emulsion test for

Lipids

Test for lipids

1- Add ethanol

2- Shake

3- Add to water

4- Lipids will precipitate out as a milky white emulsion

Monomers of proteins

Amino acids

Dipeptite

Two amino acids joined together

Polypeptide

When more than two amino acids join together

Proteins

One or more polypeptides

Amino acid general structure

Carboxyl group, amine group and variable side group

Carboxyl group

COOH

Amine group

NH₂

How many different types amino acids are there (that make up proteins)

20

What molecule is this?

Amino acid

Describe how polypeptides are formed

Amino acids are linked together by condensation reactions

What happens to polypeptides during digestion

They are broken down into amino acids

Peptide bond

The chemical bond between amino acids

How many structural levels are there of a protein

4

Primary structure of a protein

The sequence of amino acids in a polypeptide chainrotP

Explain the secondary structure of a protein

Hydrogen bonds form between amino acids which cause it to coil into an alpha helix or a beta pleated sheet

Tertiary structure of a protein

-Coiled/folded chain coils/folds further

-More bonds form between different parts of the polypeptide chain (hydrogen and ionic)

-Disulfide bridges form

How many structural levels are there for proteins mad cup of a single polypeptide chain

3

Explain how disulphide bridge form

When two molecules of cysteine come close together the sulfur atom in one cysteine bonds to the sulfur atom in the other

Quaternary structure of a protein

Several polypeptide chains held together by bonds

Final 3D structure of a protein made up of more than one polypeptide chain

Quaternary Structure

Functions of proteins

-Enzymes

-Antibodies

-Transport proteins

-Structural proteins

Explain the structure of enzymes

Spherical due to the tight folding of polypeptide chains

Solubility of enzymes

Soluble

Antibody structure

-Two light polypeptide chains and two heavy polypeptide chains bonded together

-Has variable regions

Variable regions

Areas where the amino acid sequence varies greatly

Heavy polypeptide chain

Long chain

Light polypeptide chain

Short chain

Explain the structure of channel proteins

Hydrophobic and hydrophilic amino acids in the protein cause it to fold up, so that it can transport molecules and ions across membranes

Structural proteins

Physically strong proteins