Biological molecules: proteins and enzymes

Question 1

What are amino acids?

Answer 1

Amino acids are the basic monomer units which combine to make polypeptides.
Polypeptides can be combined to form proteins.

Question 2

How many amino acids are there?

Answer 2

There are 100 identified.
20 amino acids naturally occur in proteins.
The fact the same 20 amino acids occur in all living organisms provides indirect evidence for evolution.
They only differ by their side group.

Question 3

What is the structure of an amino acid?

Answer 3

A central carbon atom to which are attached four groups.
Amino group (-NH2): a basic group.
Carboxyl group (-COOH): an acidic group.
Hydrogen atom (-H).
R (side) group: a variety of different chemical groups. Each amino acid has a different R group.

Question 4

What is the formula for an amino acid?

Answer 4

R
{
H2N ————–C————–COOH
{
H

Question 5

How are peptide bonds formed?

Answer 5

Amino acids combine to form a dipeptide, in a condensation reaction:
The water is made by combining an OH from the carboxyl group with an H from the amino group of another.
They become linked by a peptide bond between the carbon atom of one and the nitrogen atom of the other.
The peptide bond can be broken by hydrolysis to give its two constituent amino acids.

Question 6

How are polypeptides formed?

Answer 6

Through a series of condensation reactions, many amino acid monomers can be joined together by polymerisation.
The resulting chain of hundreds of amino acids is a polypeptide.

Question 7

What is the primary structure of proteins?

Answer 7

The number and sequence of amino acids in a polypeptide chain, determined by DNA.
There are a limitless number of possible combinations of primary protein structure.
Primary structure determines its ultimate shape and function.
A simple protein may consist of a single polypeptide chain, but more commonly, a protein is made up of a number of chains.

Question 8

What happens if an amino acid changes?

Answer 8

A change in just a single amino acid in the primary sequence can lead to a change in the shape of the protein and may stop it carrying out its function or just less well.
A protein’s shape is very specific to its function.

Question 9

What is the secondary structure of proteins?

Answer 9

The linked amino acids that make up a polypeptide possess both NH and C=O groups on either side of each bond.
The hydrogen of the NH group has an overall positive charge and the O of the C=O group is negative.
These two groups readily form weak hydrogen bonds.
This causes the long chain to be twisted into a 3-D shape.
Forms an α-helix or a β-pleated sheet.

Question 10

What is the tertiary structure of proteins?

Answer 10

The α-helices of the secondary protein structure can be twisted and folded even more to give the complex, and often specific, 3-D structure of each protein.
The 3D shape is important in its functioning and makes each protein distinctive and allows it to recognise, and be recognised, by other molecules.
It can then interact with them in a very specific way.

Question 11

How do bonds hold the tertiary structure together?

Answer 11

Where the bonds occur depends on the primary structure of the protein.
Disulfide bridges - are fairly strong and therefore are not easily broken.
Ionic bonds - are formed between any carboxyl and amino groups that are not involved in forming peptide bonds. They are weaker than disulfide bonds and are easily broken by changes in pH.
Hydrogen bonds - are numerous but easily broken.

Question 12

What is the quaternary structure of proteins?

Answer 12

Large proteins often form complex molecules containing a number of individual polypeptide chains that are linked in various ways.
May also be non-protein (prosthetic) groups associated with the molecules.
For example the iron-containing haem group in haemoglobin.

Question 13

What is the test for proteins?

Answer 13

The Biuret test, which detects peptide bonds:
Place a sample of the solution in a test tube and add an equal volume of sodium hydroxide at room temperature.
Add a few drops of very dilute (0.05%) copper sulfate solution and mix gently.
A purple colouration indicates proteins, stays blue if not.

Question 14

What are the two basic types of protein?

Answer 14

Fibrous proteins, such as collagen, have structural functions.
Globular proteins, such as enzymes and haemoglobin, carry out metabolic functions.

Question 15

What are fibrous proteins?

Answer 15

They form long chains which run paralell to one another.
These chains are linked by cross-bridges so form very stable molecules.

Question 16

What is the molecular structure of collagen?

Answer 16

The primary structure is an unbranched polypeptide chain.
In the secondary structure the polypeptide chain is very tightly wound.
Lots of the amino acid, glycine, helps close packing.
In the tertiary structure the chain is twisted into a second helix.
Its quaternary structure is made up of three such polypeptide chains wound together.

Question 17

Explain why the quaternary structure of collagen makes it a suitable material for a tendon?

Answer 17

The individual polypeptide chains in the fibres are held together by bonds between amino acids of adjacent chains.

Question 18

What are enzymes?

Answer 18

Globular proteins that act as catalysts.
Catalysts alter the rate of a chemical reaction without undergoing permanent changes themselves.
They can be used repeatedly and are therefore effective in small amounts.
Enzymes speed up reactions that already occur.

Question 19

What conditions must be satisfied in a natural reaction?

Answer 19

The molecules (substrate) must collide with sufficient energy to alter the arrangement of their atoms to form the products.
The free energy of the products must be less than that of the substrates.
Many reactions require an initial amount of energy to start, the activation energy.

Question 20

How do enzymes work?

Answer 20

Enzymes lower the activation energy the reaction needs to overcome to proceed.
Enzymes allow reactions to take place at a lower temperature than normal.
This enables some metabolic processes to occur rapidly at the human body temperature 37 degrees, which is relatively low.
Without enzymes these reactions would proceed too slowly to sustain life.

Question 21

What is the structure of enzymes?

Answer 21

Enzymes have a specific 3-D shape that is the result of their sequence of amino acids.
A specific region of the enzyme is functional - the active site.
This is made up of a relatively small number of amino acids. The active site forms a small depression within the much larger enzyme molecule.
The substrate fits neatly into this depression and forms an enzyme-substrate complex.
The substrate molecule is held within the active site by bonds that temporarily form between certain amino acids of the active site and groups on the substrate molecule.

Question 22

What is the induced fit model of enzyme action?

Answer 22

The active site forms as the enzyme and substrate interact.
The proximity of the substrate (change in environment) leads to a change in the enzyme that forms the functional active site.
The enzyme is flexible and can mould itself around the substrate.
The enzyme has a certain general shape, but this alters in the presence of the substrate.
As it changes shape, the enzyme puts a strain on the substrate molecule.
This strain distorts a particular bond or bonds in the substrate and consequently lowers the activation energy needed to break the bond.

Question 23

What is the lock and key model of enzyme action?

Answer 23

Proposed that enzymes work in the same way as a key operates a lock - each key has a specific shape that fits and operates only a single lock.
A substrate will only fit the active site of one particular enzyme.
This was supported by the observation that enzymes are specific in the reactions that they catalyse.
The shape of the substrate (key) exactly fits the active site of the enzyme (lock).

Question 24

What are the limitations of the lock and key model?

Answer 24

The enzyme, like a lock, is considered to be a rigid structure.
However, scientists had observed that other molecules could bind to enzymes at sites other than the active site, and altered the activity of the enzyme.
This suggested that the enzyme’s shape was being altered by the binding molecule. The structure was not rigid but flexible.
This led to the induced fit model being introduced as a modified version.

Question 25

How does temperature affect enzyme action?

Answer 25

A rise in temperature increases the kinetic energy of molecules.
So, the molecules move around more rapidly and collide with each other more often.
In an enzyme-catalysed reaction, the enzyme and substrate molecules come together more often in a given time.
There are more effective collisions resulting in more enzyme-substrate complexes being formed and so the rate of reaction increases.

Question 26

What happens at 45°c with enzyme action?

Answer 26

The temperature rise begins to cause the hydrogen and other bonds in the enzyme molecule to break.
This results in the enzyme, and its active site, to change shape.
At first, the substrate fits less easily into this changed active site, slowing the rate of reaction.

Question 27

What happens at 60°c with enzyme activity?

Answer 27

The enzyme is denatured, by heat breaking the bonds maintaining the tertiary structure of the enzyme.
Denaturation causes the substrate to no longer fit.
Denaturation is a permanent change and, once it has occurred, the enzymes do not function again.

Question 28

Why is the optimum temperature in humans 37°c?

Answer 28

Although higher temperatures would increase the metabolic rate slightly, the advantages are offset by additional energy that would be needed to maintain the high temperature.
Other proteins, apart from enzymes, may be denatured at higher temperatures.
At higher temperatures, any further rise in temperature, for example, during illness, might denature the enzymes.

Question 29

How does pH affect enzyme action?

Answer 29

The pH of a solution is a measure of its hydrogen ion concentration.
An increase in pH reduces the rate of enzyme action.
If the change in pH is more extreme then, beyond a certain pH, the enzyme becomes denatured.

Question 30

How is the pH of a solution calculated?

Answer 30

pH = -log¬10[H^+).
A hydrogen ion [H^+] concentration of 1 x 10^-9 therefore has a pH of 9.

Question 31

How does pH affect how an enzyme works?

Answer 31

A change in pH alters the charges on the amino acids that make up the active site of the enzyme.
As a result, the substrate can no longer become attached to the active site and so the enzyme-substrate complex cannot be formed.
Depending on how significant the change in pH is, it may cause the bonds maintaining the enzyme’s tertiary structure to break. The active site therefore changes shape.

Question 32

How does change in pH cause the active site to change shape?

Answer 32

The arrangement of the active site is partly determined by the hydrogen and ionic bonds between NH2 and COOH groups of the polypeptides that make up the enzyme.
The change in H+ ions affects this bonding, causing the active site to change shape.
pH fluctuations are usually small, so are far more likely to reduce an enzyme’s activity than than to denature it.

Question 33

How does enzyme concentration affect enzyme activity?

Answer 33

Once an active site on an enzyme has acted on its substrate, it is free to repeat the procedure on another substrate molecule.
This means enzymes are not used up in the reaction and therefore work efficiently at very low concentrations.
A single enzyme can act on up to millions of substrate molecules in one minute.
As long as there is an excess of substrate, an increase in the amount of enzyme leads to a proportionate increase in the rate of reaction.

Question 34

What are the two changes most frequently measured in enzyme-catalysed reactions?

Answer 34

The formation of the products of the reaction, for example, the volume of oxygen produced when the enzyme catalase acts on hydrogen peroxide.
The disappearance of the substrate, for example, the reduction in concentration of starch when it is acted upon by amylase.

Question 35

How can the shapes of enzyme-catalysed reactions be explained?

Answer 35

At first there is lots of substrate but no product.
It is very easy for substrate molecules to come into contact with the empty active sites on the enzyme molecules.
All enzyme active sites are filled at any given moment and the substrate is rapidly broken down into its products.
The amount of substrate decreases as it is broken down, resulting in an increase in the amount of product.

Question 36

What happens in enzyme-catalysed graphs as the reaction proceeds?

Answer 36

As the reaction proceeds, there is less and less substrate and more and more product.
It becomes more difficult for the substrate molecules to come into contact with the enzymes because there are fewer substrate and also the product molecules may get in the way and prevent them reaching the active site.
It therefore takes longer for the substrate molecules to be broken down by the enzyme and so its rate slows.

Question 37

What happens in enzyme-catalysed graphs/reactions at the end?

Answer 37

The rate of reaction continues to slow until there is so little substrate that any further decrease in concentration cannot be measured.
The graphs flatten out because all the substrate has been used up and so no new product can be produced.

Question 38

Why does enzyme concentration effect the rate of reaction in this way?

Answer 38

There is more substrate than the enzyme’s active sites can cope with.
If you therefore increase the enzyme concentration, some of the excess substrate can now also be acted upon and the rate of reaction will increase.
If, however, the substrate is limiting, then any increase in enzyme concentration will have no effect on rate of reaction, and the graph levels off.
This is because the available substrate is already being used as rapidly as it can be by the existing enzyme molecules.

Question 39

How does substrate concentration effect rate of enzyme action?

Answer 39

If the enzyme concentration is fixed and substrate concentration is slowly increased, the rate of reaction increases proportionally to substrate concentration.
Once the active sites are all filled, the rate of reaction is at its maximum.
After that, the addition of more substrate will have no effect on the rate of reaction.

Question 40

Why does substrate concentration effect rate of enzyme action?

Answer 40

At low substrate concentrations, the enzyme molecules have only a limited number of substrate molecules to collide with, and therefore the active sites of the enzymes are not working to full capacity.
As more substrate is added, the active sites become filled, until the point where all of them are working as fast as they can.
The rate of reaction is at its maximum.

Question 41

What are enzyme inhibitors?

Answer 41

Substances that directly or indirectly interfere with the functioning of the active site of an enzyme and so reduce its activity.

Question 42

What are the types of enzyme inhibitor?

Answer 42

Competitive inhibitors - which bind to the active site of the enzyme.
Non-competitive inhibitors - which bind to the enzyme at a position other than the active site.

Question 43

How do competitive inhibitors work?

Answer 43

They have a similar molecular shape to the substrate.
This allows them to occupy the active site of an enzyme.
They therefore compete with the substrate for the available active site.

Question 44

How is the effect on enzyme activity by inhibitor determined?

Answer 44

The difference between the concentration of the inhibitor and of the substrate.
If the substrate concentration is increased, the effect of the inhibitor is reduced.
The inhibitor is not permanently bound to the active site and so, when it leaves, another molecule can take its place.
This could be a substrate or competitive inhibitor, depending on how much of each type is present.
All the substrate molecules will occupy an active site, but the greater the concentration of inhibitor, the longer this will take.

Question 45

What is an example of competitive inhibition?

Answer 45

Occurs within an important respiratory enzyme that acts on succinate.
Another compound, called malonate, can inhibit the enzyme because it has a very similar molecular shape.
It therefore easily combines with the enzyme and blocks succinate from combining with the active site.
Another example is the inhibition of transpeptidase by penicillin.

Question 46

How do non-competitive inhibitors work?

Answer 46

They attach themselves to the enzyme at a binding site which is not the active site.
Upon attaching to the enzyme, the inhibitor alters the shape of the enzyme and thus its active site so the substrate molecules can no longer occupy it.
As the substrate and inhibitor are not competing, an increase in substrate concentration does not decrease the effect of the inhibitor.