Proteins and enzymes

Question 1

Amino acids are the basic monomer unit of what polymer?

Answer 1

peptides

Question 2

What can polypeptides be combined to form?

Answer 2

proteins

Question 3

How do amino acids provide evidence for evolution?

Answer 3

the fact that the same 20 amino acids occur in all living organisms support evolution

Question 4

What are the features of all amino acids?

Answer 4

central carbon atom attached to 4 different chemical groups:

• amino group (-NH2)
• carboxyl group
• hydrogen atom
• R group

Question 5

What if the structure of an amino acid and what does R represent?

Answer 5

The R can be one of twenty different chemical groups

Question 6

How many amino acids are used in a protein and what do they contain?

Answer 6

20 different amino acids - contain carbon, hydrogen, oxygen, and nitrogen and some contain sulfur.

Question 7

What do amino acids combine to make? (name the reaction)

Answer 7

dipeptide = condensation reaction

Question 8

How are proteins held together?

Answer 8

The amino acids in a protein chain are attracted to each other by these strong peptide bonds, between the carbon atom of one amino acid and the nitrogen atom of the other

Question 9

What is meant by the primary structure of a protein and what is its significance?

Answer 9

The order in which the amino acids are arranged in a protein chain (its sequence)

it determines the protein’s ultimate shape and hence its function

Question 10

What is the sequence of amino acids determined by?

Answer 10

DNA

Question 11

What is meant by the secondary structure of a protein? (Mention the bonds involved)

Answer 11

The coils and pleats of amino acid chains are held together by weak forces of hydrogen bonds, forming 3d structures: a- helix and beta-pleated sheet

Question 12

What is meant by the tertiary structure of a protein? (Mention the bonds involved)

Answer 12

This refers to the 3D shape of the protein ( e.g. a protein being folded into a ball). This is held together by a mixture of disulfide bridges, ionic bonds and hydrogen bonds. Also hydrophobic and hydrophilic interactions

Question 13

Tell me about the ionic bonds in the tertiary structure of proteins?

Answer 13

formed between carboxyl and amino groups that are not involved in forming peptide bonds, They are easily broken by changes in pH

Question 14

What are disulfide bonds?

Answer 14

Where two Cysteine amino acids are found together, a strong double bond (S=S) is formed between the Sulphur atoms within the Cysteine monomers.

Question 15

What is the significance of the 3D structure of a protein?

Answer 15

• important to how the protein functions
• makes each protein distinctive and allows it to recognise, and be recognise by, other molecules.
• can then interact with them in a very specific way

Question 16

How are proteins denatured (tertiary structure)?

Answer 16

tertiary structure can be broken by the action of heat. Increasing the kinetic energy of protein with a tertiary structure makes it vibrate more, and so the bonds that maintain its shape (which are mainly weak, non-covalent bonds) will be more likely to break.

Question 17

What is the Quaternary structure of proteins?

Answer 17

large proteins that have formed complex molecules of individual polypeptide chains linked in various ways.

two or more polypeptide chains together

There may also be non-protein (prosthetic) groups associated with the molecules

Question 18

How do you test for proteins?

Answer 18

1) place a sample of the solution to be tested in a test tube and add an equal volume of sodiu hydroxide solution at room temperature
2) Add a few drops of biuret reagent and mix gently
3) a purple coloration indicates the presence of peptide bonds and hence a protein. No proteins = stays blue

Question 19

What are the two different types of molecular shapes for proteins and describe them?

Answer 19

• **Globular** - These tend to form ball-like structures, caused by tightly folded polypeptide chains where hydrophobic parts are towards the centre and hydrophilic are towards the edges, which makes them water soluble. They usually have metabolic roles
• **Fibrous** - They proteins form long fibres, which are parallel to one another and mostly consist of repeated sequences of amino acids. These chains are linked by cross-bridges and so form very stable molecules. Insoluble in water and have high tensile strength. They usually have structural roles, *such as: Collagen in bone and cartilage, Keratin in fingernails and hair.*

Question 20

What are enzymes?

Answer 20

They are globular proteins that act as catalysts to both anabolic (building up) and catabolic (breaking down) reactions. They work both in intracellular and extracellular conditions

Question 21

What must happen for a chemical reaction to happen?

Answer 21

• The enzyme must collide with the substrate with suffient energy
• The substrate must fit into the active site

Question 22

What is the induced fit model?

Answer 22

An enzyme-substrate complex forms when the active site changes shape slightly so it is complementary to the substrate

this reduces the activation energy

Question 23

What is the effect of temperature on enzyme action?

Answer 23

Increase in temp = increase in kinetic energy= molecules moving around more rapidly and colliding with each other more frequently= more enzyme-substrate complexes= increase in the rate of reaction

Optimum temperature = highest number of collisions and enzyme - substrate complexes

High temperatures to very high temperatures = lots of kinetic energy = Hydrogen bonds holding the 3d structure together breaking = the substrate fits less easily into the active, causing the reaction to slow down = eventually the enzyme doesnt have an active site that fits the substrate anymore- no more enzyme- substrate complexes made due to the enzyme denaturing

Question 24

What is the effect of pH on enzyme action?

Answer 24

• Slight change in pH = slightly alters the charge = harder for enzyme-substrate complexes to form
• change in pH = alters the charge on the amino acid that makes up the active site of the enzyme = substrate can no longer become attached o the active site enzyme-substrate complex cannot be formed
• change in pH can cause the bonds maintaining the enzyme’s tertiary structure (Hydrogen and ionic bonds) to break.

Question 25

How is the arrangement of the active site determined?

Answer 25

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, casing the active site to change shape

Question 26

Why is it unlikely for enzymes to denature via pH?

Answer 26

because pH fluctuations inside organisms are usually small

Question 27

Why aren’t enzymes used up?

Answer 27

Because once an active site on an enzyme has acted on its substrate, it is free to repeat the procedure on another substrate molecule = not used up

Question 28

What is the effect of ENZYME concentration on the rate of reaction?

Answer 28

• low enzyme concentration = too few enzyme molecules to allow all substrate molecules to find an active site at one time= rate of the reaction low
• intermediate enzyme concentration = all the substrate molecules can occupy an active site at the same time = high rate of reaction
• very high enzyme concentration = the addition of further enzyme molecules has no effect as there are already enough active sites to accommodate all the available substrate molecules. This is because it is a LIMITING FACTOR