Topic 1- Proteins

Question 1

What are proteins?

Answer 1

Proteins are biological molecules that are composed of carbon, hydrogen, oxygen and nitrogen.

Question 2

What are the monomers of proteins?

Answer 2

Amino acids.

Question 3

What bond is formed via a condensation reaction of 2 amino acids?

Answer 3

Peptide bond.

Question 4

What do you form when two amino acids join together?

Answer 4

A condensation reaction takes place forming a dipeptide.

Question 5

What do you form when more than two amino acids join together?

Answer 5

A condensation reaction takes place between the amine group of one amino acid and the carboxyl group of another forming a polypeptide.

Question 6

Describe the structure of an amino acid.

Answer 6

• Amine Group (H2N)
• Carboxyl Group (COOH)
• A variable carbon-containing group (R)
• A hydrogen (H)

Question 7

How many different amino acids can you get?

Answer 7

There are 20 different amino acids, each determined by their different R groups.

Question 8

What does a functional protein contain?

Answer 8

One or more polypeptides.

Question 9

What are the 4 structures that proteins are called?

Answer 9

Primary
Secondary
Tertiary
Quaternary

Question 10

What is meant by the primary structure of proteins?

Answer 10

The sequence of amino acids in the polypeptide chain.

Question 11

What is meant by the secondary structure of proteins?

Answer 11

The way in which the chain of amino acids of the polypeptides of a protein is folded. Hydrogen bonds form between the amino acids, to form 3D shapes like an alpha helix or beta pleated sheet.

Question 12

What is meant by the tertiary structure of proteins?

Answer 12

Further folding of a whole polypeptide chain in a precise way. The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is.
There are three kinds of bonds involved:
1. Hydrogen bonds, which are weak.
2. Ionic bonds between R-groups with positive or negative charges, which are quite strong.
3. Disulphide bridges - covalent S-S bonds between two cysteine amino acids, which are strong.

Question 13

What is meant by the quaternary structure of proteins?

Answer 13

More than one polypeptide chains linked together and held by bonds.

Question 14

What determines the function of a protein?

Answer 14

The shape of the protein.

Question 15

Describe the test for proteins.

Answer 15

The test for proteins is known as the biuret test
The steps are:
- Add the test sample to a test tube.
- Then add sodium hydroxide solution as the test solution needs to be alkaline.
- Then add a few drops of copper(II) sulfate solution.
- If the solution turns from blue to purple, then it indicates that protein is present.

Question 16

What is an enzyme?

Answer 16

Enzymes are biological catalysts that increase the rate of reaction by lowering the activation energy of the reaction they catalyse without being used up.

Question 17

Which protein structure does enzymes have?

Answer 17

Tertiary, which is why enzymes are highly specific.

Question 18

What reactions do enzymes catalyse?

Answer 18

Metabolic reactions (intracellular and extracellular).

Question 19

What is the active site on an enzymes?

Answer 19

The active site, which has a specific shape, is the part of an enzymes where the substrate molecules complementary to it bind to.

Question 20

What is formed when a substrate fits into an enzyme’s active site?

Answer 20

An enzyme-substrate complex.

Question 21

Explain the induced-fit model.

Answer 21

When an enzyme and a substrate interacts with each other, a change is induced in the shape of the active site, moulding around the substrate molecule.
The change in shape of the active site puts pressure/strain on certain bonds in the substrate, lowering the activation energy required to break the bond.

Question 22

How are the properties of enzymes relate to their tertiary structure?

Answer 22

Their tertiary structure allows enzymes to be highly specific, meaning that it will usually catalyse one reaction since their active site is complementary to a specific substrate.
Each different enzyme has a different tertiary structure and so a different active site.

Question 23

What are the 6 factors that affect enzyme activity?

Answer 23

• Temperature
• pH
• Enzyme concentration
• Substrate concentration
• Concentration of competitive inhibitors
• Concentration of non-competitive inhibitors

Question 24

How does temperature affect the enzyme activity from start to optimum?

Answer 24

• Increases kinetic energy of molecules
• Molecules move more rapidly
• Increase in chances of successful
  collisions
• Increases chance of forming enzyme- substrate complex
• increase rate of reaction

Question 25

How does temperature affect the enzyme activity beyond optimum?

Answer 25

• Bonds holding the tertiary structure
  break
• Active site shape is lost
• Substrate can no longer be
  complementary
• Enzyme-substrate complex cannot be
  formed
• Enzyme denatured and rate of reaction
  decreases

Question 26

How does the substrate concentration affect the enzyme activity?

Answer 26

Increasing the substrate concentration means that:
- more chance of successful collisions
- more chance of forming enzyme-substrate complex, therefore increasing rate of reaction
- this continues until the maximum rate of reaction is reached (when all the active sites are full/occupied)

Question 27

How does the enzyme concentration affect the enzyme activity?

Answer 27

Increasing the enzyme concentration means that:
- more chance of successful collisions
- more chance of forming enzyme-substrate complex, therefore increasing rate of reaction
- this continues until the maximum rate of reaction is reached (when all the substrates are used)

Question 28

What is a competitive inhibitor?

Answer 28

A substance with a similar shape to the substrate and a complementary shape to the enzyme’s active site.

Question 29

What is a non-competitive inhibitor?

Answer 29

A substance, with a different shape that binds to another site on the enzyme other than the active site.

Question 30

How does the concentration of competitive inhibitors affect the enzyme activity?

Answer 30

A competitive inhibitor binds to the active site, blocking substrates to bind instead, preventing enzyme-substrate complex to form, and rate of reaction is at a lower rate.

Question 31

How does the concentration of non-competitive inhibitors affect the enzyme activity?

Answer 31

A non-competitive inhibitor binds to the another site on the enzyme and this causes the active site’s shape to change, meaning that the substrate is not complementary and less enzyme-substrate complexes are formed, meaning that rate of reaction is at a lower rate.

Question 32

How does pH affect the enzyme activity?

Answer 32

• All enzymes have an optimum pH.
• When an enzyme has a pH above or below their optimum pH, H+ and OH-ions found in the acid or alkali cause the ionic and hydrogen bonds that hold the tertiary structure to break.
• Therefore the active site shape is lost and enzyme-substrate complexes can no longer be formed.
• The enzyme is denatured.

Question 33

What is the lock and key model and how is it criticised?

Answer 33

This model suggested that the active site has a rigid shape and that only a substrate with the correct complementary shape can bind to the active site. However, this has its
limitations.
It does not easily explain how activation energy is lowered.
‒ It does not easily explain the role of competitive inhibitors.
‒ It does not easily explain the role of non-competitive inhibitors.