Proteins and Enzymes

Question 1

What is the monomer that proteins are made from?

Answer 1

Amino acids

amino acids are combined to from polypeptides, many polypeptides combine to form proteins

Question 2

What is the structure of an amino acid?

Answer 2

• Central Carbon atom
• Amino group (H2N)
• Carboxyl group (COOH)
• Hydrogen atom (H)
• R group

Each amino acid has a different R group

Question 3

What is the bond between amino acids?

Answer 3

Peptide bond

Question 4

How does a peptide bond form?

Answer 4

Condensation reaction which removes a water molecule (made from combining an -OH from the carboxyl groups of amino acid A with the -H from the amino group of amino acid B) to form a peptide bond.

Question 5

What is the primary structure of proteins? + how are they formed

Answer 5

Polypeptides - formed through many condensation reactions so many amino acid (monomers) are joined together through polymerisation.

The sequence of amino acids in a polypeptide chain is a proteins primary structure.

Question 6

What does primary structure determine?

Answer 6

The shape and therefore function of a protein. A change in one amino acid can lead to a change in shape of the protein.
-> shape is specific to function

Question 7

What is the secondary structure of proteins? + how is it formed

Answer 7

There are weak hydrogen bonds between the amino acids that make up a polypeptide, which causes a long polypeptide chain to be twisted into a 3D shape called an alpha helix.

Question 8

What is the tertiary structure of proteins?

Answer 8

Alpha helix can be twisted and folded to form a more complex and specific 3D structure of a protein which is the tertiary structure of a protein.

Question 9

What are the bonds which maintain a tertiary structure?

Answer 9

Disulfide bridges- Strong and not easily broken

Ionic bonds- Formed between any carboxyl and amino groups which do not form peptide bonds, easily broken by pH changes

Hydrogen bonds- easily broken

Question 10

What is the quaternary structure of proteins?

Answer 10

Large proteins which form complex molecules containing a number of polypeptide chains linked in different ways. There can also be a non-protein group within the molecule (like iron containing harm group in haemoglobin|)

Question 11

What determines the 3D shape of a protein?

Answer 11

Sequence of amino acids (primary structure)

Question 12

What is the test for proteins?

Answer 12

Biuret test- detects peptide bonds

• Place sample test tube and add an equal volume of hydroxide solution at room temperature
• Add drops of dilute copper sulphate solution and mix
• Purple solution indicates the presence of peptide bonds. If no proteins are present, solution will stay blue

Question 13

What are the two basic molecular shapes of proteins?

Answer 13

Fibrous Proteins (like collagen) - structural functions

Globular proteins (like enzymes and haemoglobin) - metabolic functions

Question 14

What do fibrous proteins form?

Answer 14

Long chains that run parallel to each other

Question 15

What is the structure of collagen?

Answer 15

• Primary structure- unbranched polypeptide chain
• Secondary structure- polypeptide is tightly wound
• Lots of Amino acid
• Tertiary structure- chain is twisted into a second helix
• Quaternary structure- 3 polypeptide chains which are wound together like a rope

Question 16

Where is collagen found and what is its function?

Answer 16

Found in tendons, these join muscles to bones. When muscles contract the bone moves to the direction of the contraction.

Question 17

Why is collagen’s quaternary a suitable molecule for a tendon?

Answer 17

Individual polypeptide chains in fibres are held together by bonds between amino acids of adjacent chains.

Question 18

What is an enzyme and what does it do?

Answer 18

Globular proteins which lower the activation energy for a reaction to take place.

Question 19

What is the structure of an enzyme?

Answer 19

Tertiary structure - have a specific 3D shape due to their sequencing of amino acids in their primary structure

Active site is specific and made up of amino acids

Substrate fits into active site to form an enzyme-substrate complex

Question 20

What is the induced fit model of enzymes?

Answer 20

Enzyme can change shape in order to fit substrate.

Enzyme colliding with a substrate is a change in the environment which causes a change in shape

Enzyme puts strain on substrate when changing shape, causing bonds to be distorted and activation energy to be lowered (needed to break the bond)

Question 21

What are the stages of the induced fit model?

Answer 21

Enzyme-substrate molecule->
Enzyme-substrate complex->
Enzyme + product molecule

Question 22

What is the lock and key model?

Answer 22

A substrate will only fit the active site of one particular enzyme

They both fit each other exactly

Question 23

What are the limitations of the lock and key model?

Answer 23

Enzymes structure is not rigid, as suggested in the model, it is flexible and will change shape when other molecules bind to it, at places other than the active site therefore the induced fit model is more accurate.

Question 24

What factors are needed for an enzyme to work?

Answer 24

• Needs to come into physical contact with substrate

- Have an active site that fits the substrate

Question 25

How are enzyme-catalysed reactions measured?

Answer 25

(How long the reaction takes)

• The formation of products of reaction
• Disappearance of the substrate

Question 26

Explain an enzyme-catalysed reaction graph

Answer 26

• Lots of substrate at first but no product
• Therefore it is easy for substrate molecules to come into contact with empty active sites/enzyme molecules
• All enzyme active sites are filled with substrates, which are rapidly broken down into products
• This decreases substrate concentration but increases product concentration
• The more the reaction goes on, there less substrate but more product
• So it is more difficult for enzyme-substrate complexes to form
• As a result, it takes more time for substrate molecules to be broken down by the enzyme so rate of disappearance/formation slows and graph begins to level off
• Rate of reaction continues to slow down until there is no substrate left, so the graph levels off as no new product can be produced

Question 27

How is rate of change measured?

Answer 27

• Draw a tangent on curve

- Find the gradient using the straight lines which form a right angled triangle (change of y / change in x)

Question 28

How does temperature affect enzyme action?

Answer 28

• Rise in temperature increases kinetic energy of molecules
• Therefore molecules move around and collide with each other more often
• There are more effective collisions and thus more enzyme-substrate complexes being formed
• As temperature begins to increase more, hydrogen bonds begin to break, causing a change in shape. At around 60 C, the enzyme becomes denatured.

Question 29

How does pH affect enzyme action?

Answer 29

pH - measure of hydrogen ion concentration
Increasing/decreasing pH reduces the enzyme action
-Change in pH alters the charges on amino acids in primary structure of enzyme so an enzyme-substrate complex cannot be formed as the active site changes shape.

Question 30

How does enzyme concentration affect the rate of reaction?

Answer 30

• Increase in amount of enzyme, increases the rate of reaction as long as there is enough substrate to bind to form an enzyme substrate complex.
• This is because there is always more substrate than enzymes so excess substrate can be acted upon by increasing the concentration of enzymes

Question 31

What happens if the substrate is limiting?

Answer 31

The increase in enzyme concentration will not affect the rate of reaction and so graph will level off

Question 32

How does substrate concentration affect the rate of enzyme action

Answer 32

• The rate of reaction increases as substrate concentration increases
• This is because at low substrate concentrations, active sites are not working at full capacity but as more substrate is added, more active sites are filled until they are working as fast as possible

Question 33

What happens when all active sites are filled but more substrate is added ?

Answer 33

The rate of reaction does not change, there will be an excess of substrate so the graph will level off.

Question 34

What are enzyme inhibitors?

Answer 34

Substances which directly and indirectly interfere with the functioning of the active site and therefore reduce activity.

Question 35

What is a competitive inhibitor?

Answer 35

Bind to active site of an enzyme

Question 36

What is a non competitive inhibitor?

Answer 36

Bind to the enzyme on a part other than the active site

Question 37

How do competitive inhibitors work?

Answer 37

They have a molecular shape similar to substrate so they are able to fit the active site of the enzyme. Therefore they have to compete with substrates for available active sites.
They are not permanent

Question 38

What happens when substrate concentration is increased?

Answer 38

The effect of a inhibitor is reduced

Question 39

What happens when the concentration of competitive inhibitor increases?

Answer 39

The longer it will take for substrates to occupy all active sites

Question 40

How do non-competitive inhibitors work?

Answer 40

Attach themselves to a part of the enzyme which is not the active site
This changes the tertiary structure of the enzyme and therefore the active site so substrate molecules are no longer able to fit it
As a result the enzyme cannot function + fewer enzyme substrate complexes

Question 41

Does an increase in substrate concentration have an effect on the non-competitive inhibitor?

Answer 41

No because they are not competing for the same site