12.2 - proteins & enzymes

Question 1

Proteins are made of what monomers?

How many different types of them are there?

What do they all have the same of?

Answer 1

Amino Acids.

20.

Same general structure

Question 2

What is the general structure of an amino acid and what are the groups called in its structure?

Answer 2

H H O
/ / //
N - C - C - OH
| |
H R

NH2 = amino group, COOH = carboyxlic group, R = variable group.

NH2-CH(R)-C=OOH

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Question 3

What is the R group?

Answer 3

It’s what makes AAs different, can be positively charged, negatively charged, hydrophobic or hydrophilic.

Question 4

Describe how a peptide bond is formed between two amino acids to form a dipeptide. (2)

Answer 4

1) Condensation reaction/ loss of water
2) Between NH2 and COOH

(hydroxyl (OH) group from one AA and H from amine group of another AA)

Question 5

Describe the structure of proteins. (7)

Answer 5

1) Polymer of amino acids
2) Joined by peptide bonds
3) Formed by condensation reaction
4) Primary structure = number and order of AAs
5) Secondary structure = the folding of the polypeptide chain into alpha helices and beta-pleated sheets due to weak hydrogen bonding
6) Tertiary structure = 3-D folding due to H bonding, Ionic bonding, and Disulfide bridges.
7) Quartenary structure = 2 or more polypeptide chains joined together.

Question 6

Describe how the structure of a protein depends on the amino acids it contains. (6)

Answer 6

1) Structure is determined by the position of amino acids / R group interactions
2) Primary structure = sequence and no. of AAs
3) Secondary structure = formed by hydrogen bonding between AAs
4) Tertiary structure = formed by interactions between R groups
5) Creates active site in enzymes OR specific shapes in carrier proteins/antibodies
6) Quarternary structure = >1 polypeptide chain, formed by interactions between PPs.

Question 7

Describe how monomers join to form the primary structure of a protein. (3)

Answer 7

1) Condensation reaction between AAs
2) Forming peptide bonds
3) Creating specific sequence of AAs

Question 8

What is the test for proteins?

Answer 8

The biuret test.
Add Biuret’s solution and the colour change to purple = presence of protein,
stays blue = no proteins present.

Question 9

What type of proteins are enzymes?

What do they act as?

What do they do?

Answer 9

Globular proteins (soluble in water)

Biological Catalysts

Increase the rate of chemical reactions by lowering the activation energy needed for the reaction, without being changed or affected, they do not get used up.

Question 10

What is Activation Energy (Ea)?

How do enzymes lower it?

Answer 10

The minimum energy required for a successful chemical reaction.

They stress/distort/weaken the bonds in the substrate during the formation of an enzyme-substrate complex, allowing reactions which would normally require higher temperatures, to work at lower temperatures.

Question 11

Describe how an ESC increases the RoR. (2)

Answer 11

1) Reduces activation energy
2) Due to bending bonds

Question 12

An enzyme catalyses only one reaction, explain why. (2)

Answer 12

1) Enzyme has an active site which has a specific shape
2) Only one substrate binds/fits

(enzymes have a specifically complementary active site to their substrate)

Question 13

Describe one way that the lock and key model is different from the induced fit model. (3)

Answer 13

1) Active site doesn’t change shape
2) Substrate already fits the active site
3) Complementary before binding

Question 14

Describe the induced fit model of enzyme action (3)

Answer 14

1) Active site not complementary
2) Active site changes shape
3) Change in enzyme allows substrate to fit / ESC to form

Question 15

Describe the induced fit model of enzyme action and how an enzyme acts as a catalyst (3)

Answer 15

1) Substrate binds to the active site / ESC forms
2) Active site changes shape slightly to be complementary to the substrate (by distorting/weakening bonds)
3) Reduces activation energy

Question 16

As enzymes are proteins, they are affected by:

Answer 16

• Temperature
• pH
• Inhibitors
• Enzyme conc.
• Substrate conc.

Question 17

Anything that alters the shape of the active site will affect the number of…

Answer 17

ES complexes formed (per second / s-1) and therefore the rate of reaction

Question 18

What happens when you increase the temperature up to the optimum?

The KE of…
More likely to..
RoR…

Answer 18

• The enzyme and substrate molecules increase their KE and are more likely to successfully collide and react.
• The RoR increases because more ESC form per second.

Question 19

What happens if you increase the temperature BEYOND the optimum?

The atoms…
The bonds..
The A.S…

Answer 19

The atoms within the AA structure of the enzyme vibrate faster as they have more KE.

• Causing the weak H bonds and ionic bonds between R groups of adjacent AAs to break = change in tertiary structure, changing the shape of the active site.
• Shape of A.S is changed = no longer complementary to substrate, less/no ESC formed.
• Enzyme is DENATURED.

Question 20

What happens if the pH is changed from the optimum?

The charge..
The A.S…
ESCs…

Answer 20

• The charge on the R groups of the AAs is altered and ionic bonds (and weak H bonds) in the tertiary structure are broken.
• Enzyme’s A.S changes shape and can no longer bind to the substrate (not complementary)
• Less/no ESC can be formed, RoR decreases either side of the optimum.
• The enzyme is DENATURED.

Question 21

(PPQ) Insulin is a protein. Suggest why insulin cannot be taken orally. (2)

Answer 21

1) Broken down by enzymes / digested / denatured (by PH changes)
2) Insulin will no longer be functional.

Question 22

What happens when the substrate conc. is low?

What happens when the substrate conc. increases?

What happens when you increase the substrate conc. even further?

[in terms of RoR, ESCs and the limiting factor]

Answer 22

• When it’s low, the RoR is low as there are less collisions so few ESCs form per second, the substrate conc. is the limiting factor.
• When it increases, more active sites are filled, and the RoR increases, due to more ESC forming. The substrate conc. is the limiting factor.
• The RoR shows no further increase at “x” (plateaus) even when the substrate conc. increases as all the enzyme active sites are saturated (filled with substrate) so now the enzyme conc. is the limiting factor.

Question 23

What is the effect of increasing substrate concentration on the rate of an enzyme controlled reaction. (3)

Answer 23

1) Increases then plateaus
2) Plateaus as all active sites are occupied / saturated.
3) Maximum number of ESCs have formed per second

Question 24

What happens at low enzyme concentration?

What happens at medium enzyme concentration?

What happens at high enzyme concentration?

Answer 24

• There are too few enzyme molecules to allow all substrate molecules to find an active site at one time, all enzymes active sites are saturated, enzyme conc. is the limiting factor.
• More enzymes available = more ESC can form per second, RoR increased, enzyme conc. is the limiting factor.
• This has no effect as there are already enough active sites to accomodate all the available substrate molecules, no increase in the RoR, all substrate has been converted into product. The initial RoR will only increase when the conc. of the substrate increases (substrate conc. = limiting factor.)

Question 25

How do you calculate the RoR (if X axis is the time):

1) At a specific point
2) Initial rate
3) Between 2 points

What is the formula?

Answer 25

1) Draw a tangent on the curve
2) Draw a tangent on the curve
3) No tangent, read off the graph / difference

Change in y / change in x

Question 26

What are inhibitors?

Answer 26

Substances that DECREASE the RoR.

Question 27

What is a competitive inhibitor?

What is its shape?

Where does it bind, what does it do?

What is the effect of this on the RoR and ESCs?

How is it overcome?

Answer 27

• Has a similar shape to the substrate
• Binds to the active site to prevent substrate from binding temporarily
• Fewer ESCs can form per second, fewer products, reduced RoR.
• Takes longer for all substrates to form products
• Overcome by increasing substrate concentration (overcomes chances of inhibitor binding)

Question 28

What is a non-competitive inhibitor?

What is its shape?

Where does it bind?

What effect on the enzyme?

What is the effect of this on the RoR and ESCs?

How is it overcome?

Answer 28

• Different shape to substrate
• Binds to the allosteric site (away from the active site)
• Causes a conformational change to the shape of the active site when it binds to the enzyme, so substrate cannot bind - changes tertiary structure of enzyme
• Can be temporary or permanent
• Fewer ESCs formed, lower RoR, fewer produced.
• Increasing substrate conc. will NOT overcome the effect of the inhibitor
• Overcome by increasing enzyme conc.

Question 29

Explain how a competitive inhibitor works (3)

Answer 29

• Inhibitor is similar shape to substrate
• Inhibitor competes with substrate and binds to active site
• Less substrates bind / less ESCs form per second.

Question 30

Describe how a non-competitive inhibitor works. (3)

Answer 30

• Attaches to the enzyme at a site other than the active site (allosteric site)
• Changes shape of A.S / alters tertiary structure
• A.S and substrate no longer complementary, less/no ESCs form.