1.4- Proteins

Question 1

1) Draw the structure of an amino acid and label the amino, carboxyl and R group

Answer 1

0

Question 2

1) Describe the reaction which forms a dipeptide.

Answer 2

A condensation reaction between two amino acids produces a dipeptide linked by a peptide bond

Question 3

1) raw a dipeptide and circle the peptide bond.

Answer 3

0

Question 4

1) Describe the formation of a polypeptide

Answer 4

A polypeptide is formed by the condensation of MANY amino acids.

Question 5

Pei,are structure

Answer 5

Primary sequence of amino acids form a polypeptide chain

peptide bonds between the amino group and the carboxyl group of the adjacent (neighbouring) amino acid

Question 6

Secondary

Answer 6

polypeptide chain is folded to form an alpha-helix or beta-pleated sheet Hydrogen bonding between NH of one amino acid and C=O of another amino acid

Question 7

Tertiary

Answer 7

Further folding of the secondary structure forms a unique 3-D structure (can be globular or fibrous) disulphide bonds, hydrogen bonds and ionic bonds between different R groups

Question 8

Quaternary

Answer 8

Two or more different polypeptide chains folded and twisted. (Can also contain non-protein (prosthetic) groups.)

Question 9

1) The primary structure is fundamental in the formation of the subsequent structures. Explain why.

Answer 9

• A different sequence of amino acids means
• There are different R-groups present
• So there is different hydrogen, ionic, disulphide bonds in different places
• which gives the tertiary structure a different shape
• which can ultimately affect the function of the protein.

Question 10

1) Describe the Biuret Test for Proteins

Answer 10

The Biuret Test
• Add the NaOH
• copper sulphate (too)
• If it turns purple there’s a protein (for you)!

Question 11

1) What is an Enzyme?

Answer 11

Enzymes are proteins with a specific tertiary structure.

Question 12

1) What is the active site of an enzyme and what is it’s function?

Answer 12

It is the functional part of the enzyme that binds to the substrate by becoming complementary to the shape of the substrate. This allows the formation of an Enzyme-Substrate Complex (E-S complex).

Question 13

1) How do enzymes affect the activation energy?

Answer 13

Enzymes lower the activation energy allowing chemical reactions to take place at lower temperatures than they would otherwise occur (e.g. body temperature).

Question 14

1) Describe the INDUCED FIT model

Answer 14

• Enzymes have an active site with a specific shape.
• Before the reaction the active site is not complementary to the substrate.
• The active site changes shape and becomes complementary as substrate binds
• An enzyme- substrate complex is formed
• This stresses and bends the bonds in the substrate which allows the reaction to occur

Question 15

1) How might a change in the primary structure result in a non-functional enzyme?

Answer 15

• A change in amino acid sequence results in different R groups
• Results in a change in hydrogen / ionic / disulfide bonds
• Which results in a change in the tertiary structure
• Which changes the shape of the active site;
• Substrate is not complementary to the active site so no enzyme-substrate complexes form.

Question 16

Temperature graph

Answer 16

As the temperature increases, rate of reaction increases
• E and S have more KINETIC ENERGY
• so there are more collisions
• more E-S complexes formed per second
When temperature exceeds optimum, the rate of reaction decreases
Because enzymes molecules have more KINETIC ENERGY  so H-Bonds break so tertiary structure changes  shape of active site changes  no E-S complexes can form

Question 17

Graph ph

Answer 17

• Changing pH changes the CHARGES on the R groups of amino acids
• leads to changing the hydrogen and ionic bonds holding tertiary structure
• active site changes shape (it is denatured) and is no longer complementary or specific to the substrate
• substrate will not bind with active site;
• fewer/no ES complexes formed;

Question 18

Substrate conc graph

Answer 18

• As substrate concentration increases, rate increases because more E-S complexes are being made per second
• Substrate concentration is the limiting factor
• Then as substrate concentration increases further, there is no further increase in rate of reaction because ALL ACTIVE SITES are OCCUPIED
• Enzyme concentration is the limiting factor

Question 19

Enzyme concept

Answer 19

• As enzyme concentration increases, rate increases because the amount of enzyme is the limiting factor
• Then as enzyme concentration increases further, there is no further increase in rate of reaction BECAUSE the rate is limited by something else, e.g. the amount of substrate available
• Also the rate might be limited because the temperature is not high enough for the reaction to happen any faster

Question 20

Compatible inhibitor grqph

Answer 20

The competitive inhibitor has a similar shape to the substrate and is complementary to the active site. The active sites will be occupied. Fewer enzyme-substrate complexes can be formed.

The inhibitor no longer affects the rate of reaction at HIGH concentration of substrate. There is more chance of the substrate binding to the active site (instead of the inhibitor) and therefore forming E-S complexes

Question 21

Non compatible graph

Answer 21

Non-competitive inhibitor binds to the allosteric site of the enzyme (not the active site).
• This changes the tertiary structure of the enzyme
• so the shape of active site has changed
• so the substrate is no longer complementary
• so fewer E-S complexes form
Even increasing the concentration of substrate does not allow the rate of reaction to reach the same rate as with no inhibitor. This is because the non-competitive inhibitor reduces the number of functional enzymes present

Question 22

1. Describe the similarities and differences between a non-competitive inhibitor and competitive inhibitor

Non comp

Answer 22

Non-competitive
Where does it bind? binds at allosteric site / a site away from active site
What happens to the active site? Binding causes change in the shape of active site
How will the above affect the number of functional enzymes? At high substrate concentration there will not be any functional enzymes available
How will a high substrate concentration affect the number of collisions? At high substrate concentrations there are less enzyme-substrate collisions

Question 23

Compatible

Answer 23

binds to active sites of enzyme
Binding does not cause change in shape of active site
At high substrate concentration there will be functional enzymes available
At high substrate concentrations there are more enzyme-substrate collisions