3.1.4 Proteins

Question 1

What are the monomers of proteins ?

Answer 1

Amino acids

Question 2

Why are they called amino acids ?

Answer 2

They have both amino groups and acid groups, which
have opposite charges.

Question 3

How many different amino acids are there ?

Answer 3

20

Question 4

How are polypeptides formed and what chemical bond is formed ?

Answer 4

Polypeptides are formed via condensation reactions between the amine group of one
amino acid and the carboxyl group of another , A molecule of water is released during reaction. The bonds formed between amino
acids are called peptide bonds. The reverse reaction happens during digestion.

Question 5

What is the sequence of an amino acids in a polypeptide determined by ?

Answer 5

The sequence of the
genetic code on mRNA being translated in the ribosomes.

Question 6

Draw the general structure of an amino acid

Answer 6

Amino acids have a central asymmetric carbon to which an amino group, a carboxyl
group, a hydrogen atom, and a side chain (R group) are attached

Question 7

How do you test for proteins ?

Answer 7

Using the biuret test
‒ The test solution needs to be alkaline, so you first need to add sodium or
potassium hydroxide solution.
‒ Next you add a few drops of copper sulfate solution.
‒ If protein is present, the solution turns purple. If there is no protein, it will remain
blue

Question 8

Define the primary structure

Answer 8

The unique sequence of amino acids in the polypeptide chain is its primary structure

Question 9

Define the secondary structure

Answer 9

Folding of primary structure
The secondary structure is held together by hydrogen bonds between the
carboxyl groups and the amino groups in the polypeptide backbone.

Question 10

What are the two polypeptide structures ?

Answer 10

Alpha helix and Beta pleated sheet

Question 11

How is the alpha helix held together ?

Answer 11

hydrogen bonds running parallel with the long helical
axis

Question 12

How is the tertiary structure formed and what bonds are involved ?

Answer 12

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. sulphur bridges - covalent S-S bonds between two cysteine amino acids, which are
strong.

Question 13

How is the quaternary structure formed ?

Answer 13

some proteins are formed from several polypeptides, also known as subunits,
and the interaction of these subunits forms the quaternary structure

Question 14

How do we identify and separate amino acids ?

Answer 14

Using thin layer chromatography

Question 15

Describe the method of thin layer chromatography

Answer 15

Preparation of Container:

Fill container with chromatography solvent to a depth of 2 cm.
Seal container to allow solvent to saturate the atmosphere, preventing evaporation.
Preparation of Chromatography Paper:

Draw a pencil line slightly more than 2 cm from the bottom.
Mark small crosses on the line for amino acid spots.
Application of Amino Acids:

Apply amino acid spot using a capillary tube (spot ≤ 2 mm in diameter).
Dry the spot with a hair dryer and reapply to build a concentrated dot.
Label the amino acids with pencil below each spot.
Running the Chromatogram:

Place the chromatography paper in the container without submerging the line.
Allow solvent to rise by capillary action, carrying amino acids at different rates.
Finishing the Chromatogram:

Remove paper when solvent nearly reaches the top and mark the solvent front.
Dry the chromatogram in a fume cupboard and spray with ninhydrin.
Observe and note purple spots indicating the positions of amino acids.

Question 16

Define a catalyst

Answer 16

A catalyst is a substance which speeds up a chemical reaction without actually being
used up in the reaction itself.

Question 17

How can enzymes act ?

Answer 17

An enzyme action can be intracellular (within the cells) or extracellular (outside the
cells).

Question 18

Where does the substrate bind to ?

Answer 18

Enzymes have an active site, which is a specific shape. It’s part of the enzyme where
the substrate molecules bind to.

Question 19

What is the lock and key model ?

Answer 19

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

Question 20

What are the limitations of the lock and key model ?

Answer 20

‒ 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

Question 21

Describe the induced fit model

Answer 21

As the enzyme and substrate come together, their interaction causes a mild shift in the
enzyme’s structure that confirms an ideal binding arrangement between the enzyme
and the transition state of the substrate.
This ideal binding maximizes the enzyme’s ability to catalyze its reaction.
( substrate enters the AS of the enzyme , E-S complex forms , enyzme/product complex and the products leave the AS of enzyme )

Question 22

What are the advantages of the induced fit model ?

Answer 22

‒ Can explain how the activation energy is lowered, the stretching and distorting of
bonds or causing the closer orientation of reactive groups.
‒ Explain how non-competitive inhibitors can bind to a region away from the active
site and change its shape so that substrate can no longer bind to the active site.
‒ Explains how competitive inhibitors can bind to the active site or other molecules
with similar shapes to the substrate.

Question 23

How does temperature affect the enzyme activity ?

Answer 23

‒ Increase in temperature increases kinetic energy
‒ so more enzyme substrate complexes form
‒ High temperatures cause denaturation, due to the breaking of breaking of bonds
holding the tertiary structure together (H bonds/disulphide bridges/ionic bonds)
‒ Active site altered (changes shape) substrate cannot bind, no enzyme substrate
complexes form

Question 24

How does pH affect enzyme activity ?

Answer 24

‒ Deviations from the optimum pH cause a decrease in enzyme activity.
‒ Small deviations change the charge at the active site and affect the binding of the
substrate
‒ Larger deviations can cause the hydrogen and ionic bonds holding the tertiary
structure together to change and the enzyme denatures, meaning enzyme
substrate complexes can no longer form

Question 25

How does the enzyme concentration affect rate of enzyme activity ?

Answer 25

‒ As enzyme concentration increases so will the rate: as there are more enzyme substrate complexes forming. ‒ At very high concentrations of enzyme the rate remains constant as substrate becomes the limiting factor Add more enzyme will cause rate to increase again.

Question 26

How does substrate concentration affect enzyme activity

Answer 26

‒ As the substrate concentration increases, the rate increases because more substrate molecules can collide with enzyme molecules, so more reactions will take place. ‒ At higher concentrations the enzyme molecules become saturated with substrate, so there are few free enzyme molecules, so adding more substrate doesn't make much difference.

Question 27

What do inhinitors do ?

Answer 27

Inhibitors prevent the binding of substrate to active site; therefore fewer enzyme-substrate complexes formed, reducing the rate of their reactions.

Question 28

Describe competitive inhibitors

Answer 28

They have a similar shape to that of the substrate molecules. ‒ They compete with the substrate molecules to bind to the active site, but no reaction takes place. ‒ Instead of a reaction, they block the active site so no substrate molecules can fit in it. ‒ The level of activity inhibited depends on the relative concentrations of the inhibitor and the substrate.

Question 29

How do high concentrations of competitive inhibitors work ?

Answer 29

‒ High concentration of the inhibitor means it will take up nearly all of the active sites and hardly any substrate will get to the enzyme.

Question 30

How does low concentration of enzyme inhibitors work ?

Answer 30

With a lower concentration, the chances of the substrate getting to an active site before the inhibitor increase

Question 31

Describe how non competitive inhibitors work ?

Answer 31

‒ They bind to the enzyme away from its active site. ‒ This causes the active site to change shape so the substrate molecules cannot bind to it. ‒ They don’t “compete” with the substrate molecules to bind to the active site because they are different shapes. ‒ Increasing the concentration of substrate doesn’t affect the reaction rate - enzyme activity is still inhibited.