3.6 Structure of proteins

Question 1

What are peptides?

Answer 1

Polymers made up of two or more amino acid molecules

Question 2

What do proteins consist of?

Answer 2

One or more polypeptides arranged as complex macromolecules

Question 3

*What elements do proteins contain

Answer 3

Carbon, hydrogen, oxygen, nitrogen

Question 4

What are R-groups?

Answer 4

Variable groups on amino acids

Question 5

How many amino acids are found in cells?

Answer 5

20

Question 6

How many amino acids are non-essential? What does this mean?

Answer 6

5 - our body can make them from different amino acids

Question 7

How many amino acids are essential? What does this mean?

Answer 7

9 - only obtainable from food

Question 8

How many amino acids are conditionally essential? What does this mean?

Answer 8

6 - only needed by growing children

Question 9

Describe what happens during synthesis of peptides

*(Refer to Figure 2 on p.g. 59)

Answer 9

-Amino acids join when amine and carboxylic acid groups react
-Hydroxyl in the carboxylic acid group of one amino acid reacts with a hydrogen in the amine group of another amino acid
-Peptide bond forms between amino acids and water is produced (this is an example of a condensation
reaction)
-The resulting compound is a dipeptide

Question 10

What is a peptide bond?

Answer 10

The bond formed between 2 amino acids

Question 11

What happens when many amino acids are joined by peptide bonds?

Answer 11

A polypeptide forms

Polypeptide - chains of 3 or more amino acids

Question 12

What enzyme catalyses the reaction which forms peptide bonds?

Answer 12

Peptidyl transferase, found in ribosomes

Question 13

Define R-group interaction. What does this result in?

Answer 13

1. Different R-groups in the amino acids making up one protein can interact
2. Forming different types of bonds
   -These bonds cause the long amino acid chains (polypeptides) to fold into complex structures
   (proteins)

Question 14

What does the presence of different amino acid sequences lead to?

Answer 14

Different structures with different shapes being produced

Question 15

Why does a protein’s shape have to be specific?

Answer 15

Vital for the protein to carry out its function

Question 16

*What is thin layer chromatography (TLC) used for?

Answer 16

To separate individual components of a mixture

e.g. identify a mixture of amino acids in a solution

Question 17

*What are the 2 phases in TLC? What happens at each phase?

Answer 17

1. Stationary phase
   - Thin layer of silica gel/any other adhesive substance is applied to a rigid surface e.g. sheet of glass
   - Amino acids are added to one end of the gel
   - This end is submerged in organic solvent
2. Mobile phase
   - The organic solvent moves through the silica

Question 18

*What is the rate at which amino acids move dependent on?

Answer 18

1. Interactions the amino acids have with the silica during the stationary phase
2. Amino acid’s solubility during the mobile phase
   - Since these vary, the amino acids move different distances in the same period of time

Question 19

*How do you carry out the procedure to separate and identify a mixture of amino acids in solution?

Answer 19

1. Whilst wearing gloves, draw a baseline 2cm from the bottom in pencil on the chromatography plate (handle the plate by its edges)
2. Mark 4 equally spaced points along the baseline
   3.

Question 20

Explain what the primary structure of a protein is

Answer 20

1. Sequence in which amino acids are joined
   - Directed by information carried within DNA
   - Amino acids in the sequence influence how the polypeptide folds to give the protein’s final shape - this determines its function
   - Only contains peptide bonds

Question 21

Explain what happens in the secondary structure of a protein

Answer 21

• Oxygen, hydrogen and nitrogen atoms of the amino acid structure interact
• Hydrogen bonds form within the amino acid chain, pulling it into a coil shape known as ‘alpha helix’
• Result of hydrogen bonds

Question 22

What is the secondary structure a result of?

Answer 22

Hydrogen bonds

Question 23

Where does the secondary structure form?

Answer 23

At regions along long protein molecules, depending on the amino acid sequence

Question 24

What forms a beta pleated sheet?

Answer 24

Polypeptide chains parallel to each other joined by hydrogen bonds, forming sheet-like structures

Question 25

What happens in the tertiary structure?

Answer 25

The protein is folded into its final shape