3.1.4 Proteins

Question 1

How do two amino acids bond?

Answer 1

Condensation reaction. OH from amino acid 1 reacts with H from amino acid 2 creating water. The C from amino acid 1 and N from aa2 bond.

Question 2

General structure of an amino acid

Answer 2

central carbon bonded to
* H
* H2N (amine group)
* COOH (carboxylic acid group)
* R group (only thing that changes, positive R group = positive amino acid)

Question 3

How many different naturally occurring amino acids are there?

Answer 3

20

Question 4

What is the monomer of polypeptides?

Answer 4

Amino acids

Question 5

What bond forms between 2 amino acids?

Answer 5

Peptide

Question 6

What is the secondary structure of proteins?

Answer 6

Folding of the polypeptide chain into an alpha helix (or beta pleated sheet) due to hydrogen bonds.

Question 7

What is the tertiary structure of a protein?

Answer 7

Further 3d folding of the polypeptide chain due to new bonds.

Question 8

Describe the quaternary structure of a protein.

Answer 8

Two or more polypeptide chains. Sometimes contain prosthetic (non protein) groups (eg haem - iron).

Question 9

What types of bonding are in the tertiary structure of proteins?

Answer 9

Disulfide bridges, ionic bonds, MORE hydrogen bonds

Question 10

What type of bonding is present in the primary structure of a protein?

Answer 10

Peptide bonds

Question 11

What is the primary structure of a protein?

Answer 11

The sequence of amino acids in a polypeptide

Question 12

What types of bonding are in the quaternary structure of proteins?

Answer 12

Disulfide bridges, ionic bonds, more hydrogen bonds.

Question 13

Describe and explain the effect of pH on an enzyme controlled reaction

Answer 13

pH below 7/ above 7 rate of reaction decreases
* more hydrogen H+ ions (BELOW 7)
* more hydroxide OH- ions (ABOVE 7)
breaks ionic and hydrogen bonds, tertiary structure changes, active site shape changes, not complementary, denatured, no enzyme substrate-complexes

Peak at pH 7
* optimum

Question 14

What 2 types of molecule interfere with enzyme activity?

Answer 14

Activators - switching on enzymes
Inhibitors - permanently or temporarily stopping enzyme action

Question 15

How do competitive inhibitors interfere with enzyme action?

Answer 15

Similar shape to substrate, binds to active site, blocks substrate form binding with active site, less enzyme-substrate complexes.

Question 16

How do non-competitive inhibitors interfere with enzyme activity?

Answer 16

Binds to enzyme away from active site (allosteric site), changes tertiary structure, changes active site shape, no longer complementary, substrate can’t bind, no enzyme-substrate complexes

Question 17

What is the induced fit hypothesis?

Answer 17

The substrate binds to the active site. The active site shape changes slightly to become complementary to the substrate to allow an enzyme-substrate complex to form. The change in shape puts a strain on the substrate which lowers the activation energy needed to break the bonds.

Question 18

Why is the induced fit model better?

Answer 18

It explains how other molecules affect enzyme activity and how activation energy is lowered.

Question 19

What is the lock and key hypothesis?

Answer 19

• Enzyme (lock) has an active site shape that is already complementary to the substrate (key).
• Substrate binding to the active site leads to the formation of the enzyme-substrate complex
• The enzyme is rigid and doesn’t change shape

Question 20

What are advantages and limitations of the lock and key model?

Answer 20

• Explains how enzymes are specific to one substrate - only one substrate fits into the active site shape.
• States enzymes are rigid, when they’re actually flexible.
• Doesn’t explain how other molecules (eg activators and inhibitors) can bind at sites other than the active site and change its activity.

Question 21

What are the features of globular and fibrous proteins

Answer 21

Globular
* spherical shape due to tightly folded polypeptide chains
* folded so hydrophobic on inside, hydrophilic outside so often water soluble
* eg enzymes and haemoglobin (roles in metabolic reactions)

Fibrous
* parallel polypeptide chains held together by regular hydrogen bond cross links
* form long, strong fibres
* usually insoluble in water
* eg keratin and collagen (structural roles)

Question 22

How does the structure of a protein depend on the amino acids it contains?

Answer 22

• structure determined by relative position of amino acids / r groups
• primary structure is sequence of amino acids
• secondary structure formed by folding of polypeptide chain into alpha helix/ beta pleated sheet due
  to hydrogen bonds
• tertiary structure formed by further 3d folding due to more hydrogen bonds, ionic bonds and disulphide bridges caused by interactions between R groups
• creates active site in enzymes (eg)
• quaternary structure two or more polypeptide chains