Biological Chemistry - From Amino Acids To Proteins (9.3)

Question 1

How doe amino acids react with one another?

Answer 1

In a nucleophilic addition-elimination reaction - a peptide bond is formed (water is also lost)

Question 2

What is a protein?

Answer 2

It is a polypeptide that has long chains of amino acids (generally n>50)

Question 3

What is the primary structure of a protein?

Answer 3

The order of amino acid residues in the chain (these residues are often referred to by their 3 letter code)

Question 4

How do you name the primary structure of proteins?

Answer 4

• Naming starts from the N-terminus (the end w/ the free NH2 group)
• Naming ends w/ the C-terminus (the end w/ the free COOH group)

Question 5

What is the secondary structure of a protein?

Answer 5

• Where different part of the chain interact via hydrogen bonds
• This forms a regular pattern
• Can have the structures: alpha helix and beta-pleated sheet

Question 6

What is the tertiary structure of a protein?

Answer 6

• The 3D arrangement of the proteins
• Controls how the alpha helices, beta sheets & random coils fold into shape
• This arrangement is due to different types of bonding

Question 7

What types of bonding does the tertiary structure involve?

Answer 7

• Hydrophilic/hydrophobic interactions
• Hydrogen bonds
• Covalent bonds (disulphide bridges)
• Ionic bonds

Question 8

What is the quaternary structure of a protein?

Answer 8

• Only found in proteins that consist of more than one polypeptide chain
• The quaternary structure is similar to the tertiary structure, but it involves involves interactions btw. two separate chains

Question 9

How can peptide bonds be broken down?

Answer 9

Hydrolysis reaction using an acid catalyst

Question 10

What are proteins?

Answer 10

They are protein based catalysts

They are often very specific & catalyse only one reaction

Question 11

What is the active site of an enzyme?

Answer 11

• Given rise to by the tertiary & quaternary structure

- An area in space that is perfectly shaped to accept a reactant molecule (substrate)

Question 12

What is meant by the ‘optimum temperature’ of an enzyme?

Answer 12

The temperature where the rate of reaction is the highest for the enzyme (increased collisions)

Question 13

What happens to the enzyme when you increase the temperature? How does this affect the rate of the reaction

Answer 13

• It breaks the H bonds
• Changes tertiary & quaternary structure of the protein
• Disrupts the shape of active site
• Slows the rate of reaction

Question 14

What is meant by the ‘optimum pH’ on an enzyme?

Answer 14

The pH where the rate of the reaction is highest

Question 15

The optimum temperature & pH is unique to each enzyme. True or false?

Answer 15

True

Question 16

Which has more of an acute affect on the rate of reaction? pH or temperature?

Answer 16

pH - slight change in pH can have much more of an effect than slight change in temp.

Question 17

Explain the effect of pH on enzymes

Answer 17

• It can protonate/deprotonate the amine & carboxylate functional groups
• This can disrupt the tertiary & quaternary structure of the enzyme
• This might also prevent the substrate from adsorbing onto the active site

Question 18

Can the effects of small changes of pH or temperature be reversible?

Answer 18

Yes

• Covalent, ionic & H bonds can reform
• Carboxylate/amine groups are reprotonated/deprotonated

Question 19

What is meant when an enzyme has been ‘denatured’?

Answer 19

When the change in pH or temp. is large, it is not reversible so the enzyme can no longer function

Question 20

What type of catalyst are enzymes usually?

Answer 20

Homogenous catalysts

Question 21

What is inhibition of an enzyme?

Answer 21

• When the active site of the enzyme is poisoned
• An inhibitor prevents the substrate from binding & therefore prevents the reaction taking place
  (Inhibition can be reversible/irreversible)

Question 22

What is the difference between a non-competitive & competitive inhibitor?

Answer 22

Competitive - binds to the active site where the substrate would usually bind to prevent substrate binding
Non-competitive - binds to a different site on the enzyme that alters the shape of the active site so substrate can’t bind