Biochemical reactions 1

Question 1

What is a biochemical reaction (4)

Answer 1

1. enzymes provide a surface/environment to react
2. initiation: reactants bind to the active site in a specific orientation, forming an enzyme-substrate complex.
3. Transition state facilitation: interactions between enzyme and substrate lower the activation energy required.
4. Termination: products have a lower affinity for the active site and are released. The enzyme is unchanged after the reaction.

Question 2

What is the Enzyme Nomenclature (7)

Answer 2

1. oxidoreductases - oxidation or reduction
2. Transferases - Transfer of a small group from one molecule to another
3. Hydrolases - Hydrolysis
4. Lyases - Split molecules by any mechanism except hydrolysis
5. Isomerases - Isomerisation
6. Ligases - Join two molecules
7. These functions are examples of biochemical reactions.

Question 3

How enzymes catalyse chemical reactions in the body (3)

Answer 3

1. The oxidation of ethanol to ethanal is a very slow reaction.
2. in the liver, ethanol is oxidised by alcohol dehydrogenase to ethanal with the cofactor NAD+ turning into NADH + H+, which is a fast reaction.
3. Proximity also helps speed up or facilitate a reaction.

Question 4

How do enzymes facilitate a biochemical reaction (8)

Answer 4

1. Provides a reaction surface (active site)
2. Positions reactants correctly for reaction
3. Provides a suitable environment
4. Weakens bonds in the reactants
5. Brings reactants together
6. Stabilises transition state with intermolecular bonds
7. Provides nucleophilic groups
8. Provides acid/base catalysis

Question 5

What are the properties of enzyme active sites (4)

Answer 5

1. Biochemical reactions take place in the active site.
2. There is a hydrophobic pocket on the enzyme surface.
3. Accepts reactants (substrates and cofactors)
4. Contains amino acids that bind reactants (substrates and cofactors) and participate in the enzyme-catalysed reaction

Question 6

What are enzymes’ use of amino acids (4)

Answer 6

1. Important for their functions
2. Hold enzyme in shape.
3. Binding substrates
4. Chemical reactions

Question 7

What are examples of substrate binding (5)

Answer 7

1. Bonding forces: hold proteins in shape & hold substrates in place
2. Ionic bonds
3. H-bonds
4. van der Waals
5. Induced fit - Active site alters shape to maximise intermolecular bonding. (e.g. binding of pyruvate in LDH, stronger H-bond weakens C=O bond).

Question 8

How does the shape and size of the substrate affect substrate specificity (2)

Answer 8

1. Substrate specificity due to the precise interaction of the enzyme with the substrate
2. result of the 3-D structure of the enzyme active site where the substrate has to bind and be properly oriented for catalysis to occur

Question 9

How does thrombin work (6)

Answer 9

1. Involved in the blood clotting cascade
2. Serine protease (uses serine OH)
3. Catalyzes hydrolysis of peptide bonds between Arg and Gly residues
4. Only in specific sequences in specific protein substrates
5. Activated only where blood needs to clot
6. Works only on very specific target protein

Question 10

How does chymotrypsin work (3)

Answer 10

1. Serine protease
2. Catalyses hydrolysis of peptide bonds on the carboxyl side of bulky aromatic groups (e.g. phenylalanine)
3. Metabolises small proteins in the small intestine

Question 11

How do enzymes being 3D affect substrate specificity (3)

Answer 11

1. Correct substrate binds
2. Incorrect substrate does not bind.
3. Molecules (e.g. substrates) are 3D enzymes that selectively bind the correct substrate.

Question 12

How do acids and bases work as catalytic mechanisms (3)

Answer 12

1. Acid: a chemical group that donates a hydrogen ion (H+)
2. Base: a chemical group that accepts a hydrogen ion (H+)
3. Note: a hydrogen ion (H+) is sometimes called a ‘proton’

Question 13

Nucleophiles and electrophiles act as a catalytic mechanism (3)

Answer 13

1. Nucleophile: a chemical group with lots of electrons and is willing to share with an acceptor with not enough to form a chemical bond. Often negatively charged or polar
2. Electrophile: a chemical group with not enough electrons and is willing to share with a donor with lots of electrons to form a chemical bond. Often positively charged or polarised
3. Nucleophiles react with electrophiles to form a covalent bond.

Question 14

How do catalytic mechanisms work? (5)

Answer 14

1. Non-ionised - acts as a base catalyst (proton ‘sink’)
2. Ionised - acts as an acid catalyst (proton source)
3. Histidine can ionise cysteine/serine to make them more reactive in an enzyme-active site.
4. Non-ionised - less nucleophilic
5. Ionised - more nucleophilic

Question 15

How does hydrolysis of proteins/peptides act as a catalytic mechanism?

Answer 15

Chymotrypsin enhanced the rate of peptide bond hydrolysis by a factor of at least x10⁹