Biochemical reactions

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 lower affinity for the active site and are released. 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 reactions (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 shape and size of 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

Question 16

How is enzyme activity controlled/regulated (5)

Answer 16

1. Enzymes sometimes need to be controlled. An organism can create its own molecules to slow down and stop the activity of enzymes and proteins.
2. Activators: Makes enzymes work faster. Your body/food can then create activators. Hormones (e.g. adrenaline) can trigger responses that activate enzymes (i.e. glycogen phosphorylase).
3. Inhibitors: Opposite of activators - slow down or stop the activity of an enzyme. Bond to the protein, changing the overall shape of the enzyme - when the shape changes, the enzyme will not work the same way.
4. Temperature: Proteins change shape as temperatures change. High enough temperatures will cause the enzyme to denature and have its structure start to break up.
5. pH Levels: The acidity of the environment changes the shape of proteins in the same way that temperature does. Also, affects the ionisation of amino acids.

Question 17

What is the effect of pH on enzyme activity (3)

Answer 17

1. Usually effective in a narrow pH range – denature beyond this – disruption of intermolecular interactions
2. Optimal pH may be due to the exact nature of the chemical reaction it performs
3. Chymotrypsin ph optimum: 7.8 (ph 6.0: about 35% of maximal activity, ph 9.3: 40% of maximal activity)

Question 18

How is enzyme activity regulated via activators and inhibitors (4)

Answer 18

1. An allosteric regulator binds reversibly to an allosteric binding site
2. Intermolecular bonds are formed
3. Induced fit alters the shape of the enzyme
4. The active site is distorted and is/is not recognised by the substrate

Question 19

How are cofactors/coenzymes used as ‘reagents’ for biochemical reactions (6)

Answer 19

1. Non-protein chemical compounds or “helper molecules” are required for the enzyme’s biological activity.
2. Subdivided into either: inorganic ions or a complex organic or metalloorganic molecule called a coenzyme;
3. Most are derived from vitamins and from required organic nutrients in small amounts.
4. A cofactor that is tightly or even covalently bound is termed a prosthetic group.
5. Sometimes “cofactor” is limited to inorganic substances.
6. An inactive enzyme without a cofactor is called an apoenzyme - a complete enzyme with a cofactor called a holoenzyme.

Question 20

How do Apoenzymes work (2)

Answer 20

1. Apoenzyme (inactive) → Haloenzyme via coenzyme.
2. Haloenzyme binds with the substrate.

Question 21

How is NAD+/NADH used as enzyme cofactors (2)

Answer 21

1. Niacin (Vitamin B3) is oxidised to form NAD+
2. NAD+ is reduced to form NADH.

Question 22

How does Lactate dehydrogenase (LDH) use NADH to make lactate (4)

Answer 22

1. LDH catalyzes the conversion of pyruvate to lactate and back, as it converts NADH to NAD+ and back.
2. A dehydrogenase is an enzyme that transfers a hydride from one molecule to another.
3. LDH is of medical significance because it is found extensively in body tissues, such as blood cells and heart muscle.
4. LDH has been of medical significance because it is found extensively in body tissues, such as blood cells and heart muscle. Because it is released during tissue damage, it is a marker of common injuries and diseases such as heart failure.