Biochemistry I - Enzymes

Question 1

Enzymes

Answer 1

• starting and end points don’t change
• the enzyme isn’t used up in the reactions
• specific to certain substrates and reactions
• induced fit corresponds with transition state; the substrate itself changes the enzymes active site to ensure a good fit
• lock and key model: the active site of an enzyme matches the binding site of the substrate - specificity
• allosteric inhibitor changes the shape of the active site

Question 2

Types of enzymes

Answer 2

Transferase: groups are being transferred
Ligase: joining compounds to each other through the elimination of water
Oxidoreductase: transferring electrons from molecule B to molecule A or molecule A to molecule B
Isomerase: a molecule is converted to one of its isomers
Hydrolase: break bonds using water
Lyase: break bonds without using water or redox reactions

Question 3

Cofactor/coenzyme

Answer 3

Bind to enzymes to support catalysis; not all enzymes can function alone
Coenzymes are organic carrier molecules (NADH)
Cofactors non-protein molecule that directly assists with catalysis
Vitamins: organic cofactors and coenzymes (B3-NAD; B5-CoA)
Minerals: inorganic cofactors (Mg2+- DNA polymerase)

Question 4

Rate of reaction

Answer 4

You can increase the substrate or enzyme concentration. The k constant is constant.
At high substrate concentrations, enzymes will be saturated and increasing the substrate concentration wouldn’t have much of an effect.

Question 5

Assumptions

Answer 5

• solutions are behaving ideally so we can categorise them into distinct steps (substrate enzyme complex formation and then forming the product)
• our constants (enzyme concentration and rate constant) are staying constant
• the substrates forming products without enzymes are negligible

Question 6

Michaelis-Menten kinetics and steady state

Answer 6

• Steady state assumption means that we’re at the point we’re the enzyme substrate concentration is constant, so it’s formation and loss are equal.
• Km is the Michaelis constant, it is a substrate concentration specific to the situation. The smaller it is, the better enzymes are at working with low substrate concentration.
• Higher catalytic efficiency means higher Kcat (the amount of substrate an enzyme can turn into product in one second at its max speed) and lower Km.
• every different enzyme has different catalytic efficiency in different situations
• the x-intercept on an Lineweaver-Burk plot is -1/Km
• Michaelis-Menten equation in notes

Question 7

Cooperativity

Answer 7

• some proteins can bind to more than one substrate and have more than one active site.
  *substrate binding changes substrate affinity
  *positive cooperative binding is when substrate binding increases affinity for subsequent substrate e.g. haemoglobin
  *negatively cooperative binding is when substrate binding decreases affinity for subsequent substrate
  *noncooperative binding is when substrate binding does not affect affinity for subsequent substrate e.g. myoglobin
  *effect only seen once some substrate is bound so difference is smaller at smaller values

Question 8

Allosteric regulation

Answer 8

• an allosteric site is a place on an enzyme where an enzyme regulator (allosteric activators which increase enzyme activity and allosteric inhibitors which decrease enzyme activities) can bind
• regulators can influence an enzymes kinetics by increasing or decreasing Km of Vmax
• feedback loops are when downstream products regulate upstream reactions; good control steps are those with very negative delta G.
  Homotropic inhibitor: substrate and inhibitor are the same molecule e.g. ATP
  Heterotrophic activator: a regulator but not a substrate
  *reversible and non covalent

Question 9

Non-enzymatic protein function

Answer 9

Proteins bind specifically and tightly to various molecules.
- receptors/ion channels
- transport: need to have a high affinity for their ligand when the ligand is present in high concentrations e.g. haemoglobin
- motor e.g. myosin (muscle contraction), kinesin (intracellular transport) dynein (intracellular transport, cilia motility - primary ciliary dyskinesia)
- antibodies: adaptive immune system; affinity is very strong

Question 10

Covalent modifications to enzymes

Answer 10

• not all enzymes are proteins like inorganic metals or small organic molecules (flavin)
• small post translational modification: methylation, acetylation, glycosylation
• zymogens: inactive enzymes that require covalent modification to be activated e.g. trypsinogen from pancreas that is modified by enterokinase in the intestine
• suicide inhibition: covalently bind an enzyme and prevent it from catalysing enzyme. They form covalent linkages and so don’t often unbind