Enzyme 1 biochem

What do enzymes do to a reaction's activation energy?

They lower activation energy by stabilizing the transition state, increasing the rate of reaction.

Do enzymes change ΔG or the equilibrium constant (Keq)?

No. Enzymes change reaction rate but do not change ΔG or Keq; they accelerate forward and reverse reactions equally.

What is the lock-and-key model of enzyme specificity?

The active site is treated as a relatively rigid shape already complementary to the substrate.

What is the induced-fit model?

Substrate binding triggers a conformational change that aligns catalytic residues for efficient transition-state stabilization.

What determines enzyme specificity?

Complementarity between the substrate and active-site shape and chemistry.

Which enzyme class performs redox/electron-transfer reactions?

Oxidoreductases.

Which enzyme class transfers functional groups between molecules?

Transferases.

Which enzyme class hydrolyzes bonds?

Hydrolases.

Which enzyme class adds or removes groups by non-hydrolytic mechanisms?

Lyases.

Which enzyme class catalyzes intramolecular rearrangements?

Isomerases.

Which enzyme class joins molecules using ATP energy?

Ligases.

Which enzyme class moves solutes across membranes?

Translocases.

What high-yield distinction separates oxidoreductases from ligases?

Oxidoreductases perform redox reactions; ligases join molecules using ATP.

Which enzyme is an example of an oxidoreductase in the guide?

Lactate dehydrogenase or glucose-6-phosphate dehydrogenase.

Which enzymes are examples of transferases?

Aspartate aminotransferase, alanine aminotransferase, and hexokinase.

Which enzymes are examples of hydrolases?

Lipases and lysosomal enzymes.

Which enzyme is an example of a lyase?

Aldolase B.

Which enzyme is an example of an isomerase?

Phosphohexose isomerase.

Which enzymes are examples of ligases?

Pyruvate carboxylase and DNA ligase.

Which membrane proteins are examples of translocases?

Na+/K+-ATPase and ATP synthase.

What is a cofactor?

Any non-protein helper required by an enzyme, including inorganic metal ions or organic coenzymes.

What is a coenzyme?

An organic cofactor, often derived from a vitamin.

What is a cosubstrate?

A coenzyme that binds transiently and is released after participating in the reaction, such as NAD+.

What is a prosthetic group?

A cofactor that remains tightly or covalently associated with the enzyme, such as FAD or biotin.

What is a holoenzyme?

The catalytically active complex consisting of an apoenzyme plus its required cofactor.

What is an apoenzyme?

The protein portion of an enzyme without its required cofactor; by itself it is inactive.

Which vitamin produces thiamine pyrophosphate (TPP)?

Vitamin B1 (thiamine).

What reactions depend on TPP?

Oxidative decarboxylation reactions such as pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase.

What deficiency is associated with vitamin B1?

Wernicke–Korsakoff syndrome and beriberi.

Which vitamin produces FAD and FMN?

Vitamin B2 (riboflavin).

What type of chemistry uses FAD and FMN?

Redox reactions, including succinate dehydrogenase and electron-transport reactions.

What oral findings are associated with riboflavin deficiency?

Cheilosis and glossitis.

Which vitamin produces NAD+ and NADP+?

Vitamin B3 (niacin).

What type of chemistry uses NAD+ and NADP+?

Redox reactions catalyzed by dehydrogenases.

What deficiency disease is associated with niacin?

Pellagra, classically summarized by the three Ds.

Which vitamin produces coenzyme A?

Vitamin B5 (pantothenate).

What does coenzyme A primarily participate in?

Acyl-group transfer, including reactions in the TCA cycle and fatty-acid metabolism.

Which vitamin produces pyridoxal phosphate (PLP)?

Vitamin B6 (pyridoxine).

What reactions depend on PLP?

Transamination and decarboxylation.

What deficiency effects are associated with vitamin B6?

Neuropathy and sideroblastic anemia.

Which vitamin supplies biotin for carboxylation reactions?

Vitamin B7 (biotin).

Which enzyme is a classic biotin-dependent carboxylase in the guide?

Pyruvate carboxylase.

What deficiency finding is associated with biotin deficiency?

Dermatitis; raw egg white exposure is a classic risk because avidin binds biotin.

Which vitamin produces tetrahydrofolate (THF)?

Vitamin B9 (folate).

What does THF carry?

One-carbon units.

What deficiency is associated with folate?

Megaloblastic anemia and neural-tube defects.

Which vitamin provides methyl- and adenosyl-cobalamin?

Vitamin B12 (cobalamin).

Which reactions use vitamin B12?

Methionine synthase and methylmalonyl-CoA mutase reactions.

What deficiency pattern is characteristic of vitamin B12 deficiency?

Megaloblastic anemia plus neurologic deficits.

How does chronic alcohol use relate to thiamine?

Chronic alcohol use can impair thiamine absorption/metabolism and predispose to Wernicke–Korsakoff syndrome.

What is the basic Michaelis–Menten reaction scheme?

E + S ⇌ ES → E + P.

What happens during the E + S binding step?

Enzyme and substrate associate to form the enzyme–substrate complex; forward and reverse binding are described by k1 and k−1.

What happens during ES → E + P?

Catalysis converts substrate into product and regenerates free enzyme; the catalytic step is characterized by kcat/k2.

What is the steady-state assumption?

The concentration of ES remains approximately constant because its rate of formation equals its rate of breakdown.

What is the Michaelis–Menten equation?

V0 = (Vmax × [S]) / (Km + [S]).

What is Vmax?

The maximum reaction velocity reached when enzyme is saturated with substrate.

What determines Vmax?

Total enzyme concentration and catalytic turnover: Vmax is proportional to [Etotal] × kcat.

What is Km in the Michaelis–Menten model?

The substrate concentration at which V0 equals one-half of Vmax.

What does a low Km generally indicate?

Higher apparent affinity because half-maximal velocity is reached at lower substrate concentration.

What does a high Km generally indicate?

Lower apparent affinity because more substrate is required to reach half-maximal velocity.

At what substrate concentration is V0 exactly one-half Vmax?

[S] = Km.

What happens when [S] is much less than Km?

Reaction velocity is approximately first-order with respect to substrate and rises nearly linearly as [S] increases.

What happens when [S] is much greater than Km?

The enzyme is saturated and reaction velocity approaches Vmax, producing zero-order behavior with respect to substrate.

Does increasing enzyme concentration change Km?

No. Km is an intrinsic property of the enzyme–substrate system in this model, whereas Vmax changes with enzyme amount.

Why is calling Km simply 'affinity' an approximation?

Km = (k−1 + kcat)/k1; it approximates the inverse of affinity only when kcat is much smaller than k−1.

Two substrates reach half-maximal velocity at 0.2 mM and 5 mM. Which has higher apparent affinity?

The substrate with Km = 0.2 mM because lower Km corresponds to higher apparent affinity.

What does a Lineweaver–Burk plot graph?

1/V0 versus 1/[S].

What is the y-intercept of a Lineweaver–Burk plot?

1/Vmax.

What is the x-intercept of a Lineweaver–Burk plot?

−1/Km.

What is the slope of a Lineweaver–Burk plot?

Km/Vmax.

What is the key advantage of a Lineweaver–Burk plot in this lecture?

It linearizes Michaelis–Menten behavior and helps diagnose inhibition type by comparing lines with and without inhibitor.

What happens to Km and Vmax in competitive inhibition?

Apparent Km increases; Vmax remains unchanged.

Where does a competitive inhibitor bind?

At the active site, competing directly with substrate.

Can competitive inhibition be overcome by increasing substrate concentration?

Yes; it is surmountable because sufficiently high substrate can outcompete the inhibitor.

What Lineweaver–Burk pattern indicates competitive inhibition?

Lines intersect on the y-axis because Vmax is unchanged.

What happens to Km and Vmax in pure noncompetitive inhibition?

Km is unchanged and Vmax decreases.

Where does a pure noncompetitive inhibitor bind?

At an allosteric site on both free enzyme and enzyme–substrate complex.

Can pure noncompetitive inhibition be overcome by increasing substrate?

No, because Vmax is reduced.

What Lineweaver–Burk pattern is expected for pure noncompetitive inhibition?

Lines intersect on the x-axis because −1/Km is unchanged.

What happens to Km and Vmax in uncompetitive inhibition?

Both Km and Vmax decrease.

Where does an uncompetitive inhibitor bind?

Only the enzyme–substrate complex.

Can uncompetitive inhibition be overcome by increasing substrate?

No.

What is the Lineweaver–Burk pattern for uncompetitive inhibition?

Parallel lines.

What happens to Km in mixed inhibition?

It may increase or decrease depending on whether the inhibitor favors free enzyme or ES.

What happens to Vmax in mixed inhibition?

Vmax decreases.

Where do mixed-inhibition Lineweaver–Burk lines intersect?

Off-axis.

What defines irreversible inhibition?

Covalent or effectively permanent inhibition that removes functional enzyme activity.

What happens to functional Vmax with irreversible inhibition?

It decreases because the amount of active enzyme is reduced.

Can increased substrate overcome irreversible inhibition?

No.

Give an example of a competitive inhibitor from the guide.

Fomepizole inhibiting alcohol dehydrogenase; statins and methotrexate are additional examples.

Give an example of an irreversible inhibitor from the guide.

Aspirin inhibiting cyclooxygenase; organophosphates inhibiting acetylcholinesterase; proton-pump inhibitors inhibiting H+/K+-ATPase; penicillin inhibiting transpeptidase.

Why should irreversible inhibition not be treated as simply another reversible equilibrium inhibitor?

The inhibitor permanently removes functional enzyme, so classic reversible-equilibrium assumptions do not strictly apply.

A drug increases apparent Km but leaves Vmax unchanged. What inhibition type is this?

Competitive inhibition.

A drug decreases Vmax but leaves Km unchanged. What inhibition type is this?

Pure noncompetitive inhibition.

A drug decreases both Km and Vmax and produces parallel Lineweaver–Burk lines. What inhibition type is this?

Uncompetitive inhibition.

What is kcat?

The turnover number: the number of substrate molecules converted to product per active site per unit time at saturating substrate.

What is the equation for kcat?

kcat = Vmax / [E]total.

Does kcat depend on how much enzyme is present?

No. kcat is an intrinsic catalytic rate for the enzyme under saturating substrate conditions.

Vmax is 100 µmol/min and total enzyme is 0.01 µmol. What is kcat?

10,000 min−1.

What is catalytic efficiency?

kcat/Km.