BIOCHEM MIDTERM 2

How do enzymes speed up reactions?

By lowering the activation energy (Ea) without changing ΔG or the reaction equilibrium.

What does the active site do?

Binds the substrate, positions reactive groups correctly, stabilizes the transition state, and catalyzes the reaction.

What is a catalytic triad?

Three amino acids (commonly Ser-His-Asp) that work together through a charge relay system to increase nucleophile reactivity.

What is the oxyanion hole?

A region of the enzyme that stabilizes negatively charged oxygen atoms in reaction intermediates through hydrogen bonding.

Why is transition-state stabilization important?

It lowers activation energy, allowing the reaction to proceed faster.

What are cofactors?

Non-protein molecules or metal ions required for enzyme activity.

Give examples of enzyme cofactors.

Metal ions (Fe2+, Zn2+, Mg2+) and coenzymes such as NAD+ and FAD.

What types of reactions require cofactors?

Electron transfer, radical reactions, hydride transfer, and oxidation-reduction reactions.

What is reaction velocity (v)?

The rate of product formation or reactant disappearance.

What is the general rate equation?

v = kf[A]^a[B]^b − kr[P]^p[Q]^q

What happens if the reverse reaction is negligible?

The rate equation simplifies to v = k[A]^a[B]^b.

What is the equation for a first-order reaction?

v = k[A]

What are the units of a first-order rate constant?

s⁻¹

What is the equation for a second-order reaction?

v = k[A][B]

What are the units of a second-order rate constant?

M⁻¹ s⁻¹

How is a rate constant determined experimentally?

Measure initial reaction rates at varying substrate concentrations and determine the slope.

What are the two steps in the Michaelis-Menten model?

1. Substrate binds the enzyme. 2. Product is formed and released.

What is the Michaelis-Menten reaction scheme?

E + S ⇌ ES → E + P

Michaelis-Menten Assumption #1.

Substrate binding is fast, catalysis is slow, and catalysis is the rate-limiting step.

Michaelis-Menten Assumption #2.

Initial velocity is measured when product concentration is approximately zero ([P] ≈ 0).

Michaelis-Menten Assumption #3.

The ES complex remains at steady state (its concentration stays constant).

Michaelis-Menten Assumption #4.

Substrate concentration is much greater than total enzyme concentration ([S] >> [E]T).

Michaelis-Menten Assumption #5.

Total enzyme concentration equals free enzyme plus enzyme-substrate complex: [E]T = [E] + [ES].

What is the equation for initial velocity?

v₀ = k₂[ES]

Why is initial velocity measured?

Product has not accumulated, so the reverse reaction is negligible.

What is the steady-state assumption?

The rate of ES formation equals the rate of ES breakdown.

At steady state, what is d[ES]/dt?

Zero.

What is the equation for Km?

Km = (k−1 + k2)/k1

What does Km represent?

The substrate concentration at one-half of Vmax.

What does a low Km indicate?

High substrate affinity.

What does a high Km indicate?

Low substrate affinity.

What is Vmax?

The maximum reaction velocity when all enzyme active sites are saturated with substrate.

When is Vmax reached?

When substrate concentration is much greater than Km ([S] >> Km).

What happens to enzyme active sites at Vmax?

All active sites are occupied (enzyme saturation).

What is the equation for Vmax?

Vmax = k2[E]T

What is the Michaelis-Menten equation?

v₀ = (Vmax[S])/(Km + [S])

What happens when [S] << Km?

Velocity increases approximately linearly with substrate concentration.

What happens when [S] >> Km?

Velocity approaches Vmax.

At what substrate concentration is v = ½Vmax?

When [S] = Km.

Why is Km useful?

It estimates enzyme-substrate affinity and allows comparison of enzymes.

Do enzymes change ΔG?

No.

Do enzymes change the equilibrium constant?

No.

Do enzymes lower activation energy?

Yes.

What limits the reaction rate in Michaelis-Menten kinetics?

The catalytic step (k₂).

Why is product concentration ignored when measuring initial velocity?

Because [P] ≈ 0, making the reverse reaction negligible.

What are the four major classes of biological macromolecules?

Proteins, nucleic acids, lipids, and carbohydrates.

What are the major learning goals for this lecture?

Understand carbohydrate structure/function, nucleic acid structure/function, and how both relate to biology.

What are carbohydrates commonly called?

Sugars.

Why are carbohydrates called carbohydrates?

Many have the empirical formula Cn(H2O)n.

Name four major functions of carbohydrates.

Energy storage, structural support, cell signaling, and glycosylation.

What is glycosylation?

The attachment of carbohydrates (glycans) to proteins or lipids.

What functional group defines an aldose?

An aldehyde.

What functional group defines a ketose?

A ketone.

What is the difference between an aldose and a ketose?

Aldoses contain an aldehyde; ketoses contain a ketone.

How many carbons are in a triose?

3

How many carbons are in a tetrose?

4

How many carbons are in a pentose?

5

How many carbons are in a hexose?

6

Name an important hexose sugar.

Glucose.

Name an important ketose sugar.

Fructose.

Which carbohydrate names should you recognize for metabolism?

Glucose, fructose, ribose, and deoxyribose.

How are carbohydrate carbons numbered?

Start numbering from the end closest to the carbonyl group.

How are carbohydrates commonly drawn?

Using Fischer projections.

Why are Fischer projections useful?

They clearly show stereochemistry.

What does a Fischer projection represent?

A three-dimensional molecule shown in two dimensions.

What do horizontal bonds in a Fischer projection represent?

Bonds projecting toward the viewer.

What do vertical bonds represent?

Bonds projecting away from the viewer.

What is a chiral carbon?

A carbon attached to four different groups.

Why are carbohydrates often chiral?

They contain one or more chiral carbons.

What are enantiomers?

Non-superimposable mirror images.

What is an epimer?

Two sugars differing at only one stereocenter.

What is a diastereomer?

Stereoisomers that are not mirror images.

What organic chemistry reaction is important for carbohydrate ring formation?

Nucleophilic attack of an alcohol on a carbonyl carbon.

What is a hemiacetal?

The product formed when an alcohol reacts with an aldehyde.

Which type of sugar forms a hemiacetal?

An aldose.

What is a hemiketal?

The product formed when an alcohol reacts with a ketone.

Which type of sugar forms a hemiketal?

A ketose.

How do carbohydrate rings form?

Through intramolecular nucleophilic attack.

What is the most common ring formation mechanism for carbohydrates?

Formation of cyclic hemiacetals or hemiketals.

What is the anomeric carbon?

The carbon that was the carbonyl carbon before ring formation.

What is the difference between α and β anomers?

The orientation of the OH group on the anomeric carbon.

What are pyranoses?

Six-membered carbohydrate rings.

What are furanoses?

Five-membered carbohydrate rings.

Which sugars typically form pyranoses?

Most hexoses.

What is mutarotation?

The spontaneous interconversion between α and β anomers in solution.

Which conformation is generally most stable for six-membered carbohydrate rings?

The chair conformation.

Why are carbohydrates structurally diverse?

They vary in stereochemistry, ring size, linkage type, and branching.

What is a glycosidic bond?

A covalent bond linking two carbohydrate molecules.

How are glycosidic bonds formed?

Through a condensation (dehydration) reaction.

What is a monosaccharide?

A single sugar unit.

What is a disaccharide?

Two monosaccharides linked together.

What is an oligosaccharide?

A short chain of sugars.

What is a polysaccharide?

A long chain of more than about 20 sugar units.

How is a glycosidic bond formed between two sugars?

Between the alcohol of one sugar and the hemiacetal of another during condensation.

Name one example of a disaccharide.

Sucrose.

What type of reaction breaks glycosidic bonds?

Hydrolysis.

What determines the type of glycosidic bond formed between sugars?

The orientation (α or β) of the anomeric carbon and which carbons are linked.

Can glycosidic bonds form between different carbon atoms?

Yes, common linkages include α(1→4), β(1→4), α(1→6), and α,β(1→2).

What is a reducing sugar?

A sugar with a free anomeric carbon that can open into its linear form.

What is required for a sugar to be reducing?

At least one anomeric carbon must not participate in a glycosidic bond.