chapter 6 pt 1 full

What genetic mutation causes sickle cell anemia?

Substitution of glutamate at position 6 with valine at position 6 in the beta subunit of hemoglobin.

Why is the glutamate-to-valine substitution in sickle cell anemia significant?

Glutamate is negatively charged and hydrophilic, while valine is hydrophobic, causing abnormal protein interactions.

What causes hemoglobin molecules to aggregate in sickle cell anemia?

Hydrophobic interactions involving valine 6.

Why do red blood cells become sickle-shaped?

The formation of elongated hemoglobin fibers distorts the cell membrane

What would happen if glutamate 6 remained in hemoglobin?

Hydrophobic aggregation of hemoglobin molecules would not occur.

What is the result of hemoglobin fiber formation inside red blood cells?

Sickle-shaped, elongated red blood cells.

What is an enzyme?

A biological catalyst that increases the rate of a chemical reaction without being consumed.

What is the primary role of enzymes?

To accelerate chemical reactions.

Are all enzymes proteins?

No. Most enzymes are proteins, but some are RNA molecules.

What are ribozymes?

RNA molecules with catalytic activity.

What are ribosomal RNAs capable of doing?

Acting as enzymes.

What type of protein structure do most enzymes have?

Globular proteins.

What are examples of RNA-based enzymes?

Ribozymes, including ribosomal RNA molecules with catalytic activity.

What conclusion was drawn from Buchner's fermentation experiments?

Molecules rather than living cells could catalyze fermentation.

What enzyme is responsible for the glowing effect in jellyfish?

Aequorin.

What does aequorin catalyze?

The oxidation of an organic compound called a chromophore.

What are the products of the reaction catalyzed by aequorin?

Release of CO2 and production of light.

What is required for aequorin's reaction to occur?

Oxygen and calcium cations.

What is a cofactor?

A metal ion required for enzyme activity.

What is a coenzyme?

An organic or metallo-organic molecule required for enzyme activity.

Which metal ions commonly serve as cofactors?

Iron, zinc, copper, manganese, and nickel.

Why are cofactors important?

Without them many enzymes lose catalytic activity.

What cofactor is required by cytochrome c oxidase?

Copper (Cu2+).

What reaction does cytochrome c oxidase help catalyze?

Reduction of oxygen to water during electron transport.

What cofactor is required by pyruvate kinase?

Potassium ion (K+).

What reaction does pyruvate kinase catalyze?

Transfer of phosphate from phosphoenolpyruvate (PEP) to ADP to form ATP and pyruvate.

Why is pyruvate kinase important during cellular respiration?

It generates ATP during glycolysis.

What cofactor is required by hexokinase?

Magnesium ion (Mg2+).

What reaction does hexokinase catalyze?

Conversion of glucose to glucose-6-phosphate.

Why is the hexokinase reaction important?

It traps glucose inside the cell.

How does glucose become trapped inside the cell?

Phosphorylation adds a negatively charged phosphate group.

What reaction is catalyzed by urease?

Conversion of urea into ammonia and carbon dioxide.

Which cofactor is required by carbonic anhydrase?

Zinc ion (Zn2+).

What are oxidoreductases?

Enzymes that catalyze oxidation-reduction reactions.

What are transferases?

Enzymes that transfer functional groups between molecules.

What are hydrolases?

Enzymes that cleave bonds using water.

What are lyases?

Enzymes that remove atoms to form double bonds or add atoms to double bonds.

What are isomerases?

Enzymes that move functional groups inside a molecule.

What are ligases?

Enzymes that join two molecules together using ATP.

What are translocases?

Enzymes that move molecules or ions across membranes.

What is a holoenzyme?

The complete catalytically active enzyme including its cofactor.

What is an apoenzyme?

The protein portion of an enzyme without its cofactor.

What is a prosthetic group?

A tightly bound non-protein component necessary for enzyme activity.

What is an enzyme active site?

The region where substrate binding and catalysis occur.

What model best describes enzyme-substrate binding?

Induced fit.

What forms the environment of an enzyme active site?

The amino acid side chains that line the active site

What are common properties of enzyme active sites?

Three-dimensional clefts, small fraction of enzyme volume, substrate specificity, and weak interaction binding.

Why are enzyme active sites highly specific?

Only particular substrates fit and interact properly.

What forces commonly form enzyme-substrate complexes?

Multiple weak intermolecular interactions.

What is the enzyme-substrate complex?

The intermediate formed when an enzyme binds its substrate.

What happens after product formation?

The product is released and the enzyme is regenerated.

What are proteolytic enzymes?

a type of hydrase that hydrolyze peptide bonds.

What are the products of peptide bond hydrolysis?

An amino component and a carboxyl component.

How specific is papain?

It cleaves peptide bonds with little regard for neighboring amino acids.

What is chymotrypsin?

A digestive protease with high substrate specificity.

Where does chymotrypsin cleave peptide bonds?

On the carboxyl side of aromatic amino acids.

What is trypsin?

A digestive protease.

Where does trypsin cleave peptide bonds?

On the carboxyl side of lysine or arginine residues.

What is thrombin?

A protease involved in blood clotting.

What peptide bond does thrombin cleave?

The bond between arginine and glycine in that order.

Does thrombin cleave a Gly-Arg sequence?

No. Thrombin specifically recognizes and cleaves an Arg-Gly sequence.

Why are enzymes preferred over many inorganic catalysts in biological systems?

They provide greater specificity,

mild conditions,

high reaction rates,

regulation.

How does enzyme specificity reduce side products?

Only the intended reaction pathway is favored.

Why is enzyme regulation important?

it ensures that cells produce the right amount of products at the right time and conserve energy and resources.

Do all enzymes operate optimally at pH 7.4?

No. Some enzymes, such as digestive enzymes in the stomach, function best at lower pH values.

What is chorismate?

A metabolic intermediate used to produce aromatic compounds.

What is prephenate?

A precursor for aromatic amino acid synthesis.

Which amino acids can be synthesized from prephenate-derived pathways?

Tyrosine, phenylalanine, and tryptophan.

Do enzymes change chemical equilibrium?

No.

What effect do enzymes have on equilibrium?

They increase speed of reaction but does not change equilibrium(ΔG)

Can enzymes catalyze both forward and reverse reactions?

Yes.

Why does equilibrium remain unchanged in enzyme-catalyzed reactions?

Enzymes accelerate both directions equally.

What is the relationship between reaction equilibria and thermodynamics?

Reaction equilibria are linked to the standard free-energy change (ΔG).

What is the relationship between reaction rates and thermodynamics?

Reaction rates are linked to the activation energy (ΔG‡).

What does the equilibrium constant represent?

the ratio of products to reactants

What is the transition state?

The highest-energy and least stable state reached during a chemical reaction.

What is activation energy?

The energy barrier separating reactants from products.

What symbol is often used for activation energy in biochemistry?

ΔG‡.

What is the highest-energy species during a reaction?

The transition state.

What is the difference between the ground state energy level and the transition state energy level?

The activation energy.

How do enzymes speed up reactions?

By stabilizing the transition state and lowering activation energy.

What happens to reaction pathway in the presence of an enzyme?

A lower-energy pathway becomes available.

What remains unchanged when enzymes lower activation energy?

The overall ΔG and equilibrium position.

What determines the reaction rate in a multistep reaction?

The slowest step.

Which step usually has the highest activation energy?

The rate-determining step.

transition state

What are the two major characteristics of enzymatic reactions?

Binding and catalysis.

What is catalysis?

Conversion of substrate into product or vise versa

What does KD describe?

Binding affinity through the dissociation constant.

What is binding energy (ΔGb)?

The free energy released when an enzyme binds its substrate.

What causes binding energy to be released?

Formation of weak interactions between enzyme and substrate.

What does a more negative ΔGb indicate?

Higher binding affinity.

Why is binding energy important?

It helps lower activation energy.

What is the major source of free energy used by enzymes to lower activation energy?

Binding energy (ΔGb).

What types of interactions generate binding energy?

Mostly noncovalent intermolecular interactions.

What is acid-base catalysis?

Catalysis involving proton donation or proton acceptance by molecules other than water.

What does specific acid-base catalysis use?

H+ or H3O+ ions from water.

Why is histidine often involved in enzyme catalysis?

It can both donate and accept protons.

How does histidine help in chymotrypsin catalysis?

It acts as a base to enhance serine nucleophilicity.

What is covalent catalysis?

Catalysis involving temporary covalent bonding between enzyme and substrate.

What does the formation and breakdown of a covalent intermediate create?

A new reaction pathway with lower activation energy.