Amino Acids, Protein Structure, Enzymes, Nucleic Acids, and Metabolic Pathways

50 flashcards covering topics in amino acids, protein structure, enzyme function, nucleic acids, and metabolic pathways to aid in exam preparation.

What are the phosphorylatable amino acids?

Serine, Tyrosine, Threonine.

What is the mnemonic for phosphorylatable amino acids?

Some Tigers Yell (S – serine, T – threonine, Y – tyrosine).

What are cyclic amino acids?

Tryptophan, Phenylalanine, Tyrosine, Proline, Histidine.

What is the approximate weight of a polypeptide composed of 11 residues?

1100 Da.

What interactions are disrupted by denaturing in quaternary structure?

Hydrophobic interactions.

What interactions are disrupted by denaturing in tertiary structure?

Ionic interactions.

What interactions are disrupted by denaturing in secondary structure?

Hydrogen bonding.

What is Kd in relation to protein and ligand?

Dissociation constant, where low Kd indicates high binding affinity.

What are prosthetic groups in enzymes?

Non-amino acids that connect to their proteins via covalent bonds.

What are coenzymes?

Non-polypeptide organic molecules that assist enzymes.

What occurs at the active site of an enzyme?

Binding to a specific substrate for reaction catalysis.

What characterizes a low Km value in enzyme kinetics?

High binding affinity.

What does an increase in temperature do to enzyme activity?

May increase the Vmax of the reaction.

What are purines?

Adenine and Guanine.

What distinguishes pyrimidines from purines?

Pyrimidines have one ring structure, while purines have two.

Which phosphate is removed during ATP hydrolysis?

Gamma phosphate.

What type of reaction forms disaccharides from monosaccharides?

Dehydration reaction that releases water as a byproduct.

What indicates a sugar is a reducing sugar?

Presence of Aldehyde, ketone, or hemiacetals.

What is the main structural difference between glycogen and cellulose?

Glycogen has alpha-1,6 glycosidic linkages, while cellulose has beta-1,4 linkages.

What is a triacylglycerol made up of?

A glycerol backbone and three fatty acids.

What effect does increasing fatty acid tail length have on cell membrane fluidity?

It decreases fluidity.

What characterizes rate-limiting enzymes in metabolic pathways?

They catalyze reactions with significantly favorable Gibbs free energy (ΔG much less than zero).

What is oxidative phosphorylation?

Energy production from the oxidation of electron carriers.

What differentiates substrate-level phosphorylation from oxidative phosphorylation?

Substrate-level phosphorylation involves direct transfer of a phosphate group.

What happens during the reaction of NADH being converted to NAD+?

NADH is oxidized and acts as a reducing agent.

How do coenzymes differ from prosthetic groups?

Coenzymes are loosely associated, while prosthetic groups are tightly bound.

What is the role of an allosteric site on an enzyme?

It is where regulatory molecules bind to bring conformational change.

What type of reaction does maltase catalyze?

Converts maltose into glucose.

What does a high Kd indicate about protein-ligand binding?

Low binding affinity.

How does temperature affect enzyme kinetics?

Temperature changes can affect both Km and Vmax.

How many rings do purines have?

Two rings.

What is a characteristic of ketoses?

They have a carbonyl group in the middle of the carbon chain.

What is the significance of the active site on a enzyme?

It is where the substrate binds and the reaction occurs.

What is the outcome when a reaction involves a favorable ΔG?

The reaction is spontaneous and tends to proceed forward.

What type of bonding do prosthetic groups utilize in enzymes?

Covalent bonding.

What defines a reducing sugar?

Presence of a hemiacetal group that can donate electrons.

What can increase the stability of a cell membrane?

Increasing cholesterol at low temperatures.

What is an example of a reducing agent?

NADH, which donates electrons.

What is the main role of ATP in biochemical reactions?

It serves as an energy carrier.

How is glucose from maltose generated?

By the enzyme maltase catalyzing the reaction.

In a metabolic pathway what is the target of regulation?

Rate-limiting enzymes.

In metabolic reactions, what does high ΔG suggest?

The reaction is unfavorable and not likely to occur spontaneously.

What is the rate-limiting step in glycolysis?

Fructose 6-phosphate to Fructose 1,6-bisphosphate, catalyzed by Phosphofructokinase-1 (PFK-1).

Enzyme thermodynamics

Is if a reaction will occur by determining stability

Enzyme kinetics

How fast a reaction will occur by controlling activation energy

Components of thermodynamics

Spontaneity, equilibrium, and free energy

Components of enzyme kinetics

Activation energy (Ea)

Michaelis-Menten constant

m = Km/Vmax

Michaelis-Menten, X-int.

Km = [1/S]

Michaelis-Menten, y-int.

Vmax = 1/V0 or Km/m