Lec 5 Enzyme Fundamentals and Metabolic Thermodynamics

Comprehensive practice flashcards covering enzyme fundamentals, thermodynamics, vitamin-coenzyme relationships, and clinical applications from BMS 527 Lecture 5.

How do enzymes function in metabolic pathways relative to spontaneous reactions?

Enzymes serve as essential engines of life, providing the necessary acceleration to maintain homeostasis because spontaneous reactions occur too slowly under physiological conditions.

What is the consequence of biochemical reactions occurring without enzymatic catalysis?

Biochemical reactions would essentially stagnate, leading to systemic collapse.

what are the four high-yield reasons to study enzymes?

1. Essentiality of Life

2. Clinical Significance

3. Pharmacological Targets

4. Diagnostic Utility.

What is an example of pathology caused by aberrant enzyme activity?

Phenylketonuria (PKU).

What percentage of FDA-approved drugs specifically target enzymes?

$50\%$.

How are enzymes used for diagnostic utility in medicine?

Enzyme levels in the blood serve as critical markers for tissue damage and metabolic disorders.

In what temperature range do enzymatic catalysts operate compared to chemical catalysts?

• Enzymatic catalysts operate under mild conditions (<100%)

• chemical catalysts often require high temperatures (>100%).

What are Ribozymes?

Catalytic RNA molecules that act as enzymes.

What are the common atmospheric conditions for enzymatic catalysis?

Atmospheric pressure and a nearly neutral pH.

How does the specificity of enzymatic catalysis compare to chemical catalysis?

Enzymatic specificity is vastly greater, reactions are highly specific, and they rarely produce side products.

By what means are enzymes regulated in biological systems?

via:

• allosteric control,

• covalent modification, and

• synthesis rates.

How much can enzymes increase the rate of a reaction?

Up to 1 trillion fold (10^12)

Do enzymes change the final ratio of products to reactants (equilibrium)?

No; enzymes do not alter reaction equilibrium or thermodynamic favorability.

What is the First Law of Thermodynamics as applied to biochemistry?

Energy is neither created nor destroyed, only converted (Conservation of Energy).

What is the Second Law of Thermodynamics?

The universe spontaneously tends toward increasing disorder, also known as entropy.

Why is the hydrolysis of $ATP$ to $ADP + P_i$ favored by the Second Law of Thermodynamics?

The products ($ADP$ and free phosphate) are less ordered than the original $ATP$ molecule.

What are the three variables used to evaluate the directionality of metabolic reactions?

• Enthalpy ($\Delta H$)

• Entropy ($\Delta S$)

• Gibbs Free Energy ($\Delta G$)

State the formula for Gibbs Free Energy.

$\Delta G = \Delta H - T\Delta S$.

What is the ultimate predictor of reaction spontaneity?

Gibbs Free Energy ($\Delta G$).

What does a negative $\Delta G$ indicate?

A spontaneous (exergonic) reaction.

Define Enthalpy ($\Delta H$) in the context of metabolic reactions.

Enthalpy is the total heat content of a system.

What is an Exothermic reaction?

A reaction where the energy released > energy used to break bonds, resulting in a negative ($-$) $\Delta H$.

What is an Endothermic reaction?

A reaction where the energy used to break bonds is greater than the energy released, resulting in a positive ($+$) $\Delta H$.

Define the Active Site of an enzyme.

A three-dimensional pocket formed by the protein's tertiary structure containing residues that directly catalyze bond breaking/making.

What is the Binding Site of an enzyme?

The region where substrate molecules interact with the enzyme.

What is an Apoenzyme?

The inactive protein portion of an enzyme, lacking its required non-protein partner.

Define a Zymogen.

An inactive precursor requiring structural cleavage to become an active enzyme.

What is Activation Energy ($\Delta G^\ddagger$)?

The energy barrier that must be overcome for a reaction to proceed.

How do enzymes specifically lower the activation energy barrier?

Enzymes stabilize the transition state.

Explain the Lock and Key model of interaction.

A model where the active site is rigid and perfectly pre-shaped for a specific substrate.

Explain the Induced Fit model of interaction.

A model where the enzyme has a flexible structure and binding induces a conformational change.

Why do enzymes exhibit stereospecificity?

They are built from L-amino acids, which results in the formation of asymmetric active sites.

Provide a clinical example of stereospecificity involving Trypsin.

Trypsin hydrolyzes polypeptides of L-amino acids but ignores D-amino acids.

Which isomer of glucose do metabolic enzymes typically target?

$\text{D-glucose}$.

What are enzyme Cofactors?

Inorganic components, such as divalent metal cations, that help facilitate catalysis.

What is a common cofactor for DNA Polymerase?

$Mg^{2+}$.

What are Coenzymes?

Complex organic molecules that serve as enzyme assistants.

Distinguish between Prosthetic Groups and Co-substrates.

Prosthetic groups are permanently or tightly bound; co-substrates are loosely associated and must be regenerated after being changed during a reaction.

Which vitamin is the precursor for Thiamine Pyrophosphate (TPP)?

$\text{B1 (Thiamine)}$.

What is the primary chemical function of Thiamine Pyrophosphate (TPP)?

Decarboxylation and aldehyde transfer.

Which vitamin is the precursor for FMN and FAD?

$\text{B2 (Riboflavin)}$.

What is the primary chemical function of coenzymes derived from Vitamin B2?

$\text{Oxidation-Reduction (Redox)}$.

Which vitamin is the precursor for NAD and NADP?

$\text{B3 (Niacin)}$.

Which vitamin corresponds to Coenzyme A (CoA)?

$\text{B5 (Pantothenic Acid)}$.

What chemical function does Coenzyme A (CoA) perform?

Acyl group transfer.

Which vitamin is the precursor for Pyridoxal Phosphate?

$\text{B6 (Pyridoxine)}$.

What chemical function does Pyridoxal Phosphate perform?

Amino group transfer.

Which vitamin is involved in Carboxylation ($CO_2$ transfer)?

$\text{B7 (Biotin)}$.

Which vitamin corresponds to Tetrahydrofolate?

$\text{B9 (Folic Acid)}$.

What is the chemical function of Tetrahydrofolate?

One-carbon group transfer.

Which vitamin corresponds to Methylcobalamin?

$\text{B12 (Cobalamin)}$.

What is the chemical function of Vitamin B12?

Methylation.

What are the six functional classes of enzymes abbreviated as O.T.H.L.I.L.?

1. Oxidoreductases, 2. Transferases, 3. Hydrolases, 4. Lyases, 5. Isomerases, 6. Ligases.

Describe the reaction type of Oxidoreductases.

Electron transfer (Redox), often using Carriers like $NAD^+/NADH$.

What is the strategic role of Transferases?

Moving functional groups, such as Kinases transferring phosphates.

What is the function of Hydrolases?

Cleavage of bonds using water.

How do Lyases differ from Hydrolases regarding bond cleavage?

Lyases cleave bonds without the use of water.

What is the function of Isomerases?

Rearranging internal bonds to convert constitutional isomers.

What is the function of Ligases?

Joining two large molecules, usually requiring $ATP$ (e.g., DNA Ligase).

In bisubstrate terminology, what is a Uni Ter reaction?

A reaction that starts with 1 substrate ($\text{Uni}$) and yields 3 products ($\text{Ter}$).

What characterizes Sequential (Single Displacement) mechanisms?

All substrates must bind to the enzyme before any product is released.

Define Ordered Sequential reactions.

A mechanism with a compulsory order of substrate addition (e.g., A then B).

Define Random Sequential reactions.

A mechanism where there is no preference for the order of substrate addition.

What characterizes a Ping Pong (Double Displacement) mechanism?

A product is released before the second substrate binds.

In a Ping Pong mechanism, what is 'Form F'?

A stable enzyme intermediate where a functional group is temporarily bound ($E-X$) before being passed to the second substrate.

What is Allosteric Control?

Regulation where binding at an allosteric site (not the active site) causes protein vibrations that change the active site's affinity.

Define Homoallosteric effectors.

The substrate serves as its own effector; binding at one subunit increases affinity in others (Cooperativity).

Explain Heteroallosteric control.

A different molecule (modulator) binds to an allosteric site to stimulate or inhibit the enzyme.

What is Covalent Modification?

The addition or removal of chemical groups to regulate an enzyme, such as Phosphorylation.

Define Negative Feedback (Feedback Loops).

A mechanism where a downstream product inhibits an upstream enzyme.

Which metabolic disorder is linked to HMG-CoA Reductase?

Familial Hypercholesterolaemia.

What is the pharmacological mechanism of Statins?

They inhibit the enzyme HMG-CoA Reductase.

Why is HMG-CoA Reductase a strategic target for Statins?

It is the rate-limiting step in cholesterol synthesis; blocking it shuts down the entire production line.

What is the memory mnemonic for enzyme classes?

O.T.H.L.I.L. (Over The Hill Life Is Long).

What is the memory trick for identifying a Ping Pong mechanism?

Identify the existence of a 'Stable Intermediate' or 'Form F'.

What does a positive $\Delta S_{reaction}$ indicate?

An increase in disorder ($S_{products} - S_{reactants}$).

Define 'system' in the context of enthalpy.

Enthalpy is the total heat content of a specific 'system'.

Does a catalyst like an enzyme alter $\Delta G$?

No, there is no difference in $\Delta G$ between a reaction with or without an enzyme.

What is the approximate lifetime of a transition state?

On the order of a picosecond ($10^{-12}\text{ s}$).

Define Holoenzyme.

The complete, active complex consisting of the enzyme (protein) plus its necessary cofactor or coenzyme.

What are the SI units for energy commonly used in biochemistry?

The Joule ($\text{J}$) and Calorie ($\text{cal}$).

How much energy is released during the hydrolysis of ATP to ADP + Pi?

$\sim 30.5\text{ kJ}$.

What is an Exergonic reaction?

A reaction that releases energy, making it thermodynamically favorable (spontaneous).

What is an Endergonic reaction?

A reaction that requires an input of energy to proceed (non-spontaneous).

Define Orthosteric site.

Another term for the Active site where the substrate binds.

How does $\Delta S$ relate to spontaneity at high temperatures in an endothermic reaction?

If $\Delta S > 0$, the reaction may become spontaneous at high temperatures ($\text{when } T\Delta S \text{ is large}$).

What is the primary role of Vitamin C in collagen synthesis?

It acts as a necessary cofactor for prolyl hydroxylase, which hydroxylates proline residues.

Why is hydroxyproline essential for collagen?

It facilitates the formation of interchain hydrogen bonds that stabilize the collagen triple helix.

What percentage of biochemcial reactions are bisubstrate reactions?

$60\%$.

What logic dictates transferases as bisubstrate reactions?

To move a group from point A to point B, the enzyme needs both a donor (Substrate A) and an acceptor (Substrate B).

What logic dictates oxidoreductases as bisubstrate reactions?

Redox reactions require one substrate to be oxidized (losing electrons) and another to be reduced (gaining electrons).

In sequential mechanisms, how are affinity and concentration related?

Changing the concentration of one substrate can change the enzyme's apparent affinity for the other substrate.

What is the 'bus ride' memory tip for Sequential reactions?

All passengers (substrates) must get on the bus (enzyme) before reaching the final stop (product release).

What is the 'table tennis' memory tip for Ping Pong reactions?

One player hits the ball, changing the enzyme state, then the other player hits it back to regenerate the enzyme.

What are vitamins defined as in biochemistry?

Organic compounds essential for normal growth that cannot be synthesized by the body and must be obtained via diet.

What class of enzymes often uses NAD+ coenzymes?

Oxidoreductases.

Define 'Stable Intermediate Form (F)' in the Ping Pong mechanism.

The temporary state where the enzyme has picked up a functional group from the first substrate and is waiting for the second substrate.

What is the primary goal of a reaction schematic (general)?

To show the overall transformation of reactants to products, often focused on thermodynamics (equilibrium, $\Delta G$).

What is the primary focus of a Bisubstrate Reaction Mechanism map?

Kinetics and the specific order of substrate binding and product release.

Are enzymes used up in a chemical reaction?

No; an enzyme increases the rate of a reaction without itself being consumed.