Lecture 3: Enzymes and biochemical pathways

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Questions and Answers

Which statement accurately describes an exergonic reaction?

It has a positive delta G.

It is a nonspontaneous process.

It proceeds with a net release of free energy. (correct)

It absorbs free energy from its surroundings.

What is the relationship between spontaneous processes and work?

Spontaneous processes only occur inside a closed system.

Spontaneous processes are unrelated to work.

Spontaneous processes can be harnessed to perform work. (correct)

Spontaneous processes cannot be used to perform work.

In a closed system, what is the overall change in Gibbs free energy (∆G) for a total reaction?

∆G is greater than 0.

∆G is less than 0.

∆G varies based on the reactants.

∆G is equal to 0. (correct)

Which of the following is NOT necessarily true for a spontaneous reaction?

It occurs rapidly. (C) Signup and view all the answers

If the hydrolysis of ATP is used to drive the synthesis of amino acids, what can be said about the overall delta G for the reaction and the processes?

Overall delta G is zero, the hydrolysis is exergonic and the synthesis is endergonic. (C) Signup and view all the answers

Why does the increased order within a cell require the release of heat?

Heat is a byproduct of the processes that keep the cell organized. (C) Signup and view all the answers

Which statement accurately describes how energy conversion happens in a cell?

The cell breaks down sugar molecules to form ATP, which can then be used for processes like ion transport. (B) Signup and view all the answers

What are the products of energy conversion in cells?

ATP and water are the main products, while carbon dioxide is a waste product. (D) Signup and view all the answers

What is the role of redox reactions in energy transfer within cells?

Redox reactions involve the transfer of electrons, which helps move energy from one step to another. (C) Signup and view all the answers

What happens to a molecule when it is oxidized?

It loses electrons and becomes more polar. (C) Signup and view all the answers

Which of the following is NOT a valid example of a redox reaction?

The transport of ions across a cell membrane. (A) Signup and view all the answers

What is the reason why photosynthesizers are essential for life on Earth?

They are the primary source of energy for nearly all life forms on Earth. (D) Signup and view all the answers

What is the relationship between the first law of thermodynamics and the energy flow through the biosphere?

The first law of thermodynamics dictates that energy cannot be destroyed, so all energy from the sun is eventually released as heat. (D) Signup and view all the answers

How does a cell maintain its internal order?

By consuming energy to counter entropy. (C) Signup and view all the answers

How is the energy flow through the biosphere a demonstration of the first law of thermodynamics?

Energy from the sun is converted and passed through the biosphere but never truly lost. (A) Signup and view all the answers

What does the equilibrium constant (K) indicate about a chemical reaction?

The concentrations of reactants and products when equilibrium is reached. (A) Signup and view all the answers

In a metabolic pathway, what is the relationship between changes in free energy for sequential reactions?

They are additive. (D) Signup and view all the answers

What role do noncovalent interactions play in enzyme catalysis?

They enable enzymes to bind to specific molecules. (D) Signup and view all the answers

What is the key characteristic of an exergonic reaction?

It occurs spontaneously. (B) Signup and view all the answers

Under what condition can an endergonic reaction occur spontaneously?

When coupled with an exergonic reaction by the breaking of covalent bonds. (C) Signup and view all the answers

What does a negative ΔG value indicate about a reaction?

The reaction will proceed spontaneously. (D) Signup and view all the answers

In the equation ΔG = ΔH – TΔS, what does ΔS represent?

The change in total disorder (entropy). (B) Signup and view all the answers

What does a value of 0 for the change in free energy (ΔG) indicate for a reaction?

The reaction is at equilibrium and no net change occurs. (B) Signup and view all the answers

Which of the following best describes the role of cellular structures in metabolic pathways?

They help organize and bring order to the different steps of metabolic pathways. (D) Signup and view all the answers

According to the information given, where would one most likely find the enzymes responsible for cellular respiration in eukaryotic cells?

Exclusively in the mitochondria. (C) Signup and view all the answers

What is the primary function of digestive enzymes in the context of cellular compartmentalization?

To break down cellular and extracellular materials within lysosomes. (C) Signup and view all the answers

What is the term given in the extra credit section that describes a barrier that chemical reactions must overcome to proceed?

Activation energy (B) Signup and view all the answers

According to the extra credit section, what do enzymes physically do during a reaction?

They lower the activation energy needed for a reaction to proceed. (D) Signup and view all the answers

What is the primary role of ATP in cellular energy coupling?

To mediate the transfer of free energy from exergonic reactions to endergonic reactions. (D) Signup and view all the answers

Why does a dead cell represent a state of equilibrium in terms of energy?

Because it cannot maintain order or perform any work since it lacks energy input, thus being at the state of maximal stability (A) Signup and view all the answers

What best describes a catabolic pathway within a cell?

A series of reactions where each releases energy to drive the next reaction. (D) Signup and view all the answers

How do enzymes affect the activation energy ($E_A$) of a reaction?

Enzymes reduce the $E_A$ barrier, resulting in rapid reactions. (C) Signup and view all the answers

Which of the following is NOT a way an enzyme's active site lowers the activation energy barrier?

By increasing the kinetic energy of the substrates. (A) Signup and view all the answers

What is the term for the molecule upon which an enzyme acts?

Substrate (B) Signup and view all the answers

What is a ribozyme?

A catalytic molecule made of RNA. (C) Signup and view all the answers

What does the term 'induced fit' refer to regarding enzyme-substrate interactions?

The conformational change of the enzyme upon binding the substrate. (C) Signup and view all the answers

If a reaction has a $\Delta G$ of -7.3 kcal/mol, what can be determined about the reaction?

The reaction is exergonic and will proceed spontaneously. (A) Signup and view all the answers

What is the primary function of enzymes in metabolic reactions?

To increase the speed of reactions (A) Signup and view all the answers

What is a major role of ATP hydrolysis in cellular work?

To provide the energy driving force for endergonic activities. (B) Signup and view all the answers

Which of the following correctly describes catabolic pathways?

They break down molecules to release energy. (D) Signup and view all the answers

What determines the optimal activity of an enzyme?

The unique environmental conditions that result in the most active conformation. (B) Signup and view all the answers

According to the laws of thermodynamics, what happens to energy in biological systems?

Energy transfers increase the overall entropy of the universe. (D) Signup and view all the answers

A car on a steep hill rolls without any energy input. What does this exemplify?

A spontaneous process proceeding towards equilibrium. (B) Signup and view all the answers

What is a consequence of entropy increasing over time in biological systems?

More energy is required for metabolism to occur. (B) Signup and view all the answers

Why is cellular metabolism in an open system, rather than a closed system?

Metabolism must have a constant flow of materials into and out of the cell. (C) Signup and view all the answers

Which statement is true regarding anabolic pathways?

They consume energy to build larger molecules. (A) Signup and view all the answers

Which of these is NOT a main type of work performed by cells?

Electrical work such as nerve impulses. (D) Signup and view all the answers

What role do intermediate metabolites play in metabolism?

They serve as building blocks for larger molecules. (B) Signup and view all the answers

What is the composition of ATP?

A ribose sugar, a nitrogenous base, and three phosphate groups. (D) Signup and view all the answers

What does the conservation of energy principle state about energy in biological systems?

Energy can neither be created nor destroyed. (C) Signup and view all the answers

Which of the following best describes the interaction of enzymes with substrates?

Enzymes decrease the activation energy needed for a reaction. (C) Signup and view all the answers

Study Notes

Enzymes & Biochemical Pathways

Enzymes are biological catalysts that facilitate metabolic reactions, but do not add energy. They only speed up the rate of reactions.
Catabolic pathways break down molecules to release energy and produce intermediate metabolites.
Anabolic pathways use energy to build up molecules.
Metabolism refers to all chemical reactions within an organism.

Metabolism & Cellular Environment

Metabolic pathways are either catabolic or anabolic.
Enzymes are biological catalysts, facilitating metabolic reactions, but not adding energy to the reactions.
They increase the speed of reactions.
Enzymes only use the activation energy for reactions and then are reusable.

How Cells Use Energy

Biological systems obey the laws of thermodynamics.
Conservation of energy: energy cannot be created or destroyed. Energy must be put into a system for work to occur.
Entropy (disorder) tends to increase over time; energy flows down a gradient (high to low).
Energy is always required to create organization or to decrease entropy.
Examples include organized metabolic pathways, cytoskeleton structure, organelles, DNA sequences, and active transport.
Heat energy is always present.

Types of Energy

Energy is the capacity to cause change (to do work).
Energy exists in various forms, falling into two categories:
- Kinetic energy—energy associated with motion, including heat energy due to random molecular motion.
- Potential energy—energy that matter possesses due to its structure or location.
  - Chemical energy—potential energy stored in chemical bonds that can be released in chemical reactions.
- Molecules or ions concentrated on one side of a membrane can represent potential energy.

How Cells Use Energy (Conversion of Energy)

Not all forms of energy are useful to a cell
Cells convert energy from one form to another.
Examples include: the energy stored in the bonds of a sugar molecule, which cannot pump ions across a membrane but can be broken and transformed to make ATP
This ATP can be used by an active transport pump that moves ions
Small molecule waste products such as CO2 and H2O carry away energy as heat.

Photosynthesis

Cells that can carry out photosynthesis use the energy of sunlight to drive biochemical reactions that transform electromagnetic energy into chemical energy (covalent bonds).

Redox Reactions

Oxidation and reduction reactions (redox reactions) involve electron transfer; these reactions are used to ferry energy between reactions
Photosynthesis and cell respiration involve redox reactions

Free Energy and Catalysis

In complex reactions, the equilibrium constant (K) includes the concentrations of all reactants and products. K will tell you the concentrations when equilibrium is reached.
The change in free energy (ΔG) is related to the equilibrium constant.
For sequential reactions, free energy changes are additive.
The change of Gibb's free energy is written as ΔG and tells how much energy is needed for a reaction to occur
Reactions that occur spontaneously have a negative ΔG whereas reactions that are not spontaneous have a positive ΔG.
Enzyme-catalyzed reactions depend on rapid molecular collisions.

Enzymes

Enzymes are biological catalysts made of proteins.
Some enzymes are simple and others have multiple polypeptide subunits.
Most enzymes require cofactors (ions or organic molecules) for activity: these cofactors are in the active site
Some biological catalysts are built from RNA, called ribozymes.
The active site of an enzyme is a region where substrates bind and catalyze reactions.
Induced fit of the substrate brings groups closer, making enzymes more efficient.

Lowering the EA Barrier

The active site lowers the activation energy barrier needed for reactions.
The active site changes the substrate into a more favorable state for the reaction and the breaking of bonds
The active site orients the substrates correctly
The active site strains substrate bonds
The active site provides a favorable microenvironment
The active site forms covalent bonds temporarily with the substrate

Enzyme Activity and Regulation

Enzyme activity can be affected by environment, pH, optimal conditions and temperature. A specific temperature is best for catalysis in the enzyme's environment.

Cofactors and Regulation

Cofactors are non-proteins that help enzymes function. These include inorganic molecules such as magnesium.
Coenzymes are organic molecules, often vitamins
Enzymes without cofactors are called apoenzymes, and are inactive.
Enzymes with cofactors are called holoenzymes.

Enzyme Inhibitors

Competitive inhibitors bind to the active site, blocking substrates from binding.
Noncompetitive inhibitors bind to a site other than the active site, causing a conformational change that lowers the effectiveness of the enzyme
- Irreversible inhibitors covalently bind to the enzyme, permanently inhibiting it.
- Allosteric inhibitors bind to the allosteric site and change the conformation of the enzyme, decreasing the ability of the enzyme to function optimally.
Allosteric activators bind to the allosteric site; the shape changes into a more favourable configuration for the reaction to occur

Enzyme Allosterism

Some enzymes have multiple subunits
Enzyme activators and inhibitors bind to allosteric sites, altering the enzyme shape and thus its activity or ability to function.
Activator = shape change to an active form
Inhibitor = shape change to an inactive form
Cooperativity—a substrate binding to one enzyme subunit can enhance the binding of substrates to other subunits.

Enzyme Feedback

In feedback inhibition, the end product of a metabolic pathway regulates its own production by inhibiting an enzyme involved in an earlier step, preventing an overproduction of the end product.
Iso/glutamine conversion

Enzyme Compartmentalization

Structures within cells help order metabolic pathways.
Some enzymes are structural components of membranes or organelles
Enzymes related to respiration are in mitochondria, and digestive enzymes are in lysosomes.

Activation Energy Extra Credit Discussion

Activation energy describes the energy needed to overcome a barrier in chemical reaction, or the initial energy required for a reaction to occur.
Catalyst reduce activation energy requirements = increases reaction rates

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Description

Test your knowledge on essential biochemistry concepts related to energy reactions, Gibbs free energy, and redox processes in cells. This quiz covers spontaneous reactions, ATP hydrolysis, and the role of photosynthesis in energy flow. Dive deep into how cellular processes relate to thermodynamics.