BIO 112 Metabolism (Chapter 8)

Define metabolism and identify its major components

totality of an organism’s chemical reactions

most reactions arranged as intersecting pathways; each step of pathway is controlled by an enzyme that converts a specific molecule to a product

consist of two pathways: catabolic and anabolic

Ex: Bioluminescence in mushrooms, which have thousands of chemical reactions occurring within their cells

Catabolic (Breakdown) Pathway

break down complex molecules into simpler ones

release energy

“downhill” (high to low)

Ex: Hydrolysis reactions: Proteins to AAs, Polysaccharides to monosaccharides

Anabolic (Biosynthetic) Pathways

build complex molecules from simpler ones

consume energy

“uphill” (low to high)

Ex: Dehydration reactions, AAs to Proteins, Monosaccharides to Polysaccharides

What can energy released from catabolic pathways be used for?

can be stored and used to drive anabolic pathways (endogonic) in cells

Define Bioenergetics and its relevance to metabolic processes

the study of how organisms transform energy (important in metabolism)

What is Energy?

the capacity to cause change

What is Kinetic Energy?

energy associated with the relative motion of objects. Moving matter can perform work by imparting motion to other objects

Ex: Heat - random motion of atoms or molecules in a body of matter

What is Potential Energy?

energy that is the capacity of the matter to cause change due to its location or arrangement

Ex: Chemical energy is the potential energy available for release in chemical reactions

Thermodynamics

study of energy transformation

1st Law: Energy can be transferred or transformed, but it cannot be created or destroyed

Ex: Chemical reactions in a brown bear will convert the chemical (potential) energy in food to the kinetic energy of the brown bear’s environment.

2nd Law: Every energy transfer or transformation increases the disorder (entropy) of the universe

Ex: As a brown bear runs, disorder is increased around the brown bear by the release of heat and small molecules that are products of cellular respiration

For a process to occur in an energetically favorable manner (spontaneously), it must increase the entropy of the universe

Open Systems vs IsolatedSystems— Thermodynamics

In open systems, energy and matter can be exchanged between the system and the surroundings

In Isolated system, systems cannot do work when equilibrium is reached

Cells exist in open system where metabolic reactions never reach equilibrium as reactants and products are constantly moving in and out of cells

What can cellular respiration be described as?

A catabolic pathway where glucose is broken down in a series of reactions that power work of cell, releases energy.

Multistep Open System: products of reactions do not build up, they become reactants in the next step. Equilibrium is not reached and cells keep living

According to the second law of thermodynamics, what happens to the entropy of the universe during a spontaneous process?

It increases

What is true of exergonic reactions?

They release free energy

Define free energy change (ΔG), calculate it, and interpret positive versus negative ΔG values.

Free Energy Change (ΔG): A living system’s free energy is the energy that can do work under cellular conditions

ΔG=ΔH - TΔS

• ΔH = Change in Enthalpy (total energy)

• T = Absolute Temp in Kelvin (K = C+273)

• ΔS = Change in Entropy

Spontaneous processes have a -ΔG (<0)

High Free Energy (G) vs Less Free Energy (G)

ΔG= G_final - G_initial (measures systems instability)

High Free Energy (G) —> Less Stable —> Great Work Capacity

Less Free Energy (G) —> More Stable —> Less Work Capacity

Once at equilibrium, a system is at a minimum of free energy and will not change spontaneously

Exergonic Reactions (-ΔG)

Spontaneous

Reactants have more free energy than products

Amount of energy released (ΔG<0) represents maximum amount of work reaction can do

Ex: Cellular respiration (C₆H₁₂0₆ + 6O₂ —> 6CO₂ + 6H₂O) has -686 kcal/mol of free energy (releases a lot of energy)

Endergonic Reactions (+ΔG)

Not Spontaneous

Must absorb free energy from surroundings:

6CO₂ + 6H₂O —> C₆H₁₂0₆ + 6O₂

ΔG = 686 kcal/mol

Key Point: Energy released by exergonic reaction is equal to energy required by the reverse endergonic reaction

Why it is essential that metabolic reactions do not reach equilibrium?

. At equilibrium, ΔG = 0 → No free energy is available to do work

Cells rely on exergonic reactions (-ΔG) to power reactions, however at equilibrium:

• ΔG = 0

• No net reaction occurs

• No energy released

A cell with no usable free energy is a cell that cannot function.

What does ATP consist of? What does it do?

Adenine Triphosphate: Consists of 3 phosphate groups attached to a ribose sugar, which is attached to a base of adenine

ATP powers cellular work by coupling exergonic reactions endergonic reactions, used as immediate source of energy for:

• Mechanical Work: Ex: contraction of muscle

• Transport Work: Ex: active transport of molecules against their concentration gradient

• Chemical Work: Ex: pushing endergonic reactions such as the synthesis of proteins from AAs

Describe how ATP couples exergonic and endergonic reactions to power cellular work

Energy produce by hydrolysis of ATP would be in form of heat (insufficient energy for cells)

Instead, cells use energy produced by hydrolysis of ATP to do cellular work:

Free energy is released from the hydrolysis of ATP is used to transfer a phosphate group to another molecule, producing a phosphorylated molecule that is more reactive (less stable)

Mechanical Work— Cellular work powered by ATP

Indirect Effect: ATP binds noncovalently to motor protein

Hydrolysis of ATP changes shape of motor protein and allows it to interact with cytoskeleton

Ex: Dynein/microtubule

Transport Work— Cellular work powered by ATP

Direct Effect: Hydrolysis of ATP phosphorylates membrane protein

Changes its shape and often its ability to bind another molecule (binding affinity)

Ex: Na⁺/K⁺ pump

Chemical Work— Cellular work powered by ATP

Synthesis of amino acid Glutamine:

Glutamic Acid + Ammonia —> Glutamine (ΔG = 3.4 kcal/mol) —> Endergonic reaction - not spontaneous

Reaction occurs in 2 steps: Glutamic Acid + ATP —> Phosphorylated (less stable intermediate) of Glutamic Acid + ADP —> Ammonia is added to produce Glutamine + ADP + P_i

Explain the ATP cycle and how ATP is regenerated

ATP is a renewable resource and can be synthesized from ADP and P_i but requires energy (ΔG = +7.3 kcal/mol)

Energy comes from energy yielding processes (catabolic processes)

ATP hydrolysis to ADP and P_i yields energy (ΔG = -7.3 kcal/mol)

Energy is used for cellular work (anabolic processes)

Key Points:

• Chemical potential energy stored in ATP drives most cellular work

• ATP cycle moves at astonishing pace

• Ex: A working muscle cell recycles its entire pool of ATP in less than one minute

How do enzymes speed up metabolic reactions?

Enzymes speed up metabolic reactions by lowering energy barriers, rate of chemical reactions important

Some spontaneous reactions do not require energy but occur at very slow rates

Ex: Hydrolysis of Sucrose (ΔG= -7 kcal/mol)

• Solution of sucrose takes years to break down

• If enzyme, Sucrase, added then sucrose will be hydrolyzed in seconds

Key Point: An enzyme is a macromolecule that acts as a catalyst which speeds up reactions without being consumed by the reaction

Activation Energy Barrier

Reaction: AB + CD —> AC + BD

Every reaction must overcome activation energy (EA); the minimum amount of energy required to push reactant molecules into a highly unstable, contorted state called the transition state.

Reactants must absorb energy to reach transition state, uphill process (highly unstable)

Once transition state reached, bonds can be broken and new bonds can form, releasing energy to surroundings

-ΔG indicates reaction is spontaneous

However, E_A provided the barrier that determines the rate of the reaction

Heat can speed up reactions

Enzymes lower E_A barrier

Most macromolecules in cells are high in free energy and have potential to decompose spontaneously

However, they persist in cells because few molecules can make it over the hump of activation energy

Key Points: Enzymes catalyze reactions by lowering the E_A

• However, Enzymes do not change the ΔG OR turn an endergonic reaction into an exergonic reaction

Why would it be inappropriate to speed up reactions by applying heat?

Heat will denature proteins and kill cells

Heat would also speed up all reactions, not just needed ones

Substrate Specificity of Enzymes

Substrates: reactants that enzymes act on

Enzyme + Substrate ⇆ Enzyme - Substrate Complex ⇆ Enzyme + Product

Example:

Sucrase + Sucrose +H₂O ⇆ Sucrase - Sucrose-H₂O Complex ⇆ Sucrase + Glucose + Fructose

A reaction catalyzed by an enzyme is very specific

Enzymes can differentiate closely related molecules and isomers due to their specific shape that dictate their unique functions

Example: Sucrase is specific for sucrose but not maltose

Active Site

Where an enzyme binds to its substrate

Contains only a few AAs, rest of protein molecule provides framework that determines configuration of active site

In active site, chemical groups on substrate interact with R-groups of amino acids

This interaction causes the enzyme to change shape slightly, so the active site fits more snuggly around the substrate (induced fit)

Induced fit increases the catalytic ability of the enzyme

Catalytic Cycle of an Enzyme

1. Active site is available for two new substrates in Enzyme

2. Substrate bind to enzyme at active site - “Induce Fit”

3. New shape where Substrates are held in active site by weak interactions (ionic bonds, hydrogen bonds, hydrophobic interactions), forms Enzyme-substrate complex

4. Various Mechanisms function within active site to lower E_A and speed up reactions

5. Substrates are converted to products

Key Points: Single enzyme can act on thousand substrate molecules/sec

Identify and describe mechanisms used at the active site to accelerate reactions (lower E_A)

1. Active site provides a template for substrate orientation

2. Active site stress the substrates towards their transition state by stretching and bending critical chemical bonds that must be broken during the reaction

3. Active site provides a favorable microenvironment for the reaction (e.g. active site may be more acidic than the neutral cell)

4. Active site can participate directly in the catalytic reaction by forming brief covalent bonds with the substrate

Most metabolic reactions are reversible

Enzymes can catalyze both forward and reverse reactions - depends on which direction has a -ΔG

Direction of reaction depends on relative concentration of reactants and products

Net effect is always direction of equilibrium

Rate of a reaction will increase with increasing substrate concentration

Sucrose + H₂O ⇆ Glucose +Fructose (Rate of reaction increases with Sucrase)

Saturated:

• When all enzyme molecules are saturated with substrate molecules and working at full speed

• To increase rate of reaction further, more enzyme needed

Enzyme activity: how efficient an enzyme functions

Depends on optimal conditions: Temperature, pH, Specific chemicals

Optimal conditions are significant because they favor the most catalytically active shape of enzyme

Why do reaction rates drop quickly at temperatures greater than the optimal temperature?

Higher temperatures will disrupt the hydrogen, ionic, and hydrophobic interactions that stabilize the active site (denatures proteins)

Most enzymes have an optimal pH between 6-8

Explain the role of cofactors and differentiate between the two major types

Cofactors: a non-protein molecule that aids catalytic activity of enzymes

1. Inorganic ions such as magnesium, zinc, iron, and copper

Example: Enzyme Glucose 6 - phosphatase requires Mg²⁺ as a cofactor

2. Organic Molecules (Coenzyme): Most vitamins are important nutritional factors because they act as coenzymes and aid in chemical reactions in body

Example: NAD⁺ (an electron carrier) is a coenzyme derived from vitamin niacin

Irreversible and Reversible Enzyme Inhibitors (Attach to enzymes)

Irreversible Inhibitions: inhibitors bind covalently to the enzyme and block activity

Reversible Inhibition: when inhibitors bind to an enzyme via weak interaction and block activity

Types of Reversible Inhibition:

1. Competitive Inhibitors: Blocks substrates from binding to active site, can overcome inhibition if: [substrate] > [inhibitor]

2. Noncompetitive Inhibitors: Impede (slow down) enzyme activity by binding to another part of the enzyme, changes shape so active site is less catalytic

Feedback Inhibition: Example Isoleucine synthesis

The end product isoleucine, binds to the allosteric site on Enzyme 1

Binding changes Enzyme 1 shape and prevents it from binding threonine

Pathway is turned off until isoleucine levels are low again

Isoleucine leaves allosteric site of Enzyme 1

Enzyme 1 active again, more isoleucine is synthesized

Key Point: Inhibition prevents the cell from wasting chemical resources by making more isoleucine than is necessary