IB Biology 8.

Metabolism

The totality of an organism's chemical reactions.

Metabolism is NEVER at equilibrium.

Enzymes

Catalysts for chemical reactions in living things.

Proteins that speed up chemical reactions

Protein that speeds up chemical reactions by lowering activation energy

Anabolic Pathway

A metabolic pathway that consumes energy to synthesize a complex molecule from simpler compounds.

Catabolic Pathway

A metabolic pathway that releases energy by breaking down complex molecules to simpler compounds. Ex. Breaks down cellular respiration pathways

Thermodynamics

The study of energy transformations that occur in a collection of matter.

Entropy

A measure of disorder or randomness.

Energy

The capacity to cause change or do work

Kinetic Energy

Energy related tot he motion of an object

Potential Energy

Not kinetic energy

Thermal Energy

Kinetic energy associated with random movement of molecules and atoms

First Law of Thermodynamics

Energy can be transferred and transformed, but it cannot be created or destroyed.

Second Law of Thermodynamics

Every energy transfer or transformation increases the entropy of the universe.

Spontaneous Process

A process that occurs without an overall input of energy; a process that is energetically favorable. Spontaneous processes increase entropy.

Spontaneous

A process is energetically favored

Free Energy

Measures the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell.

Equation for change and free energy

ΔG = ΔH - TΔS

G

Free Energy

H

Enthalpy

T

Temperature

S

Entropy

Enthalpy

The heat content of a system at constant pressure

Sponteanity of ΔG

ΔG > 0 = spontaneous

ΔG < 0 = not spontaneous

ΔG for Cellular Respiration

-686 kcal/mol

Equilibrium

When the rate of the products and the reactants are equal.

A process is spontaneous and can perform work only when it is _____________ ___________ _________________.

moving towards equilibrium

ATP

Adenosine Triphosphate

Composed of a ribose, adenine, and phosphate groups

Enhances cellular respiration

Glucose→ broken down into ATP → negative feedback → inhibits glucose

ADP

Adenosine Diphosphate

Energy storing molecule

Inhibits cellular respiration

Glucose → ATP (positive feedback)→ ADP → activates Glucose

Positive Feedback

A type of regulation that responds to a change in conditions by initiating responses that will amplify the change. Takes organism away from a steady state.

Negative Feedback

A primary mechanism of homeostasis, whereby a change in a physiological variable that is being monitored triggers a response that counteracts the initial fluctuation.

Ribozyme

RNA that can act as self-replicating enzymes.

ATP powers cellular work by...

coupling exergonic reactions to endergonic reactions.

Energy Coupling

In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction.

Exergonic Reaction

Reaction that proceeds with a net release of free energy.

Endergonic Reaction

Reactions that have more free energy in the products are termed.

3 types of cell work managed by energy coupling:

Chemical

Transport

Mechanical

Hydrolysis

Breaking down the phosphate groups in ATP's tail by the chemical addition of water. Makes ATP into ADP.

Catalyst

A substance that initiates or accelerates a chemical reaction without itself being affected.

Activation Energy

Energy required to initiate both Exothermic and Endothermic reactions. Contorts the reaction molecules so the bonds can change.

Lock and Key Hypothesis

The idea that enzymes are specifically shaped to fit only one type of substrate.

Induced Fit Hypothesis

Theory of enzyme catalysis which states that the partial binding of a substrate to an enzyme alters the structure of the enzyme so that its active site becomes complementary to the structure of the substrate, enabling binding.

Characteristics of Enzymes

Most are globular proteins that act as biological catalysts, Enzymes are chemically specific, Frequently named for the type of reaction they catalyze, Lower activation energy, end in -ase.

4 ways active sites work:

Orienting substrates correctly

Straining substrate bonds/tension/clutching (keying contortion)

Providing a favorable micro-environment

Covalently bonding to the substrate/participation in the reaction

What affects the activity of an enzyme?

Heat (denaturation)

pH

Cofactors

Non-protein helpers in catalyst activity.

Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.

Often minerals like iron or zinc.

Bound tightly to the enzyme; bind loosely and reversibly along with the substrate; inorganic molecule

Coenzymes

An organic molecule that is a necessary participant in some enzymatic reactions; helps catalysis by donating or accepting electrons or functional groups; e.g., a vitamin, ATP, NAD+. Organic substances needed to work with enzymes.

Irreversible Inhibition

Alters the enzyme in such a way that the active site is unavailable for a prolonged duration or permanently; new enzyme molecules must be synthesized for the reaction to occur again. Often poisons such as serin, penicillin, pesticides, etc.

Competitive Inhibition

An inhibitor blocks the active site from the substrate but is reversible.

Noncompetitive inhibition.

A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate. Reversible process (except for toxins).

Allosteric Activity/Regulation

When a molecule binds and a conformational change occurs and the primary binding site will no longer bind to its usual substrate. Changes the shape of a protein.

A change in shape of an enzyme that effects the rate of an enzyme pathway.

The process of using a noncompetitive inhibitor.

ADP __________ cellular respiration.

Enhances (speeds up)

ATP ___________ cellular respiration.

Inhibits (slows down)

Coopertivity

Sub-chemicals allosterically activates makes an enzyme more receptive to accepting a substrate. In an enzyme has 2 or more subunits, a substrate molecule causing induced fit in on subunit can trigger the same favorable conformational change in all the other substrates of an enzyme

Feedback Inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

Krebs Cycle

1. Acetyl CoA combines with Oxaloacetate, result is 6-carbon citrate.

2. Citrate is oxidized to form 5-carbon compound. Carbon is released from cell as CO2. NAD+ is reduced to form NADH.

3. The 5-carbon compound is oxidized and decarboxylated to form 4-carbon compound. Removed carbon combines with O2 and is released as co2. NAD+ is reduced to form NADH.

4. The 4-carbon compound results in several products. One is NADH. FAD is reduced to form FADH2. ADP is reduced to form ATP. The 4-carbon compound is changed to reform Oxaloacetate.

Normal Enzyme Reaction

A substrate binds to an enzyme (via the active site) to form an enzyme-substrate complex

The shape and properties of the substrate and active site are complementary, resulting in enzyme-substrate specificity

When binding occurs, the active site undergoes a conformational change to optimally interact with the substrate (induced fit)

This conformational change destabilizes chemical bonds within the substrate, lowering the activation energy

As a consequence of enzyme interaction, the substrate is converted into product at an accelerated rate

Competitive inhibition

involves a molecule, other than the substrate, binding to the enzyme's active site

The molecule (inhibitor) is structurally and chemically similar to the substrate (hence able to bind to the active site)

The competitive inhibitor blocks the active site and thus prevents substrate binding

As the inhibitor is in competition with the substrate, its effects can be reduced by increasing substrate concentration

Noncompetitive inhibition

Non-competitive inhibition involves a molecule binding to a site other than the active site (an allosteric site)

The binding of the inhibitor to the allosteric site causes a conformational change to the enzyme's active site

As a result of this change, the active site and substrate no longer share specificity, meaning the substrate cannot bind

As the inhibitor is not in direct competition with the substrate, increasing substrate levels cannot mitigate the inhibitor's effect

Where is CO2 produced in the mitochondrion?

The inner membrane

In the mitochondrial electron transport chain, what is the last electron acceptor

02

Which of the following is true about enzymes

Lower activation energy of reaction

What does NADH + H+ do in cell respiration

Transfers hydrogen to the electron transport chain

What is the link reaction in aerobic respiration

Pyruvate is decarboxylated, acetyl reacts with coa, forming NADH + H+

Glycolosis

1. the glucose ring is phosphorylated. Phosphorylation is the process of adding a phosphate group to a molecule derived from ATP. As a result, at this point in glycolysis, 1 molecule of ATP has been consumed. result of this phosphorylation is a molecule called glucose-6-phosphate (G6P)

2. he conversion of glucose-6-phosphate to fructose-6-phosphate (F6P). This reaction occurs with the help of the enzyme phosphoglucose isomerase (PI). As the name of the enzyme suggests, this reaction involves an isomerization reaction. Involves the rearrangement of the carbon-oxygen bond to transform the six-membered ring into a five-membered ring. To rearrangement takes place when the six-membered ring opens and then closes in such a way that the first carbon becomes now external to the ring.

3. fructose-6-phosphate is converted to fructose- 1,6-bisphosphate (FBP). Similar to the reaction that occurs in step 1 of glycolysis, a second molecule of ATP provides the phosphate group that is added on to the F6P molecule.

4. The final step of the first stage of glycolysis utilizes the enzyme aldolase, which catalyzes the cleavage of FBP to yield two 3-carbon molecules. One of these molecules is called glyceraldehyde-3-phosphate (GAP) and the other is called dihydroxyacetone phosphate (DHAP). all of the DHAP molecules produced are further acted on by the enzyme triphoshpate isomerase (TIM), which reorganizes the DHAP into GAP so it can continue in glycolysis. At this point in the glycolytic pathway, we have two 3-carbon molecules, but have not yet fully converted glucose into pyruvate