METABOLISM, PHOTOSYNTHESIS,

AND CELLULAR RESPIRATION

Chapters 8, 9, and 10

Chapter 8 8.1: An organism’s metabolism

transforms the matter and energy, subject to the laws of thermodynamicsMetabolism – totality of an organism’s

chemical reactions○ Emergent property of life that comes from

molecular interactions

Organization of the Chemistry of Life into Metabolic Pathways Metabolic pathway – begins with a specific

molecule, molecule is altered in a series of steps, results in a specific product

One enzyme per step

Startingmolecule

A

Catabolic Pathways Degradative processes Release energy Complex molecules into simpler

molecules Think: CATs (CATabolic pathways) tear

things apart

Anabolic Pathways Consume energy Simpler molecules combined into a

more complex one Sometimes called biosynthetic pathways Example: protein synthesis from amino

acids Bioenergetics: study of how energy

flows through living organisms

Forms of Energy Energy – the capacity to cause change

The ability to arrange a collection of matterCan be used to do work

Kinetic energy – energy associated with the relative motion of objects

Heat (thermal energy) – kinetic energy associated with the random movement of atoms or molecules

Light is also energy

Forms of Energy Potential energy – energy that is not

kinetic; energy that matter possesses because of its location or structure

Chemical energy – term used by biologists to refer to the potential energy available for release in a chemical reactionE.g. potential energy available through a

catabolic reaction

Laws of Energy Transformation Thermodynamics – the study of energy

transformations that occur in a collection of matter

Systems – matter under study Surroundings – everywhere outside of the

system Isolated system – unable to exchange energy or

matter with surroundings Open system – exchanges energy and matter

with surroundingsorganisms

First Law of Thermodynamics The energy of the universe is constant Energy can be transferred and

transformed, but it cannot be created or destroyed

Also known as the principle of conservation of energy

Second Law of Thermodynamics Every energy transfer or transformation

increases the entropy of the universe Entropy – measure of disorder or

randomness Spontaneous – process that can occur

without input of energyMust increase entropy of the universeFor a process to occur spontaneously, it

must increase the entropy of the universe

Biological Order and Disorder Living systems increase the entropy of

their surroundings Ordered structures created from less

organized materials Can go the other way as well Entropy of a particular system can

decrease, as long as the universe becomes more random at the same time

8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously Free-Energy Change, Delta G

Gibbs free energy, or free energy – portion of s system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell

Delta G = delta H – TdeltaS○ DeltaH – change in the systems enthalpy

(equivalent to total energy)○ DeltaS - entropy

Free Energy, Stability, and Equilibrium DeltaG = final G – initial G

Negative G is spontaneous Tendency of a system to change to a more

stable state Equilibrium

ReversibleDoes not mean that forward and backward reactions

stopSame rate or reaction, relative concentrations stay

constant Refer to Figure 8.5

Free Energy and Metabolism Exergonic and Endergonic Reactions in

MetabolismExergonic

○ “Energy outward”○ Proceeds with a net release of free energy○ DeltaG is negative

Endergonic○ “energy inward”○ Absorbs free energy from its surrounding○ DeltaG is positive

Refer to Figure 8.6

Equilibrium and Metabolism Reactions in an isolated system would

reach equilibrium and not be able to do any workA cell that has reached metabolic

equilibrium is deadMetabolism as a whole is never at

equilibrium

8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions Three main kinds of work

Chemical work – pushing of endergonic reactionsTransport work – pumping of substances across

membranes against the direction of spontaneous movement

Mechanical work – actions such as beating of cilia, contracting of muscles, etc.

Energy coupling – the use of an exergonic reaction to power an endergonic oneATP usually responsible

The Structure and Hydrolysis of ATP ATP (adenosine triphosphate)

Contains ribose, adenine, and three phosphate groups

One of the nucleoside triphosphates used to make ATP

Bonds broken by hydrolysisATP + H2O ADP + HOPO3

2-

High energy phosphate bonds

How ATP Performs Work Hydrolysis of ATP releases heat

ShiveringHeat usually harnessed to perform cellular work

Phosphorylation – the transfer of a phosphate group from ATP to some other molecule; the other molecule is now phosphorylated

Transport and mechanical work are nearly always powered by ATP hydrolysisLeads to a change in shape in the protein

The Regeneration of ATP

ADP P+

ATP + H2O

Energy fromcatabolism (exergonic,energy-releasingprocesses)

Energy fromcatabolism (exergonic,energy-releasingprocesses)

8.4: Enzymes speed up metabolic reactions by lowering energy barriers Figure 8.13 Enzyme – macromolecule that acts as a

catalyst Catalyst – a chemical agent that speeds

up a reaction without being consumed by the reaction

The Activation Barrier Activation energy (free energy of

activation) – The initial investment of energy for starting a reactionenergy required to contort reaction

molecules so that they can breakOften supplied in the form of heat from

surroundings Refer to Figure 8.14

How Enzymes Lower the EA Barrier

Figure 8.15 Heat can be used to speed up a

reaction, but most organisms would die. Lowering the EA barrier enables the

reactants to absorb enough energy to reach the transition state without reaching high temperatures.

Substrate Specificity of Enzymes Substrate – the reactant an enzyme

acts on Forms an enzyme-substrate complex

when the enzyme and substrate have joined together

Enzyme + Substrate Enzyme-substrate complex Enzyme+Products

Most enzyme names end in -ase

Substrate Specificity of Enzymes Active site – region where the enzyme

binds to the substrate; where catalysis occurs

Induced fit model

Catalysis in the Enzyme’s Active Site Figure 8.17 Occurs very quickly Reusable

Catalysis in the Enzyme’s Active Site Variety of mechanisms to lower EA

1. Provides template for substrates to come together

2. Enzyme can stretch substrates to transition-state form

3. Active site provides optimal microenvironment

4. Direct participation of active site in reaction Rate related to initial substrate

concentration

Effects of Local Conditions on Enzyme Activity Temperature pH Chemicals

Effects of Temperature and pH Up to a point, ROR increases with

temperature Optimal pH value usually between 6 and

8 Figure 8.18

Cofactors Cofactors – nonprotein helpers for

catalytic activityMay be tightly bound to enzyme

permanently, or loosely bound with substrateInorganic

Coenzyme – cofactor that is an organic moleculevitamins

Enzyme Inhibitors Certain chemicals inhibit the action of

specific enzymes Two kinds:

Competitive inhibition○ Block substrates from entering active sites

Noncompetitive inhibition○ Bind to another part of the enzyme so that it

changes its shape, preventing the substrate from binding

Figure 8.19

8.5: Regulation of enzyme activity helps control metabolism REGULATION IS IMPORTANT

Allosteric Regulation of Enzymes Allosteric regulation – term used to

describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to another siteLike reversible noncompetitive inhibition

Figure 8.20

Allosteric Activation and Inhibition Enzymes made up of subunits Subunits made up of polypeptide chains The binding of an activator stabilizes the

active form of the enzyme The binding of an inhibitor stabilizes the

inactive form of the enzyme

Identification of Allosteric Regulators Not that many metabolic enzymes are

allosterically regulated Pharmaceutical companies interested in

allosteric regulatorsExhibit higher specificity than do inhibitors

binding to the active site Figure 8.21

Feedback Inhibition Feedback inhibition – in which a

metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme early in the pathway

Figure 8.22

Specific Localization of Enzymes Within a Cell “The cell is not a bag of chemicals with

thousands of different kinds of enzymes and substrates in a random mix.”

Compartmentalized

Chapter 9Cellular Respiration: Harvesting Chemical Energy

9.1: Catabolic pathways yield energy by oxidizing organic fuels The breakdown of organic molecules is

exergonic Fermentation – a partial degradation of

sugars that occurs without O2 Aerobic respiration – consumes

organic molecules and O2 and yields ATP

Anaerobic respiration is similar to aerobic respiration but consumes compounds other than O2

Cellular Respiration Contains both aerobic and anaerobic

processes, but usually used to refer to aerobic respiration

C6H12O6 + 6 O2 6 CO2 + 6 H2O + Energy (ATP + heat)

The breakdown of glucose is exergonic

Redox Reactions Oxidation and Reduction

Releases energy stored in organic molecules

LEO the lion says GER Oxidizing agent gets reduced, and

reducing agent gets oxidized Changing of electron sharing as

opposed to transferring

Stepwise Energy Harvest via NAD+ and the Electron Transport Chain In cellular respiration, glucose and other

organic molecules are broken down in a series of steps

Electrons from organic compounds are usually first transferred to NAD+, a coenzyme

As an electron acceptor, NAD+ functions as an oxidizing agent during cellular respiration

Each NADH (the reduced form of NAD+) represents stored energy that is tapped to synthesize ATP

Electrons passed to ETC by NADH Series of steps instead of all at once

Stages of Cellular Respiration

Glycolysis – breaks down glucose into two molecules of pyruvate

The citric acid cycle – completes the breakdown of glucose

Oxidative phosphorylation -most of the ATP synthesis

9.2: Glycolysis harvests chemical energy by oxidizing glucose to pyruvate Glycolysis means “sugar splitting” Glucose (six-carbon sugar) is split into

two three-carbon sugars Smaller sugars oxidized

Remaining molecules turned into pyruvate

Glycolysis Occurs in the cytoplasm Divided into:

Energy investment ○ Cell spends ATP

Energy payoff ○ ATP is produced with substrate-level

phosphorylation and NAD+ is reduced to NADH

Figure 9.9

9.3: The citric acid cycle completes the energy yielding oxidation of organic molecules Pyruvate enters mitochondrion Must be converted to acetyl coenzyme A

(acetyl CoA) before the citric acid cycle can begin

Figure 9.10 Citric acid cycle also called the Krebs

cycle or the tricarboxylic acid cycle

The Citric Acid Cycle Takes place within the mitochondrial

matrix Figure 9.11 Figure 9.12