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