1. Metabolism, Photosynthesis, and Cellular Respiration
Chapters 8, 9, and 10
Metabolism, Photosynthesis, and Cellular Respiration

2. Chapter 8
8.1: An organism’s metabolism transforms the matter and energy, subject to the laws of thermodynamics
Metabolism – totality of an organism’s chemical reactions
Emergent property of life that comes from molecular interactions

3. 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 A
Starting
molecule

4. Catabolic Pathways Degradative processes Release energy
Complex molecules into simpler molecules
Think: CATs (CATabolic pathways) tear things apart

5. 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

6. Forms of Energy Energy – the capacity to cause change
The ability to arrange a collection of matter
Can 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

7. 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 reaction
E.g. potential energy available through a catabolic reaction

8. 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 surroundings
organisms

9. 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

10. 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 energy
Must increase entropy of the universe
For a process to occur spontaneously, it must increase the entropy of the universe

11. 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

12. Free-Energy Change, Delta G
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

13. 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
Reversible
Does not mean that forward and backward reactions stop
Same rate or reaction, relative concentrations stay constant
Refer to Figure 8.5

14. Free Energy and Metabolism
Exergonic and Endergonic Reactions in Metabolism
Exergonic
“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

15. Equilibrium and Metabolism
Reactions in an isolated system would reach equilibrium and not be able to do any work
A cell that has reached metabolic equilibrium is dead
Metabolism as a whole is never at equilibrium

16. Three main kinds of work
8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions
Three main kinds of work
Chemical work – pushing of endergonic reactions
Transport 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 one
ATP usually responsible

17. 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 hydrolysis
ATP + H2O  ADP + HOPO32-
High energy phosphate bonds

18. How ATP Performs Work Hydrolysis of ATP releases heat
Shivering
Heat 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 hydrolysis
Leads to a change in shape in the protein

19. The Regeneration of ATP+
H2O
Energy from
catabolism (exergonic,
energy-releasing
processes)
Energy from
catabolism (exergonic,
energy-releasing
processes)
ADP + P

20. 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

21. The Activation Barrier
Activation energy (free energy of activation) – The initial investment of energy for starting a reaction
energy required to contort reaction molecules so that they can break
Often supplied in the form of heat from surroundings
Refer to Figure 8.14

22. 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.

23. 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

24. Substrate Specificity of Enzymes
Active site – region where the enzyme binds to the substrate; where catalysis occurs
Induced fit model

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

26. Catalysis in the Enzyme’s Active Site
Variety of mechanisms to lower EA
Provides template for substrates to come together
Enzyme can stretch substrates to transition-state form
Active site provides optimal microenvironment
Direct participation of active site in reaction
Rate related to initial substrate concentration

27. Effects of Local Conditions on Enzyme Activity
Temperature pH
Chemicals

28. Effects of Temperature and pH
Up to a point, ROR increases with temperature
Optimal pH value usually between 6 and 8
Figure 8.18

29. Cofactors Cofactors – nonprotein helpers for catalytic activity
May be tightly bound to enzyme permanently, or loosely bound with substrate
Inorganic
Coenzyme – cofactor that is an organic molecule
vitamins

30. 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

31. 8.5: Regulation of enzyme activity helps control metabolism
REGULATION IS IMPORTANT

32. 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 site
Like reversible noncompetitive inhibition
Figure 8.20

33. 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

34. Identification of Allosteric Regulators
Not that many metabolic enzymes are allosterically regulated
Pharmaceutical companies interested in allosteric regulators
Exhibit higher specificity than do inhibitors binding to the active site
Figure 8.21

35. 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

36. 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

37. Cellular Respiration: Harvesting Chemical Energy
Chapter 9

38. 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

39. 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

40. Redox Reactions Oxidation and Reduction LEO the lion says GER
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

42. 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

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

44. 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

45. 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

46. Glycolysis Occurs in the cytoplasm Divided into: Figure 9.9
Energy investment
Cell spends ATP
Energy payoff
ATP is produced with substrate-level phosphorylation and NAD+ is reduced to NADH
Figure 9.9

47. 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

48. The Citric Acid Cycle Takes place within the mitochondrial matrix
Figure 9.11
Figure 9.12