Biology I for Non-Majors

1. Biology I for Non-Majors Metabolic Pathways

2. Metabolic Pathways • A metabolic pathway is a series of chemical reactions that takes a starting molecule and modifies it, step-by-step, through a series of metabolic intermediates, eventually yielding a final product • Composed of synthesis (anabolism) and degradation (catabolism) • Chemical reactions of metabolic pathways do not take place on their own: each step is catalyzed by an enzyme

3. Thermodynamics • Thermodynamics refers to the study of energy and energy transfer involving physical matter • The matter relevant to a particular case of energy transfer is called a system, and everything outside of that matter is called the surroundings • In an open system, energy can be exchanged with its surroundings • A closed system cannot exchange energy with its surroundings

4. First Law of Thermodynamics • The total amount of energy in the universe is constant and conserved • There has always been, and always will be, exactly the same amount of energy in the universe • Energy exists in many different forms.  • Plants perform one of the most biologically useful energy transformations on earth • Converting the energy of sunlight to chemical energy stored within organic molecules

5. Second Law of Thermodynamics • All energy transfers and transformations are never completely efficient • In every energy transfer, some amount of energy is lost in a form that is unusable • In most cases, this form is heat energy • Some energy is lost as heat energy during cellular metabolic reactions

6. Types of Energy • Kinetic energy is the energy of motion • Potential energy is energy associated with location and structure of matter • A ball on a raised platform • The bonds that hold the atoms of molecules together exist in a particular structure • There is potential energy stored within the bonds of all the food molecules we eat, which is eventually harnessed for use • Because these bonds can release energy when broken • The type of potential energy that exists within chemical bonds, and is released when those bonds are broken, is called chemical energy

7. Types of Reactions • Exergonic reactions have a negative change in free energy, releasing free energy • If energy is released during a chemical reaction, then the change in free energy, signified as ∆G (delta G) will be a negative number • A negative change in free energy also means that the products of the reaction have less free energy than the reactants, because they release some free energy during the reaction • Endergonic reactions have a positive change in free energy, requiring the addition of free energy • If a chemical reaction absorbs energy rather than releases energy on balance, then the ∆G for that reaction will be a positive value • In this case, the products have more free energy than the reactants

8. Cells and Free Energy • A living cell cannot store significant amounts of free energy • Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell • A cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed • Cells use ATP as the main energy storage molecule • When ATP is broken down, energy is released • When ATP is built, energy is stored

9. Cellular Respiration • Cellular respiration is a process that all living things use to convert glucose into energy • A collection of three unique metabolic pathways • Glycolysis • The citric acid cycle • The electron transport chain with oxidative phosphorylation

10. Glycolysis • Nearly all the energy used by living things comes in the bonds of sugar, especially glucose • Glycolysis is the first step in the breakdown of glucose to extract energy for cell metabolism • Many living organisms carry out glycolysis as part of their metabolism • Glycolysis takes place in the cytoplasm of most prokaryotic and all eukaryotic cells

11. Glycolysis to Generate ATP

12. Pyruvate to CoA • In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, the sites of cellular respiration • If oxygen is available, aerobic respiration will go forward • In mitochondria, pyruvate will be transformed into a two-carbon acetyl group that will be picked up by a carrier compound called coenzyme A (CoA)

13. The Citric Acid Cycle • The citric acid cycle in eukaryotic cells takes place in the matrix of the mitochondria • Unlike glycolysis, the citric acid cycle is a closed loop: the eight steps of the cycle are a series of chemical reactions that produces: • 2 carbon dioxide molecules • 1 ATP molecule (or an equivalent) • Reduced forms (NADH and FADH2) of NAD+ and FAD+ • It takes two turns of the cycle to process the equivalent of one glucose molecule

14. Oxidative Phosphorylation • Most of the ATP generated during the aerobic catabolism of glucose derives from a process that begins with passing electrons through a series of chemical reactions to a final electron acceptor, oxygen • These reactions take place in specialized protein complexes located in the inner membrane of the mitochondria of eukaryotic organisms and on the inner part of the cell membrane of prokaryotic organisms • The energy of the electrons is harvested and used to generate a electrochemical gradient across the inner mitochondrial membrane • The potential energy of this gradient is used to generate ATP • The entirety of this process is called oxidative phosphorylation

16. What about Macromolecules other than Carbohydrates? • The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism

17. Fermentation: Energy Production in Low Oxygen Conditions • Lactic Acid Fermentation: used by animals and certain bacteria • Alcohol Fermentation: produces alcohol as a by-product

18. Photosynthesis • Through photosynthesis, certain organisms convert solar energy (sunlight) into chemical energy, which is then used to build carbohydrate molecules • This chemical energy is then released when the food is broken down and harvested in cellular respiration • Photosynthesis also results in the release of oxygen into the atmosphere

19. Light Energy • In the case of photosynthesis, light energy is transformed into chemical energy, which autotrophs use to build carbohydrate molecules • Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun • Light energy enters the process of photosynthesis when pigments absorb the light • Violet and blue have shorter wavelengths and higher energy • Red has longer wavelengths and lower energy

20. Photosynthesis Begins with Light-Dependent Reactions • The overall purpose of the light-dependent reactions is to convert light energy into chemical energy • This chemical energy is then used to fuel the assembly of sugar molecules • In the first part of photosynthesis, the light-dependent reaction, pigment molecules absorb energy from sunlight • A photon strikes photosystem II to initiate photosynthesis • Energy travels through the electron transport chain, which pumps hydrogen ions into the thylakoid space • This forms an electrochemical gradient • The ions flow through ATP synthase from the thylakoid space into the stroma in a process called chemiosmosis to form molecules of ATP • Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule

21. Light-Dependent Reactions

22. The Calvin Cycle • Using the energy carriers formed in the first stage of photosynthesis, the Calvin cycle reactions fix CO2 from the environment to build carbohydrate molecules • RuBisCO catalyzes the fixation reaction by combining CO2 with RuBP • Three basic stages: • Fixation • Reduction • Regeneration • It takes six turns of the Calvin cycle to fix six carbon atoms from CO2 • These six turns require energy input from 12 ATP molecules and 12 NADPH molecules in the reduction step and 6 ATP molecules in the regeneration step

23. The Calvin Cycle

24. Quick Review • What are the two basic types of metabolic pathways? Which produces energy and which consumes it? • Define an open versus a closed system. • Relate the First and Second Laws of Thermodynamics to biological systems. • What are the two main types of energy? • Define the types of reactions in terms of free energy • Discuss the three major pathways of cellular respiration and list the major products of each. • What are the two main types of fermentation? • How does the wavelength of light relate to its energy? • Describe the basic steps of the light-dependent reactions of photosynthesis. • What occurs during the Calvin cycle?