BSC 2010 C - Exam 3 Study Guide PDF

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Chapter 8 Metabolism: an emergent property of life that arises from orderly interactions between molecules (totality of an organism’s chemical reactions) Metabolic Pathway: begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product  Each step of the pathway is catalyzed by a specific enzyme:

Catabolic Pathways: a degradative process in which some metabolic pathways release energy by breaking down complex molecules to simpler compounds  A major pathway of catabolism is cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water.

Anabolic Pathways: consume energy to build complicated molecules from simpler ones; they are sometimes called biosynthetic pathways  Ex: the synthesis of amino acids from simpler molecules and the synthesis of a protein from amino acids

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Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways. Energy: The capacity to cause change (does work) Kinetic Energy: Energy of motion  Forms: o Light Energy o Heat Energy (movement of molecules) Potential Energy: Stored in location of matter  Includes chemical energy stored in molecular structure Chemical Energy: a term used by biologists to refer to the potential energy available for release in a chemical reaction. Thermodynamics: the study of the energy transformations that occur in a collection of matter 1. Energy can be transferred and transformed, but it cannot be created or destroyed a. Principle of conservation of energy

2. Every energy transfer or transformation increases the disorder (entropy) of the universe a. Quality of energy decreases Free Energy: 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  Symbolized as variable “G” Non-Spontaneous Reaction: Free energy increases; G is positive Spontaneous Reaction: Free energy decreases; G is negative Exergonic Reaction: a net release of free energy  G decrease  Spontaneous reaction (it is energetically favorable, DOES NOT occur rapidly)

Endergonic Reaction: absorbs free energy from its surroundings  Stores free energy in molecules (G increases; G is positive)  Nonspontaneous (magnitude of G is the quantity of energy required to drive the reaction)  Uphill

Catabolic Pathways Recap:  Spontaneous  Exergonic  Break big molecules into small ones  Release Energy  G is negative  Cell respiration is a catabolic pathway Anabolic Pathways Recap:  Non-Spontaneous  Endergonic  Build big molecules from smaller ones  Require energy  G is positive  Photosynthesis is an anabolic pathway  ATP powers cellular work by coupling exergonic reactions to endergonic reactions Chemical Work: the pushing of endergonic reactions that would not occur spontaneously, such as synthesis of polymers from monomers Transport Work: the pumping of substances across membranes against the direction of spontaneous movement

ATP (adenosine triphosphate): Cell’s energy shuttle  Provides energy for cellular functions

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ATP is a renewable source that can be regenerated by the addition of phosphate to ADP. The free energy required to phosphorylate ADP comes from exergonic breakdown reactions(catabolism) in the cell

 Enzymes speed up metabolic reactions by lowering energy barriers Enzyme: a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction  Catalytic Protein o Some enzymes can be RNA  Catalyzed reactions by lowering barrier  Most enzyme names often end in ”ase” Activation Barrier: Every chemical reaction involves both old bonds breaking and new bonds forming Activation Energy: the initial investment of energy for starting a reaction – the energy required to contort the reactant molecules so the bonds can break 

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Ex: the amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the “downhill” part of the reaction can begin. Often supplied by heat from environment

 An enzyme CANNOT change the G for a reaction; it cannot make and endergonic reaction exergonic Substrate: Reactant enzyme acts on Substrate + Enzyme = Enzyme-Substrate complex  Substrate is held in the active sight by weak interactions, such as hydrogen and ionic bonds Active Site: Region on enzyme where substrate binds  Active sight is “lock” & substrate is “key”

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Induced fit: brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction (snug)

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Enzyme Saturation: Occurs when all active sites occupied with substrate  Need to add more enzyme to increase product production, not more substrate

 Temperature and pH are environmental factors important in the activity of an enzyme

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The higher the temperature the faster enzymatic activity happens, but each enzyme has its own optimal temperature, the temperature at which that enzyme works the best.

Chapter 9 Cellular respiration: The most prevalent and efficient catabolic pathway (exergonic, release energy) for the production of ATP, in which oxygen is consumed as a reactant along with the organic fuel.  Catabolic pathways yield energy by oxidizing organic fuels  Cell respiration is a series of chemical reactions in which the overall goal is to break down large, energy rich macromolecules and release the stored energy in order to make many ATP molecules which can be used to power cell jobs Redox reaction: A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction.  Redox reactions play an important role in cell respiration as electrons are stripped from molecules and transferred to others Oxidation: The loss of electrons from a substance involved in a redox reaction (reducing agents)  Releases energy from chemical bonds Reduction: The addition of electrons to a substance involved in a redox reaction (oxidizing agents)  Stores energy from chemical bonds

Summary Equation for Cell Respiration: (does not happen in one reaction)

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Glucose: Oxidized Oxygen: Reduced

More bonds= More potential energy Stepwise Harvesting of Energy  Inefficient way: releasing all energy from glucose at once  Better way: energy slowly stripped away from glucose in steps  Electron shuttles: move electrons (energy) slowly o Ex. Nicotinamide adenine dinucleotide o NAD+ (oxidized): Ready to accept hydrogens and electrons o NADH (reduced): carrying electrons o Dehydrogenase: Enzyme that reduces NAD+ to NADH 3 Major steps in cellular respiration 1. Glycolysis (splitting of sugar) a. Occurs in cytosol b. Breaks glucose into 2 molecules of pyruvate c. Initial series of endergonic reactions requiring ATP d. Second series of exergonic reactions make a net 2 molecules of ATP for every glucose e. ATP is made by substrate level phosphorylation

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Some electrons from glucose are also transferred to electron shuttle NAD+, reducing it to NADH with the help of dehydrogenase

2. Citric Acid Cycle (Krebs Cycle) a. Occurs in mitochondrial matrix b. Before citric acid cycle begins, pyruvate is first converted into acetyl Co-A in precitric acid step i. A molecule of carbon dioxide is produces ii. More electrons are transferred to NAD+ to make NADH iii. Co-enzyme A helps the formation of acetyl Co-A

c. The citric acid cycle joins acetyl Co-A to a 4-carbon molecule called oxaloacetate to form the 6-carbon molecule citrate d. Series of reactions converts citrate back into oxaloacetate but in the process: i. More carbon dioxide is produces ii. More electrons are shuttled to form NADH and FADH2 (reduced form of a different electron shuttle, FAD) iii. Some ATP is made by substrate level phosphorylation

e. By end of citric acid cycle, all the original energy of glucose has been released either to make ATP in glycolysis or the citric acid cycle or carried in the electrons being shuttled by FADH2 or NADH

3. Electron Transport Chain (ETC) a. Series of carrier molecules embedded in inner membrane of mitochondria b. Electron shuttles NADH and FADH2 drop off their electrons (becoming oxidized NAD+ and FAD) and reducing the carrier molecules c. In a series of redox reactions, carrier molecules pass the electrons down the chain until they are received by the final electron acceptor, oxygen i. Oxygen plus the electrons plus H+ become water ii. The role of this oxygen is the reason aerobic organisms need to breath oxygen d. Each redox reaction in the chain allows some energy to be released which can be used to pump H+ from the mitochondrial matrix to the intermembrane space i. This buildup of H+ stored potential energy that can be used by cell ii. The H+ ions are allowed to flow back down their concentration gradient, through the inner membrane into the matrix but only through the enzyme ATP synthase iii. ATP synthase can then be powered to make ATP from ADP and inorganic phosphate groups by oxidative phosphorylation e. Chemiosmosis is the process of building up of the H+ gradient in order to do a job—the job in this case is making ATP i. Couples potential energy from H+ gradient generated by ETC to make ATP by oxidative phosphorylation f. The vast majority of ATP from cell respiration is made during the electron transport chain stage

ATP Synthase: Protein embedded in the membrane; the only place hydrogen can come back in the cell  Enzyme that makes ATP Substrate level phosphorylation: The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism  Method used during glycolysis & citric acid cycle Oxidative phosphorylation: The production of ATP using energy derived from the redox reactions of an electron transport chain  Method used during electron transport chain stage

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Energy flows in this sequence: o Glucose to NADH to ETC to ATP About 34% energy transfer efficiency 1 glucose= around 32 ATP’S

Chapter 10 Photosynthesis: The conversion of light energy to chemical energy that is stored in glucose or other organic compounds Autotrophs: “self-feeders”-An organism that obtains organic food molecules without eating other organisms or substances derived from other organisms. Autotrophs use energy from the sun or from the oxidation of inorganic substances to make organic molecules from inorganic ones  Producers of the biosphere because they are the ultimate sources of organic compounds for all nonautotrophic organisms.  Specifically, use light energy Heterotrophs: An organism that obtains organic food molecules by eating other organisms and their by-products  Consumers of the biosphere  Decomposers: Feed on organic litter such as dead organisms, feces, and fallen leaves Mesophyll: the ground tissue of a leaf, sandwiched between the upper and lower epidermis and specialized for photosynthesis

Stoma: A microscopic pore surrounded by guard cells in the epidermis of leaves and stems that allows gas exchange between the environment and the interior of the plant  Carbon dioxide enters the leaf, and oxygen exits Stroma: the fluid of the chloroplast surrounding the thylakoid membrane Thylakoid: a flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy Chlorophyll: a green pigment, that gives the leaves their color, located in the thylakoid membranes of the chloroplasts.  It is the light energy absorbed by chlorophyll that drives the synthesis of organic molecules in the chloroplast.  Chlorophyll A: a type of blue-green photosynthetic pigment that participates directly in the light reactions  Chlorophyll B: a type of yellow-green accessory photosynthetic pigment that transfers energy to chlorophyll a. Photosynthesis Summary Equation

 Water: Oxidized  Carbon Dioxide: Reduced (Follow H and their electrons)  Anabolic Pathway  Requires Energy Light Energy: a form of kinetic energy and a subtype of electromagnetic energy  Only the visible light range (380nm-750nm wavelengths) is used by photosynthesis o Within the visible light, only purple/blue and orange/ red light waves are used by photosynthesis o The green light waves are NOT used by photosynthesis Photosynthetic Pigments:  Absorb light waves used in photosynthesis o Purple, blue, orange, red  Reflect light waves NOT used in photosynthesis o Green

Wavelength: the distance between crests of waves, such as those of the electromagnetic spectrum

Visible Light: the portion of the electromagnetic spectrum detected as various colors by the human eye, ranging in wavelength from about 38nm-750nm Photosystem: Light-capturing unit located in the thylakoid membrane of the chloroplast, consisting of a reaction center surrounded by numerous light-harvesting complexes  Photosystem I: One of two light-capturing units in a chloroplast’s thylakoid membrane; it has two molecules of P700 chlorophyll A at its reaction center  Photosystem II: One of two light-capturing units in a chloroplast’s thylakoid membrane; it has two molecules of P680 chlorophyll A at its reaction center Light Reactions 1) Cyclic Electron Flow: A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and that produces ATP but not NADPH or oxygen

2) Non-cyclic Electron flow(linear): A route of electron flow during the light reactions of photosynthesis that involves both photosystems and produces ATP, NADPH and oxygen.

Stages of Photosynthesis: 1. Light Reactions: a. Occurs in green thylakoid membranes inside the chloroplast b. When light energy hits chlorophyll pigment molecules, that energy is captured by raising the electrons in the chlorophyll to an excited state c. Chlorophyll is organized into photosystems, I (700) and II (680)

d. In non-cyclic electron flow, the excited electrons from chlorophyll molecules are captured by primary electron acceptors in photosystem II. i. These electrons are passed down a short ETC and through chemiosmosis, ATP is generated (phosphorylation) e. Electrons removed from chlorophyll in PSII are replaced by splitting water i. Oxygen is made as a byproduct f. Meanwhile, light energy also excites electrons in photosystem I which are captured by a primary electron acceptor in PSI i. These electrons are replaced by the ones moving down the ETC from PS II ii. PS I’s primary acceptor passes its electrons to NADP+ reducing it to NADPH g. The ATP AND NADPH made by the light reactions are then used by the next stage, Calvin Cycle, to make sugar h. In cyclic electron flow, only Photosystem I is used so no NADPH or oxygen is produced i. Electrons stay in a “loop” of moving through the ETC to make ATP only. 2. Calvin Cycle: a. Occurs in stroma (fluid area around thylakoids) b. With energy provided by ATP and reducing power of NADPH from light reactions, carbon dioxide is fixed into sugar (specifically G3P) 3 stages of Calvin Cycle 1) Carbon Fixation a. Inorganic carbon dioxide is “fixed” into organic form with help of enzyme rubisco which joins CO2 to ribulose bisphosphate (RuBP) 2) Reduction a. Gradual reduction of using ATP AND NADPH from light reactions to make Glyceraldehyde 3-phosphate (G3P) b. One molecule of G3P leaves the cycle and can be converted to other organic molecules such as glucose 3) Regeneration a. Remaining 5 G3P molecules are converted with more ATP from light reactions back into RuBP to start cycle over again as long as more CO2 enters and ATP AND NADPH keeps coming from light reaction...