Biol 215 Test 3

Describe a redox reaction. Identify the species undergoing oxidation and those undergoing reduction in such a reaction.

A redox reaction involves one molecule being oxidized (loses electrons, gains O, loses H) and another being reduced (gains electrons, loses O, gains H).

Mnemonic: OIL RIG – Oxidation Is Loss, Reduction Is Gain (of electrons)

Explain why metabolic pathways are comprised of many, small steps from reactants to products rather than just one large step.

Small steps allow for controlled energy release instead of a large, explosive reaction. This makes the energy usable by the cell.

Explain the role(s) of electron carriers in the cell and describe their general structure.

Carry electrons and protons through redox reactions. Easily oxidized/reduced. Allow for controlled energy transfer.
Structure enables reversible electron gain/loss (e.g., NAD⁺/NADH, FAD/FADH₂).

Provide an overview of the process of aerobic respiration. Describe specifically where all of the events are taking place (i.e. which subcellular location).

Three steps:

Glycolysis (cytoplasm)

Citric Acid Cycle (mitochondrial matrix)

Oxidative Phosphorylation (inner mitochondrial membrane) Generates ATP; most energy comes from step 3.

Describe the glycolytic pathway, highlighting the driving forces behind the steps of the pathway.

Glycolysis is a cytoplasmic pathway that breaks down one glucose (6C) into two pyruvate (3C) molecules through a series of enzyme-catalyzed steps. Driving forces include phosphorylation (to destabilize glucose), redox reactions (oxidation of G3P), and substrate-level phosphorylation (to generate ATP).

What is involved in the energy investment phase of glycolysis?

The cell uses 2 ATP to phosphorylate glucose and convert it into two molecules of G3P. This prepares the molecule for later energy extraction.

What is involved in the energy payoff phase of glycolysis?

Each G3P is oxidized, forming 2 NADH and 4 ATP (net gain: 2 ATP). The result is the production of two pyruvate molecules and water.

What are the overall inputs and outputs of glycolysis?

Inputs: 1 glucose, 2 ATP, 2 NAD⁺
Outputs: 2 pyruvate, 2 NADH, 4 ATP (net 2 ATP), 2 H₂O

Describe the fate of pyruvate in both aerobic and anaerobic environments.

In aerobic conditions, pyruvate enters the mitochondria and becomes acetyl-CoA for the Krebs cycle. In anaerobic conditions, pyruvate undergoes fermentation into lactate (animals) or ethanol and CO₂ (yeast).

Differentiate between organisms/cells based on their oxygen usage.

Obligate aerobes require oxygen to survive. Obligate anaerobes cannot tolerate oxygen. Facultative anaerobes can switch between aerobic respiration and anaerobic fermentation depending on conditions.

Describe in detail the structure of the mitochondria.

Mitochondria have a double membrane: the outer membrane (OMM) and the inner membrane (IMM), which folds into cristae. The matrix contains enzymes for the Krebs cycle, mitochondrial DNA, and ribosomes. The IMM holds the ETC and ATP synthase.

How is mitochondrial structure related to its function?

Cristae increase surface area for ATP production. Compartments separate processes: matrix for Krebs, IMM for ETC/OxPhos. High concentration in energy-demanding tissues like liver and muscle.

Describe PDH and the oxidative decarboxylation of pyruvate.

a large enzyme complex in the mitochondrial matrix that converts pyruvate (3C) into acetyl-CoA (2C). It removes one carbon as CO₂ and transfers electrons to NAD⁺ → NADH, linking glycolysis to the Krebs cycle.

Describe the fate of pyruvate in both aerobic and anaerobic environments

In aerobic conditions, pyruvate enters the mitochondria and is converted to acetyl-CoA for use in the Krebs cycle. In anaerobic conditions, it is converted to lactate in animals or ethanol and CO₂ in yeast through fermentation to regenerate NAD⁺ for glycolysis.

Describe in detail the structure of the mitochondria. Explain how this structure is related to its functions

Mitochondria have a double membrane: the outer membrane (OMM) and inner membrane (IMM). The IMM folds into cristae to increase surface area. The matrix contains Krebs cycle enzymes, mitochondrial DNA, and ribosomes. The IMM houses the ETC and ATP synthase, critical for oxidative phosphorylation.

Provide an overview of the process of aerobic respiration. Describe specifically where all of the events are taking place (i.e. which subcellular location)

Glycolysis occurs in the cytoplasm. Pyruvate oxidation and the Krebs cycle take place in the mitochondrial matrix. The electron transport chain and ATP synthase function in the inner mitochondrial membrane. Oxygen acts as the final electron acceptor to form water.

Describe PDH and the oxidative decarboxylation of pyruvate by PDH

Pyruvate dehydrogenase (PDH) is a multi-enzyme complex in the mitochondrial matrix. It converts pyruvate (3C) into acetyl-CoA (2C) by removing CO₂ and transferring electrons to NAD⁺ to form NADH. This step links glycolysis to the Krebs cycle.

Describe the form and fate of the carbons in the Krebs cycle

Acetyl-CoA (2C) combines with oxaloacetate (4C) to form citrate (6C). Through a series of reactions, two carbons are released as CO₂. Oxaloacetate is regenerated at the end of the cycle. Inputs: acetyl-CoA, NAD⁺, FAD, ADP. Outputs: 2 CO₂, 3 NADH, 1 FADH₂, 1 ATP (per cycle).

Explain the role of Coenzyme A in aerobic respiration

Coenzyme A carries acetyl groups into the Krebs cycle by forming acetyl-CoA. It acts as a carrier molecule for acyl groups and is essential for the link between glycolysis and the Krebs cycle.

Explain the driving force behind electron movement through the electron transport chain. What drives the concomitant movement of protons across the IMM?

Electrons move through the ETC due to increasing electronegativity of the complexes. Energy released during this transfer powers proton pumping from the matrix to the intermembrane space, creating a proton gradient.

Explain how membrane structure is related to membrane function in chemiosmosis

The inner mitochondrial membrane is selectively permeable and contains ETC proteins and ATP synthase. Its structure allows a proton gradient to form, which drives ATP synthesis as protons flow back through ATP synthase.

Differentiate between substrate-level phosphorylation and oxidative phosphorylation

Substrate-level phosphorylation directly transfers a phosphate group to ADP to form ATP (e.g., in glycolysis and Krebs). Oxidative phosphorylation uses the proton gradient and ATP synthase in the mitochondria to produce ATP indirectly.

Summarize the net ATP yield from the oxidation of glucose in aerobic respiration. Compare that to the net ATP yield from glycolysis alone

Aerobic respiration yields about 30–32 ATP per glucose: 2 from glycolysis, 2 from Krebs cycle, and ~26–28 from oxidative phosphorylation. Glycolysis alone yields only 2 net ATP.

Describe the pathways of alcoholic fermentation and lactate (lactic acid) fermentation. Explain why fermentation is necessary

Alcoholic fermentation (in yeast) converts pyruvate to ethanol and CO₂. Lactic acid fermentation (in animals) converts pyruvate to lactate. Both regenerate NAD⁺ to keep glycolysis running in the absence of oxygen.

Explain why fermentation is important economically

Fermentation is used to produce bread, alcohol, yogurt, cheese, and biofuels. It's also essential in biotechnology and food industries for anaerobic microbial growth and production.

Compare the cellular processes of fermentation and aerobic respiration. Speculate on the types of cells/organisms that carry out these processes

Fermentation is anaerobic, yields 2 ATP, and occurs in some bacteria, yeast, and muscle cells. Aerobic respiration uses oxygen, yields ~30 ATP, and occurs in most plants, animals, and aerobic microbes.

Be able to generate the 'big picture' of chemotropic energy metabolism by linking together the processes of glycolysis, Krebs cycle, ETC and oxidative phosphorylation. Include a link to fermentation to explain energy conversion under anaerobic conditions. Your picture should also include the subcellular locations of these processes

Glycolysis (cytoplasm) breaks glucose into pyruvate. In aerobic conditions, pyruvate is oxidized to acetyl-CoA (mitochondrial matrix), enters the Krebs cycle (matrix), and provides NADH/FADH₂ to the ETC (inner membrane) where ATP is produced via oxidative phosphorylation. In anaerobic conditions, fermentation occurs in the cytoplasm to regenerate NAD⁺ for glycolysis.

Describe the molecular biology/chemistry involved in yogurt production

Yogurt is made by lactic acid bacteria fermenting lactose into lactic acid. The acid lowers pH, causing milk proteins to coagulate and form the texture of yogurt. The fermentation also gives yogurt its tangy flavor.

Describe the Warburg effect. How can the Warburg effect be used in the study of cancer?

The Warburg effect describes how cancer cells preferentially use glycolysis for energy, even in the presence of oxygen. This high glucose uptake is used in cancer diagnosis via imaging techniques like PET scans.

What is PDG-PET?

PDG-PET (Fluorodeoxyglucose Positron Emission Tomography) is a diagnostic imaging tool that uses a radioactive glucose analog to detect areas of high glucose uptake, such as tumors, based on the Warburg effect.

Explain how alternative carbohydrates (i.e. other than glucose) and other organic molecules (e.g. glycerol) are metabolized and from where they are derived

Fructose and galactose enter glycolysis as intermediates. Glycerol from triglycerides becomes DHAP (a glycolysis intermediate). Fatty acids undergo beta-oxidation to form acetyl-CoA. Amino acids are deaminated and enter glycolysis or the Krebs cycle.

Analyze the regulatory effects of different molecules on glycolysis and the Krebs cycle

ATP and citrate inhibit glycolysis; AMP activates it. NADH and ATP inhibit the Krebs cycle; ADP and Ca²⁺ activate it. Enzymes like phosphofructokinase and isocitrate dehydrogenase are key regulation points.

Describe the Cori cycle. Describe the abnormal conditions that occur when the Cori cycle takes place

The Cori cycle transfers lactate from muscles to the liver, where it is converted back to glucose, then sent back to muscles. During intense activity or oxygen deprivation, excessive lactate can accumulate, leading to acidosis.

Describe the Cori cycle. Describe the abnormal conditions that occur when the Cori cycle takes place

The Cori cycle converts lactate produced by muscles during anaerobic glycolysis into glucose in the liver. This glucose returns to the muscles for energy. Under abnormal conditions like prolonged anaerobic activity or oxygen deficiency, lactate accumulates and may cause acidosis.

Regarding glucose usage by the cell, describe the scenarios that would result in glycolysis compared to glycogenesis, and vice versa. Why does the cell decide to use one over the other

Glycolysis occurs when energy is needed and ATP levels are low. Glycogenesis occurs when energy and glucose are abundant. The cell decides based on ATP levels and hormone signals like insulin and glucagon.

Explain specifically the role of phosphoglucomutase in glucose metabolism

Phosphoglucomutase converts glucose-1-phosphate to glucose-6-phosphate and vice versa, connecting glycogen metabolism to glycolysis and glucose release.

Define and differentiate the various G words glycolysis glycogenesis glycogenolysis gluconeogenesis

Glycolysis is the breakdown of glucose to pyruvate. Glycogenesis is the formation of glycogen from glucose. Glycogenolysis is the breakdown of glycogen to glucose. Gluconeogenesis is the formation of new glucose from non-carbohydrate sources.

Outline the general fate of food molecules protein lipids carbohydrates

Carbohydrates are broken into glucose for ATP production. Lipids are broken into glycerol and fatty acids for energy. Proteins are broken into amino acids, which are deaminated and used for energy or biosynthesis.

Describe the catabolism of triglycerides

Triglycerides are broken into glycerol and fatty acids. Glycerol enters glycolysis. Fatty acids undergo beta-oxidation to form acetyl-CoA for the Krebs cycle.

Describe the process of beta-oxidation of fatty acids. How many rounds are required for a given fatty acid

Beta-oxidation occurs in the mitochondria and breaks fatty acids into 2-carbon acetyl-CoA units. The number of rounds equals the number of carbon atoms divided by 2 minus 1. Each round produces NADH and FADH₂.

Explain why fats contain more extractable energy per gram compared to carbohydrates or proteins

Fats are more reduced and contain more high-energy C-H bonds, allowing them to release more electrons during oxidation and generate more ATP.

Describe the catabolism of proteins

Proteins are broken into amino acids, which are deaminated to remove the nitrogen. The remaining carbon skeletons enter glycolysis or the Krebs cycle depending on their structure.

Explain phenylketonuria PKU. Why do individuals with PKU have to avoid aspartame

PKU is a genetic disorder where phenylalanine cannot be broken down due to a missing enzyme. Aspartame contains phenylalanine, which can build up and cause brain damage in individuals with PKU.

List the different types of phototrophs photoautotrophs and photoheterotrophs

Photoautotrophs use light energy and CO₂ to produce their own food, like plants and algae. Photoheterotrophs use light for energy but consume organic compounds for carbon, like some bacteria.

Revisited Describe how energy and matter move through the biosphere. Differentiate between autotrophs and heterotrophs

Energy flows one way from the sun to producers to consumers and is lost as heat. Matter cycles through organisms and the environment. Autotrophs produce their own food. Heterotrophs consume others for energy.

Write a summary equation for photosynthesis

6 CO₂ + 6 H₂O + light energy produces C₆H₁₂O₆ + 6 O₂

Differentiate between oxygenic and anoxygenic photosynthesis

Oxygenic photosynthesis uses water and releases oxygen, common in plants and algae. Anoxygenic photosynthesis uses other electron donors like hydrogen sulfide and does not release oxygen, seen in some bacteria.

Explain why the evolution of photosynthesis was so important in organismal evolution

Photosynthesis increased atmospheric oxygen, allowing aerobic respiration and enabling the evolution of complex multicellular organisms.

Describe in detail the structure and function of the chloroplast

Chloroplasts have a double membrane and contain internal thylakoids stacked into grana. The stroma surrounds the thylakoids. Light-dependent reactions occur in the thylakoids and the Calvin cycle occurs in the stroma. Chloroplasts also have DNA and ribosomes.

Describe in general the two main stages of photosynthesis

The light-dependent reactions capture light energy to produce ATP and NADPH. The Calvin cycle uses ATP and NADPH to fix carbon dioxide into glucose.

Describe the structure of the chlorophyll molecule

Chlorophyll has a porphyrin ring with a central magnesium ion that absorbs light, and a hydrophobic tail that anchors it in the thylakoid membrane.

Describe the accessory pigments used by phototropic organisms

Accessory pigments like carotenoids and phycobilins absorb additional light wavelengths and transfer energy to chlorophyll, expanding the range of usable light.

Explain how light energy is absorbed by the different plant pigments to generate the colors we see

Plant pigments absorb certain wavelengths of light and reflect others. The reflected wavelengths determine the color we perceive, such as green from chlorophyll.

Describe the biochemical changes that give rise to fall leaf color

As chlorophyll breaks down in the fall, carotenoids and anthocyanins become visible. These pigments were present or produced in response to sugar accumulation and changing light.

Describe the two photosystems used in photosynthesis. Explain how the structure of the photosystems is designed to funnel light energy to the reaction centers. Describe the special pair of chlorophyll molecules found in each reaction center

Photosystem II (P680) and Photosystem I (P700) are complexes that absorb light. Antenna pigments funnel light to a special pair of chlorophyll a molecules in each reaction center. These special pairs release excited electrons to start the electron transport chain.

Explain the possible fates of photoexcited electrons

Photoexcited electrons can return to their ground state and release heat or fluorescence, be transferred to another pigment, or be donated to an electron acceptor to begin electron transport.

Describe electron flow during the light reactions. Specifically explain the driving force behind the flow of electrons, what happens as a result of the electrons moving through the electron transport system of photosynthesis, and what are the products of the light reaction

The flow is driven by photon energy exciting electrons in PSII. Electrons pass through the ETC to PSI, creating a proton gradient. Water is split to replace lost electrons, releasing O₂. Electrons from PSI reduce NADP⁺ to NADPH. Products are ATP, NADPH, and O₂.

Describe the general structure and function of NADP⁺/NADPH. Compare its structure and function to that of NAD⁺/NADH

NADP⁺ and NADPH are electron carriers. NADPH has a phosphate group and functions in biosynthesis and photosynthesis. NAD⁺/NADH are used in catabolic reactions like respiration. Both carry electrons and hydrogen ions.

Describe the process of photophosphorylation. Again, you should be able to explain what is driving the process

Photophosphorylation is ATP synthesis driven by a proton gradient across the thylakoid membrane. The gradient is created by electron transport from PSII through the cytochrome complex. Protons flow back through ATP synthase, generating ATP.

Compare and contrast electron transport during aerobic respiration and photosynthesis

In respiration, electrons from food pass through the mitochondrial ETC to oxygen. In photosynthesis, light excites electrons from water in PSII, and they pass through a chloroplast ETC to NADP⁺. Both chains create a proton gradient for ATP synthesis.

Compare and contrast chemiosmosis during oxidative phosphorylation in mitochondria and photophosphorylation in chloroplasts

Both use a proton gradient and ATP synthase. In mitochondria, the gradient is in the intermembrane space and protons flow into the matrix. In chloroplasts, the gradient is in the thylakoid lumen and protons flow into the stroma.

Describe the structure and function of a leaf. What are the stomata and guard cells? Describe their structure and function

Leaves have a flat structure to absorb sunlight and contain chloroplasts for photosynthesis. Stomata are pores on the underside of the leaf. Guard cells control the opening and closing of stomata to regulate gas exchange and water loss.

From where is the CO₂ derived that is fixed in the Calvin Cycle

CO₂ is taken from the atmosphere through the stomata and enters the chloroplasts where it is fixed in the Calvin cycle.

Summarize the reactions of the Calvin cycle, specifically the three phases, and describe changes that occur in the carbon skeletons of intermediates

The Calvin cycle includes carbon fixation (CO₂ combines with RuBP), reduction (3-PGA is converted to G3P using ATP and NADPH), and regeneration (RuBP is regenerated). Carbon atoms are rearranged to eventually form G3P and reform RuBP.

Describe the role of ATP and NADPH in the Calvin cycle

ATP provides energy and NADPH provides reducing power to convert 3-PGA into G3P during the reduction phase of the Calvin cycle.

Link together the processes of photoreduction, photophosphorylation and carbon fixation to generate a complete picture of phototrophic energy conversion

Light reactions occur in the thylakoid membrane. Photoreduction reduces NADP⁺ to NADPH. Photophosphorylation generates ATP using a proton gradient. These products enter the Calvin cycle in the stroma where CO₂ is fixed into sugars.

Describe the various ways that the Calvin Cycle is regulated

The Calvin cycle is regulated by light (activates enzymes), pH (alkaline pH in stroma activates enzymes), and the availability of substrates like ATP, NADPH, and CO₂. Thioredoxin also activates enzymes in response to light.