Exam 2 bio

• Distinguish between free and bound ribosomes in terms of location and function.

- Bound: attached to the rough ER (protein synthesis that goes to golgi and leave cell) -free: in cytosol, ( fluid part of the cytoplasm.) (proteins the cell is going to use)

• What are some examples of specialized internal membranes in prokaryotic cells. How do these compare to eukaryotic organelles?

- internal membranes that perform metabolic functions have been discovered in a number of bacterial species. • not true organelles: • Typically composed of infoldings of the plasma (cell) membrane • Do not demonstrate the complex compartmentalization found in eukaryotic cells • Infoldings perform generalized tasks and are species specific -presence of these internal membranes in bacteria support the theory that eukaryotic cells arose from prokaryotic cells.

• Why are the hydrocarbon bonds found in carbohydrates and fats so important to cellular respiration in terms of redox reactions?

- main energy-yielding foods, (carbohydrates / fats) are reservoirs of electrons associated with hydrogen (H ) -- they can release a lot of free energy when broken down

• Explain the terms 'proton-motive force' and chemiosmosis

- proton-motive force: exergonic movement of protons across the membrane during chemiosmosis provides the direct energy needed for the endergonic process of ATP synthesis. -chemiostasis: protons diffuse down their electrochemical gradient back across the membrane. During chemiosmosis, the protons are forced to move through the enzyme ATP synthase, driving the production of ATP from ADP and Pi.

• Explain where and how the electron transport chain creates a proton gradient.

--The ETC acts as an energy converter that uses the exergonic movement of electrons to pump protons (H+) into the intermembrane space. -Cells that cannot use oxygen as an electron acceptor cannot generate such a large potential energy difference - they produce smaller proton gradients, smaller proton- motive force, and thus make less ATP than cells that use aerobic respiration.

• Summarize the stages and products of glucose oxidation.

-1st 3 steps of cellular resp. 1. glycolisis products: 2 ATP, 2 NADH, 2 pyruvate 2. pyruvate processing products: 2 CO2, 2 NADH 2 Acetyl coA 3. citric acid cycle products: 6 NADH, 2 FADH2, 2 ATP, 4 CO2 -Glucose oxidation produces ATP, NADH, FADH2, and CO2. • Glucose oxidation only produces 4 ATP (2 (net) from glycolysis, 2 from the Citric acid cycle)

• Distinguish between aerobic and anaerobic respiration and fermentation.

-Aerobic Respiration: Eukaryotes (and many prokaryotes) use oxygen as the final electron acceptor in the electron transport chain -Anaerobic Respiration: Some prokaryotes use final electron acceptors other than oxygen; Common in oxygen poor or anoxic environments -Fermentation: metabolic pathway that uses pyruvate or a molecule derived from pyruvate to accept electrons from NADH. (not cellular respiration) --> in most organisms, cellular respiration cannot occur without the electron transport chain (ETC), however, some organisms can use a process called fermentation to make ATP. not as efficient

• A molecule of ATP has a great deal of potential energy that can be released, why?

-All three phosphate groups are negatively charged (have oxygens with extra electrons) • The electrons associated with the oxygens of the phosphate groups have high potential energy because of their locations -- close to other electrons. There is mutual repulsion between the crowded electrons, causing instability in this region of ATP.

• Explain why smaller cells have a greater surface area to volume ratio.

-As a cell increases in size, its volume (V) grows proportionally more than its surface area (SA). • A smaller object/cell has a greater SA:V ratio compared to a large object/cell. -transport become less efficient as cell size increases.

• Briefly describe the primary functions of the plasma membrane.

-Creates a stable environment inside the cell despite fluctuating conditions outside. -selectively permeable: controls the flow of materials into and out of the cell (e.g. oxygen, nutrients, and wastes).

• How does ATP drive endergonic reactions? Describe energy-coupling and substrate activation.

-During oxidative phosphorylation, ETC provides a proton gradient, while chemiosmosis provides a proton-motive force to build ATP. -ATP hydrolysis can drive endergonic (energy-requiring) reactions when ATP phosphorylates (transfers a phosphate group to) target molecules (e.g. reactants or enzymes). -As long as the ΔG (change in free energy) of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that the coupled reactions are exergonic. -After ATP hydrolysis, the released phosphate group is transferred to a substrate (phosphorylation). Phosphorylation usually causes a change in the molecule's shape and the molecule become less stable (more reactive) than the original molecule (substrate activation), allowing for the endergonic reaction to proceed.

• Distinguish between obligate and facultative anaerobes.

-Facultative anaerobes: can switch between fermentation and cellular respiration but do not use fermentation if an appropriate electron acceptor is available for cellular respiration. (ex. Human skeletal muscle cells, Saccharomyces (Yeast) -Obligate anaerobes : only utilize fermentation (or anaerobic respiration) and may die in the presence of oxygen (toxic to cells). (Ex. Bacteria group responsible for botulism, tetanus, and types of food poisoning)

• Give an overview of how fermentation works.

-Fermentation : metabolic pathway that uses pyruvate or a molecule derived from pyruvate to accept electrons from NADH.

• Explain how different factors affect membrane behavior (i.e. fluidity and permeability) o How does temperature, hydrocarbon tail saturation, and presence of cholesterol affect membrane fluidity? Why is cholesterol called a 'fluidity buffer'? o How does hydrocarbon tail saturation, hydrocarbon tail length, presence of cholesterol, and temperature affect membrane permeability? edit!

-How quickly molecules move within and across membranes is a function of temperature and the structure of the lipids in the bilayer. -Many factors influence the behavior (fluidity and permeability) of the membrane: • Temperature • Proportion of phospholipids with saturated and unsaturated hydrophobic fatty acid tails • Length of the phospholipid hydrophobic tails • Number of cholesterol molecules in the membrane -Membrane fluidity decreases with temperature because molecules in the bilayer move more slowly. (decreased permeability.) -Membranes can remain fluid at lower temperatures if they have a high proportion of phospholipids with unsaturated hydrocarbon tails - the kinks decrease packing. -Membranes with unsaturated phospholipid tails are much more permeable than those formed by phospholipids with saturated tails. -Membranes containing phospholipids with longer tails have reduced permeability due to increased hydrophobicity. -Cholesterol buffers effects of temperature on membrane fluidity in animal cells (e.g. acts as a fluidity buffer): • At high temperatures (37°C in humans), cholesterol molecules make the membrane less fluid by restraining phospholipid movement. At low temperatures, cholesterol molecules can hinder the close packing of phospholipids, which maintains fluidity. Adding cholesterol to membranes increases the density of the hydrophobic section, which decreases membrane permeability

• Describe the evidence that mitochondria and chloroplasts are semiautonomous organelles (i.e. not always dependent on the nucleus for regulation and protein synthesis).

-Mitochondria have their own DNA and manufacture their own ribosomes. -Chloroplasts have their own DNA, specialized enzymes, and manufacture their own ribosomes.

• Are the bacterial and eukaryotic flagella closely related evolutionarily (i.e. it is likely that they arose from the same structure in a common ancestor)?

-Not closely related evolutionarily bc are made of different components and move differently. (convergent evolution--common ancestor had no flagella) -Eukaryotic flagella: made of microtubules, wave back and forth -Bacterial flagella: made of flagellin (protein) and rotate like a propellor

• Review the characteristics of osmosis and tonicity.

-OSMOSIS: Water moves from regions of low solute concentration to regions of high solute concentration. -The solute concentration of a solution outside a cell may differ from the solute concentration inside the cell. -Tonicity is how we describe the effect the outside solute concentration will have on the process of osmosis and "shape" of the cell (e.g. grow, shrink, no change): -An outside solution with a higher solute concentration is said to be hypertonic to the inside of a cell. -An outside solution with a lower solute concentration is hypotonic to the cell. -If solute concentrations are equal on the outside and inside of a cell, solutions are isotonic to each other.

• Distinguish between substrate level phosphorylation and oxidative phosphorylation.

-Oxidative phosphorylation: process which ATP is built using the electron transport chain and chemiosmosis collectively. (where most ATP is produced)--4th step -Substrate-level phosphorylation: when an enzyme catalyzes the transfer of a phosphate group from an intermediate (phosphorylated) substrate to ADP to form ATP. (how ATP is produced in glycolysis and the citric acid cycle.)--4 produced, 2 from each.

• Know the difference between active and passive transport and be able to categorize the types of transport that are discussed into these categories

-Passive transport: movement of molecules along a concentration gradient (diffusion), which does not require an input of energy. -Active transport: movement of molecules against a concentration gradient, which requires an input of energy.

• What constrains cell size?

-SA:V ratio -Metabolic requirements of the cell impose a limit on size; only a limited amount of any substance can diffuse across a cell's membrane in a fixed amount of time. • Cells must shuttle oxygen, nutrients, and wastes in and out to perform vital cellular functions - transport become less efficient as cell size increases.

• Describe the structure and function of ATP synthase. How does it interact with the process of chemiosmosis? How does the movement of ATP synthase produce ATP?

-Structure: • eukaryotes: many copies of this protein complex are found on the inner mitochondrion membrane that forms the cristae. • ATP synthase consisting of two large components: A membrane-bound, proton- transporting base (F0 unit), An ATPase "knob" (F1 unit) -Function: ATP synthase is an enzyme complex used during chemiosmosis to make (synthesize) ATP. -Movement: ATP synthase acts as a turbine powered by protons: The units are connected by a rotor, which spins the F1 unit, and a stator, which interacts with the spinning F1 unit. • The ATP synthase F0 unit provides the only route through the membrane for H+ • Protons flowing through the F0 unit spin the rotor and the F1 unit. • As the F1 unit spins, its subunits change shape, and catalyze the phosphorylation of ADP to ATP.

• Give a general overview of how the citric acid cycle is regulated.

-The citric acid cycle can be slowed down or turned off at multiple points via several different mechanisms of negative feedback inhibition. • ATP and NADH can allosterically inhibit different enzymes in the cycle.

• Why is the peroxisome a good example of the advantages of compartmentalization?

-able to break down hydrogen peroxide (harmful byproduct of fatty acid breakdown), brings catalase and H2O2 together in a small area so reaction can happen

• Describe the functions of the cytoskeleton.

-cell shape and structural stability • aids cell movement and transport of materials within the cell. • organizes all of the organelles and other cellular structures into a cohesive whole. -The eukaryotic cytoskeleton is dynamic - it changes to alter the cell's shape, to transport materials in the cell, or to move the cell itself.

• Define organelle.

-membrane-bound compartments in eukaryotic cells; contain enzymes or structures specialized for a particular function • e.g. nucleus, mitochondria, chloroplast, endomembrane system

• Know the general characteristics of membrane proteins. edit!

-move throughout the membrane but much more slowly than the phospholipids. • Two major types of membrane proteins: Integral, Peripheral

• What type of molecules require energy to move around the cell.

-movement of large molecules, like proteins, is energy demanding and tightly regulated. • Small molecules can be easily moved around the cell with diffusion (e.g. ions, ATP, amino acids) The endomembrane system is a specialized system of internal membranes responsible for protein and lipid synthesis and transport.

• Be able to determine the tonicity of a solution surrounding a cell and be able to predict which direction water will move (in or out) and what could happen to the "tone" of the cell.

-outside solution hypertonic (more solute): water flows outside of cell, cell shrinks -outside solution hypotonic (more water outside, more solute inside cell): water flows inside of cell, cell expands (and may burst) -isotonic (equal concentrations of solute and water): no change

• Summarize the overall net yield of ATP from substrate level phosphorylation and oxidative phosphorylation.

-oxidative phosphorylation: ATP synthase produces 25 (approx. 25-28) of the 29 (approx. 29-32) ATP molecules produced per glucose molecule during cell respiration. -substrate level phosphorylation: 1st 3 steps: 4 total (2 in 1st, 2 in 3rd)

• What is another function of adenine triphosphate, other than providing energy for cellular work?

-used to polymerize RNA nucleic acids

• Name and distinguish between the three major domains of life.

1. Bacteria • Prokaryotes • Single-celled only 2. Archaea • Prokaryotes • Single-celled only • Many extremophiles 3. Eukarya • Eukaryotes • Unicellular and multicellular organisms

• What are the major differences between eukaryotes and prokaryotes?--compare

1. Eukaryotic chromosomes are inside a membrane-bound nucleus. 2. Eukaryotic cells are often much larger. 3. Eukaryotic cells contain extensive amounts of internal, specialized membrane- bound compartments (organelles); based on this definition, prokaryotes lack organelles 4. Eukaryotic cells feature a diverse and dynamic cytoskeleton.

• Name the four steps of cellular respiration and state the region of the eukaryotic cell where each stage occurs. Outline which molecules are oxidized and which are reduced in each step. edit!!

1. Glycolysis Region: cytosol Oxidized: glucose is broken down (oxidized) to pyruvate. Reduced: Two molecules of NAD+ are reduced to NADH 2. Pyruvate processing Region: mitochondrial matrix Oxidized: pyruvate is oxidized to form acetyl CoA. Reduced: 3. Citric acid cycle Region: mitochondrial matrix Oxidized: acetyl CoA is oxidized to CO2. Reduced: Steps 1-3 collectively called glucose oxidation 4. Electron transport (and chemiosmosis) - compounds that were reduced in steps 1-3 (i.e. the electron carriers) are oxidized in reactions leading to ATP production.

• Compare the structure and functions of microtubules, microfilaments, and intermediate filaments.

1. MICROFILAMENTS/actin -smallest cytoskeletal elements. -Found underneath cell membrane to help define cell shape -Actin-Myosin (motor protein) interactions are responsible for some cellular movements: cell crawling, cytokinesis, cytoplasmic streaming -can also be involved in movement by interacting with the motor protein myosin 2. INTERMEDIATE FILAMENTS -defined by size rather than composition, Many types of intermediate filaments exist, each consisting of a different protein subunit. -provide structural support for the cell. They are not involved in movement, more permanent structures than microfilaments and microtubules -Form more permanent structures that help shape the cell and hold cell structures in place 3. MICROTUBLES -structure: large, hollow tubes--made of tubulin -provide a stable, structural framework for the cell as well as individual organelles. Also involved in movement: Act as "railroad tracks" to carry vesicles, Separate chromosomes during cell division, Form flagella and cilia -Provide structural support in cells and form motility structures (flagella, cilia) Involved in cellular movements: • Interact with motor protein kinesin to carry vesicles around the cell • Separate chromosomes during cell division • Interact with motor protein dynein to cause bending of flagella and cilia

• What motor protein is associated with what cytoskeletal structure? What is the collective function of motor proteins?

1. Microfilament: Actin-Myosin (motor protein) interactions are responsible for some cellular movements: cell crawling, cytokinesis, cytoplasmic streaming 2. Microtuble: Interact w/ kinesin to carry vesicles around the cell, Interact with motor protein dynein to cause bending of flagella and cilia -collective function: movement (thats why theres no motor proteins associated with intermediate filaments--theyre involved in structure, not movement)

• Briefly describe the energy conversions carried out by mitochondria and chloroplasts.

1. Mitochondria: produces ATP (the major cellular energy currency) by coupling exergonic breakdown of molecules with the endergonic process of building ATP molecules. 2. Chloroplasts: Contain the green pigment, chlorophyll, along with enzymes and other molecules that function in the photosynthetic production of sugar (captures light energy to build sugars)

• What are the two main types of passive transport used by cells? How do they differ?

1. Osmosis: Diffusion of water molecules across lipid bilayers • only occurs across a selectively permeable membrane. • maintains a balance of water between the internal and external environment. 2. Dialysis: Diffusion of solute molecules across lipid bilayers. • Specific characteristics of the solute (size, presence of polarity or charge) will determine its ability to diffuse across a selectively permeable membrane.

• Distinguish between prokaryotic and eukaryotic cells.--classify

1. Prokaryotes: lack a membrane-bound nucleus and other organelles 2. Eukaryotes: have a membrane-bound nucleus and other organelles

• Compare the structure and functions of smooth and rough ER.

1. Rough STRUCTURE: • membrane-bound tubes and sacs studded with ribosomes. • interior is called the lumen. • continuous with the nuclear envelope. FUNCTION: • Ribosomes associated with the rough ER synthesize proteins. • New proteins (particularly proteins to be secreted by the cell) are folded and processed in the rough ER lumen. • Builds more membrane 2. Smooth STRUCTURE: • membrane-bound tubes and sacs, No ribosomes are attached to its exterior • The interior is called the lumen. FUNCTION: -Synthesize lipids and steroids, drug/toxin detoxification, and ion storage • Serves different functions in different types of cells: Hormone production in testes and ovarian cells, Detoxification in liver cells

• Explain the advantages of compartmentalization in eukaryotic cells.

1. Separate incompatible chemical reactions 2. Increase the efficiency of chemical reactions

• Describe the three major types of cellular work.

1. Transport work: moving substances across membranes against the direction of passive movement. 2. Mechanical work: beating of cilia or flagella, muscle cell contraction. 3. Chemical work: pushing endergonic reactions, which would otherwise not occur spontaneously (e.g. synthesis of polymers from monomers).

• Describe three examples of intracellular digestion by lysosomes.

1. autophagy: break down own cell material (breaking down damaged organelle, brought to it by a vesicle) 2. Endocytosis: process by which the cell membrane can pinch off a vesicle or vacuole to bring outside material into the cell then merge the vesicle or vacuole with a lysosome -- material from outside taken into the cell(two types): -Receptor-mediated endocytosis: module-specific endocytosis (directed--particular substance) -phagocytosis: endocytosis of solid material (undirected/random)

• Explain the physical and functional differences of the two types of membrane proteins.

1. integral proteins penetrate the hydrophobic interior of the lipid bilayer -have many regulatory (cell communication, transport) and structural functions. -Majority are transmembrane proteins that span the membrane. • Other integral proteins only extend part way into the hydrophobic region. • All integral proteins have hydrophobic and hydrophilic regions. 2. Peripheral proteins are not embedded in the lipid bilayer - these proteins are loosely bound to the surface of a membrane (interior or exterior). -often have regulatory functions, especially in cell communication.

• List the components of the endomembrane system, and describe the structure and function of each component.

1. smooth and 2. rough ER 2. Golgi apparatus -structure: formed by a series of stacked flat membranous sacs called cisternae. -function: receives synthesized proteins from the rough ER and processes, sorts, then ships the proteins. -Membranous vesicles carry materials to and from the organelle. 3. lysosomes -structure: single-membrane-bound structures containing different digestive enzymes. (animal cells.) -function: Digestion and waste processing: Hydrolyze macromolecules, Contain an acidic environment 4. the nuclear envelope -structure: double-membrane that surrounds the nucleus -function: rough ER is continuous with the nuclear envelope 5. plasma membrane -structure: phospholipid bilayer with interspersed proteins. An external membrane made by the cell's internal membrane system -function: Creates a stable environment inside the cell despite fluctuating conditions outside. • Is selectively permeable: controls the flow of materials into and out of the cell (e.g. oxygen, nutrients, and wastes).

• Know how concentration gradients and equilibrium relate to diffusion.

A difference in solute concentrations creates a concentration gradient for both the solute and water. Molecules and ions move randomly when a concentration gradient exists, but there is a net movement from high concentration regions to low concentration regions, a process called diffusion. • Diffusion along a concentration gradient increases entropy (disorder) and is thus spontaneous (no energy input required). • Equilibrium is established once the molecules or ions are randomly distributed throughout a solution. (Molecules are still moving randomly but there is no more net movement.)

• Describe the procedure used in gram-staining and how this technique can be used to differentiate groups of bacteria.

A gram staining test can be used to classify illness-causing bacteria based on the composition of their cell walls: first washed with a pink dye then a purple 1. Gram-positive bacteria: simpler walls with large amounts of peptidoglycan (purple, bc peptidoglycan traps the violet) 2. Gram-negative bacteria: more complex walls -- less peptidoglycan, plus an extra outer glycolipid membrane (pink, violet color rinses away, revealing red/pink dye)

• What are the major differences between animal and plant cells?--compare

Animal cells: • Do not have cell walls or chloroplasts, or a large central vacuole -Do have centrioles and centrosomes, lysosomes Plant cells: • Have cellulose cell walls to maintain structural support • Have chloroplasts - the organelle used in photosynthesis • Contain a large central vacuole to maintain cell structure and store water • No centrioles or centrosomes, no lysosomes

• Write the summary equation for cellular respiration. Describe cellular respiration as a redox reaction.

C6H12O6 + 6O2 --> 6CO2 + 6H2O + Energy (to build ATP) -O2 is an oxidizing agent in this reaction - (causes glucose to lose electrons)--becomes reduced -the oxygen atoms in oxygen are reduced (GER) to form water -the carbon atoms of glucose are oxidized (LEO) to form carbon dioxide

• Is the term cellular respiration synonymous with the term anaerobic respiration, fermentation, or aerobic respiration?

Cellular respiration: reactions that use an electron transport chain to produce ATP. • Aerobic respiration (requires O2 as a final electron acceptor) and Anaerobic respiration (uses molecules other than O2 as final electron acceptors) are examples of cellular respiration. - NOT synonymous with fermentation. -Fermentation: production of ATP without the use of an electron transport chain (no oxygen required)

• Name the point at which glucose is completely oxidized during cellular respiration.

Citric Acid Cycle

• What is the overall function of the ETC if it does not make ATP directly?

During oxidative phosphorylation, ETC provides a proton gradient, while chemiosmosis provides a proton-motive force to build ATP. -coupled with chemiosmosis which actually synthesizes ATP. -eases the fall of electrons from glucose to oxygen (makes the process of harnessing that energy more efficient.)

• Give a general overview of how glycolysis is regulated.

Feedback inhibition: occurs when an enzyme in a pathway is inhibited by the product of that pathway. -when ATP is abundant: more feedback inhibition, glycolysis slows down, a cell can conserve its stores of glucose for times when ATP is scarce. -When ATP is scarce: less feedback inhibition, glycolysis speeds up, utilizing the stores of glucose in the cell.

• Compare the processes of aerobic and anaerobic respiration and fermentation in terms of metabolic pathways utilized and ATP yields. edit!

Fermentation is extremely inefficient compared to cellular respiration. • Fermentation produces two 2 ATP molecules per glucose molecule, compared with about 29 (to 32) ATP molecules per glucose molecule in aerobic respiration.

• Describe the structure of cilia and flagella and relate motor protein-microtubule interactions to their overall movement.

Flagella - long, hair-like projections from the cell surface that move cells. If cells have flagella, they usually have only one or two. -Eukaryotic flagella are made of microtubules and wave back and forth. -Bacterial flagella are made of flagellin (a protein) and rotate like a propeller. CILIA -Closely related to eukaryotic flagella: short, filament-like projections also composed of microtubules. -Cells with cilia typically have many cilia. **** microtubles Interact with motor protein dynein to cause bending of flagella and cilia

• Outline, in terms of redox reactions, how the electron carriers and O2 interact with the ETC complexes.

Fourth step in cellular respiration: • High potential energy of the electrons carried by NADH and FADH2 is gradually decreased as they move through a series of redox reactions (the electron carriers become oxidized as they lose electrons). • These redox reactions involve a series of protein complexes called an electron transport chain (ETC). • O2 is the final electron acceptor of the ETC -- the transfer of electrons along with protons to oxygen forms water (O2 is reduced (GER), thus acts as an oxidizing agent)

• Write the specific chemical equation for the breakdown of glucose.

Glucose is oxidized: loses electrons (and protons) C6H12O6 + 6O2 --> 6CO2 + 6H2O+ energy (to build ATP) oxygen is reduced: gains electrons (and protons)

• Explain how secondary active transport (or cotransport) works (see figure on slide)

In addition to moving materials against their concentration gradients, pumps can set up electrochemical gradients. • These gradients make it possible for cells to engage in secondary active transport, or cotransport.

• Describe how organelle (and cell) structure is correlated with function.

In multicellular organisms with specialized tissue types, overall cell structure (e.g., type, size, and number organelles) typically correlates with cell function. -muscle cells (move or contract) have more mitochondria per volume than cells with less activity.

• What is the most common way phospholipids move within the membrane?

Individual phospholipids can travel laterally throughout the lipid bilayer but rarely flip between layers

• List the initial reactant(s) and final products of the citric acid cycle. Explain why it is called a cycle.

Initial Reactants: Acetyl CoA Final products: Oxaloacetate Why its a cycle: The end product is necessary to start a new cycle: The molecule Oxaloacetate reacts with Acetyl CoA to produce Citrate. Citrate is then broken down and rearranged until Oxaloacetate is the final product...picking up a new Acetyl CoA...

• Compare the fate of pyruvate in alcohol fermentation and lactic acid fermentation. Name an example of a cell type that uses alcohol fermentation and one that uses lactic acid fermentation.

Lactic acid fermentation: • Pyruvate produced by glycolysis accepts electrons from NADH. • 2 Lactate, 2 NAD+, and 2 ATP are produced per glucose molecule. -cell type: skeletal muscle cells Alcohol fermentation: • Pyruvate is enzymatically converted to acetaldehyde (aka acetylaldehyde) and CO2. • Acetaldehyde accepts electrons from NADH • 2 ethanol, 2 NAD+, 2 CO2, and 2 ATP are produced per glucose molecule -cell type: yeast cells

• Describe the location and function of the electron transport chain.

Location: inner membrane of the mitochondrion (e.g. walls of the cristae) Function: Fourth step in cellular respiration: • High potential energy of the electrons carried by NADH and FADH2 is gradually decreased as they move through a series of redox reactions (the electron carriers become oxidized as they lose electrons). • These redox reactions involve a series of protein complexes called an electron transport chain (ETC). • O2 is the final electron acceptor of the ETC -- the transfer of electrons along with protons to oxygen forms water (O2 is reduced (GER), thus acts as an oxidizing agent)

• Explain why it is not possible to state an exact number of ATP molecules generated by the oxidation of a molecule of glucose. What is the total theoretical yield and the more realistic range of yield for oxidation of a single glucose molecule?

Many sources state that 38 ATP can be produced per oxidized glucose molecule during cellular respiration Glycolysis (2), Citric Acid Cycle (2), Oxidative Phosphorylation (34) • Above is the theoretical yield given ideal conditions - in reality, this maximum is never reached. • Thus, current estimates suggest ~ 29-32 ATP molecules are typically produced per glucose molecule during cell respiration. -potential reasons theoretical yields are not obtained: Losses (e.g. leaky membranes) Costs of moving pyruvate, ADP, and electrons into the mitochondrial matrix, Costs of moving ATP out into the cytosol after production

• How are lipid bilayers bound together?

Membranes are held together primarily by hydrophobic interactions, which are much weaker than covalent bonds.

• How do glycolysis and the citric acid cycle contribute to anabolic pathways? edit!

Molecules associated with glucose oxidation (e.g. intermediates and products of glycolysis, pyruvate processing, and the citric acid cycle) can also be used by cells to synthesize macromolecules - such as glycogen or starch, RNA, DNA, fatty acids, amino acids, and other cell components. -anabolic pathways: endergonic (building)

• By the end of glucose oxidation, which molecules contain most of the energy derived from the original molecule of glucose.

Most of glucose's original energy is contained in the electrons transferred to NADH and FADH2, which then carry them to oxygen, the final electron acceptor.--go to next step: electron transport chain (where the energy released powers ATP synthesis.)

• What types of organisms typically form physical connections between cells - unicellular or multicellular?

Multicellular • Cells of multicellular organisms adhere to one another and have specific, distinct structures and functions. • Groups of similar cells performing similar functions in multicellular organisms are called tissues.

• Is CO2 produced during this step of cellular respiration? (glycolysis)

No

• What is the specific final electron acceptor used in cellular respiration?

O2 (aerobic)

• Distinguish between: o Oxidation and reduction o Oxidizing agent and reducing agent

Oxidation: loss of electron, more positive, REDUCING AGENT Reduction: gain of electron, more negative, OXIDIZING AGENT Reducing agent: oxidized molecule (because it causes another molecule to gain an electron when it loses one.) oxidizing agent: reduced molecule (it causes another molecule to lose an electron when it gains one.)

• Which players in redox reactions gain potential energy and which lose potential energy?

Oxidized molecule (LEO) • loses an electron (and a proton) and has LOWER potential energy. Reduced molecule (GER) • gains an electron (and a proton) and has HIGHER potential energy.

• Why is the lysosome a good example of the advantages of compartmentalization?

Placing a substrate/enzyme in a small space increases the efficiency of chemical reactions

• What structures allow bacterial cells to adapt to unusual environmental conditions?

Plasmids: small, supercoiled, circular DNA molecules that contain genes for adapting to unusual/stressful environmental conditions (e.g. provide antibiotic resistance).

• Describe where pyruvate is oxidized to acetyl CoA, what molecules are produced, and how this process links glycolysis to the citric acid cycle.

Pyruvate processing (2nd step) Molecules produced: 2 NADH, 2 CO2, 2 Acetyl coA -2nd step in cellular respiration (in between 1. glycolisis and 3. citric acid cycle)

• Give an overview of the process of cellular respiration (reactants, products).

Reactants: Glucose, O2 Products: CO2 ,H2O, ATP 1. glycolisis reactants: 1 glucose products: 2 ATP, 2 NADH, 2 pyruvate 2. Pyruvate processing reactants: 2 pyruvate products: 2 NADH, 2 CO2, 2 Acetyl coA 3. citric acid cycle reactants: 2 Acetyl coA products: 6 NADH, 2 FADH2, 4 CO2, 2 ATp

• Nucleus: Describe the structures of and their functions.

STRUCTURE: • Large and highly organized • Surrounded by a double-membrane nuclear envelope. • Contains a distinct region called the nucleolus. • FUNCTION: • Information storage and processing • Contains the cell's chromosomes (structures carrying genetic information) • Directs protein synthesis (makes messenger RNA) • Ribosomal RNA synthesis (in the nucleolus)

• Briefly describe the structure and functions of this organelle.(peroxisome)

STRUCTURE: • globe-shaped organelles bound by a single membrane (NOT part of the endomembrane system.) FUNCTION: • Breaks down long fatty acid chains (the smaller fatty acids can be sent to the mitochondria to produce energy) • Breaks down hydrogen peroxide (H2O2) - a harmful by-product of fatty acid break-down (Uses enzyme catalase)

• What are the structural components and function of ribosomes?

STRUCTURE: • non-membranous (not considered organelles). • Have large and small subunits, both containing RNA molecules and protein (subunits made in nucleolus) FUNCTION: • Protein synthesis

• Describe the structure of a mitochondrion and explain the importance of the folded inner membranes (cristae) in mitochondrial functioning.

STRUCTURE: • two membranes; the inner one is folded into a series of sac-like cristae. The solution inside the cristae is called the mitochondrial matrix. • Mitochondria have their own DNA and manufacture their own ribosomes. FUNCTION -Acts as a powerhouse: produces ATP (the major cellular energy currency) by coupling exergonic breakdown of molecules with the endergonic process of building ATP molecules. • Some of the enzymes that catalyze steps of cellular respiration are found in the mitochondrial matrix, others that function in ATP production are built into the inner membrane walls.

• What is selective permeability? What types of molecules can/cannot pass through cell membranes? Study the permeability figure.

Selective permeability of the membrane controls the flow of materials into and out of the cell. (Keep damaging materials out of the cell, Allow entry of materials needed by the cell) -Size and charge affect the rate of diffusion across a membrane -Small nonpolar (e.g. lipid- soluble) and polar molecules move across phospholipid bilayers fairly quickly. • H2O is polar BUT small enough to pass through (but not very fast!) -Large polar or charged molecules (e.g. ions) cross slowly, if at all.

• Give a structural overview of prokaryotic cells, focusing on the size, shape, major internal structures, and diverse external structures of bacteria cells.

Size-bacterial cell diameters typically range from 0.5-5 μm - much smaller than eukaryotic cells (10-100 μm ) Shape (3 main categories): spherical (cocci), rod (bacilli), spiral (Spirochetes) -Major internal structures: A circular chromosome, Plasmids, Ribosomes, (structures composed of protein and RNA, which synthesize proteins), A rigid cytoskeleton (internal skeleton) composed of protein filaments, Plasma (cell) membrane, Stiff cell wall External structure -tough, fibrous cell wall surrounding the plasma membrane to maintain shape and protect the cell. bacteria=peptidoglycan, Archaea = polysaccharides and proteins but lack peptidoglycan. -Some bacterial groups have an extra outer membrane attached to their cell wall (gram - only, glycolipid layer) -capsule: sticky protein or polysaccharide layer that allows attachment -fimbrae: hair-like structures allow attachment -some prokaryotes have tail-like flagella/um (made of the protein flagellin) that spin around to move the cell

• Describe how substrate-level phosphorylation creates ATP.

Substrate-level phosphorylation: when an enzyme catalyzes the transfer of a phosphate group from an intermediate (phosphorylated) substrate to ADP to form ATP. (how ATP is produced in glycolysis and the citric acid cycle.)

• Is the building or decomposition of ATP an endergonic process?

The BUILDING of ATP (from ADP and Pi) is an ENDERGONIC reaction (requires energy)

• Explain how the exergonic movement of electrons down the electron transport chain is coupled to the endergonic production of ATP by chemiosmosis.

The energy released as electrons move through the ETC is used to pump protons (H+) across the inner membrane into the intermembrane space, forming a strong electrochemical gradient. The protons then diffuse down their electrochemical gradient back across the membrane through a process called chemiosmosis. During chemiosmosis, the protons are forced to move through the enzyme ATP synthase, driving the production of ATP from ADP and Pi.

• Explain the relationship between catabolic and anabolic pathways and cellular respiration. edit!

The pathways of cellular respiration can interact with many catabolic and anabolic pathways in the cell to meet these fundamental requirements. 1. A catabolic pathway involves breaking down molecules into smaller units, which releases energy. Exergonic pathways (hydrolisis) 2. An anabolic pathway involves building molecules, which requires energy. Endergonic pathways (condensation/dehydration reac)

• Why is NAD/NADH+ called an electron carrier?

They carry electrons from one reaction to another. • (NAD+) can accept two electrons and a proton (H+) from molecules that are being oxidized to become NADH (i.e. becomes reduced, acts as a oxidizing agent) • NADH can then donate electrons to other molecules (i.e. becomes oxidized, acts as a reducing agent).

• Describe the ATP cycle.

ch 6 slide 15 https://lms.uconn.edu/bbcswebdav/pid-49045-dt-content-rid-261447_1/courses/1155-UCONN-BIOL-1107-SECH10-1043/Lecture%206%287%29.pdf

• What is the fluid mosaic model and how is it related to membrane phospholipids and proteins?

describes the membrane as a fluid structure with proteins embedded in or attached to the phospholipid bilayers

• Which phase of glycolysis requires an expenditure of ATP?

energy investment phase (first 5 reactions): • Two molecules of ATP are consumed

• Identify where substrate-level phosphorylation and the reduction of NAD+ occur in glycolysis (energy investment or energy pay-off phase?).

energy payoff phase (second 5 reactions)

• Describe how food molecules other than glucose can be oxidized to make ATP. Which is typically used first and which is typically a last resort? edit!

for ATP production, cells first use carbohydrates, then fats, and lastly proteins

• Describe ATP hydrolysis. What are the products?

hydrolysis of the bond between the two outermost phosphate groups results in formation of ADP and Pi (inorganic phosphate, H2PO4−ADP AND PI ARE PRODUCTS) in a highly exergonic reaction (the potential energy of the products is much lower than that of the reactants).

• What type of molecules (for the most part) make up the ETC complexes? edit!

protein

• Give a general overview of how pyruvate processing is regulated.

pyruvate processing is under both positive and negative feedback control: -Positive Feedback: stimulate pyruvate processing (when large supplies of reactants, such as pyruvate and NAD+, and low supplies of ATP, stimulate pyruvate processing.) -Negative Feedback: inhibit/slow down pyruvate processing( Abundant ATP reserves in the mitochondrial matrix inhibit the enzyme complex.)

• Review the summary of membrane transport

slide 33 ch 8

• In general terms, what is an organism's metabolism?

totality of chemical reactions that occur within an individual (organism or cell) -Metabole (greek) = change

• Explain in general terms how redox reactions are involved in energy exchanges.

• Electrons are transferred during redox reactions - the relocation of electrons releases energy stored in organic molecules. -The released energy can then be harnessed by the cell to build ATP from ADP and Pi -catabolic pathways decompose glucose / other organic compounds to release energy

• Describe the efficiency of respiration in generating ATP. What happens to the energy from glucose that is not used to make ATP during cellular respiration?

• Roughly 34% of the potential chemical energy in glucose can be transferred to ATP. • The rest of the energy stored in glucose is lost as heat during cellular respiration -The mechanisms of cellular respiration carried out by the mitochondria are quite efficient in their energy transforming capacities.