Unit 2 Exam

Compare and contrast the two laws of thermodynamics we discussed, and give examples of both laws using chemical reactions or processes from cells. IOW, make connections between these general principles and biology to enhance your understanding.

1st law- Conservation of energy -energy can't be created or destroyed, only transformed from one form to another 2nd law- Energy cannot be changed from one form to another without a loss of USEABLE energy (heat). -increase in disorder in UNIVERSE (entropy)

What is the full name and chemical structure of ATP (i.e., parts (review from last exam material) and why do we call it an energy carrier? IOW, what do cells do with the energy ATP carries? WHERE does ATP carry the energy, (the EXACT place, 'THE BOND', this is why you need to know the parts)? What type of reaction is the breakdown of ATP (endergonic or exergonic)? How about the making of ATP (endergonic or exergonic)? {Hey, they are opposite. Yes, yes they are. Need to understand this idea of the two reactions being opposite to understand cellular respiration that you both make and break ATP in the cells.

Adenosine triphosphate, the main energy source for cells. ATP releases energy when its phosphate bonds are hydrolyzed.

What are metabolic reactions {do not make this too difficult}? What types of factors affect their rates of reaction? {HEY! There is that rate business, again, do you think it is important?}

All of a cell's chemical reactions. Dependent on surface area to volume ratio which controls the rate of molecular diffusion across the membrane.

Why should you "follow the hydrogens" to figure out if a reaction is a reduction or oxidation?

Hydrogen atoms represent electron transfers because each hydrogen atom consists of both an electron and a proton

Understand the meaning of hypertonic, hypotonic, and isotonic solutions when describing osmosis. (IOW, how would you use these words to describe solutions on different sides of a membrane?) The terms always refer to a comparison of solutions in at least two compartments.

Hypertonic- a solution that, when surrounding a cell, will cause the cell to lose water & shrivel. Hypotonic- " " will cause the cell to take up water (swell) Isotonic- " " causes no net movement of water into or out of the cell.

Explain where O2 is used and CO2 is produced in cellular respiration.

O2 accepts electrons at the end of the ETC. CO2 is released during the oxidation of intermediate compounds in pyruvate oxidation and the citric acid cycle.

REVIEW: What two words do I want you to think of when I say, "food or cellular fuel"? What word do I want you to think of when I say, "materials" in the context of cells and living organisms? Why are both energy and building materials so important in living things {i.e., its essential function should be review & it has to do with several common properties of life?}

energy and atoms

What are the four stages of aerobic respiration, and where does each take place within a cell? {Yes, your book says three, but it is four for this class.}

1. Glycolysis 2. Pyruvate Oxidation 3. Citric Acid Cycle 4. Oxidative Phosphorylation

Remember what the chemical structure of phospholipids is!!! What functional groups of the phospholipids account for their hydrophobic end and their hydrophilic end? How does this structure account for their aquatic behavior? {Hint: see next question} What does amphipathic mean?

-Hydrophobic tails (lipids) point towards the inside of the cell -Hydrophilic heads (phosphate groups) point towards the cytoplasm of the cell and interact with other molecules -Amphipathic means that there is a separation of charge within the same molecule.

What is the difference between active and passive transport?

-Passive doesn't require energy to transport substances that are diffusing down their concentration gradients. -Active requires specific transport proteins and an input of energy (often as ATP) to move molecules against its concentration gradient.

FOR EMPHASIS:What types of energy transfer occur during chemiosmosis?List them and identify the form of energy each starts with and what type that energy transforms into.{example, chemical energy (bond) to mechanical energy, etc. There will be several}.FOCUS ON THIS ONE TO MAKE THE CONNECTIONS BETWEEN LECTURES AND CONCEPTS.

-Potential energy of the concentration gradient of H+ across the inner mitochondria membrane.

What is diffusion? What are the physical factors that determine the rate of diffusion?

-The random movement of particles that results in the net movement of a substance down its concentration gradient from a region of high to low concentration.

What are the two processes that provide the energy TO RUN life {think ecosystem level, not asking about storage}? How are they connected? IOW, compare the products and reactants for these two processes and use them explain why the two pathways are said to be interdependent. {Think about the commonalities and differences between the two.}

1. Breathing 2. Cellular respiration

Give examples of Red-Ox reactions in living systems{we discussed several}. Take the time to understand what is going on with the major molecules in cell respiration and photosynthesis(inputs and outputs). We will be adding the details in the next few lectures. And, prepare yourselves to look for where to use the information on RedOx as we move forward.

1. Cotransportation (symporter and antiporters) 2. Endergonic and exergonic reactions (cellular respiration in substrate level phosphorylation of ADP-> ATP and visa versa. 3. Transferring electrons to different states

What are two methods of potential energy storage in cells? {These concepts will help you understand everything else we are studying in this unit and all of biology.} And, name a few examples of kinetic energy you find in biological systems.

1. Covalent chemical bonds 2. Proton gradients across a semi-permeable membrane.

What are the reactants, products, and the OVERALL objective of cellular respiration? (Use the summary equation.)IOW, what is being done during cellular respiration and for what purpose?

6O2+ C6H12O6---> 6CO2 + 6H20 + ATP + heat

What percentage of our cellular energy is used to maintain the health of our cells (i.e., homeostasis, active transport to set up ion gradients, etc.)? To do external activities? Does this surprise you?

75% maintain health 25% power physical activities

Describe the GENERAL location, structure(what is it exactly), and function of an electron transport chain (include in your description the analogy of a staircase).

A series of electron carrier molecules that shuttle electrons during a series of redox reactions that release energy used to make ATP; located in the inner membrane of mitochondria, the thylakoid membranes of chloroplasts, and the plasma membranes of prokaryotes.

Explain the process of chemiosmosis. What is its function? How does it work? Explain the steps and the cellular machinery involved. What structures must be present for it to work?{critical information for you to understand ATP synthesis using an ETC}

An energy-coupling mechanism that uses energy of hydrogen ion (H+) gradients across membranes to drive cellular work, such as the phosphorylation of ADP; powers most ATP synthesis in cells.

How does osmosis differ from simple diffusion {not talking about passive transport here}? IOW, what structure must be present for osmosis to work? AND, what molecule does the moving in osmosis? Why only that substance {has to do with the structure that must be present in osmosis and the phospholipid bilayer}?

Aquaporins are protein pumps that use energy to move molecules against the concentration gradient.

Distinguish between autotrophs and heterotrophs, and give examples of each. {review & your general knowledge} Are plants the only photoautotrophs? What type of organism does the majority of photosynthesis on Earth?

Autotrophs- main photosynthesizers (plants, protists, algae, cyanobacteria, diatoms)

What is a phospholipid bilayer? Why does it form spontaneously in water?

Cellular membrane composed of lipids and phosphate groups, integral/channel proteins, cholesterol, etc. Since the hydrophobic lipid tails repel the electronegativity of water molecules, the bilayer forms spontaneously in water.

What is the difference between breathing and cellular respiration? In your body, how are they connected?

Cellular respiration is the oxidation of glucose and it releases CO2 which is used to power the Citric Acid cycle, ETC, and chemiosmosis for ATP synthesis. O2 from breathing is the final electron receptor.

What are cofactors? Explain the difference between cofactors and coenzymes.

Cofactors: A nonprotein molecule or ion that is required for the proper functioning of an enzyme Coenzyme: An organic molecules serving as a cofactor. Most vitamins function as coenzymes in important metabolic reactions.

Describe how inhibitors control enzymes by describing the following terms: competitive and noncompetitive inhibition, allosteric site, feedback inhibition, and the interaction of inhibitors & enzymes. IOW, how do feedback loops control metabolic pathways?

Competitive: A substance that reduces the activity of an enzyme by entering the active site in place of the substrate. A competitive inhibitor's structure mimics that of the enzyme's substrate. Noncompetitive: substance that reduces the activity of an enzyme without entering an active site but by binding elsewhere on the enzyme. Changes the shape of the enzyme so that the active site no longer effectively catalyzes the conversion of substrate to product. Feedback inhibition: A method of metabolic control in which a product of a metabolic pathway acts as an inhibitor of an enzyme within the pathway. Enzymes: A macromolecule, usually a protein, that serves as a biological catalyst, changing the rate of a chemical reaction without being consumed by the reaction.

Plasmolysis

Contraction of the protoplast of a plant cell as a result of loss of water from the cell. Aka: the process in which cells lose water in a hypertonic solution.

Connecting concept: What is the advantage of releasing energy during metabolic pathways in living cells instead of all at once? IOW, what would happen if you release the energy in a molecule all at once {uncontrolled release}?

Controlled release; we would explode if all the energy in a molecule was released at once.

Photosynthesis and cell respiration: what role does NADP+ play in photosynthesis and NAD+ and FAD play in cell respiration?{two word answer, it is the idea I want to pop into your head when I say either of them}

Electron carrier

What is the difference between endocytosis and exocytosis, and the difference between phagocytosis and pinocytosis?

Endocytosis- cellular uptake of molecules or particles via formation of new vesicles from the plasma membrane. Exocytosis- the movement of materials out of the cell by the fusion of vesicles with the plasma membrane. Phagocytosis- cellular "eating"; a type of endocytosis in which a cell engulfs macromolecules, other cells, or particles into its cytoplasm Pinocytosis- cellular "drinking"

Define energy and distinguish between potential and kinetic energy. Give cellular examples of each.

Energy is the ability to do work. Potential energy- stored in covalent chemical bonds Kinetic energy- energy associated with the movement of objects.

Explain the differences among exergonic, endergonic, and coupled metabolic reactions. MOST IMPORTANT, what does "coupling" reactions mean? Do you need to couple exergonic rxn with endergonic rxn or can you couple exergonic with exergonic and endergonic with endergonic {energy coupling is the essential concept}? Just like we saw in the iClicker questions, be able to figure out exo- vs endergonic reactions.

Exergonic- release energy Endergonic- require energy and yield products rich in potential energy Coupling- ATP drives cellular work by coupling exergonic and endergonic reactions. The hydrolysis of ATP, and often the transfer of a phosphate group, is involved in chemical, transport, and mechanical work. The energy harvested from one reaction is used to power the other.

What is free energy? What does comparing the free energy of reactants and products tell you? How do you calculate a change in free energy {the equation, you will need to learn it for the exam}?

Gibb's Free Energy Δ G= Gp - Gr

What is the net energy yield (# ATPs) of each stage of aerobic respiration?

Glycolysis- 2 ATP Citric Acid Cycle- 2 ATP Oxidative phosphorylation- ~28 ATP

REVIEW: How does energy move through ecological systems? IOW, flow or cycle? Why is it one and not the other? What about materials moving through ecological systems, flow or cycle?

It flows and does not cycle unlike materials.

What are the two stages (i.e., sets of reactions) of photosynthesis and where do they occur? What are the reactants and the products of each stage, and how are the two stages linked {yes, some are the answer to question 3}?

Light reaction (thylakoid membrane) -O2, ATP, NADPH Calvin Cycle (stroma) -Sugar, NADP, ADP

What are the raw materials (reactants) that plants need to do photosynthesis, and how do plants get each one? Relate it to leaf anatomy. IOW, which structures are used to obtain each type of raw material?

Light, H20, CO2

What coenzymes (2 main ones mentioned in this lecture, 4 total) are used in aerobic cellular respiration, and what are their reduced and oxidized forms{just their abbreviations, NOT their full structure, although that would be great to know.}

NAD+ (becomes reduced to NADH) -Nicotinamide adenine dinucleotide FAD (becomes reduced to FADH2)

Give the main function of plasma membranes. How is it related to homeostasis?

Regulation of material passing through the cell; both inputs and outputs.

What does it mean to say that a membrane is "selectively or differentially permeable?"

Only certain molecules can pass through the membrane due to cellular regulation.

Explain how receptor-mediated endocytosis works. What is special about this type of endocytosis?

Pick and choose which molecules to bring in, need a receptor protein to shape-match and bind to specific molecules.

Review: What is the difference between reactants and products?

Reactants are inputs; products are outputs

Define reduction-oxidation reactions(RedOx). What happens during reduction?What happens during oxidation? {two ways of answering last two questions} Are these types of reactions always paired together?

Redox: Short for reduction-oxidation reaction; a chemical reaction in which electrons are lost from one substance (oxidation) and added to another (reduction). Oxidation: The loss of electrons from a substance involved in a redox reaction; always accompanies reduction. Reduction: The gain of electrons by a substance involved in a redox reaction; always accompanies oxidation. Yes, oxidation and reduction always go together because an electron transfer requires both a donor and an acceptor.

Turgor pressure

The pressure of exerted by water inside the cell pushing against the cell wall.

What is aerobic respiration?

Respiration in the presence of oxygen

If the environment of an enzyme is not at its optimal temperature and pH, what feature of the enzyme is affected and why? {Although the feature affected by each condition is the same, the reason why it is affected is not. Think back to macromolecule structure.}

Since enzymes are proteins, the 3rd level of the protein's macromolecular structure is denatured.

Important terms to know and understand that relate to enzymes: substrate, activation energy, active site, enzyme-substrate complex, optimum temperature and optimum pH.

Substrate: 1. A specific substance (reactant) on which an enzyme acts. Each enzyme recognizes only the specific substrate or substrates of the reaction it catalyzes. 2. A surface in or on which an organism lives. Activation energy: The amount of energy that reactants must absorb before a chemical reaction will start. Active site: The part of an enzyme where a substrate molecule attaches; typically, a pocket or groove on the enzyme's surface.

Tonicity

The ability of a solution surrounding a cell to cause that cell to gain or lose water.

Give a complete description of the Fluid-Mosaic Model. Why is the plasma membrane said to be asymmetrical and not static (it is dynamic instead)?

The currently accepted model of cell membrane structure, depicting the membrane as a mosaic of protein molecules suspended in a fluid bilayer of phospholipid molecules. It is constantly moving because of cholesterol molecules spaced in between phospholipids, forcing it to remain fluid.

Osmosis

The diffusion of free water across a selectively permeable membrane

Osmotic pressure

The pressure necessary to prevent osmosis into a given solution when the solution is separated from the pure solvent by a semipermeable membrane.

Understand how the concentration of the substrate and product of an enzymatic reaction affects the direction and rate of the reaction.

The rate of a chemical reaction increases as the substrate concentration increases. Enzymes can greatly speed up the rate of a reaction. However, enzymes become saturated when the substrate concentration is high.

Explain how ATP cycles with ADP, and what does phosphorylation mean? REPEAT: Which bond is 'THE BOND' in ATP that we care about? IOW, which one matters to doing cellular work?

The transfer of a phosphate group, usually from ATP, to a molecule. Nearly all cellular work depends on ATP energizing other molecules by phosphorylation.

How do cells extract the energy in glucose to use for their cellular processes (work)?Why stepwise?IOW, review, what advantage is there for breaking down glucose slowly? Why not break it down all at once?Why do we need ATP at all?Why not use glucose directly?

We would explode if it was all broken down at once- too much energy would be released

What are the basic reactants {answer to question 3} and products of photosynthesis? Which reactant is reduced and which is oxidized in photosynthesis?

light energy + 6CO2 + 6H20 -> C6H12O6 + 6O2