Biology Study Guide

Study guide for exam 2. Chapter 7 ‐ Membrane Structure and Function  Define  fluid mosaic model  semi‐permeability  amphipathic molecules  What is the effect of unsaturated fatty acids on membrane structure and properties?  What is the effect of cholesterol on membrane structure and properties?  Membrane Proteins and Their Functions  peripheral  Integral proteins  Classification based on function (transport, enzymatic activity, cell‐cell interactions, etc.)  How do proteins get to cell surface?  The role of ribosomes, ER, Golgi  Semipermeability  Which molecules pass through membrane easily (polar vs. non‐polar, hydrophobic vs. hydrophilic, etc.)  The role of ion channels, transport proteins, etc.  Diffusion – what is it? How does it work? Does it require energy? Is it a type of active or passive transport? What is concentration gradient? What is facilitated diffusion?  Osmosis – what is it? How does it differ from diffusion?  Tonicity – hypotonic, isotonic, hypertonic – what does it mean?  Active transport – does it require energy? Movement of substances down or against their concentration gradient? How does sodium‐potassium pump work? What is electrochemical gradient?  Cotransport – what is it?  Bulk transport – exocytosis vs. endocytosis (pinocytosis, phagocytosis, receptor‐ mediated endocytosis) Chapter 8 ‐ Introduction to Metabolism  Define  What is metabolism? What is metabolic pathway? Substrate? Product? Enzyme? Catalyst? Active site? Cofactor? Coenzyme?  Catabolic vs. anabolic; exorgenic vs. endorgenic reactions?  Types of energy (kinetic, heat, chemical, potential )  Thermodynamics, open vs. closed system  The first and second law of thermodynamics  What is free energy?  What is energy coupling?  What is activation energy?  How do enzymes catalyze reactions (by lowering activation energy)

 Chapter 9 – Cellular respiration  What is the difference between fermentation and aerobic respiration? (one is a partial degradation of sugars that occurs without O2, the other needs O2 to produce ATP)  General formula of cellular respiration: C6H12O6 + 6 O2  6 CO2 + 6 H2O + Energy (ATP + heat)  The principle of redox reactions – energy is released when electrons are transferred during chemical reactions  what is oxidation? Reduction? What gets oxidized? Reduced? (substance that gains electrons becomes reduced, substance that looses electrons become oxidized)  What becomes oxidized during cellular respiration? (glucose)  What becomes reduced during cellular respiration? (oxygen)  What is NAD+ ? (captures electrons released during glucose oxidation)  What is electron transport chain? How does it work? What does it do? (passes electrons in a series of steps onto O2 and the released energy is used to produce ATP)  Stages of cellular respiration –  Glycolysis (breaks down glucose into two molecules of pyruvate)  The citric acid cycle (completes the breakdown of glucose)  Oxidative phosphorylation (accounts for most of the ATP synthesis)  What is the difference in substrate‐level phosphorylation and oxidative phosphorylation?  ATP formed in glycolysis and the citric acid cycle is produced by substrate level phosphorylation = transfer of a phosphate from one molecule onto ADP  ATP formed during the transfer of electrons down the electron transport chain is produced by oxidative phosphorylation (oxygen and ATP synthase are involved) – 90% of ATP in cellular respiration is produced this way  Glycolysis –  What is it? (Breaking down glucose into two molecules of pyruvate)  What do you gain during glycolysis? (invest 2 ATP molecules and gain 4 ATP molecules and 2 NADH  How many carbons does the product of glycolysis have? (3)  Oxidation of pyruvate to acetyl CoA –  when does it occur? (only when oxygen is available) What happens when oxygen is not available?  How many carbons does the product of have? (Acetyl CoA has 2 carbons)

Competitive vs. non‐competitive inhibition. What is allosteric regulation? Saturation of enzyme with substrate – what does that mean? What is equilibrium? What can you do to disturb equilibrium and move reaction if forward or reverse direction? What is ATP? Structure of ATP.

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What do you gain during oxidation of pyruvate into acetylCoA? (CO2 and 1 NADPH molecule) Citric acid cycle –  What does it do? (The cycle oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH2 per turn)  how many turns are needed per one molecule of glucose? (2 turns) Oxidative phosphorylation –  Where is the energy at this step? (NADH and FADH2)  What happens next? NADH and FADH2? (They donate electrons to the electron transport chain, which powers ATP synthesis via oxidative phosphorylation)  What happens when the electrons when they are passed down the electron transport chain? (Electron transfer in the electron transport chain causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space)  How is ATP made during oxidative phosphorylation? (ATP synthase uses the flow of H+ down their concentration gradient to drive phosphorylation of ATP)  What is chemiosmosis? (the use of energy in a H+ gradient to drive cellular work) How many molecules of ATP are produced during cellular respiration? (32 at most) Fermentation –  What is it? (Fermentation consists of glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis)  When do cells use it? What types are there? (Fermentation occurs when the cells experience lack of oxygen and it uses substrate‐level phosphorylation instead of an electron transport chain to generate ATP. There are multiple types. Two common types are alcohol fermentation and lactic acid fermentation) Comparing Fermentation with Anaerobic and Aerobic Respiration  All use glycolysis (net ATP = 2) to oxidize glucose and harvest chemical energy of food  In all three, NAD+ is the oxidizing agent that accepts electrons during glycolysis  The processes have different final electron acceptors: an organic molecule (such as pyruvate or acetaldehyde) in fermentation and O2 in cellular respiration  Cellular respiration produces 32 ATP per glucose molecule; fermentation produces 2 ATP per glucose molecule What is the difference between obligate and facultative anaerobes

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Chapter 10 – Photosynthesis  What is photosynthesis?  Autotrophs vs. heterotrophs

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Structure of the leaf and chloroplasts (stomata, mesophyll, grana, thylakoids, stroma, etc. ) Chemical reaction of photosynthesis: 6 CO2 + 6 H2O + Light energy  C6H12O6 + 6 O2  Where does the oxygen come from? Water or CO2?  Which substrate becomes reduced and which becomes oxidized? What substrate donates electrons?  Which molecule becomes oxidized and which reduced in cellular respiration?  When you look at the reaction, where does the dry mass of the plant come from? Air? Water? Sun? Soil? All of those? Stages of photosynthesis?  What exactly happens in the light phase? 4 things – o Split H2O o Release O2 o Reduce NADP+ to NADPH o Generate ATP from ADP by photophosphorylation  What exactly happens in the dark phase/Calvin cycle? 2 things‐ o forms sugar from CO2, using ATP and NADPH o begins with carbon fixation, incorporating CO2 into organic molecules What is light? Wavelength? Visible lightwavelength ? Absorption? Reflection? What is the wavelength that chlorophyll a and b absorb? Why do chloroplast and chlorophyll appear grean? What is a photosystem? Parts of a photosystem? (reaction‐center complex and light‐ harvesting center) What is the difference between photosystem I and II (PSI and PSII)? Describe linear flow of electrons. Utilizes both systems (PSI and PSII), both systems harvest light in form of a photon and transfer the photon to the main pigment (P680 or P700), which then become excited. Their natural tendency to come back to ground state results in loss of a electron (they transfer it to primary electron acceptor). This creates an electron hole that needs to be filled. The PSII system pigment (P680) becomes filled by an electron coming from splitting of H2O (releasing O2 in the process), while PSI system pigment (P700) fills its hole by obtaining the electron originally released by PSII pigment (P680). When the electron is moved from PSII to PSI it is handed down by a system of protein complexes similar to electron transport chain in mitochondria and during the transfer from PSII to PSI, ATP is produced. Describe cyclic electron flow Basics about Calvin cycle –  Carbon fixation (catalyzed by rubisco)  Reduction  Regeneration of the CO2 acceptor (RuBP) Photorespiration – what is it? When does it occur? (when there is not enough CO2 available – rubisco will use O2 instead of CO2) What is the product of photorespiration (2 carbon product, release of CO2, no sugar, no ATP  how do plants deal?

 Chapter 11 – Cell communication  Understand the difference between local and long distance signaling  What is a ligand? What is a hormone? Why some cells respond to a ligand and some don’t?  The three stages of cell signaling pathway (reception, transduction, response)  Reception  Ligand binds to a receptor ‐> what happens to the receptor?  Plasma membrane‐bound vs. nuclear membrane‐bound receptors –  What is different about their ligands? (nuclear receptors bind ligands that can pass through the plasma membrane – non‐ polar and small molecules)  What is different in their mode of action? (nuclear receptors act as transcription factors meaning they do not activate cytoplasmic proteins)  Three types of plasma membrane receptors (G protein‐coupled, Receptor tyrosine kinases, Ion channel receptors)  Understand G protein‐coupled signaling in detail  Transduction – multistep process  Frequently based on protein activation and inactivation by phosphorylation and dephosphorylation, respectively (what are kinases and phosphatases?)  What are second messengers? (small, nonprotein, water‐soluble molecules or ions that spread throughout a cell by diffusion, like cyclic AMP and calcium ions)  Response –  What types of responses are there? (it could be activation or inactivation of genes, regulation of activity of enzymes, or change in shape of the cell)  Fine‐Tuning of the Response via amplification of the signal, specificity of the response, overall efficiency of response, and termination of the signal  Apoptosis – What is it? How is it achieved? Why is it important? What triggers it?

C4 plants – mesophyll cells fix CO2 and deliver it to bundle‐sheath cells that use it in Calvin cycle (ATP is used in the process, so it “costs” the plants energy to do this)  CAM plants ‐ open their stomata at night, incorporating CO2 into organic acids, CO2 is released from organic acids and used in the Calvin cycle during the day Compare and contrast how ATP is produced in mitochondria vs. chloroplasts

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