Biology 1 Exam 2 Study Guide
Biology 1 Exam 2 Study Guide BSC2010
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This 11 page Study Guide was uploaded by clb13m on Monday February 15, 2016. The Study Guide belongs to BSC2010 at Florida State University taught by Dr. Steven Marks in Fall 2015. Since its upload, it has received 58 views. For similar materials see Biological Science 1 in Biological Sciences at Florida State University.
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Date Created: 02/15/16
Objectives for Lecture 9 Know the difference in resolution and magnification between light and electron microscopes. o Light Microscopes: up to 1000x magnification, 0.2 micrometers resolution o Electron microscope: 1,000,000x magnification; ~1nm resolution Understand the process of cell fractionation based on centrifugation and know what the purpose of cell fractionation is. o Cell fractionation allows the purification and study of cellular components (organelles). You centrifuge for a certain period of time, the longer the time the heavier mass separates more. Pellet on the bottom forms with cellular debris/organelles. Know what the differences in cell structure are between prokaryotic cells and eukaryotic cells o Bacteria are prokaryotes. Animals, fungi, protists, and plants are eukaryotes. o Similarities: Selectively permeable plasma membrane; cytoplasm (semifluid mixture of water and organic and inorganic compounds); chromosomes (carry genes; made of DNA and protein); ribosomes (make proteins) o Differences: Eukaryotes have internal, membrane bound organelles – particularly a nucleus, prokaryotes do not Know that most eukaryotic cells are between 10100 micro meters in diameter, whereas most prokaryotic cells are about 1 micro meters in diameter. Know the following terms, plasma membrane, cytoplasm, nucleus, cell wall, ribosomes, chromosomes. o Plasma membrane – membrane of lipids and proteins that forms the external boundary of the cytoplasm of a cell or encloses a vacuole, and that regulates the passage of molecules in and out of the cytoplasm. o Cytoplasm – fluid (water/organic/inorganic compounds) in cell o Nucleus – a dense organelle present in most eukaryotic cells, typically a single rounded structure bounded by a double membrane, containing the genetic material. o Cell wall – a rigid layer of polysaccharides lying outside the plasma membrane of the cells of plants, fungi, and bacteria. In the algae and higher plants, it consists mainly of cellulose. o Ribosomes – free ribosomes (loose in cytoplasma); bound ribosomes (attached to ER); made in nucleolus. o Chromosomes DNA; chromatin is the chromosome fibers Know the general structure and function Be able to identify each of these organelles in photographs or drawings of cells. o Plasma membrane – is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. o Nucleus – double membrane; prorated by nuclear pores; ribosomes & mRNA made in nucleolus. o Ribosomes – synthesize proteins (free or bound); get transported to other parts of the cell by transport vesicles. o Rough ER – ribosomes in RER make membrane proteins and proteins to be secreted; these proteins are transported to other parts of cell by transport vesicles; membrane factory for cell. o Smooth ER – synthesis of lipids; storage of calcium o Golgi – sorts and moves membranes and proteins made in ER; vesicle merges and dumps sack from the ER to the golgi. The stuff in the sack gets sorted/relocated to its correct place. o Lysosome – contain enzymes that help digest food or defective macromolecules or organelles to recycle their components Phagocytosis – lysosome digests food in the food vacuole that was taken into the cell Autophagy picks up organelles thats dying o Mitochondria – membrane bound organelle; have own DNA/ribosomes for making its own proteins; transforms energy from one form to another; used for cellular respiration o Chloroplast – membrane bound organelle; have own DNA/ribosomes for making its own proteins; transforms energy from one form to another; used for photosynthesis Understand that the pathway for the flow of materials to the cell surface is from ER to the Golgi, to Golgi vesicles, to the plasma membrane o Vesicle goes from rough ER to cis Golgi, gets transported to transexual golgi, then is determined whether it gets transported to the lysosome, plasma membrane, or wherever the protein inside the vesicle tells it to go (mRNA) Know that cell shape and cellular movements are mediated by the cytoskeleton, which is composed of microtubules (tubulin protein), microfilaments (actin protein), and intermediate filaments (keratin protein) Know the major structural differences between animal and plant cells. o Plant cells have central vacuoles (bag of salty fluid that increases size of cell) with minimal cytosol increase, thylakoids (in the chloroplast), chloroplasts, and cell walls. o Animal cells doesn’t have any of that. Lecture 10 Be able to describe the structure of biological membranes (lipid bilayers + membrane proteins). o The core of the cell membrane is a phospholipid bilayer (hydrophilic head, hydrophobic tail). o There are integral membrane proteins (embedded in the phospholipid bilayer); parts of protein that does not touch water is hydrophobic. o There are peripheral membrane proteins (attached to integral proteins); they’re hydrophilic. o Fluidity is the ability of the phospholipids (and membrane proteins) to move. Most phospholipid movement is lateral. Membrane fluidity is affected phospholipid composition – saturated versus unsaturated. Unsaturated means more fluidity; saturated means more viscous. Cholesterol buffers change fluidity against changes in temperature (keeps it more fluid even if temperature drops) Be able to list the functions of membrane proteins o Transport moves molecules across membrane o Surface for chemical reactions – enzymes o Hormone perception receptors; listens and responds , makes protein receptor respond to hormone signals. o Celltocell attachment they attach o Cellcell recognition recognizes each cell to build tissue o Attachment points of cytoskeleton and Extracellular proteins to membrane – attaches protein to cytoskeleton and extracellular matrix (ECM) Know that biological membranes are semipermeable (more permeable to some solutes than others) and know how the size., polarity, and charge affects the permeability of solutes through membranes. o Bigger substance/more charge = less permeable o Nonpolar substances move easiest = more permeable (O2 and CO2 move easily without transport proteins) o Increase in size restricts movement across membrane (needs transport proteins) o Increase in charge restricts movement across membrane (needs transport proteins) o More polar the molecule restricts the movement across the membrane because bilayer has hydrophobic (nonpolar) tail. Understand the terms passive transport and diffusion, and osmosis. Be able to make predictions about the direction that solutes or water will move if given the concentrations of solutes across a membrane. o Passive transport – transports small molecules without the requirement of ATP; moves substances from high to low concentration o Diffusion – moves small molecules from high to low concentration o Simple diffusion – doesn’t use transport proteins/channels/carrier proteins; substances pass through semipermeable membrane o Facilitated diffusion – needs channels/carrier proteins o Active transport – cell uses energy to move substances o Osmosis – diffusion of water from lower solute concentration to higher solute concentration Be able to correctly use the terms hypotonic, isotonic and hypertonic. o Hypotonic – solute concentration outside cell is less than that inside of the cell; cell gains water; in animal cell its lysed (Bursts); in plant cell its turgid (best state) o Isotonic – solute concentration is same as that inside cell; no net water movement across plasma membrane; in animal cell its normal; in plant cell its flaccid (thirsty) o Hypertonic – solute concentration is greater than that inside the cell; cell loses water; in animal cell its shriveled; in plant cell its plasmolyzed (real thirsty) Lecture 11 Be able to explain the difference between simple diffusion and facilitated diffusion. o Simple diffusion – movement of molecules from regions of high concentration to regions of low concentration o Facilitated diffusion – use of channels and carrier proteins. Channels provide a pore for movement of substances. Carrier proteins flipflop substances across membrane. Both proteins are highly specific and are regulated o Except for gases like O2, N2, and CO2, nearly all substances that diffuse across cell membranes move by facilitated diffusion through channels or carriers. Channels and carriers are highly specific for the molecules or ions they transport and they are regulated. o Water moves through the channel aquaporin. Understand active transport is the transport of a substance against its chemical (or electrochemical) gradient; it requires the input of energy. Proteins that actively transport ions are often called ion pumps. The SodiumPotassium pump is the main ion pump in animal cell membranes. It pumps 3 NA+ out and 2 K+ in the cell. So the cell becomes more negative inside. Other organisms mostly use proton pumps (H+ is pumped out). Understand that the active pumping of ions creates both a chemical gradient of the pumped ion and a membrane voltage (membrane potential). Most cells have a membrane potential of about 100 mV (inside is more negative). Understand that the electrochemical gradient of the pumped ion can be coupled to the movement of other substances by means of cotransport. o Cotransport – uptake of sugars, amino acids, or ions, is coupled to uptake of the pumped ion Know what endocytosis is and what types of substances are taken up by phagocytosis, pinocytosis, and receptormediated endocytosis o Exocytosis – used to transport materials out of the cell o Endocytosis – used to transport materials into the cell. 3 types: phagocytosis (larger molecules; eats) pinocytosis (small molecules; drinks) receptormediated endocytosis (vesicle is coated by receptors and only has receptors and corresponding ligands in vesicle) Lecture 12 Be able to define metabolism and know the difference catabolism, and anabolism and whether they consist of energy generating or consuming reactions o Metabolism is the sum total of all the chemical reactions that occur in an organism. o Catabolism – energy generating (releases energy) by breaking down complex molecules into simpler compounds. EXOTHERMIC Ex: Cellular respiration o Anabolism – energy consuming to build complex molecules from simpler ones. ENDOTHERMIC Ex: photosynthesis Know the difference between potential and kinetic energy, and know that for most situations in biology potential energy is the energy in chemical bonds. Cleaving those bonds releases that energy, which can be used to do work (drive a chemical reaction, cause movement, etc.). o Potential Energy – energy that matter possesses because of its location or structure. In biology PE is mostly in the form of chemical energy. Energy is stored in chemical bonds. o Kinetic Energy – is energy associated with motion. Heat, which is associated with the random movement of atoms or molecules, is a form of kinetic energy. Be able to state the first and second laws of thermodynamics and understand what entropy is o First law: energy can be transferred or transformed from one form to another, but it can’t be created or destroyed. The amount of energy in the universe is constant. o Second law: every energy transfer or transformation increases the entropy of the universe. o Entropy is a measure of disorder or chaos. During every energy transfer or transformation, some energy becomes unusable, and is often lost in the form of heat. Heat dissipates randomly in the universe, it is more chaotic than the energy in its original form, and thus increases the entropy of the universe. Know what free energy is, how it relates to chemical reactions, what DG is, and what a positive or a negative DG means in terms of the direction of a chemical reaction (spontaneous vs nonspontaneous) o Free energy (G) – amount of energy that is available to do work. Not all the energy in a system is usable, some is entropy. o ∆G – change in free energy. For chemical reactions, at equilibrium is 0. o If negative – there is a net release of energy the reaction occurs spontaneously.. If positive, there is a net gain of energy during the reaction then energy must be added for the reaction to occur. Be able to correctly use the terms exergonic and endergonic when describing a chemical reaction. Understand how cells couple the hydrolysis of ATP to driving unfavorable (anabolic,nonspontaneous, +DG) chemical reactions o Exergonic rxn – release energy, negative ∆G, occurs spontaneously. In general, catabolic reactions are exergonic. o Endergonic – requires energy, positive ∆G, does not occur spontaneously. In general, anabolic reactions are endergonic o To do work, which requires energy; cells couple these endergonic processes (transport, chemical) to exergonic processes (mechanical). This is energy coupling. Most energy coupling in cells is mediated by ATP. o Hydrolysis of ATP is exergonic. ∆G of 7.3 kcal/mol. ATP + H20 = ADP + P + Energy. o Transport work – ATP phosphorylates transport proteins o Mechanical work – ATP binds noncovalently to motor proteins, then is hydrolyzed Understand the ATP cycle – energy from catabolic reactions (exergonic, energyreleasing processes) is used to regenerate ATP. o Cells hydrolyze ATP to ADP + P and couple the energy that is released in this exergonic reaction to doing work. Then the ADP + P has to be converted back into ATP, this reaction is endergonic and requires energy. Lecture 13 Know that o Virtually all biochemical reactions are catalyzed by an enzyme. o A catalyst is an agent that increases the rate of a chemical reaction, without being consumed by the reaction. It is reusable. Enzymes are a class of proteins that act as catalysts. Know what activation energy refers to and what affect enzymes have on activation energies. Be able to interpret plots of energy changes during an enzyme reaction and identify the activation energy and Delta Gamma o Activation energy – an energy barrier that must be overcome to start the reaction. o Enzymes don’t provide the energy to overcome the energy of activation, they actually lower the energy of activation. Enzymes catalyze reaction. o Reactants energy higher than products energy = exergonic reaction; ∆G is negative o Reactants energy lower than products energy = endergonic reaction; ∆G is positive Understand that each enzyme is highly specific for the reaction it controls. Be able to correctly use the terms substrates and products when talking about enzyme catalyzed reactions. o Substrate is the reactant. Product is the product. Specificity of enzyme activity is because only the proper substrate fits into the enzyme’s active site like a key fits into a lock. Know what an enzyme's active site is and know the generalized catalytic cycle of enzymes and the role of changes in enzyme shape (conformation) to the reaction it controls o Enzyme activity can be affected by anything that alters the 3D structure of the enzyme or the accessibility of the enzyme’s active site. Heat and pH cause denaturation of the enzyme Know what a cofactor is. o Cofactors are nonprotein enzyme helpers. Cofactors may be inorganic (such as the metals zinc and iron) or organic (an organic cofactor is called a coenzyme). Most vitamins are important in your diet because they’re coenzymes. Know how the activity of enzymes depends on temperature and pH and be able to explain why enzyme activity varies with changing temperature and pH. o Higher temperatures promote faster reactions, but only up to a point. Excess heat disrupts chemical bonds that hold enzyme in its active configuration. pH is important for enzyme structure and function. H+ concentration (pH) is needed for ionic and hydrogen bonds of proteins secondary and tertiary structure. Main Point: Enzymes speed the rate of chemical reactions by reducing the activation energy of that reaction. Each enzyme is specific for a certain chemical reaction. The substrate binds to a pocket on the enzyme (active site). This results in a change in the enzymes shape and causes the substrate to be turned into the product. The product is then released from the enzyme and the enzyme returns to its original shape and the process is repeated with a new molecule of the substrate. Lecture 14 Enzyme Regulation Cells can control enzymatic reactions by controlling the production of the enzyme (regulation of gene activity) and by regulating the activity of the enzyme itself. Know what allosteric regulation of enzymes means, how enzymes are controlled by activators and inhibitors, the difference between competitive and noncompetitive inhibition. o Noncompetitive inhibitor – allosteric inhibitor, does not bind to the active site, does not compete with the substrate. Noncompetitive inhibitors are more potent because they cannot be overpowered by an increased amount of substrate. Alters shape of enzyme once it binds to nonactive site. o Competitive inhibitor binds to the active site, competes with substrate of the enzyme. A competitive inhibitor can be overpowered by increasing the concentration of the substrate. Redox Reactions: Be able to state what a reduction is and what an oxidation is, know that: o In redox reactions electrons are transferred from less electronegative atoms to ones that are more electronegative along with the release of energy (exergonic). Spontaneous chemical reactions (exergonic) move toward increased oxidation state. o Reduction – reactions in which an electron is gained o Oxidation – reaction in which an electron is lost Know that NAD+ is a temporary electron acceptor (is reduced to NADH, which is an electron donor) in many biological redox reactions. o NAD+ is a temporary electron acceptor (is reduced to NADH, which is an electron donor (H+)) in many biological redox reactions. Respiration and Glycolysis Know that in respiration glucose is oxidized to CO2 and oxygen is reduced to water and that the energy released is used to make 32 ATPs Know that respiration takes place in three sets of reactions (glycolysis, Krebs cycle, and electron transport chain). o Glycolysis – cytosol o TCA – mitochondrial matrix o ETC – inner mitochondrial membrane Be able to write the overall reaction for glycolysis and for respiration. o Glucose + 2 ADP + 2 NAD+ → 2 pyruvate + 2 ATP + 2 NADH + 2H+ o Second part of respiration: 2 pyruvate → 6CO2 + 6H2O + 30 ATP Lecture 15 Know that the pyruvate produced by glycolysis is transported into the mitochondrion, cleaved to CO2 + acetyl CoA in a reaction generates a reduced NADH. The acetyl CoA is then attached to a 4 carbon acid (oxaloacetate) to form the 6 carbon acid (citrate). Be able to outline the major events in the citric acid cycle (TCA cycle, Krebs cycle), you don’t need to be able to name all the compounds or the reactions in order but you should know that a 4 carbon acid is converted to a six carbon acid by addition of an acetyl group, then the six carbon acid is converted back into the 4 carbon acid and along the way 2 CO2s are released, and 3 NADH, one FADH, and one ATP are formed. o A 4 carbon acid is converted to a 6 carbon acid by addition of an acetyl group, then the 6 carbon acid is converted back into the 4 carbon acid (releasing 2 CO2s, 3 NADH, 1 FADH, and 1 ATP) From original molecule of glucose (2 pyruvate = 2 acetyl CoA) yields 2 ATP, 6 NADH, 2 FADH2, 4 CO2 from 2 turns in the TCA. CO2 is only released in the conversion of the acetyl CoA (1 CO2 for each pyruvate 2 CO2 released total), and in the citric acid cycle (2 CO2 for each acetyl CoA 4 CO2 total) ONLY 6CO2 is released. none is released in glycolysis or electron transport chain. Lecture 16 The mechanism by which electron transport synthesizes ATP. o The NADH and FADH formed by glycolysis and the citric acid cycle transfer their electrons to the electron transport chain, which is a series of proteins in the inner mitochondrial membrane. These electrons are passed from one member of the chain to the next, releasing little bits of energy along the way. Finally the electrons are passed to oxygen (the final electron acceptor) to make water. The energy released during electron transport is used by the electron transport proteins to move protons from the mitochondrial matrix across the inner mitochondrial membrane into the intermembrane space (between inner membrane and outer membrane). This results in a pH and electrical gradient across the inner mitochondrial membrane. The energy in this electrochemical gradient is used to make ATP from ADP + Pi. Protons flow through an ATP synthase enzyme (a proton channel in the inner mitochondrial membrane) back into the mitochondrial matrix. The energy released as the protons diffuse back into the matrix is used by the ATP synthase to convert ADP + Pi into ATP. Essentially what is happening is that a proton pump is being run backwards to make ATP. You should understand what fermentation is, what it produces, under what conditions does it occur. Know that organisms do fermentation to regenerate NAD+ in order to keep glycolysis running in the absence of O2. Know that the product of fermentation is ethyl alcohol in yeast (and many bacteria) but is lactic acid in our muscle cells. o Fermentation – alternative pathway for energy production that is used when oxygen is scarce. Purpose: to regenerate NAD+ so glycolysis can continue. 2 ATP and 2 NADH is produced. Occurs when there is no oxygen. Happens in anaerobic organisms, facultative anaerobes, and active muscle cells. Lecture 17 Know what a photoautotroph, and a heterotroph are and which organisms fall in each category. o Photoautotroph – selffeeders; use light energy to synthesize organic compounds. Plants. o Heterotrophs – consumers; live on compounds produced by other organisms. Not plants. Be able to write an overall reaction for photosynthesis and know which molecules are oxidized and which are reduced. Know what molecule the oxygen comes from that is formed in photosynthesis. o Photosynthesis – the process that converts solar energy into chemical energy. Directly or indirectly, photosynthesis nourishes almost the entire living world. It takes place in the chloroplasts. o Water is oxidized (lose e) ; CO2 is reduced (gain e) o O2 comes from H20 not CO2. Know what stomates are and what their role is in photosynthesis in land plants. o Stomates – pores on the leaf that takes in CO2 and releases O2 and water Be able to describe the structure of a chloroplast, be able to name its parts and identify them in a picture (inner and outer membranes, stroma, thylakoid membranes, thylakoid space) and know which reactions take place in each compartment. o Role photosynthesis occurs here nigga o Chloroplast: has stack of thylakoids, inside thylakoid is the thylakoid space, stoma (fluid in the chloroplast), inner and outer membranes. o Light reactions on the thylakoid membranes. Energy used to split water. H+ ions and electrons from the split of water are used to make ATP and reduced NADPH. o Calvin cycle in stroma. Energy in ATP and reducing power of NADPH used to synthesize sugar from CO2. Know what is formed by the light reactions and the Calvin cycle reactions, know where each of these reactions takes place. o ATP, O2, and NADPH is formed by the light reactions, which takes place in the thylakoid stacks o NADP, CH2O, and ADP + P is formed from calvin cycle, which takes place in the stroma. Understand the relationship between an absorption spectrum and an action spectrum, know what colors (wavelengths) of light are absorbed by chlorophyll and what change occurs in chlorophyll when it absorbs light. o Absorption spectrum – wavelengths of light absorbed by chloroplast pigments o Action spectrum – rate of photosynthesis measured in the lab (amount of O2 released) when plants exposed to visible light of specific wavelengths. o Chlorophyll A – absorbs violetblue o Chlorophyll B – absorbs redblue Both reflect green o Carotenoids – absorb bluegreen and violet. Reflects yellow, red, and orange Know the role of the light harvesting complex and chlorophyll b and carotenoid pigments in photosynthesis and know the structure of the photosystems (light harvesting complex containing proteins and chlorophyll a, and carotenoids surrounding the reaction center, which consists of proteins holding a chlorophyll a). o Light harvesting complexes – proteins, chlorophylls, and carotenoids AKA photosystems o Energy from light is transferred to a chlorophyll a at the reactioncenter complex. This chlorophyll loses an electron to an electron transport chain. The lost electron is replaced from water. Be able to describe the path taken by an electron during the light reactions and know where ATP is made, NADP+ is reduced and where water is split. o Electrons move from PSII through electron transport to PSI, the electrons are boosted to an even higher energy level by a second photon and that energy is used to reduce NADP+ o ATP is produced in ETC o Water is split in photosystem 2 o NAP+ is reduced in photosystem 1 with the help of NADP+ reductase Be able to compare the reactions in respiration and photosynthesis in terms of their energetics, where the electrons for the redox reactions come from, what compartment protons are pumped into for ATP production, and where the electrons and protons ultimately end up. Lecture 18 Know that the Calvin cycle takes place in the stroma of the chloroplast and uses the products of the light reactions (ATP and NADPH) to fix CO2 into carbohydrates. Know the reaction that is catalyzed by the enzyme Rubisco (ribulose bisphosphate or RuBP + CO2 forms 2 molecules of the 3 carbon acid 3phosphoglycerate) and know how many turns of the Calvin cycle are required to synthesize one glucose molecule. o The Calvin cycle takes place in the stroma of the chloroplast and uses the products of the light reactions (ATP and NADPH) to fix CO2 into carbohydrates. o The enzyme rubisco (ribulose biphosphate carboxylase) catalyzes the reaction where CO2 is joined with the 5 carbon sugar RuBP to make 2 molecules of the 3 carbon acid 3 phosphoglycerate. o It takes 3 turns of the calvin cycle to make one net G3P and 6 turns to fix enough carbon for one glucose molecule. 9 ATP and 6 NADPH are needed to make one G3P. Therefore, 18 ATP and 12 NADPH are needed to make one glucose molecule. Know what photorespiration is and under what conditions it occurs. o In photorespiration CO2 is released without formation of ATP or NADH and the products of the calvin cycle are wasted. Be able to explain the differences between C3, C4 and CAM photosynthesis and how C4 and CAM avoid the problem of photorespiration. o On hot dry sunny days 30% or more of the carbon fixed by the photosynthesis can be lost through photorespiration in C3 Plants. C3 photosynthesis is probably more efficient when temperatures are low and water is abundant o C4 photosynthesis avoids photorespiration – tropical grasses like corn and sugar cane. Uses more ATP than C3 photosynthesis. o CAM photosynthesis – cacti and other succulents have this type. They open their stomates at night, fix CO2 into malic acid, close their stomates in the day, break malic acid down to pyruvate + CO2 and run the Calvin cycle. Be able to explain the endosymbiotic hypothesis of the origin of mitochondria and chloroplasts and be able to provide four pieces of evidence that support this hypothesis. o Endosymbiotic hypothesis – chloroplasts and mitochondria are thought to be descendants of bacteria taken up and adopted by host cells in two separate events. o Evidence for the Origin of chloroplasts: 1) Chloroplasts: arise only by division of other chloroplasts 2) Are surrounded by a double membrane 3) Contain DNA for making some of their own proteins 4) DNA sequence comparisons shows chloroplasts arose from a cyanobacterial endosymbiont (prokaryote)
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