BIOL 150 Lecture Exam II Study Guide PDF

BIOL 150 LECTURE EXAM II STUDY GUIDE MEMBRANE STRUCTURE 10 exam questions Know the 3 types of molecules that are important for cell membrane structure: lipids, proteins, carbohydrates Know the particular types of lipids found in membranes: phospholipids Know why this lipid is important: it is an...

BIOL 150 LECTURE EXAM II STUDY GUIDE MEMBRANE STRUCTURE 10 exam questions Know the 3 types of molecules that are important for cell membrane structure: lipids, proteins, carbohydrates Know the particular types of lipids found in membranes: phospholipids Know why this lipid is important: it is an amphipathic molecule -- has both hydrophilic & hydrophobic regions Know an important property of membrane proteins: they have both hydrophilic & hydrophobic regions Know what the current model of membrane structure is: fluid -- mosaic model Know 2 important properties of membranes: membranes are fluid because the components can move; membranes are held together mainly by hydrophobic interactions Know which features affect membrane fluidity: Phospholipids with double bonds are fluid at lower temperatures; cholesterol in the membrane makes it less fluid at body temperature Know other properties of membranes: phosphate head group of the phospholipid is hydrophilic so it interacts with a watery environment; fatty acid tails of the phospholipid are hydrophobic so they avoid a watery environment & form the interior of the phospholipid bilayer Know the 2 main groups of membrane proteins: integral & peripheral proteins Know the difference between the 2 groups: integral proteins are embedded in the membrane & often span the entire membrane; peripheral proteins are attached to the inside or outside of the membrane but are not embedded in the membrane Know why membrane carbohydrates are important: cell -- cell recognition Know properties of membrane oligosaccharides: less than 15 residues long & attached to membrane lipids (called glycolipids) or mostly attached to membrane proteins (called glycoproteins) Know the functions of membrane proteins: transport, enzyme activity, signal transduction, intercellular joining, cell -- cell recognition, attachment to cytoskeleton & to the extracellular matrix MEMBRANE TRANSPORT 10 exam questions Know what selective permeability of membranes means: hydrophobic molecules pass through the membrane; ions & polar molecules cannot pass through the membrane due to the phospholipid bilayer Know how hydrophilic substances cross membranes: use protein channels & protein carriers Know the difference between active & passive transport processes: active transport needs ATP for energy & moves substances against concentration gradients; passive transport does not need energy & always moves substances from high concentration to low concentration regions Know what drives passive transport processes: inherent kinetic energy called thermal motion or heat Know what a hypertonic, hypotonic, isotonic solution is: hypertonic -- higher solute concentration; hypotonic -- lower solute concentration; isotonic -- equal solute concentration Know the definition of osmosis: movement of water across selectively permeable membrane Know which way water moves during osmosis: water moves from hypotonic to hypertonic Know how water moves in isotonic solutions: no net movement of water but equal movement of water in both directions Know what happens to a cell placed in hypertonic, hypotonic, isotonic solutions: hypertonic -- cell shrinks; hypotonic -- cell swells & bursts; isotonic -- no cell volume changes Know what mechanisms cells use to maintain a stable volume: cells in fresh water can have a contractile water vacuole; plant cells have a cell wall Know how plant cells react in hypertonic, hypotonic, isotonic solutions: in isotonic solution cell is limp & wilts; in hypertonic solution cell shrinks & pulls away from the cell wall (called plasmolysis); in hypotonic solution cells fills & pushes against cell wall (called turgor pressure) Know what facilitated diffusion is: polar molecules & ions move across membranes passively with the help of transport proteins; aquaporins (water channel proteins) allow large move of water across membranes; some transport proteins change shape to move molecules across membranes Know what active transport is: requires energy & pumps solutes against concentration gradients Know how large molecules such as polysaccharides & proteins cross membranes: use vesicles & exocytosis to move substances out and endocytosis to move substances in Know the 3 types of endocytosis: phagocytosis --moves large particles in; pinocytosis -- moves drops of fluid in; receptor mediated endocytosis -- need a specific receptor protein to move a specific substance in CELLULAR RESPIRATION 15 exam questions Know the 3 stages of cellular respiration & where each occurs in the cell: glycolysis occurs in cytoplasm; Krebs cycle occurs in mitochondria; electron transport chain occurs in mitochondria Know the starting substances & end products of glycolysis: starting substance is glucose & end products are pyruvic acid, net 2 ATP, 2 NADH; no carbon dioxide is produced & no oxygen is used so glycolysis can occur in the presence or absence of oxygen Know which compound can enter the Krebs cycle: acetyl Co-enzyme A Know what co-enzyme A is: a sulfur containing derivative of a B vitamin Know which high energy electron carriers are formed during the Krebs cycle: NADH & FADH~2~ Know why these molecules are important: they carry high energy electrons from glycolysis & Krebs cycle to the electron transport chain Know where the components of the electron transport chain are located: in the inner mitochondrial membrane Know what type of reactions occur in the electron transport chain: redox or oxidation/reduction reactions Know how the electron transport chain is coupled to ATP production: mechanism is called chemiosmosis Know what the energy from the high energy electrons from glycolysis & Krebs cycle is used for: that energy is used to make a hydrogen ion gradient Know what protein complex is needed for ATP production: ATP synthase Know where this protein complex is located: in inner mitochondrial membrane Know which molecule accepts the electron at the end of the electron transport chain: oxygen Know which substance is formed at the end of the electron transport chain: water Know the 3 parts of ATP synthase: cylindrical rotor, internal rod, knob with catalytic sites Know which substances can be used in cellular respiration to generate ATP: amino acids from proteins, carbohydrates, fatty acids & glycerol from fats Know how metabolic pathways are controlled & what is an important control point: pathways controlled by feedback inhibition & ATP inhibits the enzyme phosphofructokinase in glycolysis Know what fermentation produces: ethanol & carbon dioxide or lactic acid Know which stage of cellular respiration produces the most ATP: electron transport chain Know which stage produces the carbon dioxide during cellular respiration: Krebs cycle PHOTOSYNTHESIS 20 exam questions Know the difference between autotrophs & heterotrophs: autotrophs make organic molecules from carbon dioxide & water so they make glucose & oxygen as by products; heterotrophs cannot make glucose from carbon dioxide & water & so are dependent for food & oxygen on autotrophs Know the site of photosynthesis: chloroplasts Know the structural details of chloroplasts: small holes for carbon dioxide entry -- stomata; dense fluid inside the chloroplast called stroma; thylakoid membranes -- separate stroma from the thylakoid space; thylakoid membranes stacked like pancakes -- stacks called grana Know what chlorophyll is: the pigment that captures the light energy Know where the chlorophyll is located: in thylakoid membranes in 2 different photosystems Know the overall equation for photosynthesis: carbon dioxide + water + light energy -\> glucose + oxygen + water Know where the carbon & oxygen atoms in the reactants carbon dioxide & water end up in the product molecules: carbon atoms in carbon dioxide end up as carbon atoms in glucose; oxygen atoms in carbon dioxide end up as oxygen atoms in glucose & as oxygen atoms in water; oxygen atoms in reactant water end up as oxygen atoms in oxygen gas in products Know the 2 main parts of photosynthesis: light reactions & Calvin cycle Know the function of each part of photosynthesis: light reactions convert solar energy to chemical energy; Calvin cycle converts carbon dioxide to sugar molecules Know the function of the pigment molecules in photosynthesis: pigment molecules absorb some wavelengths of visible light & reflect (not absorb) other wavelengths of visible light; reflected wavelengths are the colors we see Know the function of a spectrophotometer: instrument that measures the amount of light absorbed or transmitted through a pigment solution Know what happens when a pigment molecule absorbs a photon of light energy: energy is transferred to an electron of the pigment molecule; so electron is activated or excited to high energy state; when electron loses the energy it gives off heat or fluorescence Know what a photosystem in chloroplasts is: a cluster of protein & other organic molecules Know what a light gathering antenna is: group of several hundred chlorophyll a & b & carotenoid molecules in a photosystem Know what happens when a photosystem absorbs light energy: light energy activates an electron in a chlorophyll a molecule which passes the activated electron to other pigment molecules until it is passed to a reaction center chlorophyll a molecule which can pass the electron to a primary electron acceptor molecule Know the difference between photosystem I & photosystem II: chlorophyll a molecules in photosystem I absorb light best at wavelengths of 700nm; chlorophyll a molecules of photosystem II absorb light best at wavelengths of 680 nm Know what happens when photosystem II absorbs light energy: light energy activates a chlorophyll a electron which is passed eventually passed from a reaction center chlorophyll a molecule to a primary electron acceptor Know what happens to the chlorophyll a molecule that lost the high energy electron to the primary electron acceptor: chlorophyll a molecule that lost its electron (oxidized chlorophyll a) must gain an electron so an enzyme splits water to get the replacement electron & by splitting water it generates molecular oxygen (O~2~) as a by product Know what happens to the activated (energized) electron generated by photosystem II: high energy electron is passed from the primary electron acceptor to an electron transport chain that connects photosystem II to photosystem I & has several components including plastoquinone, a complex of 2 cytochrome proteins & a copper containing protein called plastocyanin; energy from the high energy electron is removed in discrete steps & used to generate a hydrogen ion gradient in the chloroplast across the thylakoid membrane & the potential energy of the hydrogen ion gradient is used to generate ATP using ATP synthase just as in cellular respiration Know what happens to the electron from photosystem II after it goes down the electron transport chain between photosystem II & photosystem I: the electron which is now a low energy electron is used to replace an activated electron that was generated by light absorbance in photosystem I Know what happens to the activated electron generated by light absorbance in photosystem I: the now high energy electron is passed to the reaction center chlorophyll a molecule which passes it to the primary electron acceptor which sends it down a different electron transport chain which passes the electron to an iron containing protein called ferredoxin which passes the electron to the enzyme NADP+ reductase which forms NADPH from NADP+ products of light reactions are ATP & NADPH NADPH carries the high energy electron to the Calvin cycle Know why the high energy electron from photosystem I is sometimes passed to ferredoxin which then passes this electron back to the cytochrome complex of electron transport chain between photosystem II & photosystem I instead of passing the electron to NADP+ reductase: Calvin cycle uses more ATP than NADPH so need to generate additional ATP from the electron transport chain that makes ATP Know what molecules are used by the Calvin cycle & which specific molecules are generated in the Calvin cycle: Calvin cycle uses ATP & NADPH from the light reactions; Calvin cycle uses carbon dioxide from the air to produce a 3 carbon sugar molecule called glyceraldehyde 3 phosphate Know the 3 phases of the Calvin cycle: carbon fixation phase where carbon dioxide is attached to 5 carbon molecule called ribulose bis phosphate by enzyme called RuBP carboxylase or rubisco; phase IIis reduction phase & uses ATP & NADPH from the light reactions to generate glyceraldehyde 3 phosphate; phase II is the regeneration phase & uses more ATP from the light reactions to regenerate the ribulose bis phosphate Know what the direct product of the Calvin cycle is & what it is used for: direct product of the Calvin cycle is glyceraldehyde 3 phosphate & it is used to make glucose & other organic molecules LAST 3 SECTIONS 5 exam questions ENERGY HARVESTING Know the central molecule in cellular energy needs: ATP Know why ATP is important: 3 negatively charged phosphate groups of ATP make it unstable & losing the terminal phosphate group makes it more stable Know what happens to the terminal phosphate group when ATP loses it: terminal phosphate group is transferred to other molecules which become activated & are 'phosphorylated' Know what oxidation/reduction reactions are & what happens when a molecule is oxidized or reduced: oxidation reduction reactions involve the gain or loss of electrons; a molecule is oxidized when it loses an electron & a molecule is reduced when it gains an electron METABOLISM Know the difference between a catabolic reaction & an anabolic reaction: catabolic reactions involve the breakdown of complex molecules to simple molecules with release of energy; anabolic reactions involve the making of complex molecules from simple molecules & require energy input Know the definition of energy, kinetic energy, potential energy, chemical energy: energy is the capacity to do work; kinetic energy is the energy of motion; potential energy is energy that matter has due to location or structure; chemical energy is a form of potential energy that molecules have due to the arrangement of the atoms in the molecule Know the definition of free energy: portion of a system's energy that can perform work when the temperature is uniform Know the relation between free energy & exergonic & endergonic reactions: exergonic reactions proceed with net release of free energy as products have less free energy than reactants; endergonic reactions absorb free energy from the surroundings so products have more free energy than reactants Know what energy coupling is: linking of energy release of exergonic reactions to energy required in endergonic reactions ATP, ENZYMES, METABOLIC CONTROL Know the 3 main types of work done by the cell: mechanical -- muscle contraction, cilia beating; transport -- pumping ions against concentration gradients; chemical -- pushing endergonic reactions Know the structure of ATP: nitrogenous base called adenine attached to 5 carbon sugar called ribose that has 3 phosphate groups attached Know where the energy is stored in the ATP molecule: energy is stored in the bonds between the phosphate groups Know how ATP works: terminal phosphate group is removed & attached to another molecule which becomes activated & is said to be phosphorylated Know what an enzyme is & what a catalyst is: an enzyme is a catalytic protein & a catalyst is a chemical agent that changes the rate of a reaction without being consumed in the reaction process Know what the activation energy is: initial energy required to break the chemical bonds of the reactants in a chemical reaction Know how a catalytic enzyme works: catalytic enzyme works by lowering the activation energy for a reaction Know what the active site of an enzyme is: small part of the enzyme that actually binds the substrate molecules Know what factors affect enzyme activity & why: enzyme activity is affected by temperature, pH, ionic concentrations, anything that affects the 3 dimensional shape of the enzyme affects the activity Know what a co-factor is & what a co-enzyme is: co-factor is a nonprotein helper of catalytic activity such as ions like zinc, copper, iron; co-enzyme is an organic molecule such as a vitamin or a molecule derived from a vitamin Know what enzyme inhibitors are & what types of inhibitors exist & how they work: inhibitors are reversible if they bind using weak bonds or irreversible if they bind using covalent bonds; competitive inhibitors bind to the active site of the enzyme & prevent the substrate from binding; noncompetitive inhibitors bind to another part of the enzyme but they change the shape of the enzyme so the substrate cannot bind to the active site Know what allosteric regulation of enzymes is: allosteric regulation involves enzymes with more than 1 polypeptide chain that each have an allosteric site between the polypeptides & activators or inhibitors bind to the allosteric sites & keep the proteins in the active or inactive conformation Know what feedback inhibition is: most common type of metabolic control where end product inhibits a pathway Know what enzyme cooperativity is: 1 substrate molecule primes the enzyme to accept additional substrate molecules