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BIO1002 - Term Test 1 Outcomes.docx

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Western University
Biology 1002B
Tom Haffie

Lecture Outcomes – Term Test 1 Lecture 1 1) Roles of light as used by life  Source of energy and source of information about the environment 2) Characteristics of Chlamydomonas that make it a useful model system  Based on the genome sequence, it has attributes of both an animal and plant 3) Function of basic components of Chlamydomonas cells  Nucleus, basal body, ER, ribosomes, golgi, mitochondrion, chloroplast – pyrenoid (where carbon fixation occurs)  Eyespot (within outer membrane of chloroplast): enables cell to orientate itself in relation to light to harvest for photosynthesis 4) Relative usefulness of various biological characteristics as measures of complexity  Genome size can mislead you, PCG (protein-coding genes)?  Evolution of multicellularity 5) Advantages to Chlamydomonas being phototactic  Want to move towards light to harvest photons for photosynthesis, eyespots maximize this with phototaxis 6) Reasons why Chlamydomonas might move AWAY from a light source  Too much light is damaging  protein will denature, might damage the photosynthetic apparatus, free radicals (ROS) 7) Basic structure of rods and cones as photoreceptor cells  Modified neuron photoreceptor cells that sit on the retina (cone – colour vision, rod – black & white)  One photoreceptor cell within the disk contain many individual photoreceptors 8) Major components involved in phototransduction and their role  Photoreceptor cells generate electrical signals in response to captured photons  Channels are open in dark, provides both an inward and outward current (presence of cyclic GMP keeps channel open)  Single photon of light activates photopigment rhodopsin (changes shape from cis to trans)  activates transducing molecules (protein)  activates phosphodiesterase (enzyme)  Phophodiesterase hydrolyzes cyclic GMP (5’ GMP) molecule by cleaving 3’ phosphate bond  Ion channels (sodium in the outer membrane of photoreceptor cell) close because of the reduced number of cyclic GMP  Inward channels close while outward channels remain open, Na can’t enter  Photoreceptor becomes hyperpolarized because of change in inward current (voltage becomes even higher)  Leads to an electric current (signal) running down the membrane surrounding the photoreceptor cell  200 million bits per second – optic nerve  brain Lecture 2 1) Relationship between excited states of a pigment and its absorption, fluorescence emission spectra  Pigment absorb photons of light  excited state to produce energy and emit light  Energy of fluorescence is always lower than excited state due to loss of heat 2) Region of the electromagnetic spectrum known as “visible light”  Represents a very narrow region of the entire EM spectrum (400 – 700 nm) 3) Relationship between wavelength and energy content of a photon  Energy of light is inversely related to the wavelength  The shorter the wavelength, the more energy that light has 4) Molecular characteristic of visible pigments that make them able to absorb light  Made up of conjugated system: alternation of a double bond and single bond (carbon in chlorophyll), indicates a specific electron configuration  Represent an abundance of electrons which are non-boding Pi orbital electrons  Interact with the photons of light, thus readily accessible to trap energy 5) Relationship between pigments and associated protein  Pigment is bound non-covalently specifically to proteins creating pigment-protein complexes (not floating around in cell) 6) Four “fates” of the excited state of chlorophyll resulting from absorption of photons  Lose energy as heat (10 -1s)  Lose little energy as heat to reach the lower excited state, lose the rest as fluorescence – emission of light (slightly longer wavelength)  Use light to do work – photochemistry (change molecule / structure of a pigment)  Transfer energy to another molecule (neighboring pigment) 7) Reason(s) why relative fluorescence is different in isolated chlorophyll vs. intact cells when exposed to light  Cell requires a lot of energy to run cell processes to function properly  Energy produced by excitation could be used by essential organelles, drive photochemistry as part of photosynthesis  Isolated chlorophyll has no pathway to be utilize energy so it is released via fluorescence (producing higher amount) 8) What accounts for the fact that chlorophyll is green in colour  There is no green excited state, nothing can absorb a green photon (just lost)  Can’t absorb = reflects green photon / transmitted through that pigment 9) Quantitative relationship between photons and excited electrons  1 to 1 ratio – one photon cannot excite more than one electron 10)Relationship between energy of photon and energy required to excite electrons in order for photons to be absorbed  Energy of photon must match perfectly the energy required to excite electrons 11)General structure of photosystem  Unit of photochemistry in photosynthesis is a photosystem  Created of antenna (outside) where energy transfer happens and reaction center (middle) where photochemistry occurs 12)Similarities and differences of the light capturing and photochemistry of phototransduction (retinal) VS photosynthesis (chlorophyll)  Phototransduction: photon of light activates ion channels to send electric current signal to brain to provide information  Photosynthesis: photon of light transfer energy to excite electrons and emit energy / light  Photochemistry occurs in both, both use photons of light 13)How are excited states of antennae pigments organized to provide for energy transfer to reaction center  Pigments are very close together, organized to fall down (A  B  C  D, A is the highest excited state and D is the lowest) 14)Structure of rhodopsin  Pigment-protein complex – pigment retinal is bound specifically to the protein opsin (rhodopsin – photosensitive pigment in retina) 15)Effect of photon absorption by 11-cis retinal on retinal structure followed by association with opsin protein followed by interaction of transducin with opsin  In the dark, 11-cis retinal is present and absorbing photon of light leads to photoisomerization and produces all-trans retinal  Energy of light breaks the pi bond and enables the molecule to swivel, pi bond is reformed in an all-trans configuration (photochemistry when it comes to retinal)  Cleft in opsin where cis retinal can fit, opsin cannot accommodate trans and the protein changes shape, opening up a clef where transducin can interact  Retinal leaves the opsin, trans cannot longer bind to the opsin so it just leaves and then there’s a regeneration pathway that has to take place  Once the activation occurs, opsin gets a new retinal  In the trans configuration, molecule is lost from the opsin 16)Reasons why life has evolved to detect the narrow band of energy represented by “visible light”  Most dominant form of electromagnetic radiation that hits the earth (evolved to use most abundant molecule)  Energy in visible light is just perfect, enough energy to excite a pigment to an higher state / drive isomerization of retinal Lecture 3 1) Reasons why photosystems have antenna proteins while the eye doesn’t  Image-forming eye doesn’t just harvesting huge amount of photons, every photoreceptor wants to be hit  Photosystem wants to harvest as much light as possible (antennas harvest) 2) Points of controls for regulation of protein abundance  Transcription, translation, mRNA decay 3) Factors affecting mRNA transcript abundance  Dependent on the rates of transcription, also dependent on how long this mRNA sticks around (decay / breakdown) 4) Steps in making a Northern Blot for measuring mRNA transcript abundance  Isolate total RNA and run on gel  transfer to solid surface (membrane), all RNAs are on surface of a solid matrix – nylon  incubate membrane with a probe solution (single stranded molecule of DNA complementary in sequence) that washes over  probe hybridizes complementary sequence on membrane  each DNA probe molecule has radioactive group attached to detect location and abundance by exposing to x-ray photographic film 5) Relative abundance of various types of RNA in typical cells  Ribosomal RNA – most dominant form of RNA in cells  3% of total RNA is mRNA, of 20,000 human expressed genes 6) Steps in making a Western Blot for measuring protein abundance  Western blots are done using antibodies, pour antibody on a membrane and it will bind very specifically to the proteins which it is raised against 7) Characteristics of constitutive vs. induced vs. repressed gene expression kinetics  Constitutive – doesn’t change / Induced – go up / Repressed – go down 8) Varieties of defects that might account for lower levels of functional photoreceptors  Simple mutation in the opsin gene  Protein made is just not the right one, not folded correctly  Problem with translation affects the amount of functional receptors  mRNA decay – defect in enzyme catalyzed process (don’t have transcript)  Protein abundance could be oppressed or decay – breaks down much faster  Absorb too much light? Opsin could be perfect but what if there’s no retinal? 9) Relationship among polypeptide, apoprotein, cofactor and functional protein  Cofactor (retinal) + Apoprotein (opsin)  Functional Protein (rhodopsin) 10)Relationship between protein folding and function  Polypeptide is simply a string of amino acids, protein is a polypeptide folded into specific 3D shape required for function 11)Factors affecting proper protein folding (Anfensen’s dogma)  Spontaneous in milliseconds, dependent solely on primary sequence Lecture 4 1) Meaning of potential, kinetic, chemical energy, closed, open vs. isolated systems, First Law of Thermodynamics, Second Law of Thermodynamics, entropy, spontaneous reaction, enthalpy (H), DH, exothermic, endothermic, Gibbs Free Energy, exergonic, endergonic, DG, catalyst, rate of reaction, energy of activation (EA), transition state, kinetic stability, active site, catalytic cycle  Potential Energy: energy possessed by a system  Kinetic Energy: energy released due to motion  Chemical Energy: energy contained within a chemical bond  Entropy: measure of the disorder of a system and its surroundings  Spontaneous Reaction: reactants  products without energy input  Enthalpy: measure of total energy of system  H: change in potential energy from reactants to products  Exothermic: heat is released/energy is lost by the reactants (-H)  Endothermic: heat is absorbed/energy is gained by the products (+H)  Gibbs Free Energy: energy available to do things  Exergonic: negative G, reaction is spontaneous  Endergonic: positive G  G: change in free energy  Catalyst: substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change  Rate of Reaction: the speed at which a reaction proceeds  Energy of Activation (EA): the energy needed to reach the transition state  Transition State: a state of higher energy that must be reached by the reactants before they can form the products of a reaction  Kinetic Stability: the energy needed to reach the transition state. A large energy of activation means a higher kinetic stability and vice versa  Active site: the location on an enzyme where the reaction occurs  Catalytic Cycle: the process of enzyme binding to the substrate to form the enzyme-substrate complex and catalyzing the reaction to form the products 2) Why life does not go against the second law  Cell is an open system – allows for free exchange of energy and compounds between the system and surroundings (increase disorder by giving off waste & CO ) 2 3) Why life needs to consume energy  Maintain low entropy because of huge amounts of energy input, low levels of disorder by bringing in energy (high entropy = death) 4) Components of Gibbs Free Energy equation  ∆G = ∆H -T∆S 5) Whether or not a given reaction will be spontaneous, given DG  Potential energy of B is less than A – exothermic (-∆G)  Products are more disordered, entropy goes up 6) Role of enzymes in endergonic vs. exergonic reactions  Enzymes speed up rate of a spontaneous reaction (only exergonic) 7) Relationship between activation energy and rate of reaction  Activation Energy: how much energy is needed to get to the transition state  Lower activation energy = higher rate of reaction 8) How enzymes increase rate of chemical reactions  Enzymes lower activation energy  Precise orientation of two substrates – mimic transition state  Charge interactions – provide a charge to active site  Conformational strain – distort substrate molecule 9) Why biological systems need enzymes  Enzymes can make reactions fast without raising temperature or pressure  Biological molecules can’t deal with high temperatures 10)Importance of tertiary structure to enzyme function  Induced Fit: flexible tert (tertiary structure) – enzyme must have the right shape, must be flexible and not rigid or won’t work properly 11)Link between enzyme function and growth rate  Rate of molecular motion increases with temperature (optimum) so then catalysis occurs at a faster rate  Growth rate is a function of enzyme activity  If temperature is too high, enzyme will denature (protein) 12)How tertiary structure bonding arrangements are different depending upon the temperature habitat of the organism  Hyperthermophiles live at high temps and have stronger intramolecular forces = higher disassociation temperature  Psychrophiles live at low temps and have weaker bonds, dissociate at lower temperature  Bond energies associated with bonds in tertiary bonding arrangements of enzymes, if bond energy is exceeded – bond will break Lecture 5 1) Meaning of hydrophilic, hydrophobic, fatty acid, saturated, membrane fluidity, hydrogenation, desaturase, membrane permeability, transmembrane protein, simple diffusion, facilitated diffusion, active transport, “ATP-Binding Cassette” (ABC) transporter, cystic fibrosis, Cystic Fibrosis Transconductance Regulator (CFTR), ∆F508, chaperone protein, “ER quality control”, proteasomes, proteases  Hydrophilic: water-loving (polar head group)  Hydrophobic: water-fearing (fatty acid tails)  Fatty Acid: carboxylic acid with a long carbon tail  Saturated: every carbon has the maximum amount of hydrogens (2)  Membrane Fluidity: viscosity of the lipid bilayer of a cell membrane  Hydrogenation: addition of a hydrogen to a fatty acid  Desaturase: enzymes catalyzing the formation of double bonds in fatty acids  Membrane Permeability: quality of a membrane that allows for diffusion  Simple Diffusion: diffusion along a concentration gradient through a membrane  Facilitated Diffusion: diffusion down a concentration gradient through a molecule specific protein “pore”  Active Transport: transport against a concentration gradient requiring energy  “ATP-Binding Cassette” (ABC) Transporter: transmembrane proteins that utilize ATP hydrolysis to transport substances across the membrane  Cystic Fibrosis: a recessive genetic disease caused by mutation in the CFTR gene  Cystic Fibrosis Transconductance Regulator (CFTR): a chloride ion active transporter that functions to keep epithelial linings moist  ∆F508: phenylalanine deletion at position 508, the most common mutation to the CFTR causing cystic fibrosis (70% of all cases)  Chaperone Protein: detects protein folding stability in the ER  “ER Quality Control”: process in the ER screening proteins for folding stability  Proteosomes: complex of proteases functioning to degrade proteins  Proteases: enzymes which break down proteins 2) Role of fatty acids in membrane structure  Position themselves away from aqueous environments to form lipid membrane spontaneously 3) Relationship of fatty acid saturation levels on membrane fluidity  Saturated molecule pack close together and the membrane is less fluid  More unsaturation = more fluid your membrane will be at any given temperature 4) Relationship of temperature on membrane fluidity  Higher temperature = more fluid membrane 5) Relationship of fluidity to membrane functions such as transport  Maintaining proper fluidity is important for electron transport  Too fluid = membrane fall aparts, too little fluid = ETC stops 6) Properties of saturated vs. unsaturated fats  Fully saturated – saturated with hydrogen, very linear  Unsaturated fatty acid by introducing a C-C double bond, reducing number of hydrogens – changes the shape of the molecule (kink) 7) Role of desaturases in fatty acid biosynthesis  Synthesized by a biosynthetic pathway in a saturated form (completely linear)  To be unsaturated, desaturases introduce double bonds 8) Relationship of bacterial desaturase expression vs. temperature  Higher temperature = lower desaturase expression (membrane is already fluid enough) 9) Role of size and charge in movement of molecules across biological membranes  Size and charge impede diffusion across the membrane 10)Characteristics of transmembrane proteins that enable them to interact with hydrophobic core of membrane  Interact with the lipid bilayer by producing a channel (inner charge is different from outer charge)  Inner part of the channel is hydrophilic, the outside is hydrophobic  Membrane protein – made of nonpolar amino acids (hydrophobic)  Alpha helical structure minimizes the charge of the backbone groups, thus the protein is much more easily able to interact with hydrophobic core 11)Factors influencing simple and facilitated diffusion  Simple diffusion goes down concentration gradient (free energy change drives this, more free energy = more ability to do work)  Facilitated diffusion uses pores specific to certain molecules to let one in 12)Transport against a concentration gradient (active transport)  Uses an ABC Transporter that requires energy to go from low to high 13)Role of electrochemical gradient in determining equilibrium concentration of ions  Ions diffuse along electrochemical gradient, doesn’t move to equal concentrations on both sides  Charged = down the concentration gradient  Electrical difference between the two – inside in relation to outside 14)Basis for electrical gradient across photoreceptor cell  Charge difference across a photoreceptor membrane – lots on anions inside the cell which impart a negative charge to the interior of the cell  Lots of sodium leaks in and lots of potassium leaks out  Ions pumped against their gradient by a potassium / sodium transporter  cGMP gated channel allows influx of sodium ions, which keeps the membrane polarized at -30mV  When light hits a photoreceptor, phosphodiesterase metabolizes cGMP, causing the membrane to hyperpolarize (at -60mV) because sodium cannot get in  Triggers inhibition of glutamate and triggers the action potential that signals the presence of light to the brain 15)Basic structure of ABC transporter  Used in active transport composed of two parts: transmembrane domain (part transports molecule) and ATP binding cassette (binds ATP and uses energy of breakdown to fuel transport) 16)Genetics underlying cystic fibrosis  Homozygous recessive disease caused by a mutation to CFTR (ABC transporter)  6000 bases, 1480 amino acids – most common ∆F508 (70% of cases) 17)Cystic fibrosis phenotype  CFTR is located on membrane on epithelial cells linked with mucus cilia (keep wet to get good clearance  With CF, mucus is dry and brittle and lung tissue sticks together 18)Physiological function of CFTR  ATP
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