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Biology 1001A
Tom Haffie

Bio Outcomes Lecture1 stromatolite: fossilized remains of ancient cyanobacterial mats that carried out photosynthesis by the water-splitting reaction extremophile: a microbe that lives in an environment once thought to be uninhabitable panspermia: seeds of life from outer space, theory that life exists and is distributed throughout the universe in the form of germs and spores that develop in the right environment abiotic synthesis: the preparation of a compound, often of biological relevance, without the use of biological agents such as enzymes or nucleic acids, inorganic molecules reacted to make organic molecules prebiotic evolution: the theory of how life on Earth could have arisen from inanimate matter redox terminology: atmosphere was reduced and is now oxidized chirality: one that is not superimposable on its mirror image enantiomers: isomers that are mirror images of each other (optical isomers), cells use one over the other teratogen: a drug or other substance capable of interfering with the development of a fetus, causing birth defects racemic: of, concerned with, or being a mixture of equal amounts of enantiomers and consequently having no optical activity polymerization: process in which monomers link together to form a polymer transcription: the mechanism by which the information in DNA is made into a complementary RNA copy translation: the use of the information encoded in the RNA to assemble amino acids into a polypeptide RNA world: - came first: information, structure, catalysis - if can fold like a protein, complementary base pairing, can acquire very elaborate 3D shapes - ribosomes, ancient organelle (2/3 RNA and 1/3 protein) ribozyme: an RNA-based catalyst that is part of the biochemical machinery of all cells micelle: a sphere composed of a single layer of lipid molecules vesicle: a small, membrane bound compartment that transfers substances between parts of the endomembrane system basic characteristics of life a. display order: all forms of life are arranged in a highly ordered manner, with the cell being the building block of life b. harness and utilize energy: all forms of life acquire energy from the environment and use it to maintain their highly ordered state c. reproduce: all organisms have the ability to make more of their own kind d. respond to stimuli: organisms can make adjustments to their structure, function and behaviour in response to changes in the external environment 1 e. exhibit homeostasis: organisms are able to regulate their internal environment such that conditions remain relatively constant f. growth and development: all organisms increase their size by increasing the size/number of cells, many organisms also change overtime g. evolve: populations of living organisms change over the course of generations to become better adapted to their environment general timing of the appearance of various life forms: january 1st - world started started (4,600 mya) march 2nd - prokaryotes, 4 billion years ago (3,800 mya) april 28 - oxygen (2,700 mya) june 13 - eukaryotes (2200 mya) august 12 - multicellular eukaryotes (1400 mya) october 15 - animals (600 mya) december 31 - humans 150 thousand years ago stages of prebiotic evolution: - geophysical stage: what was the composition on the earth and atmosphere? - early atmosphere h2o, h2, ch4, nh3, h2s - energy source: ultraviolet, lightening - reducing atmosphere (building complex molecules from reduced, electron rich molecules) - chemical stage: how could the building blocks be synthesized? - Miller-Urey experiment: set up an artificial atmosphere - important monomers (amino acids, sugars, purines and pyrimidines) - cannot do abiotic synthesis now because there is so much oxygen in the atmosphere - biological stage: how did the building blocks organize into living cells? connection between cyanobacteria and atmospheric oxygen levels - cyanobacteria could harness electrons from water - the “splitting of water” released protons and electrons but it also resulted in the formation of oxygen - oxygen started being released and over of millions of year slowly accumulated in the atmosphere physical/chemical conditions of primordial earth with respect to atmosphere, energy - deep sea vents, hot, nutrient rich, extremophiles - panspermia, seeds of life from space basic principles of oxidation/reduction chemistry - oxidation loses electrons, reduction gains electrons Miller-Urey experiment - lack of oxygen in the atmosphere meant there was no ozone layer to potentially block the Sun’s energetic ultraviolet light from reaching Earth’s surface - they hypothesized that the ultraviolet light/lightning provided the energy that, combined with the reducing conditions in the atmosphere, would lead to the accumulation of the simple “building blocks” required for life 2 - Stanley Miller created a laboratory simulation of the reducing atmosphere believed to exist on early Earth - Miller placed the components of a reducing atmosphere (hydrogen, methane, ammonia, water vapour) in a closed apparatus and exposed the gases to and energy source - water vapour was added to the “atmosphere” in one part of the apparatus and subsequently condensed back into water by cooling in another part - after running the experiment for a week, a large assortment of organic compounds were found in the water (urea, amino acids, lactic, formic and acetic acids) - as much as 15% of the original carbon was now in the form of organic compounds **** abiotic synthesis cannot occur in the modern atmosphere because of the abundance of oxygen possible explanations for homochirality in life 1. random chance 2. extraterrestrial origin - we don’t fully understand how homochirality came about which homochiral form of sugars and amino acids are used in life - L amino acids - D sugars relationship between homochirality and enzyme activity - the active site on an enzyme is very specific to the type of amino acid, it could bind the L form but not it’s D form stages of biological evolution 1. development of DNA, RNA, protein triad 2. synthesis of polymers 3. the first cells (the protein formation steps require enzymes to catalyze those steps but you need proteins to have enzymes - which came first? we think RNA) evidence for various roles of RNA in early biological evolution - RNA: information, structure, catalysis - carrie information for protein synthesis - RNA can fold into very elaborate 3D shapes through complementary base pairing - ribosome, ancient organelle (2/3 RNA, 1/3 protein) - ribozymes molecules that can catalyze chemical reactions that are RNA reasons why DNA is preferred over RNA - DNA is more stable than RNA due to the presence of the sugar deoxyribose instead of ribose - the base uracil found in RNA is not found in DNA; it has been replaced by thymine, by utilizing thymine in DNA any uracil is easily recognized as a damaged cytosine and can be repaired - DNA is double stranded, so in case of mutation, the complementary strand can be used to repair the damaged strand role of clay particles in formation of organic polymers - large surface area that is charged 3 - attract molecules to them and polymerization can occur on the surface of the clay role of clay particles served in the formation of early cells - formation of vesicles - free-living fatty acids are attracted to the charged clay surface and form a micelle, and speeds up the formation of a vesicle basic strategy used by Craig Venter to create synthetic cells - created the first cell that didn’t have a parent cell, didn’t get its chromosome from another cells - he manufactured the chromosome himself and made the cell from scratch - recombination (pasting) Lecture2 Proxima Centauri: closest star to us (4.22 lightyears away) SETI: search for extraterrestrial intelligence galaxy: a large system of stars held together by mutual gravitation and isolated from similar systems by vast regions of space extrasolar planet: planet that orbits a star other than the Sun habitable zone: a special zone where one would predict the conditions would be right for the development of life cohesion: the force of attraction that holds molecules of a given substance together heat capacity: the heat required to raise the temperature of a substance one degree heat of vapourization: energy required to transform a given quantity of a substance into a gas at a given pressure hydration shell: a “covering” of water molecules with surrounds polar or charged substances in aqueous solutions sublimation: process of changing from a solid to a gas without passing through an intermediate liquid phase Fermi paradox: the contradiction between high estimates of the probability of the existence of life on other planets and the lack of evidence Drake Equation - N = N s × f p × n e × f l × f i × - N = number of advanced civilizations in our galaxy (100) - Ns = number of stars (100 billion) - p= the fraction of those stars that have planets (0.5) - half of the stars have planets around them - e= number of planets that can potential support life (2) - factor: how far is the planet from the star/the habitable zone - = the fraction of those planets that develop life (1) - all planets capable of developing life do indeed develop life - = the fraction of planets that develop intelligent life (10%) - estimate planets with intelligent and communicating life 4 - c = the fraction of planet willing and able to communicate (10%) - L = average lifetime of civilization (100 years) - our communicating civilization lasts 100 yrs mechanism by which the “transit method” detects extrasolar planets - when a planet passes between a parent star and earth, the star will dim, so there is a regular oscillate so we can tell there is a planet in the way mechanism by which astrometry/doppler spectroscopy detects extrasolar planets - we can detect the wobbling of a parent star, explained by planet orbiting around the star mechanism by which optical telescopes can detect extrasolar planets - can detect large massive planets surrounding stars characteristics of the habitable zone that promote life - how far the planet is from the star - as the star gets brighter, the habitable zone moves farther away and vise versa - also defined by the presence of liquid water chemical characteristics of liquid water - dipole moment, polar covalent but unequal sharing of electrons - oxygen is slightly negative and hydrogen is slightly positive - based on its molecular weight, water should be gas on earth at our temperatures but due to hydrogen bonding, its bp is 100 degrees - cohesion cause high heat capacity and high heat of vapourization - hydration shells minimize electrostatic interactions (water is attracted to the large molecules) role of hydration shells in chemistry of life - protein interaction in sophisticated ways that are required for life - minimizes the electrostatic interactions evidence of water on mars - mars rover dug a hole and took pictures of it, the rocks disappeared 4 days later - this is evidence of sublimation, therefore evidence of frozen water on mars - which also means, there could have been liquid water on mars at some point Fermi paradox resolutions 1. we can’t detect them - distances are far too great - technological incompatible 2. no other civilizations exist Lecture3 constitutive expression: a gene that is always being transcribed at a constant rate induced expression: only transcribed as needed transcription factor: protein that binds to specific DNA sequences, thereby controlling the movement of genetic information from DNA to mRNA Northern blot: technique used in molecular biology research to study gene expression by detection of RNA in a sample 5 Western blot: analytical technique used to detect specific proteins in the given sample of tissue peptide bond: a link formed by a dehydration synthesis reaction between the -NH2 group of one amino acid and the -COOH group of a second amino: consisting of, or containing the group of atoms -NH2 carboxylic group: the characteristic functional group of organic acids, formed by the combination of carbonyl and hydroxyl groups R group: where the amino acids differ aqueous: of, like, or containing water polarity: the condition of having two opposite poles, or of having opposite properties or characteristics hydrophobic: having little or no affinity for water hydrophilic: having a strong affinity for water primary: linear sequence of amino acids secondary: produced by regular repeated interactions between atoms of the backbone (nothing to do with the R group) tertiary: gives overall 3D shape of protein (interaction between R groups) quaternary: the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex, polypeptides come together alpha helix: corkscrew, about every 5 amino acids that can interact beta sheet: zigzag hydrogen: colourless, odorless, flammable gas that combines chemically with oxygen to form water ionic: of, containing, or involving an ion or ions disulfide: a sulfide containing two atoms of sulfur VanderWaals bond: bond formed by weak molecular attractions over short distances nascent peptide: new, denatured than transcribed again native conformation: shape protein should take under normal conditions in vitro: may occur in a laboratory vessel or other controlled experimental environment rather than within a living organism or natural setting in vivo: occurring or made to occur within a living organism or natural setting urea: a compound occurring in urine and other body fluids as a product of protein metabolism denaturation: to treat a protein by chemical or physical means so as to alter its original state macromolecular crowding: too many other amino acids around, you haven’t isolated the peptide chaperones: interacts with and stabilizes non-native forms of protein but not part of the final assembly heat shock protein (HSP): related proteins whose expression is increased when cells are exposed to elevated temperatures or other stress prosthetic group(cofactors): non-protein chemical compound that is bound to a protein and is required for the protein’s biological activity 6 examples of constitutive vs. induced genes - actin, carotin, chaperones - induced: HSP process by which Northern and Western blots measure transcript and protein abundance - northern: RNA is separated out by RNA gel electrophoresis, subsequent transfer to membrane, hybridization with probe and finally detection - western: separate the macromolecules using gel electrophoresis, separated molecules are transferred onto a second matrix, an appropriate substrate is then added to the enzyme and together they produce a detectable product relationship between polarity and +/- charge with respect to interaction with water - amino acids are polar, and cytosol is aqueous (water) - interact very well, the R groups are polar, some are positively charged and some are negatively charged - when they are non-polar (hydrophobic), these amino acids do not want to interact with aqueous environment (the hydrophobic effect), unstable, just want to interact with other hydrophobic molecules how to measure transcript/protein abundance - transcript: use Northern blot - protein abundance: use Western blot factors that influence mRNA transcript abundance - temperature size of typical peptide - chains of under 40 amino acids difference between peptide and protein - peptides are shorter chains of amino acids than proteins (500 amino acids) main factors that contribute to - primary structure: held together by covalent or peptide bonds - secondary structure: defined by patterns of hydrogen bonds between the main-chain peptide groups - tertiary structure: driven by non-specific hydrophobic interactions, structure is only stable when the parts of a protein domain are locked into place - quaternary structure: stabilized by same non-covalent interactions as tertiary relative strength of bonds - VanderWaals is the weakest of the bonds because they are just weak molecular forces over long distances - ionic bonds are weaker than covalent bonds because each molecule gets a charge and that is was keeps them attracted whereas in covalent bonds, the molecules share the electrons - hydrogen bonds are the strongest physico-chemical conditions leading to protein folding - attractions between amino acids cause the protein to fold - proteins must be folded in order to be functional 7 physico-chemical conditions leading to denaturation - presence of a denaturant examples of denaturants - heat: breaks weak bonds - pH: disrupts ionic bonds - organic solvents, urea mechanisms underlying denaturation - disrupting bonds and attractions between amino acids causes the protein to unfold itself and become dysfunctional factors or conditions required for proper protein folding - depends on the solvent - the concentration of salts, the temperature and the presence of molecular chaperones - chaperones assist in folding and assembly, modulation and conformation, transport, disaggregation of protein aggregations relative timing of protein folding relative to translation - protein folding occurs after translation factors that “drive” protein folding - non-specific hydrophobic interactions - amino acid attractions - hydrogen bonds in main chain groups relationship between folding and free energy - native conformation has the lowest free energy consequences of denaturation - incorrect molecular activities and loss of activity - hydrophobic become exposed and interactions occur that wouldn’t normally - misfolding (with itself or aggregation(with other protein molecules)) - aggregation, interacts with other protein molecules role of chaperones - interacts and stabilizes non-native forms of protein - not part of the final assembly - assist in folding and assembly, modulation conformation - ATP-dependent role of heat shock proteins - play an important role in protein-protein interactions such as folding and assisting in the establishment of proper protein conformation and prevention of unwanted protein aggregation - members are expressed at low to moderate levels in all organisms because of their essential role in protein maintenance Lecture4 potential energy: has energy associated with it (gravity) kinetic energy: energy in motion chemical energy: sugars, gasoline 8 closed systems: only energy can be exchanged with the surroundings, no matter is exchanged open systems: matter and energy can be exchanged with the surroundings isolated systems: neither matter or energy can be exchanged first law of thermodynamics: total energy in the universe is constant, you can transform energy but not destroy or create it second law of thermo: every energy transformation increases the disorder of the universe entropy: measure of the disorder of the universe enthalpy: the sum of the internal energy of the system spontaneous reaction: reactions that occur naturally change in enthalpy: the change in internal energy of a system exothermic: releases heat endothermic: absorbs heat Gibbs Free Energy: the capacity of a system to do non-mechanical work exergonic: free energy of the reactants are higher than the products endergonic: free energy of products is higher than the reactants dG: change in the capacity of a system to do non-mechanical work stability: resistance or the degree of resistance to chemical change or disintegration work capacity: the capacity to perform work-related activities phosphoryl group transfer potential: transfers the phosphate and becomes unstable and wants to react equilibrium: the condition existing when a chemical reaction and its reverse reaction proceed at equal rates relationship between entropy change and open, closed and isolated systems - closed: entropy always increases or remains constant because energy can be let in - open: entropy increases because energy is let in - isolated: entropy will tend not to decrease because the second law says it doesn’t conditions needed for a reaction to be spontaneous - products have lower potential energy than the reactants - products are less ordered than the reactants Gibbs free energy equation - ∆G = ∆H - T∆S - ∆H: change in enthalpy - T: temperature - ∆S: change in entropy whether or not a reaction will be spontaneous based on ∆G - if ∆G is -ve, the reaction will occur spontaneously - products have lower potential energy than the reactants - -ve ∆H is exothermic, +ve ∆H is endothermic - products are less order than the reactant molecules, entropy increases - if ∆G is +ve, the reaction will not occur spontaneously 9 - exergonic reaction the free energy of the products is less than the free energy of the reactants, has a negative ∆G - endergonic has a positive ∆G, reactants have a lower free energy than the products, non-spontaneous relationship between phase changes and entropy - whenever you have a phase change (solid to liquid or liquid to gas), the entropy goes up because there is more disorder, more heat, more random molecular motion role of enzymes in coupling ATP hydrolysis with other reactions - requires an enzyme to trap the energy from the ATP, no heat is lost - energy coupling is linking an exergonic reaction to drive a endergonic process - enzyme brings molecules very close together, so the ATP isn’t free, it’s right beside the substrate, does not allow water in the site so breakdown occurs instead of hydrolysis why “ATP breakdown” is not “ATP hydrolysis” - in breakdown, ATP is not actually being hydrolysized - ATP is being broken down and energy is used to drive endergonic reaction - ATP hydrolysis (conversion of ATP to ATD in aqueous solution) is the repulsion between phosphate ions causes it to be very unstable and makes it easy to break the bonds, liberates free energy - ATP hydrolysis’s energy is lost as heat, and does not occur in cells because they cannot handle the heat relationship between life and the 2nd law of thermo - life goes against the second law - life is highly ordered - constant energy influx - living things increase the disorder of the surroundings by giving off heat why life needs to consume energy - to maintain low entropy - proteins are constantly getting synthesized and broken down Lecture5 catalyst: substance with the ability to accelerate a spontaneous reaction without being changed by the reaction rate of reaction: the speed of the reaction energy of activation: the initial output of energy required to start a reaction transition state: an intermediate arrangement of atoms and bonds that both the reactants and the products of a reaction can assume kinetic stability: active site: the region of an enzyme that recognizes and combines with a substrate molecule turnover rate: enzyme kinetics: the study of the chemical reactions that are catalyzed by enzyme 10 substrate: the particular reacting molecule or molecular group that an enzyme catalyzes reaction velocity: the rate of reaction for a reactant or product in a particular reaction is intuitively defined as how fast a reaction takes place Vmax: an amount of substrate where the enzyme can’t work any faster Km: substrate concentration that gives you 1/2 Vmax enzyme affinity: substrate affinity: attractiveness between the two molecules competitive inhibition: inhibition of an enzyme reaction by an inhibitor molecule that resembles the normal substrate closely enough so that it fits into the active site of the enzyme penicillin: an antibiotic medication used to treat certain infections peptidoglycan: a polymer found in the cell walls of prokaryotes that consists of polysaccharide and peptide chains in a strong molecular network transpeptidase: an enzyme that catalyzes the transfer of an amino acid residue or a peptide residue from one amino compound to another covalent inactivation: chlamydomonas: solitary doubly-flagellated plant-like algae common in fresh water and damp soil nitrate reductase: molybdoenzymes that reduce nitrate to nitrite prosthetic group: tightly-bound cofactors cofactor: a non-protein chemical compound that is bound to a protein and is required for the protein’s biological activity apoprotein: a conjugated protein from which the prosthetic group has been removed roles of enzymes in exergonic reactions vs. endergonic reactions - exergonic: reacting molecules need to acquire a transition state of higher energy than original reaction conditions - need “activation energy” to get to that transition state - enzymes lower the activation energy, this is how they speed up the reaction because you need less energy to get to the transition state (changes the pathway) relationship between activation energy and rate of reaction - rate is proportional to the number of activated molecules - activation energy represents a barrier that keeps the reaction from going quickly why biological systems need enzymes - we need reactions to go faster - can’t use massive amounts of heat all the time - enzymes do not provide energy, they just lower the activation energy characteristics of active site - site where the substrate attaches itself - enzyme must be flexible so that substrate can bind - active site is where the reaction occurs, site of catalysis 11 comparison of “induced fit” and “lock and key” - induced fit: enzyme changes its shape to fit the substrate (flexible) - lock and key: enzyme and substrate are not like a lock and key, the enzyme must be flexible for substrate binding effect of temperature on substrate binding - if temperature increases, rate of substrate binding increases 3 mechanisms enzymes use to lower activation energy and mimic transition state 1. precise orientation of two substrates - enzyme allows the two to acquire a specific orientation 2. charge interactions - enzyme allows specific charge on substrate 3. conformational strain - maybe bonds need to be strained graphical relationship between [S] and velocity - rate of reaction is directly proportional to concentration of substrate - eventually you reach an amount of substrate where the enzyme can’t work any faster (Vmax) identify families of curves with higher vs. lower Km for given Vmax - Km is the substrate concentration at 1/2Vmax - the steeper the graph, the lower the Km, the flatter the graph, the higher the Km mechanism for competitive inhibition - a competitive inhibitor is fighting for the active site with a substrate - at high substrate concentrations, inhibitor becomes relatively irrelevant effect of competitive inhibitor on velocity at increasing [S] - Vmax remains the same - Km becomes higher - need more substrate to reach 1/2 Vmax mechanism of action of penicillin - transpeptidase enzyme required to form the bonds between amino acids - inhibits bacterial cell wall - competitive inhibitor examples for prosthetic groups - chlamydomonas (green alga) - nitrogen assimilation - both grow well on ammonia but mutant doesn’t grow on nitrate relationship between growth rate curve and enzyme activity 12 relationship between growth rate curve of phychrophile, mesophile, thermophile and enzyme activity Lecture6 amphipathic: contains a region that is hydrophobic and a region that is hydrophilic hydrophilic: polar molecule that associate with water hydrophobic: nonpolar substances that are excluded by water and other polar molecules fatty acid: one of two components of a neutral lipid, containing a single hydrocarbon chain with a carboxyl group linked at one end saturated: fatty acid with only single bonds linking the carbon atoms, linear membrane fluidity: very important if you want membrane to work (ie. things to pass through it) hydrogenation: to undergo or cause to undergo a reaction with hydrogen desaturase: enzyme that synthesize unsaturated fatty acids membrane permeability: charge and size effects ability for molecule to move through membrane transmembrane protein: a protein that spans a membrane (17-22 amino acids that are highly nonpolar) simple diffusion: go right through membrane facilitated diffusion: use a channel or pore to go through, for molecules that can’t interact with the hydrophobic core active transport: pump this against the concentration gradient “ATP-Binding Cassette” (ABC) transporter: one of the largest group of transporter proteins, facilitated diffusion against gradient, which consumes ATP 13 cystic fibrosis: impairment of lung and intestinal function, caused by mutation Cystic Fibrosis Transconductance Regulator (CFTR): pumps chloride into the epithelial lining dF508: most common CFTR chaperone protein: assist in the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures “ER equality control”: proteosomes: a form of vaccine that can be administered by an inhaler role of fatty acids in membrane structure - the fatty acids align with their hydrophilic heads facing outwards and their hydrophobic tails inwards - the fatty acids create a membrane with fluidity because they are not rigidly bonded together cis vs. trans unsaturation - cis: the hydrogens bonded on the carbons with the double bond are on the same side - trans: the hydrogens bonded to the carbons with the double bond are on opposite sides relationship of fatty acid saturation levels on membrane fluidity - the more saturated the fatty acids are the less fluid the membrane is because saturated fatty acids have linear tails and can pack together more tightly - unsaturated fatty acids have bent tails and the more unsaturated they are the more crooked they become, making them unable to pack together as tightly and leaving space between them, cause the membrane to be very fluid relationship between gene, transcript abundance and protein abundance - changes in the transcription of a gene often result in changes in the abundance of its transcript (mRNA) and resulting protein abundance relationship of temperature on membrane fluidity - if the temperature drops low enough, the phospholipid molecules become closely packed and the membrane forms a highly viscous semis
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