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Biology Notes - Final

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Biology 1001A
Tom Haffie

Lecture 1: Origin of Life - Stromatolite – fossilized remains of ancient cyanobacterial mats that carried out photosynthesis by the water –splitting reaction - Extremophile – organisms that thrive in and may even require physically or geographically extreme conditions that are detrimental to most life on earth - Panspermia – hypothesis that life exists throughout the universe and proposes that life can survive the effects of space - Abiotic synthesis – molecules that were synthesized from non-living/non-biological agents - Prebiotic evolution – life oriented gradually from interaction between different chemicals in the earth’s atmosphere – led to first amino acids, which formed complex molecules; proteins/DNA - Chirality – lacking an internal plane of symmetry and thus having a non-superimposable mirror image - Enantiomers – isomers that are mirror images of one another - Teratogen – a drug or other substance capable of interfering with the development of a fetus; causing birth defects - Racemic – concerned with, or being a mixture of equal amounts of enantiomers and consequently having no optic activity - Polymerization – process in which monomers link together to form a polymer - Transcription – the mechanism by which the information encoded in DNA is made into a complementary RNA strand - Translation – the use of information encoded in the RNA to assemble amino acids into a polypeptide - RNA world – hypothesis that a world filled with life based on RNA predates the current world based on DNA and protein - Ribozyme – an RNA-bases 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 General Timing - Jan 1 – - Mar 2 – Prokaryotes – 3800mya - Apr 28 – oxygen – 2700mya - Jun 13 – eukaryotes – 2200mya - Aug 12 – multi-cellular eukaryotes – 1400mya - Oct 15 – animals – 600mya - Dec 31 – homosapiens – 150000ya Stages of Pre-biotic Evolution 1. Abiotic synthesis – making building blocks of life from non-biological process 2. Heritable information – for cell to divide passing information to generations below 3. Formation of cells – produce cells to contain reactions – to keep from external environment Early Atmosphere - Water, hydrogen, methane, ammonia, hydrogen sulphide - Energy – lightning, ultraviolet - Reducing atmosphere – have an atmosphere conducive to building large complex reduced molecules Miller-Urey Experiment - Made artificial reducing atmosphere - Important monomer: o Amino acid, sugar, purines, pyrimidines Homochirality - Essential to evolution of life - Specificity required – highly complex interactions – can’t swap out for one another - Random chance and extraterrestrial origin Stages of Biological Evolution - Development of the DNA,RNA, protein triad - Synthesis of polymers - The first cell  Need enzymes  Need ‘product’ to catalyze previous reaction DNA over RNA - RNA information, structure, catalyst and can fold to acquire a structural function you wouldn’t normally have - Protein was able to take over structure and catalyst from RNA - DNA is more stable for holding information o Deoxyribose, thymine replaces uracil, complementary strands Clay Particles - Monomers – polymers o Catalyzed by clay particles o Accelerated by clay due to:  High surface charge  Enhances the formation of the vesicle  Spontaneous Lecture 2: Biochemistry - Proxima Centauri – stars that are closest to the sun - SETI – search for extraterrestrial intelligence - Galaxy – massive, gravitationally bound system that consists of starts, stellar remnants, gas dust and dark matter - Extrasolar planet - planet outside of out solar system - Habitable zone – a region capable of supporting life in a solar system - Cohesion – molecular attraction by which the particles of a body that are united throughout the mass - Heat capacity – characterizes the amount of heat required to change a body’s temperature by a given amount - Heat of vaporization – the heart required to give water molecules enough energy of motion to break loose from liquid water and form a gas - Hydration shell – partially positive; it surrounds the solute and attaches to make bonds with the atoms of the solute, breaking them apart and making them part of the solution - Sublimation – transition of phases directly from a solid to a gas - Fermi paradox – apparent contradiction between estimates of high probability of existence of extraterrestrial civilizations and lack of evidence for or contact with the civilizations The Drake Equations - N = number of advanced civilizations in our galaxy - Ns = number of stars - Fp = fraction of those starts that have planets - Ne = number of planets that can potentially support life - Fe = number of planets that can potentially support life - Fi = fraction of planets that develop intelligent life - Fc = fraction of planets willing and able to communicate - L = average lifetime of a civilization Transit Method - Periodic Brightness o When a planet moves the star dims, the planet moves back out of the way, the star brightens Astrometry/Doppler Spectroscopy - Planet has the ability to have gravitational pill and they pull the star so that it moves (wobbles) Direct Imaging - Actually imaging the planet – optical telescopes o Not used often, works for very big planets Water - Emergent properties o Cohesion o High heat capacity o High heat of vaporization Mars - Project Phoenix o Evidence there is ice on mars o Chemical signature Resolutions of Fermi Paradox - Mainstream astronomy and SETI - Radio emissions - Direct planetary observation Lecture 3: Introductory Biochemistry - Constitutive expression – a gene that is transcribed continually compared to a facultative gene which is only transcribed as needed - Induced expression – responsive to environmental change or dependent on the position of the cell cycle - Transcription factor – proteins that recognize and bind to the TATA box and then recruit the polymerase - Northern Blot – use to study gene expression by detection of RNA or isolated mRNA in a sample - Western Blot – used to detect specific proteins in a given sample of tissue - Peptide bond – a link formed by a dehydration synthesis reaction between the ammonium group of one amino acid and the –COOH group of another - Amino – group that acts as an organic base - Carboxyl group – characteristic functional group of organic acids formed by the combination of carbonyl/hydroxyl group - Aqueous – dissolved in water - Polarity – describes how equally bonding electrons are shared between atoms - Hydrophobic – water hating - Hydrophilic – water loving - Primary structure – refers to an amino acid sequence of a polypeptide chain - Secondary – alpha helix and beta strand - Tertiary – folded protein – into a globule - Quaternary structure – several protein molecules/polypeptide chains - Hydrogen – colourless, odourless, gas - Ionic – electrostatic attraction between two oppositely charged ions - Disulphide – liked sulphide bonds; covalent bonding - Vander Waals – weak molecular attractions over short distances - Nascent peptide – a protein as its being formed by a ribosome before it folds into its active shape - Native conformation – a protein in its operative or functional form - In vitro – a state of being an artificial environment outside the living organism - In vivo – using a whole, living organism in a controlled environment - Urea – organic compound, used in the metabolism of nitrogen-containing compounds - Denaturation – a loss of both the structure and function of a protein due to extreme condition that unfolds it from its conformation - Macromolecular crowding – alters the properties of molecules in a solution when high concentrations of proteins are present - Chaperones – proteins that assist the non-covalent folding/unfolding and the assembly or disassembly of other macromolecular structures - Heat shock proteins – expression is increased when exposed to elevated temperatures or other stressors - Prosthetic group; co-factor – an inorganic/organic non-protein group that is necessary for catalysis to take place Polarity - Polar = negative charge - Non-polar = positive charge - Non-polar – have the hydrophobic effect, becomes unstable, they do not want to interact with water, problem when synthesizing proteins Protein - Molecules that carry out most of the activities of life,
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