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bio 112 midterm.odt

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University of British Columbia
BIOL 112

Cell theory 1.1 robert hooke uses weak microscopes composed of same fundamental building block—cell cell - highly organized compartment that is held with plasma membrane in watery solution all cells arise from previous cells all organisms made of cells all cells are connected by common ancestry natural selection - survival of fittest- more offspring Tree of life 1.3 eukaryotic- have membrane bound nucleus prokaryotic-free floating nucleus/genetic material phylogeny- tribe source—actual genealogical relationships studied rRNA, used it to compare the ribonucleotide order phylogenetic tree-- shows relationships among species more similar - closer together on tree 3 domains: BACTERIA, ARCHAEA, EUKARYA Doing Biology 1.4 Hypothesis, prediction, tests, observations, results need control group to be accurate+ repetition Building Blocks of Chemical Evolution 2.1 O>>N>C-H make up 96% of organisms theory of chemical evolution- simple compounds in ancient atmosphere + ocean- complex substances electrons(much smaller than protons) - negative charge atomic number- number of protons( positive charge) isotopes- same element diff mass number( prot+ neut) electrons move around in regions called orbitals each orbital-2 electrons grouped into electron shell 1,2,3............ valence- unpaired electrons in outer shell atom is stable when valence shell filled-- uses Chemical bonds covalent- shared electrons electronegativity- amount of nrg want e- Ionic bonds- transfer of electrons cation- positive charge anion- negative charge polar bonds- unequal sharing of electrons double bond- share 2 triple- share 3 CH4-tetrahedron H20- bent molecular formula- numbers and types of atoms in mlcl structural formula-shows the bonds ball and stick - shows angles space filling models-actual representative of model Early oceans and properties of water 2.2 most important to life - water water- solvent (dissolves substances into solution) polar so makes hydrogen bonds between other water mlcls hydrophillic- water loving hydrophobic- water hating cohesion- binding with like molecules adhesion- binding with unlike molecules(not straight if held in a cup - meniscus) surface tension- elastic membrane formed from cohesion and adhesion Density- liquid > solid high capacity for absorbing heat acids - proton donor base - proton acceptor ph= -logH H= antilog(-ph) Buffers- maintains pH by becoming weak base or acid Importance of Carbon 2.4 carbon- most versatile atom because of 4 valence electrons can from many covalent bonds contains C- organic no C- inorganic functional groups- attaches to C and gives characteristics * refer page 41 What do proteins do 3.1 Proteins are used for: Defense- antibodies destroy disease Movement- motor and contractile proteins moves the cells Catalysis- speed up a chemical reaction using enymes Signalling- peptide hormones carry and receive signals Structure- gives mechanical support Transport- Passage of specific molecules/ions Amino Acids and Polymerization 3.3 Amino acids- 21 types that make up proteins carbon attaches to amino group (NH2), carboxyl group(C-OOH), H and R group Hydrophobic R groups (nonpolar) cannot form h bonds with water polar or charged R groups can form H bonds with R groups ( hydrophillic) *Refer p 49 If R groups are not charged/ polar the chemical behaviour depends on size/ shape Structural isomers- same atoms but different order of bonds Geometric isomers- same atoms but diff arrangements of atoms around dbl bond Optical isomers- same atoms but diff arrangements around C atoms amino acids are called monomers lots of them are called polymers polymerization- joining of amino acids protein- macromolecule and a polymer polymerize through condensation reactions AKAdehydration synthesis- monomers in water out hydrolysis- water in monomer out C of carboxyl group combines with N of amino groups peptide bond forms ( as strong as dbl) when a.a are linked by peptide bonds into chain they are called residues resulting molecule is polypeptide peptide bonded backbone a.a always numbered starting from N terminus single bonds beside peptide bonds - flexible and rotates <50 - oligopeptide/ peptide >50- protein What do proteins look like 3.4 Proteins serve diverse functions because of their diverse size and shape underlying structure of protein - same 4 lvl of organization Primary structure- unique sequence of amino acids 21^n fundamental to function and to determine higher lvls of protein structure Secondary structure- Created by H bonding between carboxyl group + amino group not by R group forms- alpha helix and beta pleated sheets formation depends on primary structure esp the geometry of a.a increase stability and define shape Tertiary structure- created from interactions between R groups causes peptide bonded backbone to bend and phone → 3d shape of polypeptide hydrogen bonds between R group and carboxyl when hydrophobic chains are close to each other makes van der waals interaction(weak chrg) covalent bonds between sulfur containing R groups makes disulfide bond ionic bond form between full opposing charges Quaternary structure- combination of several polypepties held together by interactions of R groups, bonds, peptide backbone protein with 2 polypeptide called dimers *refer p 59 protein structure is hierarchical. Higher lvls based on previous ones folding is spontaneous in some cases- bonds that occur makes mlcl more stable so it can be exergonic denature- protein can be unfolded and no longer functional folding facilitated by specific protein called molecular chaperones proteins function depends on shape; shape depends on folding Enzymes 3.5 brings substrates together in precise orientation into a transition state and finally products activation energy- nrg required to reach transition state need kinetic energy to reach the state so higher temp - faster catalyst - lowers activation energy can increase rxns up to trillions times faster enzymes bring reactants together and stabilize transition states. Proposed theory - lock and key substrate fits into active site of enzyme actual- induced fit theory enzyme changes shape slightly to bind substrate interactions with R groups at active site lowers activation nrg *refer p 64 enzyme catalysts - initiation(precise collision), transition state facilitation(lower nrg), termination(products less affinity so releases) Cofactors and organic mlcls called coenzymes help with enzymes they stabilize transition state enzymes are regulated by mlcls that change the protein structures competitive inhibition- slows down rxn by competing with substrates allosteric regulation- mlcl binds with enzyme and changes the shape of it substrate concentration low - increases in linear fashion substrate concentration high- levels out at max speed (saturated) pH and temperature affects enzyme for better or for worse Lipids 6.1 carbon containing compound which are non polar and hydrophobic can still dissolve in liquids with non polar organic compounds mlcls that contain only H and C - hydrocarbons non polar fatty acid- type of compound consists of hydrocarbon chain bonded to carboxyl group key building blocks of lipids Lipids defined by solubility so structures varies fats- 3 fatty acids linked to glycerol thru dehydration synthesis AKAtriglycerides joined by an ester linkage page 101 fats are not polymers and fatty acids arent monomers steroids-
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