BioChem(Final(Review(PART%I:%INTRODUCTION%I. Foundations(of(Biochemistry(a. Properties(that(distinguish(organisms:(i. High(degree(of(chemical(complexity(and(microscopic(organization(ii. Systems(for(extracting,(transforming(and(using(energy(1. Counteracts(entropy((moving(towards(disorder)(iii. Functions(for(each(component(of(an(organism(and(regulated(integration(of(functions(iv. Mechanisms(for(sensing(and(responding(to(external(stimuli(v. Capacity(for(exact(selfGreplication(and(assembly(vi. Capacity(to(change(over(time(via(evolution(II. Cellular(Foundations(a. The(Cell(i. Plasma(membrane(–(defines(the(periphery(of(the(cell;(barrier(between(the(cell(and(the(environment(1. Composed(of(lipid(and(protein(molecules(that(form(a(hydrophobic(barrier(around(the(cell.((2. Allows(passage(of(charged((polar)(particles,(receptor(proteins,(and(enzymes.(3. Incredibly(flexible,(can(grow(with(the(cell(by(adding(additional(lipid(and(protein(molecules(4. Never(loses(membrane(integrity((never(a(hole)(ii. Cytoplasm(1. Composed(of(an(aqueous(solution(called(the(cytosol(a. Cytosol(is(concentrated(with(enzymes(and(RNA(molecules,(component(molecules((amino(acids,(nucleotides,(etc.),(metabolites((small(organic(molecules),(coenzymes,(inorganic(ions,(ribosomes(and(proteasomes%(which(degrade(proteins)(iii. Nucleus(1. Stores(the(genome(–(composed(of(DNA(a. Eukaryotes(have(a(membrane(separating(nucleus(from(cytosol(called(nuclear(envelope(b. Prokaryotes(have(no(double(membrane(b. Cell(Size(Limits(–(Diffusion(i. Smallest(cells(have(a(volume(of(~(10G14(mL(ii. Upper(limit(of(cell(size(is(due(to(rate(of(diffusion(of(solute(molecules(c. Three(Distinct(Domains(i. Archae,(Bacteria(and(Eukarya(1. Archae(and(Bacteria(Classifications(a. Aerobic(vs.(Anaerobic(i. Obligate(Anaerobes((oxygen(is(poisonous)(ii. Facultative(Anaerobes((“ambidextrous”)(b. Energetic(Classification(i. Phototrophs((use(sunlight)(1. Autotrophic(or(heterotrophic(ii. Chemotrophs((oxidation(of(chemicals)(1. Autotrophic(or(heterotrophic(iii. Organotrophs((use(organic(compouds)(d. Membrane(Bound(Organelles(of(Eukarya(i. Mitochondria(–(energy(production(ii. Endoplastic(Reticullum(–(transport(and(ribosome(synthesis(iii. Golgi(complexes(–(packaging(and(transport(iv. Peroxisomes(–(used(for(breakdown(of(fatty(acids(v. Lysosomes(–(breakdown(everything(else(vi. Separated(by(fractionation(1. Fractionation(–(using(many(different(staged(centrifuge(speeds(to(separate(out(components(of(the(cell(by(density(to(isolate(these(components(e. Cytoskeleton(i. The(three(dimensional(mesh(of(protein(filaments(that(forms(the(skeletal(structure(of(a(eukaryotic(cell(ii. Contains(three(types(of(filaments(differing(in(width,(composition,(and(function(1. Actin(filaments((used(for(locomotion)(2. Microtubules((used(for(locomotion)(3. Intermediate(filaments(iii. Endomembrane(system(–(segregates(specific(metabolic(processes(and(provides(surfaces(for(reactions(1. Exocytosis(–(transports(materials(out(the(cell(via(membrane(fusion(and(fission;(used(for(secretion(2. Endocytosis(–(transports(materials(into(the(cell(via(membrane(fusion(and(fission;(used(for(extracellular(upta k e((ingestion)(f. Supramolecular(Structures(i. Differ(greatly(in(size,(from(just(0.5(nm(to(1(μm(ii. Subunits(of(proteins,(nucleic(acids,(and(poly(saccharides(are(joined(by(covalent%bonds(iii. Supramolecular(structures(are(held(together(mainly(by(weaker,(nonGcovalent(bonds,(hydrogen%bonds((between(polar(groups),(ionic(interactions,(hydrophobic(((among(nonpolar(groups(in(aqueous(solution),(and(van(der(Waals(interactions((London(forces)(III. Chemistry(Foundations(a. Carbon(in(Biomolecules(i. Carbon’s(Bonding(Capacity(1. Carbon(can(form(single(bonds(with(hydrogen(atoms(2. Forms(doubles(bonds(with(oxygen(and(nitrogen(3. Forms(stable(single(bonds(with(up(to(four((4)(other(carbon(atoms(4. It(can(also(share(double(bonds(with(two(other(Carbon(atoms,(or(a(triple(bond(with(another(Carbon(atom.(ii. Structure(of(bonds(1. Four(single(bonds(with(other(carbon(atoms(forms(a(tetrahedron(with(bond(angles(of(109.5°((2. This(formation(allows(for(free(rotation(depending(on(the(functional(groups(that(are(attached(3. Double(bonds(are(shorter(than(single(bonds(iii. Functional(Groups(1. All(biomolecules(are(derivatives(of(hydrocarbons(2. Functional(groups(replace(hydrogen(atoms(3. Most(common(are(alcohols,(amines,(aldehydes,(ketones,(and(carboxylic(acids(4. Many(are(polyfunctional((more(than(one(functional(group)(with(unique(chemical(characteristics(and(reactions(b. Universal(Set(of(Small(Molecules(i. Primary%metabolites((small(organic(molecules(in(every(cell)(1. Includes(amino(acids,(nucleotides,(sugars,(carboxylic(acids,(and(derivatives(of(each(of(the(listed(molecules(2. Generally(polar,(waterGsoluble,(and(present(in(very(small(concentrations(ii. Secondary%metabolites(1. Metabolites(that(are(not(present(in(every(cell(but(are(rather(unique(to(certain(types(of(cells(a. Ex.(Nicotine,(morphine,(quinine(and(caffeine(in(plants(2. Entire(collection(of(small(molecules(is(known(as(metabolome(c. Macromolecules((i. Major(constituents(of(cells(–(polymers(assembled(from(simple(precursor(molecules(1. Shorter(polymers(are(called(oligomers(2. Proteins,(nucleic(acids,(and(poysaccharides(are(examples(ii. Proteins((sum(of(all(is(called(the(cell’s(proteome)(1. Polymers(of(amino(acids(2. Compose(largest(fraction(of(the(cell((besides(water)(3. Some(have(catalytic(activity;(function%as%enzymes(4. Also(can(be(structural(elements,(signal(receptors,(or(transporters(5. Most(versatile(biomolecule(iii. Nucleic(acids((1. Store(genetic(material(in(the(form(of(DNA(and(RNA(2. RNA(molecules(can(have(both(structural(and(catalytic(roles(iv. Polysaccharides(1. Polymers(of(simple(sugars(such(as(glucose(2. Three(main(functions(a. Sources(of(energy((contain(large(amounts(of(energy)(b. Rigid(structural(components(of(cell(walls(c. Extracellular(recognition(elements(–(can(be(located(on(proteins(or(on(cell(surface(to(provide(signal(v. Lipids(1. Water(insoluble(hydrocarbon(derivatives(2. Structural(components(of(membranes((phospholipid(bilayer)(3. Energy(rich(fuel(sources(4. Can(act(as(pigments(and(intracellular(signals(vi. Proteins(and(nucleic(acids(are(considered(informational(macromolecules(d. 3GD(Structure(–(Configuration(and(Conformation(i.