Tuesday(9/13(prokaryotes(• Rna(folds(up(into(these(stems(and(loops(• Small(rnas(are(involved(in(splicing(and(regulation(• Transcription(–(making(an(rna(molecule(from(the(dna(template,(made(in(5’(to(3’(direction,(means(template(is(running(3’(to(5’.(The(nontemplate(strand(has((the(same(sequence(as(the(rna.(• Rna(polymerase(causes(the(promoter(to(start(synthesizing.((• Terminal(genes(stop(the(rna(polymerase(so(it(doesn’t(go(all(the(way(around(the(genome.(• Rna(polymerases(don’t(need(a(primer(they(can(start(on(a(bare(strand(of(dna(• Rna(polymerase(can(recognize(the(gene(and(will(start(transcribing.(• Can(alrign(a(bunch(of(genes(and(form(a(consensus(sequence.(c/g(they(use(when(they(are(50/50.((• First(base(transcribed(is(labeled(as(+1(• The(closer(the(gene(matches(the(consensus,(the(more(highly(the(gene(expression(is(going(to(be(• Core(rna(polymerase(–(2(alpha(and(2(beta(subunits,(the(sigma(factor(is(an(additional(protein(that(recognizes(the(consensus(sequence(and(increasing(the(binding(to(those(particular(sites.(Gives(specificity(to(consensus(sequence(• To(stop(transcription,(one(mechianism(is(rhoMindependent(mechanism.(Relies(ona(particular(sequence(at(the(end(of(the(gene,(a(pair(of(inverted(repeats(that(form(a(step(loop(structure(in(the(transcript.(AU(bonds,(less(tightly(bound(to(make(rna(not(very(well(attached(to(the(template.((• Other(mechanism(–(rho(dependent,(requires(a(rho(protein.(Rho(protein(chases(the(polymerase(and(dislodges(it.(Rna(pauses(from(the(hair(pin(loop(and(gives(time(for(the(rho(protein(to(catch(up.((Eukaryotes(• Have(4(polymerases(to(transcribe(different(classes(of(genes(• Promoters(are(bigger(and(more(complex(• Core(promotor(has(a(M25(box((• Upstream(also(have(recognizable(consenuses(sequences.(Show(if(a(gene(is(going(to(be(highly(expressed.((• Transcription(complex(–(tata(binding(protein,(binds(2(core(promotor,(together(with(tfiid(are(the(first(to(bind(and(recognize(core(promotor.(Must(recrut(all(the(other(elements(of(rna(polymerase(II.((• Footprinting(experiments(–(piece(of(dna(,(mix(some(of(this(dna(with(proteins(of(choice,(dnaseI(chews(up(all(of(the(dna(that(is(not(protected(by(a(protein(wrapped(around(it,(leaves(over(a(set(of(fragments,(bands(indicate(where(dnaseI(cut(the(bases((0(with(slash(through(it).(As(we(increase(the(amount(of(protein(there(are(no(cuts,(showing(that(protein(is(protecting(a(part(of(the(sequence.(Seeing(footprints(of(where(protein(is(nteracting(dna(and(protecting(it(from(degredation.(• Termination(–(not(as(tightly(regulated(as(prokaryotes,(mrna(as(its(being(transcribed(downstream(will(have(a(consensus(sequence(that(will(initate(protein(cleavage(to(release(mrna,(but(rna(polymerase(is(still(running(along.(The(rat1(endonuclease(chases(the(polymerase(down(and(will(dislode(it(so(it(doesn’t(continue(transcribing(to(the(next(gene.((Chapter(14MRNA(molecules(and(rna(processing(• Basic(prok(messanger(rnaM(start(of(transcription,(usually(first(part(isn’t(translated(into(protein,(then(a(consensus(sequence(called(shine(dalgarno(sequence(which(is(where(the(ribosome(recognizes(where(it(shoud(start(translating.(Start(and(stop(codon.(Then(after(there(is(also(an(uncoded(region.(• Euk(mrnas(have(3(different(modifications:(5’(cap(–(a(guanine(that(is(put(on(backwards(5’(to(5’(linkage.(After(the(5’(is(added,(the(bases(get(metyl(groups.((• The(3’(end(also(gets(modified(with(a(poly(a(tail.(A(long(stream(of(A’s(that(protects(the(3’(end(and(is(important(in(regulation(of(translation.((• Central(dogma(isn’t(true(in(euks.(Introns(–(intervening(regions.(Mrna(gets(chopped(down(to(eliminate(introns.(Called(splicing.(Splicing(the(exons(together(and(in(the(process(removing(the(introns.((• GtMag(rule(–(first(2(and(last(2(bases(in(an(intron.(Look(for(that(structure(to(find(the(boundary(of(the(introns.((• 90%(of(ur(genes(at(alternitavely(splices(((9/15(lecture(• there(are(some(introns(that(can(splice(out(themselves,(first(evidence(of(rna(acting(as(an(enzyme.(• Gives(some(insight(into(the(early(stages(of(life(of(the(RNA(world,(could(be(the(entire(genetic(system(all(by(themselves.(• Cleaving(is(when(you(cut(a(piece(on(t he(end(off,(splicing(is(cutting(out(something(in(the(middle(and(putting(the(pieces(back(together.(• Substitution(editingM(substitutes(one(base(for(another(to(produce(a( different(protein.((Transfer(RNA(• Transfer(rnas(have(a(clover(leaf(structure.(4(arms,(one(is(an(acceptor(arm,(at(3’(end(ACC(is(the(amino(acid(acceptor.(Anticodon(arm(interacts(with(the(mrna(to(help(get(the(right(bases.(• Trna(is(transcribed(as(a(regular(rna(but(modifers(come(in(to(change(some(of(the(bases.((• Tnra(has(a(precursor(that(has(to(be(cleaved(off(and(an(intron(that(has(to(be(spliced(out,(brings(you(to(the(basic(trna,(t hen( thers(there(addition(of(the(ACC(added(to(the(end(of(the(3’(and(some(modification(of(the(bases.((rRna(• Bacterical(rubisomes(have(2(subunits(to(make(a(70s(ribosome(that(includes(rna(components(and(protein(components.(((• Start(with(double(stranded(rna(that(gets(processed(and(associated(with(a(protein(that(somehow(inhibits(the(message(in(your(body.(• miRNAs(are(important(to(development(and(gene(expression(• rna(transcribed(in(nucleus,(processed(mostly(in(the(nucleus,(3(regions(found(in(all(mrna(–(5’(untranslated(region,(3’(untranslated(region,(start(codon,(stop(codon.(Be(able(to(draw((a(prokaryotic(mrna(and(eukaryotic(one.(• Intron(–(in(between(region(with(no(genetic(info(• Modificatiosn(on(an(mrna((((Chapter(15(–(Genetic(Code(and(Translation(• Series(of(arguments(and(experiments(that(led(to(the(genetic(code(1) Logic(–(have(4(nucleotides(and(need(20(amino(acids.(Must(be(a(triplet(code(=(64(different(codes,(which(is(more(than(enough(to(code(for(20(different(amino(acids.((2) Insertional(MutagensM(a(set(of(experiments,(drugs(proflavin(which(are(mutagins(and(insert(themselves(into(the(helix,(acts(as(a(nucleotide,(causes(intsertion,(mutations(and(deletions.(THE(BIG(DOG(ATE(THE(FAT(CAT(–(experminets(that(an(be(associated(with(a(certain(amino(acid(triplet,(found(that(whenever(they(had(an(insertion(of(one(base(it(was(a(mutant(changed(the(entire(code,(if(they(combined(a(+1(mutiation(with(a(M1(mutation(then(it(becomes(normal(wild(type,(+3(or(M3(were(also(wild(type.(Code(is(not(overlapping.((3)