chapter 12 gene transcription and rna modification

gene, transcription, copy, not, store

• transcription overview

  • at the molecular level, a …. is a segment of DNA used to make a functional product

    • either an RNA or a polypeptide

  • …. is the first step in gene expression

    • transcription literally means the act or process of making a ….

  • the structure of dna is … altered as a result of this process

    • it continues to …. information

parent, offspring, stores, genes, rna copy, temporary, polypeptide, polypeptide, mrna, functional

• central dogma

  • dna replication: makes dna copies that are transmitted from cell to cell and from …. to …..

  • chromosomal dna: …. information in units called ….

  • transcription: produces an …. …. of a gene

  • messenger rna: a …. copy of a gene that contains information to make a …..

  • translation: produces a … using the information in ….

  • polypeptide: becomes part of a … protein that contributes to an organism’s traits

beginning, end, rna synthesis, regulatory, recognize, act, functional, environmental, trait

• important concepts of transcription

  • dna base sequences define the …. and …. of a gene and regulate the level of … …

    • …. regions

  • many proteins must … and … on DNA for transcription to occur

  • gene expression is the overall process by which the information within a gene is used to produce a … product which can, in concert with ……. factors, determine a …..

regulatory, rate, rna polymerase binding, beginning, end

• DNA transcription:

  • regulatory sequences: site for the binding of … proteins ; the role of regulatory proteins is to influence the … of transcription

    • regulatory sequences can be found in a variety of locations

  • promoter: site for … … … ; signals the …. of transcription

  • terminator: signals the …. of transcription

ribosome binding, begins, eukaryotes, start, first, formylmethionine, methionine, 3 nucleotide, sequence, polypeptide, polycistronic

• mRNA translation:

  • ribosome - binding site: site for … … ; translation …. near this site in the mRNA

    • in ….. , the ribosome scans the mRNA for a …. codon

  • start codon: specifies the … amino acid in a polypeptide sequence, usually a …. (in bacteria) or a …. (in eukaryotes)

  • codons: .. …. sequences within the mRNA that specify particular amino acids

    • the sequence of codons within mRNA determines the …… of amino acids within a polypeptide

  • stop codon: specifies the end of … synthesis

  • bacterial mrna may be …… , which means it encodes 2 or more polypeptides

template, complementary, coding, nontemplate, rna, uracil, thymine, proteins, promoter, regulatory, transcription, translation

• DNA strands, TFs, and regulatory regions

  • the dna strand that is actually transcribed (used as the template) is termed the …. strand

    • the rna transcript is …. to the template strand

  • the opposite dna strand is called the …. strand (….. strand)

    • the base sequence is identical to the …. transcript (except for the substitution of …. in rna for … in the dna template)

  • transcription factors are …. that recognize the …. and …. sequences of genes to control …

  • mrna sequences such as the ribosomal binding site and codons direct …..

dna, template, 3, 5, coding, 5, 3, mrna

• template vs. non template strand

  • transcription: the synthesis of mrna instructions from …

  • rna polymerase transcribes only the … strand (…’ - …’ strand)

  • the non template (…) strand (…’ - …..’ strand) matches the sequence of the …..

phosphodiester, pairing occurs

…. bond is formed by rna polymerase after base … ….

recognition, rna polymerase, denatured, open, dna, open, rna, polymerase, transcript, dissociate, dna, protein, dna

• 3 steps of transcription

  • 1) initiation: the promoter functions as a …. site for transcription factors

    • the transcription factors enables … … to bind to the promoter

    • following binding, the dna is … into a bubble known as the … complex

  • 2) elongation / synthesis of the rna transcript: rna polymerase slides along the … in an … complex to synthesize ….

  • 3) termination: a terminator is reached that causes rna … and the rna …. to … from the …

  • these steps all involve … - …. interactions

structural, mrna, polypeptides, never, rna molecules

• rna transcripts have different functions

  • once they are made, rna transcripts play different functional roles

  • over 90% of all genes are …. genes

    • transcribed into …, and translated into ….

  • the other rna molecules are …. translated

    • final functional products are … ….

nonstructural, not translated, cellular, traits, complex, protein subunits, ribosomes, spliceosomes, signal recognition particles, telomerase

• rna transcripts have different functions

  • the rna transcripts from …. genes are … …

  • they do have various important …. functions, and can still confer …

  • in some cases, the rna transcript becomes part of a … that contains … …

    • …

    • ….

    • … …. …

    • …..

expression, exact, initiation, upstream, begins, bases, start

• bacterial promoters

  • promoters are dna sequences that promote gene ….

    • more precisely, they direct the … location for the … of transcription

  • promoters are typically located just … of the site where transcription of a gene actually ….

    • the … in a promoter sequences are numbered in relation to the transcription …. site

rate, -35, -10, consensus, more, occur

• for many bacterial genes, there is a strong correlation between the .. of transcription and how close the …. and …. sequences are to the … sequences

  • the closer to consensus sequence

    • …. gene expression

    • transcription is more likely to ….

rna polymerase, holoenzyme, core, 5, binding, dna, rna synthesis, sigma, 1, recognizes, promoter

• initiation of bacterial transcription

  • … … is the enzyme that catalyzes the synthesis of rna

  • in E. coli, the rna polymerase … is composed of

    • 1) … enzyme

      • … subunits: alpha2betabeta'primew

      • important in …. to the ….. and catalyzing … ….

    • 2) … factor

      • ….. subunit = sigma

      • …. the …. sequence

holoenzyme, loosely, dna, scans, promoter, sigma, -35, -10, helix, turn, helix, tighter, -35, -10

• initiation of bacterial transcription

  • the rna polymerase …. binds … to the ….

  • it then …. along the dna, until it encounters a … region

  • when it does, the …. factor recognizes both the …. and … regions

    • a region within the sigma factor that contains a .. - … - … structure is involved in a .. binding to the dna in the …. and … regions

sigma, promoter, closed, open, tataat, -10, unwound, separated, 2, short rna, open, sigma, released, end, core, dna, rna, elongation

• transcription initiation

  • initiation occurs when the rna polymerase (… factor) binds to the …. ; forms the …. complex

  • then the … complex is formed when the … box in the … region is ….

    • A-T bonds are more easily …. (only … hydrogen bonds)

  • a … … strand is made within the …. complex, then the … factor is .. at this point which marks the … of initiation

  • the … enzyme now slides down the … to synthesize an … strand (…. phase)

transcript, elongation, template, antisense, coding, transcript, u, open, 17, double, 43

• elongation in bacterial transcription

  • the rna … is synthesized during the ….. stage

  • the dna strand used as a template for rna synthesis is termed the … or …. strand

  • the opposite dna strand is called the … strand

    • it has the same base sequence as the rna ….

      • except that T in dna corresponds to …. in rna

  • the …. complex formed by the action of rna polymerase is about … bases long

    • behind the open complex, the dna reqinds back into a …. helix

  • on average, the rate of rna synthesis is about …. nucleotides per second

dna, open, template, complementary, hybrid, 3, 5, 5, 3, nucleoside triphosphates, pyrophosphate

• elongation in bacterial transcription

  • rna polymerase slides along the …, creating an … complex as it moves

  • the dna strand known as the … strand is used to make a … copy of rna, resulting in an rna-dna …

  • rna polymerase moves along the template strand in a …’ to …’ direction, and rna is synthesized in a …’ to …’ direction using … …. as precursors

    • …. is released

end, short, hybrid, open, separate, newly, rna, polymerase, dependent, rho, independent, not

• termination of bacterial transcription

  • termination is the …. of rna synthesis

    • it occurs when the …. rna-dna … of the … complex is forced to …

      • this releases the …. made .. as well as the rna …..

  • E. coli has 2 different mechanisms for termination

    • 1) rho … termination

      • requires a protein known as p (…)

    • 2) rho … termination

      • does …. require p

utilization, p, rut, rna, 3, helicase, separate, polymerase, stem loop, terminator, pause, open, separates, hybrid

• p dependent termination

  • rut (rho …. site)

  • …. protein binds to the .. site in … and moves toward the …’ end

    • rho protein is a ….. - will … the rna/dna hybrid

  • rna …. transcribes a region that forms a …. … and then proceeds to the ….

    • the stem loop causes rna polymerase to ….

  • during this pause, p protein catches up to the … complex and …. the rna-dna ….

rna, uracil rich, 3, stem loop, upstream, uracil rich

• p independent termination is facilitated by 2 adjacent sequences in the …

  • 1) a … … sequence located at the …’ end of the rna

  • 2) a … … structure …. of the … … sequence

pol, pause, NusA proteins, u, a, dna, weak, dissociates, dna, weak, termination, no, rna, dna, intrinsic

• p independent termination

  • stem loop causes rna … to ….., which is stabilized by … …

  • at this point, the …. rich region is bound to the …. rich …. region, which is …. = rna pol spontaneously .. from the ….

  • U rna - A dna hydrogen bonds are relatively ….

  • while rna polymerase pauses, the weakly bound u rich sequence is not able to hold the rna-dna hybrid together

    • …. occurs

  • …. protein is required to physically remove the …. from the …

  • this type of termination is also called …

eukaryotic transcription

bacteria, more complex, large, organelles, proteins, multicellularity, correct, time

• transcription in eukaryotes

  • basic features are very similar in …. and eukaryotes

  • however, gene transcription in eukaryotes is .. …

    • ……., more complex cells (….0

      • more genes that encode ….. are required

    • ….. adds another level of regulation

      • expression of genes is restricted to the …. cells at the proper …

nuclear, rrna, 5s, structural, mrnas, snrna, splicing, trna, 5s rrna, microrna

• eukaryotic rna polymerases

  • ….. dna is transcribed by 3 different rna polymerases

    • RNA pol 1

      • transcribes all …. genes (except for the …. rrna)

    • rna pol 2

      • transcribed all protein encoding (….) genes

        • thus synthesizes all …..

      • transcribes some …. genes needed for …..

    • rna pol 3

      • transcribes all …. genes

      • the … …. gene

      • ….. genes

similar, many, jaw, rudder, hybrid apart, clamp, movement, enzyme, bend, addition, nucleotides, template

• structure of rna polymerase

  • all 3 euk pols are very …. structurally and are composed of …. subunits

  • remarkable similarity between the bacterial rna pol and euk rna pols

  • notes

    • dna enters through …

    • …. forces rna-dna …. …..

    • …. controls … of dna through ….

    • rna-dna hybrid forced to … facilitating … of … to ….

promoter, tata, transcriptional start, enhancer, silencers

• sequences of eukaryotic structural genes

  • eukaryotic promoter sequences are variable and often more complex than those of bacteria

  • most eukaryotic genes have 2 features

    • 1) core ….

      • typically sequence TATAAA (….. box)

      • … … site

    • 2) regulatory elements

      • …. / …..

short, TATA, transcriptional start, precise, low, basal

• the core promoter is relatively …

  • it consists of the …. box and … …. site

    • important in determining the … start point for transcriptional

• the core promoter by itself produces a … level of transcription

  • this is termed …. transcription

short dna sequences, polymerase, promoter, rate, stimulate, inhibit, -50, -100, upstream

• regulatory elements are … .. … that affect the binding of rna … to the …..

• regulatory transcription factors bind to these elements and influence the … of transcription

  • 2 types of regulatory elements

    • enhancers - ….. transcription

    • silencers - … transcription

• they vary widely in their locations but are often found in the … to … regions that is … from the core promoter

action, cis, dna sequences, particular, tata, enhancers, silencers, trans, regulatory proteins, cis

• regulators of gene expression

  • factors that control gene expression can be divided into 2 types, based on their …

    • 1) … acting elements

      • …. … that exert their effect only over a …. gene

      • example: …. box, …. and …

    • 2) … acting elements

      • ….. …. that bind to …. acting elements

promoter, 2, general transcription factors, mediator

• rna polymerase 2 and its transcription factors

  • 3 categories of proteins are required for basal transcription to occur at the ….

    • rna polymerase …

    • 5 different proteins called … … .. (GTFs)

    • a protein complex called …..

tfiid, proteins, tata, tfiib, binding, polymerase 2, promoter, tfiif, polymerase 2, tfiie, tfiih, polymerase 2, preinitiation, closed, helicase, open, phosphorylates, c, polymerase 2, tfiib, polymerase 2, tfiib, tfiie, tfiih, elongation

• assembly of transcription factors and rna polymerase 2 at the TATA box

  • …. binds to the TATA box. It is a complex of ….. that includes the ….-binding protein (TBP) and several TBP associated factors (TAFs)

  • …. binds to TFIID

  • TFIIB promotes the …. of rna … … to the core …

  • …. is bound to rna … ….

  • …. and …. bind to rna …. … to form a …. or … complex

  • TFIIH acts as a …. to form an …. complex

  • TFIIH also … the …-terminal domain of rna …. …

  • c terminal domain phosphorylation breaks the contact between … and rna … …

  • …, …, and … are released

  • rna polymerase 2 can now proceed to the ….. stage

2, gtfs, large protein, mediator, 2, regulatory, enhancers, silencers, complex, partially, 2, phosphorylate, ctd, tfiih, ctd, initiation, elongation

• basal transcription apparatus

  • = rna polymerase …. + the five …..

• the 3rd component required for transcription is a … … complex termed ….

  • mediates interactions between rna polymerase …. and various …. TFs that bind …. or …

  • its subunt composition is …. and variable

  • core subunits … wraps around rna polymerase …

  • mediator may ….. the ….. of rna polymerase 2 and it may regulate the ability of …… to phosphorylate the …

    • therefore, it plays a pivotal role in the switch between transcriptional …. and …..

pre, 3, adenines, downstream, polyA, 2

• RNA pol 2 transcriptional termination

  • ….-mRNAs are modified by cleavage near their ….’ end with subsequent attachment of a string of ….

  • transcriptions terminates 500 to 2000 nucleotides ….. from the …. signal

  • there are …. models for termination

    • further research is needed to determine if either, or both are correct

2, polyadenylation, past, polyadenylation, transcribing, destabilized, dissociates, elongation, termination, occurs

• Allosteric model (mechanism for pol 2 termination)

  • rna polymerase … transcribes a gene past the …. signal sequence

  • the rna is cleaved just … the …. signal sequence

  • rna polymerase continues …… the dna

  • after transcribing the polyadenylation signal sequence, rna polymerase 2 is …. and …. from the dna

    • this may be caused by the release of …. factors or the binding of … factors

    • termination ….

2, polyadenylation, past, polyadenylation, transcribing, exonuclease, 5, 5, 3, 2, termination

• torpedo model (mechanism of rna pol 2)

  • rna polymerase … transcribes a gene past the …. signal sequence

  • the rna is cleaved just … the …. signal sequence

  • rna polymerase continues …… the dna

  • an …. binds to the …’ end of the rna that is still being transcribed and degrades it in a …’ to …’ direction

  • exonuclease catches up to rna pol .. and causes ….

rna modification

coding, nucleotides, mrna, sequence, polypeptide, colinearity, eukaryotic, not, functional

• colinear or not?

  • analysis of bacterial genes in the 1960s and 1970 revealed the following:

    • the sequence of dna in the …. strand corresponds to the sequence of … in the ….

    • the sequence of codons in the mrna provides the instructions for the …. of amino acids in the …

  • this is termed … of gene expression

  • analysis of …. structural genes in the late 1970s revealed that genes are …. always colinear with their … mrnas

exons, introns, pre, entire, excised, connected, spliced, splicing, eukaryotes, occasionally

• rna modifiation

  • coding sequences (….) in eukaryotes, are interrupted by intervening sequences (….)

  • transcription produces a …-mrna corresponding to the …. gene sequence

    • introns are later removed (…)

    • exons are …. together (….)

  • this phenomenon is termed rna ……

    • it is a common genetic phenomenon in …..

    • occurs …. in bacteria as well

rrna, trna, smaller, 5, capping, 3, polyA tailing, mrna

• other rna modifications

  • aside from splicing, rna transcripts can be modified in several ways

    • for example

      • processing of … and … transcripts to …. functional pieces

      • …’ …. and …’ … … of …. transcripts

nonstructural, large, smaller

• processing of mammalian ribosomal rna

  • many …. genes are initially transcribed as a … rna which is then enzymatically cleaved into …. functional pieces

transfer, 5, 3, functional, exonucleases, endonucleases, phosphodiester, 2, end, within

• processing

  • …. rnas are also made as large precursors

    • these have to be cleaved at both the …’ and ….’ ends to produce mature, …. trnas

  • cleaved by …. and ….

    • exonucleases cleave a … bond between … nucleotides at one … of a strand

    • endonucleases can cleave bonds … a strand

RNaseP, endonuclease, 5, rnasep, rna, protein, RNaseD, exonuclease, 9

• trimming of a precursor trna

  • …., an …., makes a cut here that creates the …’ end of the mature trna

    • ….. contains both …. and … subunits

  • …., an …., removes … nucleotides

methylguanosine, 2, isopentenyladenosine, pseudouridine, 4, thiouridine

• trimming of a precursor trna

  • covalently modified bases of the trna

    • mG = ….

    • IP = …-…..

    • P = ….

    • T = ….-…..

1 intron, 2 intron, spliceosome, intron, exon, phosphodiester

• splicing

  • 3 different splicing mechanisms have been identified

    • group … … splicing

    • group … … splicing

    • …..

  • all 3 cases involve:

    • removal of the … rna

    • linkage of the … rna by a …. bond

1, 2, self, splicing, enzymes, ribozyme, rrnas, trna, removed, connected, vitro without, maturases, enhance

• splicing among group … and …. introns is termed …-….

  • this does not require the aid of …

  • instead the rna itself functions as its own …

  • occurs mainly in … and …

• group 1 and 2 differ in the way that the intron is … and the exons are …

• group 1 and 2 self-splicing can occur in … ….. the additional proteins

  • however, in vitro, proteins known as …. often … the rate of splicing

guanosine, within, intron, exon 1, intron, 5, intron, exon 1, 2, phosphodiester, linear intron

• group 1 (self splicing)

  • free … binds to a site …. the ….

    • breaks the bond between … … and …

      • becomes attached to …’ end of ….

  • results in … … and … covalently joined by … bond and free, … ….

2, hydroxyl, adenine, intron, exon 1, intron, linkage, lariat

• group 2 (self splicing)

  • …’ … from … within … breaks bond between … … and …

  • results in exon 1 and 2 …. and intron as …..

long, pre, splicing, before, nucleus, spliceosome, snrnps, small nuclear rna, proteins

• pre-mRNA (splicing via a spliceosome)

  • in eukaryotes, the transcription of structural genes produces a … transcript known as …-mRNA

  • this rna is altered by … and other modifications, … it leaves the …

  • splicing in this case requires the aid of a multicomponent structure known as the …

    • this structure is composed of several subunits known as …

      • each snRNP contains … .. … and a set of …..

bind, intron, recognize, intron, exon, hold, pre, configuration, catalyze, remove, link

• pre-mrna splicing

  • the subunits of a spliceosome carry out several functions

    • 1) … to an … sequence and precisely … the …-… boundaries

    • 2) … the …-mRNA in the correct …

    • 3) … the chemical reactions that …. introns and covalently … exons

5, branch

…’ splice site and … site serve as recognition sites for the binding of the spliceosome

5, branch, 4, 6, 5, loops, closer, 5, 5, intron, a, branch, lariat, 1, 4, snrna, 2, 6, 3, 1, 2, intron, 2, 5, 6, degraded, exons

• pre-mRNA splicing mechanism

  • U1 binds to …’ splice site

  • U2 binds to …. site

  • U…/U…. and U…. trimer binds

  • intron … out and exons are brought … together

  • …’ splice site is cut

  • ….’ end of … is connected to the … in the … site to form a …

  • U… and U… are released

  • cleavage may be catalyzed by … molecules within a U…. and U….

  • …’ splice site is cut

  • exon … is connected to exon …

  • the …. (in the form of a lariat) is released along with U…, U…, and U…

  • the intron will be …

  • two connected ….

alternative splicing, multiple, mature, exons, types, development

• intron advantage?

  • one benefit of genes with introns is a phenomenon called … ..

  • a pre-mRNA with … introns can be spliced in different ways

    • this will generate …. mRNAs with different combinations of …

  • this variation in splicing can occur in different cell … or during different stages of …..

2, more, polypeptides, single, fewer, genome

• intron advantage?

  • the biological advantage of alternative splicing is that … (or ….) … can be derived from a … gene

  • this allows an organism to carry … genes in its ….

eukaryotes, 2, protein, species, baker’s yeast, 5, 23,000, 70

• alternative splicing

  • biological advantage of introns in … is alternative splicing

  • pre-mRNA can be splicing in more than one way

    • …. alternative versions of a …. that have similar functions

    • each protein with its own unique characteristics

  • the degree of splicing varies greatly among different ….

    • …. … contains about 6,300 genes

      • ~300 (….%) encode mrnas that are spliced

    • humans contain ~….

      • most of these encode mRNAs that are spliced

        • …% are alternatively spliced

7, methylguanosine, 5, capping, 2, 20, 25

• capping

  • most mature euk mRNAs have a ..-… covalently attached at their ..’ end

    • this event is known as ….

  • capping occurs as the pre-mRNA is being synthesized by rna pol …

    • usually when the transcript is only …. to …. long

5, triphosphate, phosphate, guanylyltransferase, gtp, gmp, 5, ppi, methyltransferase, methyl, finished

• 3 step capping process

  • rna …’ … removes a …

  • …. hydrolyzes …

  • the … is attached to the ..’ end and …. is released

  • … attaches a …. group

  • occurs before transcription is …

7, methylguanosine, proteins, movement, cytoplasm, early, translation, splicing, introns

• consequences of capping

  • the ….-… cap structure is recognized by cap-binding ….

  • cap-binding proteins play roles in the:

    • …. of some RNAs into the …

    • …. stages of …

    • ….. of …..

adenine, 3, polyA tail, not, enzymatically, transcribed

• polyadenylation

  • most mature mRNAs have a string of …. nucleotides at their ..’ ends

    • this is termed the … …

  • the polyA tail is … encoded in the gene sequence

    • it is added … after the gene is completely ….

higher, endonuclease, 20, downstream, polyA, adenine, 3, export, nucleus, stability, mrna, translation, polypeptide, 250

• polyadenylation

  • polyadenylation signal sequence = AAUAAA

    • consensus sequence in …. eukaryotes

  • …. cleavage occurs about …. nucleotides … from the AAUAAA sequence

  • …-polymerase adds …. nucleotides to the …’ end

  • polyA tail important in … from the …., the … of …, and the … of the ….

    • length varies between mRNAs

    • max length around … nucleotides

leder, electron, beta, hybridization, double, cloned, denatured, mature, complementary, hybridize, reformation, double

• introns were discovered via microscopy

  • phillip … used …. microscopy to identify introns in the …-globin gene, which had been previously cloned

    • he used a strategy that involved …

  • … stranded dna of the …. beta globin gene is first …

    • then mixed with … beta globin gene

  • the mRNA is … to the template strand of the dna

    • so the 2 will bind or .. to each other

      • if the dna is allowed to renature, this complex will prevent the …. of the dna …. helix