RNA Synthesis: Transcription

Question 2

Gene

The entire __ ___ sequence that is necessary for the ____ of a ___ ___ or the synthesis of a particular ___transcript (__ __ or ___)

Answer 2

The entire nucleic acid sequence that is necessary for the synthesis of a functional polypeptide or the synthesis of a particular RNA transcript (rRNA, tRNA and microRNA)

Question 3

The Genetic Code

• 3 bases code for each amino acid known as codons
• No ___ or “___”
• __ reading frames
• ___ starting point

Answer 3

• 3 bases code for each amino acid known as codons
• No overlap or “punctuation”
• 3 reading frames
• Fixed starting point

Question 4

The Genetic Code

•Code is ____
•Codon Usage table for all codons
•Some amino acids are coded for by more than 1 codon
•6 codons for ___ ___ ___
•Others only 1 codon for ___ ___
•AUG codon - initiator codon
•Codes for the amino acid methionine
•A special ___ ____ recognizes this codon
___ ____ ___ are used as stop codons to signal the end of translation
•___ termination tRNA

Answer 4

• Code is degenerate
• Codon Usage table for all codons
• Some amino acids are coded for by more than 1 codon
• 6 codons for Leu, Arg, Ser
• Others only 1 codon for Trp, Met
• AUG codon - initiator codon
• Codes for the amino acid methionine
• A special initiator tRNA recognizes this codon
• UAA, UAG, UGA are used as stop codons to signal the end of translation
• No termination tRNA

Question 5

Colinearity:Evidence

___ sequence determines the ___ sequence.
•Evidence is carried in ___. (Changes in the DNA sequence results in changes in the ___ and___of the polypeptide chain)

Answer 5

• DNA sequence determines the protein sequence.
• Evidence is carried in mutations. (Changes in the DNA sequence results in changes in the composition and length of the polypeptide chain)

Question 6

RNA Polymerases

•Bacterial
___ RNA polymerase transcribes all genes.
•Consists of __ subunits (____) and a ____factor s which ___ ____of RNA polymerase to the promoter.
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•Eukaryotes
•__ different enzymes; each transcribes a differen___ of ___
•Type I
•Type II
•Type III

Answer 6

•Bacterial
•1 RNA polymerase transcribes all genes.
•Consists of 4 subunits (a2bb’) and a sigma factor s which directs binding of RNA polymerase to the promoter.
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•Eukaryotes
•3 different enzymes; each transcribes a different type of gene
•Type I (rRNA)
•Type II (mRNA and microRNAs)
•Type III (tRNA)

Question 7

RNA Polymerase Functions

•Scans for ___ ___, ___ synthesis
•___short stretches of DNA
•Selects ___
•Catalyzes____ bond formation (___’)
•Interacts with ____ ___ ____ to regulate transcription.
___ __!

Answer 7

• Scans for initiation sites, initiates synthesis
• Unwinds short stretches of DNA
• Selects nucleotides
• Catalyzes phosphodiester bond formation (5’ to 3’)
• Interacts with transcription regulatory proteins to regulate transcription.
• CANNOT PROOFREAD!

Question 8

Organization of Prokaryotic Promoters

•Sequences in the ___ that ____ _____ binds and initiates transcriptions are known as promoters.
•Start of transcription is denoted by ___ site.
•Polymerase binds at the ___and ___ sites.
____ and ___ of transcription bind _________to the start of transcription.

Answer 8

• Sequences in the DNA that RNA polymerase binds and initiates transcriptions are known as promoters.
• Start of transcription is denoted by +1 site.
• Polymerase binds at the -10 and – 35 sites.
• Activators and repressors of transcription bind upstream and downstream to the start of transcription.

Question 9

Transcription: Initiation

•Occurs at promoter site on the DNA template where RNA polymerase binds
•Open complex with ____ unwound base pairs forms
•A nucleotide triphosphate base-pairs to template at +1 site
•First phosphodiester bond formed (No ___needed)
___ ____influence RNA polymerase in eukaryotes

Answer 9

• Occurs at promoter site on the DNA template where RNA polymerase binds
• Open complex with ~17 unwound base pairs forms
• A nucleotide triphosphate base-pairs to template at +1 site
• First phosphodiester bond formed (No primer needed)
• Transcription factors influence RNA polymerase in eukaryotes

Question 10

Transcription: Elongation

•Transcription bubble
____ bases of unwound DNA
•Progresses along DNA template
•New RNA synthesized from template (____) strand as polymerase travels along DNA (_____’ synthesis)
•No____
•Coupling of

Answer 10

• Transcription bubble
• ~17 bases of unwound DNA
• Progresses along DNA template
• New RNA synthesized from template (noncoding) strand as polymerase travels along DNA (5’ to 3’ synthesis)
• No proofreading
• Coupling of transcription and translation

Question 11

Transcription: Termination

Rho independent

• Signals are in ____
• RNA ____ (stem loop structure) followed by ___-rich region.
• Hairpin structure ___ the ___ ___
• ____ and ____ genes

Rho dependent

• Rho protein binds to ___ ____ in nascent ___ and ___ ____ from template strand
• ____genes

Answer 11

Rho independent

• Signals are in RNA
• RNA hairpin (stem loop structure) followed by U-rich region.
• Hairpin structure disrupts the transcription bubble.
• Structural and metabolic genes

Rho dependent

• Rho protein binds to signal sequences in nascent RNA and pulls RNA from template strand
• Ribosomal genes

Question 12

Polycistronic vs. Monocistronic

Answer 12

Several genes are transcribed from a single promoter results in the formation of a polycistronic mRNA strand. (In prokayotes, ralely occurs in eukaryotes)

Question 13

Transcription in Eukaryotes

•Transcription occurs in____
•Transcription and translation in eukaryotes are
•Much more
•Different
•Upstream regions contain
____ ______specify where transcription ends.
•Very extensive _____ of eukaryotic RNA which will become mRNA.
•Almost all eukaryotic mRNA____

Answer 13

• Transcription occurs in nucleus.
• Transcription and translation in eukaryotes are not coupled.
• Much more complex.
• Different promoters.
• Upstream regions contain enhancers.
• Termination sequences specify where transcription ends.
• Very extensive processing of eukaryotic RNA which will become mRNA.
• Almost all eukaryotic mRNA spliced.

Question 14

Organization of Eukaryotic Promoters

Cis-elements = ____ or ___ ___ on the DNA that is transcribed. (___ _____ _____ and _____)

Trans-elements = ___________

Answer 14

Cis-elements = promoter or enhancer sequences on the DNA that is transcribed. (TATA box, GC rich regions, CAAT box and regions where enhancers bind)

Trans-elements = proteins that bind to cis-elements

Question 15

Transcription Initiation

•Transcription factors that bind to ___acting elements are also required for the initiation of transcription
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•These factors form a___ with ___ ___ (____ ___ ____)
•RNA polymerase is ____to the start site by this set of transcription factors (Ex – TFIIA-F)
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Answer 15

•Transcription factors that bind to cis acting elements are also required for the initiation of transcription
•
•These factors form a complex with RNA polymerase (Basal Transcription Complex).
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•RNA polymerase is guided to the start site by this set of transcription factors (Ex – TFIIA-F)
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Question 16

Enhancers of Transcription

• Some DNA regulatory ____hat are specific to a gene/genes can ____e transcription. (known as Enhancers)
• Interact with the transcription complex via ____

Answer 16

• Some DNA regulatory sequences that are specific to a gene/genes can increase transcription. (known as Enhancers)
• Interact with the transcription complex via activators.

Question 17

Termination of Transcription in Eukaryotes

• Polymerase I is terminated by a
• Polymerase II termination is
• Polymerase III terminates

Answer 17

• Polymerase I is terminated by a specific termination factor that binds to the DNA rather than the RNA synthesized.
• Polymerase II termination is coupled to the process that cleaves and polyadenylates the 3′ end of a transcript.
• Polymerase III terminates after polymerizing a series of U residues. No secondary structures for termination.

Question 18

Processing of mRNA

•Initial transcript contains introns & exons
•Pre-mRNA (________________)
•5’ end of the RNA molecule “____” by addition of ____ ____ nucleotide (_______)
•Increase ____ & ___ ____

•Adenylate (poly A) added to 3’ end
•Signal at _’ end of RNA
________residues
____
•Processing to remove introns (splicing).

Answer 18

• Initial transcript contains introns & exons
• Pre-mRNA (hnRNA - heterogenus nuclear RNA)
• 5’ end of the RNA molecule “capped” by addition of methylated Guanine nucleotide (5’-5’ linkage)
• Increase stability & ribosome binding
• Adenylate (poly A) added to 3’ end
• Signal at 3’ end of RNA
• 100 to 200 residues
• Stability
• Processing to remove introns (splicing).

Question 19

Splicing of Genes

•Introns intervene between exons
•Actin gene–309-bp intron separates first three amino acids and the other 350 or so
•Chicken pro-alpha-2 collagen gene is 40-kbp long, with 51 exons of only 5 kbp total.
•Exons range from _______bases
•Requires accurate “_____” mechanism

Answer 19

• Introns intervene between exons
• Actin gene–309-bp intron separates first three amino acids and the other 350 or so
• Chicken pro-alpha-2 collagen gene is 40-kbp long, with 51 exons of only 5 kbp total.
• Exons range from 45 to 249 bases
• Requires accurate “splicing” mechanism

Question 20

RNA splicing

_____
___ ____ _____
•Complex of ____ and ___ ___ ____ (snRNA)
______ splicing of a transcript can alter protein expressed
•Many ______(____ _____) and other diseases caused by aberrant splicing.

Answer 20

• Spliceosome
• Small nuclear ribonucleoproteins (snRNPs)
• Complex of protein and small nuclear RNA’s (snRNA)
• Alternative splicing of a transcript can alter protein expressed
• Many thalassemias (blood disorders) and other diseases caused by aberrant splicing.

Question 21

RNA splicing

•The 5’ end of introns have a ___ sequence while the 3’ end the sequence is ___.
•Upstream of the AG sequence within the intron is a____ ___ ____ consisting of branch residue ____.
•Splicing is preformed by Small Nuclear RNAs (snRNAs) _____
•snRNAs from a complex known as the splicesome, which keeps pre-mRNA in the ___ ____ for splicing.
•Splicing takes place in ___ steps.
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Answer 21

•The 5’ end of introns have a GU sequence while the 3’ end the sequence is AG.
•Upstream of the AG sequence within the intron is a branch-point sequence consisting of branch residue adenine.
•Splicing is preformed by Small Nuclear RNAs (snRNAs) U1-U6.
•snRNAs from a complex known as the splicesome, which keeps pre-mRNA in the correct confirmation for splicing.
•Splicing takes place in two steps.
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Question 22

RNA splicing

First step

• The _’ splice site is attacked by____ group of the____ ___ ____ nucleotide.
• Forms a ___ ____ molecule known as a __
• Results in the ____________

Second step

•Resulting hydroxyl group of ____ attacks the___splice site which results in ___________
•Intron is released in the lariat form and eventually is degraded.
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•

Answer 22

First step

• The 5’ splice site is attacked by hydroxyl group of the branch site adenine nucleotide.
• Forms a closed circular molecule known as a lariat.
• Results in the release of exon 1.

Second step

•Resulting hydroxyl group of exon 1 attacks the 3’ splice site which results in the joining of the two exons.
•Intron is released in the lariat form and eventually is degraded.
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Question 23

Alternate splicing results in protein variants

•The primary transcript (pre-mRNA) can spliced into different ways, giving rise to distinct mRNAs resulting in ____ proteins.
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•Splicing pattern for a primary transcript is specific form_____ ___ ___ to ____

Answer 23

•The primary transcript (pre-mRNA) can spliced into different ways, giving rise to distinct mRNAs resulting in variant proteins.
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•Splicing pattern for a primary transcript is specific form one cell type to another.

Question 24

Summary

•RNA polymerase synthesizes a polynucleotide chain using a ___ ____strand as a template.
•In prokaryotes, initiation of transcription occurs by the binding of RNA polymerase to ____ sequences.
•Transcription is terminated via ____ or ____mechanisms in prokaryotes.
•In eukaryotes the promoters are ____ and consists of multiple ___ ___ ___
•The primary transcript in eukaryotes is further processed by ___ ___ and ___
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Answer 24

•RNA polymerase synthesizes a polynucleotide chain using a single DNA strand as a template.
•In prokaryotes, initiation of transcription occurs by the binding of RNA polymerase to promoter sequences.
•Transcription is terminated via Rho dependent or independent mechanisms in prokaryotes.
•In eukaryotes the promoters are diverse and consists of multiple upstream regulatory sequences.
•The primary transcript in eukaryotes is further processed by splicing, capping and addition of a poly A tail.
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