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Flashcards in Transcription Deck (53):
1

DNA-->mRNA-->Polypeptide
(transcribed) (translated)

Central Dogma of Molecular Biology

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Label nucleotides with (-) numbers

Upstream of the +1 site

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Label nucleotides with (+) numbers

Downstream of the +1 site

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Place where transcription starts
-NOT the start codon

+1 site

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Where transcription stops
-NOT stop codon

Stop

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Molecules involved in transcription

mRNA
DNA
transcription factors
RNA polymerase
nTPs (ATP, CTP, GTP, UTP)

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Strand involved with transcription

DNA template strand

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Strand not involved with transcription

DNA coding strand

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1. DNA is locally ______.

denatured

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2. ______assembles NTPs completemtary to the template strand

RNA polymerase

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-Reads the template 3' to 5'
-no primer needed
-synthesizes 5' to 3'

RNA polymerase

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3. RNA/DNA duplex ________ when bigger than ______ base pairs.

dissociates; 20.

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4. ____________ template reannealed behind bubble.

Coding

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RNA transcript is the same as _______ strand except it has uracil instead of thymine

coding

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Major steps in transcription

1. Initiation
2. Elongation
3. Termination

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Sequence with a specific function

consensus sequence

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- It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.
-Positions polymerase in the correct location

sigma subunit of bacterial RNA polymerase

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Step 1: Initiation in E. coli

1. Sigma binds to 2 consensus sequences -10 box and -35 box.
-this orients polymerase at the +1 site.
2. RNA polymerase synthesizes RNA
-no primer is needed

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The sigma subunit of bacterial RNA pol. ______.
a. binds to a bacterial gene's promoter
b. is composed of both polypeptide and RNA molecules
c. is required for RNA polymerization
d. is required for termination of transcription
e. is required for ribosomal binding

a. binds to a bacterial gene's promoter

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"new strand"

nascent strand

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______ in mRNA causes RNA to stop transcribing.

Hairpin

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Step that occurs when RNA/DNA duplex is dissociated by a helicase called Rho

termination

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Differences between prokarytoic and eukaryotic transcription

prokaryotes:
-1 RNA pol.
-no RNA processing
-Coupled transcription and translation
-polycistronic RNA

Eukaryotes:
-3 RNA
-Introns removed
-Transcription and translation not coupled
-Nuclear export (due to nuclear envelope & membrane)
-Capping
-Polyadenlation
-monocistronic RNA

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Many genes encoded in same RNA molecule.
(prokaryotes)

Polycistronic

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One gene encoded in same RNA molecule.
(eukaryotes)

Monocistronic

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RNA pol I in Eukaryotes

RNA in nucleolus

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RNA pol II in Eukaryotes

mRNA + snRNA
-found in nucleoplasm

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small nuclear RNA
- their primary function is in the processing of pre-mRNA in the nucleus.
-They have been shown to aid in the regulation of transcription factors, and maintaining the telomeres.

snRNA

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RNA pol III in Eukaryotes

tRNA + one kind of rRNA
found in nucleoplasm

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Polymerases in Eukaryotes

1. RNA pol I
2. RNA pol II
3. RNA pol III
-none can bind directly to DNA, need txn factors

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Major steps in transcription

1. Initiation
2. Elongation
3. Termination

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Step 1: Initiation in Eukaryotes

-general transcription factors bind to the core promoter
-GTFs recruit polymerase to form the preinitiation complex (PIC)

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Are name according to the polymerase the recruit.
ex TF II A where II= RNA pol II interacion and A=1st to be discovered

General Transcription Factors

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Recruitment of polymerase by GTFs is __________.

increased by activators bound to enhancer sequences.

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A region of DNA that recognizes the transcription machinery and binds one or more proteins that regulate transcription initiation.
-are necessary for transcription to be initiated accurately and at a basal level.
-located immediately adjacent to the genes they regulate.

Promoter

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Subcategories within Eukaryotic promoter

1. Core Promoter
2. Proximal Promoter Elements

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Determines the accurate initiation of transcription by RNA pol. II

Core promoter

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Modulate the efficinecy of basal levels of transcription.

Proximal promoter elements

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These proteins bind to genes at sites known as enhancers and speed the rate of transcription

Activators

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These proteins bind to selected sets of genes at all sites known as silencers and thus slow transcription

Repressors

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These "adapter" molecules integrate signals from activators and perhaps repressors

Coactivators

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In response to injunctions from activators, these factors position RNA pol. at the start of transcription and initiate the transcription process.

Basal transcription factors

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Step 2: Elongation in Eukaryotes

-RNA pol. II can denature DNA to form a transcription bubble
*catalyzes NTP addition to 3' end of RNA
*during transcription (cotranscriptionally):
1. 5' methyl G cap added to RNA
2. Splicing of introns

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Short nucleotide sequences that bind specific regulatory factors

Promoter Elements

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Sequence that is located on the same chromosome as the gene that it regulates

Cis-acting sequence

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Can regulate a gene on any chromosome
-ex. DNA-binding protein

Trans-acting factors

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-Protect RNA from exonucleases
-Correct position of ribosome during translation
-Exonucleases cannot work with this 5' to 5' linkage

5' methyl G capping

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Many eukaryotic genes contain long insertions of non-coding sequences called ________.
-intervening
-transcribed but not translated

Introns

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Expressed sequence
-transcribed and often times translated

Exons

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Complex of proteins and RNA that performs the removal of introns

Spliceosome

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Step 3: Termination in Eukaryotes through polyadenylation

-mRNA is cleaved at a polyA site
-mRNA released
-50 to 250 adenine nucleotides added to the 3' end by polyA polymerase
*protection from 3' to 5' exonucleases
*aids in translation

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Structure of a mature eukaryotic mRNA

5' cap-------5' UTR-------protein coding region--------3' UTR-------3' polyA tail

*UTR= untranslated region
*translational start site btwn 5' UTR and protein coding region
*translational stop site btwn 3' UTR and protein coding region

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The polyA tail of mRNAs __________.
a. is added to the 3' end of mRNAs
b. is found on mature eukaryotic mRNAs
c. is added at the end of transcription
d. helps prevent degradation of eukaryotic mRNAs
e. all of the above are correct

e. all of the above are correct