Transcription Flashcards
Transcription is the process where ____ is made using ___ as a ____.
- RNA
- DNA
- template
RNA polymerization requires an enzyme called:
-RNA polymerase
RNA polymerase can start a chain without a ___, incorporates nucleotides into a growing chain in the ___ to __ direction using ___ bonds, and uses ___, ___, ___, and ___ as starting compounds.
- primer
- nucleotides
- 5’ to 3’
- phosphodiester
- ATP, GTP, CTP, UTP
Cells have three main types of RNA-
what are the functions?
mRNA (carries message to be translated into protein), tRNA (carries amino acids to ribosomes for incorporation into protein), and rRNA (components of ribosomes).
In E. coli, all of the RNAs are made by:
a single RNA Polymerase.
E. coli RNA Polymerase has five distinct:
distinct polypeptide subunits.
Promoters in E. coli (___ ___ binding sites adjacent to genes) function with widely varying rates of efficiency - some stimulating ___ of transcription every ___ ___, others only one or twice per ___ ___.
- RNA polymerase
- initiation
- few seconds
- life cycle
One way for a promoter to control such events is via ___ in ___ sequences. E. coli genes have two conserved sequences- one at ___ relative to the transcription start site (___) and another at ___ relative to the transcription start site (___).
- variation
- conserved
- -10
- TATAAT
- -35
- TTGACA
The more closely a given promoter’s sequence matches the consensus sequence of the ___ sequence, the more ___ the promoter is at ___ transcription.
- -10
- active
- initiating
Different ___ ___ (such as the one made during ___ ___) allow the cell to turn ___ sets of ___ with different sequences in the -10/-35 sequences as needs arise.
- sigma factors
- heat shock
- on
- genes
The strand of DNA being copied is known as the ___ ___. It runs ___ to ___, since the RNA is being made ___ to ___, _____ to it.
- template strand
- 3’ to 5’
- 5’ to 3’
- complementary
The strand of DNA that is NOT copied in transcription is called the ___ ___, since it has the ___ sequence as the ___ except for having ___ instead of ___.
- coding strand
- same
- RNA
- T
- U
Transcription occurs under the ‘control’ of ___. The more strongly RNA Polymerase (in ___) binds to the ___, the more ___ are made of that particular gene.
- promoters
- prokaryotes
- promotor
- transcripts
The more transcripts are made, the ___ is referred to as being ‘___.’
- promoter
- stronger
Transcription ___ occurs by both ___ ___ means (requires a ___ ___) and ___ ___ means (no extra ___ required). The factor independent method relies on formation of a ___ sequence of ___ base pairs immediately ahead of a stretch of ___.
- termination
- factor dependent
- protein factor
- factor independent
- protein
- duplex
- GC
- Us
The ___ destabilizes the ___-___-___ _____ complex and this is favored by the relatively weak ___ bonds of the ___ interactions.
- duplex
- RNA-DNA-RNA polymerase
- hydrogen
- U-A
The factor involved in factor dependent transcription termination in E. coli is called ___. It binds to the ___ end of an ___ being made and (using ___ energy) “climbs” the RNA until it reaches the ___ ___.
- rho
- 5’
- RNA
- ATP
- RNA polymerase
There it destabilizes the ______ ___, favoring the release of the ___ ______ from the DNA and the ___ from the DNA, as well.
- RNA/DNA complex
- RNA polymerase
- RNA
In prokaryotes, ___ are the most altered (___) RNAs. Modifications start with their being ___ from a larger RNA containing both ___ and ___.
- tRNAs
- processed
- cleaved
- tRNAs
- rRNAs
___ ___ is a ribozyme (catalytic RNA) that cleaves the ___’ end of ___ from the larger RNA. ___ ___ catalyzes ___ of ___ from the larger molecule.
- Ribonuclease P
- 5’
- tRNAs
- Ribonuclease III
- excision
- rRNAs
Transcription and translation are targets of ___. In transcription,___ binds to the open ___ complex and ___ the movement of the ___, thus stopping ___.
- antibiotics
- rifampicin
- promoter
- inhibits
- RNA polymerase
- elongation
___ ___ binds to DNA and also prevents the ___ of the transcription complex.
- Actinomycin D
- movement
Eukaryotes and prokaryotes differ significantly in the relationship between ___ and ___.
- Transcription
- Translation
Prokaryotes have no ___. In them, translation starts oftentimes ___ a message is being ___. There are no significant ___ to mRNAs in prokaryotes.
- nucleus
- WHILE
- transcribed
- modifications
In eukaryotes, transcription and translation are ___ ___. Transcription occurs in the ___, whereas translation occurs in the ___.
- spacially separated
- nucleus
- cytoplasm
Eukaryotic mRNAs are modified at the ___ end (capping), the ___ end (___) and even in the ___ (___ and s___).
- 5’
- capping
- 3’
- polyadenylation
- middle
- editing and splicing
Eukaryotes have 3 specialized RNA polymerases. They differ in their sensitivity to ___-___ (a ___ from some mushrooms).
- alpha-amanitin
- poison
RNA polymerase II (makes mRNAs) is the most ___. RNA polymerase III (makes ___ and ___ ___) has ___ sensitivity and RNA polymerase I (makes ___ ___) has ___ sensitivity.
- sensitive
- tRNAs and small rRNAs
- moderate
- large rRNAs
- low
Sequence elements affect transcription of eukaryotic genes. They include the ___ ___ (positioned approximately ___ to ___), and a ___ box and ___ box (___ to ___).
- TATA box
- -30 to -100
- CAAT box
- GC box
- -40 and -150
The promoters for each RNA polymerase are:
different in structure
Enhancer sequence elements are DNA sequences that are:
bound by enhancer (transcription factor) proteins.
Enhancer proteins act in this way to enhance transcription of genes located up to many thousands of base pairs ___ (___ __), ____ (__ ___ ) or even in the ___ of genes.
- upstream (ahead of)
- downstream (down from)
- middle
RNA Polymerase II in eukaryotes differs from RNA polymerase in E. coli in not binding to the ___ ___, but rather, it must bind to another ___ that binds to the ___ first.
- DNA directly
- protein
- promoter
In eukaryotes, rRNA is made by the action of ___ ___ ___. It is made as a ___ and then processed, like what occurs in prokaryotes.
- RNA Polymerase I
- precursor
tRNAs in eukaryotes are made by action of ___ ___ ___. Processing of them includes ___ of a ___ leader sequence and part of a ___ tail, as well as addition of a ___ sequence at the new ___ end. The amino acid gets attached to the ___ end of the tRNA.
- RNA Polymerase III
- removal
- 5’
- 3’
- CCA
- 3’
- 3’
Micro RNAs affect the amount of ___ ___ - note that the term ‘___ ___’ refers ultimately to the amount of ___ ___ made from a particular gene.
- gene expression
- gene expression
- functional protein
Micro RNAs and silencing RNAs are made as ___ ___ ___ that get processed ultimately to produce a ___ ___ ___ that is ___ to a target sequence in a given ___. When it binds to that sequence, it may result in either ___ of the mRNA or in ___ translation of the mRNA.
- double stranded RNAs
- single stranded stranded RNA
- complementary
- mRNA
- degradation
- inhibiting
RNA editing occurs when a base in an ___ is altered. An example is the ___/___ system in our bodies. apoB100 codes for a ___ ___ protein. An enzyme can recognize a ___ codon inside of the ___ and ___ the C to make it a U. That makes ___
- mRNA
- apoB100/apoB48
- 100 kilodalton
- CAA
- mRNA
- deaminate
- UAA
UAA is a stop codon and stops ___, making a ___ ___ protein instead. Thus, the same ___ can make two different proteins.
- translation
- 48 kilodalton
- mRNA
Transcription factors are proteins that bind to specific sequences in ___ and affect transcription of the ___ near them. Specifically, they bind to ___ ___.
- DNA
- genes
- sequence elements
Eukaryotic mRNAs are significantly modified. At the ___ end, a cap is added in the form of a ___ ___ that is attached in a ___ to ___ linkage to the ___ base of the transcript. This linkage is important for ___, performs a role in ___, and protects against ___ ___.
- 5’
- modified GTP
- 5’ to 5’
- first
- recognition
- translation
- exonuclease degradation
At the ___ end of eukaryotic mRNAs, a long sequence of ___ is added. This too plays a role in ___ and also provides a “buffer” against ___ ___. The longer the sequence of poly-A, the longer a transcript tends to ___.
- 3’
- As
- translation
- exonuclease degradation
- poly-A
- exist
___ is another modification that happens to eukaryotic mRNAs. Splicing also occurs to ___ and ___ in eukaryotes.
- Splicing
- tRNAs
- rRNAs
Splicing involves removal of ___ ___ from RNA followed by ___ of ends. The removed sequences are called ___. The segments that make it into the final RNA are called ___.
- internal sequences
- joining
- introns
- exons
The only sequences common to all spliced RNAs are a ___ ___ at the ___ end of the intron and an ___ at the ___ end of the intron. A third sequence - an ___ residue surrounded by ___ also is common.
- GU sequence
- 5’
- AG
- 3’
- A
- pyrimidines
Protein/RNA complexes called ___ mediate the ___ process in higher eukaryotes. ___ contain small ___ ___ (___) and ___.
- snRNPs
- splicing
- snRNPs
- nuclear RNAs (snRNAs)
- proteins
In splicing, the ___ of the A residue attacks the ___ of the phosphodiester bond at the ___ end of the intron, creating a 5’-2’ bond (part of the ___ structure). Attack by the released 3’ end of the ___ on the 3’ end of the intron joins the two exon ends and releases the intron as a ___.
- hydroxyl
- phosphate
- 5’
- lariat
- Attack
- exon
- 3’
- lariat
In splicing, the ___ ___ forms base pairing with the ___ end of the ___ ___.
- U1 snRNA
- 5’
- intron sequence
In splicing, the ___ ___ forms base pairs with the ___-___ region in the ___ and with the ___ of ___. Pairing with the intron forces outwards the ‘___’ residue that attacks the ___.
- U2 snRNA
- pyrimidine-rich
- intron
- snRNA
- U6
- ‘A’
- phosphate
Transcription factors assist ___ ___ __ in binding. For genes with a ___ ___, the transcription factor ___ binds first. It contains a subunit called ___ (___ ___ ___) that recognizes and binds to the ___ sequence.
- RNA polymerase II
- TATA box
- TFIID
- TBP (TATA binding protein)
- TATA
