Chapter 8 Flashcards
How do you distinguish different nitrogenous bases
- if purine (double ring), G is more decorated (think GO!)
- if pyrimidine (single ring), T has more O’s (think TOO)
- if ribose sugar and pyrimidine, U has the 2 O’s
What are the 3 parts of RNA ribonucleotides
1) ribose sugar
2) a nucleotide base
3) one or more phosphate groups
_______ catalyzes the addition of each ribonucleotide to the 3’ end of the growing RNA strand
RNA polymerase
What kind of bond does RNA polymerase make?
phosphodiester bond
_______ inhibits RNA synthesis in prokaryotes by inhibiting the formation of the _______ phosphodiester bond
Rifampicin
first
_______ is produced by protein-encoding genes and is a short-lived intermediary between DNA and protein
mRNA
mRNA is the only type of RNA that undergoes _______
translation
transcription of mRNA is often followed by _______
post-transcriptional processing
_______ are encoded in dozens of forms and are responsible for binding an amino acid and depositing it for inclusion into a growing protein chain
transfer RNA
_______ combines with numerous proteins to form ribosomes
ribosomal RNA
_______ of various types is found in the nucleus of eukaryotes and plays a role in mRNA processing
small nuclear RNA
_______ is active in plant and animal cells and is involved in post-transcriptional regulation of mRNA
micro RNA
_______ protects plant and animal cells from production of viruses and movement of transposons
small interfering RNA
Certain RNA’s in eukaryotic cells have catalytic activity; these are called _______
ribozymes
Transcription is the synthesis of a single-stranded RNA molecule by _______
RNA polymerase
RNA polymerase reads the _______ of the DNA to assemble a complementary, antiparallel strand of ribonucleotides
template strand
what is another name for the template strand
non-coding
what is another name for the coding strand
non-template
What are the 4 stages of transcription in bacteria?
1) promoter recognition
2) transcription initiation
3) chain elongation
4) chain termination
The _______ is immediately upstream (5’ of the coding strand) to the start of transcription
promoter
The _______ of the gene is the portion that contain the information needed to synthesize the protein product
coding region
the _______ of the gene regulates the cessation of transcription
termination region
The bacterial RNA polymerase holoenzyme is composed of a _______ and a _______ subunit
pentameric core
sigma
The large core enzyme of RNA polymerase holoenzyme is composed of _______, _______, _______, _______, _______
alpha 1
alpha 2
beta
beta’
w
several types of sigma subunits are available called _______
alternative sigma subunits
How do you make a consensus sequence
Take the most common letter in each column
a promoter is a _______-stranded DNA sequence that is the RNA polymerase binding site and is required for the initiation of transcription
double
_______ or ___ consensus sequnce and __ consensus sequence make up the promotor region in prokaryotes
pribnow box or -10
-35
What are the 2 steps in prokaryote transcription initiation
1) RNA polymerase holoenzyme makes the closed promoter complex
2) Then unwinds 18bp to make the open promotor complex
After how many bp polymerized does the sigma subunit disassociate?
8-10 RNA nucleotides
What are the two different types of transcription termination methods in prokaryotes? Explain each.
1) intrinsic termination (most common)
- invert repeat sequence makes hairpin and string of U’s unstablizes the polymerase allowing the hairpin to pull the RNA out
2) rho-dependent termination
- invert repeat makes hairpin however since there are no U’s, the rho protein binds to the RUT sequence (made of C’s) which pulls the RNA out
Eukaryotic genes carry _______ and_______ and require the process of removing _______
introns
exons
introns
Eukaryotic DNA is associated with proteins to form _______ which affects its transcription
chromatin
What does RNA polymerase I transcribe?
3 ribosomal RNA genes
What does RNA polymerase II transcribe?
mRNA and most snRNA genes
What does RNA polymerase III transcribe?
tRNA
1 snRNA
1 rRNA
Most common eukaryotic promoter consensus sequence? What is its position?
TATA box or Goldberg-Hogness box
Position -25
Which consensus sequence is found near the -80 position in eukaryotes?
CAAT box
Which consensus sequence is found near -90 position in eukaryotes?
GC-rich box
RNA pol II recognizes and binds to promoter sequences with the aid of proteins called _______
Transcription Factors (TFs)
TFs bind to nearby _______ sequences and interact with _______
Regulatory
RNA Polymerase
TF’s that interact with pol II are called _______ factors
TF II
What is TFIID composed of
Multisubunit protein containing TBP (TATA-binding protein) (2x) and TAF (TBP -associated factor)
What is the initial committed complex composed of?
TFIID binded to the TATA box
What makes up the minimal initiation complex?
TFIID, with the addition of TFIIB, TFIIF, and RNA pol II (image adds TFIIA)
What makes up the complete initiation complex?
the minimal initiation complex + TFIIE and TFIIH
The complete initiation complex contains multiple proteins commonly referred to as _______
General Transcription Factors (GTFs)
How do we experimentally determine what DNA sequences are binding sites for RNA Polymerase and/or other Transcription factors? (2)
Using Band Shift Assay and DNA Footprint Protection Assay
How does the Band Shift Assay work? What does it allow us to do?
1) Fragments of DNA are isolated and mixed with RNA Polymerase
2) The Fragments that bind to pol will have slower electrophoretic migration
- allows us to determine which DNA fragments are bound by transcriptional proteins
How does the Footprint Protection Assay work? What does it allow us to do?
1) Fragments are end-labeled with 32P
2) Fragments of DNA are isolated and mixed with RNA polymerase
3) Dnase 1 is added and cleaves DNA not protected by proteins
- Allows us to determine where within fragments a transcriptional protein binds
Describe what each variable is in the hardy weinberg equations: p+q = 1 and p^2 + 2pq + q^2 = 1
p is frequency of dominant allele
q is frequency of recessive allele
Describe what each variable is in the binomial probability equation: (n!/s!t!)p^s q^t
n is the total number
s is outcome 1
t is outcome 2
p is the probability of outcome 1
q is the probability of outcome 2
What happens if mutations occur inside the consensus region?
Reduce levels of transcription
What happens if mutations occur outside the consensus region?
Nonsignificant effects on transcription
What do enhancer sequences do?
Increase the level of transcription of specific gene
How do enhancer sequences form protein bridges?
Bind activator proteins and co-activators that link to the promoter
The enhancer and silencer proteins make a bridge that _____ the DNA so that proteins are close enough to interact
bends
What do silencer sequences do?
Repress transcription by using repressor proteins that induce bends in DNA
(These bends reduce transcription of the target gene)
How do silencer sequences form their protein bridges?
Bind repressor proteins and co-repressors that link to the promoter
Ribosomal genes are found in the _______
nucleolus
What are the 2 functional sequences near the transcription start for RNA Pol I promoters? And what binds to each?
1) core element (sigma like factor 1)
2) upstream control element (upstream binding factor 1)
Most RNA pol III promoters have an _______
Internal Control Region (ICR)
What are the 2 scenarios of short DNA sequences for ICR
1) box A + box B
2) box A + box C
Describe archaeal promoters sequence (2)
1) TATA_binding protein (TBP) binds to the TATA box and Transcription factor B (TFB) binds to TFB-recognition element (BRE)
2) RNA polymerase binds
What are the 3 steps in eukaryotic post-transcriptional processing?
1) 5’ capping
2) 3’ adenylation
3) intron splicing
A special enzyme, _______, adds a guanine to the 5’ end of the pre-mRNA
guanylyl transferase
What kind of bond does guanylyl transferase make?
5’ to 5’ triphosphate linkage
5’ capping functions
- _______ of RNA from rapid degradation
- facilitating _______ of mRNA out of the nucleus
- facilitating subsequent intron _______
- enhancing _______ efficiency by orienting the ribosome on the mRNA
1) protections
2) transport
3) splicing
4) translation
Functions of 3’ Polyadenylation
- facilitating _______ of mature mRNA across the nuclear membrane (through nuclear pore complex) to the cytoplasm
- _______ the mRNA from degradation
- Enhance _______ by enabling the ribosomal recognition of mRNA
1) transport
2) protect
3) translation
Describe the steps to polyadenylation (6)
1) cleavage and polyadenylation specificity factor (CPSF) binds near the polyadenylation sequence
2) cleavage-stimulating factor (CstF) binds to U-rich region downstream of the polyadenylation sequence
3) CFI, CFII, and polyadenylate polymerase bind
4) The pre-mRNA is cleaved 15-30 nucleotides downstream of the polyadenylation sequence
5) Cleavage and polyadenylation specificity factor and polyadenylate polymerase add the A’s
6) after 10 adenines poly-A-binding protein (PABII) joins
Polyadenylation and transcription termination are connected by the activity of a specialized _______
RNase (torpedo RNAse)
Pre-mRNA transcript introns are the most common type of intron and are removed by a _______
spliceosome complex
The presence of intron sequences can be demonstrated by a technique called _______
R-looping
The 5’ splice site contains a consensus sequence with an invariant _____ dinucleotide at the 5’ most end of the intron
GU
The 3’ splice site has a consensus with a pyrimidine region and a nearly invariant _______ dinucleotide at the most 3’ end
AG
The _______ is 20-40 nucleotides upstream of the 3’ end of the intron and contains an invariant adenine called the _______ near the 3’ end of the consensus
branch site
branch point adenine
Introns are removed from the pre-mRNA by an _______ complex called the spliceosome
snRNA-protein
The 5’ splice site is cleaved first and a _______ intron structure is formed
lariat
What does snRNP’s stand for?
small nuclear ribonucleoprotein particle (U1-U6)
Spliceosome components are recruited to 5’ and 3’ splice sites by _______; these bind to sequences on the exons called _______ and ensure accurate splicing
SR proteins
exonic splicing enhancers (ESE’s)
What is the difference between cis and trans splicing?
Cis: connects exons from single mRNA
Trans: connects exons from multiple mRNA’s
What is the difference between intragenic and intergenic splicing? (both are examples of trans splicing)
intragenic: exons from a single TYPE of mRNA (can duplicate an exon)
intergenic: exons from more than one TYPE of mRNA fused together
The _______ of RNA polymerase II functions as an assembly platform and regulator of pre-mRNA processing machinery
Carboxyl-terminal domain (CTD)
What are the 3 mechanisms for alternative pre-mRNA processing
1) spliced in alternative patterns
2) alternative promoters
3) alternative sites for polyadenylation
Group 1 intron SELF-splicing produces a _______ intron sequence, while group 2 intron SELF-splicing produces a _______ intron sequence
linear
lariat
Some _______ tRNA’s are produced simultaneously with rRNA’s while each _______ tRNA gene is individually transcribed
bacterial
eukaryotic
Bacterial tRNA processing
1) tRNA’s are _______ from their large precursor transcripts (several tRNA’s can be produced from one transcript)
2) _______ are trimmed from the 3’ and 5’ ends of the molecule
3) certain _______ nucleotides are chemically modified
4) tRNA’s _______ into a precise 3d structure
5) tRNA’s undergo posttranscriptional _______ of bases most commonly CCA at the 3’ end
1) cleaved
2) nucleotides
3) individual
4) fold
5) addition
in one kind of RNA editing, uracils are added with the assistance of _______ which contains a sequence complementary to the RNA that it edits
guide RNA (gRNA)
A second type of RNA editing is _______, the frequent replacement of cytosine with uracil
base substitution
(can make premature stop codon)
Describe how each RNA pol (RNA pol I, II, and III) terminate
1) RNA pol I terminates by a string of uracils but no inverted repeat
2) RNA pol II terminates poly-A tail then by torpedo RNAse
3) RNA pol III terminates by Trancription Termination Factor 1
