RNA Synthesis and The Genetic Code Flashcards
mRNA carries the information encoded in the DNA to the ___ where it is ____ into proteins
cytoplasm; translated
tRNAs serve as ___ for AAs
carriers
rRNA is a major component of the protein synthesizing machinery, the ____
ribosome
All RNAs are synthesized by RNA polymerases in the ____. An exception to this is the small percentage of RNA that is synthesized in ____
nucleus; mitochondria
True or false? All three classes of RNA require processing of the initial product of transcription to yield a mature RNA molecule
true
note: processing occurs in nucleus
Bacteria contains about ____ genes and man perhaps ____ genes.
2000; 25000
What are the 5 steps in transcription?
- location of the segment of DNA to be transcribed (formation of open-promoter complex)
- synthesis of RNA
- termination of synthesis
- processing of the primary transcript
- prokaryotic vs. eukaryotic
Upstream from the transcription start site are sequences of nucleotides called ____ sequences that signal RNA polymerase to bind. This region of DNA is called the ___
consensus; promoter
Binding of RNA polymerase to the promoter region causes localized unwinding of the DNA template called an ___ complex
open
RNA polymerase is a huge protein, about _____ kDa
500,000
RNA synthesis, as with DNA synthesis, proceeds in what direction?
5’ to 3’
The RNA polymerase moves along the surface of the DNA in a processive manner. What does this mean?
it stays attached throughout synthesis and elongates the RNA transcript
For each of the following RNA polymerase subunits, give its role:
Beta
Beta’
sigma
Beta: active enzyme site
Beta’: important for binding to DNA
sigma: required to recognize and bind to the promoter
In regards to the promoter region, 10 residues upstream from the transcription start site is a region known as the ____ box and a second region at -35 rich in __ and ___ known as the -35 region
TATA; A; T
Promoter sequences are consensus sequences. What does this mean?
slight variations in sequence may occur between promoters for different genes in these regions
RNA polymerase ___ the DNA, opening it into a transcription bubble. Two ribonucleotides enter the bubble and hydrogen bond to the +1 and +2 deoxyribonucleotides of the template strand. A dinucleotide is formed and synthesis has begun. This first stretch of ribonucleotide formed is called the ___.
denatures; primer
note: if this process does not reach 10 nucleotides quickly, transcription will abort
In order for RNA polymerase to proceed out of the transcription bubble it must lose the sigma protein. Which protein displaces sigma and also plays a role in efficient elongation of the nascent RNA molecule?
Nus A protein
note: Nus A dissociates at termination step
In regards to termination, when a specific base or sequence is copied from the template, RNA synthesis stops. Theses sites posses dyad symmetry and are called ___
palindromes
In regards to termination, because the transcribed palindromes can base pair, they form ____ ____, which pull away from the template. When RNA polymers interact with these, transcription stalls.
hairpin loops
In ___ independent terminators, there is an adjacent poly A stretch to the hairpin. Poly A-poly U hybrid is very unstable, hence the ____ dissociates from the template
rho; message
Rho factor binds to the ___ end of messages as they are being transcribed.
5’
When a ribosome “stalls” at a rho termination site, rho factor is able to do what?
“catch up” to the ribosome and termination occurs
For each of the following polymerases, give its location, product, and relative activity %:
RNA poly I
RNA poly II
RNA poly III
RNA poly I: nucleolus; rRNA; 50-70%
RNA poly II: nucleoplasm; hnRNA (precursor of mRNA); 20-40%
RNA poly III: nucleoplasm; small RNA (5S RNA, tRNA); 10%
___-____ is a toxic compound from certain poisonous mushrooms that inhibit RNA synthesis by RNA polymerase ___
alpha-amanitin; II
TATA box directs RNA polymerase to what?
correct start site
The CAAT box is present around -__ and is also an important part of the promoter - it controls what?
80; frequency of initiation of transcription
mRNA carries the ___ for synthesis of specific proteins.
message
In regards to prokaryotes, the message often codes for multiple proteins; this is called being ____. Since there is no nucleus, the message is immediately translated - often when it is still attached to ___
polycistronic; DNA
In regards to eukaryotes, the message only codes for one protein, this is called being ____. The sections that carry the necessary code are called ____. The sections which do not carry information for protein synthesis must be removed and are called ____.
monocistronic; exons; introns
The prokaryotic mRNA is ___-lived, while the eukaryotic mRNA is ___-lived
short; long
mRNA is synthesized in the nucleus as a high molecular weight precursor named ____. This precursor is also always present as a ____
hnRNA (heterogenous nuclear RNA); RNP (protein + RNA)
Correct processing of an hnRNA to the mature mRNA is a prerequisite for transport of mRNA to the ___
cytoplasm
All hnRNAs and mRNAs contain a structure termed a cap at the __’ end of the molecule. The cap consists of what two methylated things?
5; methylated guanine and methylated riboses
What is the methyl donor for the methylation reactions forming the 5’ cap?
S’-Adenosylmethionine
What is the two functions of the cap in eukaryotic mRNA?
- to protect the 5’ end from attack by RNase
- to permit binding of mRNAs to the 40S ribosomal subunit - without caps, the translation of mRNA is drastically reduced
Most hnRNAs contain a sequence of 20-200 adenine residues at the 3’ end of the molecule. This stretch of adenine residues is termed the ___(__) tail
poly (A)
Not all hnRNAs, and therefore not all mRNAs, contain poly(A) tails at their 3’ end. Give an example of an mRNA that doesn’t contain a poly(A) tail
mRNA coding for histones
What is the function of a poly(A) tail?
to confer stability to the message - messages which have had their tail removed are degraded rapidly
When the consensus sequence AAUAAA is read, what does RNA polymerase do?
cleaves the chain followed by addition of poly(A’s) at the new 3’ end
RNA sequences corresponding to the introns are found in what RNAs?
hnRNAs
note: means one of the requirements for hnRNA to become mature mRNA is for the introns to be spliced out
In regards to the mechanism of splicing mRNA precursors, in all eukaryotic genes, the sequence __ is found where the 5’ end of the intron meets the 5’ exon
GU
In regards to the mechanism of splicing mRNA precursors, the dinucleotide sequence __ marks where the 3’ end of the intron joins the 3’ exon
AG
An adenosine is part of the ___ site (a place important in splicing) and is located approximately 35 nucleotides upstream from the 3’ splice site
branch
Splicing must be precise. A mutation in the consensus sequence can cause what?
the intron to be retained in the message and result in a nonfunctional protein
This is a large protein plus RNA complex (45 protein complexes and 5000 nucleotides of RNA) which catalyzes splicing out the intron.
spliceosome
The spliceosome removes the intron by two transesterfication reactions. Where do these transesterfircations take place?
- between the 5’ splice site and a branch-site adenylate
2. between the 5’ exon and the 3’ splice site
The spliceosome contains a group of proteins that catalyze the transesterfication reactions at the correct sites. What are these proteins called?
SNRPs (small nuclear ribonucleotproteins, “snurps”)
How many complexes of SNRPs are involved in the formation of a spliceosome?
4
Each SNRP comlex is associated with one or more small RNA molecule. List these molecules
U1, U2, U4/6, or U5
Catalytic RNA molecules are referred to as ____
ribozymes
How does self-splicing occur in lower eukaryotes?
nucleolytic attack by a free GTP molecule on a splice junction which undergoes internal rearrangement to generate the final spliced product
Alternative splicing is used to create different mRNA from what?
the same initial hnRNA
In Troponin T, alternative splicing allows ___ different isoforms to be created
32
What is the function of an intron?
not fully established; maybe protein diversity
Since there are 4 nitrogenous bases and 3 code words for an AA, there are ___ possible code words
64 (4^3)
How many code words code for AAs and how many code for termination?
61 for AAs; 3 for termination (UAA, UAG, UGA)
note: AUG codes for initiation and methionine
The base pairing between the codon (in the mRNA) and the anticodon (in the tRNA) is ______
antiparallel
The genetic code contains no punctuation - there are no signals required to indicate the end of one codon and the beginning of the next. True or false?
true - therefore it is imperative that translation of the codons in mRNA begin at the correct place
The genetic cod is degenerate. What does this mean?
there is more than one code word for most of the amino acids
ex: arginine = 6, valine = 4, tryptophan = 1
____ indicates that there is less specificity in the third position of the codons than in the first two positions. Therefore base pairing between the codon and anticodon is very specific at the first two positions and not very specific at the third.
wobble
The genetic code is almost universal. The various codons code for the same amino acids in all prokaryotic and eukaryotic cells. Exceptions include codons in mito and chloroplasts. True or false?
true
The ___ in tRNA is complementary to the codon in the mRNA
anticodon
ex: 5’ CUA 3’ in the codon is matched by 3’ GAU 5’
For eukaryotes, the spontaneous mutation rate is what?
1 in 10^10 to 1 in 10^11
In this type of mutation, a purine is replaced by another purine or pyrimidine is replaced by another pyrimidine
transition
In this type of mutation, a purine is changed to a pyrimidine or a pyrimidine is changed to a purine
transversion
A mutation that results in a change in codon but no change in AA meaning there is no effect is called what?
silent mutation
A mutation that results in alternation of a single base pair in the DNA which leads to insertion of a different AA during protein synthesis is called what?
missense mutation
ex: sickle cell disease - a missions mutation might result in a protein of improved function
This is the type of mutation that results in the introduction of a stop codon
nonsense mutation
Insertions and deletions are _____ mutations, which change the translation of the genetic code for all codons downstream from the mutation
frameshift
