Which of the following initially determines which DNA strand is the template strand, and therefore in which direction RNA polymerase II moves along the DNA?

A) the location along the chromosome where the double-stranded DNA unwinds
B) the location of specific proteins (transcription factors) that bind to the DNA
C) which of the two strands of DNA carries the RNA primer
D) the position of the gene’s promoter on the chromosome
E) the specific sequence of bases along the DNA strands

E) the specific sequence of bases along the DNA strands
Where are magnesium ions found in RNA polymerase holoenzyme?
Two Mg++ ions are located in the active site. Many other Mg++ ions coat the outside of the enzyme.
Which of the following lists steps of mRNA production in eukaryotes in the correct order?

A) 5′ cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane, transcription
B) Transcription, 5′ cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane
C) Transcription, 5′ cap addition, addition of poly-A tail, passage through nuclear membrane, exon splicing
D) Transcription, addition of poly-A tail, 5′ cap addition, exon splicing, passage through nuclear membrane

B) Transcription, 5′ cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane
Which of the following is characteristic of transcription in eukaryotes but not in prokaryotes?

A) A single transcript may be transcribed and translated simultaneously.
B) A 5′ untranslated leader sequence
C) A 3′ untranslated trailer sequence
D) Exon splicing

D) Exon splicing
Which of the following best describes the function of the 5’mRNA cap?

A) It provides a site for ribosome binding in the cytoplasm.
B) Termination of transcription
C) To provide a binding site for poly(A) polymerase

A) It provides a site for ribosome binding in the cytoplasm.
Messenger RNA is usually polycistronic in eukaryotes.

A) True
B) False

B) FALSE
In which cellular organelle do the three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes occur?
nucleus
Introns are known to contain termination codons (UAA, UGA, or UAG), yet these codons do not interrupt the coding of a particular protein. Why?

A) These triplets cause frameshift mutations, but not termination.
B) UAA, UGA, and UAG are initiator codons, not termination codons.
C) Introns are removed from mRNA before translation.
D) Exons are spliced out of mRNA before translation.
E) More than one termination codon is needed to stop translation.

C) Introns are removed from mRNA before translation.
Which of the following is a characteristic of RNA splicing in Eukaryotes?

A) It involves removal of introns from a gene sequence followed by transcription and subsequent splicing of exons.
B) Exon/intron boundaries are typically characterized by a 5′ GU splice junction and a 3′ AG splice junction.
C) After splicing occurs, the U1, U2, U5, U6 snRNP complex removes remaining exons for degradation.
D) It involves recognition of sequence-specific intron/exon boundary sites by cytoplasmic proteins.

B) Exon/intron boundaries are typically characterized by a 5′ GU splice junction and a 3′ AG splice junction.
A snRNP is best described as _______.

A) short mRNA transcripts combined with nuclear protein complexes
B) a specific sequence of 7 bases in the mRNA transcript
C) small RNAs associated with protein complexes in the nucleus
D) the loop structure that forms when two exons are brought into close proximity

C) small RNAs associated with protein complexes in the nucleus
Which of the following is most likely attributable to a base substitution at a 5′ splice junction?

A) Failure of the U2 snRNP to bind the transcript
B) An amino acid substitution in the final protein product
C) A longer than usual final transcript
D) A shorter than usual final transcript

C) A longer than usual final transcript
The genetic code is degenerate, meaning that a codon can specify more than one amino acid.

A) True
B) False

B) False
A DNA sequence produces a mutant protein in which several amino acids in the middle of the protein differ from the normal protein. What kind of mutation could have occurred?

A) No mutation
B) A nonsense mutation
C) An addition or deletion mutation
D) An addition and a deletion mutation

D) An addition and a deletion mutation
Which of the following statements about eukaryotic transcription is false?

A) Transcription initiation occurs when RNA polymerase binds to a complex of transcription factors at the TATA box.
B) The transcripts produced contain both exons and introns.
C) Eukaryotic promoter regions contain a TATA box and a CAAT box.
D) A polycistronic mRNA may be transcribed if the gene products are used in the same pathway or needed at the same time.

D) A polycistronic mRNA may be transcribed if the gene products are used in the same pathway or needed at the same time.
The mRNA formed from the repeating tetranucleotide UUAC incorporates only three amino acids, but the use of UAUC incorporates four amino acids. Why?

A) The UAC triplet, produced from the first sequence, does not code any amino acid.
B) The first sequence has a “double U” fragment.
C) The second sequence is more random.
D) The triplets UUA and CUU, produced from the first sequence, code the same amino acid.

D) The triplets UUA and CUU, produced from the first sequence, code the same amino acid.
In studies using repeating copolymers, AC . . . incorporates threonine and histidine, and CAACAA . . . incorporates glutamine, asparagine, and threonine. What triplet code can definitely be assigned to threonine?

A) ACC
B) ACA
C) CAC
D) CAA

B) ACA
What is the initiator triplet in both prokaryotes and eukaryotes? Which amino acid does this triplet recruit?

A) UAA; no amino acid called in
B) UAA; methionine
C) AUG; arginine
D) UAA or UGA; arginine
E) AUG; methionine

E) AUG; methionine
In an overlapping code, what is the maximum number amino acid(s) that would be affected by a point mutation?
3
In a non-overlapping code, what is the maximum number of amino acid(s) that would be affected by a point mutation?
1
The genetic code is fairly consistent among all organisms. The term often used to describe such consistency in the code is ________.
universal
mRNA
messenger RNA bears transcribed region of DNA in the form of coded information
Unambiguous
Each triplet specifies 1 amino acid
Degenerate
A given amino acid can be specified by more than one triplet codon
nonoverlapping
each ribonucleotide is part of only one triplet
Jacob and Monod
postulated existence of mRNA
Frameshift mutations
result from addition or deletion of one or more nucleotides within a gene, so the remaining code shifts
RNA homopolymers
Nirenberg and Matthaei synthesized them each with one type of ribonucleotide. Identified codons.
RNA heteropolymers
used calculated frequencies of ribonucleotides and found mRNA triplet compositions
anticodon
tRNA specifies a complimentary sequence to mRNA called an anticodon
Khorana
found identity of triplets and filled in gaps of knowledge by finding STOP codons and a START codon
Wobble Hypothesis
Crick saw a pattern in the third codon– the first two codons are far more important and hydrogen bonding in the third codon is less strict so base-pair rules are more relaxed. (U can pair with more things)
Ordered genetic code
Chemically similar amino acids often share one or two middle bases (hydrophillic or hydrophobic for example)
GUG
is special in that it usually codes for valine but sometimes can become methionine (start codon)
nonsense mutation
when a stop codon is specified too early because of a base pair change
Exceptions to the coding dictionary
mtDNA has some exceptions, but other than that the code is universal
Overlapping genes
Different initiation points mean that several reading frames of mRNA could occur simultaneously– some viruses do this.
Transcription
RNA molecules are synthesized on a DNA template in the nucleous. RNA then moves to the cytoplasm where translation occurs
RNA polymerase
No primer required to initiate synthesis, makes mRNA sequence bind to template strand
Holoenzyme
active form of RNA polymerase
beta and beta prime subunits
provide catalyst and active site for transcription
sigma factor
regulates initiation of RNA transcription
promoters
regions on the DNA which the sigma factor recognizes and joins to. Upstream from transcription start site.
Consensus Sequences
Pribnow Box and -35 region promote transcription.
Cis-acting elements
adjacent parts of the same DNA molecule.
Trans-acting factors
molecules that bind to DNA elements
TATA box
consensus sequence in eukaryotes
Initiation
insertion of the first 5′ ribonucleoside triphosphate
Chain elongation
goes 5′–> 3′
Hairpin secondary structure
when the new RNA transcript folds back on itself and is held together by hydrogen bonds
termination factor p
terminates the synthesis of the RNA transcript
hnRNA
pre-mRNA’s found only in the nucleous and are very large primary transcripts and form hnRNP’s but only 25% of these are converted to mRNA which are spliced
RNA polymerase II
responsible for transcription initiation
core-promoter
decides where RNP II binds to the DNA
poly-A tail
added to 3′ end of mRNA after the transcript is cleaved from the sequence. AAUAAA
self-splicing RNA’s
Ribozymes. introns are removed from RNA sequences and a ligation enzyme binds the remaining exons together
Spliceosome
mediates splicing reactions and it is a huge molecular complex. snRNPs form an intermediate (a lariat which is a loop) by joining the 5′ end of the intron to the A, and the loop pops off.
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