Exam 3: Transcription Flashcards
Describe the general features of the genetic code.
-RNA “letters” are complementary to a DNA template and colinear to the encoded protein sequence
-Triplets are unambiguous: each triplet specifies only one amino acid
-Amino acids are degenerate: A given AMINO acid can be specified by more than one triplet codon
-Contains start and stop signals: triplets that initiate and terminate translation
-read without overlap and without breaks
-nearly universal to all viruses, prokaryotes, and eukaryotes
Does RNA or DNA have a 2’-OH group?
RNA– this is what makes it less stable and shortens half-life.
Describe a typical gene layout
-Promoter
-Transcription start site: This marks the specific point where the transcription of the gene begins. RNA polymerase binds.
-Introns
-Exons
-Terminator
-Transcription termination site: This signals the end of the transcription process and the release of the newly synthesized pre-mRNA molecule.
Describe the regions of a message RNA molecule (a mature one in eukaryotes)
-5’ untranslated region
-Shine-Dalgarno sequence in bacteria only
-protein coding region
-3’ untranslated region
Eukaryotic pre-mRNA processing is a series of modifications and editing steps that occur after transcription and before the mature mRNA (messenger RNA) molecule is ready for translation into protein.
Describe the different kinds of eukaryotic pre-mRNA processing.
-5’ Methyl Capping:
The 5’ end of the pre-mRNA molecule is modified by the addition of a 7-methylguanosine (m7G) cap (5’-5’) and a removal of one the three phosphates. The 5’ cap serves several purposes, including protecting the mRNA from degradation, increasing stability, promoting efficient translation, and facilitating the binding of ribosomes to the mRNA.
-Polyadenylation:
The 3’ end of the pre-mRNA is modified by the addition of a poly-A tail, a string of adenine (A) nucleotides after cleavage downstream of the consensus sequence. The poly-A tail serves to increase stability, facilitate mRNA export from the nucleus, and assist in ribosomal binding to mRNA.
-Splicing:
Introns are removed by splicing. Exons are then joined together in mature mRNA. Mature mRNA is smaller than initial RNA. Splicing is carried out by a complex called the spliceosome, which consists of snRNPs and other proteins. The spliceosome recognizes specific sequences at the boundaries of introns (5’ splice site and 3’ splice site) and removes the introns, ligating the exons together. Helps to remove noncoding introns from pre-mRNA, facilitate export of mRNA to cytoplasm, and allow for multiple proteins to be produced through alternative splicing.
-RNA Editing (substitution or insertion/deletion)
Relate alternative splicing to multiple poly-peptide production from a single gene.
Once thought to be rare, alternative
splicing is found to be used by many genes. One gene can encode several protein isoforms.
Relate the Wobble hypothesis to the degeneracy of the codon table
Not all three positions within the codon are equally important to the actual code. Third position is less spatially constrained. Need not adhere as strictly to established base-pairing rules.
A codon in mRNA has three nucleotides, and the anticodon in tRNA, which is complementary to the codon, also has three nucleotides.
The first two nucleotides in the codon-anticodon interaction follow strict Watson-Crick base-pairing rules.
The third nucleotide in the codon (the “wobble” position) and the first nucleotide in the anticodon do not have to follow strict base-pairing rules.
This relaxed base-pairing at the wobble position allows for some flexibility in the codon-anticodon interaction. As a result, a single tRNA molecule with a specific anticodon can recognize and bind to multiple codons that code for the same amino acid, even if the wobble position differs.
Provide examples of the role of consensus sequence in transcription
A consensus sequence is a representative sequence derived from a set of similar sequences by indentifying the most common bases at each position. They are often used to identify conserved regions within a set of related sequences. These conserved regions often correspond to functional or structurally important elements, such as transcription factor binding sites, protein domains, or active sites.
E. coli promoters have two consensus sequences
–TTGACA and TATAAT (Pribnow box)
–Positioned at -35 and -10 with respect to the transcription initiation site
Another example is the TATA box which serves as a binding site for transcription factors for eukaryotes.
The recognition of these consensus sequences by RNA polymerase allows for the formation of the transcription initiation complex, where RNA polymerase binds to the promoter and begins transcribing the DNA into RNA.
Describe mRNA coding frame and how it is established
The mRNA coding frame, also known as the reading frame, refers to the correct grouping of nucleotides in an mRNA molecule to specify the translation of a protein. The coding frame is established through the proper selection of a start codon and the subsequent reading of codons in groups of three nucleotides (triplets) without any frameshift mutations.
Contrast overlapping genes in pro- and eukaryotes
Prokaryotic genomes are generally more compact and have a higher gene density compared to eukaryotic genomes. Overlapping genes are relatively common in prokaryotes, and multiple genes can be packed closely together on the same DNA strand.
Overlapping genes in prokaryotes often occur as a result of reading frameshifts or alternative start codon usage. In some cases, a portion of one gene’s coding sequence can be contained within another gene’s coding sequence in a different reading frame.
Describe the process of transcription
-RNA synthesized on DNA template, and genetic information stored in DNA is transferred to RNA
– Serves as intermediate molecule between DNA and proteins
– Each triplet codon is complementary to anticodon of tRNA
Compare and contrast pro- and eukaryotic transcription
-Transcription in eukaryotes occurs within the nucleus
under the direction of three separate forms of RNA
polymerase. Unlike the prokaryotic process, in eukaryotes the RNA transcript is not free to associate with
ribosomes prior to the completion of transcription. For the mRNA to be translated, it must move out of the nucleus into the cytoplasm.
-For eukaryotic transcription, chromatin must uncoil to
make DNA accessible to RNA Polymerase.
-RNA Polymerase 2: Responsible for transcription of wide range of genes in eukaryotes. Regulatory sequences influence efficiency of transcription initiation by RNAP II: Proximal-promoter elements, Enhancers, Silencers
-Termination is simpler for prokaryotes. Termination sequence transcribed into RNA causes newly
formed transcript to fold back on itself (hairpin).
-Eukaryotes may have a TATA box: Core-promoter element. Binds TATA-binding protein (TBP) of
transcription factor TFIID: determines start transcription start site
-Alteration of the primary RNA transcript to produce
mature eukaryotic mRNA involves many complex stages referred to generally as “processing.”
You can’t have an intron unless you have two
exons
Explain how overlapping genes work.
A single mRNA may have multiple initiation points for translation. If so, it would create multiple different open reading frames (ORFs). This means it can specifies more than one polypeptide.
RNA Polymerase comes from the
5’ end
