Transcription (Lec. 10.5) Flashcards
Chapter 8 + 9
What is genomic DNA?
The set of instructions governing cell activity, which are used by the cell via synthesis of RNA and proteins
What is a polymerase?
A type of enzyme that catalyzes the formation of new DNA or RNA acting as a template.
Describe bacterial RNA polymerase
A complex enzyme with multiple subunits; the sigma subunit (aka the sigma factor) positions RNA polymerase at the site of transciption initiation; catalyzes growth of an RNA chain in the 5’ to 3’ direction.
What is a bacterial promoter?
A DNA sequence that RNA polymerase binds to in order to initiate transcription
Describe bacterial transcription elongation
RNA pol continues to unwind the DNA in the 3’ direction while winding in the 5’ direction
What are the steps of bacterial transcription initiation?
The sigma factor guides RNA pol to the promoter by binding to the -10 and -35 regions (closed-promoter complex: DNA is not unwound).
RNA pol unwinds 12-14 bp of the DNA (open-promoter complex: ssDNA is now available to use as a template for transcription).
Initiation starts when RNA pol joins two free nucleotides together.
After ~10 nucleotides are joined, the sigma factor leaves the polymerase and RNA pol leaves and continues to elongate the growing RNA chain.
Describe bacterial transcription termination
Elongation continues until RNA pol hits a termination signal. The RNA formed from the transcription of the termination site will form a stable stem-loop structure through base pairing. After transcription of these residues, the RNA is released from RNA pol, and RNA pol then dissociates from the DNA template
What types of RNA are associated with protein-coding genes?
mRNA
What types of RNA are used for regulation of gene expression in eukaryotes?
miRNA (micro RNA) and lncRNA (long non-coding RNA)
What types of RNA are associated with RNA processing, translation, and protein transport?
rRNA, tRNA, snRNA (small nuclear RNA), and scRNA (small cytoplasmic RNA)
What does RNA pol I do?
Transcribes the three largest rRNAs
What does RNA pol II do?
Transcribes protein-coding genes to yield mRNA
What does RNA pol III do?
Transcribes genes for tRNAs, the smallest rRNA, and RNAs involved in splicing and protein transport
What are the five general transcription factors required at minimum?
A general transcription factor that binds to the promoter; this binding recruits a second GTF; RNS pol II binds to this complex with a third factor; two more factors are added, forming the preinitiation complex
What are GTFs?
General transcription factors are needed for transcription of all genes.
What is required for eukaryotic transcription?
RNA pol + additional proteins (RNA pol II requires transcription factors to find eukaryotic promoters and initiate transcription as a whole)
What is required for bacterial transcription?
RNA pol + DNA with promoter (sigma factor NOT required, but does help with accuracy and efficiency)
Describe eukaryotic transcription termination
A specific residue in the C-terminal domain is phosphorylated, which creates a binding site for RNA endonuclease, which will recognize and cleave a non-coding sequence after the mRNA, freeing it and degrading the remaining RNA sequence and causing RNA pol II to dislodge from the DNA
What is the initial product of transcription?
pre-mRNA
What is added to pre-mRNA during mRNA processing?
Addition of a 5’ cap and a poly-A tail
What does a 5’ cap do?
Helps mRNA to be exported; prevents degradation of mRNA; assists ribosomal binding during translation
What does a poly-A tail do?
Prevents degradation of mRNA, helps regulate translation
What is RNA splicing?
Removal of introns, joining of exons
What happens if introns are not removed?
The noncoding sequences will be translated, resulting in a nonfunctional protein
What are spliceosomes?
A variety of proteins and several small RNAs that recognize splice sites. and catalyze the splicing reaction
What is alternative RNA splicing?
When different segments are treated as exons during splicing, which means that some genes can encode more than one kind of polypeptide, which means that the number of different proteins an organism can produce is much greater than its number of genes
What is the significance of the lac operon?
It encodes a protein that allows bacteria to metabolize lactose. However, many bacteria prefer glucose, so in the presence of glucose in the environment, the lac operon is repressed (catabolite repression).
What are enhancers?
Sequences that interact with polymerase and allow for more efficient transcription
What do NELF and DSIF do?
They’re negative regulatory factors that pause transcription soon after initiation
What does a positive regulatory factor do?
Re-initiates transcription after NELF or DSIF pause it
What does histone acetylation do?
Causes chromatin to decondense, which increases transcription
What do chromatin remodeling factors do?
Move, remove, or exchange histones
How does DNA methylation relate to transcription?
Cytosine that precedes guanine can be methylated, which is correlated with transcriptional repression
