Quiz #10 Flashcards
What are codons and the triplet code?
DNA (and mRNA) are read as a series of non-overlapping three-letter words (a triplet code)
3 letter words = codons
in order to interpret the triplet code, the code must be read in the correct reading frame
codons are read in the 5’ –> 3’ direction along the mRNA, so codons are usually written in the 5’ –> 3’ direction
What is the genetic code?
a table that shows which codons form which amino acids
there is redundancy in the genetic code
each codon has a specific meaning except for AUG, which has a dual function (codes for both methionine and signals to start translation)
three codons: UAA, UGA, and UAG, do not specify an amino acid, but are used as signals to stop translation
What is the RNA polymerase (RNA pol)?
adds RNA nucleotides (5’ –> 3’)
does not require a primer (3’ OH)
has its own helicase activity
catalyzes phosphodiester bonds
reactants are ATP, GTP, CTP, and UTP
How many RNA pol do bacteria, archaea, and eukaryotes have?
bacteria and archaea have one RNA pol for all transcription
eukaryotes have 3 classes of RNA pol for transcription
What are the three classes of RNA pol used for transcription in eukaryotes?
RNA pol I: synthesizes rRNA
RNA pol II: synthesizes mRNA
RNA pol III: synthesizes tRNA
What are promotors in transcription?
RNA pol initially binds to a specific DNA sequence called a promoter
said to “upstream” of the genetic information to be transcribed
provide a “target” for other proteins to bind to, which then recruit RNA pol in the correct orientation
direct the timing and frequency of initiation
What is required for initiation of transcription?
the recruitment of a RNA pol, unwinding DNA helix, and beginning transcription
RNA pols do not require a primer to start synthesizing RNA, so initiation is usually the rate-limiting step in gene expression
What does the promoter sequence look like in bacteria?
a typical bacterial promoter contains two consensus sequences, the Pribnow box (also called the -10 element) on coding strand and the -35 element
What does the promoter sequence look like in eukaryotes and archaea?
many eukaryotic promoters contain a TATA box located 25-35 base pairs upstream of transcription start site
What helps the RNA pol bind to the promoter in bacteria?
a protein called sigma binds directly to the -10 and -3 elements
RNA pol associates with sigma protein on the promoter
once transcription begins, sigma dissociates
What helps RNA pol bind to the promoter sequence in eukaryotes?
none of the 3 classes of RNA pols can bind promoters of their own
several proteins called general transcription factors (GTFs) bind to promoter regions, and help recruit RNA pol to promoter
RNA pol I, II, and III each have their own set of GTFs
as transcription begins, some GTFs dissociate and are replaced by proteins required for elongation
What are the three stages of transcription?
Initiation, Elongation, and Termination
What happens in the initiation step of transcription?
DNA strands unwind, polymerase initiates RNA synthesis at the start point
What happens at the elongation phase of transcription?
RNA pol catalyzes formation of phosphodiester bonds to synthesize the RNA polymer
the transcription “bubble” closes as the RNA pol moves forward
RNA pol moves downstream, making RNA transcript (5’ –> 3’ direction)
What happens in the termination phase of transcription?
RNA transcript is released
What does the termination of transcription look like in bacteria?
requires a sequence in the newly transcribed RNA that signals the end (called a terminator sequence)
Intrinsic: stem-loop forms because of GC-rich inverted repeat, this displaces RNA from template
Extrinsic: uses a nonstem-loop terminator sequence, and requires a protein with helicase activity, called rho (p) which binds to the transcript, and travelling faster than RNA pol, reaches the DNA/RNA duplex and unwinds it, RNA pol falls off
What does the termination of transcription look like in eukaryotes?
RNA pol II transcribes a sequence in DNA called the polyadenylation signal sequence, in the pre-mRNA, this signal (AAUAAA) causes cleavage of the transcript and further processing, RNA pol keeps going, an RNA exonuclease eventually removes the trailing RNA and helps knock the polymerase off
RNA pol I is terminated when a protein binds to DNA downstream of coding region, and simply blocks it from proceeding further until it falls off
RNA pol III mechanism is not well understood
Why can a single gene be transcribed simultaneously by several molecules of RNA pol?
happens in both eukaryotes and prokaryotes
allows a cell to produce a lot of RNA molecules in a short amount of time
the ability of a promoter to recruit RNA pol (initiation) can determine how much RNA is made in a given amount of time
What post-transcriptional modifications occur to pre-mRNAs (in the nucleus)?
- Addition of a 5’ cap: a modified form of guanosine is added to the 5’ end of the RNA polymer via an unusual 5’ to 5’ phosphate linkage
- Addition of 50-250 adenine nucleotides to the 3’ end, known as the poly-A tail, the same enzymes that cut the RNA and add the poly-A tail
- RNA splicing: large portions of pre-mRNA are removed (introns) and the remaining sections (exons) are pasted together in order, almost all eukaryote genes have introns
What are the functions of the 5’ cap and the poly-A tail?
Facilitate the export of mRNA from nucleus
Protect the RNA from degradation by exonucleases
Help ribosomes attach to 5’ end of mRNA (occurs in cytoplasm)
What are spliceosomes?
in some cases, RNA splicing is carried out by spliceosomes
spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize splice sites
What are the steps of the RNA splicing reaction?
snRNPs and other proteins form a complex called the spliceosome
snRNA base pairs with nucleotides at specific sites along the intron
the spliceosome cuts the RNA, releasing the intron for rapid degradation, and ligates the exons together
What are introns?
can vary in size (from 50 nucleotides to several thousand)
some evidence suggests that introns could have evolved from a mobile self-splicing element called a group II intron
What are two possible reasons why introns have been retained in eukaryotic genes?
some introns contain sequences that help regulate the expression of genes (mechanism is not always clear)
alternative splicing allows for an increase in the diversity of proteins
