lecture 14- transcription Flashcards
central dogma
DNA —transcription–> RNA —translation–> protein
(DNA->mRNA–>protein–>function)
majority of DNA is coding or non-coding?
non-coding
what is the importance of non-coding DNA?
becomes ncRNA, can’t encode protein, but important for translation process and gene expression –> function
describe RNA structure
- composed of nucleotides
- sugar = ribose
- presence of 2’ OH group
- nitrogenous bases = A, G, C, U
- nucleotides joined by phosphodiester bonds (5’ phosphate to 3’ hydroxyl)
- usually single-stranded
- secondary structure varies a lot- gives RNA diverse functions
- stability: easily degraded
RNA ___ enables RNA molecules to fold into many different shapes that lend themselves to many functions
secondary structure
RNA’s nucleotides are joined by ___ bonds, which is
phosphodiester
5’ phosphate to 3’ hydroxyl
describe RNA secondary structure
- RNA’s have helical secondary structures- tRNA forms a cloverleaf with 4 helices
- double-helical characteristics of RNA:
. right-handed helical conformation dominated by base-stacking conformations
. internal loops where nucleotides don’t pair
. hairpins
. non-watson crick base pairing important to stabilize secondary structure
. helical portions have overall geometry of A-form duplex
name 4 interactions that contribute to stability of secondary 3D RNA structure
1- non- Watson Crick interactions
2- additional unusual interactions (base triples)
3- 2’ hydroxyl group
4- base stacking
describe non- Watson Crick interactions
contribute to stability of RNA secondary structure
- adenine pairing with adenine by 2 hydrogen bonds
- guanine pairing with uracil
describe additional unusual interactions that contribute to stability of RNA secondary structure
C:G:C base triple
U:A:U base triple
(purine in the middle)
describe how 2’ hydroxyl group stabilizes secondary structure
2’ OH can form hydrogen bonds with the oxygen of the ribose on the following nucleotide
- also hydrogen bonding through a water molecule between 2’ hydroxyl and the phosphate oxygen
how does base stacking contribute to stability of secondary structure
nucleotide bases stacked one on top of the other is favored
___ is the entire set of RNA transcripts produced in a cell
transcriptome
which DNA strand is transcribed to RNA
template (noncoding, antisense) strand
- RNA sequence will be exact same as nontemplate (coding, sense) strand but with uracil
how does rate of transcription vary
very different for different genes
- genes that promote high rates of expression called housekeeping genes (usually genes of metabolic pathways- glycolysis, etc.)
brief overview of transcription process
- RNA polymerases synthesize RNA
- RNA synthesis always in 5’ to 3’ direction, meaning DNA template copied from 3’ to 5’ because antiparallel
- use rNTP’s to synthesize RNA complementary to template
- add ribonucleotides to 3’ OH end only (same as DNA poly’s)
- no primer required
- product does not remain paired with template
- less accurate than DNA replication
does RNA polymerase require primer
no
how many RNA polymerases are needed in prokaryotes and eukaryotes
prokaryotes: a single RNA poly synthesizes all RNA’s
eukaryotes: have at least 3- RNA poly I, II, III
what is a transcription unit
sequence of nucleotides in DNA that codes for a single RNA molecule, along with the sequences necessary for its transcription- normally contains a promoter, a RNA-coding sequence, and a terminator
RNA polymerase attaches and initiates transcription at the ___, which is located where?
promoter
upstream of the information contained in the gene
what signals the end of transcription?
terminator
promoter is the RNA polymerase binding site on the DNA and determines…
which strand is going to be transcribed
+1 and +10 sites
+1 site is the start site in the promoter
+10 is the 10th nucleotide downstream of the start side
everything before the coding region in DNA is considered ___
upstream
describe the general steps of transcription
- similar in prokaryotes and eukaryotes
- step 1: RNA polymerase binds at promoter of gene- this forms a closed complex
- step 2: promoter melting- double helix DNA melts in promoter region (not bound by hydrogen bonds anymore) - forms open complex
- step 3: transcription initiated within complex
- step 4: promoter clearance and elongation- RNA polymerase moves along DNA, leaving promoter (RNA polymerase bound to DNA so tightly, synthesizes RNA very fast)
- step 4: RNA polymerase finds terminator site, dissociates, and releases the new RNA, recycled
describe the formation of transcription bubble in initiation
promoter melting- DNA duplex is unwound for about 17 bp, forming the open complex bubble, which enables RNA polymerase to access template strand
- DNA supercoiling occurs both in front and behind the bubble (pos supercoils ahead of RNA poly and neg supercoils behind in the DNA)
the addition of an rNTP to a growing transcript is a ___ dependent reaction that produces a ___ linkage
Mg2+
5’-3’ phosphodiester linkage
the presence of the 2’ OH makes RNA vulnerable to ___ but also allows additional ___ bonding between segments of molecule
hydrolysis
hydrogen
base-paired segments of RNA generally adopt the compact geometry of ___ helices
A-form
