RNA: Transcription and Processing Flashcards
transcription
- DNA directed synthesis of RNA by RNA polymerase
RNA polymerase similarities to DNA polymerase (2)
- requires Mg+
- catalytic mechanism
RNA polymerase differences to DNA polymerase (4)
- doesn’t require primer
- does not have proof-reading activity
- does not use topoisomerase to relieve supercoils
- does not require helicase (built into RNA pol.)
types of RNA (3)
- mRNA
- tTNA
- rRNA
mRNA (4)
- full name
- percentage of all RNA
- function
- number of possible sequences
- messenger RNA
- about 5% of RNA
- encodes proteins
- thousands - millions of different sequences
tRNA (5)
- full name
- percentage of all RNA
- function
- number of possible sequences
- size
- transfer RNA
- about 15% of all DNA
- transfers amino acids to ribosomes
- at least 1 sequence per amino acid (usually about 40 tRNAs)
- smaller than mRNA usually
rRNA (3)
- full name
- percentage of all RNA
- function
- ribosomal RNA
- about 80% of all RNA
- major part of ribosomes: play structural and catalytic role in ribosomes
other RNA (3)
- examples
- percentage of all RNA
- function
- miRNA, snRNA
- less than 1%
- involved in regulation of gene expression, studied in epigenetics
what are the main components of a gene (4)
- protein coding region
- transcription start site/+1 site
- promoter region
- terminator sequence
promoter region
- location
- function
- sequence of DNA upstream of TSS
- binding of RNA polymerase occurs heres
terminator sequence
- involved in termination of transcription
RNA transcript
- protein coding region, 5’ untranslated region, and 3’ untranslated region
template strand/non-coding strand (2)
- strand of DNA that serves as a template during transcription
- complementary to coding strand
coding strand/non-template strand (2)
- has exact same sequence as unprocessed DNA (preRNA) except U is used instead of T
- gene sequences are always written as the coding sequence
what are the common features of bacterial promoters (3)
- -10 sequence
- -35 sequence
- UP element
- 10 sequence (2)
- consensus sequence TATAAT
- recognized by sigma-factor
- 35 sequence
- consensus sequence: TTGACA
UP element (2)
- less common
- associated with strong transcription, so it is usually found in housekeeping genes
RNA polymerase holoenzyme
RNA polymerase core + sigma-factor
sigma-factor (2)
- can attach to DNA
- different sigma-factors recognize different -10 sequences
sigma-switch
- change in sigma-factor on an RNA polymerase
closed complex
- RNA polymerase holoenzyme bound to promoter on coding strand
open complex
- RNA polymerase bound to coding strand when DNA double helix is opened
what direction does the RNA chain grow in elongation of transcription
- 5’ -> 3’ direction
NasU protein
- binds to core RNA polymerase during elongation instead of sigma/replaces sigma
transcription bubble
- where transcription occurs
- region of denatured DNA enclosed by RNA polymerase that contains nascent RNA and RNA-DNA hybrid double helix
how long is the RNA-DNA hybrid double helix
- 8bp
what are the 2 common mechanisms used during transcription termination? (2)
- rho-independent termination
- rho-dependent termination
what is unique to pho-independent termination?
- palindromic sequence that causes the formation of a stem-loop structure
what is unique to pho-dependent termination?
- rut element that binds rho-helicase
what are the key differences between transcription in eukaryotes vs prokaryotes (4)
- chromatin must be reorganized prior to transcription
- activation of transcription can occur over long distances
- there are 3 different RNA polymerases
- RNA must be processes before it is ready for translation
what does RNA polymerase I produce (3)
- 18S rRNA
- 58S rRNA
- 28S rRNA
what does RNA polymerase II produce (3)
- mRNA
- miRNA
- snRNA
what does RNA polymerase III produce (2)
- tRNA
- 5S rRNA
what is the unit “s” that is used to classify rRNA? (2)
- 1 svedberg
- centrifugation unit
how is DNA accessibility regulated in eukaryotes?
- changing state of histone proteins
euchromatin (2)
- definition
- enzyme
- describes DNA when it is “wrapped” loosely around histones and is actively transcribed
- this DNA type of produced by histone acetyl transferases
heterochromatin (2)
- definition
- enzyme
- describes DNA when it is “wrapped” tightly around histones and is not transcribed
- this DNA type of produced by histone deacetylases
histone acetyl transferases (HATs) (3)
- enzymes that add acetyl groups to lysine residues of histones
- makes histones less positive and electrostatic forces between histones and DNA weaker
- this enzyme turns the gene “on”
histone acetylases (HDACs)
- enzymes that remove acetyl groups from lysine residues of histones
- makes histones more positive and electrostatic forces between histones and DNA stronger
- this enzyme turns the gene “off”
how do cells characterize their genome into heterochromatin and euchromatin (2)
- euchromatin and heterochromatin are specific to each cell type
- can change over time and in different environments
how can chromatin be modified? (3)
- methods (2)
- affect
- acetylation of histones
- methylation of chromatin and DNA
- this will affect transcription rate
cis elements (3)
- definition
- examples (3)
- effect
- parts of DNA that can affect transcription over long distances in eukaryotes
- enhancers, silencers, and insulators
- binding sites for different trans-factors (proteins) that will interact with the promoter and affect transcription initiation
enhancers
- enhance transcription
silencers
- inhibit transcription
isulators
- prevent action of other cis-elements
eukaryotic promoters and RNA polymerase
- each RNA polymerase has its own type of promoter
common elements of RNA polymerase promoters (2)
- TATA box (-30 region)
- CAAT box (-40 to -150 region; varies)
promoter
- binding site for RNA polymerase and transcription factors
what is required for transcription (2)
- RNA polymerase and help from transcription factors
- usually gene-specific TFs are needed to initiate transcription
transcription factors for RNA polymerase II
- TFII
transcription factors for RNA polymerase I
- TFI
TATA binding proteins (2)
- TFIID
- TFIIA
eukaryote closed complex
- TFII and RNA polymerase II bound to the promoter with no DNA unwinding
eukaryote open complex
- TFII and RNA polymerase II bound to the promoter with DNA unwinding
RNA polymerase II “tail” (2)
- what it is
- what happens to it during transcription initiation
- C-terminus of RNA polymerase
- phosphorylated at multiple sites by TFIIs
what happens to RNA polymerase and the TFs after transcription starts? (2)
- RNA polymerase II leaves the promoter and begins synthesis of RNA
- general TFs are left behind and dissociate with DNA
example of a gene-specific transcription factor
- SREBP binds to SRE to initiate transcription of HMG-CoA reductase
how does elongation differ in eukaryotes from prokaryotes? (2)
- more complex
- require elongation factors
how does termination differ in eukaryotes from prokaryotes?
- can require termination factors or be done in factor-independent way
pre-mRNA (2)
- nascent mRNA that must undergo modifications before it is ready for translation
- present in eukaryotic cells
capping
- definition
- purpose
- addition of 5’ cap
- helps ribosomes recognize RNA
what enzymes are used for capping pre-mRNA (2)
- step 1: phosphohydrolase
- step 2: guanylyltransferase
polyadenylation
- addition of polyadenine (polyA) tail at 3’ end of mRNA
purpose of polyadenylation (2)
- helps ribosome to recognize mRNA
- plays role in RNA stability
how does polyA tail length affect mRNA
- longer tails lead to longer lifespan for mRNA as tail is degraded over time and tail confers stability of the RNA
splicing
- removal of introns from pre-mRNA prior to translation in eukaryotic cells
exons
- amino acid coding sequences in eukaryotic pre-mRNA
introns
- amino acid non-coding sequences in eukaryotic pre-mRNA
alternative splicing
- splicing of different exons out of pre-mRNA to produce different proteins
group I introns (2)
- free guanosine serves as 1st nucleophile
- 3’ OH of upstream exon serves as 2nd nucleophile
group II introns (3)
- 2’ OH of adenosine in middle of intron serves as first nucleophile
- 3’ OH of upstream exon serves as 2nd nucleophile
- lariat is formed as product
ribozymes (2)
- catalytic RNAs
- ex. group I and group II introns
spliceosome mediated introns (2)
- requires several proteins and Mg2+
- evolved from group II, so lariat is formed
how are tRNAs and rRNAs processed?
- bases can be modified
RNA editing
- change in nucleotide sequence after transcription that leads to change in protein sequence
example of RNA editing
- ApoB 100 in LDL (100% of protein) - no editing
- ApoB 48 in chylomicrons (48% of protein) - post transcriptional editing of C -> U (deamination) in the intestines, leading to a premature stop codon
