2.13 Transcription Flashcards
Process of synthesizing RNA from a DNA template
Transcription
Transcription is the first step of ___
Gene expression
Runs from 3’ -> 5’ direction
Template/antisense/non-coding strand
Synthesized RNA appears similar to the ____ strand, which runs from 5’-> 3’ direction
Non-template/sense/coidng strand
Corresponds to the first nucleotide expressend in the 5’ end of the synthesized RNA
+1
Serves as the apoenzyme
Protein component of the RNA polymerase
Core enzyme
Core enzyme is composed of 5 units: __
alpha-alpha-beta-beta’-omega
Assembly of subunits
alpha (1)
Promoter-binding site
Recognizes the promoter region
alpha (2)
Nucleotide binding site
beta
Catalytic site
Possesses inherent DNA-DNA helicase activity in the breakage of hydrogen bonds
Also binds incoming NTPs to the growing mRNA strand via phosphodiester bonds
beta’
Stabilizes RNA molecule
omega
The only responsible for RNA elongation
5’->3’ RNA polymerase
Non-protein component that activates the core enzyme
Coenzymes
Increase RNA polymerase affinity for promoter region
Unique for each RNA synthesized
Sigma factor
Signal end of transcription only for rho-dependent termination
Termination factors
Termination factors are also called the ___
rho factor
3 processes of prokaryotic transcription
Initiation
Elongation
Termination
Occurs at the promoter region
Initiation
Usually located -8 to -10 bases to the left of +1 (downstream)
Pribnow Box
Base sequence of Pribnow box
5’-TATAAT-3’
Usually located -35 bases to the left of +1 (downstream)
-35 sequence
Base sequence of -35 sequence
5’-TTGACA-3’
Sigma factor is released
Takes place through the RNA polymerase
Elongation
Recognizes the C-rich regions near the 3’ end
rho-dependent termination
rho factors has the ____, to separate the template DNA stand and the synthesized RNA strand at the end of transcription
RNA-DNA helicase activity
RNA forms a hairpin turn via palindromic sequences
rho-independent temination
Bonds have high melting point and as strong and stable
G-C rich regions
Facilitates the separation of newly synthesized RNA strand
U-A rich regions
Binds to and changes the morphology of beta subunits of bacterial RNA polymerase
Blocks or suppresses the initiation step
Rifampin
Binds to the DNA-RNA complex which results to a barricade on the template strand
Prevents further elongation of strand
Dactinomycin
Basically, eukaryotic transcription follows the same processes as prokaryotic transcription; however, eukaryotic transcription:
- Affected by chromatin structure
- Affected by DNA methylation
- Affected by histone acetylation
- HasTATA box and CAAT box as promoter regions
- Has TFIID as transcription factors
Relaxed form, actively transcribed
Euchromatin
Condensed form
Tightly packed
Inactive segments, transcriptionally silenced
Heterochromatin
Interconversion of the two forms (euchromatin and heterochromatin)
Chromatin remodeling
Chromatin remodeling involves acetylation of lysine residues at amino terminus of histones, which is mediated by
Histone acetyltranserases
Chromatin remodeling also involves removal of acetyl group in lysine residues, mediated by __
Histone deacetylases
Presence of methyl groups in DNA (enhances/inhibits) eukaryotic transcription
Inhibits
Methyl groups can physically prevent binding of transcriptional proteins
Presence of acetyl groups in the DNA (enhances/inhibits) eukaryotic transcription
Enhances
Presence of acetyl groups reduces interaction between histone tails and nucleosomes, making it relazed and transcriptionally active
Another term for TATA box
Goldberg-Hogness Box
Base sequence of TATA box
5’-ATATAAAA-3’
Location of TATA box
-25 region
Base sequence of CAAT box
5’-GGCCAATCT-3’
Location of CAAT box
-70 region
Eukaryotic promoter regions
TATA box
CAAT box
Binds to TATA box
Similar to alpha subunit in prokaryotes
TFIID
Eukaryotic transcription factors
TFIID
Type of eukaryotic RNA polymerase in nucleolus
RNA polymerase I
Product
RNA polymerase I
Large rRNA
Type of eukaryotic RNA polymerase that uses different promoter regions and affected by enhancers and silencers
RNA polymerase II
RNA polymerase II is inhibited by ___
Amanita phalloides
Product
RNA polymerase II
mRNA
snRNA
Product
RNA polymerase III
tRNA
5S rRNA
snRNA
Type of eukaryotic RNA polymerase that resembles prokaryotic RNA polymerase
Mitochondrial polymerase
Reasons for modification of eukaryotic RNA
Complexity of RNA
Cell compartment issues
Transcription-export
Introns are removed from anticodon loop via ____
tRNA splicing endonuclease
Intervening sequences
Introns
Expressed sequences
Exons
5’ and 3’ are trimmed
tRNA modifications
Addition of certain sequences at 3’ end and modification to unusual bases
tRNA modifications
4 mRNA modifications
5’ capping
3’ Poly-A Tail
Removal of introns
Alternative splicing
Used for translation initiation and stabilizes mRNA
5’ capping
5’ capping is facilitated by ___
guanylyltransferase
guanine-7-methyltransferase
In 5’ capping, the cap is ___
7-methylguanosine triphosphate
Addition of 40-200 adenine bases
3’ Poly-A tail
Facilitates 3’ Poly-A Tail
Polyadenylate polymerase
3’ poly-A tail is used for protection against ___
Exonuclease
Facilitates exit of mRNA from nucleus
3’ Poly-A tail
Facilitated in a spliceosome
Removal of introns
Removal of introns forms a ___– bonds will form on the loop and spliceosome will cut loop leaving RNA
Lariat loop
snRNA + other protein
snRNP
mRNA + snRNP
spliceosome
Forms antibodies that attack snRNPs
SLE
Systemic lupus erythematosus
Due to aberrant beta-globin mRNA splicing a lot of introns that aren’t removed properly
beta thalassemia
Combination of different exons from pre-mRNA will yield different combinations of mRNAs and different proteins
Alternative splicing
Testament to efficiency of eukaryotic mRNA in creating more proteins
Alternative splicing
