BIOB11 NOTES
LECTURE 2
- Nucleotide= P group, sugar, base
o Sugar has a 5’ and 3’, 5’ is P group and 3’ a hole to
make the next sugar attach
o Base pairing:
▪ Purine- 2 rings A&G
▪ Pyrimidine- 1 ring T&C
LECTURE 3
- RNA pol makes RNA in the 5’à3’ direction
- Nucleoside= sugar, base
- mRNA= coding RNA
- Transcription (varies for bacteria & eukaryotes)
o Bacteria
▪ RNA pol core enzyme + sigma = holoenzyme
▪ Transcription bubble, RNA pol opens the strand
and sigma factor holds onto one strand, RNA pol
core enzyme starts transcription & it fails 10
nucleotides at first, once moved away from the
promoter it lets go of the sigma factor
LECTURE 4
- Transcription
o Eukaryotic
▪ Requires initiation factors (does not want to fail 10
nucleotides at the start)
▪ GTFs: help position euk. RNA pol at the promoter,
called general bc any promoter needs it
▪ TFII= transcription factor for pol II and it binds to
the TATA box and carries TBP
, ▪ Transcription initiation complex:
• TFIID comes with its TBP to bind to TATA
box
• TFIIB attaches to all (box and TFIID)
• RNA pol comes in with its TFIIF
• TFIIE&TFIIH (one of the 9 subunits of IIH
is DNA helicase) join
o It works to get away from the promoter
by tail phosphorylation and this will
release factors. The name of the tail is
C-terminal Domain/CTD
▪ Transcriptional activators
• Bind to enhancers found in the DNA, helps
to attract RNA pol II
▪ Mediator is btw RNA pol II & GTFs to allow
indirect communication
▪ Chromatin modifying enzymes include 2 things:
• Chromatin remodelling complexes
• Histone modifying enzymes
- RNA pol
o I = rRNAs, makes rRNA
o II = transcription, makes mRNA
o III = rRNA, makes tRNA
LECTURE 5
- RNA processing (5’ cap, RNA splicing, Poly A tail)
o 5’ cap:
▪ Addition of modified guanine nucleotide
▪ 3 enzymes involved: phosphatase (remove one p
of ATP in the sugar), guanine transferase (adding
P&G to sugar), methyl transferase (adding
methyl to G)
o RNA splicing
, ▪ Exons- coding sequences, Introns- noncoding
sequences
▪ Remove of intron by phosphoryl transfer reactions
(transesterifications) by the enzyme phosphoryl
transferase
▪ The joining of the 2 exons leading to a lariat
▪ Spliceosome:
• U1 snRNP bins to 5’ splice site
• U2F & BBP bind to branch site “A”
• U2snRNP replaces U2F&BBP
• U4/U6 . U5 “triple” snRNP come in
• U6 breaks apart from U4
• U4&U1 snRNP leave the complex
• U6 snRNP replaces U1 snRNP
• The intron is removed by reactions of
phosphoryl transferase
• EJC joins the exons
• Intron is degraded in the nucleus and snRNPs
get replaced
▪ RNA splicing errors
• Exon skipping
• Cryptic splice site (part of the exon is
included and not fully)
▪ Splicing accuracy
• Check-recheck: U6 replaces U1 both read the
sequence
• Splicing is coupled with transcription
• Exon definition (exon is around 150
nucleotides)
▪ SR proteins
• Rich in serine and arginine
LECTURE 2
- Nucleotide= P group, sugar, base
o Sugar has a 5’ and 3’, 5’ is P group and 3’ a hole to
make the next sugar attach
o Base pairing:
▪ Purine- 2 rings A&G
▪ Pyrimidine- 1 ring T&C
LECTURE 3
- RNA pol makes RNA in the 5’à3’ direction
- Nucleoside= sugar, base
- mRNA= coding RNA
- Transcription (varies for bacteria & eukaryotes)
o Bacteria
▪ RNA pol core enzyme + sigma = holoenzyme
▪ Transcription bubble, RNA pol opens the strand
and sigma factor holds onto one strand, RNA pol
core enzyme starts transcription & it fails 10
nucleotides at first, once moved away from the
promoter it lets go of the sigma factor
LECTURE 4
- Transcription
o Eukaryotic
▪ Requires initiation factors (does not want to fail 10
nucleotides at the start)
▪ GTFs: help position euk. RNA pol at the promoter,
called general bc any promoter needs it
▪ TFII= transcription factor for pol II and it binds to
the TATA box and carries TBP
, ▪ Transcription initiation complex:
• TFIID comes with its TBP to bind to TATA
box
• TFIIB attaches to all (box and TFIID)
• RNA pol comes in with its TFIIF
• TFIIE&TFIIH (one of the 9 subunits of IIH
is DNA helicase) join
o It works to get away from the promoter
by tail phosphorylation and this will
release factors. The name of the tail is
C-terminal Domain/CTD
▪ Transcriptional activators
• Bind to enhancers found in the DNA, helps
to attract RNA pol II
▪ Mediator is btw RNA pol II & GTFs to allow
indirect communication
▪ Chromatin modifying enzymes include 2 things:
• Chromatin remodelling complexes
• Histone modifying enzymes
- RNA pol
o I = rRNAs, makes rRNA
o II = transcription, makes mRNA
o III = rRNA, makes tRNA
LECTURE 5
- RNA processing (5’ cap, RNA splicing, Poly A tail)
o 5’ cap:
▪ Addition of modified guanine nucleotide
▪ 3 enzymes involved: phosphatase (remove one p
of ATP in the sugar), guanine transferase (adding
P&G to sugar), methyl transferase (adding
methyl to G)
o RNA splicing
, ▪ Exons- coding sequences, Introns- noncoding
sequences
▪ Remove of intron by phosphoryl transfer reactions
(transesterifications) by the enzyme phosphoryl
transferase
▪ The joining of the 2 exons leading to a lariat
▪ Spliceosome:
• U1 snRNP bins to 5’ splice site
• U2F & BBP bind to branch site “A”
• U2snRNP replaces U2F&BBP
• U4/U6 . U5 “triple” snRNP come in
• U6 breaks apart from U4
• U4&U1 snRNP leave the complex
• U6 snRNP replaces U1 snRNP
• The intron is removed by reactions of
phosphoryl transferase
• EJC joins the exons
• Intron is degraded in the nucleus and snRNPs
get replaced
▪ RNA splicing errors
• Exon skipping
• Cryptic splice site (part of the exon is
included and not fully)
▪ Splicing accuracy
• Check-recheck: U6 replaces U1 both read the
sequence
• Splicing is coupled with transcription
• Exon definition (exon is around 150
nucleotides)
▪ SR proteins
• Rich in serine and arginine
