Biochemistry
Dept. of Biochemistry and
Molecular Biology
Professor Wu Yaosheng
2009-11
小船上的人定是不知道，自己竟也成了美景的一部分。
2
发现决定人类语言功能
关键基因
为什么人能说话而其生物学近亲黑猩猩却不能？英国《自然》杂志11月12日刊登
研究报告说，答案可能就在基因FOXP2上，这个基因的人类版本与黑猩猩版本仅有
两点小小的不同，但却因此赋予人类独特的语言能力。
美国加利福尼亚大学等机构的研究人员报告说，他们发现FOXP2基因在人类语言
功能形成过程中发挥着核心作用。这个基因会指导合成一种特殊蛋白质，这种蛋白质
又会与DNA（脱氧核糖核酸）结合，对其他基因的功能造成影响。因此，虽然实验显
示这个基因的人类版本与黑猩猩版本只有两处氨基酸不同，但在同样的培养环境下，
该基因的人类版本会增强61个基因的作用，同时抑制另外51个基因的作用。
在这些受影响的基因中，一些与大脑发育有关，FOXP2基因可以通过它们影响大
脑中的语言功能区域和神经网络。另一些受影响的基因与咽喉部位的软组织发育有关，
FOXP2基因可以通过它们来影响与语言功能有关的器官结构
我国科学家首提“人类泛基因组”
人类基因组存在着种群特异甚至个体独有的DNA序列和功能基因
经过不懈研究和攻关，我国科研人员在人类基因组研究中获得新的重大进展――
发现人类基因组中存在着种群特异甚至个体独有的DNA序列和功能基因。科研人员还
首次提出了“人类泛基因组”的概念。
由深圳华大基因研究院领衔，华南理工大学参与的研究论文《构建人类泛基因组
序列图谱》12月7日在国际著名科学期刊《自然—生物技术》（Nature
Biotechnology）上发表。
在研究中，科研人员运用第二代测序技术和自主研发的基因组组装工具，对“炎
黄一号”基因组――首个亚洲人个人基因组进行了进一步的深度测序和拼接，发现人
类基因组中除原先公认的单核甘酸多态性、插入删除多态性和结构性变异以外，还存
在着种群特异甚至个体独有的DNA序列和功能基因，例如主要在亚洲人群内特有的基
因序列。
我国科学家首提“人类泛基因组”
人类基因组存在着种群特异甚至个体独有的DNA序列和功能基因
科研人员同时对近两年发表的非洲人基因组和韩国人基因组进行了重新组装，也
得到类似结论。科研人员还首次提出了“人类泛基因组”的概念，即人类群体基因序
列的总和。
国际人类基因计划基于欧洲人DNA完成的参考基因组序列，是目前绝大多数人类
基因组学研究的数据基础。多年来，大多数科学研究都认为每个个体的基因组均与这
一参考基因组相似，仅有替换或重排性质的变化。
专家指出，这一研究树立了新的人类基因组测序标准，进一步证明自主构建中国
人群医学基因组学图谱、推进个人基因组研究和个体化医学研究的必要性，是中国科
学家在人类基因组研究领域的又一重要贡献。
在论文同行匿名审稿过程中，一名科学家评价说：“这是一篇激动人心，发人深
思，严谨清晰的文章。除了对新序列的检出和分类，这篇文章还通过使用相当有趣的
独创的分析方法，增强了我们对这些新序列中所能展示的种群多样性和进化保守性的
认识。”
Chapter 11
RNA Biosynthesis
6
Two kinds of RNA biosynthesis
in organisms:
Transcription
RNA replication
7
7
Transcription----to synthesize RNA with
DNA single strand as template
Introduction
1. Transcription is the first stage of the process
of gene expression.
2. Transcription processes have to suffer strictly
regulation to meet the need of development,
morphogenesis and physiological functions of
organisms .
3. The products of transcription are RNA
8
8
General picture of transcription
9
9
Main Contains
★ Overview of Transcription
★ Transcription in Eukaryotes
★ Processing of Eukaryotic RNA
★ Transcription in Prokaryotes
★ RNA Dependent RNA Synthesis
10
10
Key Points
★ Transcription characteristics
★ Transcription system
★ RNA polymerases
★ Transcription initiation
★ Postranscription modification
11
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Section One
Overview of Transcription
12
Transcription
The process which RNA polymerase
catalyzes the yield of RNA (tRNA, mRNA,
rRNA ) with one of double strands of DNA as
template, NTPs as precursors, in the light of
the rule of complementary base pairing.
DNA
RNA
13
13
The requirements of transcription
Precursors : NTP (ATP, UTP, GTP, CTP)
Template : DNA （one strand )
Enzyme: RNA polymerase, RNA-pol
Other proteins
(transcriptional factors et al )
14
14
Comparison of Replication and Transcription
Comparison
Replication
Transcription
Template
Both strands of
DNA
One strand of
DNA
Precursors
dNTP
NTP
Base pairing
A→T, G→C
A→U, T→A, G→C
Polymerase
DNA polymerase
RNA polymerase
Products
DNA
tRNA, mRNA,
rRNA
Primers
Needed
No need
15
15
1. General characters of transcription
• Only one strand of DNA molecule
serves as template
• Asymmetric transcription
• No primer needed
• Initiation at promoter site
16
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DNA Transcription plot
5’……GCAGTACATGTC…………3’
3’……c g t c a t g t a c a g…………5’
DNA
transcription
5’……GCA GUA CAU GUC………3’
mRNA
translation
N…... Ala Val
His Val.. ………….C
peptide
Note：capital letters means the code strand, small
letters means the template strand
17
17
Some important concepts
DNA template
Template strand, antisense strand, Watson
strand
Coding strand, sense strand, Crick strand
Structural gene
Asymmetric transcription
18
18
Direction of transcription: 5’ →3’
Direction of template reading: 3’ →5’
19
19
Asymmetry transcription
5’
5’
3’
5’
3’
5’
5’
Structure gene
Template strand
Coding strand
Arrowhead means the direction of transcription
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20
For asymmetric transcription,
there are two meanings:
(1) Only one strand of a gene can serve as
template, the other which is complimentary to
the template strand can’t be transcripted.
(2) Not all the template strands of genes are
found in the same strand on DNA molecule.
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2. DNA Dependent RNA Polymerase
The enzyme related to transcription is RNA
polymerase, which is termed as DNA
dependent RNA polymerase (DDRP) or RNA
pol, or transcriptase.
It catalyzes the following reaction:
(NTP)n
DNA template
RNA pol
Mg2+, Zn2+
pppN(pN)n-1 + (n-1)PPi
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22
DNA template
strand
DNA template
strand
5`
direction
3`
OH
OH
U
U
OH
OH
Transcription by RNA polymerase. In each step the incoming
ribonucleotide selected is that which can base-pair with the next base
of the DNA template strand.
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23
A 3`-5`phosphodiester bond is formed, extending the RNA chain by one
nucleotide, and pyrophosphate is released. Overall the RNA molecule grows in
a 5`3`direction.
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Eukaryotic RNA polymerase
Class
Pol I
Pol II
Pol III
Mitochondrial Pol
Location
Nucleolus
Nucleus
Nucleus
Mitochondria
Transcripts
Pre-rRNA
(18, 5.8, 28S)
Pre-mRNA,
specialized
RNAs
tRAN, 5S
rRNA, U6
snRNA
Mitochondrial
RNA
Sensitive to
α-amanitin
Insensitive
Strongly
sensitive
Sensitive
Insensitive
Sensitive to
Refampicin
Insensitive
Insensitive
Insensitive
Sensitive
Amanitin，鹅膏蕈碱；refampicin, 利福平
25
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Prokaryotic RNA polymerase ( E. coli)
Subunit
Num. of subunit
Functions
α
2
Control transcription
β
1
To catalyze the synthesis
of RNA
β’
1
To bind to DNA template
ω
1
Unclear
σ
1
To recognize the start site
(promoter )
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RNA polymerase in prokaryotes
only one RNA pol has been found:
α2ββ’ ω σ (holoenzyme )
α2ββ’ ω ( core enzyme )
Holoenzyme

ω 

 
Core enzyme

ω

 
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Core enzyme: the RNA polymerase without the 
subunit is called core enzyme (2 ω).
Holoenzyme: It can initiate transcription
specifically at promoter sites and catalyze
polymerization of two free NTPs.
Core enzyme: It can not initiate transcription
specifically at promoter sites but can catalyze
RNA elongation.
28
28
There are more than one kind of 
factor in prokaryotes
 70 carries out the promoter recognition
process on their own, mainly responsible for the
housekeeping gene expression.
‘Housekeeping’ genes are those that encode
many proteins needed for routine cell functions
and which are therefor expressed at low rates in
all cells.
 32 is responsible for the heat-shock gene
expression under some emergent cases.
29
29
RNA polymerase binds to DNA at the
Transcriptional start point
How many kinds of RNA
polymerase have been found
in prokaryotesωor in eukaryotes?
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30
Questions
1. The RNA polymerases that transcribe
bacterial DNA or eukaryotic nuclear DNA are
A. multisubunit enzymes and partially homologous.
B. monomeric and very large.
C. multimeric and interchangeable.
D. only active inside the cell.
E. highly glycosylated in their active forms.
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Questions
2. RNA chain elongation can be inhibited
by
A. Repressors.
B. Rifampicin (a Rifamycin derivative).
C. Actinomycin D.
D. RNases.
E. 0.5 M NaCl.
32
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Section Two
Transcription
in Eukaryotes
33
The process of transcription is
generally divided into three steps:
Initiation
Elongation
Termination
34
34
Requirements of transcription initiation
RNA pol, promoter, TFs, precursors (NTP)
Transcription factors and promoters
RNA pol (location)
Transcription
factors
Promoters
RNA pol I (nucleolus)
TF I
Class I promoter
RNA pol II (nucleus )
TF II
Class II promoter
RNA pol III ( nucleus)
TF III
Class III promoter
35
35
1. Synthesis of mRNA in Eukaryotes
RNA polymerase II is responsible for biosynthesis
of mRNA in eukaryotes
It contains 12 subunits:
The largest one
contains carboxylterminal domain, CTD
Rbp2
Rbp1 Rbp4
Rbp3
Rbp7
Rbp5
Rbp6
Rbp12 Rbp11
Rbp9 Rbp8 Rbp10
RNA pol II
36
36
Structures of gene in eukaryotes:
Promoter, cis-action elements, exon, intron
Structural gene
Promoter
CAAT
-110bp
GC
TATA
- 40bp
-25bp
AATAA
exon intron
Enhancer
Initiation site
Modification site
(A point for cutting and
adding a tail )
Real termination site
37
37
Genes in eukaryotes are split gene (断裂基因）
A gene consists of exons and introns.
enhancer P
E1
I1
E2
I2
Promoter structure:
5’
3’
-110
CAAT box
- 40
GC box
Upstream elements
RNA pol II
E3
+1
-25
TATA box
T
YYAN YY
A
BRE
3’
5’
Inr
Class two of promoter
BRE (TF II B recognition element ); Inr (initiator)
TF II
38
38
Class and functions of TF II
Class
Functions
TF II A
To stabilize the combination of TF II B and TBP to
promoter
TF II B
To bind with TBP and serve as a bridge between other
factors and pol II
TF II D(TBP)
To recognize specifically and to bind with TATA box
TF II E
To recruit TF II H, it has ATPase and helicase activity
TF II F
To bind to TF II B, and Pol II to prevent the wrong binding
of pol II with nonspecific DNA sequence
TF II H
Helicase activity
39
39
1.1 Initiation of mRNA Synthesis
◆To form pre-transcription initiation complex(PIC)
First, a closed complex (闭合复合物），Secondly, an
open complex ( 开放复合物）
◆ To form a transcription bubble (转录泡)---transcription initiation complex
◆ To join two nucleotides to form pppGpNOH with first phosphodiester bond
40
40
The forming of transcription initiation complex
(1) TFIID binds to the TATA box.
The key subunit of TF II D is TBP(TATA box-binding
protein).
(2) TFII A binds, followed by TF II B.
(3) RNA polymerase II, which has already complex with
TFIIF,binds followed by the binding of TFIIE,H.
(4) The transcription begins when forming of
transcription initiation complex.
(5) It is a basal transcription apparatus.
Transcription is only at a low rate. For a high rate of
transcription, other transcription factors are required.
41
41
TATA
TF II D
D
TATA
TFIIA, TFIIB, TFIIF,
RNA polymerase II
D Pol II
A
TATA
B F
TFIIE, TFIIH, TFIIJ
D Pol II
A
TATA
B F E H
Transcription starts
Initiation of transcription by RNA
polymerase II. TFIID binds to the
TATA box followed in order by the
binding of TFIIA,TFIIB and a preformed complex of TFIIF-RNA
polymerase II. Subsequently TFIIE,
TFIIH bind in order and transcription
then starts about 25 bp downstream
from the TATA box.
Note that the placement of the
the various factors in this diagram
is arbitrary; their exact position in
the complex are not yet known.
PIC formation in order:
TFIID→A →B →F →pol II →E →H
42
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43
43
1.2 Elongation of mRNA transcription
Elongation
When the transcription initiation complex is
formed, the transcription begins and the
elongation of the RNA chain continues until
termination occurs.
44
44
1.3 Termination of mRNA transcription
Unlike RNA polymerase in prokaryotes, RNA polymerase II
does not terminate transcription at specific sites but rather
transcription stops at varying distances downstream of the
gene.
Adding of poly A tail
AAAAA------AAAA
5’
5’
Termination site
Cleavage site
Modification
signal
3’
5’
TTATTT
RNA pol II
5’
3’
45
45

Transcription termintation and adding of tail at
3’-end in eukaryotes
46
46
2. Synthesis of rRNA in Eukaryotes
rRNA is synthesized in nucleolus.
Each transcriptional unit contains sequence for 18S, 5.8S,
and 28S rRNA.
Several hundred copies of transcriptional units occur
tandem in chromosome. Transcriptional units are
separated by gene spacer sequences(基因间隔序列）
DNA
Transcription
Pre-RNA 5’
3’
18S rRNA
5.8S rRNA
28S rRNA
Class I promoter and RNA pol I are required
47
47
3. Synthesis of tRNA and 5S rRNA in Eukaryotes
RNA pol III and TF IIIs are required
One unusual feature of RNA pol III action is the location
of TF III binding site within DNA sequence called as
“internal control region”(内部控制区）
The internal promoter of tRNA gene is split into two parts:
box A and box B but those of 5S rRNA gene split into
three parts: box A, a short intermediate element, box C
Box A
Box B
tRNA gene
5S rRNA gene
Box A
Intermediate
element
Box C
48
48
Questions
What are requirements for mRNA
biosynthesis in eukaryotes ?
Specially for initiation stage?
49
49
Questions
1. A promoter is
A. a manager for a sports team.
B. a specific sequence of DNA to which RNA
polymerase binds.
C. a specific sequence of DNA to which a
catabolic repressor binds.
D. a specific DNA sequence to which a restriction
endonuclease binds.
E. not found in eukaryotic cells.
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50
Questions
2. When σ subunit dissociates from an initiated
RNA polymerase,
A. it can bind a core enzyme to reform
holoenzyme.
B. it leaves behind an elongating species
complexed with Rho factor.
C. it hydrolyzes ATP until rebound by core
enzyme.
D. it remains bound to the promoter consensus
sequence.
E. None of the above are correct.
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Section Three
Processing of
Eukaryotic RNA
52
1. Processing of Eukaryotic mRNA
Including:
◆Capping of mRNA at 5’-end
◆ Adding of poly A tail at 3’-end ( polyadenylation )
◆ Removal of introns from mRNA precursor
◆ Alternative pre-mRNA splicing
◆ mRNA editing
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Expression of a protein-coding gene in eukaryotes
Exon 1
promoter
Exon 2
Intron1
Exon 3
termination
region
Intron2
Primary RNA transcript (hnRNA)
5`ppp
5`cap added
3`poly(A) added
5`
cap
AAAA200 3`
poly(a) tail
RNA slicing
1
5`
Cleavage by endonuclease
and addition of poly(a) tail
2
3
AAAA200 3`
Transport to cytoplasm
via nuclear pore
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1.1 Capping of mRNA at 5’-end

Cap structure of mRNA at 5’-end：
Guanine
55
55

Process to form cap structure
Phosphotase
5 pppGp…
5 ppGp…
Pi
pppG
ppi
Guanosin
e
transferas
e
5 GpppGp…
SAM
Methyl
transferase
5 m7GpppGp…
56
56
57
57
The roles of capping
A. Protecting mRNA from degradation by
ribonuclease that have specificity for 3`-5`
phosphodiester bonds and cannot hydrolyze
the 5`-5` bond in the cap structure.
B. The cap plays a role in the initiation step of
protein synthesis in eukaryotes.
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1.2 Adding of poly A at 3’-end of mRNA

Polyadenylation
The endonuclease cleaves the RNA transcript
at a site approximately 10-30 nucleotides on the
3’-side of a AAUAAA sequence that is called a
polyadenylation signal. Poly(A) polymerase
then adds 100-200 adenosine monophosphate
residues to the new 3’-end using ATP as
precursor.
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Termination of mRNA transcription
Unlike RNA polymerase in prokaryotes, RNA polymerase II
does not terminate transcription at specific sites but rather
transcription stops at varying distances downstream of the
gene.
Adding of poly A tail
AAAAA------AAAA
5’
5’
Termination site
Cleavage site
Modification
signal
3’
5’
RNA pol II
TTATTT
5’
3’
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The roles of polyadenylation
◆To protect the 3’-end of the final mRNA
against ribonuclease digestion and hence
stabilizes the mRNA.
◆To increase the efficiency of translation of the
mRNA.
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1.3 Removal of Introns from mRNA Precursors

RNA splicing (RNA 剪接）
To remove introns and to ligate exons together,
making hnRNA become mature mRNA
Spliceosome (剪接体）is required for RNA splicing
Spliceosome
snRNP(小核核蛋白）
snRNA (U1,U2,U4,U5,U6 )
more than 50 proteins
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U2
U1
spliceosome
UCCAUACAUA
AGGUAUGU
5’
P P P -G3m
Exon1
P P P -G3m
AUGUUGU
UACUACA
3’
AG
Exon2
Intron
5’donor junction
3’acceptor junction
pre-mRNA
GpGU
2’-OH
A
GpGU
OH
A
G--OH
U
G
P
A
Exon 1
5’-Cap
5’-Cap
5’-Cap
Exon 2
AGp
An-3’
Step 1
AGp
An-3’
2’,5’-phophodiester bond
AGp
An-3’
Step 2
5’-Cap
Gp
An-3’
+
U
G
P
A
63
AG-OH
63
The splicing chart of ovalbumin transcript (hnRNA)
64
64
1.4 Alternative Pre-mRNA Splicing

Differentially splicing transcripts
Approximately two-thirds of genes in a genome
give rise to differentially spliced transcripts
So, one gene can be transcripted and differentially
spliced to produce several transcripts
Tropomyosin
(原肌球蛋白) pre-mRNA
10 of 13 exons used in striated
muscle (横纹肌)
9 of 13 exons used in smooth
muscle (平滑肌)
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65
Primary transcript
E1
E2
E3
E4
E5
E6 E7 E8
E9 E10 E11 E12
E13
3’
5’
Striated poly (A) site
Smooth poly (A) site
Striated mRNA
Smooth mRNA
E1 E3 E5 E6 E8 E9E10E11E12
An
E1E3 E4 E5 E6 E8 E9 E10E13
An
Alternative splicing of tropomyosin primary transcrip
results in family of tissue-specific mRNA
66
66
Calcitonin generelated peptide (CGRP)
Calcitonin (降钙素)
67
67
1.5 mRNA Editing

A base in mRNA is altered enzymatically
The nucleotide sequence on an mRNA molecule may be
changed by several reactions other than RNA splicing.
Therefore, the codons on mRNA would be changed to
create alternative polypeptide transcripts from the same
gene in different cell types.
apoB
Apolipoprotein B
apoB100 be synthesized in liver
apoB48 be synthesized in intestine
Because CAA is turned to be UAA (a terminal codon)
6666
68
68
apo B gene
6666 C→U
CAA→UAA
(glutamine)
apo B mRNA
( liver)
apo B100
(Mw 500 000)
4,536 AA
apo B mRNA
( small intestine)
apo B48
(Mw 240 000)
2,152 AA
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69
2. Processing of Eukaryotic rRNA
Primary transcript from rRNA gene is 45S rRNA
◆location in nucleolus
◆self-splicing intron called group I intron
◆ ribozyme involved in this splicing
◆ snoRNAs (小核仁RNA)
◆ snoRNPs (small nucleolar ribonucleoproteins, 小核
仁核蛋白)
70
70
Processing of Eukaryotic rRNA
71
71
3. Processing of Eukaryotic tRNA
To form a special cloverleaf structure
◆tRNA molecules from all organisms are base-paired
internally to give a ‘clover-leaf’ structure ( secondary
structure). This consists of three stem-loop. Each
tRNA has a 5`-phosphate group and the nucleotide
sequence CCA at its 3` end with a 3`-OH group.
◆ The cloverleaf structure folds further into an Lshaped conformation (tertiary structure).
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72
◆To cut out excess sequences from 3’-end, 5’-end, and
middle part
◆ To add CCA-OH to 3’-end
◆ To modify some bases on special sites to create rare
bases in tRNA molecule
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73
Questions
1. mRNA in eukaryotes is similar to that
in prokaryotes as follows
A. the 5' ends of the primary transcript are
triphosphorylated.
B. the 5' ends become capped with 7-Methyl G.
C. a polyA tail is added to the 3' end.
D. the RNAs are spliced to form mature mRNA.
E. the mRNAs are translated before completion
of RNA synthesis.
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Section Four
Transcription in
Prokaryotes
75
1. Proceeding of Transcription in Prokaryotes
Initiation
Elongation
Termination
76
76
1.1 Initiation of transcription
The transcriptional unit in prokaryotes is
operon that consists of two regions on DNA
Regulation region
Operon
Structural gene region
77
77
Operon structure
Regulation region
I
P
Structural gene region
O
1
2
Inhibitor gene
Promotor, the region Operator gene
Inhibitive protein for binding of RNA pol
substrate
-50
-40
-30
TTGACA
-20
-10
1
pppG
TATAATPu
Pribnow box
10
mRNA
NH2
78
78
Initiation of transcription
◆Recognition of promoter
◆Start of synthesis
During initiation, RNA polymerase
recognizes promoter site, and then unwinds
DNA locally to expose a single-stranded
DNA template that can be transcripted.
79
79
The steps of transcription initiation
(1) The sigma factor(σ) in holoenzyme of RNA
pol recognizes the promoter and let the whole
enzyme to bind with the promoter sequence.
(2) To unwind the local region of promoter on
DNA and to form a transcription initiation
bubble .
(3) To form a initiation complex of transcription.
Holoenzyme- DNA-pppGpN-OH
80
80
81
81
Transcriptional start site
+1
RNA pol
3’
-35
TTGACA
pppGpN-OH
-10
Transcriptional bubble
Holoenzyme of RNA pol
pppG-OH + pppN-OH
pppGpN-OH + PPi
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RNA pol
-10
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Two important sequence in prokaryotic promoters:
-10 sequence:
Located about 10 nucleotides upstream of
where transcription will begin.
-35 sequence:
Located about 35 nucleotides upstream.
5`
-35
-10
TTGACA
TATAAT
?
+1
Transcriptional
start site
By convention, the first nucleotide of the
template DNA that is transcribed into RNA is
denoted +1, the transcriptional start site.
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Promoter
Pribnow box
Consensus sequence of promoter in E. coli
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1.2 Elongation of transcription
The elongation phase of RNA synthesis,
which begins after formation of the first bond,
is carried out by core enzyme.
The transcriptional complex:
Core enzyme of RNA pol-DNA template-new RNA
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-subunit dissociates from the enzyme, once
transcription has been initiated .
Core enzyme(2) moves along the gene,
synthesizes a complementary RNA copy to the
DNA template, using four ribonucleoside 5`
triphosphates (ATP,CTP,GTP,UTP) as precursors.
3`-OH at the end of the growing RNA chain attacks
the  phosphate groups of the incoming
ribonucleoside 5` triphosphate to form a 3`5`
phosphodiester bond.
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Transcription bubble
The complex of RNA polymerase, DNA
template and new RNA transcript is called a
transcription bubble. Because within it there is a
region where the DNA double helix has opened up
to allow transcription to occur.
The RNA transcript forms a transient RNADNA hybrid helix with its template strand but then
peels away from the DNA as transcription
proceeds.
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transcription bubble
RNA-pol （core enzyme） ···· DNA ····
RNA
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The DNA is unwound ahead of the
transcription bubble, and after the
transcription complex has passed , the
DNA rewind.
Direction :
RNA is synthesized in the 5`3`direction. DNA
template is read in the 3`  5` direction.
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DNA template
strand
DNA template
strand
5`
direction
3`
OH
OH
U
U
OH
OH
Overall the RNA molecule grows in a 5`3`direction.
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1.3 Termination of transcription in prokaryotes
There are two forms in termination
(1) Rho () factor dependent termination
(2) Rho () factor independent termination
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(1) Rho () factor dependent termination
Those that lack such a structure require an
additional protein, called rho (), to allow
recognition of the termination site and stop
transcription.
Rho (), can bind to the 3’ end of RNA and to
change the conformation of RNA pol, therefore to
loose the binding RNA pol with DNA template,
then release out from the bubble.
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
Mechanism of ρfactor action
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(2) Rho () factor independent termination
The simplest termination signal is a GC-rich
region in the template that is a palindrome,
followed by an AT-rich sequence. The RNA
made from the DNA palindrome is selfcomplementary and so base-pairs internally to
form a hairpin structure followed by a few U
residues.
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5`---------GCCGCCAGTTCGGCTGGCGGC-------ATTTT-OH 3`
3`---------CGGCGGTCAAGCCGACCGCCG-------TAAAA-OH 5`
template
Transcription
5`---------GCCGCCAGUUCGGCUGGCGGC-------AUUUU-OH 3`
RNA
C
5`
U
G
U
G
A typical hairpin structure
G•C
formed by the 3` end of an
A•U
RNA molecule during
C•G
termination of transcription.
C•G
G•C
C•G
C•G
G•C
A-U-U-U-U-OH 3`
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DNA
5TTGCAGCCTGACAAATCAGGCTGATGGCTGGTGACTTTTTAGTCACCAGCCTTTTT... 3
5`UUGCAGCCUGACAAAUCAGGCUGAUGGCUGGUGACUUUUUAGUCACCAGCCUUUUU... 3`
RNA
UUUU...…
UUUU...…
It’s a universal phenomena to terminate transcription
by the formation of hairpin near terminal region and rho
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independent.
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rho () factor independent model
The hairpin structure alters
RNA pol conformation,
transcription stop;
Transcription complex is
divided and RNA is released
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2. Processing of Post Transcription in Prokaryotes
mRNA:
In prokaryotes, mRNA requires little or no
modification prior to translation.
rRNA:
(1) Cleavage: the rRNA precursor molecule
is cleaved by specific ribonucleases to yield
mature 23s,16s and 5s rRNA.
(2) Methylation of some bases and ribose
moieties of rRNA also occurs.
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DNA
5
RNA
3
RNA pol
Ribosome
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16S rRNA
tRNA
23S rRNA
5S rRNA
An RNA precursor molecule that is cleaved
to yield the 23S, 16S and 5S rRNA and a tRNA
molecule; the spacer RNA( open blocks) is
degraded during these processing steps.
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tRNA:
(1) Cleavage: the tRNA precursor molecule is
cleaved by specific ribonucleases .
(2) Some tRNA molecules further require the
addition of the three nucleotides CCA to the 3`
end before they can function.
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Questions
What are differences of
transcription between in
eukaryotes and in prokaryotes?
How to compare the two
transcriptions?
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Questions
1. During transcription initiation the
template DNA strands are separated
("melted") from about positions
A. -35 to +1 after chain initiation.
B. -9 to +2 after chain initiation.
C. -35 to +1 prior to chain initiation.
D. -9 to +2 prior to chain initiation.
E. -1 to +1 during ATP or GTP binding.
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Questions
2. An operon is a transcriptional unit in
bacteria that contains
A. a promoter site, an operator site, and one or
more regulatory genes.
B. a promoter site, an operator site, and two or
more structural genes.
C. cis-acting elements adjacent to trans-acting
factors.
D. RNA polymerase loading zones.
E. The 2nd and 3rd choices are both correct.
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Section Five
RNA-Dependent RNA
Synthesis
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It’s a process of RNA replication
Specially for the genetic information transmission
of RNA viruses.
RNA-dependent RNA polymerase is required.
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RNA negative
strand (-)
RNA replication
RNA positive
strand (+)
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Questions
1. Describe the process of transcription in
prokaryotes, how does it be terminated?
2. Compare RNA polymerases in prokaryotes
with those in eukaryotes
3. What are the characters of RNA
transcription?
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4. Compare transcription with replication
from template, enzyme, precursors, baseparing, products, characters
5. How do the primary transcripts of mRNA
genes be modified in eukaryotes?
6. How do the primary transcripts of tRNA
genes be modified in eukaryotes?
7. What is asymmetric transcription?
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此時無聲勝有聲……
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