Title: Chapter Eleven Transcription of the Genetic Code: The Biosynthesis of RNA
1Chapter ElevenTranscription of the Genetic Code
The Biosynthesis of RNA
2Transcription
- Overview of Transcription
- synthesized on a DNA template, catalyzed by
DNA-dependent RNA polymerase - ATP, GTP, CTP, and UTP are required, as is Mg2
- no RNA primer is required
- the RNA chain is synthesized in the 5 -gt 3
direction the nucleotide at the 5 end of the
chain retains its triphosphate (ppp) group - the DNA base sequence contains signals for
initiation and termination of RNA synthesis the
enzyme binds to and moves along the DNA template
in the 3 -gt 5 direction - the DNA template is unchanged
3Transcription in Prokaryotes
- E. coli RNA Polymerase
- molecular weight about ______________________
- four different types of subunits
_____________________ - the _____________ enzyme is ?2??
- the _____________ is ?2??s
- the role of the s subunit is recognition of the
______________ the s subunit is released after
________________ - of the two DNA strands, the one that serves as
the template for RNA synthesis is called the
template strand or ____________ strand the other
is called the coding (or nontemplate) strand or
_____________ strand - the __________ binds to and transcribes only the
___________
4The Basics of Transcription
5Promoter Sequence
- Simplest of organisms contain a lot of DNA that
is __________________________ - RNA polymerase needs to know which strand is
_____________strand, which part to _____________,
and where first _____________ of gene to be
transcribed is - _____________ - DNA sequence that provide
direction for RNA polymerase
6Promoter Sequence
7Chain Initiation
- First phase of transcription is _____________
- _____________begins when RNA polymerase binds to
_____________and forms ________________ complex - After this, DNA unwinds at _____________ to form
open complex, required for chain ____________
8Initiation and Elongation in Transcription
9Chain Elongation
- After strands separated, transcription
_____________ of 17 bp moves down the DNA
sequence to be transcribed - RNA polymerase catalyzes formation of
_____________bonds between the incorporated
_____________ - Topoisomerases _____________ _____________ in
front of behind __________ bubble __________
10Chain Elongation (Contd)
11Chain Termination
- Two types of termination mechanisms
- 1. intrinsic termination- controlled by specific
sequences called _____________ _____________,
characterized by two _____________ _____________
12Chain Termination (Contd)
- 2. Other type of termination involves rho (?)
protein - ?-dependent termination sequences cause hairpin
loop to form
13Transcription Regulation in Prokaryotes
- In prokaryotes, transcription regulated by
- __________________________________
- __________________________________
- __________________________________
- __________________________________
- Alternative s factors
- ___________ ____________ exert control over
which genes are expressed by producing different
s-subunits that direct the RNA _____________ to
different genes.
14Control by Different ? Subunits
15Enhancers
- Certain genes include sequences upstream of
____________________________________ - These genes for ribosomal production have _____
upstream sites, _________ sites - Class of DNA sequences that do this are called
______________ - Bound by proteins called _________ _________
16Elements of a Bacterial Promoter
17Operon
- _________ a group of operator, promoter, and
structural genes that codes for proteins - the control sites, promoter, and operator genes
are physically adjacent to the structural gene in
the DNA - the regulatory gene can be quite far from the
operon - operons are usually not transcribed all the time
- __________________, an inducible protein
- coded for by a structural gene, _________
- structural gene _________ codes for lactose
permease - structural gene _________ codes for
transacetylase - expression of these 3 structural genes is
controlled by the regulatory gene ______ that
codes for a repressor
18How Does Repression Work
- Repressor protein made by lacI gene forms
tetramer when it is translated - Repressor protein then binds to operator portion
of operon - Operator and promoter together are the control
sites
19Binding Sites On the lac operon
- Lac operon is induced when E. coli has _________
as the carbon source - Lac protein synthesis repressed by ____________
(catabolite repression) - E. coli recognizes presence of glucose by
promoter as it has 2 regions RNA polymerase
binding site, _________ _________ _________ (CAP)
binding site
20Binding Sites On lac operon (Contd)
21Catabolite Repression
- CAP forms complex with _________
- Complex binds at CAP site
- RNA polymerase binds at available binding site,
and _____________ occurs
22Basic Control Mechanisms in Gene Control
- Control may be _________ or _________, and these
may be _________ or _________ controlled
23Control of the trp operon
- Trp operon codes for a leader sequence (trpL) 5
polypeptides - The 5 proteins make up 4 different enzymes that
catalyze the multistep process that converts
chorisimate to tryptophan
24Alternative 2 structures can form in trp operon
- These structures can form in the leader sequence
- Pause structure- binding between regions 1 and 2
- Terminator loop- binding between regions 3 and 4
- Antiterminator structure- Alternative binding
between regions 2 and 3
25Attenuation in the trp operon
- Pause structure forms when ribosome passes over
Trp codons when Trp levels are high - Ribosome stalls at the Trp codon when trp levels
are low and antiterminator loop forms
26Transcription in Eukaryotes
- Three RNA polymerases are known each transcribes
a different set of genes and recognizes a
_____________________________________ - RNA Polymerase I- found in the _________ and
synthesizes precursors of most _________ - RNA Polymerase II- found in the _________ and
synthesizes _________ precursors - RNA Polymerase III- found in the _________ and
synthesizes _________, other RNA molecules
involved in mRNA _________ and _________ _________
27RNA Polymerase II
- Most studied of the polymerases
- Consists of 12 subunits
- ______ - RNA Polymerase B
28How does Pol II Recognize the Correct DNA?
- 4 elements of the Pol II promoter allow for this
phenomenon
29Initiation of Transcription
- Any protein regulator of transcription that is
not itself a subunit of Pol II is a _________
_________ - Initiation begins by forming a _________
_________ - Transcription control is based here
30General Transcription Initiation Factors
31Transcription Order of Events
- Less is known about _________ than _________
- The phosphorylated Pol II synthesizes RNA and
leaves the promoter region behind - GTFs are left at the promoter or dissociate from
Pol II
32Elongation and Termination
- Elongation is controlled by
- _________ sites, where RNA Pol will hesitate
- _________, which proceeds past the normal
termination point - _________ _________ _________ _________ (P-TEF)
and _________ _________ _________ _________
(N-TEF) - Termination
- begins by stopping RNA Pol the _____________
consensus sequence for termination is ___________
33Gene Regulation
- _________ _________ - regulatory sequences that
augment or diminish transcription, respectively - DNA _________ brings _________ into contact with
transcription _________ and ____________
34Eukaryotic Gene Regulation
- _________ _________ are enhancers that respond to
certain metabolic factors - _________ _________ _________(HSE)
- _________ _________ _________(GRE)
- _________ _________ _________(MRE)
- _________ _________ _________(CRE)
- Response elements all bind _________(transcription
factors) that are produced under certain cell
conditions
35Response Elements
36Activation of transcription Via CREB and CBP
- _________________ CREB does not bind to CREB
binding protein, and no transcription occurs - _________________ of CREB causes binding of CREB
to CBP - Complex with basal complex (RNA polymerase and
GTFs) activates _________________
37Structural Motifs in DNA-Binding Proteins
- Most proteins that activate or inhibit RNA Pol II
have two _________ _________ - DNA-binding domain
- transcription-activation domain
- DNA-Binding domains have domains that are either
- _________________________
- _________________________
- _________________________
38Helix-Turn-Helix Motif
- Hydrogen bonding between amino acids and DNA
39Zinc Finger Motif
- Motif contains 2 cysteines and 2 His --12 amino
acids later - Zn binds to the repeats
40Basic Region Leucine Zipper Motif
- Many transcription factors contain this motif,
such as CREB (Biochemical Connections, page 315) - Half of the protein composed of basic region of
conserved Lys, Arg, and His - Half contains series of Leu
- Leu line up on one side, forming hydrophobic
pocket
41Helical Wheel Structure of Leucine Zipper
42Transcription Activation Domains
- _________________________ domains - rich in Asp
and Glu. Gal4 has domain of 49 amino acids, 11
are acidic - _________________________ domains - Seen in
several transcription factors. Sp1 has 2
glutamine-rich domains, one with 39 Glu in 143
amino acids - _________________________ domains - Seen in CTF-1
(an activator). It has 84 amino acid domain, of
which 19 are Pro
43Post Transcriptional RNA Modification
- ____________________________________ are all
modified after transcription to give the
functional form - the initial size of the RNA transcript is greater
than the final size because of the leader
sequences at the 5 end and the trailer sequences
at the 3 end - the types of processing in prokaryotes can differ
greatly from that in eukaryotes, especially for
_______________ - Modifications
- ____________________ of leader and trailer
sequences - addition of _____________ _________ (after
transcription) - modification of the structure of specific bases
(particularly in _______________)
44Posttranscriptional Modification of tRNA Precursor
45Modification of tRNA
- tRNA- the precursor of several tRNAs is can be
transcribed as ________ polynucleotide sequence - _________________________________________________
___________ all take place - ____________________ ________________ of
____________________ are the two most usual types
of base modification
46Modification of rRNA
- Ribosomal RNA
- processing of rRNA is primarily a matter of
________________________________________ - in _______________, 3 rRNAs in one intact
ribosome - in _______________, ribosomes have 80s, 60s, and
40s subunits - base modification in both prokaryotes and
eukaryotes is primarily by _____________________
47Modification of mRNA
- Includes the capping of the 5 end with an
N-methylated guanine that is bonded to the next
residue by a 5?5 triphosphate. - Also, 2-O-methylation of terminal ribose(s)
48mRNA Modification
- A polyadenylate tail that is usually100-200
nucleotides long, is added to the 3 end before
the mRNA leaves the nucleus - This tail protects the mRNA from nucleases and
phosphatases - Eukaryote genes frequently contain intervening
base sequences that do not appear in the final
mRNA of that gene product - Expressed DNA sequences are called exons
- Intervening DNA sequences that are not expressed
are called introns - These genes are often referred to as split genes
49Organization of Split Genes in Eukaryotes
50The Splicing Reaction
- Exons are separated by intervening
_______________ - When the exons are spliced together, a
_______________ forms in the intron
51Ribozymes
- The first ribozymes discovered included those
that catalyze ______________________________ - More recently, ribozymes have been discovered
that are involved in _______________
_______________ - _______________ribozymes
- require an external guanosine
- example pre-rRNA of the protozoan Tetrahymena
(next screen) - _______________ribozymes
- display a ______ mechanism similar to mRNA
splicing - no requirement for an external nucleotide
52Self-splicing of pre-rRNA