Download Chapter 14: Gene Transcription and RNA Modification

Chapter 14: Gene Transcription and RNA Modification
Student Learning Objectives
Upon completion of this chapter you should be able to:
1.
2.
3.
4.
Understand the role of transcription in gene expression.
Know the initiation, elongation, and termination stages of transcription in bacteria.
Understand how eukaryotic transcription differs from bacterial transcription.
Understand the importance of regulatory elements and transcription factors to
eukaryotic transcription.
5. Understand the processes of RNA modification and why each of these processes is
needed in a eukaryotic cell.
14.1 Overview of Transcription
Overview
The central dogma of molecular biology, also known as the central dogma of genetics
(Figure 14.1), describes the process by which the genetic information is interpreted to form a
functional protein. Gene expression is actually a two stage process. In this chapter we will
examine the biochemical process of transcription. The basic purpose of transcription is to make a
copy of the protein-building instructions of a gene. The next chapter will examine the process of
translation, in which the instructions contained within the copy are used to construct a functional
protein.
This initial section of the chapter serves as an important overview to transcription. The
terms and processes described within this section are used for both prokaryotic and eukaryotic
transcription. You should master these terms before proceeding to the next sections.
Outline of Key Terms
Gene organization
Promoter
Terminator
Template strand
Antisense strand
Coding strand
Sense strand
Regulatory sequences
Transcription factors
mRNA organization
Ribosomal binding site
Codons
Start codon
Stop codon
Gene
Structural genes
Nonstructural genes
Central dogma of genetics
Gene expression
Transcription
mRNA
Translation
Polypeptide
Transcription stages
Initiation
Elongation
Termination
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Focal Points




Central dogma of genetics (Figure 14.1)
Organization of a bacterial gene and its mRNA transcript (Figure 14.2)
Stages of transcription (Figure 14.3)
Functions of RNA molecules (Table 14.1)
Exercises and Problems
For questions 1 to 7, match the term to its correct definition.
_____ 1. Terminator
_____ 2. Codons
_____ 3. Regulatory sequences
_____ 4. Promoter
_____ 5. Template stand
_____ 6. Gene
_____ 7. Structural genes
a.
b.
c.
d.
e.
f.
g.
Binding sites for proteins that control transcription.
Contains genetic information that is complementary to the RNA transcript.
Groups of three nucleotides within the mRNA.
The site that controls the start of transcription.
The site that controls the end of transcription.
A transcriptional unit that can be transcribed into RNA.
Produces mRNA when transcribed.
For questions 8 to 11, indicate whether the statement is associated with the initiation (I),
elongation (E), or termination (T) of transcription.
_____ 8. The RNA polymerase synthesizes a mRNA transcript.
_____ 9. The RNA polymerase interacts with the promoter.
_____ 10. The DNA forms an open complex.
_____ 11. The RNA polymerase and mRNA dissociate from the DNA.
For each of the following statements, indicate the type of RNA from Table 14.1 that best matches
the statement.
12. Targets the proteins to the endoplasmic reticulum of eukaryotes.
13. Small nuclear RNA that is involved in the splicing of eukaryotic mRNA.
14. Contains the instructions for a protein sequence.
15. Cytoplasmic RNA of prokaryotes that is used in protein secretion.
16. A component of the ribosome.
17. Transfer RNA.
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14.2 Transcription in Bacteria
Overview
This section outlines the process of transcription in bacteria. As was the case with
replication, it is better to understand the simpler bacterial transcription system before proceeding
to the more complex eukaryotic one. Before entering into the discussion of initiation, elongation,
and termination, the section takes a good look at the structure of a bacterial promoter. A promoter
is a regulatory sequence that plays a central role in transcriptional regulation. There are two
things that you should focus on with regards to the promoter. The first is the numbering of
nucleotides (Figure 14.4) and the second is the concept of a consensus sequence (Figure 14.5).
Notice that not all promoters have the same nucleotide sequence, although they are very similar.
The best way to understand transcription initiation, elongation, and termination is to first
read the sections of the text, and then study the appropriate diagrams. Remember that these are
three-dimensional systems, and it is a complex interaction of proteins and nucleic acids (both
DNA and RNA) that makes the process possible.
Outline of Key Terms
Promoter complexes
Closed complex
Open complex
Transcription termination
-dependent termination
Rho () factor
-independent termination
Intrinsic termination
Promoter
Sequence elements
Pribnow box
Consensus sequence
RNA polymerase
Holoenzyme
Core enzyme
Sigma () factor
Helix-turn-helix motif
Focal Points



Transcription initiation (Figure 14.7)
Synthesis of the RNA transcript (Figure 14.8)
Transcription termination (Figures 14.10 and 14.11)
Exercises and Problems
For questions 1 to 6, match the term with its correct definition.
_____ 1. Helix-turn-helix
_____ 2. Transcription factors
_____ 3. RNA polymerase
_____ 4. Holoenzyme
_____ 5. Closed complex
_____ 6. Promoter
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a.
b.
c.
d.
e.
f.
An RNA polymerase that has sigma factor attached.
The region of a gene between -10 and -35 that contains the Pribnow box.
Occurs when the holoenzyme is bound to the promoter region.
Proteins that influence the relationship of the holoenzyme with the promoter.
A four subunit molecule that catalyzes the synthesis of RNA.
A region of the sigma factor that facilitates binding to the DNA.
For questions 7 to 14 indicate whether the statement is associated with initiation (I), elongation
(E), or termination (T) of bacterial transcription.
_____ 7. Disrupts the hydrogen bonding between the DNA and RNA.
_____ 8. Starts with the formation of a closed complex.
_____ 9. May occur either dependently or independently of the rho protein.
_____ 10. Actively uses the template strand for RNA synthesis.
_____ 11. Unraveling of the DNA occurs in AT-rich regions
_____ 12. The RNA polymerase moves along the DNA.
_____ 13. RNA is synthesized in a 5′ to 3′ direction.
_____ 14. The sigma factor within the holoenzyme binds to the DNA.
14.3 Transcription in Eukaryotes
Overview
Transcription in eukaryotes is slightly more complicated than in bacteria, although the
principles remain the same. During initiation, the RNA polymerase must still bind to the promoter
and form an open complex. However, unlike the bacterial systems, eukaryotic systems employ
three different RNA polymerases to transcribe the various categories of genes. These include
RNA polymerase II, which transcribes mRNAs. Moreover, eukaryotes utilize a variety of
proteins, called transcription factors, which regulate the binding of the polymerase to the
promoter (Figure 14.14). Other types of transcription factors bind regulatory elements and allow
for a fine tuning of the transcription process. Also, note how the termination of transcription
occurs after the mRNA is released from the DNA template (Figure 14.15).
Outline of Key Terms
Regulatory elements
Enhancers
Silencers
Cis-acting elements
DNA sequences
Trans-acting factors
Proteins
Core promoter
TATA box
Transcriptional start site
Basal transcription
Basal transcription apparatus
General transcription factors
Preinitiation complex
Mediator
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Focal Points



Promoter regions of a eukaryotic structural gene (Figure 14.13)
Interactions of transcription factors and RNA polymerase in initiation (Figure 14.14)
Possible models for transcription termination (Figure 14.15)
Exercises and Problems
For questions 1 to 7, match each of the components of a eukaryotic structural gene to its correct
definition.
_____ 1. trans-acting factor
_____ 2. TATA box
_____ 3. enhancer
_____ 4. core promoter
_____ 5. regulatory element
_____ 6. cis-acting element
_____ 7. silencer
a.
b.
c.
d.
e.
f.
g.
Any sequence that effects the ability of the RNA polymerase to bind the promoter.
A regulatory sequence that inhibit the level of transcription.
A general term for regulatory elements that influence the activity of a nearby gene.
A regulatory sequence that increase the level of transcription.
This will produce a low level of transcription even in the absence of regulatory elements.
This determines the precise start site of transcription.
A gene that controls a second gene from a distance.
For each of the following components of the transcription preinitiation complex, match the
protein with its correct function.
_____ 8. TFIIB
_____ 9. TFIID
_____ 10. TFIIF
_____ 11. Mediator
_____ 12. TFIIH
_____ 13. TFIIE
a.
b.
c.
d.
e.
f.
Interacts with the transcription factors and the RNA polymerase.
Serves as a junction between the RNA polymerase, TFIIB and the promoter.
This protein binds to the TATA box in the promoter.
Binds to TFIID, allows the RNA polymerase to bind to the core promoter.
Plays the major role in the formation of the open complex.
Maintains the open complex.
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14.4 RNA Modification
Overview
In eukaryotic organisms, transcription does not directly produce a functional mRNA.
Instead, following transcription, the pre-mRNA molecule is modified by a number of different
processes that can drastically alter the size and function of the pre-mRNA produced by the RNA
polymerase (Table 14.3).
These processes can be divided into two general categories. The first form of
modification is a chemical change to the RNA transcript. This is usually in the form of 5′ capping
or 3′ polyA tailing, and sometimes even editing changes that alter the base sequence after it has
been synthesized. The second form of modification involves alterations in the RNA length. This
includes trimming of large transcripts into smaller pieces, and the removal of non-coding or
intervening sequences. These sequences, called introns, are removed by RNA splicing. You need
to familiarize yourself with all these modifications and the terminology associated with them.
Outline of Key Terms
Self-splicing
Group I introns
Group II introns
Maturases
Spliceosome
Pre-mRNA
Heterogeneous nuclear RNA
(hnRNA)
snRNPs
Alternative splicing
Other RNA modifications
Capping
5′ cap
Polyadenylation
3′ poly A tail
Editing
Colinearity
RNA splicing
Exons
Introns
Intervening sequences
rRNA processing
Nucleolus
tRNA processing
Endonuclease
Exonuclease
Ribozyme
Focal Points







Overview of RNA modifications (Table 14.3)
The processing of ribosomal RNA in eukaryotes (Figure 14.16)
The processing of a precursor tRNA molecule in E. coli (Figure 14.17)
RNA splicing (Figures 14.18-14.20)
Capping (Figure 14.21)
PolyA tailing (Figure 14.22)
RNA editing (Figure 14.23)
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Exercises and Problems
For questions 1 to 9, use the following answers. Some answers may be used more than once.
a. 5′ capping
b. 3′ polyA tailing
c. Splicing
_____ 1. May involve the use of snRNPs.
_____ 2. Usually serves to shorten the length of the RNA transcript.
_____ 3. This process may occur while the transcript is being made by the RNA polymerase.
_____ 4. This plays an important role in the early stages of translation.
_____ 5. This provides stability to the mRNA molecule.
_____ 6. Removes the introns from the pre-mRNA.
_____ 7. May produce an mRNA with different combinations of introns.
_____ 8. Identifies the consensus sequence AAUAAA in the pre-mRNA.
_____ 9. Attaches a guanosine monophosphate to the pre-mRNA.
For questions 10 to 14, identify the type of splicing that is involved in the statement.
a. group II
b. spliceosome
c. group I
d. all of the above
_____ 10. Involves the use of snRNPs.
_____ 11. Uses a free guanosine to enable splicing.
_____ 12. Produces a conformational change in the pre-mRNA to enable splicing.
_____ 13. Identifies consensus sequences in the pre-mRNA.
_____ 14. Utilizes an adenine nucleotide present within the intron.
For questions 15 to 17, provide the correct term that completes the statement.
15. An enzyme that is composed of RNA, not protein, is called a _________.
16. In eukaryotes, the coding information for a protein is contained within the _______ of a gene.
These are separated by DNA sequences called _______ that are not translated into protein.
17. In eukaryotes, one gene may produce many similar proteins due to the process of _________.
Chapter Quiz
1. Which of the following would reduce the overall level of transcription?
a. transcription factors
b. enhancers
c. silencers
d. core promoter
e. none of the above
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2. Sigma factor is associated with transcription in ________.
a. bacteria
b. eukaryotes
c. viruses
d. all organisms
3. This process increases the stability of the mRNA.
a. 5′ capping
b. alternative splicing
c. 3′ polyA tailing
d. spliceosomes
e. none of the above
4. The transcription factor that binds to the TATA sequence in eukaryotes is ________.
a. sigma
b. rho
c. TFIIB
d. TFIID
e. mediator
5. This process involves the use of snRNPs.
a. 3′ polyA tailing
b. initiation of transcription
c. spliceosome activity
d. transcription termination
6. The Pribnow box is located where?
a. the bacterial promoter
b. the core promoter of eukaryotes
c. eukaryotic introns
d. the end of the coding sequence
e. none of the above
7. Which of the following is NOT associated with the initiation of transcription in eukaryotes?
a. rho
b. mediator
c. formation of an open complex
d. transcription factors
e. RNA polymerase II
8. In RNA editing, the most common modification is
a. decarboxylation.
b. deamination.
c. methylation.
d. phosphorylation.
9. The allosteric and torpedo models have been proposed to describe which of the following?
a. transcription initiation in bacteria
b. transcription termination in bacteria
c. transcription initiation in eukaryotes
d. transcription termination in eukaryotes
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10. The information for producing a functional protein is contained within the _______ of a
eukaryotic gene.
a. introns
b. exons
c. polyA tail
d. 5′ cap
e. group I introns
Answer Key for Study Guide Questions
This answer key provides the answers to the exercises and chapter quiz for this chapter. Answers
in parentheses ( ) represent possible alternate answers to a problem, while answers marked with
an asterisk (*) indicate that the response to the question may vary.
14.1
1. e
2. c
3. a
4. d
5. b
6. f
7. g
8. E
9. I
10. I
11. T
12. 7S RNA
13. snRNA
14. mRNA
15. scRNA
16. rRNA
17. tRNA
14.2
1. f
2. d
3. e
4. a
5. c
6. b
7. T
8. I
9. T
10. E
11. I
12. E
13. E
14. I
14.3
1. g
2. f
3. d
4. e
5. a
6. c
7. b
8. d
9. c
10. b
11. a
12. e
13. f
14.4
1. c
2. c
3. a
4. a
5. b
6. c
7. c
8. b
9. a
10. b
11. c
12. d
13. d
14. a
15. ribozyme
16. exons; introns
17. alternative splicing
1. c
2. a
3. c
4. d
5. c
6. a
7. a
8. b
9. d
Quiz
10. b
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