1. Central dogma of Genetics
A Gene is a DNA sequence
A Gene encodes for a protein
A protein could function as an enzyme or a biocatalyst that is responsible for allowing chemical reactions to take place in a cell.
Many chemical reactions together produce a trait or characteristic like flower color.

2. Genes ----->proteins -----> Traits (Red flower color)
Genes to Traits

3. Gene expression occurs in two steps
The Information Within the DNA Is Accessed During the Process of Gene Expression
Gene expression occurs in two steps
Transcription
The genetic information in DNA is copied into a nucleotide sequence of ribonucleic acid (RNA)
Translation
The nucleotide sequence in RNA is converted (using the genetic code) into the amino acid sequence of a protein
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5. Transcription literally means the act or process of making a copy
In genetics, the term refer to the copying of a DNA sequence into an RNA sequence
The structure of DNA is not altered as a result of this process
It can continue to store information
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6. Structural genes encode the amino acids of a polypeptide
Gene Expression
Structural genes encode the amino acids of a polypeptide
Transcription of a structural gene produces messenger RNA, usually called mRNA
Polypeptide synthesis is called translation
The mRNA sequence determines the amino acids in the polypeptide
The function of the protein determines traits
This path from gene to trait is called the central dogma of genetics
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7. The central dogma of genetics

8. Signals the end of protein synthesis

9. Gene Expression Requires Base Sequences
The strand that is actually transcribed (used as the template) is termed the template strand
The opposite strand is called the coding strand or the sense strand as well as the nontemplate strand
The base sequence is identical to the RNA transcript
Except for the substitution of uracil in RNA for thymine in DNA
Transcription factors recognize the promoter and regulatory sequences to control transcription
mRNA sequences such as the ribosomal-binding site and codons direct translation
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10. The Stages of Transcription
Transcription occurs in three stages
Initiation
Elongation
Termination
These steps involve protein-DNA interactions
Proteins such as RNA polymerase interact with DNA sequences
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11. Transcription

13. The conventional numbering system of promoters
Most of the promoter region is labeled with negative numbers
Bases preceding this are numbered in a negative direction
There is no base numbered 0
Bases to the right are numbered in a positive direction
The conventional numbering system of promoters
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14. Sequence elements that play a key role in transcription
The promoter may span a large region, but specific short sequence elements are particularly critical for promoter recognition and activity level
Sequence elements that play a key role in transcription
Sometimes termed the Pribnow box, after its discoverer
\The conventional numbering system of promoters
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15. The most commonly occurring bases
For many bacterial genes, there is a good correlation between the rate of RNA transcription and the degree of agreement with the consensus sequences
The most commonly occurring bases
Examples of –35 and –10 sequences within a variety of bacterial promoters
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16. Initiation of Bacterial Transcription
RNA polymerase is the enzyme that catalyzes the synthesis of RNA
In E. coli, the RNA polymerase holoenzyme is composed of
Core enzyme
Five subunits = a2bb’
Sigma factor
One subunit = s
These subunits play distinct functional roles
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17. Binding of factor protein to DNA double helix
Amino acids within the a helices hydrogen bond with bases in the promoter sequence elements
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19. Similar to the synthesis of DNA via DNA polymerase

20. Rho protein is a helicase
rho utilization site
Rho protein is a helicase
r-dependent termination

21. r-dependent termination

22. r-independent termination is facilitated by two sequences in the RNA
1. A uracil-rich sequence located at the 3’ end of the RNA
2. A stem-loop structure upstream of the Us
Stabilizes the RNA pol pausing
URNA-ADNA hydrogen bonds are very weak
This type is also called intrinsic
r-independent termination

23. Eukaryotic RNA Polymerases
Nuclear DNA is transcribed by three different RNA polymerases
RNA pol I
Transcribes all rRNA genes (except for the 5S rRNA)
RNA pol II
Transcribes all structural genes
Thus, synthesizes all mRNAs
Transcribes some snRNA genes
RNA pol III
Transcribes all tRNA genes
And the 5S rRNA gene
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24. Eukaryotic RNA Polymerases
All three are very similar structurally and are composed of many subunits
There is also a remarkable similarity between the bacterial RNA pol and its eukaryotic counterparts
Structure of
RNA polymerase
© From Patrick Cramer, David A. Bushnell, Roger D. Kornberg. "Structural Basis of
Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution." Science, Vol.
292:5523, , June 8, 2001.
© From Seth Darst, Bacterial RNA polymerase.
Current Opinion in Structural Biology.
Reprinted with permission of the author.
(a) Structure of a bacterial
RNA polymerase
Structure of a eukaryotic
RNA polymerase II (yeast) 5′ 3′
Transcribed DNA
(upstream)
Lid
Exit
Clamp 5′
Rudder
Entering DNA
(downstream)
Wall 3′ 5′
Mg2+
Bridge
Jaw
Catalytic
site
through a pore
NTPs enter
Transcription
(b) Schematic structure of RNA polymerase
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25. The core promoter is relatively short It consists of the TATA box
Usually an adenine
The core promoter is relatively short
It consists of the TATA box
Important in determining the precise start point for transcription
The core promoter by itself produces a low level of transcription
This is termed basal transcription
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26. The core promoter is relatively short It consists of the TATA box
Usually an adenine
The core promoter is relatively short
It consists of the TATA box
Important in determining the precise start point for transcription
The core promoter by itself produces a low level of transcription
This is termed basal transcription
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27. Regulatory elements affect the binding of RNA polymerase to the promoter
They are of two types
Enhancers
Stimulate transcription
Silencers
Inhibit transcription
They vary widely in their locations but are often found in the –50 to –100 region
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29. Released after the open complex is formed
A closed complex
RNA pol II can now proceed to the elongation stage
Released after the open complex is formed
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30. Transcription termination RNA polymerase II
RNA polymerase II transcribes a gene
past the polyA signal sequence.
The RNA is cleaved just past the
polyA signal sequence. RNA
polymerase continues transcribing
the DNA.

31. Transcription produces the entire gene product
RNA MODIFICATION
In eukaryotes, the genes are interrupted: the coding sequences, called exons, are interrupted by intervening sequences or introns
Transcription produces the entire gene product
Introns are later removed or excised
Exons are connected together or spliced
This phenomenon is termed RNA splicing
It is a common genetic phenomenon in eukaryotes
Occurs occasionally in bacteria as well
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32. Aside from splicing, RNA transcripts can be modified in several ways
RNA MODIFICATION
Aside from splicing, RNA transcripts can be modified in several ways
For example
Trimming of rRNA and tRNA transcripts
5’ Capping and 3’ polyA tailing of mRNA transcripts
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34. This processing occurs in the nucleolus
Functional RNAs that are key in ribosome structure
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35. Found to contain both RNA and protein subunits
Covalently modified bases
Therefore, it is a ribozyme
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36. The spliceosome is a large complex that splices pre-mRNA
Pre-mRNA Splicing
The spliceosome is a large complex that splices pre-mRNA
It is composed of several subunits known as snRNPs (pronounced “snurps”)
Each snRNP contains small nuclear RNA and a set of proteins
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37. Intron RNA is defined by particular sequences within the intron and at the intro-exon boundaries
The consensus sequences for the splicing of mammalian pre-mRNA are shown here
Corresponds to the boxed adenine
Sequences shown in bold are highly conserved
Serve as recognition sites for the binding of the spliceosome
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38. Intron loops out and exons brought closer together
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39. Intron will be degraded and the snRNPs used again
Cleavage may be
catalyzed by RNA
molecules within U2
and U6
Intron will be degraded and the snRNPs used again
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40. Capping of pre-mRNA

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43. RNA editing
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44. Possible mechanisms for Pol II termination
RNA polymerase II transcribes a gene
past the polyA signal sequence. 5′ 3′
PolyA signal sequence
The RNA is cleaved just past the
polyA signal sequence. RNA
polymerase continues transcribing
the DNA. 5′ 3′ 3′ 3′
Allosteric model: After passing the polyA signal sequence,
RNA polymerase II is destabilized due to the release of
elongation factors or the binding of termination factors (not
shown). Termination occurs.
Torpedo model: An exonuclease
binds to the 5′ end of the RNA
that is still being transcribed and
degrades it in a 5′ to 3′ direction. 5′ 5′ 3′ 3′ 5′ 3′
Exonuclease catches
up to RNA polymerase II
and causes termination.
Exonuclease 3′ 5′ 3′
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