RNA and RNA Transcription

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RNA and RNA Transcription

• September 9, 2003

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Flow of Genetic Information
DNA
RNA Transcription
DNA Replication
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The Plan- RNA Transcription

• Today (9/9)
• Structure of RNA
• How is RNA made
• Types of different RNAs
• rRNA and tRNA
• A brief intermission
• Monday (9/15)
• Structure of mRNA
• Details of Transcription (mRNA)

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Definition of RNA
RNA Ribonucleic Acid

• A polymer of ribonucleoside 5-monophosphates
  (i.e., ribonucleotides)

OH
5
Structure of RNA

• RNA is a polymer of ribonucleotides as opposed to
  the deoxyribonucleotides that make up DNA

5
1
4
5
1
4
2
3
2
3
Our old friend Deoxyribose
Ribose
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Bases Found in RNA
Guanine
Adenine
Uracil
Cytosine
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Information is encodedin the order of the Bases
U
1

• Bases attach to the 1 Carbon just as was seen in
  the DNA chain
• Remember that although the RNA chain looks very
  similar to the DNA chain there are
  differences!!!!!!!!!!!!!!!!!

C
1
1) RNA is chemically less stable than DNA 2) RNA
is single-stranded
U
1
RNA just doesnt need to hang around as long
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Secondary Structure of RNA

• Unlike DNA, RNA is technically a single-stranded
  molecule
• The bases can pair with one another through
  intramolecular base pairing to give different
  structures
• Hairpins
• Double-stranded regions
• Helices (A type)
• Often bound to proteins

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How does Information get Transferred from DNA to
RNA?

• DNA serves as a template for RNA polymerase
• As you might expect RNA polymerase is a DNA
  directed polymerizer of RNA
• Can anyone guess in which direction the RNA chain
  grows?

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One strand of DNA serves as the template

• The RNA polymerase copies one of the strands of
  DNA in a process known as RNA transcription

C A T T A G T A C T A T A C T
3
5
DNA
G T A A T C A T G A T A T G A
3
5
5
3
RNA
C A U U A G U A C U A U A C U
Template Strand
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RNA Polymerases

• Reaction catalyzed is chemically identical to
  that described for DNA polymerases
• Add a ribonucleotide to the 3-OH of an RNA chain
• RNA polymerases have 5-3 polymerase activity
  (No other activities)
• Unlike DNA polymerases they can simply initiate
  the chain on their own (i.e., they dont need any
  kind of priming)

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Chemical Mechanism is Identical to that described
for DNA polymerase
5 RNA Chain
G
5
U
OH
3
OH
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RNA Polymerization

• Requirements for RNA Synthesis
• DNA template
• RNA polymerase
• All four NTPs (N Nucleotide)
• ATP, CTP, GTP, UTP

(RNA)N NTP (RNA)N1 PPi
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Recurring ThemeConservation of Mechanism

• The cell figures out a good way to do something
  and applies that mechanism to multiple processes
• An efficient way to synthesize nucleic acid
  chains is to add an activated (phosphorylated)
  ribonucleotide or deoxyribonucleotide to the
  3-OH group of an existing chain
• That mechanism is used for both
• DNA and RNA

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How do RNA polymerases copy Chromatin?

• RNA polymerases require accessory factors to
  initiate synthesis
• After initiation they can move along without the
  aid of any other proteins
• Topisomerases probably still function to relax
  supercoils in front of the machine

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RNA Polymerase Does Not Require Accessory Factors
Topisomerases
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Different Classes of RNAs Cooperate to Direct
Protein Synthesis

• rRNA (80 of cellular RNA)
• Ribosomal RNA is a component of the ribosomes
  that mediate protein synthesis
• tRNA (15 of cellular RNA)
• Transfer RNA - acts as a cellular adapter
  between nucleic acids and proteins
• mRNA (5 of cellular RNA)
• Messenger RNA - takes the information encoded by
  the DNA to the protein translation machinery so
  that it can be read
• Others- snRNAs, scRNAs, mt rRNA

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Synthesis of Different Classes of RNA Molecules

• Bacteria have a single RNA polymerase that
  synthesizes all the different types of RNAs
• Eukaryotic cells have polymerases specific for
  each type of RNA
• rRNA RNA polymerase I
• mRNA RNA polymerase II (topic for Monday)
• tRNA and others RNA polymerase III

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Classes of RNA

• rRNA
• tRNA
• mRNA (covered Monday in gory detail)
• Other classes of RNA

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Properties of rRNA

• rRNA is the most abundant form of RNA in the cell
  (80 of cellular RNA)
• Plays a structural role in building the ribosomes
  which are the machines that synthesize proteins
• Some catalytic roles
• Very stable RNAs due to
• Association with proteins
• Methylation of the 2-OH
• (antibiotic resistance)

OCH3
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Ribosomal RNAs are Synthesized Simultaneously

• Different size ribosomal RNAs are needed to make
  the ribosomes
• 16S, 23S, 5S (sizes in prokaryotes)
• 18S, 28S, 5.8S, 5S (sizes in eukaryotes)
• Equal amounts of each of these RNAs are required
• The cell has devised a clever way to assure that
  equal amounts of these RNAs are made

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In eukaryotes rRNA is synthesized in the Nucleolus

• In eukaryotes, the rRNA genes are repeats located
  in a special region of one chromosome
• rRNAs are transcribed in the Nucleolus

This makes sense because ribosomes are assembled
in the nucleolus
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Some Common Antibiotics Interact with Ribosomal
RNAs

• These antibiotics work by inhibiting prokaryotic
  protein synthesis- dont affect the distinct
  eukaryotic ribosomes
• Streptomycin
• 16S RNA
• Chloramphenicol
• 23S RNA

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Classes of RNA

• rRNA
• tRNA
• mRNA (to be covered Monday)
• Other classes of RNA

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RNA-type Properties of tRNA

• tRNAs are relatively short RNA molecules 75-80
  nucleotides
• Bases are extensively modified (1of 10)
• Synthesized as longer pieces and then trimmed and
  spliced
• Highly structured molecules

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Role of tRNA

• Transfer RNAs (15 of cellular RNA)
• tRNAs function as the decoders so that messenger
  RNA can serve as the template for making proteins
• tRNAs carry the amino acids that are going to be
  linked together in the process of protein
  synthesis
• One end reads the code in the messenger RNA and
  the other end carries the amino acid

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tRNAs are Modified by Addition of an Amino Acid
to a 3-OH
Amino Acid
-OH

• The 3-OH is modified by addition of an amino
  acid
• The anticodon recognizes the codon in the
  messenger RNA
• tRNA serve to decode the genetic code

AAAA
Much much more to come on the function of tRNAs
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Tertiary structure of tRNA
Amino acid
Messenger RNA
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Classes of RNA

• rRNA
• tRNA
• mRNA (to be covered Monday)
• Other classes of RNA
• snRNAs
• snoRNAs
• RNPs
• ribozymes

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Other Roles for RNA

• Many RNAs play a role in catalyzing other nucleic
  acid reactions- ribozymes
• Often these RNAs give sequence specificity to
  different reactions- such as helping to identify
  the region of another RNA molecule that needs to
  be modified

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Take Home Message

• Structure of RNA (similarities to and differences
  from DNA)
• Transfer of information from DNA to RNA
• Classes of RNA
• rRNA
• tRNA
• mRNA (still to come- you can hardly wait )

More info on what I said about selectively
reading the DNA