Ribonucleic Acid2

The versatility of RNA
RNA: types & structure
• Polymer of nucleotides
– What is the difference?
• Five RNA types:

– rRNA
– mRNA
– tRNA
– snRNA
– snoRNA
Components of RNA
The versatility of RNA
• RNA folds into unique 3-D structures which act similarly to
globular proteins; “tRNA looks like natures attempt to make RNA do
the job of a protein” -Francis Crick
• Generally the pathway of gene expression from DNA to

functional product via an RNA intermediate overemphasizes
proteins as the ultimate goal;
• However, RNAs are involved in a variety of cellular processes
along the pathway of gene expression including;
– DNA replication; RNA processing; mRNA turnover; protein synthesis;
protein targeting
• RNA catalyzes chemical reactions in living cells (ribozymes)

Relationship between the 5 RNA
types during gene expression
tRNA
Adaptor like molecule that decodes mRNA
codons into amino acids
Brings amino acid corresponding to the appropriate

mRNA codon
D-loop Each amino acid has unique tRNA
T-loop
Anticodon-loop
tRNA structure
The three tRNA loops form the cloverleaf secondary structure;
each loop has a specific function
1. The T-loop; involved in recognition by the ribosomes

2. The D-loop; associated with recognition by the aminoacyl
tRNA synthatase
3. The Anticodon loop; base pairs with the codon in mRNA
• Every tRNA has the sequence ACC on the 3’-End to which

the amino acid is attached
• The anticodon loop in all tRNAs is bounded by U on the 5’-
side and a modified purine on the 3’-side
tRNA: secondary and tertiary structures
rRNA
Component of the ribosome, the site of protein synthesis in all living cells
Provides a mechanism for decoding mRNA into amino acids and interacts
with tRNAs during translation by providing peptidyltransferase activity
Type Size Large subunit Small subunit
Prokaryotic 70S 50S (5S rRNA, 23S 30S (16S rRNA)

rRNA)
Eukaryotic 80S 60S (5S rRNA, 40S (18S rRNA)

5.8S rRNA, 28S rRNA)
RNAs are in parenthesis

-Sites of attack for several antimicrobials, especially TB drugs
-16S RNA used to classify microorganisms; the Microbiome / Metagenomics
Ribonucleoproteins (RNPs)
• Most RNAs are associated with proteins as RNA-
protein complexes called ribonucleotpoteins
– One important RNP is the ribosome
• RNA-based catalytic reactions occur in conjunction

with proteins
• Catalytic RNAs are called ribozymes; they catalyze

a number of reactions in cells ranging from cleavage
of phosphodiester bonds to peptide formation
RNPs are involved in a wide range of
cellular processes
Types of naturally occurring ribozymes
mRNA
Sense; Template DNA strand;
Non-template DNA strand; Antisense, Non-coding strand
Coding strand
Reverse Primer
Forward Primer
Information in DNA is copied

(transcribed) into mRNA, which
goes to ribosome for translation
mRNA is;
-unstable in cells (why?)
-<5% total RNA
-Methylated heads (CH3 cup)
-Polyadenylated tails: utilized in
biotech
-Represents expressed genes in

cells
2. Fundamental Molecular
Biology II
The processes governing flow of genetic info
-DNA replication
-Transcription
-Translation
DNA replication
Re-cap; the dogma of biology
Each process governing the flow of genetic info is given a
specific name;
• Replication; the process of making an exact copy of DNA

from the original DNA
• Transcription; the process of being copied to generate a
ssRNA identical in sequence to one strand in dsDNA
– The info is rewritten (transcribed), but in basically the same language
of nucleotides
• Translation; the process in which the RNA nucleotide

sequence is converted into the amino acid sequence of a
protein
– The term denotes that the info in the language of nucleotides is copied
(translated) into another language of amino acids
DNA replication
• The regulation of DNA replication is fundamental
to understanding of the continuity of life
• As cells multiply and give rise to new cells, the

genome must be accurately duplicated so that
information is passed on to each new generation
with minimal error
• Understanding DNA replication helps to

understand molecular tests e.g. PCR, Sequencing
DNA polymerases
• Polymerize nucleotides into growing DNA strands
• Bacteria have 5 DNA pols, mammals 14
• Eukaryotes have 3 DNA pols for chromosomal DNA
replication;
– DNA polymerase α
– DNA polymerase δ Chromosomal
– DNA polymerase ε
– DNA polymerase γ: mtDNA replication
• The above 4 are called replicative DNA pols; other

types of DNA pols are used in DNA repair processes (e.g.
Klenow, etc.; have 3’ – 5’ activity)
All DNA pols add nucleotides in the 5’-
3’ direction
• DNA pol catalyzes formation of phosphodiester bond
between the 5’C-PO4 of a new dNTP and the 3’C-
OH of the last nucleotide in the newly synthesized
strand
• DNA pol cannot initiate DNA synthesis de novo

– Except for DNA pol α that’s involved in primer synthesis,
all DNA pols require a primer
– DNA pol recognize and bind the free 3’-OH at the end of
the primer
– Once primed, the pol extends pre-existing chains rapidly
DNA polymerase works in 5’ – 3’ direction
DNA polymerase works in
5’ – 3’ direction
22
Semi-conservative nature of DNA
replication: gives two daughter duplex
DNAs, each with one original strand
and one new strand
Transcription
Transcription
• The copying of the sequence of the template
strand of the gene into a complementary RNA
transcript (mRNA)
– The beginning of gene expression
– Transcription and translation are coupled in

bacteria
– In eukaryotes, mRNA and protein synthesis are

separated between two cellular compartments
Transcription and translation
coupled in prokaryotes
Transcription and translation
uncoupled in eukaryotes
Regulation at each level

Sense and Antisense strands
• A DNA sequence is read in triplets using the
antisense (non-coding) strand;
– Called the template strand, directs the synthesis
of RNA via complementary base-pairing
• The other non-template strand is the sense

(coding) strand;
– Bears the same sequence as the mRNA (except
for possessing U instead of T)
Sense and antisense strands
Promoters: in bacteria they have two
distinct “Consensus” Sequences
A promoters is a sequence to which RNA polymerase

binds to begin transcription
Structure of bacterial RNA pol
• Comprised of;
– Core Enzyme, and
– A transcription factor called the Sigma factor, δ
• Together, the core enzyme and δ form a

functional enzyme complex called the
“Holoenzyme”
The core enzyme, cont’d
• The core enzyme catalyzes polymerization
– It is conserved from bacteria to humans

– Has high affinity for most DNA; in absence of δ it
initiates synthesis anywhere on a DNA template
in vitro
• The δ is responsible for decreasing the non-

specific binding affinity of RNA pol
The sigma factor (δ)
• Recognizes the promoter
• The -35 and -10 sequences are required for

recognition
• -10 region is responsible for initial melting of the

template strand
• There several δ per species

E. coli sigma factors
Types of DNA-dependent RNA
polymerases
Sites for antibiotic attack (RIF, etc.)
RNA polymerases catalyze RNA synthesis using DNA as a

Template; they initiate RNA synthesis de novo
(in contrast to DNA pol)
The mechanism of transcription
• Occurs in three stages
– Initiation
– Elongation
– Termination
Initiation
Further divided into three stages;
• Formation of a closed promoter complex
– The DNA remains DS and the complex is reversible
• Formation of an open promoter complex

– Melting occurs to expose the template strand
– AT rich -10 region and negative supercoiling helps
– Irreversible; polymerization is initiated
• Promoter clearance
– There is a staged disruption of δ-core enzyme interaction
Elongation
• Transcription bubble is formed as RNA pol winds
and unwinds strands
• The catalytic site of the RNA pol has both;
– A Substrate Binding Sub-site at which the incoming NTP is
bound to the pol and to the complementary nt residue of the template
– And a Product Binding Sub-site, at which the 3’-
terminus of the growing RNA chain is positioned
• NTP and a phosphodiester bond forms with the 3’-

OH of the last nt in the RNA chain
• Transcription also proceeds in 5’ – 3’
Transcription elongation

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The versatility of RNA

RNA: types & structure

• Five RNA types:

• Generally the pathway of gene expression from DNA to

• RNA catalyzes chemical reactions in living cells (ribozymes)

Brings amino acid corresponding to the appropriate

D-loop Each amino acid has unique tRNA

1. The T-loop; involved in recognition by the ribosomes

• Every tRNA has the sequence ACC on the 3’-End to which

Type Size Large subunit Small subunit

Prokaryotic 70S 50S (5S rRNA, 23S 30S (16S rRNA)

Eukaryotic 80S 60S (5S rRNA, 40S (18S rRNA)

RNAs are in parenthesis

• RNA-based catalytic reactions occur in conjunction

• Catalytic RNAs are called ribozymes; they catalyze

Information in DNA is copied

-Represents expressed genes in

The processes governing flow of genetic info

• Replication; the process of making an exact copy of DNA

• Translation; the process in which the RNA nucleotide

• As cells multiply and give rise to new cells, the

• Understanding DNA replication helps to

• The above 4 are called replicative DNA pols; other

• DNA pol cannot initiate DNA synthesis de novo

– Transcription and translation are coupled in

– In eukaryotes, mRNA and protein synthesis are

Regulation at each level

• The other non-template strand is the sense

A promoters is a sequence to which RNA polymerase

• Together, the core enzyme and δ form a

– It is conserved from bacteria to humans

• The δ is responsible for decreasing the non-

• Recognizes the promoter

• The -35 and -10 sequences are required for

• -10 region is responsible for initial melting of the

• There several δ per species

Sites for antibiotic attack (RIF, etc.)

RNA polymerases catalyze RNA synthesis using DNA as a

• Formation of an open promoter complex

• NTP and a phosphodiester bond forms with the 3’-

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