LS2202!

March to April 2016!
Outline of course!
•  RNA!
•  Transcription (prokaryote and eukaryote)!
•  Basic Lac-operon!
•  Bacterial genetics (mutation,
transformation, conjugation and
transduction)!
•  Phages (small ssDNA, lamda phage, p1-
phage) !
Book!

•  Introduction to genetic analysis, by
Griffiths, Wessler, Lewontin and Carroll!

•  GENES VIII by LEWIN.!

•  Biochemistry by Voet and Voet!
Central Dogma!
What is a gene?

DNA

How does genetic
information transferred to
gene product?
Central Dogma!
What is a gene?

DNA

How does genetic
information transferred to
gene product?

Through an intermediate
RNA!

The process is called transcription, use DNA as a template!
Central Dogma!
What is a gene?

DNA

RNA!

Translation!

protein!

Function!
Replica)on, Transcrip)on and
Transla)on
Informa)on stored in RNA can be
transferred to DNA
•  Modifica)on to the central dogma

RNA act as a template for DNA synthesis, using RNA-dependent DNA
polymerase or reverse transcriptase
Retroviruses store gene)c informa)on
in RNA, which is then copied into DNA
But RNA is more than an intermediate!
Properties of RNA !
Ø RNA is produced as single strand
Ø RNA is usually a single stranded polynucleo)de
chain
Ø RNA are flexible and form a much greater
variety of complex 3D structure

Structure of transfer RNA
Properties of RNA !
Ø RNA is produced as single strand
Ø RNA is usually a single stranded polynucleo)de
chain
Ø RNA are flexible and form a much greater
variety of complex 3D structure
Ø RNA can form intramolecular base pairing,
which is important determinant of RNA shape
Ø RNA has hydroxyl group (-OH) at 2` posi)on
Ø Form base pairing between purin and pyrimidin,
for example Adenine pairs with Uracil, and
Guanine pairs with Cytosine.
Ø Some RNA can func)on as enzyme or switch,
for example ribozyme and riboseswitch
Class of RNA!

Messenger RNA (mRNA)! Non-coding RNA!
Coding ! Or!
Functional RNA !

protein
Class of RNA!

Messenger RNA (mRNA)! Non-coding RNA!
Coding ! Or!
Functional RNA !

Transfer RNA (tRNA)!
protein Ribosomal RNA (rRNA) !
Small nuclear RNA (sn RNA): they are part of the system in eukaryotic
cells that further process mRNA!
!
Micro RNA (miRNA): regulate protein expression in eukaryotic genes!
!
Small interferes RNA (SiRNA) inhibit the production of viruses and
prevents the spread of transposable elements to other chromosomal loci !
!
Chemical structure of RNA!

Ø  T h e n u c l e o t i d e i n R N A a r e j o i n e d b y
phosphodiester linkage between 3`carbon of one
nucleotide and the 5` carbon of another!

Ø  Like DNA, RNA can form double-stranded helical
structure!
Chemical structure of DNA/RNA!
Polynucleotide chain of DNA and RNA!
RNA DNA

•  Similar strand structure
•  Can define a 5’ and 3’ end
•  2’ hydroxyl in RNA
•  (causes stability differences)
•  Uracil in RNA not in DNA
Base pairing in RNA
double-strand!
Why DNA is suitable for storing genetic material than RNA?!

All known living cells use DNA rather than RNA to store genetic
information!
DNA is chemically more stable than RNA!

RNA undergo spontaneous hydrolysis in aqueous
solution. The 2` -OH group can attack and break the
phosphodiester linkage at the 3`position.!
DNA is chemically more stable than RNA!

!
!
Structure of RNA!

•  RNA can form discontinuous stretches of double
helix!
•  Hydrogen-bonding between the bases are
important for the formation of double helices. !
•  These H-bonds are cooperative.!
•  Major driving force that stabilizes a double helix
is base stacking interaction!
Structure of RNA!

Purine and Pyrimidine are flat and planar, so they can stack on top of one
another. The Van der Waals and electrostatic interactions between stacked
bases contribute to the strong interaction !
Structure of RNA!

•  RNA can form discontinuous stretches of double
helix!
•  Hydrogen-bonding between the bases are
important for the formation of double helices. !
•  These H-bonds are cooperative.!
•  Major driving force that stabilizes a double helix
is base stacking interaction!
•  Metal ion helps shield electrostatic repulsion
between the phosphate group!
Structure of RNA!

•  The backbone phosphate group are negatively charge and will tend to
repel each other!

•  Both monovalent (Na+ and K+) and divalent (Mg2+) ions have been found
to shield the negative charge of RNA!
RNA cannot adopt the standard Watson-Crick
double helical structure!

Alternate conformation of ribose ring is define by
sugar pucker!
5` 5`
2` 3`
4` 1` 4` 1`
3` 2`

C2` and C5` are in same plane C3` and C5` are in same plane
Found in B-form of double-helix Found in A-form of double-helix
What are A-form and B-form of helix?!

Major groove

Minor groove

•  A- and B-form are right handed double –
helix
•  In B-form of double-stranded helix major
groove is wider
•  In A-form of double-stranded helix
major groove is deeper and narrower
RNA adopts the A-form of double helical
conformation!
DNA can take B-form of double helix, and under limited
water spontaneously switch to A-form of DNA
5`
3`
4` 1`
2`

C2`-edo

In RNA, due to C2`-OH steric hindrance with PO42- on C3`,
C2`-edo sugar pucker is not observed

The major groove of A-form of double helices is less accessible
to proteins than that of B-form of DNA
Non-standard base-pairing is common in RNA !

Wobble base pair are often seen in RNA!
Non-standard base-pairing is common in RNA !

Hoogsteen base pairs:
named after Karst
Hoogsteen!

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