Molecular Genetics

The study of chemical and physical structure of biological

macromolecules is known as molecular biology
Central Dogma of Molecular Biology

Transcription + Translation =
Gene expression
Deoxyribonucleic acids
• Main parts:
• Sugar-phosphate backbone
• Chains are formed by the binding of phosphodiester
bonds between phosphates and sugars.
• Nucleic acid base
• Covalently bound on sugars
• Complementary base pairing (A = T; C ≡ G)
• Purines – two rings (AG)
• Pyrimidines – one ring (CUT)
• 5’ and 3’ ends based on the sugar
• Chargaff’s rule
• Number of purines = number of pyrimidines
Directionality of DNA
• DNA is antiparallel
• Can either be 5’ to 3’ or 3’ to 5’
Organization of DNA into chromosomes
DNA Replication
• In eukaryotes
• In the nucleus
• Starts in multiple origins
• In prokaryotes
• In the cytosol
• Starts in a single origin
• Replication is semi-conservative
Helicase
The unzipping
enzyme
Breaks H-bond
that binds DNA
bases together
Topoisomerase
Prevents
supercoiling of
DNA
SSB proteins
Keeps opposite
strands separate
Prevents
degradation due
to endonucleases
DNA
polymerase
The builder
Replicates DNA
molecules to build
a new strand of
DNA
DNA is produced
only in the 3’ to 5’
direction
Has error
correcting
mechanisms
When the polymerase adds an
incorrect nucleotide, the newly synthesized
DNA strand (red) transiently unpairs from
the template strand (orange), and its 3′ end
moves into the editing site (E) to allow the
incorrect nucleotide to be removed.
DNA primase
The initializer
Makes primers
to delineate
start of
replication
Primers are
made of RNA
Ligase
The gluer
DNA Replication
Initiation
• Initiated by the ORC
(Origin recognition
complex) which leads to
the sequence of events
shown
• Occurs in the G1
phase
Central Dogma of Molecular Biology

Transcription + Translation = Gene expression

Parts of an mRNA
• Very similar to DNA
• 5’ end has methyl guanosine cap
• 3’ end has a poly(A) tail
Transcription
• Occurs in the nucleus
• RNA transcriptase makes a
sequence of pre-mRNA based
on the DNA
• Pre-mRNA is modified to mRNA
• mRNA can then exit the
nucleus for translation
RNA polymerase
• Active site is indicated
by the Mg2+ ion
• A 9 nucleotide long
RNA-DNA complex is
formed transiently
• DNA helix reforms
• The energy required for
these reactions come
from the phosphate
bonds of the
nucleotides.
Transcription Initiation
• Many promoters contain a DNA
sequence called the TATA box
• located about 30 nucleotides
away from the site at which
transcription is initiated.

• Through its subunit TBP, TFIID

recognizes and binds the TATA
box, which then enables the
adjacent binding of TFIIB and
TFIIA.

…and then other things happen.

Eukaryote Bacteria
Transcripts contain both No introns or exons
exons and introns
Modifications: 5’ capping, No modification
RNA splicing, 3’
polyadenylation
Compartmentalization of No compartmentalization
processes
Comparison between bacterial and eukaryotic
translation
Bacterial mRNA
Unmodified mRNA
A single transcript can for
multiple proteins
Eukaryotic mRNA
Modified with 5’cap and
poly(A) tail
A single transcript codes for a
single protein
RNA splicing can lead to different mRNAs
Translation
• In the cytoplasm
• Uses a ribosome
• Elongation of
peptides due to
formation of peptide
bonds
Ribosome
Each ribosome has one binding site
for mRNA and three binding sites
for tRNA: the A, P, and E sites
• aminoacyl-tRNA,
• peptidyl-tRNA, and
• exit, respectively)
tRNA
No need to memorize the table!

But remember that:

AUG = Start Codon (Met)
UAA, UAG, UGA = Stop Codon
Wobble base pairing

Codon-anticodon base pairing

is more stringent at positions 1
and 2.

If the base found on the left of

the table is found in the
wobble position (position 3), it
can pair with any of the bases
on the right of the table.
 • Step 1. an aminoacyl-tRNA
molecule binds to a vacant
A site on the ribosome
• Step 2. a new peptide bond
is formed.
• Step 3. The large subunit
translocates relative to the
small subunit, leaving the
Translating an two tRNAs in hybrid sites: P
mRNA molecule on the large subunit and A
on the small, for one tRNA;
E on the large subunit and
P on the small, for the other
tRNA.
• Step 4. the small subunit
translocates carrying its
mRNA a distance of three
nucleotides through the
ribosome.
Structure of a typical bacterial mRNA

Unlike eukaryotic ribosomes, which typically require a capped 5′ end on the mRNA,
prokaryotic ribosomes initiate translation at ribosome-binding sites (Shine–Dalgarno
sequences), which can be located anywhere along an mRNA molecule. This property
of their ribosomes permits bacteria to synthesize more than one type of protein from a
single mRNA molecule.
Don’t memorize this
Gene regulation and Order of the Operon
Differentiated
cells contain
all the genetic
instructions
necessary
to direct the
formation of a
complete
organism
 Gene regulation and Order of the Operon

an operon is a
functioning unit
of DNA containing a
cluster of genes under
the control of a
single promoter.
Seven steps at which eukaryotic gene expression can be controlled.