Lesson

Bases
In DNA there are four bases: adenine
(abbreviated A), guanine (G), thymine, (T) and
cytosine (C).
Adenine and guanine are purines;
Thymine and cytosine are pyrimidines.

Nucleoside
A nucleoside is a pyrimidine or purine base
covalently bonded to a sugar.
In DNA, the sugar is deoxyribose and so this is a
deoxynucleoside.
There are four types of deoxynucleoside in DNA;
deoxyadenosine, deoxyguanosine,
deoxythymidine and deoxycyGdine

NucleoGde
A nucleoGde is base + sugar + phosphate
covalently bonded together.
In DNA, where the sugar is deoxyribose, this
unit is a deoxynucleoGde.

Phosphodiester Bond
In DNA the nucleoGdes
are covalently joined
together by 3-5
phosphodiester bonds
to form a repeGGve
sugarphosphate chain
which is the backbone
to which the bases are
aPached.

DNA Sequence
The DNA sequence is
the sequence of A, C, G
and T along the DNA
molecule which carries
the geneGc informaGon.
In a DNA double helix,
the two strands of DNA
are wound round each
other with the bases on
the inside and the
sugarphosphate
backbones on the
outside.

DNA Double Helix

The two DNA chains are held together by
hydrogen bonds between pairs of bases;
adenine (A) always pairs with thymine (T) and
guanine (G) always pairs with cytosine (C).

ProkaryoGc Chromosomes
The DNA in a bacterium is a supercoiled
double-stranded circular molecule that is
packaged in the nucleoid region of the cell.
The DNA is negaGvely supercoiled, complexed
to several histone-like proteins and organized

Circular and Coiled DNA

(b)

(c)

15

DNA ReplicaGon in Bacteria

E. coli DNA polymerase I requires all four deoxynucleoside 5
triphosphates (dNTPs) as precursors, Mg2+, a DNA template and a
primer with a 3-OH end.
DNA synthesis occurs in a 5 3 direcGon.
DNA polymerase I also has a 35 exonuclease (proof-reading)
acGvity and a 53 exonuclease acGvity.
E. coli DNA polymerases II and III lack the
53 Fexonuclease
acGvity.
158
Section
DNA structure
and replication
1111
5'
5'
3'
3'
2
DNA template
DNA template
3
strand
strand
O
O
4
G
C
H2 C
G
C
H 2C
O
O
5
4
4
6
H H
H H
H H
H H
7
PPi
8
H
H
HO
O
..
O
O
O
9

O
P
O
P
P
O
P
O
10111 O

O
O
O
O
1
O
2
T
A
H2 C
O
T
A
H2C
O
3
H H
H H
4
H H
H H
5
H
HO
H
HO
5'
5'
6
7
Fig. 1. DNA synthesis. In this schematic diagram, the incoming dTTP hydrogen bonds with the adenine on the
8
template DNA strand and a 3!5! phosphodiester bond is formed, releasing pyrophosphate.
9

ReplicaGon Forks

F3 DNA replication in bacteria

ReplicaGon starts at
1111origin, is bi-
a single
2
direcGonal
and
3
semi-conservaGve.
4
Each r5eplicaGon
6 (or eye)
bubble
7
consists
8 of two
replicaGon
forks.
9
10111
1
2

(a)

Replication bubble

(b) Replication forks

Fig. 2. Replication of the bacterial circular chromosome. Re

origin and proceeds bi-directionally (a) moving around the ch
two replication forks eventually meet and fuse. The two circu

polymerases make DNA only in the 5!3! direction

direction. What actually happens is that on the tem
orientation, new DNA is made in a continuous piece i
tion. This new DNA is called the leading strand (Fig.
DNA synthesis proceeds in a 53 direcGon on each strand of
strand
(that Dhas
the parental
NA. a 5!3! orientation), DNA polymeras
new
On the DNA
strand with
35 orientaGon
(the leading strand)
the in the 5!
of
(about
1000 nucleotides
long)
new DNA is synthesized conGnuously.
then
these
together.
small
On joins
the strand
that hpieces
as 53 orientaGon
(the The
lagging
strand) fragments
the
DNA is after
synthesized
disconGnuously
as a sThe
eries of new
short DNA strand
ments
their
discoverer.
Okazaki fragments
that are then
oined together.
discontinuous
method
is jcalled
the lagging strand.

Okazaki Fragment

3'
5'

5'
3'

Leading strand

Okazaki fragments

3' Lagging strand

5'

RNA Primer
160

1111
2
3
4
5
6
7
8
9
10111
1
2
3
4
5
6
7
8
9
20111
1
2
3
4
5
6
7
8
9

DNA replicaGon requires an

RNA primer that is
synthesized by an RNA
polymerase called primase.
This is extended by DNA
polymerase III, which makes
the DNA for both the leading
and lagging strands.
DNA polymerase degrades
the primer and replaces it
with DNA.
DNA ligase then joins DNA
ends.

(a)

Section F DNA structur

Parental DNA template

3!

5!

Primase
(b)

5!
3!
RNA primer

Synthesis of new DNA

by DNA
polymerase III

(c)
5!

3!

(d)
RNA primer removed
and gap filled with
DNA by DNA polymerase I
(e)

(f)
DNA fragments
joined by
DNA ligase
(g)

Fig. 4. Details of DNA replication. (a) Primase binds to the DNA templa
and (b) synthesizes a short RNA primer (dotted line); (c) DNA polymeras
RNA primer by synthesizing new DNA (thick line); (d) during synthesis of
adjacent Okazaki fragments are separated by the RNA primers; (e) the R

7
8
9
10111
1
2
3
4
5
6
7
8
9
20111
1
2
3
4
5
6
7
8
9
30111
1
2
3
4
5
6
7
8
9
40111
1
2
3
4
5
6
7

separates them as follows. This enzyme works in a similar

merase I but causes a transient break in each strand (a dou
a double-stranded DNA molecule. Thus topoisomerase II b
stranded DNA circle and causes a transient double-strand
gate through which the other DNA circle can pass (Fig. 5
then re-seals the strand breaks.

Accessory Proteins

A helicase unwinds the DNA

double helix and single-
stranded DNA-binding (SSB)
protein stabilizes the single-
stranded regions during
replicaGon.
DNA topoisomerase I is
needed to allow the helix to
unwind without causing
extensive rotaGon of the
chromosome.
DNA topoisomerase II
separates the two daughter
DNA circles following
replicaGon.

Two interlocked
daughter DNA molecules

Binding of topoisomerase II

Topoisomerase causes double-strand

break, allowing the other DNA circle
to pass through the break, then re-joins
the DNA strands to recreate the DNA circle

!
Fig. 5.

Separation of daughter DNA circles by topoisomerase II.

Replica(on
3
3

5
3
5

Helicase protein binds to DNA sequences called

origins and unwinds DNA strands.
Binding proteins prevent single strands from rewinding.
Primase protein makes a short segment of RNA
complementary to the DNA, a primer.

Replica(on
Overall direction
of replication

3
3

5
3
5

3
5

DNA polymerase enzyme adds DNA nucleotides

to the RNA primer.

Replica(on
Overall direction
of replication

3
5

3
5
3
5

3
5

DNA polymerase enzyme adds DNA nucleotides

to the RNA primer.
DNA polymerase proofreads bases added and
replaces incorrect nucleotides.

Replica(on
Overall direction
of replication

3
3

5
3
5

Leading strand synthesis continues in a

5 to 3 direction.

3
5

Replica(on
Overall direction
of replication

3
3

5
Okazaki fragment

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

3 5

3
5

Replica(on
Overall direction
of replication

3
3

5
Okazaki fragment

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

35

3
5

Replica(on
3
5

3
5
3
5

3 5

35

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

Replica(on
3
5

3
5
3
5

35

35

3
5

Leading strand synthesis continues in a

5 to 3 direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.

Replica(on
3
5

3
5
3
5

35

35

3
5

Exonuclease activity of DNA polymerase I removes RNA primers.

Replica(on
3
3
5
3
5

35

3
5

Polymerase activity of DNA polymerase I fills the gaps.

Ligase forms bonds between sugar-phosphate backbone.

TranscripGon in Prokaryotes
TranscripGon by E. coli RNA polymerase occurs in three
phases; iniGaGon, elongaGon and terminaGon.
IniGaGon involves binding of the enzyme to a promoter
upstream of the gene.
During elongaGon, the anGsense DNA strand is used as
the template so that the RNA made has the same base
sequence as the sense (coding) strand, except that U
replaces T.
A terminaGon signal is eventually encountered that
halts synthesis and causes release of the completed
RNA.

between species. Using the convention of calling the first nucleotide

scribed sequence as "1, these two promoter elements lie at position
35, that is about 10 and 35 bp, respectively, upstream of where tra
will begin (Fig. 1).

Promoters and IniGaGon

The 10 sequence has the consensus TATAAT. Because this ele

discovered by Pribnow, it is also known as the Pribnow box. It is
RNA polymerase holoenzyme (containing 2
tant recognition site that interacts with the factor of RNA polym
iniGates
ranscripGon
y binding
to ais importan
Thesubunits)
35 sequence
has tthe
consensus b
TTGACA
and
4060 bduring
p region
that contains
two conserved
unwinding
transcriptional
initiation.

promoter elements, the 10 sequence (Pribnow

The actual sequence between the 10 sequence and the 35 sequen

box) (i.e.
with
he consensus
conserved
it tvaries
from promoter to promoter) but the distance
these
sites a
isnd
extremely
for
correct
two
TATAAT
the 35 important
sequence
with
the functioning
consensus of the
Promoters
differ
TTGACA.
by up to 1000-fold in their efficiency of initiatio
scription so that genes with strong promoters are transcribed very f

The factor is essenGal for iniGaGon.

16 18 bp

T TG A C A
! 35 sequence

"1

5 8 bp
TAT A A T
!10 sequence
(Pribnow box)

Transcriptional
start site

Fig. 1. Prokaryotic promoter showing the 10 sequence and 35 sequence. By

the first nucleotide of the template DNA that is transcribed into RNA is denoted +
transcriptional start site.

ElongaGon
Following iniGaGon, the subunit dissociates from RNA polymerase
to leave the core enzyme (2) that conGnues RNA synthesis in a 5
3 direcGon
using the four ribonucleoside 5 triphosphates as precursors.
The DNA double helix is unwound for transcripGon, forming a
transcripGon bubble, and is then rewound
aber the transcripGon
Section G RNA synthesis and processing
complex has passed.
Sense strand
RNA polymerase

Direction of
transcription

Rewinding

3!
5!

Unwinding

5!
3!

3!

5ppp

Transcription
elongation
Newly synthesized
RNA strand

Antisense
strand

but then peels away from the DNA as transcription proceeds. The DNA is
unwound ahead of the transcription bubble and after the transcription
complex has passed, the DNA rewinds.

ElongaGon
5!

5!
3!
O
O

H 2C
H

P
O-

P
O

PPi

DNA
template
strand

OH

H 2C

H
HO

H
O

3!

DNA
template
strand

H
O

OH

O
O

O-

O
O

H2C
H

H
OH

U
H

H
HO

H2 C

5!

H
HO

5!

OH

Fig. 2. Transcription by RNA polymerase. In each step the incoming ribonucleotide selected is that which can basepair with the next base of the DNA template strand. In the diagram, the incoming nucleotide is rUTP to base-pair with
the A residue of the template DNA. A 3!5! phosphodiester bond is formed, extending the RNA chain by one
nucleotide, and pyrophosphate is released. Overall the RNA molecule grows in a 5! to 3! direction.

as precursor molecules that do require p

Topics G9 and G10, respectively).

TerminaGon

A common terminaGon
signal is a hairpin structure
formed by a palindromic
GC-rich region, followed by
an AT-rich sequence.
Other signals are also used
which require the
assistance of rho protein
for eecGve terminaGon.

G
G

G C
A U
C G
C G
G C
C G
C G
G C
5

A U U U U OH 3

RNA Processing
Messenger RNA (mRNA) transcripts of
protein-coding genes in prokaryotes require
liPle or no modicaGon before translaGon.

to transcription of lac repressor mRNA and hence production of lac rep

protein monomers. Four identical repressor monomers come together to

LAC Operon

P
lacI

mRNA

lac

lac

lacI

lacZ

lacY

lacA

lacI

lacZ

lacY

lacA

-Galactosidase
lac repressor lac repressor
tt

Fig. 1. Structure of the lac operon.

mRNA

Permease Transacetylase

LAC Operon
The lac operon contains lacZ, lacY and lacA genes encoding -
galactosidase, galactose permease, and thiogalactoside
transacetylase, respecGvely, preceded by an operator site (Olac)
and a promoter (Plac).
The operon is transcribed by RNA polymerase to produce a single
polycistronic mRNA that is then translated to produce all three
enzymes.
These enzymes are involved in lactose metabolism.
When lactose is absent, E. coli makes only small amounts of these
enzymes but the presence of lactose induces synthesis of large
amounts of all three enzymes.
The mechanism of inducGon is that the background level of -
galactosidase converts some lactose to allolactose which then acts
as an inducer and turns on transcripGon of the lac operon.
IPTG can also act as an inducer.
TranscripGon of the operon is controlled by the lac repressor
protein encoded by the lacI gene.

The LAC Opressor

The lacI gene has its own promoter (PlacI) to which RNA
polymerase binds and iniGates transcripGon.
In the absence of an inducer, the lacI gene is transcribed,
producing lac repressor mRNA and hence lac repressor
protein monomers.
These monomers assemble to form acGve tetramers which
bind to the lac operator site, Olac, and prevent
transcripGon of the lac operon.
In the presence of an inducer (such as allolactose or IPTG),
the inducer binds to the repressor and changes its
conformaGon, reducing its anity for the lac operator.
Thus the repressor now dissociates and allows RNA
polymerase to transcribe the lac operon.

CRP/CAP
Catabolite acGvator protein, CAP (also called cAMP receptor
protein, CRP) is an acGvator required for high level transcripGon of
the lac operon.
The acGve molecule is a CRP dimer that binds 35 cyclic AMP to form
a CRPcAMP complex.
CRPcAMP binds to the lac promoter and increases the binding of
RNA polymerase, sGmulaGng transcripGon of the lac operon.
CRP dimer without cAMP cannot bind to this DNA. The acGon of
CRP depends upon the carbon source available to the bacterium.
When glucose is present, the intracellular level of cAMP falls, CRP
cannot bind to the lac promoter and the lac operon is only weakly
transcribed.
When glucose is absent, the level of intracellular cAMP rises, the
CRPcAMP complex sGmulates transcripGon of the lac operon and
allows lactose to be used as an alternaGve carbon source.

PosiGve and NegaGve RegulaGon

In negaGve regulaGon of prokaryoGc gene
expression, bound repressor prevents
transcripGon of the structural genes.
In posiGve regulaGon of gene expression, an
acGvator binds to DNA and increases the rate
of transcripGon.
Through the lac repressor and CRP/CAP
protein, the lac operon is subject to both
negaGve and posiGve control.

tRNA
Each tRNA has a cloverleaf secondary structure
containing an anGcodon arm, a D (or DHU) arm, a
T or TC arm, and an amino acid acceptor stem
to which the relevant amino acid becomes
covalently bound, at the 3 OH group.
Some tRNAs also have a variable (or opGonal)
arm.
The three-dimensional structure is more complex
because of addiGonal interacGons between the
nucleoGdes.

tRNA

Section G RNA synthesis and processing

10

Section G RNA synthesis and processing

(b)

3!OH
I
A3!OH
C I
C A
C
C
Amino acid
5!
acceptor stem
Amino acid
5!
acceptor stem

a)

(b)

5!
3!
Acceptor
3!
stem
Acceptor
stem

TC loop
DHU loop

T loop

D loop

5!

TC arm

TC loop

T loop

D loop

TC arm

DHU loop
Optional arm

DHU arm

Optional arm

DHU arm

Anticodon arm
Variable
arm

Anticodon arm

Variable
arm
Anticodon
loop

Anticodon

Anticodon loop

Anticodon loop

Anticodon

Anticodon

Anticodon
loop

Fig. 1. (a) Cloverleaf secondary structure of tRNA; (b) tertiary structure of tRNA (from
Anticodon

Genetics: a Molecular Approach, second edition, T.A. Brown, Kluwer Academic Publishers,

Promoter

tRNA gene

tRNA gene

5!

3! DNA
Transcription
5!

3! Pre-tRNA
RNA folding

RNA processing
(cleavage and trimming by RNases)

tRNA

tRNA

TranscripGon and Processing of tRNA

in Prokaryotes
E. coli contains clusters of up to seven tRNA
genes separated by spacer
regions, as well as tRNA genes within ribosomal
RNA transcripGon units.
Following transcripGon, the primary RNA
transcript folds up into specic stem-loop
structures and is then processed by ribonucleases
D, E, F and P in an ordered series of reacGons to
release the individual tRNA molecules.

GeneGc Code
The geneGc code is the rules that specify how the
nucleoGde sequence of an mRNA is translated
into the amino acid sequence of a polypepGde.
The nucleoGde sequence is read as triplets called
codons.
The codons UAG, UGA and UAA do not specify
amino acids and are called terminaGon codons or
Stop codons.
AUG codes for methionine and also acts as an
iniGaGon (Start) codon.

The GeneGc Code is Degenerate

Most amino acids in proteins are specied by
more than one codon (i.e. the geneGc code is
degenerate).
Codons that specify the same amino acid
(synonyms) oben dier only in the third base,
the wobble posiGon, where base-pairing with
the anGcodon may be less stringent than for
the rst two posiGons of the codon.

Codon sequence

1st base

3rd base

2nd base

(5!end)

Fig. 1.

(3!end)
U

Phe
Phe
Leu
Leu
Leu
Leu
Leu
Leu
Ile
Ile
Ile
Met
Val
Val
Val
Val

Ser
Ser
Ser
Ser
Pro
Pro
Pro
Pro
Thr
Thr
Thr
Thr

The genetic code.

Ala
Ala
Ala
Ala

A
Tyr
Tyr
Stop
Stop
His
His
Gln
Gln
Asn
Asn
Lys
Lys
Asp
Asp
Glu
Glu

G
Cys
Cys
Stop
Trp
Arg
Arg
Arg
Arg
Ser
Ser
Arg
Arg
Gly
Gly
Gly
Gly

U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G

Universality of GeneGc Code

The geneGc code is not universal but is the same
in most organisms.
ExcepGons are found in mitochondrial genomes
where some codons specify dierent amino acids
to that normally encoded by nuclear genes.
In mitochondria, the UGA codon does not specify
terminaGon of translaGon but instead encodes
for tryptophan.
Similarly, in certain protozoa UAA and UAG
encode glutamic acid instead of acGng as
terminaGon codons.

TranslaGon in Prokaryotes
During translaGon the mRNA is read in a 5 to 3
direcGon and protein is made in an N-terminal
to C-terminal direcGon.
TranslaGon relies upon aminoacyl-tRNAs that
carry specic amino acids and recognize the
corresponding codons in mRNA by anGcodon
codon base-pairing.
TranslaGon takes place in three phases;
iniGaGon, elongaGon and terminaGon.

Synthesis of Amino-acyl -tRNA

H2 Translation in prokaryotes

1111
Each tRNA molecule
has a
2
3
cloverleaf secondary
structure
4
5
consisGng of three
stem loops,
6
one of which bears
the
7
anGcodon at its e89 nd.
The amino acid i10111
s covalently
1
bound to the 3 O23 H group at the
4
3 end by aminoacyl
synthetase
5
to form aminoacyl-tRNA.

6
7
The reacGon, called
amino acid
8
9
acGvaGon, occurs
in two steps
20111
1 to form an
and requires ATP
2
3
intermediate, aminoacyl-
4
adenylate.
5

Amino
acid

5"

UCC

6
7
8
9
30111
1
2
3

NH2
I
CH2
I
C!0
I
O
I
A
C
C

Anticodon

Fig. 1.

Structure of an aminoacyl-tRNA.

Synthesis of aminoacyl-tRNAs is crucially im

each amino acid must be covalently linked to a t
part in protein synthesis, which depends upon t
to ensure that the correct amino acids are inco

TerminaGon
The appearance of a UAA or UAG terminaGon
(stop) codon in the A site causes release factor
RF1 to bind whereas RF2 recognizes UGA.
The release factors trigger pepGdyl transferase to
transfer the polypepGde to a water molecule
instead of to aminoacyl-tRNA.
The polypepGde, mRNA, and free tRNA leave the
ribosome and the ribosome dissociates into its
subunits ready to begin a new round of
translaGon.

Synthesis of an RNA Transcript

The stages of
transcripGon are
IniGaGon
ElongaGon
TerminaGon

Promoter

Transcription unit

5
3

3
5

Start point
RNA polymerase

DNA
1

Initiation. After RNA polymerase binds to

the promoter, the DNA strands unwind, and
the polymerase initiates RNA synthesis at the
start point on the template strand.

5
3

Unwound
DNA

3
5

Template strand of
RNA DNA
transcript
2

Elongation. The polymerase moves downstream, unwinding the

DNA and elongating the RNA transcript 5 3 . In the wake of
transcription, the DNA strands re-form a double helix.

Rewound
RNA
5
3

3
5

3
5

RNA
transcript
3 Termination. Eventually, the RNA
transcript is released, and the
polymerase detaches from the DNA.

5
3

3
5
5

Completed RNA
transcript

MutaGon Causes and Rate

The natural replicaGon of DNA produces occasional errors.

DNA polymerase has an ediGng mechanism that decreases
the rate, but it sGll exists.\
Typically genes incur base subsGtuGons about once in
every 10,000 to 1,000,000 cells.
Since we have about 6 billion bases of DNA in each cell,
virtually every cell in your body contains several
mutaGons.
However, most mutaGons are neutral: have no eect.
Only mutaGons in cells that become sperm or eggsare
passed on to future generaGons.
MutaGons in other body cells only cause trouble when
they cause cancer or related diseases.

Point mutaGons
Point mutaGons involve alteraGons in the structure or
locaGon of a single gene. Generally, only one or a few base
pairs are involved.
Point mutaGons can signcantly aect protein structure
and funcGon
Point mutaGons may be caused by physical damage to the
DNA from radiaGon or chemicals, or may occur
spontaneously
Point mutaGons are oben caused by mutagens

Mutagens

Mutagens are chemical or physical agents that interact with DNA to cause
mutaGons.
Physical agents include high-energy radiaGon like X-rays and ultraviolet light
Chemical mutagens fall into several categories.

Chemicals that are base analogues that may be subsGtuted into DNA, but they
pair incorrectly during DNA replicaGon.
Interference with DNA replicaGon by inserGng into DNA and distorGng the
double helix.
Chemical changes in bases that change their pairing properGes.

Tests are oben used as a preliminary screen of chemicals to idenGfy those

that may cause cancer
Most carcinogens are mutagenic and most mutagens are carcinogenic.

Viral Mutagens

ScienGsts have recognized a number of tumor

viruses that cause cancer in various animals,
including humans
About 15% of human cancers are caused by viral
infecGons that disrupt normal control of cell
division
All tumor viruses transform cells into cancer
cells through the integraGon of viral nucleic acid
into host cell DNA.

Point MutaGon

The change of a single nucleoGde in the DNAs

template strand leads to the producGon of an
abnormal protein
Wild-type hemoglobin DNA
3

Mutant hemoglobin DNA

5

C T

In the DNA, the

mutant template
strand has an A where
the wild-type template
has a T.

G U A

The mutant mRNA has

a U instead of an A in
one codon.

C A

mRNA

mRNA
G A

Normal hemoglobin
Glu

Sickle-cell hemoglobin
Val

The mutant (sickle-cell)

hemoglobin has a valine
(Val) instead of a glutamic
acid (Glu).

Types of Point MutaGons

Point mutaGons within a gene can be divided
into two general categories
Base-pair subsGtuGons
Base-pair inserGons or deleGons

SubsGtuGons
A base-pair subsGtuGon is the replacement of one nucleoGde and its partner with
another pair of nucleoGdes

Silent - changes a codon but codes for the same amino acid
Missense - subsGtuGons that change a codon for one amino acid into a codon for a
dierent amino acid
Nonsense -subsGtuGons that change a codon for one amino acid into a stop codon
Wild type
mRNA
Protein

A U G
Met

A A G U U U G G C U A A
Lys

Phe

Gly

3
Stop

Amino end

Carboxyl end
Base-pair substitution
No effect on amino acid sequence
U instead of C
A U G A A G U U U G G U U A A
Met

Lys

Missense

Phe

Gly

Stop

A instead of G

A U G A A G U U U A G U U A A
Met
Nonsense

Lys

Phe

Ser

Stop

U instead of A

A U G U A G U U U G G C U A A
Met

Stop

InserGons
a
nd
D
eleGons
InserGons and deleGons

Are addiGons or losses of nucleoGde pairs in a gene

May produce frameshib mutaGons that will change the reading frame
of the gene, and alter all codons downstream from the mutaGon.
Wild type
mRNA
Protein

A U GA A GU U U GG C U A A
Met

Lys

Gly

Phe

Stop

Amino end
Carboxyl end
Base-pair insertion or deletion
Frameshift causing immediate nonsense

Extra U
AU GU A AG U U U G GC U A
Met

Stop

Frameshift causing
extensive missense

U Missing

A U G A A GU U G G C U A A
Met

Lys

Leu

Ala

Insertion or deletion of 3 nucleotides:

no frameshift but extra or missing amino acid

A A G Missing
A U G U U U G G C U A A
Met

Phe

Gly

Stop

5-TTT TTT TTT TTT TTT TTT TTT TTG CTG GTT CAA GGG CTT TAT TCC ATC TCT CTC
GGT GCA AGA GGC GGC GGG TGG GGG GCT GCC TGC GGG CTG CGT CTA
GTT GCA GTA GTT CTC CAG CTG GTA GAG GGA GCA GAT GCT GGT ACA GCA TTG
GTT CCC AAT GCC CAG CTT TTT GAA GGG CCC CTC CAG GGC CCA GGG CTT CAG
GTT GTC CTG CAC CAA GGG CCC CCC CCA ATT CCC CCT GCC CCA CCT GGA-3