NUCLEIC ACIDS

Ilag, Janella*Jane R.
ChE-4102

Transcription: RNA
Synthesis
Transcription
is the process by which DNA directs the
synthesis of hnRNA / mRNA molecules
that carry the coded information needed
for protein synthesis.
Messenger
RNA
production
via
transcription is actually a two step
process in which an hnRNA molecule is
initially produced and then is edited to
yield the desired mRNA molecule.

Gene is a segment of a DNA strand that

contains the base sequence for the
production of a specific hnRNA / mRNA
molecule.
Human Genome Project
a decade long internationally based
research project to determine the location
and base sequence of each of the genes
in the human genome.
Genome
is all of the genetic material (the total
DNA) contained in the chromosomes of an
organism.

Steps in the
Transcription Process
1.

2.

A portion of the DNA double helix unwinds,

exposing some bases (a gene). The
unwinding process is governed by the
enzyme RNA polymerase rather than by
DNA helicase (replication enzyme).
Free ribonucleotide, one nucleotide at a
time, align along one of the exposed
strands of DNA bases, the template
strands, forming new base pairs. In this
process, U rather than T aligns with A in
the baising process.

3.

RNA polymerase is involved in

the linkage of ribonucleotides,
one by one to the growing hnRNA
molecule.

4.

Transcription ends when the RNA

polymerase enzyme encounters a
sequence of bases that is read as
a sop signal.

Overall Process of
Transcription of DNA

Template Strand

strand of DNA used for hnRA/mRNA

synthesis.
it is copied proceeding in the 3to
5direction

Informational Strand

the other DNA strand (the nontemplate strand)

Gives the base sequence present in
the hnRNA strand being synthesized.

Base Pairing Associated with the

Transcription Process
From the base sequence 5A-T-G-C-C-A 3in a DNA
template strand, determine the base sequence in the
hnRNA synthesized from the DNA template strand.

DNA template Strand:

DNA informational

Strand:

5 A-T-G-C-C-A 3
3 T-A-C-G-G-T 5

hnRNA Strand:

3 U-A-C-G-G-U 5

Base Sequence in RNA: 5 U-G-G-C-A-U 3

Exercise:
From the base sequence 5T-A-A-C-C-T 3
in a DNA template strand, determine the
base
sequence
in
the
hnRNA
synthesized from the DNA template
strand.
DNA template Strand: 5 T-A-A-C-C-T 3
DNA informational Strand: 3A-U-U-G-G-A 5
hnRNA Strand:3A-U-U-G-G-A 5
Base Sequence in RNA:
3

5A-G-G-U-U-A

Post-Transcription Processing:
Formation of mRNA
The RNA produced from a gene through
transcription is hnRNA, the precursor form
RNA.
Conversion of hnRNA to mRNA involves
post-transcription processing of the hnRNA.
Exon is a gene segment that conveys
(codes for) genetic information.
Intron is a gene segment that does not
convey (code for) genetic information.
- DNA segments that interrupt a genetic
message.

A gene consists of alternating exon and

intron segments.
Exon

Intron

Exon

Intron Exon
hnRNA
snRNA

Introns are
cut out
snRNA
Exons are
joined
together

mRNA

Splicing
is the process of removing introns
from an hnRNA molecule and joining
the remaining exons together to form
an mRNA molecule.
- this involves snRNA molecules
which is never found free in a cell and
is always found complexed with
proteins in particles called small
nuclear ribonucleo-protein molecules
called
snRNPs
(pronounced
as
snurps)

Small nuclear
ribonucleoprotein particle
is a complex formed from an
snRNA molecule and several
proteins.
Spliceosome
- is a large assembly of snRNA
molecules and proteins involved
in the conversion of hnRNA
molecules to mRNA molecules.

Alternative Splicing
- is a process by which several
different proteins that are
variations of a basic structural
motif can be produced from a
single gene.

mRNA for
second
Protein

mRNA for
first Protein

hnRNA

Intron
Exon A

Intron
Exon B

Intron
Exon C

mRNA for
third Protein

hnRNA
Exon D
mRNA for
fourth Protein

Alternative Splicing

The Human Transcriptome

Transcriptome is all of the mRNA
molecules that can be generated from
the genetic material in a genome.

The Genetic Code

Codon is a three nucleotide sequence in
on mRNA molecule that codes for a
specific amino acid.
Genetic Code is the assignment of the
64 mRNA codons to specific amino acids
(or stop signals).

The Genetic Code Table

Remarkable Features of
Genetic Code Table
1.The

genetic code is highly degenerate,

that is many amino acid are
designated by more than one codon.
Codons that specify the some amino
acid are called synonyms.
2.There is a pattern to the arrangement
of synonyms in the genetic code table.
3.The genetic code is almost universal.
4.An initiation codon exits. The existence
of stop codons (UAG, UAA and UGA)
suggests the existences of start
codons.

Using the Genetic Code and mRNA

codons to Predict Amino Acid
Sequences
Using the genetic code, determine the sequence of
amino acids encoded by the mRNA codon sequence
5 GCC-AUG-GUA-AAA-UGC-GAC-CCA 3

mRNA: 5 GCC-AUG-GUA-AAA-UGC-GAC-CCA 3
Peptide: Ala-Met-Val-Lys-Cys-Asp-Pro

Exercise
Using the genetic code, determine the sequence
of amino acids encoded by the mRNA codon
sequence.
5 CAU-CCU-CAC-ACU-GUU-UGU-UGG 3

Answer:
His-Pro-Thr-Val-Cys-Trp

Relating Exons and Introns to hnRNA

and mRNA Structures
Section A, C, and E of the following base
sequence section of a DNA template strand
are exons and sections B and D are introns.
DNA: 5ATT-CGT-TGT-TTT-CCC-AGT-GCC 3
A
E

a.

What is the structure of the hnRNA

transcribed from this template?

DNA:

5 ATT-CGT-TGT-TTT-CCC-AGT-GCC 3
A

hnRNA: 3 UAA-GCA-ACA-AAA-GGG-UCA-CGG 5
A

hnRNA: 5 GGC-ACU-GGG-AAA-ACA-ACG-AAU 3
E

b.

What is the structure of the mRNA obtained

by splicing the hnRNA?
mRNA: 5 GGC-AAA-ACA-AAU 3
E

Exercise
Section A,C, and E of the following base
sequence section ofa DNA template strand
are exons and sections B and D are introns
DNA: 5CGC-CGT-AGT-TGG-CCC-GGA-GGA 3
A

a.

b.

What is the structure of the hnRNA

transcribed from this template?
What is the structure of the mRHA
obtained by splicing the hnRNA?

Answer:
a. DNA

5CGC-CGT-AGT-TGG-CCC-GGA-GGA 3
A

hnRNA 3GCG-GCA-UCA-ACC-GGG-CCU-CCU- 5
A
E

hnRNA 5 UCC-UCC-GGG-CCA-ACU-ACG-GCG 3
E

b.

mRNA 5 UCC-UCC-CCA-GCG 3
E

Relating
Protein
Amino
Acid
Sequence to the Directionality of an
mRNA Segment
The structure if an mRNA segment obtained from DNA
template strand is
mRNA 3 AUU-CCG-UAC-GAC 5
What polypeptide amino acid sequence will be
synthesized using this mRNA?

mRNA 5 CAG-CAU-GCC-UUA 3
N-end Gln-His-Ala-Leu C-end

Example
The structure of an mRNA segment
obtained from a DNA template strand is
mRNA 3 ACG-AGC-CCU-CUU 5
What polypeptide amino acid
sequence will be synthesized using this
mRNA?
Answer:

mRNA 3 ACG-AGC-CCU-CUU 5
mRNA 5 UUC-UCC-CGA-GCA 3
N-end Phe Ser Arg Ala C end

Anticodons and tRNA Molecules

tRNA molecules function as intermediaries that
deliver amino acids to the mRNA.
All tRNA molecules have the same general
shape and this shape is crucial to how they
function.
Two-dimensional cloverleaf is the shape
produced by the molecules folding and twisting
into regions of parallel strands and regions of
hairpin loops.

Two Features of the

tRNA Structure
1.

2.

The 3end of the open part of the

cloverleaf structure is where an amino
acid becomes covalently bonded to the
tRNA molecule through an ester bond.
The loop opposite the open end of the
cloverleaf is the site for a sequence of
three
bases
called
an
anticodon.
Anticodon is a three-nucleotide sequence
on
an
tRNA
molecule
that
is
complementary to a codon on an mRNA
molecule.

Determining Codon Anticodon Relationship

A tRNA molecule has the anticodon 5AAG
3with which mRNA codon will this
anticodon interact?
Answer:
3 Anticodon 5
5

Codon 3

Anticodon3 GAA
Codon 5 CUU

5
3

Exercise:
A tRNA molecule has the anticodon
5ACG 3mRNA codon will this anticodon
interact?

Answer:
Anticodon 5 ACG 3
Codon 3 UGC 5
Codon 5 CGU 3

Determining Anticodon tRNA Amino Acid

Relationships
A tRNA molecule possesses the anticodon
5 CGU 3. Which amino acid will this tRNA
molecule carry?
Anticodon 5 CGU 3
Anticodon 3 UGC 5
Codon 5 ACG 3
The amino acid that the codon ACG codes for
is Thr (Threonine)

Exercise:
A tRNA molecule possess the anticodon
5UGA 3which amino acid will this tRNA
molecule carry?
Answer:
Anticodon
Anticodon

5 UGA 3
3 AGU 5

Codon
5 UCA 3
Amino Acid Ser (Serine)

Determining Relationships Among DNA Base. Sequences, mRNA base

sequences, Codons, Anticodons and Amino Acids.

A DNA template strand is read as follows:

3 ACG-AAC-CGA-TAG-GGA 5
Determine the following:
a.

The base sequence in the DNA information strand

Template strand :
3 ACG-AAC-CGA-TAG-GGA 5
Information Strand: 5 TGC-TTG-GCT-ATC-CCT 3

b.

The codons present in the mRNA transcribed from

the DNA template strand (assuming that no introns
are present)
Informational Strand : 5 TGC TTG GCT ATC CCT
3
mRNA :
5 UGC UUG GCU AUC - CCU 3
Codons :
5 UGC UUG GCU AUC - CCU 3

c. The

tRNA anticodons that interact with the

mRNA codons
Codons :
5 UGC UUG GCU AUC CCU 3
Anticodons: 3 ACG AAC CGA UAG GGA 5
Anticodons: 5 AGG GAU AGC CAA GCA 3

d.

The amino acid that the tRNA molecules

carry
Codons:
5 UGC-UUG GCU-AUC-CCU 3
Amino Acids:

Cys Leu Ala Ile Pro

The structure of the peptide formed from

the overall translation process.
N terminal end Cys Leu Ala Ile Pro C-

e.

terminal end

Exercise:
A DNA template strand is read as follows:
3 GCA AAA CAA ATA GTG

Determine each sequence of the following using this

information.
a. The base sequence in the DNA information strand.
b. The codons present in the mRNA transcribed from the
DNA template strand (assuming no introns and present)
c. The tRNA anticodons that interact
with the mRNA
codons.
d. The amino acids that the tRNA molecules carry.
e. The structure of the peptide formed from he overall
translation process.

Answer:
a.

DNA Template Strand

Informational Strand

3 GCA-AAA-CAA-ATA-GTG 5
5 CGT-TTT-GTT- TAT-CAC 3

b.

Informational Strand 5 CGT-TTT-GTT-TAT-CAC 3

mRNA/Codons 5 CGU-UUU-GUU-UAU-CAC 3

c.

d.

Codons
Anticodons
Anticodons
Codons

5 CGU-UUU-GUU-UAU-CAC 3
3 CGA-AAA-CAA-AUA-GUG 5
5 GUG-AUA-AAC-AAA-ACG 3
5 CGU-UUU-GUU-UAU-CAC 3

e.

Amino Acid

N-endArg-Phe-Val-Tyr-His-C-end

Translation: Protein
Synthesis
Translation
The process by which mRNA codons are
deciphered and a particular protein molecule is
synthesized.
The substances needed for the translation
phase of protein synthesis are mRNA
molecules, tRNA molecules, amino acids,
ribosomes and a no. of different enzymes.
Ribosome rRNA protein complex that serves as
the site for the translastion phase of protein
synthesis.

Five General Steps to the

Translation Process
Activation of tRNA
An amino acid interacts with ATP to
become highly energized. It then forms a
covalent bond with the 3end of a tRNA
molecules. Amino acids tRNA paring is
governed by enzymes.
2. Initiation
the mRNA attaches to a ribosome so that
the first codon (AUG) is at the P site. A tRNA
carrying methionine attaches to first codon.
1.

3. Elongation

Another tRNA with

second amino acid binds at the A site.
The methionine transfer from the P-site
to the A site. The ribosome shifts to the
next codon, making its a site available.
4. Terminationthe
polypeptide chain
continues to lengthen until a stop
codon appears on the mRNA. The new
protein is cleared from the last tRNA.
5. Past-Translation
Processing

cleavage of Met (the initiation codon)

usually occurs S-S bonds between Cys
units also can form.

Mutations is an error in base sequence in a gene that is

reproduced during DNA replication.
Mutagen is a substance or agent that causes a change
in the structure of a gene.
Two Types of Mutagens
1) Radiation in the form of ultraviolet light, X-rays,
radioactivity and cosmic rays.
2) Chemical agents (HNO2) causes deamination of
heterocyclic nitrogen bases.
Point Mutation a mutation in which one nucleotide is
substituted for another.
Original DNA
TAGCAC
C has replaced
Point Mutated DNA T A C C A C
G
The effect of a point mutation can vary from no effect to a
change in primary structure to termination of protein
synthesis.

Predicting the Effect of a Point Mutation

Predict the change that occurs in amino acid identity
when each of the following point mutations occur on 3to 5
DNA base segments.
a.
GAG is point mutated to GAA
b.
AAA is point mutated to AAT
c.
ATA is point mutated to ATT
Unmutated base sequence
GAG
CTC CUC Leu
a.

Template Informational
strandStrand

mRNA amino acid

Mutated base sequence

GAA CTT CUU Leu
Template Informational
strandStrand

mRNA amino acid

Silent Mutation amino acid identity is not affected, as both

mRNA codons code for the same amino acid.

Unmutated base sequence

AAA TTT UUUPhe
b.

Template Informational
strand Strand

mRNA amino acid

Mutate base sequence

AAT TTA UUA Leu
Template Informational
strand Strand

mRNA amino acid

The point mutation has produced a codon that codes for a

different amino acid.
Unmutated base sequence
ATA TAT UAU Tyr

c.

Template Informational
strand Strand

mRNA amino acid

Mutated base sequence

ATT TAA UAA stop codon
Template Informational
strand Strand

mRNAamino acid

The point mutation has produced stop codon resulting in

termination of protein synthesis.

Exercise:
Predict the change that occurs in amino
acid identity when each of the following
point mutation occur on to 3 to 5 DNA
base segments.
a. CTA is point mutated to CTT
b. CGA is point mutated to GGA
c. GTC is point mutated to ATC

Answers:
a.
b.
c.

Asp becomes Glu

Ala becomes Pro
Gln becomes a stop codon

Nucleic Acids and Viruses

Viruses a very small disease causing agents
that are considered the lowest order of life.
- is a small particle that contains DNA or RNA
(but not both) surrounded by a coat of protein
and that cannot reproduce without the aid of a
host cell.
- do not posses the nucleotides, enzymes, amino
acids and the other molecules necessary to
replicate their nucleic acid or to synthesize
proteins.
- their only function is for reproduction, viruses
do not generate energy.

Retrovirus RNA containing virus

- reverse synthesis is governed by the
enzymes reverse transcriptase AIDS virus
in on ex. of retrovirus.
Helper T-cell virus has affinity for a
specific type of white blood cell, an
important part of the bodys immune
system.
Vaccine is a preparation containing an
inactive or weakened form of a virus or
bacterium.
If a virus contains DNA, the host cell
replicates the viral DNA in a manner
similar to the way it replicates to its own

Recombinant DNA and

Genetic Engineering
Genetic Engineering
- is the process whereby an organism is intentionally change
at the molecular (DNA) level so that it exhibits different traits.
- the first organisms to be genetically engineered were
bacteria in 1973 and mice in 1974.
- Insulin producing bacteria were commercialized in 1982,
and genetically modified crops have been available since
1974.
Bacillus thuringiensis on insect resistant that is obtained
from the presence of a gene obtained from the soil bacteria.
- amylase an enzyme that rapidly breaks down starch
into glucose.

Recombinant DNA (rDNA)

- is DNA that contains genetic material
from two different organisms.
Bacterium E. coli
found in the intestinal tract of humans
and animals is the organism most often
used in recombinant DNA.
-- contain DNA in the form of small,
circular, double stranded molecules called
plasmids.

Selected Human Proteins Produced Using

Recombinant DNA Technology and their Use
Protein

Treatment

Insulin

Diabetes

Erythropoietin (EPO)

Anemia

Human growth hormones (HGH)

Stimulate growth

Interleukins

Stimulate immune system

Interferons

Leukemia and other cancers

Lung surfactant protein

Respiratory distress

Serum albumin

Plasma supplement

Tumor necrosis factor (TNF)

Cancers

Tissue plasminogen activator

(TPA)

Heart attacks

Epidermal growth factor

Healing of wounds and burns

Fibroblast growth factor

ulcers

-END OF REPORT-