DNA & RNA

M. K. Tadjudin
Fakultas Kedokteran dan Ilmu Kesehatan
Universitas Islam Negeri Syarif Hidayatullah
Jakarta

Module description
Analysis of each cellular component in
the human body to the molecular
level in order study pathogenesis of
disease, diagnosis diseases, develop
treatment strategies including
develop new modalities of treatment

Nucleoside
Nucleotide
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Pentose
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Pentose
The chemical structure of pentose which
contains five carbon atoms, labeled as
C1' to C5'.
The pentose is called RIBOSE in RNA and
DEOXYRIBOSE in DNA, because the
DNA's pentose lacks an oxygen atom at
C2'.
Recalling that RNA stands for
"ribonucleic acid", and DNA for
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"deoxyribonucleic acid".

Nucleotide
Composed of three parts: PENTOSE,
BASE, and PHOSPHATE GROUP.
In DNA or RNA, a pentose is associated
with only one phosphate group, but a
cellular free nucleotide (such as ATP)
may contain more than one phosphate
group.
If all phosphate groups are removed, a
nucleotide becomes a NUCLEOSIDE.
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Bases of Nucleic acids

DNA
Adenine
Guanine
Cytosine
Thymine

RNA
Adenine
Guanine
Cytosine
Uracil

Deamination may change the cytosine to uracil, or the methylated cytosine to thymine.

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Why has DNA Thymine and

RNA Uracil ?
Cytosine is one of four bases in DNA molecules.
Cytosine may be mutated to uracil by
deamination.
Since uracil is not part of DNA, this mutation can
easily be detected and repaired by base excision.
Suppose DNA, like RNA, were made up of uracil,
then the cytosine to uracil mutation could be
corrected only by mismatch repair which is very
inefficient.
This may explain why DNA chooses thymine,
instead of uracil, even though the chemical
structure of uracil is simpler than thymine.
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Pairing of DNA strands

A DNA molecule has two strands, held
together by the hydrogen bonding between
their bases.
Adenine can form two hydrogen bonds with
thymine; cytosine can form three hydrogen
bonds with guanine.
Although other base pairs [e.g., (G:T) and
(C:T) ] may also form hydrogen bonds, their
strengths are not as strong as (C:G) and
(A:T) found in natural DNA molecules.
Due to the specific base pairing, DNA's two
strands are complementary to each other
the nucleotide sequence of one strand
determines the sequence of another strand.14

B form, the helix

makes a turn every
3.4 nm, and the
distance between
two neighboring
base pairs is 0.34
nm. Hence, there
are about 10 pairs
per turn. The
intertwined strands
make two grooves of
different widths,
referred to as the
MAJOR GROOVE and
the MINOR GROOVE,
which may facilitate
binding with specific
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proteins.

The normal right-handed

"double helix" structure of
DNA, also known as the B
form.

Z form, because its bases seem

to zigzag. Z DNA is lefthanded. One turn spans 4.6 nm,
comprising 12 base pairs. The
DNA molecule with alternating
G-C sequences in alcohol or high
salt solution tends to have such
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structure.

Most cellular RNA molecules are single

stranded. They may form secondary structures such
as stem-loop and hairpin.
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Classes of RNA
The major role of RNA is to
participate in protein synthesis,
which requires three classes of
RNA:
messenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)
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The secondary structure of

tRNA.
Blue color indicates modified
nucleotides, with "m"
representing "methylated".
Anticodon is the trinucleotides
complementary to a codon on
mRNA.

tRNA
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tRNA

The major role of tRNA is to translate mRNA

sequence into amino acid sequence.
A tRNA molecule consists of 70-80 nucleotides.
Some nucleotides in tRNA have been modified,
such as dihydrouridine (D),pseudouridine (Y),
and inosine (I).
In dihydrouridine, a hydrogen atom is added to
each C5 and C6 of uracil.
In pseudouridine, the ribose is attached to C5,
instead of the normal N1.
Inosine plays an important role in codon
recognition. In addition to these modifications,
a few nucleosides are methylated.
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Translation

Translation is carried out by tRNA through the

relationship between its anticodon and the
associated amino acid.
When a tRNA is brought to the ribosome by the
pairing between its anticodon and the mRNA's
codon, the amino acid attached at its 3' end will be
added to the growing peptide.
In bacteria, there are 30-40 tRNAs with different
anticodons.
In animal and plant cells, about 50 different tRNAs
are found.
However, there are 61 codons coded for amino
acids. Suppose each codon can pair with only a
unique anticodon, then 61 tRNAs would be needed.
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Wobble pairing
The reason why less than 61 tRNAs are
required is because of the "wobble
pairing" between anticodon and codon.
Base pairing does not obey the standard
Watson-Crick pairing at the wobble
position.
One base can pair with several other
bases. For example, guanine (G) can pair
with both cytosine (C) and uracil (U) ;
inosine (I) can pair with cytosine, adenine
and uracil.
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The nonstandard base

pairing at the
wobble
position.

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Aminoacyl-tRNA
The tRNA together with the amino acid
attached to its 3' end is called an
aminoacyl-tRNA.
The attached amino acid is encoded by the
codon which matches the tRNA's
anticodon.
The process is catalyzed by a class of
enzymes called aminoacyl-tRNA
synthetases, which recognize the
anticodon and its compatible amino acid.
A cell has 20 different aminoacyl-tRNA
synthetases, each can add only one of 20
amino acids to a compatible tRNA.

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Notation of aminoacyl-tRNA
"Arg-tRNA" denotes the tRNA
with arginine attached while
"tRNAArg" specifies the tRNA
which contains the anticodon for
the codon of arginine.
"Arg-tRNAArg" represents the
arginine-specific tRNA with
arginine attached.
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Ribosomal RNA (rRNA) (1)

In prokaryotes, the ribosomal RNA (rRNA) has three
types: 23S, 5S, and 16S.
In mammals, four types of rRNA have been found : 28S,
5.8S, 5S and 18S.
The unit "S" stands for Svedberg, which is a measure of
the sedimentation rate.
After rRNA molecules are produced in the nucleus, they
are transported to the cytoplasm, where they combine
with tens of specific proteins to form a ribosome.
In prokaryotes, the size of a ribosome is 70S, consisting
of two subunits: 50S and 30S.
The size of a mammalian ribosome is 80S, comprising a
60S and a 40S subunit.
Proteins in the larger subunit are designated as L1, L2,
L3, etc. (L = large). In the smaller subunit, proteins are
denoted by S1, S2, S3, etc.

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Ribosomal RNA (rRNA) (2)

During protein synthesis, the ribosome binds to
mRNA and tRNA as shown in the following figure.
Only the tRNA containing the anticodon which
matches mRNA's codon may join the complex.

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Other classes of RNA

Ribozymes:

The RNA molecules with catalytic

activity.
They were discovered in early
1980s by Thomas Cech and Sidney
Altman who shared the 1989 Nobel
Prize in Chemistry.

Small RNA molecules:

RNA interference and other
functions.

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Major types of small RNA

molecules
Small nuclear RNA (snRNA) - involved in
mRNA splicing.
Small nucleolar RNA (snoRNA) - directs
the modification of ribosomal RNAs.
Micro-RNA (miRNA) - regulates gene
expression (only 20-25 nucleotides long):

It may be divided into two subtypes: small

interfering RNA (siRNA) and small temporally
regulated RNA (stRNA).
siRNA mediates RNA interference (RNAi) which
has been widely used in functional genomics
and also has therapeutic potential.
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Chromatin
The substance which becomes visible chromosomes
during cell division.
Its basic unit is NUCLEOSOME, composed of 146 bp
DNA and eight HISTONE proteins.
The structure of chromatin is dynamically changing,
at least in part, depending on the need of
transcription
In the metaphase of cell division, the chromatin is
condensed into the visible chromosome.
At other times, the chromatin is less condensed, with
some regions in a "BEADS-ON-A-STRING"
CONFORMATION.
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Structure of chromatin fibers

The structure of chromatin fibers is dynamically
changing.
In the condensed state, each nucleosome is
associated with an H1 (or H5) to form a SOLENOID
structure. H1 and H5 are called LINKER HISTONES.
They are essential in stabilizing the solenoid
conformation. This can be demonstrated by
extracting the condensed chromatin at a low salt
concentration, which will release H1 or H5. Then,
the "beads-on-a-string" conformation may be
observed by the atomic force microscopy

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Each
nucleosome
consists of 146
bp DNA and 8
histones: two
copies for each
of H2A, H2B, H3
and H4.
The DNA is
wrapped around
the histone core,
making nearly
two turns per
nucleosome.
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Structure of chromatin
a. The 30 nm chromatin fiber is associated with
scaffold proteins (notably topoisomerase II) to
form loops. Each loop contains about 75 kb
DNA. Scaffold proteins are attached to DNA at
specific regions called scaffold attachment
regions (SARs), which are rich in adenine and
thymine.
b. The chromatin fiber and associated scaffold
proteins coil into a helical structure which may
be observed as a chromosome. G bands are rich
in A-T nucleotide pairs while R bands are rich in
G-C nucleotide pairs.
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Histone Acetylation (1)

Acetylation of the lysine residues at the N
terminus of histone proteins removes
positive charges, thereby reducing the
affinity between histones and DNA.
This makes RNA polymerase and
transcription factors easier to access the
promoter region.
Therefore, in most cases, HISTONE
ACETYLATION ENHANCES TRANSCRIPTION
while HISTONE DEACETYLATION REPRESSES
TRANSCRIPTION.
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Histone Acetylation (2)

Histone acetylation is catalyzed by histone
acetyltransferases (HATs) and histone
deacetylation is catalyzed by histone
deacetylases (denoted by HDs or HDACs).
Several different forms of HATs and HDs
have been identified.
Among them, CBP/p300 is probably the
most important, since it can interact with
numerous transcription regulators.
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Acetylation and
deacetylation of the
lysine residue.

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The standard genetic code (1)

Genetic code was deciphered by Marshall
Nirenberg and his colleagues in early 1960s
Synthesis of a peptide always starts from
methionine (Met), coded by AUG.
The stop codon (UAA, UAG or UGA) signals
the end of a peptide.
In a DNA molecule, the sequence from an
initiating codon (ATG) to a stop codon (TAA,
TAG or TGA) is called an OPEN READING
FRAME (ORF), which is likely (but not
always) to encode a protein or polypeptide.
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The standard genetic code (2)

Amino acids with close physical properties have
similar codons. For example, both Asp and Glu are
negatively charged. Their codons all contain "GA" in
the first two positions. The physical properties of
Ser and Thr are also very close. They are coded by
UCN and ACN (N = any), respectively.
One advantage for this assignment is to reduce the
damage caused by replication errors or other
mutations. For instance, if the third nucleotide of
Ser codon is mutated, the produced amino acid
remains Ser. If the first nucleotide of Ser codon is
mutated to A, it will produce Thr, which is similar to
Ser.
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The standard genetic code (3)

Such mutation will not have significant effect
on the protein's structure and function.
Let us consider a hypothetical case that
codons are randomly assigned. Suppose Ser
were coded by GAG, GUA, GCU and UGG; Thr
were coded by AAA, AGU, UUU and
CCC. Then, any mutation would produce an
amino acid different from Ser and Thr.

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Cracking the genetic code (1)

Approach used by Marshall Nirenberg and his
colleagues to crack the genetic code:
1. Synthesize a trinucleotide (e.g. UUU) which
mimics a codon in mRNA.
2. Prepare various types of aminoacyl-tRNA, e.g.,
Thr-tRNA, Phe-tRNA, Lys-tRNA, etc.
3. Radioactively label an aminoacyl-tRNA (e.g. PhetRNA) which might contain the anticodon for the
synthesized trinucleotide.
4. Place the trinucleotide, aminoacyl-tRNA and
ribosome on a nitrocellulose filter.

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Cracking the genetic code (2)

5.
6.

7.
8.

Individual trinucleotide and aminoacyl-tRNA can

pass through the filter, but the ribosome is too big
to pass through.
Therefore, if the labeled aminoacyl-tRNA contains
the anticodon for the trinucleotide, it will bind to
the trinucleotide and ribosome on the filter.
The radioactivity can be detected on the filter and
the amino acid in the labeled aminoacyl-tRNA is
likely to be encoded by the trinucleotide.
If no radioactivity was detected, the trinucleotide
is unlikely to be the codon of the amino acid. Most
of the 64 possible codons can be determined by
repeating this procedure for different
trinucleotides and labellings.
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The standard genetic code applies to most, but not all,

cases. Exceptions have been found in the mitochondrial
DNA of many organisms and in the nuclear DNA of a few
lower organisms.
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Repetitive DNA sequences

A stretch of DNA sequence often repeats several
times in the total DNA of a cell.
DNA reassociation kinetics is used to classify the
repetitive DNA sequences. The total DNA is first
randomly cleaved into fragments with an average
size of about 1000 bp. Then, they are heated to
separate the complementary strands of each
fragment. Subsequently, temperature is reduced
to allow strand reassociation. If a fragment
contains a sequence which is repeated many
times in the total DNA, it will have greater chance
to find a complementary strand and reassociate
more quickly than other fragments with less
repetitive sequences.
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 A stretch of DNA sequence often

repeats several times in the total
DNA of a cell.
An entire telomere of each human
chromosome of about 15 kb, is
constituted by thousands of the
repeated sequence "GGGTTA".

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Classes of repetitive DNA

sequences
Based on the reassociation rate, DNA sequences are
divided into three classes:
HIGHLY REPETITIVE: About 10-15% of mammalian
DNA fragments reassociate very rapidly. This class
includes tandem repeats.
MODERATELY REPETITIVE: Roughly 25-40% of
mammalian DNA fragments reassociate at an
intermediate rate. This class includes interspersed
repeats (also known as mobile elements or
transposable elements).
SINGLE COPY (OR VERY LOW COPY NUMBER): This
class accounts for 50-60% of mammalian DNA.
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Interspersed repeats
Repeated DNA sequences located at dispersed regions
in a genome.
They are also known as MOBILE ELEMENTS or
TRANSPOSABLE ELEMENTS.
A stretch of DNA sequence may be copied to a
different location through DNA RECOMBINATION.
After many generations, such sequence (the repeat
unit) could spread over various regions.
Mobile elements were first discovered by Barbara
McClintock in 1940s from the studies of corn.
Subsequently, they were found in all kinds of
organisms. In mammals, the most common mobile
elements are LINEs (Long Interspersed Nuclear
Elements) and SINEs (Short Interspersed Nuclear
Elements).
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Basic organization of LINEs:

ORF1 and ORF2 are open reading frames.
The protein product of ORF1 is called p40,
with unknown function.
ORF2 encodes a reverse transcriptase which
is necessary for copying the element to
other locations.
The red color regions on both ends are
direct repeats.
All mobile elements contain direct repeats
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Comparison between direct repeats and

inverted repeats:
Direct repeats have the same sequence
along a given direction.
Inverted repeats have complementary
sequences along opposite directions.
The most common LINEs in humans is the L1
family.
A human genome contains about 60,000 to
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100,000 L1 elements.

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