Dr Budi Enoch SpPD

• Deoxyribonucleic acid ( DNA) is a molecule that carries most of the genetic instructions used
in the
growth,
development,
functioning and
reproduction
of all known living organisms and many viruses.
• DNA and RNA are nucleic acids; alongside proteins and complex carbohydrates, they comprise
the three major types of macromolecule that are essential for all known forms of life.
• Most DNA molecules consist of two biopolymer strands coiled around each other to form a
double helix.
• The two DNA strands are known as polynucleotides since they are composed of simpler units
called nucleotides.
• Each nucleotide is composed of a nitrogen-containing nucleobase—either
• cytosine (C),
• guanine (G),
• adenine (A), or
• thymine (T)—as well as
• a sugar called deoxyribose and a phosphate group.
 History 
• DNA was first isolated by Friedrich Miescher in 1869.
• Its molecular structure was identified by James Watson and
Francis Crick in 1953, whose model-building efforts were
guided by X-ray diffraction data acquired by Rosalind Franklin.
• DNA is used by researchers as a molecular tool to explore
physical laws and theories, such as the ergodic theorem and
the theory of elasticity.
• The unique material properties of DNA have made it an
attractive molecule for material scientists and engineers
interested in micro- and nano-fabrication.
• Among notable advances in this field are DNA origami and
DNA-based hybrid materials
• Pencil sketch of the DNA double James Watson and Francis Crick
helix by Francis Crick in 1953 (right), co-originators of the
double-helix model, with
Maclyn McCarty (left).
Where’s DNA
• Within cells, DNA is organized into long structures called
chromosomes.
• During cell division these chromosomes are duplicated in the
process of DNA replication, providing each cell its own
complete set of chromosomes.
• Eukaryotic organisms (animals, plants, fungi, and protists) store
most of their DNA inside the cell nucleus and some of their
DNA in organelles, such as mitochondria or chloroplasts.
• In contrast, prokaryotes (bacteria and archaea) store their DNA
only in the cytoplasm. Within the chromosomes, chromatin
proteins such as histones compact and organize DNA.
• These compact structures guide the interactions between DNA
and other proteins, helping control which parts of the DNA are
transcribed
DNA molecules consist of two biopolymer strands coiled around each other to form a
double helix
• The nucleotides are joined to one another in a
chain by covalent bonds between the sugar of
one nucleotide and the phosphate of the next,
resulting in an alternating sugar-phosphate
backbone.
• According to base pairing rules (A with T, and C
with G), hydrogen bonds bind the nitrogenous
bases of the two separate polynucleotide strands
to make double-stranded DNA.
Chemical structure of DNA; hydrogen bonds shown as dotted lines
 Beberapa Istilah
Allele
• An allele is a variant form of a gene. When a genes varies (genes for eye color, for example, could
be blue or brown) each individual form is called an allele.
Autosome
• Autosomes are the non-sex chromosomes (carriers of DNA). Each human cell has 23 pairs of
chromosomes: 22 autosomal pairs and one sex pair.
Base
• Nucleotide bases are the chemical building blocks of DNA, which pair up in a double helix
structure and serve as a genetic alphabet with which we form sentences (or genes). There are four
kinds of bases (A, C, G, and T).
Cell
• Cells are the basic units for life. The human body is made of some 50 trillion to 100 trillion cells,
which combine to form more complex tissues and organs. Most cells have a similar basic
structure. An outer layer, called the cell membrane, contains fluid called cytoplasm. Within the
cytoplasm are many different, specialized “little organs” called organelles. The most important of
these is the nucleus, which controls the cell and houses a person’s genetic material in structures
called chromosomes. Another type of organelle is the mitochondrion. This “cellular power plant”
has its own genetic material, which we can study to trace family history.
Chromosome
• A chromosome is the carrier of DNA. Inside most of your cells there are exactly 23 pairs
of chromosomes. Chromosomes are paired because you inherit one copy from your
mother and one from your father.
DNA
• DNA (deoxyribonucleic acid) is the set of genetic instructions for creating an organism.
DNA molecules are shaped like a spiral staircase called a double helix. Each step is
composed of DNA bases (A, C, G, and T). Scientists can read your specific sequence of
DNA bases and use that information to trace your ancestors’ journey.
Double Helix
• The shape of DNA, similar to that of a spiral staircase or twisted ladder. The stairway’s
railings are composed of sugars and phosphates. Its sides contain the patterned base
pairs: A, T, C, and G. When a cell divides for reproduction, the helix unwinds and splits
down the middle like a zipper in order to copy itself.
Polymerase is an enzyme that synthesizes long chains or polymers of nucleic acid. DNA
polymerase and RNA polymerase are used to assemble DNA and RNA molecules,
respectively, by copying a DNA or RNA template strand using base-pairing interactions
• DNA stores biological information.
• The DNA backbone is resistant to cleavage, and both strands of the double-
stranded structure store the same biological information.
• Biological information is replicated as the two strands are separated.
• A significant portion of DNA (more than 98% for humans) is non-coding,
meaning that these sections do not serve as patterns for protein sequences.
• The two strands of DNA run in opposite directions to each other and are
therefore anti-parallel.
• Attached to each sugar is one of four types of nucleobases (informally, bases).
• It is the sequence of these four nucleobases along the backbone that encodes
biological information.
• Under the genetic code, RNA strands are translated to specify the sequence
of amino acids within proteins. These RNA strands are initially created using
DNA strands as a template in a process called transcription
 chromosome
• A chromosome (from Greek: χρῶμα color and σῶμα body) is a
packaged and organized structure containing most of the DNA of a
living organism.
• It is not usually found on its own, but rather is structured by being
wrapped around protein complexes called nucleosomes, which consist
of proteins called histones
• The asymmetric ends of DNA strands are called the 5′ (five prime) and
3′ (three prime) ends, with the 5′ end having a terminal phosphate
group and the 3′ end a terminal hydroxyl group.
• One major difference between DNA and RNA is the sugar, with the 2-
deoxyribose in DNA being replaced by the alternative pentose sugar
ribose in RNA.
Karyogram of a human male
 Nucleobase classification
• The nucleobases are classified into two types: the
purines, A and G, being fused five- and six-
membered heterocyclic compounds, and the
pyrimidines, the six-membered rings C and T.[14]
• A fifth pyrimidine nucleobase, uracil (U), usually
takes the place of thymine in RNA and differs from
thymine by lacking a methyl group on its ring.
• In addition to RNA and DNA a large number of
artificial nucleic acid analogues have also been
created to study the properties of nucleic acids, or
for use in biotechnology
Major and minor grooves of DNA. Minor groove is a binding
site for the dye Hoechst 33258
 Grooves
• Twin helical strands form the DNA backbone.
• Another double helix may be found tracing the spaces, or grooves,
between the strands.
• These voids are adjacent to the base pairs and may provide a binding site.
• As the strands are not symmetrically located with respect to each other,
the grooves are unequally sized.
• One groove, the major groove, is 22  Å wide and the other, the minor
groove, is 12 Å wide.
• The width of the major groove means that the edges of the bases are
more accessible in the major groove than in the minor groove.
• As a result, proteins such as transcription factors that can bind to specific
sequences in double-stranded DNA usually make contact with the sides of
the bases exposed in the major groove.
• This situation varies in unusual conformations of DNA within the cell (see
below), but the major and minor grooves are always named to reflect the
differences in size that would be seen if the DNA is twisted back into the
ordinary B form
 Base pairing
• In a DNA double helix, each type of nucleobase on one strand bonds with
just one type of nucleobase on the other strand. This is called.
[complementary base pairing.

• Here, purines form hydrogen bonds to pyrimidines, with adenine bonding

only to thymine in two hydrogen bonds, and cytosine bonding only to
guanine in three hydrogen bonds.
• This arrangement of two nucleotides binding together across the double
helix is called a base pair.
• As hydrogen bonds are not covalent, they can be broken and rejoined
relatively easily.
• The two strands of DNA in a double helix can therefore be pulled apart like
a zipper, either by a mechanical force or high temperature
• As a result of this complementarity, all the information in the double-
stranded sequence of a DNA helix is duplicated on each strand, which is
vital in DNA replication.
• Indeed, this reversible and specific interaction between complementary
base pairs is critical for all the functions of DNA in living organisms
 Left, a GC base pair with three hydrogen bonds.
Right, an AT base pair with two hydrogen bonds. Non-
covalent hydrogen bonds between the pairs are shown as
dashed lines.
• The two types of base pairs form different numbers of
hydrogen bonds, AT forming two hydrogen bonds, and GC
forming three hydrogen bonds (see figures, right).
• DNA with high GC-content is more stable than DNA with low
GC-content.
• As noted above, most DNA molecules are actually two polymer
strands, bound together in a helical fashion by noncovalent
bonds; this double stranded structure (dsDNA) is maintained
largely by the intrastrand base stacking interactions, which are
strongest for G,C stacks.
• The two strands can come apart – a process known as melting –
to form two single-stranded DNA molecules (ssDNA) molecules.
• Melting occurs at high temperature, low salt and high pH (low
pH also melts DNA, but since DNA is unstable due to acid
depurination, low pH is rarely used).
 Sense and antisense
• A DNA sequence is called "sense" if its sequence is the same as
that of a messenger RNA copy that is translated into protein.
• The sequence on the opposite strand is called the "antisense"
sequence.
• Both sense and antisense sequences can exist on different parts of
the same strand of DNA (i.e. both strands can contain both sense
and antisense sequences).
• In both prokaryotes and eukaryotes, antisense RNA sequences are
produced, but the functions of these RNAs are not entirely clear.
 Supercoiling
• DNA can be twisted like a rope in a process called
DNA supercoiling.
• With DNA in its "relaxed" state, a strand usually circles the axis of
the double helix once every 10.4 base pairs, but if the DNA is
twisted the strands become more tightly or more loosely wound.
• If the DNA is twisted in the direction of the helix, this is positive
supercoiling, and the bases are held more tightly together.
• If they are twisted in the opposite direction, this is negative
supercoiling, and the bases come apart more easily.
• In nature, most DNA has slight negative supercoiling that is
introduced by enzymes called topoisomerases.
Quadruplex structures - telomeres
• At the ends of the linear chromosomes are specialized regions of DNA
called telomeres.
• The main function of these regions is to allow the cell to replicate
chromosome ends using the enzyme telomerase, as the enzymes that
normally replicate DNA cannot copy the extreme 3′ ends of
chromosomes.
• These specialized chromosome caps also help protect the DNA ends,
and stop the DNA repair systems in the cell from treating them as
damage to be corrected.
• In human cells, telomeres are usually lengths of single-stranded DNA
containing several thousand repeats of a simple TTAGGG sequence
 The telomeres are disposable buffers at the ends of chromosomes
which are truncated during cell division; their presence protects the
genes before them on the chromosome from being truncated instead.
• A telomere is a region of repetitive nucleotide sequences at each end
of a chromosome, which protects the end of the chromosome from
deterioration or from fusion with neighboring chromosomes.
• Its name is derived from the Greek nouns telos (τέλος) 'end' and
merοs (μέρος, root: μερ-) 'part.' For vertebrates, the sequence of
nucleotides in telomeres is TTAGGG. This sequence of TTAGGG is
repeated approximately 2,500 times in humans.[1]
• During chromosome replication, the enzymes that duplicate DNA
cannot continue their duplication all the way to the end of a
chromosome, so in each duplication the end of the chromosome is
shortened (this is because the synthesis of Okazaki fragments requires
RNA primers attaching ahead on the lagging strand).
• The telomeres are disposable buffers at the ends of chromosomes
which are truncated during cell division; their presence protects the
genes before them on the chromosome from being truncated instead.
• Over time, due to each cell division, the telomere ends become
shorter. They are replenished by an enzyme,
• Three-dimensional representation of the molecular structure
of a telomere (G-quadruplex)
Human chromosomes (grey) capped by telomeres (white)
• Telomeres are critical for maintaining genomic integrity and studies
show that telomere dysfunction or shortening is commonly acquired
during the process of tumor development.
• Short telomeres can lead to genomic instability, chromosome loss and
the formation of non-reciprocal translocations; and telomeres in tumor
cells and their precursor lesions are significantly shorter than
surrounding normal tissue.
• Observational studies have found shortened telomeres in many
cancers: including pancreatic, bone, prostate, bladder, lung, kidney, and
head and neck.
• In addition, people with many types of cancer have been found to
possess shorter leukocyte telomeres than healthy controls.
• Recent meta-analyses suggest 1.4 to 3.0 fold increased risk of cancer
for those with the shortest vs. longest telomeres.
• However the increase in risk varies by age, sex, tumor type and
 chromatin.
• The expression of genes is influenced by how the DNA is packaged in
chromosomes, in a structure called chromatin.
• Base modifications can be involved in packaging, with regions that have
low or no gene expression usually containing high levels of methylation
of cytosine bases.
• DNA packaging and its influence on gene expression can also occur by
covalent modifications of the histone protein core around which DNA is
wrapped in the chromatin structure or else by remodeling carried out
by chromatin remodeling complexes (see Chromatin remodeling).
• There is, further, crosstalk between DNA methylation and histone
modification, so they can coordinately affect chromatin and gene
expression
 Damage

• DNA can be damaged by many sorts of mutagens, which change

the DNA sequence.
• Mutagens include oxidizing agents, alkylating agents and also
high-energy electromagnetic radiation such as ultraviolet light
and X-rays.
• The type of DNA damage produced depends on the type of
mutagen. For example, UV light can damage DNA by producing
thymine dimers, which are cross-links between pyrimidine bases.
• On the other hand, oxidants such as free radicals or hydrogen
peroxide produce multiple forms of damage
• Of these oxidative lesions, the most dangerous are double-strand breaks, as
these are difficult to repair and can produce point mutations, insertions and
deletions from the DNA sequence, as well as chromosomal translocations.
• These mutations can cause cancer.
• Because of inherent limitations in the DNA repair mechanisms, if humans
lived long enough, they would all eventually develop cancer.
• DNA damages that are naturally occurring, due to normal cellular processes
that produce reactive oxygen species, the hydrolytic activities of cellular
water, etc
• These remaining DNA damages accumulate with age in mammalian
postmitotic tissues. This accumulation appears to be an important
underlying cause of aging
 genome
• DNA usually occurs as linear chromosomes in eukaryotes, and circular
chromosomes in prokaryotes.
• The set of chromosomes in a cell makes up its genome; the human genome
has approximately 3 billion base pairs of DNA arranged into 46
chromosomes.
• The information carried by DNA is held in the sequence of pieces of DNA
called genes.
• Transmission of genetic information in genes is achieved via complementary
base pairing. For example, in transcription, when a cell uses the information
in a gene, the DNA sequence is copied into a complementary RNA sequence
through the attraction between the DNA and the correct RNA nucleotides.
• Usually, this RNA copy is then used to make a matching protein sequence in
a process called translation, which depends on the same interaction
between RNA nucleotides
 Genes and genomes
• Genomic DNA is tightly and orderly packed in the process called DNA
condensation to fit the small available volumes of the cell. In
eukaryotes, DNA is located in the cell nucleus, as well as small
amounts in mitochondria and chloroplasts.
• In prokaryotes, the DNA is held within an irregularly shaped body in
the cytoplasm called the nucleoid.
• The genetic information in a genome is held within genes, and the
complete set of this information in an organism is called its genotype.
• A gene is a unit of heredity and is a region of DNA that influences a
particular characteristic in an organism.
• Genes contain an open reading frame that can be transcribed, as well
as regulatory sequences such as promoters and enhancers, which
control the transcription of the open reading frame.
• Some noncoding DNA sequences play structural roles in
chromosomes.
• Telomeres and centromeres typically contain few genes, but
are important for the function and stability of chromosomes.
• An abundant form of noncoding DNA in humans are
pseudogenes, which are copies of genes that have been
disabled by mutation.
• These sequences are usually just molecular fossils, although
they can occasionally serve as raw genetic material for the
creation of new genes through the process of gene
duplication and divergence
 Transcription and translation
• A gene is a sequence of DNA that contains genetic information
and can influence the phenotype of an organism.
• Within a gene, the sequence of bases along a DNA strand
defines a messenger RNA sequence, which then defines one or
more protein sequences.
• The relationship between the nucleotide sequences of genes
and the amino-acid sequences of proteins is determined by the
rules of translation, known collectively as the genetic code.
• The genetic code consists of three-letter 'words' called codons
formed from a sequence of three nucleotides (e.g. ACT, CAG,
TTT).
• In transcription, the codons of a gene are copied into
messenger RNA by RNA polymerase.
• This RNA copy is then decoded by a ribosome that reads
the RNA sequence by base-pairing the messenger RNA to
transfer RNA, which carries amino acids.
• Since there are 4 bases in 3-letter combinations, there are
64 possible codons (43 combinations).
• These encode the twenty standard amino acids, giving most
amino acids more than one possible codon. There are also
three 'stop' or 'nonsense' codons signifying the end of the
coding region; these are the TAA, TGA, and TAG codons.
 DNA replication
• Cell division is essential for an organism to grow, but, when a cell
divides, it must replicate the DNA in its genome so that the two
daughter cells have the same genetic information as their parent.
• The double-stranded structure of DNA provides a simple mechanism
for DNA replication.
• Here, the two strands are separated and then each strand's
complementary DNA sequence is recreated by an enzyme called DNA
polymerase.
• This enzyme makes the complementary strand by finding the correct
base through complementary base pairing, and bonding it onto the
original strand.
 DNA replication.
The double helix is unwound by a helicase and topoisomerase. Next,
one DNA polymerase produces the leading strand copy. Another DNA
polymerase binds to the lagging strand. This enzyme makes
discontinuous segments (called Okazaki fragments) before DNA ligase
joins them together.
 DNA-binding proteins
• Interaction of DNA (shown in orange) with histones (shown in blue). These
proteins' basic amino acids bind to the acidic phosphate groups on DNA.
• Structural proteins that bind DNA are well-understood examples of non-
specific DNA-protein interactions.
• Within chromosomes, DNA is held in complexes with structural proteins.
• These proteins organize the DNA into a compact structure called chromatin. In
eukaryotes this structure involves DNA binding to a complex of small basic
proteins called histones, while in prokaryotes multiple types of proteins are
involved.
• The histones form a disk-shaped complex called a nucleosome, which contains
two complete turns of double-stranded DNA wrapped around its surface.
• These non-specific interactions are formed through basic residues in the
histones making ionic bonds to the acidic sugar-phosphate backbone of the
DNA, and are therefore largely independent of the base sequence.
 Nucleases and ligases
• Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of
the phosphodiester bonds.
• Nucleases that hydrolyse nucleotides from the ends of DNA strands are
called exonucleases, while endonucleases cut within strands. The most
frequently used nucleases in molecular biology are the restriction
endonucleases, which cut DNA at specific sequences. For instance, the
EcoRV enzyme shown to the left recognizes the 6-base sequence 5′-
GATATC-3′ and makes a cut at the vertical line.
• In nature, these enzymes protect bacteria against phage infection by
digesting the phage DNA when it enters the bacterial cell, acting as part of
the restriction modification system. In technology, these sequence-specific
nucleases are used in molecular cloning and DNA fingerprinting.
• Enzymes called DNA ligases can rejoin cut or broken DNA strands.
 Topoisomerases and helicases
• Topoisomerases are enzymes with both nuclease and ligase activity.
• These proteins change the amount of supercoiling in DNA.
• Some of these enzymes work by cutting the DNA helix and allowing one section
to rotate, thereby reducing its level of supercoiling; the enzyme then seals the
DNA break.
• Other types of these enzymes are capable of cutting one DNA helix and then
passing a second strand of DNA through this break, before rejoining the helix.
• Topoisomerases are required for many processes involving DNA, such as DNA
replication and transcription.
• Helicases are proteins that are a type of molecular motor.
• They use the chemical energy in nucleoside triphosphates, predominantly ATP,
to break hydrogen bonds between bases and unwind the DNA double helix into
single strands.
• These enzymes are essential for most processes where enzymes need to access
the DNA bases.
 Polymerases

• Polymerases are enzymes that synthesize polynucleotide

chains from nucleoside triphosphates.
• The sequence of their products are created based on existing
polynucleotide chains—which are called templates. These
enzymes function by repeatedly adding a nucleotide to the 3′
hydroxyl group at the end of the growing polynucleotide chain.
• As a consequence, all polymerases work in a 5′ to 3′ direction.
• In the active site of these enzymes, the incoming nucleoside
triphosphate base-pairs to the template: this allows
polymerases to accurately synthesize the complementary
strand of their template.
 Evolution
• DNA contains the genetic information that allows all modern living things to
function, grow and reproduce.
• However, it is unclear how long in the 4-billion-year history of life DNA has
performed this function, as it has been proposed that the earliest forms of life
may have used RNA as their genetic material.
• RNA may have acted as the central part of early cell metabolism as it can both
transmit genetic information and carry out catalysis as part of ribozymes.
• This ancient RNA world where nucleic acid would have been used for both
catalysis and genetics may have influenced the evolution of the current genetic
code based on four nucleotide bases.
• This would occur, since the number of different bases in such an organism is a
trade-off between a small number of bases increasing replication accuracy and a
large number of bases increasing the catalytic efficiency of ribozymes.
• However, there is no direct evidence of ancient genetic systems, as recovery of
DNA from most fossils is impossible because DNA survives in the environment for
TERIMAKASIH 