Disease and the Genome:

Genetic, Developmental,
and Neoplastic Disease
IDA BAGUS MADE SURYAWISESA
• Disease manifests in many cases as a direct
reflection of changes in patterns of gene
expression and often involves changes in the
genome
• Gene expression patterns in a given lesion type (e.g., a certain
form of cancer) will influence the clinical behavior of that lesion
and its
response to therapy
THE HUMAN GENOME
• DNA is the Source of Genetic Information
• essential building blocks of living cells were nucleic acids—long-chain
polymers composed of nucleotides
• a major constituent of the cell nucleus
• nucleic acids form the chemical basis for the transmission of genetic traits did
not occur until about 65 years ago
• It was recognized that chromosomes contained deoxyribonucleic acid (DNA)
as a primary constituent, but it was not known if this DNA carried genetic
information
RTT-replication transcription translation
• The Central Dogma of Molecular Biology
• A theory, referred to as the central dogma, describes the interrelationships among these
major processes.
• The central dogma defines the paradigm of molecular biology that genetic information is
perpetuated as sequences of nucleic acid and that genes function through their
expression in the form of protein molecules.
• Individual DNA molecules serve as templates for either complementary DNA strands
during the process of replication or complementary RNA molecules during the process of
transcription.
• In turn, RNA molecules serve as blueprints for the ordering of amino acids by ribosomes
during protein synthesis or translation.
• This simple representation of the complex interactions and interrelation- ships among DNA, RNA, and
protein was proposed and commonly accepted shortly after the discovery of the structure of DNA.
The central dogma. (A) The central dogma of molecular biology as
originally described by Crick. This schematic illustrates the flow of
genetic information from DNA to RNA and then to protein, as well as
illustrates that DNA serves as its own template in replication.
• (B) The new central dogma reflects advances in our understanding of
molecular processes that occur in normal cells. These processes include
epigenetic regulation of gene expression by DNA methylation and histone
modification,
• post-transcriptional regulation of gene expression by microRNAs, and
modification of protein functionality by post-translational modification (which
might include glycosylation, ubiquitination, phosphorylation, or other).
• This new central dogma also emphasizes the importance of DNA repair
processes in the maintenance of genome integrity.
Structure and Organization of the Human Genome

• Chemical Nature of DNA

• DNA is a polymeric molecule that is composed of repeating nucleotide
subunits.
• Each nucleotide is composed of (i) a phosphate group, (ii) a pentose (5
carbons) sugar, and (iii) a cyclic nitrogen containing compound called a base.
• In DNA, the sugar moiety is 2-deoxyribose
• Eukaryotic DNA is composed of four different bases: adenine, guanine,
thymine, and cytosine
• These bases are classified based on their chemical structure into two groups:
adenine and guanine are double-ring structures termed purines and thymine
and cytosine are single-ring structures termed pyrimidines
• Within the overall composition of DNA, the concentration of thymine is
always equal to the concentration of adenine, and the concentration of
cytosine is always equal to guanine.
• Thus, the total concentration of pyrimidines always equals the total
concentration of purines
• The constant ratio of purines to pyrimidines in DNA, and more
specifically the equal concentrations of adenine/thymine and
guanosine/cytosine, is known as Chargaff rule
• Chargaff observations related to the purine/pyrimidine composition of DNA
was validated when it was recognized that adenine/thymine (A:T) and
guanosine/ cytosine (G:C) are specifically hydrogen bond in the structure of
DNA.
• Adenine–thymine pairs are linked in the structure of DNA by double
hydrogen bonding, and guanosine– cytosine pairs are linked by triple
hydrogen bonding.
• The extensive hydrogen bonding between strands of DNA in the double
helical structure of the molecule confers great stability under physiological
conditions.
• Structure of DNA
• The structure of DNA is a double helix, composed of two poly-nucleotide
strands that are coiled about one another in a spiral.
• Each polynucleotide strand is held together by phosphodiester bonds linking
adjacent deoxyribose moieties
• The two polynucleotide strands are held together by a variety of noncovalent
interactions, including lipophilic interactions between adjacent bases and
hydrogen bonding between the bases on opposite strands.
• The sugar-phosphate backbones of the two complementary strands are
antiparallel—that is, they possess opposite chemical polarity.
• Moving along the DNA double helix in one direction, the phosphodiester
bonds in one strand are oriented 5′-3′, whereas in the complementary strand,
the phosphodiester bonds are oriented 3′-5′.
• The base pairing is always specific: adenine is always paired to thymidine,
and guanine is always paired to cytosine. This specificity results from the
hydrogen-bonding capacities of the bases themselves
• Adenine and thymine form two hydrogen bonds, and guanine and cytosine
form three hydrogen bonds
• The specificity of molecular interactions within the DNA molecule allows one
to predict the sequence of nucleotides in one polynucleotide strand if the
sequence of nucleotides in the complementary strand is known.
Sequence of the Human Genome

• The diploid genome of the typical human cell contains approx- imately 3 ×
109 base pairs of DNA that is subdivided into 23 pairs of chromosomes (22
autosomes and sex chromosomes X and Y).
• Today, the human genome is thought to contain approximately 21,000
distinct protein-coding genes. Analysis of the human genome sequence
reveals considerable variability between individuals, including in excess of
1.1–1.4 million single-nucleotide polymorphisms (SNPs) distributed
through- out the genome.
• The implications for knowing the sequence of the human genome in the
context of understanding the impact of genetic factors on human disease
are enormous.
Organization of the Human Genome

• Human genomic DNA is packaged into discreet structural units that

vary in size and genetic composition.
• The structural unit of DNA is the chromosome, which is a large con-
tinuous segment of DNA.
• A chromosome represents a single genetically specific DNA molecule
to which a large number of protein molecules are attached that are
involved in the maintenance of chromosome structure and regulation
of gene expression.
• Genomic DNA contains both coding and noncoding sequences.
Noncoding sequences contain information that does not lead to the
synthesis of an active RNA molecule or protein. This is not to suggest
that noncoding DNA serves no function within the genome.
• On the contrary, noncoding DNA sequences have been suggested to
function in DNA packaging, chromosome structure, chromatin orga-
nization within the nucleus, and/or in the regulation of gene
expression.
• A portion of the noncoding sequences represent intervening
sequences that split the coding regions of structural genes.
• Coding DNA sequences give rise to all of the transcribed RNAs of the
cell, including mRNAs that encode for protein products.
• The organization of transcribed structural genes consists of coding
regions that are interrupted by intervening noncoding regions of
DNA.
• Thus, primary RNA transcripts contain both coding and noncoding
sequences, and the noncoding sequences must be removed from the
primary RNA transcript during processing to pro- duce a functional
mRNA molecule appropriate for translation.
DNA Function

• DNA serves two essential functions with respect to cellular

homeostasis: (i) storage of genetic information and (ii) transmission of
genetic information.
• The DNA molecule serves as a template to fulfill each of these general
functions.
• During cell division, DNA serves as a template for the faithful
replication of genetic information that is ultimately passed into
daughter cells
• Likewise, the DNA molecule serves as a template for restoration of
normal DNA sequence during DNA repair processes.
• During normal cellular operations, DNA serves as a template for the
transcription of RNA.
• Transcribed RNA molecules may function directly (as is the case for
ribosomal RNAs and transfer RNAs), may function after processing (as
is the case of miRNAs), or may function as the template for synthesis
of cellular proteins (as in the case of mRNAs).
Replication of DNA

• Discovery of the double-stranded structure of DNA led rapidly to the

suggestion that DNA replication could be accomplished in a
semiconservative manner.
• In semiconservative DNA rep- lication, each strand of the DNA helix
serves as a template for the synthesis of the complementary strand. The
result is the formation of two complete copies of the DNA molecule, each
consisting of one strand from the parent DNA molecule and one newly
synthesized strand.
• Utilization of the DNA strands as templates for the synthesis of
complimentary DNA strands ensures the faithful reproduction of the
genetic material for transmission into daughter cells.
Transcription of RNA

• Transcription is the process by which RNA molecules are synthesized

with a sequence complimen- tary to the transcriptional unit of DNA.
Hence, the mRNA that encodes a specific protein is complimentary to
the DNA sequence of that specific gene.
• In similar fashion, rRNAs, tRNAs, and various other RNA species are
transcribed. The correct start and end points for transcription of a
particular gene are determined by the promoter sequence upstream
of the coding sequence of the gene and by termination signals
downstream.
• In contrast to DNA replication where both strands of the molecule
serve as templates for synthe- sis of complementary DNA strands, in
RNA transcription, only one strand of the DNA serves as template.
This strand is referred to as the sense strand.
DNA Damage and Mutagenesis

• Overview of DNA Damaging Agents

• Types of DNA Mutation
• Mutation is simply defined as any permanent change to the DNA molecule. The
various forms of spontaneous and induced DNA damage give rise to a plethora of
different types of molecular alterations to the DNA molecule, leading to stable
mutations. These various types of mutation include both gross alteration of
chromosomes and more subtle alterations to spe- cific gene sequences in
otherwise normal chromosomes.
• Chromosomal Alterations
• Gross chromosomal aberrations include large deletions, addi- tions (reflecting
amplification of DNA sequences), translo- cations (reciprocal and nonreciprocal),
and other forms of chromosomal rearrangement
• Nucleotide Sequence Alterations
• Somatic Mutations Versus Germ-Line Mutations
• When DNA damaging and mutational events affect the DNA of a somatic cell, the
resulting mutations are referred to as somatic muta- tions.
• Somatic cells represent the cells that compose all of the tissues in the organism
outside of the germ line
• Somatic muta- tions have been implicated in numerous disease types, par- ticularly
those that are characterized by clonal proliferation of altered cells (like in the case
of cancer)
• Some somatic mutations occur during development, resulting in specific kinds of
local- ized developmental abnormalities.
• Somatic mutations are not heritable.
• In contrast, DNA damaging and mutational events affecting the DNA of cells in
the germ line produce mutations that are referred to as germ-line mutations.
• This distinction is biologically and clinically significant.
• The cells of the germ line are responsible for the genesis of oocytes (in the female) and
spermatocytes (in the male).
• Hence, transmission of a germ- line mutation introduces a nucleotide sequence
alteration into the fertilized egg.
• If that egg produces a viable organism, the mutation will be found in every cell in the
organism.
• Germ- line mutations account for numerous genetic diseases, which can manifest
systemic or organ-system-specific diseases (single organ or multiorgan).
• In addition, the germ-line mutation is found in the germ line of the affected individual,
meaning that their offspring might also inherit the mutation.