INTRODUCTION AND HUMAN

GENOME

Ahmad Hamim Sadewa

INTRODUCTION TO
HUMAN GENETICS

Ahmad Hamim Sadewa

 OUTLINE

1. The principle of medical genetics

2. Genetic Disorders

3. Single-gene Disorders

4. Chromosome Disorders

5. Multifactorial Disorders
 Medical Genetics

Spesialisasi di bidang medik yang berkaitan dengan

diagnosis, treatment dan penanganan kelainan herediter
Berada pada garis terdepan penelitian-penelitian mengenai
sifat-sifat herediter dan keanekaragaman manusia
bersama-sama dengan cabang ilmu lain seperti biokimia,
biologi molekuler dan biologi sel.
Human Genome Project : menentukan urutan/isi dari
genom manusia secara lengkap 🡪 menentukan variasi-
variasi gena yang berperan dalam kondisi sehat dan sakit.
Pediatric Genetics

Pada awalnya, genetika manusia fokus pada kasus

penyakit genetik yang terdeteksi saat masa anak-anak
(pediatric genetic)
Sekarang, genetika manusia diaplikasikan pada
berbagai bidang ilmu
Royal Hemophilia
Chromosome Map
• Begun in 1990, the Human Genome Project was a 13-
year effort. The project originally was planned to last 15
years, but rapid technological advances accelerated the
completion date to 2003. Project goals were to
• identify all the approximately 30,000 genes in human
DNA,
• determine the sequences of the 3 billion chemical base
pairs that make up human DNA,
• store this information in databases,
• improve tools for data analysis,
• transfer related technologies to the private sector,
• address the ethical, legal, and social issues (ELSI) that
may arise from the project.
 Medical Genetics (cont’d)

Human Genetics : the science of variation and heredity of

human being
Medical Genetics : deals with the subset of human genetic
variation that is of significance in the practice of medicine
and in medical research, contains many disciplines :
Cytogenetics : study of chromosomes
Molecular and biochemical genetics : study of structure
and function of individual genes
Genomics : study of the genome, its organizations and
functions
 Medical Genetics (cont’d)

Population Genetics : study of genetic variation in human

populations and determine factors that determine allele
frequencies
Developmental Genetics : study of the genetic control of
human development
Clinical Genetics : the application of genetics to
diagnosis and patients care
Kepentingan Mempelajari Genetika Manusia

1. memahami fungsi gen sebagai dasar proses

kehidupan
2. memahami peran gen dalam kondisi sehat dan sakit
3. Mengetahui distribusi suatu alel dalam populasi
4. Mengetahui fenotip yang muncul akibat mutasi dan
polimorfisme
5. Memahami interaksi gen-gen dan gen-lingkungan
6. Memahami peran gen pada kanker dan proses
degeneratif
7. Diagnosis prenatal dan skrining populasi dan terapi
(DNA fingerprinting)
 Genetic Disorders

Virtually any disease is the result of the

combined action of genes and environment, but
the relative role of the genetic component may
be large or small

Disorders caused wholly or partly by genetic factors can be

divided into three main types :
1. Single-gene disorders
2. Chromosome disorders
3. Multifactorial disorders
Applications

1. Nutrigenomic
2. Pharmacogenomic
3. Immunogenetic
4. Oncogenetic
5. Population genetic
6. Forensic genetic
7. Gene therapy
Other application of Human Genetics
1. Sport Genetics
2. Prenatal Diagnostics and Counseling
3. DNA finger printing 🡪 disaster victim identification (DVI)
4. Disease risk factor and prediction
5. Etc.
Genes mutation which reduce
expression in several cancer
List of miRNA used fro clinical trial
 Single-gene Disorders

Caused by individual mutant gene; can be recognized by

family pedigree
Mutation of the genes may be present on only one
chromosome or on both chromosome (dominant or
recessive); on autosom or sex chromosom
Mutation of the genes may be present on nuclear genome
or mitochondrial genome
Mutation of the genes cause a critical error in the genetic
information carried by a single gene
 Single-gene Disorders (cont’d)

The frequencies are rare, the highest is as much as one

in 500 individuals (1:500). But, taken together in whole
population, overall frequency is around 2%.

Total frequency among population is 0.36%, among

hospitalized children is 6 – 8%.

Single-gene disorders in Indonesia : Thalassemia,

Dystrophia Musculorum Duchenne (DMD), Glucose-6
phosphate Dehidrogenase (G6PD) Deficiency
Autosomal Dominant Inheritance
X-Linked Dominant
Inheritance
X-linked Recessive
Inheritance
 Chromosome Disorders

Caused by defects in the chromosome segment (heteroploid,

aneuploid, inversion, deletion etc.)
Down Syndrome caused by trisomy chromosome no 21
Overall frequency in population is about 7 in 1000 liveborn
infants and about half of all apontaneous first-trimester
abortion
Triploidy
Chromosome Disjunction
 Multifactorial Disorders
Responsible for a number of development disorders resulting
in congenital malformations and for many common disorders
of adult life

The disease is the result of a combination of variation in genes

that together can produce or predispose to a serious defect,
often in concert with environmental factors

Multifactorial disorders tend to recur in families but do not

show the characteristic pedigree patters of single gene
disorders
The frequency is 5% in pediatric population to more than 60%
in the entire population
Multifactorial disorders tend to recur in families but do not
show the characteristic pedigree patters of single gene
disorders
The frequency is 5% in pediatric population to more than 60%
in the entire population
E.g. hypertension, diabetes mellitus
 NUCLEIC ACIDS AND
HUMAN GENOME

Ahmad Hamim Sadewa

Department of Biochemistry Faculty of Medicine

Gadjah Mada University
 Content

A. Structure of Nucleic Acids

B. Organization of Nucleic Acids
C. Function of Nucleic Acids
D. Metabolism of Nucleic Acids
 NUCLEIC ACID

Nucleic acid is a macromolecule consists of

nucleotides (polynucleotides)
Purines and pyrimidines are nitrogen-containing
heterocycles, cyclic compounds whose rings contain
both carbon and other elements (hetero atoms).
Adenine and guanine are purine; thymine, uracyl and
cytosine are pyrimidine
Nucleosides are derivatives of purines and
pyrimidines that have a sugar linked to a ring nitrogen.
The sugar is linked via a beta-N-glycosidic bond, to
N-1 of a pyrimidine or to N-9 of a purine
Mononucleotides are nucleosides with a phosphoryl
group esterified to a hydroxyl group of the sugar.
Purine, Pyrimidine and Nucleosides
 Nucleotides

Numerals with a prime (eg, 2′ or 3′) indicate the sugar,

numerals without a prime indicate the base.
The prefix “d” (deoxy) indicates that the sugar is 2′-deoxy-
D-ribose, without prefix “d” indicates that the sugar is D-
ribose.
AMP, ADP and ATP
The Nomenclature of Base, Nucleoside and Nucleotide
 NUCLEIC ACID

There are two nucleic acids based on ribose:

DNA is deoxyribose; RNA ribose
DNA is the chemical basis of heredity, organized
into genes, the fundamental units of genetic
information
DNA contains 4 deoxynucleotides : deoxy
adenilate, guanilate, cytidylate and thymidylate
RNA contains uracil instead of thymine
Basic information pathway : DNA to RNA to protein
is the central dogma of molecular biology
 DNA

Genetic materials, in eucaryotes DNA present

in the nucleus, in procaryotes DNA is dispersed
in the cytoplasma (recently known as nucleoid)
In human, DNA also exists in the mitochondria
(mitochondrial DNA = mtDNA)
DNA bound to nucleoprotein (histone) to form
nucleosome. Together with nonhistone proteins
and RNA form chromatin (eu- dan hetero-
chromatin).
Nonhistone proteins include enzymes important for
DNA replication and translation.
 Chromatin
Transcriptionally inactive chromatin is densely packed
during interphase as observed by electron microscopic
studies and is referred to as heterochromatin
Constitutive heterochromatin is always condensed
and thus inactive. It is found in the regions near the
chromosomal centromere and at chromosomal ends
(telomeres).
Facultative heterochromatin is at times condensed,
but at other times it is actively transcribed and, thus,
uncondensed and appears as euchromatin.

Transcriptionally active chromatin stains less densely

and is referred to as euchromatin.
One purpose of the molecules that comprise
chromatin, particularly the histones, is to condense
the DNA.
Genome : all DNA contain in the cell. Human have 3
billion base pairs of nuclear genome and 16,500 base
pairs of mitochondrial genome.

Chromatin demonstrated dense spherical

particles called nucleosomes, which are
approximately 10 nm in diameter and connected
by DNA filaments
Core histone : H2A, H2B, H3 and H4 make
histone octamer, bound tightly.
H1 histone least tightly bound to the core histone.
Nuclear DNA Structure
proposed by Watson dan Crick
Each linear molecule consists of 2 strand joined
by hydrogen bond between purine and
pyrimidine bases
adenine join with thymine, involve the formation of
2 hydrogen bonds
guanine join with cytosine, involve the formation
of 3 hydrogen bonds
The 2 DNA strands are complementer,
adenine = thymin and guanine = cytosine
Bases are linked with deoxyribose by mean of N-
glicosidic linkage, purine and pyrimidine bases are
held together by phosphodiester backbone between
2 deoxyribosil moeities
The 2 strands are antiparalel, one strand runs
in the 5’ – 3’, the other runs in the 3’ – 5’
The 2 strands, which bases held together by
hydrogen bond, wind around central axis to form
a double helix right handed
One strand act as a template strand, the
opposite is considered as coding strand
Double helix right handed DNA (B DNA)

major groove
Protein
binding
site
minor groove
 3’
antiparalel strand

5’

5’

3’
DNA provides a template for replication, transcription
DNA characteristic
Denaturation occurs by decreasing the salts
concentration or increasing temperature, yields
single-stranded DNA.
Decrease temperature results in renaturation or
reannealing.

Hybridization : single stranded DNA join with

other complementer DNA or RNA.
 DNA Organization
DNA (genes) are organized into coding region (exon) which
will be translated into proteins and noncoding region
(intron/intervening sequence = IVS) which will not be
translated into protein.
During mRNA maturation, noncoding region will be
removed by a process called splicing.

In human, 30,000 genes have been characterized;

however, scientists believe that the number of genes
should be at least 80,000.
All genes only comprises 3% of human genomes, others
are introns and extragenic DNA
Exon and Intron in Genes
RNA Splicing
Human Repetitive DNA
There are 3 major categories of repeated sequence or repeats:
1. Terminal repeats : e.g. telomere repeat (TTAGGG)n
2. Tandem repeats: copies which lie adjacent to each other, either directly or
inverted
• Satellite DNA - typically found in centromeres and heterochromatin
• Minisatellite - repeat units from about 10 to 60 base pairs, found in
many places in the genome, including the centromeres (e.g. VNTR)
• Microsatellite - repeat units of less than 10 base pairs; this includes
telomeres, which typically have 6 to 8 base pair repeat units (e.g. STR)
3. Interspersed repeats (or interspersed nuclear elements/transposable
elements
• DNA transposons
• Retrotransposons
• LTR-retrotransposons (HERVs)
• non LTR-retrotransposons
• SINEs (Short Interspersed Nuclear Elements)
• LINEs (Long Interspersed Nuclear Elements)
• SVAs (consist of 3 components : SINE, VNTR, Alu)
In primates, the majority of LINEs are LINE-1 and the majority of SINEs are
Alu's. SVAs are hominoid specific.
Differences between variable number of tandem
repeat (VNTR) and short tandem repeat (STR)
 Similarities between VNTR and STR

1. VNTR and STR are two types of tandem repeats.

2. Both VNTR and STR are structural regions of the eukaryotic genome.
3. Both VNTR and STR consist of noncoding DNA.
4. BothVNTR and STR are inherited from parents.
5. Both VNTR and STR are composed of repetitive sequences, arranging
adjacent to each other in an array.
6. Both VNTR and STR produce genetic polymorphism.
7. Both VNTR and STR are spread throughout the genome.
8. Both VNTR and STR are used as genetic markers in forensic genetics.
9. Mutations in both VNTR and STR lead to genetic diseases.
 Transposon/Transposable Elements
or “jumping gene”

❑ DNA sequence that can move in the genome

❑ Also called mobile DNA element or transposable element
❑ Transposition: The process by which these sequences are copied
and inserted into a new site in the genome
❑ Probably had a significant influence on evolution
How transposon was found

❑ 1940s, Barbara
McClintock discovered the
first transposable element
in maize, earned a Nobel
prize in 1983.
❑Late 1960s, transposition
was also found in Bacteria.
Barbara McClintock
http://en.wikipedia.org/wiki/Barbara_McClintock
 Two Categories :
DNA transposon and
Retrotransposon

A. DNA transposons
✔ Most mobile elements in bacteria is
DNA transposons
“cut-and-paste” “copy-and-paste”
✔ In contrast, most mobile elements
in eukaryotes are retrotransposons,
but eukaryotic DNA transposons
also occur.
✔ Around 42% of the human genome
is made up of retrotransposons,
while DNA transposons account for
about 2–3%.
Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-8
B. Retrotransposons

1. Long terminal repeat (LTR) retrotransposons:

2. Non-LTR retrotransposons: the most common type of transposons in mammals

General structure of eukaryotic LTR retrotransposons

Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-11
1. LTR transposon

Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-12

Endogenous retroviruses (ERs) are an important type of LTR

retrotransposon in mammals, including in humans where the Human
ERVs (HERVs) make up 8% of the genome.
Retrotransposons
2. Non-LTR Retrotransposons

a. long interspersed elements (LINEs) : L1 (most common), L2, L3

≈6 kb in human
account for 21% of the genome
Example : There are >500,000 L1 copies in the human genome, resulting from their continued
mobilization activity. L1 elements constitute ~17% of the human genome, which makes them
the most successful TEs in the human genome by mass.

b. short interspersed elements (SINEs) : Alu (most common), B1, B2

≈300 bp in human
account for 13% of the genome
Example : Arthrobacter luteus (Alu) family is a family of repetitive elements in the human genome.
Modern Alu elements are about 300 bp long. There are over one million Alu elements
interspersed throughout the human genome, and it is estimated that about 10.7% of the human
genome consists of Alu sequences.
 The Organization of Human Genome

Human Genome
3000 Mb

Genes and related Extragenic DNA

sequences 900 Mb 2100 Mb

Coding DNA Non-Coding Repetitive Unique and low

90 Mb DNA 810 Mb DNA 420 Mb copy number
1680 Mb

Pseudogenes Gene Introns, leaders,

fragments trailers
Mitochondrial DNA

Closed circle/circular, exist in relax and

supercoiled form, consists approximately 16,500
bp. Similar with the bacterial plasmid.
Contain 37 genes (encode 13 respiratory
complex mRNA, 2 rRNA genes and 22 tRNA
genes)
Contain no intron
Inherited only from mother
The structure of human mitochondrial DNA
 RNA

Transcribed from DNA, different structure

Involve in protein synthesis (mRNA : template

for prot synt, tRNA : adapter molecule for
transcription, rRNA : formation of ribosome)

Involve in replication (oligonucleotides) dan RNA

processing (snRNA, snRNP atau snurp,
hnRNA : mRNA precursor)
Act as an enzyme (ribozyme: peptidyl
transferase)
 DNA vs RNA
DNA RNA
deoxyribose ribose
thymine uracyl
double-strand single-strand
guanine = cytosine, adenine = Not equal
thymine
Denaturation to single strand Hydrolisis by alkali to
mononucleotides
1. mRNA
Convey information in a gene to protein-
synthesizing machinery
Synthesized in nucleus, translated in cytoplasm
Capping at 5’ terminus: 7-methylguanosine
and 2-O-methylpurine
Poly(A) tail : additional adenilate residue at the
3’ terminus(20 – 200 molecules)
Capping and poly(A) tail is important to stabilize
RNA (preventing the attack of exonuclease), also
to direct RNA to ribosome.
UTR : untranslated region, 3` and 5` part of
RNA whis is not be transcribed
mRNA
mRNA
2. tRNA
Adapter for the translation of mRNA. There are
20 species of tRNA corresponding to each of the
20 amino acids
The primary structure allow folding and intrastrand
complementarity, so appear like a cloverleaf
D-loops consists of dihydrouridine
Anticodon-loops interact with mRNA
TψC loops consists of ribothymidine and
pseudouridine
Variable loop
Acceptor arm (3’ terminus) amino acids attach here
tRNA
3. rRNA
Ribosome : nucleoprotein structure (rRNA
and protein) act as the machinery for the
protein synthesis
Mammalian ribosome contains 2 major
nucleoprotein, a large one of 60S (5S, 5,8S,
28S rRNA and 50 polypeptide) and a small one
of 40S (18S rRNA and 30 polypeptide)

4. Small-stable RNA
Small stable RNA exist as ribonucleoprotein,
distributed in the nucleus and cytoplasm
snRNA (snRNP/snurps) : RNA splicing and
gene regulation
5. Short noncoding RNA/MicroRNA (miRNA)
is a short RNA molecule, has very few nucleotides (an average
of 22). The miRNAs are post-transcriptional regulators that bind
to complementary sequences on target mRNAs, usually
resulting in translational repression, target degradation and
gene silencing
6. Long noncoding RNA (lncRNA)
Regulators of gene expression.
Ribosome 40S Ribosome 80S
References

Nussbaum RL, McInnes RR, Willard HR. 2007.

Thompson and Thompson Genetics in Medicine 7th
Ed. Saunders, Philadelphia.
Strachan T and Read AP. 2004. Human Molecular
Genetics 3rd Ed. Garland Science Publishing, USA.
Brown, TA. Genomes 3rd Ed. 2007. Garland Science
Publishing, USA.