The document summarizes the organization of the human genome and genes. It discusses the general organization of the human genome including nuclear and mitochondrial genomes. It describes gene distribution and density in the nuclear genome. It provides details on the organization of different types of genes such as rRNA, mRNA, small nuclear RNA genes, overlapping genes, and multi-gene families. It also discusses various repetitive elements in the genome including SINEs, LINEs, microsatellites, and minisatellites. Finally, it covers topics like chromatin structure, histones, heterochromatin, euchromatin, and X-inactivation.

1. Organization of human genome and genes:
• General organization of human Genome-Nuclear and Mitochondrial
• Mitochondrial Genome organization, Mitochondrial mutations and
myopathies
• Size and banding of human chromosomes
• Distribution of tandems and interspersed repetitive DNA
• Gene distribution and density in human nuclear genome
• Organization of genes:
• rRNA encoding Genes
• mRNA encoding Genes
• small nuclear RNA genes
• Overlapping genes
• Genes within genes
• Multi-gene families
• Pseudo genes
• Truncated genes and gene fragments

4. Nuclear genetic organization
• What is the shape of nucleus?
A: Nucleus appears different in interphase and mitotic phase
• What are the various parts of nucleus?
A: Chromatin, Nuclear membrane, Nuclear matrix, Nucleolus
• Chromatin material is fibrous and condensed DNA with protein structures
• Nuclear membrane is a porous double membrane with ribosomes
attached outside and outer membrane is continuous with ER
• Nucleolus: Darkly staining body eccentrically placed in the nucleus,
number can be 1-4, size varies with cell types and metabolic state of the
cell, larger in rapidly dividing and actively protein synthesizing cells; site for
ribosome precursor assembly, composed of RNA, Proteins and some
amount of DNA
• Nuclear Matrix:

5. Chromatin: DNA, Proteins – mainly histones,
RNA, certain polysaccharides
• DNA
• RNA
• Histone proteins: Isoelectric point more than 10, basic pH,
large number of arginine and lysine proteins
• Non-histone proteins: Isoelectric point less than 10,
generally 4-9, acidic pH, mixture of proteins with different
structural, enzymatic, and regulatory proteins

6. Histones
? What is the amount of histones in nuclear material?
•Ratio of Histones:DNA in chromatin is 1:1
? Types of histone and how do they differ?
• H1: Lysine-rich; H2A & H2B: Slightly Lysine-rich; H3/H4: Arginine-rich
•H3 & H4 are highly conserved in evolution
? Are there cell-specific types of histones?
•H5 – in nucleated Erythrocytes in place of H1
•Sperms – protamine instead of histones
? How histone proteins can be studied?
•Extraction with dilute acids or high molarity salt solutions

7. Histones
? What is the amount of histones in nuclear material?
•Ratio of Histones:DNA in chromatin is 1:1
? Types of histone and how do the differ?
• H1: Lysine-rich; H2A & H2B: Slightly Lysine-rich; H3/H4: Arginine-rich
•H3 & H4 are highly conserved in evolution
? Are there cell-specific types of histones?
•H5 – in nucleated Erythrocytes in place of H1
•Sperms – protamine instead of histones
? How histone proteins can be studied?
•Extraction with dilute acids or high molarity salt solutions

8. Non-histone proteins
•Amount: Less as compared to histones
•Types: Several hundred various types of proteins
•More variable and numerous
•Functions:
•Chromosomal metabolism
•In gene expression
•Higher order structure

9. • Basic unit of eukaryotic chromatin, present in
dispersed or condensed chromatin
• 10nm spheres or disks, octamers made up of 2
molecules each of H2A, H2B, H3, & H4
• H1 histones link & compact the nucleosomes
• Around 140bps of DNA wind twice around the
spherical nucleosome (~6/gene of 1200bp), followed
by 60bp linker and next nucleosome, H1 proteins
condense the beads into a 10nm fiber, coiled again
into 25nm strands
Nucleosomes

10. Nucleosome: Basic unit of chromatin
•10nm spheres or disks made up of 2
molecules each of H2A, H2B, H3, H4 make
octomers:
•~140bp of DNA wind twice around the
spherical structure (~6/gene of 1200bp)
•~60bp linker DNA and the next nucleosome
•H1 link two nucleosomes and condense the
beads into ~10nm fiber

11. • Coiled into 25-30nm strand
• Coiled to form ~300nm
chromomeres that cluster onto
chromatin structure, form ~1400nm
chromosome with 2 chromatids;
• Chromomere clusters are G-positive
bands

12. Chromosome structure

13. `

14. Distribution of tandems & interspersed repetitive DNA
• LINEs: Long Interspersed
Elements
• Length of 1-5Kb
• 20-40 thousand copy number
• 21% fraction of genome
• Contain cleavage sites for L1
located in bright bands
• Autonomous transposition
• SINEs: Short Interspersed Elements
• Length 100-300bp; smaller than
500bp
• ~15lakh copy number
• 13% fraction of genome
• Contain cleavage sites for Alu1
located in pale bands
• Nonautonomous transposition

15. 0 2 4 6 8 10 12
Microsatellite
Minisatellite
Simple Sequence Repeats
Short Interspersed Elements
Long Interspersed Elements
Chart Title
Column1 Approx. amount in % Approx. no. of basepairs

16. Chromosome structure & function details
• Proteins: Histone & Non-histone
• DNA: Chromatin material
• Euchromatin
• Heterochromatin: Facultative (X-chromatin) & Constitutive
• Satellite DNA

17. Euchromatin & Heterochromatin
• Heteropyknosis: variation in staining intensity owing to differential
degree of coiling
• Heterochromatin: Facultative and Constitutive; non-coding; both
replicate late in the synthesis phase of cell cycle
• Euchromatin: The remaining regions of DNA

18. Heterochromatin: Facultative and Constitutive;
non-coding; both replicate late in the synthesis
phase of cell cycle
Facultative Heterochromatin:
• Inactivated homologue of X-
chromosome pair
• Not stained with C-banding
• May differ from cell to cell
• Has coding DNA
• Can decondense and become
active
• Example; X-chromosome
Constitutive Heterochromatin:
• Differentially staining areas of
chromatin and chromosomes
• Stained with C-banding
• Constant from cell to cell
• Rich in repetitive DNA
• Never elongates or decondenses
• Example; Centromeric regions
mainly of 1, 9, 16, and Yq

19. Constitutive Heterochromatin
contains repetitive DNA
• Density gradient centrifugation leads to separate band from main
band hence called Satellite DNA
• Types of satellite DNA are I, II, and III etc. to denote single family of
simple repeats; & also pure sequence groups i.e. Alpha & Beta
Satellite DNA
• Alpha Satellite DNA: Consensus sequences that are same in
centromere of all the chromosomes; more specific sequences used to
identify centromere regions of specific chromosome

20. Heterochromatin contains undispersed & dispersed
repetitive sequences throughout the genome
• Microsatellites: 2-3 nucleotide tandem repeats, highly polymorphic
• Simple sequence repeats: 3-6bp repeats in coding and non-coding
DNA regions, highly polymorphic
• Minisatellites: ~10bps, usually at distal end of chromosomes
also dispersed through out the genome
{used for DNA fingerprinting due to polymorphism}
• SINES
• LINES

21. X-chromatin, facultative heterochromatin
• Dosage compensation?
• Any one of X-homologue can be inactivated randomly
• Occurs in early embryogenesis
• Inactivation is stable, can pass in descendents of a cell
• Russell-Lyon hypothesis

22. X-inactivation:
•Xq13: XIC X-inactivation centre; encodes large non-
coding RNA called XIST(X-inactivation-specific
transcript), only in case of inactive copy; XIST primary
transcript splicing & polyadenylation 17Kb
mature RNA; recruits certain proteins that organize
the chromatin into closed, transcriptionally inactive
conformation [essential for inactivation but not for
maintenance of inactivation]
•What are the molecular changes in X-Inactivation or
‘heterochromatization’ that is initiated by XIST that
propagates along the whole length?

23. X-inactivation:
•What are the molecular changes in X-Inactivation or
‘heterochromatization’ that is initiated by XIST that
propagates along the whole length? This involves
modifications of typical heterochromatin viz.,
• H3K9 – di or tri methylated
• H3K4 – unmethylated
• H4 – deacetylated
• H3K27 – trimethylated
• CpG islands at promoters of inactivated genes are methylated
• Many nucleosomes carry variant ‘Macro-H2A’ instead of normal H2A

24. X-inactivation as mechanism of gene dosage
compensation: Total of partial?
• One of the X is inactivated over most of the regions
except;
• Two Pseudo-autosomal regions; PAR1 on Xp/Yp,
and PAR2 on Xq/Yq have functional homologues,
all PAR1 and some of PAR2 genes are found to
escape inactivation
The pseudoautosomal regions at the tips of Xp and Yp are identical, as are
those at the tips of Xq and Yq. The non-recombining male-specific region on
the Y chromosome (MSY) and the equivalent, X-specific, region on the X
chromosome are rather different in sequence but nevertheless show multiple
homologous XY gene pairs (gametologs). The latter are generally given the
same gene symbols followed by an X or a Y such as SMCX on proximal Xp
and its equivalent SMCY on Yq. In some cases, however, the Y-chromosome
homologs have degenerated into pseudogenes (with symbols terminating in a
P; see examples in the gene clusters labeled a, b, and c). As a result of
positive selection, the sequence of the male-determinant SRY is now rather
different from its original gene partner on the X chromosome, the SOX3 gene
(highlighted in yellow). [Adapted from Lahn BT & Page DC
(1999) Science 286, 964-967. With permission from the American Association
for the Advancement of Science.]

26. • Separate band –other than main band of DNA on density
gradient centrifugation (&/or), highly repeated sequences,
called as classical satellites I, II, III, etc. that are made up of
a single family of simple repeats designated by 1, 2, 3, etc.
• RFLP to detect polymorphism due to mutation
• For each class there are certain ‘consensus sequences’ that
are substantially the same i.e. for all chromosome
centromere & there are specific for each chromosome also
Satellite DNA

27. Hope this is not the case with you! Good Day!!

28. • Dispersed repetitive sequences thru’ out the genome in
contrast to localized one
• ~>500bps, short interspersed elements
& long interspersed elements
• SINES: Alu-I recognized cleavage sites, on QM pale bands
• LINES: L1 recognized cleavage sites, on QM bright bands
• Microsatellites:
• Simple sequence repeats: 3-6 bp units, in coding & non coding DNAs,
highly polymorphic,
• Mini satellites: >10bps, at distal ends, highly polymorphic, used for
DNA fingerprinting
SINES & LINES / Micro Mini Simple satellites

29. Constitutive Heterochromatin

31. Figure 4: FISH with repetitive probes to human chromosomes. a) FISH with a "pan-centromeric"
probe delineates all centromeres. b) A probe containing the highly conserved repetitive sequence
hybridized to all telomeres. c) A rDNA probe hybridized to all human NOR bearing chromosomes
(chromosome 13-15, 21,22). d) FISH with the disperse repetitive Alu mimics a R banding pattern.

32. Revision checkpoints:
• How is isoelectric employed to isolate histone proteins from non-
histone proteins?
• Describe structure of nucleosomes and organization in chromosome
with diagram.
• Which are the various types of repetitive DNA sequences? Mention
the size, amount, and significance of each
• Explain facultative heterochromatin and Lyon Russel hypothesis

33. DNA
methylation,
CpG islands,

34. Mitochondrial Genome organization,
Mitochondrial mutations and myopathies
Nuclear organization
• 3.3 Billion Base pairs
• Linear
• Single copy per cell, single copy per
nucleus
• In the nucleus
• 93% non-coding
• Inherited equally from both parents
• ~25000 genes
• Usually transcription of one gene at a
time from their own mRNA
Mitochondrial organization
• 16569 Base pairs
• Circular
• Thousands of copies per cell, dozens of
copies per mitochondria
• In the cytoplasm
• 3% non-coding
• Inherited strictly from maternal
• 37 genes encode 13 proteins, 22 tRNAs, 2
rRNAs
• Polycistronic transcription, one large mRNA
encode one after the next protein

35. Mitochondrial Nuclear
Protein coding -66% 1.1%
RNA genes – 32% 4%
Other seq. – 2% 44%
Heterochromatin 0- 6.5%
Transposon-based 0 - 45%

38. • 37 genes encode 13 proteins, 22
tRNAs, 2 rRNAs
• Polycistronic transcription, one large
mRNA encode one after the next
protein
• Nuclear gene POLG (DNA polymerase
Gamma) encodes polymerase
responsible for replicating mt-DNA
• POLG: a CATALYTIC DOMAIN + an
EXONUCLEASE DOMAIN, polymerase
activity and recognition and removal
of DNA base-pair mismatches
• Imbalance in levels of dNTPs can
reduce fidelity of POLG

39. Mitochondrial or Cytoplasmic or Maternal
inheritance: Characteristics
• Codon triplets do not follow universal rules while translation into proteins
• Same nucleotide base function in overlapping position for >1 genes
• ~100 times higher mutation rate than nuclear genome
• Hence heterogeneous population of mtDNA within same cell and within
same mitochondria: Heteroplasmic
• Segregation of mitochondria in two daughter cells in a random manner
leading to similar but un-identical copies of mt-DNA

40. Mt DNA mutation rate > Nuclear DNA
• DNA polymerase gamma (POLG), a nuclear gene encodes DNA
polymerase responsible for replication of mt-DNA
• POLG – catalytic domain exhibits polymerase activity &
exonuclease domain exhibits recognition and removal of DNA
base-pair mismatches occurring during replication
• Imbalance in nucleotides can lead to decreased fidelity & higher
mutation rates

44. Disease conditions
due to
mitochondrial
mutations

45. Mitochondrial CODON: how is it different
from nuclear CODON?
• In the mitochondrial genetic code there are 60 codons that specify
amino-acids, one fewer than in the nuclear genetic code. There are
four stop codons:
• UAA and UAG (which also serve as stop codons in the nuclear genetic
code) and
• AGA and AGG (which specify arginine in the nuclear genetic code; see
Figure 1.25).
• The nuclear stop codon UGA encodes tryptophan in mitochondria,
and AUA specifies methionine not isoleucine.

46. Mitochondrial Mutations & Clinical symptoms
Why it is difficult to predict outcome of
mitochondrial mutations?
•Mutations can be homoplasmic or heteroplasmic
•Complex interplay between mitochondrial and
nuclear genomes
•Mitochondrial mutation needs to be considered
with ref. to number of mitochondria having a
mutation across the population

47. Classical mitochondrial syndromes
• Leber hereditary optic neuropathy (LHON)
• Post lingual deafness (mutation in RNR1 gene encoding ribosomal
RNA and also environmental factors like use of certain antibiotics)
• Pearson syndrome
• Leigh syndrome
• Progressive external opthalmoplagia
• Exercise-induced muscle pain
• Fatigue
• Rhabdomyolysis

48. Clinical syndromes with high probability of
Mt-DNA involvement
•Maternal family history
•Involvement of several different tissues
•Tissues with high energy demand viz., brain,
retina, skeletal muscle, cardiac muscle more
affected
•Pearson syndrome, Leigh syndrome, progressive
external opthalmoplagia

49. • Mitochondria picture • Two membranes
• Inter-membrane space

50. Gene distribution and density in human
nuclear genome

51. Organization of genes:
• rRNA encoding genes
• mRNA encoding genes
• Small nuclear RNA genes
• Overlapping genes
• Genes within genes
• Multigene families
• Pseudogenes
• Truncated genes and gene fragments: Antibody secreting mature B
cells

52. RNA genes: A twist in Central Dogma?
• Strachan & Read: Chapter:9, Page-274, [9.3] RNA genes
• Nuclear DNA codes for ~21000 protein coding genes which is XX % of
total genome
• ~85% of nuclear DNA is transcribed, whereas only XX% are protein coding
genes (~21000), thus rest are RNA coding genes (~6000)
• Multi-genic and bidirectional transcription is extensive that explains
more no. of genes in a much smaller encoded region
• ~20000 genes in human (xx billion cells) and also in C. elegans (1000
cells), thus RNA machinery seems to be more important
• ncRNA: Functional Noncoding RNA

54. Apart from the protein coding genes that are transcribed into
mRNA; Which are the other RNA genes?
• rRNA & tRNA
• snRNA: Small nuclear RNA, ~60-360 Nucleotides long, role in post-
transcriptional processing, bind various proteins to function as
ribonucleoproteins (snRNPs)
• snoRNA: Small nucleolar RNA, involved in post-transcriptional
processing of rRNA precursors in the nucleolus
• scaRNA: Small Cajal body RNAs, discrete nuclear structures associated
with maturation of snRNPs

55. miRNA:~21-22 nucleotide cytoplasmic RNA
• How does miRNA regulate gene expression?
miRNA bind to target transcript at 3’ untranslated region of mRNA,
block the translation, and down regulate the expression
• How miRNA are synthesized?
The RNAse III ribonuclease cleaves pre-miRNA i.e. dsRNA resulted from
cleavage of hairpin RNA, transported out of nucleus where the
cytoplasmic RNAse III (dicer) cleaves pre-miRNA to give miRNA duplex
with free 3’dinucleotides. RISC (RNA-induced silencing complex) that
contains endoribonuclease argonaute binds the duplex, and causes
unwinding of dsDNA, argonaute degrades ‘passenger’ strand, and the
‘Guide’ strand i.e. mature miRNA remains

56. General Scheme of Human miRNA synthesis:
The primary transcript, pri-miRNA, has a 5’ cap
(m7GpppG) and a 3’poly(A) tail. miRNA precursors have a
prominent double-stranded RNA structure (RNA hairpin),
and processing occurs through the actions of a series of
ribonuclease complexes.
In the nucleus, Rnasen, (the human homolog of Drosha)
cleaves the pri-miRNA to release the hairpin RNA (pre-
miRNA); and exported..
In the cytoplasm, dicer cleaves it to produce a miRNA
duplex.
The duplex RNA is bound by an argonaute complex and
the helix is unwound,
whereupon one strand (the passenger) is degraded by the
argonaute ribonuclease, leaving the mature miRNA (the
guide strand) bound to argonaute. miR, miRNA gene.

58. Inverted repeats are highlighted overlined by long arrows in the pri-miRNA, these
undergo base pairing to form a hairpin, usually with a few mismatches. It contains
sequences that will form the mature guide strand & passenger strand. Green
Arrows show sites of cleavage by human Drosha and dicer, that is typically
asymmetric, leaving an RNA duplex with overhanging 3’ dinucleotides
MiRNA synthesis: Example of human miR-26a1

59. piRNA:Piwi protein-interacting RNA
• 24-31 nucleotides long
• ~15000 types, most diverse family of RNA
• Processed from long RNA precursor transcribed from piRNA cluster
loci
• Limit transposition of transposons in germ-line cells in mammals
• Control gene expression
• Bind to Piwi protein in RNA interference pathway

60. siRNA: Endogenous
• Long DS RNA in mammalian cells
• Can cause non-specific gene silencing
• ~>10000 types found in mouse oocyte
• Arise from natural dsRNA in cell, also due to transcription of
pseudogenes i.e. antisense equivalent of mRNA produced by parent
gene

61. Other medium to large regulatory ncRNA
• Kilobases long
• Antisense transcripts do not undergo splicing, regulate overlapping
sense transcripts
• Many types can undergo splicing, capping, polyadenylation, but no
translation
• Some contain internal ncRNAs like snoRNA or piRNA
• Can affect gene expression by chromatin-modification

62. Role of ncRNA in epigenetic regulation:
• XIST gene encodes long ncRNA that regulates X-chromosome
inactivation in female mammals [Xq13]
• H19RNA plays a role in repressing transcription of either paternal or
maternal allele of many autosomal regions i.e. imprinting [11p15]
• PEG3RNA plays a role in tumour suppression by activating P53, and is
maternally imprinted [19q13]
• The long mRNA like ncRNA are regulated by genes that produce long
antisense ncRNA transcripts that do not undergo splicing
• HOX gene cluster of 39 genes encode ~231 different long ncRNA

63. Overlapping genes & Genes within genes
• G-C rich or pale bands on GTG are gene rich, gene density is varied among
different chromosomes – what is the mechanism?
• 6p21.3: HLA complex; 180 protein coding genes over 4Mb
• Xp21.2; dystrophin gene extends over 2.4Mb on dark band,
• ~9% of human genes overlap another genes
• Majority of overlapping genes transcribe from opposite strands
• Protein coding genes can share common promoter, transcription can take
place in opposite direction (e.g.…. ), or in same direction (e.g. multigenic or
polycistronic, Insulin A and B chains) in some cases
• Different proteins by overlapping transcription units
• RNA genes overlap protein coding genes

64. GTG [G banding by Giemsa Trypsin] banded Metaphase cell
Trypsin treatment- digests chromatin protein
 increase access to Giemsa stain - Higher
access in
AT rich regions [two Hydrogen bonds] as
compared to
GC rich regions [three Hydrogen bonds]

65. Gene families
•Sequence and structure similarities among two or
more proteins suggest evolutionary relationship
and relatedness that may be minimal or significant
•These genes can arise due to tandem duplications
•These genes can be clustered together on a same
chromosome location or can be dispersed over
different regions which may be due to translocation
or inversion

66. Gene families
•Genes coding for proteins taking part in similar
functional pathways but very little sequence similarity,
and are dispersed over different chromosomal locations
•Examples:
• Insulin on 11p & Insulin receptor on 19p
• Ferritin heavy chain on 11q & Ferritin light chain on 22q
• Steroid 11-hydroxylase on 8q & Steroid 21-hydroxylase on 6p
• JAK1 on 1p & STAT1 on 2q

67. Pseudogenes & Gene fragments
• A defective gene that contains multiple exons of a functional gene is
known as pseudogene
• A defective gene containing only one exon or very limited sequence is
known as gene fragment

68. One-Gene-One-Enzyme,
Pseudogenes
& Common Ancestry
The following animation is intended to show:
1. The one-gene-one-enzyme hypothesis
2. How a mutation in one gene (probably in some
early pre-primate) prevented the production of
Vitamin C, explaining why all primates today
require Vitamin C in their diets (not so with
other mammals).
3. The GULO pseudogene evidence for the
common ancestry of primates [Gene coding for
enzyme L-gulonolactone oxidase]
68

69. What’s a Pseudogene?
A pseudogene is a DNA sequence that is nearly
identical to that of a functional gene, but contains
one or more mutations, making it non-functional.
Much of the intron material in the genomes of
organisms is composed of recognizable
pseudogenes.
69

70. Pseudogenes and Vitamin C
Gene 1
Enzyme 1
Gene 2
Enzyme 2
Gene 3
Enzyme 3
D
B C Vitamin C
A
GULO
gene
Gulo Enz
Vitamin C
Not so in primates…
Portion of Working GULO Gene in Rat:
Matching GULO Pseudogenes in 4 Primates Note Deletion
In most mammals
70

71. Analysis
• Any one of thousands of possible mutations in the several genes for
a biochemical pathway could explain why a particular species fails to
make a particular enzyme.
• What does this suggest about the fact that Vitamin C production is
blocked in several similar species by the exact same mutation in the
Gulo gene?
• Maybe common ancestry?
71

72. Vitamin C, GULO Pseudogenes
& Primate Evolution
72
Cladogram showing sequence of
branching, based on
the decreasing number of
additional mutations found in the
species moving upwards and to
the left.

73. Note Simplification
In this presentation, three adjacent DNA segments (genes) were shown
as necessary for Vitamin C to be formed.
In reality, there can be more genes (or fewer), and they may not be
adjacent, or even in the same chromosome.
73

74. Pseudogenes: Vitamin C
& Common Ancestry
74

75. Gene: Evolving definitions from hypothetical
to functional to operational
1
Gene
1 Trait
1
Enzyme
1 Polypeptide
1 Transcript
Gregor Mendel, 1866
Archibald Garrod,
1900
George W. Beadle &
Edward L. Tatum,
1940
Encoding RNA as
final product

76. Genes, basic functional units, but what is the
elementary structural unit?: Nucleotides
• 1940s: Clarence Oliver; Recombination within gene reported leading to
acceptance of concept that nucleotides are the subunits, lozenge gene
in Drossophila
• Cis- Trans or Complementation test in Drossophila (Edward Lewis) and
bacteriophage T4 (Seymour Benzer) demonstrated that if two
independent mutations are located in the same gene or in two
different genes, and fits into one-gene one-polypeptide concept
• Archibald Garrod, 1900: Inborn errors of metabolism

77. • Archibald Garrod: Inborn errors of metabolism, example of
Alkaptonuria [his definition, one mutant gene  one metabolic block]
• George Beadle & Boris Ephrussi on Drossophila (1930s); Beadle &
Edward Tatum on Neurospora Crassa: One gene  one enzyme using
X-ray irradiation of spores and growth on complete medium, Nobel
prize in 1958

78. Enzymes or Proteins that are hetero multimeric:
Tryptophan synthetase, Haemoglobin
• Alpha polypeptide:
Gene on chromosome 16q13
• Beta polypeptide:
Gene on chromosome 11q13

79. 台大農藝系 遺傳學 601 20000 Chapter 4 slide 83
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
Fig. 4.10 The hemoglobin molecule

80. Beads-on-a-string assume
• gene as a unit of function
Controlled inheritance of a character or an attribute of phenotype
• gene as a unit of structure
Unit of genetic information not sub-divisible by recombination
Unit of genetic material capable of independent mutation

81. Beads-on-a-string proved wrong as recombination
within a gene was reported: Clarence P. Oliver, 1940
• Drossophila X chromosome – Lozenge locus studied for two
mutations lzs (spectacle eyes) or lzg (glassy eyes) that were thought to
be alleles i.e. different forms of the same gene
• Cross between the two resulted in F1 with 0.2% WT progeny 
revertants? Not possible as; frequency of reversion from lzg or lzs to
WT was less than 0.2% in lozenge hemizygous males & secondly,
when the female lzs/lzg heterozygote carried genetic markers
bracketing the loznge locus, the progeny with WT eyes always carried
X chromosome with lz+ flanked by recombinant markers always in
same combination

82. Beads-on-a-string proved wrong as recombination
within a gene was reported: Seymour Benzer
• Bacteriophage T4: Study of rIIA locus showed 199 sites of
recombination or mutable sites indicated gene as a sequence of
nucleotide pairs
• E. Coli: Study of trypA gene auxotrophs
268 AA seq. of alpha polypeptide of tetraheteromer of 2 alpha and 2
beta chains was determined; frequency of revertants of mutants and
comparison with WT done for various auxotrophs indicated the unit
of genetic material not divisible by recombination is single nucleotide
pair

83. Circular / Linearized PhiX 174 genome with gene
and intergenic regions and overlapping portion of
certain gene

84. Collinearity between genetic coding
sequence and polypeptide product

85. Bacteriophage øX174: Overlapping Genes &
Genes within genes
•5386 nucleotide- 11 genes- 2300 amino
acids
•5386/3 1795 amino acids expected [500
lesser than observed]

86. Multi-gene families
•More than one locus producing same or similar
protein
•Advantage when large amount of product
required at high rate in short time
•Examples: Actin gene in Dictyostelium
Discoidium; 10% of total protein in aggregation
stage, none later
•~17 different dispersed loci identified

87. Pseudo-gene
• Similar gene sequences not translated into protein

89. • An important example of a programmed recombination event that occurs during development is
the generation of immunoglobulin genes from gene segments that are separate in the genome.
Immunoglobulins (or antibodies), produced by B lymphocytes, are the foot soldiers of the
vertebrate immune system-the molecules that bind to infectious agents and all substances
foreign to the organism. A mammal such as a human is capable of producing many millions of
different antibodies with distinct binding specificities. However, the human genome contains only
about 100,000 genes. Recombination allows an organism to produce an extraordinary diversity of
antibodies from a relatively small amount of DNA-coding capacity.
• Vertebrates generally produce multiple classes of immunoglobulins. To illustrate how antibody
diversity is generated, we will focus on the immunoglobulin G (IgG) class from humans.
Immunoglobulins consist of two heavy and two light polypeptide chains (Fig. 24-38a).Each chain
has a variable region with a sequence that differs greatly from one immunoglobulin to the next,
and another region that is virtually constant within a class of immunoglobulins. There are also
two distinct families of light chains, called kappa and lambda, which differ somewhat in the
sequences of their constant regions. For each of the three types of polypeptide chain (heavy
chain, and kappa or lambda light chain), diversity in the variable regions is generated by a similar
mechanism. The genes for these polypeptides are divided into segments, and clusters containing
multiple versions of each segment exist in the genome. One version of each segment is joined to
create a complete gene.

90. Example of a
multi-gene family

91. In vitro culture media can be minimal or
complete, with or without serum
Minimal Medium
• Contain only inorganic salts, a
simple sugar, one vitamin i.e.
Biotin
Complete Medium
• Minimal medium supplemented
with all amino acids, purines,
pyrimidines, and vitamins

92. Genomic Medicine
Thus far, most success in identifying genomic
contributions to common disorders has been
for low frequency, high penetrance alleles; for
example:
• HNPCC (colon cancer)
• BRCA1 and 2 (breast and ovarian cancer)
• MODY 1,2,3 (diabetes)
• Alpha-synuclein (Parkinson Disease)

93. Genomic Medicine
But, on a population basis, most genomic
contributions to common disorders are from
high frequency, low penetrance alleles; for
example:
• APC I1307K and colon cancer
• ApoE and Alzheimer disease
• Factor V Leiden and thrombosis
• CCR5 and HIV resistance

94. Lesson Four
Structure of a Gene

95. Gene Structure
• What is a gene?
• Gene: a unit of DNA on a
chromosome that codes for a
protein(s)
– Exons
– Introns
– Promoter sequences
– Terminator sequences
• Other regulatory sequences (enhancers,
silencers), which may be far from major
components of a gene

96. Gene Structure
• Exons: contain the bases that are utilized in
coding for the protein
• Introns: contain bases that are not utilized in
coding for proteins and intervene between the
exons
– Introns are spliced out

97. Gene Structure
• Promoter: bases that provide a
signal to tell the cell’s machinery
where to begin transcription,
usually before or within a gene
• Terminator: bases that provide a
signal to tell the cell’s machinery
where to stop transcription, usually
at the end of a gene

98. Translation Requires Different
Types of DNA
• mRNA: messenger RNA; major product
of transcription
– Represents the code for the primary amino
acid sequence of a protein
– Only type of RNA that is translated
• tRNA: transfer RNA
– Recognizes the mRNA code (tri-nucleotide)
and brings with it (or transfers) the
appropriate amino acid to the protein
– Link between mRNA and protein
• rRNA: ribosomal RNA
– Part of the ribosomes
– Involved with translation by helping to align
the mRNAs and tRNAs

116. Protein Processing
Final transport

117. Primary control of gene
expression
Genomics to Proteomics

118. Lesson Seven
Mutations

119. Point Mutations
• Involves a single base pair
– Substitution, insertion, deletion
– SNPs
• May not affect amino acid sequence
– Same sense (silent, neutral, synonymous, same
sense)
– Due to redundancy of the genetic code
• May affect amino acid sequence
(nonsynonymous)
– Missense (results from a change in an amino
acid)
– Nonsense (results from a change to a stop
codon – truncated protein)
– Frame shift mutations (insertion or deletion of
1+ bases - alters the reading frame)

120. Missense Mutation
Sickle Cell Anemia

122. Gene Structure
• A typical gene might look something like this:
• This gene has 3 exons and 2 introns
----------
----------
= exon
= intron
= promoter
= terminator

123. The Human Genome
• the human genome consists of ~3 billion bp
and 30,000-35,000 genes (haploid state)
• it would fill about 150,000 phone book
pages with A’s, T’s, G’s, and C’s
• a disorder can be caused by variation in
one or more base pairs (among the 3
billion)
• the challenge is partly one of scale (needle
in a haystack)

124. The Human Genome
• Human genome 3 billion bp
• Average chromosome 150 million bp
• Average gene 50 thousand bp
• Average coding sequence 3 thousand bp
• Unit of the genetic code 3 bp
• Genetic variation variable

125. • Content:
• Human Chromosomes: Structure, number and classification, methods of chromosome preparation, banding patterns.
Chromosome abnormalities, Autosomal abnormalities – syndromes, Sex chromosomal abnormalities – syndromes,
Molecular and Cytogenetics.
• Organization of human genome and genes: General organization of human Genome-Nuclear and Mitochondrial,
Mitochondrial Genome organization, Mitochondrial mutations and myopathies. Size and banding of human
chromosomes; distribution of tandems and interspersed repetitive DNA, Gene distribution and density in human
nuclear genome, Organization of genes: rRNA encoding Genes, mRNA encoding Genes, small nuclear RNA genes,
Overlapping genes, genes within genes, multigene families, pseudo genes, truncated genes and gene fragments
• Gene mapping: Mapping: physical and genetic; Strategies in identifying human disease genes: Human Genome project
– History and Reality; Techniques and Technology involved in genome mapping- low and high resolution mapping ;
Strategies and milestones in mapping and sequencing of human genome approaches to physical and genetic mapping
; Principles and strategies for identifying unknown disease or susceptibility genes; Beyond genomics – the physical
and genetic mapping the post genomic era.
• Animal Models For Human Diseases: Potential of using animal models for human diseases: why animal models? ,
Types of animal models, Transgenic animals – what are they and procedures of production, detection and use in the
study of different diseases, Genes in Pedigrees, Complex diseases transgenic animals to model complex diseases.
• Molecular Cytogenetics: Molecular cytogenetic techniques, Fluorescence in situ hybridization using various types of
probes, applications of Multiplex-FISH, comparative genomic hybridization, and microarray.
• Data Mining In Genetics Research And Clinical Management: Introduction to Internet based cataloguing of Genetic
Aberrations in various diseases including Cancer, OMIM, Mitelman database of chromosome aberrations in cancer,
Borgaonkar database of chromosomal variations in man, London Dysmorphology Database, Human Variome project,
Human Phenome project, Encode project.