introductory lecture - csw.uobaghdad.edu.iq

Department of biology 2018-2019 1 st semester
3 rd
Introductory lecture:
Genetics is defined as the science that deals with heredity and
variation in organisms, including the genetic features and constitution of
a single organism, species, or group, and with the mechanisms by which
they are affected. The term genetics was proposed by the English
biologist William Bateson In 1906.
The classical principles of genetics were deduced by Gregory Mendel
in 1865, on the basis of the results of breeding experiments with peas.
Mendel studied the inheritance of a number of well-defined traits, such as
seed color, and was able to deduce general rules for their transmission. In
all cases, he could correctly interpret the observed patterns of inheritance
by assuming that each trait is determined by a pair of inherited factors,
which are now called genes. These factors are transmitted from one plant
generation to the next in a predictable pattern, each factor being
responsible for an observable trait. The trait one can observe is the
phenotype. The underlying genetic information is the genotype. The term
gene for this type of a heritable factor was introduced in 1909 by the
Danish biologist Wilhelm Johannsen (1857–1927). Theodor Boveri
(1862–1915), recognized the genetic individuality of chromosomes in
1902.
Genetics became an independent scientific field in 1910 when
Thomas H. Morgan introduced the fruit fly (Drosophila melanogaster)
for systematic genetic studies and showed that genes are arranged on
chromosomes in sequential order. Morgan summarized this in 1915 in the
chromosome theory of inheritance. This theory proposed that hereditary
factors responsible for Mendelian inheritance are located on the
chromosomes within the nucleus. This field is known as a Classic
(Mendelian) genetics.
Population genetics as a new genetic field was found as a result of the
work of the English mathematician G.H. Hardy and the German
physician W. Weinberg independently who recognized, in 1908 that
College of science for women Genetics lecture (1)
3 rd
Mendelian inheritance accounts for certain regularities in the genetic
structure of populations. Their work contributed to the successful
introduction of genetic concepts into plant and animal breeding.
Figure ( 1): Phenotype of several traits in pea.( Weinberg, Robert A. , 2014, The
biology of cancer , 2 nd
edition)
The double helix structure of DNA molecule was deduced by Watson
and crick in 1953, this structure elucidated the replication of DNA and
how could the DNA store the genetic information.
Importance of genetics:
In the last century, genetics has become an important biological tool,
using mutants to gain an understanding of specific processes. This work
has included:
b. Analyzing evolutionary processes.
d. Mapping genes.
F. Analyzing molecular features of genes and regulation of gene
expression
3 rd
1. Genetic material of both eukaryotes and prokaryotes is DNA
(deoxyribonucleic acid). Many viruses also have DNA, but some have
RNA genomes instead.
2. DNA has two chains, each made of nucleotides composed of a
deoxyribose sugar, a phosphate group and a base. The chains form a
double helix.
3. There are four bases in DNA: A (adenine), G (guanine), C (cytosine)
and T (thymine).
b. The sequence of bases determines the genetic information.
c. Genes are specific sequences of nucleotides that pass traits from
parents to offspring.
4. Genetic material in cells is organized into chromosomes (literally
“colored body” because it stains with biological dyes).
a. Prokaryotes generally have one circular, super coiled chromosome.
b. Eukaryotes generally have:
i. Linear chromosomes in their nuclei, with different species having
different numbers of chromosomes.
ii. DNA in organelles (e.g., mitochondria and chloroplasts) that is usually
a circular molecule
3 rd
class
Figure (2): the double helix structure of DNA proposed by Watson and Crick in 1953.
(Russell ,P. , I Genetics, a molecular approach , 3 rd
edition , 2009, edited by Yue-
Wen Wang. Pearsons,USA).
Branches of genetics
1- Mendelian (classic) genetics: deals with transmission (movement)
of genes and genetic traits from parents to offspring, and with
genetic recombination.
2- Population genetics: studies heredity in groups for traits determined
by one or a few genes.
3- Quantitative genetics: studies group hereditary for traits determined
by many genes simultaneously.
4- Human genetics: is the study of inheritance as it occurs in human
beings.
5- Medical genetics is the branch of medicine that involves the
diagnosis and management of hereditary disorders.
a- Cytogenetic is the study of the structure, the behavior of
the chromosomes and chromosome abnormalities
b- Biochemical genetics: Metabolic (or biochemical) genetics
involves the diagnosis and of inborn errors of metabolism in
3 rd
metabolism of carbohydrates, amino acids, and lipids
c- Cancer genetics.
of mitochondrial disorders, which have a molecular basis but
often result in biochemical abnormalities due to deficient in
energy production.
e- Developmental genetics: is the study of the process by which
animals and plants grow and develop.
f- Genetic counseling: Genetic counseling is the process of
providing information about genetic conditions, diagnostic
testing, and risks in other family members.
6- Molecular genetics: deals with the molecular structure and function
of genes.
7- Microbial genetics. It studies the genetics of very small (micro)
organisms; bacteria, archaea, viruses and some protozoa and
fungi. This involves the study of the genotype of microbial species
the phenotypes.
organism's genome using biotechnology.
studies:
Many organisms are used in genetic research. Desirable qualities for
an experimental organism include:
a. A well-known genetic history.
b. A short life cycle so generations can be studied in a relatively.
c. A large number of offspring from each mating.
d. Ease of growing and handling the organism.
e. Marked genetic variation within the population.
3 rd
Prokaryotic cells (bacteria) are typically rod shaped or spherical with
few micrometers in diameter, without a nucleus or special internal
structures. Within a cell wall consisting of a bilayered cell membrane,
most of bacteria contain an average 1000–5000 genes tightly packed in a
single super-coiled circular molecule of DNA. In addition, they usually
contain small circular DNA molecules named plasmids.
Eukaryotic Cells:
genetics are:
i. Centrioles (basal bodies) are in cytoplasm of nearly all animals,
but not in most plants. In animals, a pair of centrioles is
ii. Associated with the centrosome region of the cytoplasm where
spindle fibers are organized in mitosis or meiosis.
ii. The endoplasmic reticulum (ER) is a double membrane system that
runs through the cell. ER, with ribosome attached, collects proteins that
will be secreted from the cell or localized to an organelle.
iii. Ribosome synthesizes proteins, either free in the cytoplasm or
attached to the cytoplasmic side of the ER.
iv. Mitochondria are large organelles surrounded by double membrane
that play a key role in energy processing for the cell. They contain their
own DNA encoding some mitochondrial proteins, rRNAs and tRNAs.
v. Chloroplasts are photosynthetic structures that occur in plants. The
organelle has a triple membrane layer, and includes a genome encoding
some of the genes needed for organelle functions.
Eukaryotes have multiple linear chromosomes in a number characteristic
of the species. These chromosomes located in the nucleus which
College of science for women Genetics lecture (1)
3 rd
class
surrounded by the nuclear membrane. Most have two versions of each
chromosome, and so are diploid (2N).
a. Diploid cells are produced by haploid (N) gametes that fuse to form a
zygote. The zygote then undergoes development, forming a new
individual.
b. Examples of diploid organisms are humans (23 pairs) and Drosophila
melanogaster (4 pairs). The yeast Saccharomyces cerevisiae is haploid
(16 chromosomes).
of Genetics, 3rd edition , 2007, Thieme).
College of science for women Genetics Lecture (2)
3 rd
The Search for the Genetic Material:
In the early 1900s, chromosomes were shown to be the carriers of
hereditary information. In eukaryotes they are composed of both DNA
and protein, and most scientists initially believed that protein must be the
genetic material.
The transmission and behavior of the abstract factors of Mendel and the
physical behavior of chromosomes in mitosis, meiosis, and fertilization
led Sutton, Roux and Boveri proposed the chromosome theory of
inheritance.
As the Chromosome consists of protein and nucleic acid,
So the question was what is the genetic material? Is it the protein or
it is the nucleic acid ?
In the present facts of that:
Protein consists of 20 kinds of amino acid
Nucleic acids consist of 4 kinds of nucleotides
Complexity of life very complicated protein or nucleic acid
to account for the level of complexity?
Griffith’s Transformation Experiment
pneumoniae bacteria in mice showed that something passed from
dead bacteria into nearby living ones, allowing them to change
their cell surface.
2- He called this agent the transforming principle, but did not know
what it was or how it worked.
3 rd
class
Figure 1: Griffith’s transformation experiment, (Russell ,P. , I Genetics, a molecula
approach , 3 rd
A landmark experiment clearly pointing to DNA as the genetic
material was reported in 1944 by Oswald Avery, Colin MacLeod, and
Maclyn McCarty.
3 rd
Avery’s Transformation Experiment:
1. In 1944, Avery, MacLeod and McCarty published results of a study
that identified the transforming principle from S. pneumoniae. Their
approach was to break open dead cells, chemically separate the
components (e.g., protein, nucleic acids) and determine which was
capable of transforming live S. pneumoniae cells.
2. Only the nucleic acid fraction was capable of transforming the bacteria.
3. Critics noted that the nucleic acid fraction was contaminated with
proteins. The researchers treated this fraction with either RNase or
protease and still found transforming activity, but when it was treated
with DNase, no transformation occurred, indicating that the transforming
principle was DNA.
Figure 2: Experiment that showed that DNA, not RNA, was the transforming
principle. (Russell ,P. , I Genetics, a molecula approach , 3 rd
edition , 2009,
3 rd
material came in 1953 with Alfred
Hershey and Martha Chase’s work on E.
coli infected with bacteriophage T2.
2. In one part of the experiment, T2
proteins were labeled with 35
S, and in the
P.
Then each group of labeled viruses was mixed separately with the E. coli
host. After a short time, phage attachment was disrupted with a kitchen
blender, and the location of the label determined.
3. The 35
S-labeled protein was found outside the infected cells, while the 32
P-labeled DNA was inside the E. coli, indicating that DNA carried the
information needed for viral infection. This provided additional support
for the idea that genetic inheritance occurs via DNA.
figure 3: Lytic life cycle of a virulent phage, such as T2, ( Russell ,P. , I Genetics, A molecula
approach , 3 rd
3 rd
edition , 2009, edited by Yue-Wen Wang.
Pearsons,USA.)
3 rd
• TMV ( tobacco mosaic virus)
• Infected tobacco plant with purified RNA typical virus-infected
lesion
• RNA treated with RNAase then injected into tobacco not lesion
• 1957 Heinz Fraenkel-Conrat and B. Singer reconstitue the RNA of
one type with the protein of the other type and vice versa and
injected to two tobacco plants the progeny viruses isolated from
the resulting lesion were the type specified by the RNA, not by
the protein.
Pearsons,USA.
3 rd
1. DNA and RNA are polymers composed of monomers called
nucleotides.
a. A pentose (5-carbon) sugar.
b. A nitrogenous base.
c. A phosphate group.
3. The pentose sugar in RNA is ribose, and in DNA it’s deoxyribose.
where RNA has a hydroxyl (OH) group, while DNA has only a
hydrogen at the sugar carbon 2.
Figure (1): The Structure of Nucleotide. (Hardin,J. ; G. Bertoni And L. J. Kleinsmith,
World Of The Cell, 8 Th Edition, 2012, Beakers)
There are two classes of nitrogenous bases:
a. Purines (double-ring, nine-membered structures) include
adenine (A) and guanine (G).
b. Pyrimidines (one-ring, six-membered structures) include
cytosine (C), thymine (T) in DNA and uracil (U) in RNA.
3 rd
class
Figure (2): The compositions of nitrogen base in nucleic acids.( Russell,P. ,
I Genetics, a molecula approach , 3 rd
Pearsons,USA).
5. The structure of nucleotides has these features:
a. The base is always attached by a covalent bond between the 1′ carbon
of the pentose sugar and a nitrogen in the base (specifically, the nine
nitrogen in purines and the one nitrogen in pyrimidines).
b. The sugar-base combination is a nucleoside. When a phosphate is
added (always to the 5′ carbon of the pentose sugar), it becomes a
nucleoside phosphate, or simply nucleotide.
6. Polynucleotides of both DNA and RNA are formed by stable covalent
bonds (phosphodiester linkages) between the phosphate group on the 5′
carbon of one nucleotide, and the 3′ hydroxyl on another nucleotide. This
creates the “backbone” of a nucleic acid molecule.
7. The a symmetry of phosphodiester bonds creates 3′-5′ polarity within
the nucleic acid chain.
3 rd
1. James Watson and Francis Crick published the famous double-helix
structure in 1953. When they began their work, it was known that DNA is
composed of nucleotides, but how the nucleotides are assembled into
nucleic acid was unknown. Two additional sources of data assisted
Watson and Crick with their model:
a- Three years before Watson and Crick proposed their essentially
correct three-dimensional structure of DNA as a double helix, Erwin
Chargaff developed a chemical technique to measure the amount of each
base present in DNA. As we describe his technique, we will let the molar
concentration of any base be represented by the symbol for the base in
square brackets; for example, [A] denotes the molar concentration of
adenine. Chargaff used his technique to measure the [A], [T], [G], and
[C] content of the DNA from a variety of sources. He found that the base
composition of the DNA, d efined as the percent G + C, differs among
species but is constant in all cells of an organism and within a species.
Chargaff also observed certain regular relationships among the molar
concentrations of the different bases. These relationships are now called
Chargaff's rules:
• The amount of adenine equals that of thymine: [A] = [T].
• The amount of guanine equals that of cytosine:[G] = [C]
• The amount of purine base equals that of pyrimidine bases:
b. Rosalind Franklin’s X ray diffraction images of DNA showed a helical
structure with regularities at 0.34 nm and 3.4 nm along the axis of the
molecule.
3 rd
class
Figure ( 3): Watson and Crick, showing their DNA double helix model,( to the left),
Rosalind Franklin , (to the right). (Russell ,P. , I Genetics, a molecula approach , 3 rd
edition , 2009, edited by Yue-Wen Wang. Pearsons,USA and . Hardin,J. ; G. Bertoni
And L. J. Kleinsmith, World Of The Cell, 8 Th Edition, 2012, Beakers).
figure(4 ): X-ray diffraction analysis of DNA, (Russell ,P. , I Genetics, a molecula
approach , 3 rd
edition , 2009, edited by Yue-Wen Wang. Pearsons,USA)
2. Watson and Crick’s three-dimensional model has these main features:
a. It is two polynucleotide chains wound around each other in a right-
handed helix.
b. The two chains are anti-parallel.
c. The sugar-phosphate backbones are on the outside of the helix, and the
bases are on the inside, stacked perpendicularly to the long axis like the
steps of a spiral staircase.
3 rd
class
Figure(5): DNA double helix structure.( Russell ,P. , I Genetics, a molecula approach
, 3 rd
d. The bases of the two strands are held together by hydrogen bonds
between complementary bases (two for A-T pairs and three for G-C
pairs). Individual H-bonds are relatively weak and so the strands can be
separated (by heating, for example). Complementary base pairing means
that the sequence of one strand dictates the sequence of the other strand.
Figure(6): the base paring of DNA ant parallel strands.( Russell ,P. , I Genetics, a
molecula approach , 3 rd
3 rd
class
e. The base pairs are 0.34 nm apart, and one full turn of the DNA helix
takes 3.4 nm, so there are 10 bp in a complete turn. The diameter of a
dsDNA helix is 2 nm.
f. Because of the way the bases H-bond with each other, the opposite
sugar-phosphate backbones are not equally spaced, resulting in a major
and minor groove. This feature of DNA structure is important for protein
binding.
Different DNA Structures:
• X ray diffraction studies show that DNA can exist in different
forms .
a. A-DNA is the dehydrated form, and so it is not usually found in cells.
It is a right-handed helix with 10.9 bp/turn, with the bases inclined 13°
from the helix axis. A-DNA has a deep and narrow major groove, and a
wide and shallow minor groove.
b. B-DNA is the hydrated form of DNA, the kind normally found in cells.
It is also a right-handed helix, with only 10.0 bp/turn, and the bases
inclined only 2° from the helix axis. B-DNA has a wide major groove and
a narrow minor groove, and its major and minor grooves are of about the
same depth.
c. Z-DNA is a left-handed helix with a zigzag sugar-phosphate backbone
that gives it its name. It has 12.0 bp/turn, with the bases inclined 8.8°
from the helix axis. Z-DNA has a deep minor groove, and a very shallow
major groove. Its existence in living cells has not been proven.
3 rd
• All known cellular DNA is in the B form.
• A-DNA would not be expected because it is dehydrated and cells
are aqueous.
• Z-DNA has never been found in living cells, although many
organisms have been shown to contain proteins that will bind to Z-
DNA.
Viral genome:
1. A virus is nucleic acid surrounded by a protein coat. The nucleic
acid may be dsDNA, ssDNA, dsRNA or ssRNA, and it may be
linear or circular, a single molecule or several segments.
2. Bacteriophages are viruses that infect bacteria. Three different
types that infect E. coli are good examples of the variety of
chromosome structure found in viruses.
Prokaryotic genome:
In prokaryotes the genome is usually a single, circular, and
supercoiled chromosome. In eukaryotes, the genome is one complete
haploid set of nuclear chromosomes; mitochondrial and chloroplast
DNA are not included.
Eukaryotic genome :
1- Cellular DNA is organized into chromosomes. A genome is the
chromosome or set of chromosomes that contains all the DNA of
an organism.
2- Eukaryotic chromosomes are linear dsDNA, and by weight contain
about twice as much protein as DNA. The DNA-protein complex is
called chromatin, and it is highly conserved in all eukaryotes.
3 rd
Chromatin Structure:
1. Both histones and non-histones are involved in physical structure of
the chromosome.
2. Histones are abundant, small proteins with a net (+) charge. The
five main types are H1, H2A, H2B, H3 and H4. By weight,
chromosomes have equal amounts of DNA and histones.
3. Histones are highly conserved between species (H1 less than the
others).
4. Non-histone is a general name for other proteins associated with
DNA. This is a big group, with some structural proteins, and some that
bind only transiently.
5. Chromatin formation involves histones, and condenses the DNA so
it will fit into the cell. Chromatin formation has two components:
a. Two molecules each of histones H2A, H2B, H3 and H4 associate to
form a nucleosome core, and DNA wraps around it 1 3⁄4 times for a 7-
fold condensation factor. Nucleosome cores are about 11 nm in diameter.
b.H1 serves as the linker histone, connecting nucleosomes to create
chromatin with a diameter of 30 nm, for an additional 6-
foldcondensation. The exact mechanism used by H1 is unknown.
Figure(7): Nucleosome structure. .( Russell ,P. , I Genetics, a molecula approach , 3 rd
3 rd
Genetics, a molecula approach , 3 rd
Pearsons,USA)
3 rd
Euchromatin and Heterochromatin:
1. The cell cycle affects DNA packing, with DNA condensing for
mitosis and meiosis, and decondensing during interphase.
Chromosomes are most condensed at metaphase, when the looped
domains are further coiled and the chromatic has a diameter of about
700 nm. Non-histone proteins form the scaffold for this additional
condensation.
2. Staining of chromatin reveals two forms:
a. Euchromatin condenses and decondenses with the cell cycle. It is
actively transcribed, and lacks repetitive sequences. Euchromatin
accounts for most of the genome in active cells.
b. Heterochromatin remains condensed throughout the cell cycle. It
replicates later than euchromatin, and is transcriptionally inactive. There
are two types based on activity:
Centromeric and Telomeric DNA:
special functions.
2. Centromeres are the site of the kinetochore, where spindle fibers attach
during mitosis and meiosis. They are required for accurate segregation of
chromatids.
3. Telomeres are needed for chromosomal replication and stability.
Generally composed of heterochromatin, they interact with both the
nuclear envelope and each other. All telomeres in a species have the same
sequence. Simple telomeric sequences are short, species-specific and
tandemly repeated. (Examples: Tetrahymena is 5-TTGGGG-3, and
human is 5-TTAGGG-3).
3 rd
1. Watson and Crick DNA model implies a mechanism for
replication:
c. Make a complimentary copy for each strand.
2 .Three possible models were proposed for DNA replication:
a. Conservative model proposed both strands of one copy would be
entirely old DNA, while the other copy would have both strands of
new DNA.
b. Dispersive model was that dsDNA might fragment; replicate
dsDNA, and then reassemble, creating a mosaic of old and new
dsDNA regions in each new chromosome.
c. Semiconservative model is that DNA strands separate, and a
complementary strand is synthesized for each, so that sibling
chromatids have one old and one new strand. This model was the
winner in the Meselson and Stahl experiment.
Figure (1): Three models for the replication of DNA. (Russell, P., I Genetics, a molecular
approach , 3 rd
3 rd
The Meselson-Stahl Experiment:
1. Meselson and Stahl (1958) grew E. coli in a heavy (not radioactive)
isotope of nitrogen, 15
containing 15
N, and so can be
separated by CsCl density gradient centrifugation.
2. Once the E. coli were labeled with heavy 15
N, the researchers shifted the
cells to medium containing normal 14
N, and took samples at time points.
DNA was extracted from each sample and analyzed in CsCl density
gradients.
Figure(2 ): DNA replication models. (Russell ,P. , I Genetics, a molecular approach
, 3 rd
3 rd
N medium, all DNA had density
intermediate between heavy and normal. After two replication cycles, there
were two bands in the density gradient, one at the intermediate position, and
one at the position for DNA containing entirely 14
N.
4. Results compared with the three proposed models:
a. Does not fit conservative model, because after one generation there is a
single intermediate band, rather than one with entirely 15
N DNA and another
N DNA.
b. The dispersive model predicted that a single band of DNA of intermediate
density would be present in each generation, gradually becoming less dense
as increasing amounts of 14
N were incorporated with each round of
replication. Instead, Meselson and Stahl observed two bands of DNA, with
the intermediate form decreasing over time.
c. The semiconservative model fits the data very well.
Semiconservative DNA Replication in Eukaryotes:
To visualize DNA of eukaryotic chromosomes replicating, CHO (Chinese
hamster ovary) cells are grown in 5-bromodeoxyuridine (BUdR), a base
analog for thymine. After two rounds of replication, mitotic chromosomes
are stained with fluorescent dye and Giemsa stain.
Figure( 3): semi conservative model in Eukaryotic DNA. (Russell ,P. , I
Genetics, a molecular approach , 3 rd
Pearsons,USA).
3 rd
DNA Polymerases, the DNA Replicating Enzymes
1. All DNA polymerases link dNTPs into DNA chains .Main features of the
reaction:
a. An incoming nucleotide is attached by its 5’-phosphate group to the 3’-OH
of the growing DNA chain. Energy comes from the dNTP releasing two
phosphates. The DNA chain acts as a primer for the reaction.
b. The incoming nucleotide is selected by its ability to hydrogen bond with
the complementary base in the template strand. The process is fast and
accurate.
The properties of DNA polymerases:
a. DNA polymerase I is a single peptide encoded by polA and used for DNA
replication. Replicates DNA in the 5’3’ direction. Has 3’5’ exonuclease
activity to remove nucleotides from 3’ end of DNA or from an RNA primer.
b. DNA polymerase II is a single peptide encoded by polB. Used for DNA
repair.
c. DNA polymerase III has three polypeptide subunits in the catalytic core of
the enzyme: α (encoded by the dnaE gene), ε(dnaQ), and θ(holE).
Holoenzyme has an additional six different polypeptides. Replicates DNA in
the 5’3’ direction.
d. DNA polymerase IV is encoded by the dinB gene, and is used in DNA
repair.
e. DNA polymerase V is encoded by umuDC, and is used in DNA repair.
3 rd
Initiation of Replication
1. Replication starts when DNA at the origin of replication denatures to
expose the bases, creating a replication fork. Replication is usually
bidirectional from the origin. E. coli has one origin, oriC, which has:
a. A minimal sequence of about 245 bp required for initiation.
b. Three copies of a 13-bp AT-rich sequence.
c. Four copies of a 9-bp sequence.
2. Events in E. coli initiating DNA synthesis, derived from in vitro studies:
a. Initiator proteins attach. E. coli’s initiator protein is DnaA (from the dnaA
gene).
b. DNA helicase binds initiator proteins on the DNA, and denatures the AT-
rich region using ATP as an energy source.
c. DNA primase binds helicase to form a primosome, which synthesizes a
short (5–10nt) RNA primer.
3 rd
class
Figure(4 ): Model for the formation of a replication bubble at a replication origin in
E. coli and the initiation of the new DNA strand.( (Russell ,P. , I Genetics, a molecular
approach , 3 rd
3 rd
class
Model for the events occurring around a single replication fork of the E. coli
chromosome.
1. When DNA denatures at the oriC, replication forks are formed. DNA
replication is usually bi-directional, but will consider events at just one
replication fork:
a. Single-strand DNA-binding proteins (SSBs) bind the ssDNA formed by
helicase, preventing reannealing.
b. Primase synthesizes a primer on each template strand.
c. DNA polymerase III adds nucleotides to the 3’ end of the primer,
synthesizing a new strand complementary to the template, and displacing the
SSBs. DNA is made in opposite directions on the two template strands.
d. New strand made 5’ → 3’ in same direction as movement of the
replication fork is leading strand, while new strand made in opposite
direction is lagging strand. Leading strand needs only one primer, while
lagging needs a series of primers.
2. Helicase denaturing DNA causes tighter winding in other parts of the
circular chromosome. Gyrase relieves this tension.
3. Leading strand is synthesized continuously, while lagging strand is
synthesized discontinuously, in the form of Okazaki fragments. DNA
replication is therefore semidiscontinuous.
4. Each fragment requires a primer to begin, and is extended by DNA
polymerase III.
5. Okazaki data show that these fragments are gradually joined together to
make a full-length dsDNA chromosome. DNA polymerase I uses the 3’-OH
of the adjacent DNA fragment as a primer, and simultaneously removes the
RNA primer while resynthesizing the primer region in the form of DNA. The
nick remaining between the two fragments is sealed with DNA ligase.
3 rd
DNA Replication in Eukaryotes:
1. Eukaryotic chromosomes generally contain much more DNA than those of
prokaryotes, and their replication forks move much more slowly. If they
were like typical prokaryotes, with only one origin of replication per
chromosome, DNA replication would take many days.
2. Instead, eukaryotic chromosomes contain multiple origins, at which DNA
denatures and replication then proceeds bidirectionally until an adjacent
replication fork is encountered. The DNA replicated from a single origin is
called a replicon, or replication unit.
Figure(5):Temporal ordering of DNA replication initiation events in replication units of
eukaryotic chromosomes.( (Russell ,P. , I Genetics, a molecular approach , 3 rd
edition ,
3 rd
Eukaryotic replication enzymes
a. Three DNA polymerases are used to replicate nuclear DNA. Pol α (alpha)
extends the 10-nt RNA primer by about 30nt. Pol δ(delta) and Pol ε(epsilon)
extend the RNA/DNA primers, one on the leading strand and the other on the
lagging (it is not clear which synthesizes which).
b.Other DNA pols replicate mitochondrial or chloroplast DNA, or are used in
DNA repair.
Replicating the Ends of Chromosomes:
1. When the ends of chromosomes are replicated and the primers are
removed from the 5’ ends, there is no adjacent DNA strand to serve as a
primer, and so a single-stranded region is left at the 5’ end of the new
strand. If the gap is not addressed, chromosomes would become shorter
with each round of replication .
2. Most eukaryotic chromosomes have short, species-specific sequences
tandemly repeated at their telomeres. Blackburn and Greider have shown
that chromosome lengths are maintained by telomerase, which adds
telomere repeats without using the cell’s regular replication machinery.
3. In the ciliate Tetrahymena, the telomere repeat sequence is 5 TTGGGG-
3” .
a. Telomerase, an enzyme containing both protein and RNA, binds to the
terminal telomere repeat when it is single stranded, synthesizing a 3-nt
sequence, TTG.
b. The 3” end of the telomerase RNA contains the sequence AAC, which
binds the TTG positioning telomerase to complete its synthesis of the
TTGGGG telomere repeat.
c. Additional rounds of telomerase activity lengthen the chromosome by
adding telomere repeats.
4. After telomerase adds telomere sequences, chromosomal replication
proceeds in the usual way. Any shortening of the chromosome ends is
compensated by the addition of the telomere repeats.
3 rd
class
5. If the sequence of the telomerase RNA is mutated, telomeres will
correspond to the mutant sequence, rather than the organism’s normal
telomere sequence. Using an RNA template to make DNA, telomerase
functions as a reverse transcriptase called TERT (telomerase reverse
transcriptase).
6. Telomere length may vary, but organisms and cell types have
characteristic telomere lengths. Mutants affecting telomere length have
been identified, and data indicate that telomere length is genetically
controlled. Shortening of telomeres eventually leads to cell death,
and this may be a factor in the regulation of normal cell death.
Figure (6): Synthesis of telomeric DNA by telomerase. (Russell ,P. , I Genetics, a
molecular approach , 3 rd
3 rd
The flow of genetic information in cells generally proceeds from
DNA to RNA to protein.
DNA (more precisely, a segment of one DNA strand) first serves
as a template for the synthesis of an RNA molecule, which in most
cases then directs the synthesis of a particular protein.
Francis Crick (1956) named the principle of directional
information flow from DNA to RNA to protein by the central
dogma of molecular biology.
RNA that is translated into protein is called messenger RNA
(mRNA) because it carries a genetic message from DNA to the
ribosome, where protein synthesis takes place.
In addition to mRNA, two other types of RNA are involved in
protein synthesis: ribosomal RNA (rRNA) molecules, which are
integral components of the ribosome, and transfer RNA (tRNA)
molecules, which serve as intermediate molecules that translate the
coded base sequence of messenger RNA and bring the appropriate
amino acids to the ribosome.
There are four major types of RNA molecules:
o a. Messenger RNA (mRNA) encodes the amino acid
sequence of a polypeptide.
o b. Transfer RNA (tRNA) brings amino acids to ribosomes
during translation.
o c. Ribosomal RNA (rRNA) combines with proteins to form a
ribosome, the catalyst for translation.
o d. Small nuclear RNA (snRNA) combines with proteins to
form complexes used in eukaryotic RNA processing.
3 rd
regulatory elements associated with each gene.
• DNA unwinds in the region next to the gene, due to RNA
polymerase in prokaryotes and other proteins in eukaryotes. In
both, RNA polymerase catalyzes transcription.
Figure (1): Transcription process. (Hardin,J. ; G. Bertoni And L. J. Kleinsmith, World
Of The Cell, 8 Th Edition, 2012, Beakers)
• RNA is transcribed 5’-to-3’. The template DNA strand is read 3’-
to-5’. Its complementary DNA, the nontemplate strand, has the
same polarity as the RNA.
• RNA polymerization is similar to DNA synthesis (Figure 5.2),
except:
• b. No primer is needed to initiate synthesis.
• c. No proofreading occurs.
3 rd
Transcription is divided into three steps for both prokaryotes and
eukaryotes. They are initiation, elongation and termination.
A prokaryotic gene is a DNA sequence in the chromosome.
The gene has three regions, each with a function in transcription:
a. A promoter sequence that attracts RNA polymerase to begin
transcription at a site specified by the promoter.
b. The transcribed sequence, called the RNA-coding sequence. The
sequence of this DNA corresponds with the RNA sequence of the
transcript.
that specifies where transcription will stop.
Figure (2):Promoter, RNA-coding sequence, and terminator regions of a gene.
to bind to the promoter DNA sequence. Holoenzyme consists of:
• a. Core enzyme of RNA polymerase, containing four
polypeptides (two α, one β and one β’).
• b. Sigma factor (σ).
3 rd
• Sigma factor binds the core enzyme, and confers ability to
recognize promoters and initiate RNA synthesis. Without
sigma, the core enzyme randomly binds DNA but does not
transcribe it efficiently.
there are two types:
have two-fold symmetry that would allow a hairpin loop to
form (Figure 5.5). The palindrome is followed by 4-8U
residues in the trasncript, and together these sequences cause
termination, possibly because rapid hairpin formation
destabilizes the RNA-DNA hybrid.
the poly(U) region, and many also lack the palindrome. The
protein ρ is required for termination. It has two domains,
one binding RNA and the other binding ATP. ATP
hydrolysis provides energy for ρ to move along the transcript
and destablize the RNA-DNA hybrid at the termination
region.
Figure (3):Sequence of a -independent terminator and structure of the terminated
RNA. (Russell ,P. , I Genetics, a molecular approach , 3 rd
edition , 2009, edited by
3 rd
• Eukaryotes have three different polymerases, each transcribing a
different class of RNA. Processing of transcripts is also more complex
in eukaryotes.
a. RNA polymerase I, located in the nucleolus, synthesizes three of
the four rRNAs found in ribosomes: three of the RNAs (the 28S, 18S,
and 5.8S rRNA molecules).
messenger RNAs (mRNAs; translated to produce polypeptides) and
some small nuclear RNAs (snRNAs), some of which are involved in
R NA processing events.
c. RNA polymerase III, also located in the nucleoplasm, synthesizes
the transfer RNAs (tRNAs), which bring amino acids to the ribosome;
5S rRNA, the fourth rRNA molecule found in each ribosome; and the
small nuclear RNAs (snRNAs) not made by RNA polymerase II.
Transcription of Protein-Coding Genes by RNA
Polymerase II.
Promoters control the expression of protein-coding genes. The promoter
located upstream each gene and near the transcription start site. Examples
include:
the start point for transcription.
• ii. The initiator element (Inr), a pyramiding-rich
sequence near the transcription start site.
Higher levels are induced by activator factors that bind DNA sequences
called enhancers.
3 rd
• b. They function in either orientation.
• c. They function upstream, downstream or within the gene,
although they are usually located upstream.
• d. They may be several kb from the gene they control.
Eukaryotic mRNAs
modification. Transcription and translation are coupled in
the cytoplasm. Messages may be polycistronic.
• b. Eukaryotes modify pre-RNA into mRNA by RNA
processing. The processed mRNA migrates from nucleus to
cytoplasm before translation. Messages are always
monocistronic.
Figure (4);Processes for synthesis of functional mRNA in prokaryotes and eukaryotes.
3 rd
Eukaryotic pre-RNAs often have introns (intervening sequences)
between the exons (expressed sequences) that are removed.
5’ and 3’ Modifications by adding 7-methyl guanosine (m 7 G), to
the 5’ end using a 5’-to-5’ linkage. The cap is used for ribosome
binding to the mRNA during translation initiation.
The 3’ end of the pre-RNA has 50–250 adenines added
enzymatically to form a poly(A) tail. The poly(A) tail is important
in mRNA stability, and also plays a role in transcription
termination.
splicing.
include:
• b. Addition of the 5’ cap.
• c. Addition of the poly(A) tail.
• d. Splicing to remove introns.
• Events in splicing together two exons (designated 1 and 2) :
• a. cleavage occurs at the 5’ splice junction of exon 1 and the
intron.
• b. The G nucleotide at the free 5’ end of the intron joins with
a specific A nucleotide (18-38 nt upstream of the 3’ spice
junction) in the branch-point sequenc of the intron, forming
an RNA lariat structure.
• c. The bond forming the lariat is a 2’-5’ phosphodiester
linkage between the 5’ phosphate of the free guanine nt at
the end of introns, and the 2’ OH of the adenine nt in the
branch-point sequence.
3 rd
class
• d. The introns lariat is excised, and the exons are joined to
form a spliced mRNA. The intronsRNA is degraded by the
cell.
Figure(5):Details of intron removal from a pre-mRNA molecule. (Russell ,P. , I
Genetics, a molecular approach , 3 rd
Pearsons,USA).
1 st class 2018-2019 2
nd semester
Page 1
Chromosomal aberrations
Chromosomes are the units into which the genes are organized. In eukaryotic
cells each chromosome consists of arms, centromer and telomers. Centromer is
the point of attachment of the spindle during mitosis.
Chromosomes are classified as submetacentric, metacentric, or acrocentric
according to the location of its centromere. The centromere divides a
submetacentric chromosome into a short arm (p arm, derived from the French
petit) and a long arm (q, next letter after p). In metacentric chromosomes, the short
and long arms are equall in length. Acrocentric chromosomes carry as their short
arm a dense appendage called a satellite at the end of a stalk( ) .
Figure 1: chromosomes types.
In human chromosomes are arranged and numbered according to their length
into 22 pairs of chromosomes (autosomes) and 1 pair of sex chromosomes X and Y.
In females (karyotype 46, XX ) for males 46, XY). The arrangement of
chromosomes according to their length and their morphology under light
microscope, called chromosomal karyotype. The 22 pairs of autosomes in man are
divided into seven groups (A–G).
Figure2: karyogram human for male and female
Department of biology Genetics Lecture (6,7)
1 st class 2018-2019 2
nd semester
Page 2
Chromosomal aberration:
Chromosomal aberration: It's the change in chromosomes number or structure.
Change in chromosome number called numerical chromosomal aberration, and the
change in chromosome structure called structural chromosomal aberrations.
The normal human (diploid= 2n) cell has 2 sets of chromosomes, one set is
inherited from the mother and the other set is inherited from the father. The change
in normal number called Aneuploidy which is mean loss or gain of one or several
chromosomes, these conditions are fatal in infants or cause genetic syndromes.
Loss of chromosomes called monosomy and gain of chromosome called trisomy.
Both are resulted from chromosome frailer in separation during meiosis which is
known as nondisjunction in meosis I or II, leading to variation in chromosome
number in gametes and in the offspring arising from those gametes.
Figure 3: Mechanism of numerical aberration by chromosome nondisjunction during meiosis I or II.
Most common chromosomal syndromes in humans:
1 st class 2018-2019 2
nd semester
Page 3
Polyploidy is numerical chromosomal aberration is the triploidy=3n, and
tetraploidy=4n (all chromosomes set is triplicate or quadruplicate). Triploidy does
not result from nondisjunction at meiosis, but from one of a variety of other
processes.
1-Two sperms may have penetrated the egg (dispermia).
2-the egg or sperm may have an unreduced chromosome set as a result of
nondisjunction in the first or second meiotic division.
3-the second polar body may have reunited with the haploid egg nucleus.
Triploidy (3n) is one of the most frequent chromosomal aberrations in man, causing
17% of spontaneous abortions. Tetraploidy(4n) is rarer than triploidy.
figure 5: Triploidy
Structural chromosomal aberrations :
Mutations involving changes in chromosome structure occur in four common
types:
c. Inversions (changing orientation of a DNA segment).
d. Translocations (moving a DNA segment).
1 st class 2018-2019 2
nd semester
Page 4
All chromosome structure mutations begin with a break in the DNA, leaving
ends that are not protected by telomeres, but are “sticky” and may adhere to
other broken ends.
Chromosomal deletion (deficiency) arises from a single break with loss of the
distal fragment (terminal deletion) or from two breaks and loss of the intervening
segment (interstitial or intercalary deletion).
Figure 6: mechanism of deletion formation.
Duplications: result from doubling of chromosomal segments, and occur in a range
of sizes and locations. There are two types of dublication .
a. Tandem duplications are adjacent to each other.
b. Reverse tandem duplications result in genes arranged in the opposite order of
the original.
1 st class 2018-2019 2
nd semester
Page 5
Invertion : Inversion results when a chromosome segment excises and reintegrates
oriented 180° from the original orientation. There are two types
a. Pericentric inversions include the centromere.
b. Paracentric inversions do not include the centromere.
Figure 8: types of inversions.
Translocation: is a change in location of a chromosome segment is a translocation.
No DNA is lost or gained. Simple translocations are of two types:
a. Intrachromosomal, with a change of position within the same chromosome.
b. Interchromosomal, with transfer of the segment to a nonhomologous
chromosome.
1. If a segment is transferred from one chromosome to another, it is nonreciprocal.
2. If segments are exchanged, it is reciprocal.
Figure 9:types of Translocations.
3 rd
Mutation
A mutation defined as a change in a DNA base-pair sequence or in
chromosome number or structure.
- Mutation could be occurs in single base pair substitution (), deletion
() of one or more base pair, or as large alteration () or insertion ()
in the structure of the chromosome.
- Mutation may be occurs in protein coding region (exons) causing leading to
change protein structure and function, or it's occur in noncoding sequence
such as introns or regulatory regions of the gene.
- Mutation could occur in somatic cells and such mutation may cause change in
cell function or tumors and it's not inheritable. Other mutations may occur in
germ cell and those are heritable to next generation offering the bases for
genetic diversity and evolution. It may cause genetic diseases
Classification of mutations:-
1- According to the cause of mutation its classified into:-
A- Spontaneous M.: those mutations arise as a result of metabolic
activities of the cell that produces free radicals which change the
structure of nucleotides or its occurd during DNA replication.
B- Induced M.: those mutations results from exposure to external
mutagenic effect which could be natural (such as ultraviolet radiation
from the sun, cosmic raies, and radiation of isotopes in the ground), or
it could be Artificial (such as diagnostic X- ray, and synthetic
chemicals).
3 rd
grade 2018-2019 1 st semester
Mutation Rate : defined as the likelihood that gene will undergo a mutation in
single generation or in forming a single gamete. Mutation rate is very low for all
organisms and it's varied between species and varied within the same species
from gene to gene.
2-Classification based on location of Mutations:-
Mutations may be classified according to the cell type or chromosome locations
in which they occur. Somatic mutations are those occurring in any cell type
except germ cells. They not transmitted into the next generations, when a
recessive autosomal mutations masked by the dominant allele in the diploid cells,
but if the mutation in the dominant alleles it's expressed. In similar way the
dominant or X-linked somatic mutation will be more noticeable if they occur in
early development. The effect of mutated cells is attenuated by the very large
number of non mutated cells in the same tissue. While mutations occur in the
germ cells called germ line mutations.
Autosomal mutations: those mutations occur in the autosomal chromosomes.
While the mutations located on chromosome X or Y called X linked mutation or
Y linked mutations. Those mutations are more significant as they transmitted
into the future generations.
Classification based on type of molecular change:
The change of one base pair into another in a DNA molecule is classified as:
1- Point mutation its ocuures
a- Base substitution : when purine is replaced by another purin
(A>G) or a pyrimidine is replaced by pyrimidine (C>T) it's called
transition. When purine is replaced by pyrimidine (A> T) and vice
versa (C>G) it's called transversion. When one nucleotide
Department of biology Genetics Lecture (8)
3 rd
Figure(1): point mutation.
changed in the triplet within protein coding sequence of the gene, it may result
a different triplet that code for incorrect amino acid inserted to the synthesized
protein, this type is of mutation is called missense mutation, Leading to
genetic disease, like sickle cell anemia which caused by missense mutation
in β globine chain of the heamoglobine . heamoglobine consists of 4 chaines,
2α and 2β attached to heam group. sickle cell anemia resulting when
substation of A instead of T in the 6 th codon in the β chain , which results
in glutamic acid being substituted by valine at position 6. this mutation leads
to loss the folded shape of β globine chain and become unfolded leading to
change red blood cell shape to the crescent or sickle shape . These irregularly
shaped cells can get stuck in small blood vessels, and able to slow or block
blood flow and oxygen to parts of the body.
Figure(2): sickle cell anemia resulting from missense mutation in heamoglobine β chain.
3 rd
In other type of pint mutation is Nonsense Mutations when change of one base
pair leading to alter the codon signal to stop codon, thus shorter m RNA is
produced and resulting protein is truncated or nonfuctional.
The third type of point mutations is the Silent mutation, when the change leading
to insert the same amino acid in the protein and mutation effect is not detectable.
Its occur because several codons encode to the same amino acid, Eg: ATT, ATC,
and ATA all correspond to isoleucine, so when a mutation change the last
nucleotide (T) to C or A the resulting protein will remain same sequence and
functional.
2- Fram- Shift Mutations:
A frame-shift mutation results in the addition or deletion of nucleotides in the
DNA sequence. Three nucleotides (a triplet) are translated into an amino acid
3 rd
through the process of translation. The addition or subtraction of nucleotides will
shift the entire reading fram.
Causes of Mutations :
3 rd
Radiation (e.g., X rays and UV) induces mutations.
a. X rays are an example of ionizing radiation, which penetrates tissue
molecules, knocking.
commonly thymines (designated T^T) .
Repair of DNA Damage:
1. Both prokaryotes and eukaryotes have enzyme-based DNA repair systems that
prevent mutations and even death from DNA damage.
3 rd
2. Repair systems are grouped by their repair mechanisms. Some directly
correct, while others excise the damaged area and then repair the gap.
1.DNA polymerase proofreading corrects most of the incorrect nucleotide
insertions that occur during DNA synthesis, which stalls until the wrong
nucleotide is replaced with a correct one by its 3’-to-5’ exonuclease activity .
2.UV-induced pyrimidine dimers are repaired using photoreactivation (light
repair) by activates phtoreactivation enzyme to split the dimer.
phtoreactivation enzyme are found in prokaryotes and simple eukaryotes,
but not in humans.
3- Excision Repair
A: Base repair : Base excision repair uses a repair glycosylase enzyme to
recognize and remove damaged bases.
4- B:- Mismatch repair: Mismatch repair recognizes mismatched base
pairs, excises the incorrect bases and then carries out repair synthesis.
In E. coli, initial stages involve products of the mutS, mutL and mutH
genes.
i. MutS binds the mismatch, and determines which is the new strand by its
lack of methylation.
ii. MutL and MutH bind unmethylated GATC sequences (site of
methylation in E. coli) and bring the GATC close to the mismatch by
binding MutS.
iii. MutH then nicks the unmethylated GATC site, the mismatch is
removed by an exonuclease and the gap is repaired by DNA polymerase III
and ligase.
3 rd
Chromosomal aberrations
Chromosomes are the units into which the genes are organized. In eukaryotic
cells each chromosome consists of arms, centromer and telomers. Centromer
is the point of attachment of the spindle during mitosis.
Chromosomes are classified as submetacentric, metacentric, or acrocentric
according to the location of its centromere. The centromere divides a
submetacentric chromosome into a short arm (p arm, derived fromthe French
petit) and a long arm (q, next letter after p). In metacentric chromosomes, the
short and long arms are equall in length. Acrocentric chromosomes carry as their
short arm a dense appendage called a satellite at the end of a stalk( ) .
Figure 1: chromosomes types.
In human chromosomes are arranged and numbered according to their length
into 22 pairs of chromosomes (autosomes) and 1 pair of sex chromosomes X and
3 rd
Y. In females (karyotype 46, XX ) for males 46, XY). The arrengemnt of
chromosomes according to their length and their morphology under light
microscop, called chromosomal karyotype. The 22 pairs of autosomes in man are
divided into seven groups (A–G).
Figure2: karyogram human for male and female
Chromosomal aberration:
structure. Change in chromosome number called numerical chromosomal
aberration, and the change in chromosome structure called structural
chromosomal aberrations.
The normal human (diploid= 2n) cell has 2 sets of chromosomes, one set is
inherited from the mother and the other set is inherited from the father. The
change in normal number called Aneuploidy which is mean loss or gain of one or
several chromosomes, these conditions are fatal in infants or cause genetic
syndromes. Loss of chromosomes called monosomy and gain of chromosome
called trisomy. Both are resulted from chromosome frailer in separation during
meiosis which is known as nondisjunction in meosis I or II, leading to variation
in chromosome number in gametes and in the offspring arising from those
gametes.
3 rd
Figure 3: Mechanism of numerical aberration by chromosome nondisjunction
during meiosis I or II.
Most common chromosomal syndromes in humans:
3 rd
Figure 4: Pataue syndrome infant feture, and karyotype.
Polyploidy is numerical chromosomal aberration is the triploidy=3n, and
tetraploidy=4n (all chromosomes set is triplicate or quadruplicate). Triploidy
does not result from nondisjunction at meiosis, but from one of a variety of other
processes.
1-Two sperms may have penetrated the egg (dispermia).
2-the egg or sperm may have an unreduced chromosome set as a result of
nondisjunction in the first or second meiotic division.
3-the second polar body may have reunited with the haploid egg nucleus.
Triploidy (3n) is one of the most frequent chromosomal aberrations in man,
causing 17% of spontaneous abortions. Tetraploidy(4n) is rarer than triploidy.
3 rd
figure 5: polyploidy.
Structural chromosomal aberrations :
Mutations involving changes in chromosome structure occur in four common
types:
c. Inversions (changing orientation of a DNA segment).
d. Translocations (moving a DNA segment).
All chromosome structure mutations begin with a break in the DNA,
leaving ends that are not protected by telomeres, but are “sticky” and may
adhere to other broken ends.
3 rd
Chromosomal deletion (deficiency) arises from a single break with loss of the
distal fragment (terminal deletion) or from two breaks and loss of the intervening
segment (interstitial or intercalary deletion).
Figure 6: mechanism of deletion formation.
Duplications: result from doubling of chromosomal segments, and occur in a
range of sizes and locations. There are two types of dublication .
a. Tandem duplications are adjacent to each other.
b. Reverse tandem duplications result in genes arranged in the opposite order of
the original.
3 rd
Invertion : Inversion results when a chromosome segment excises and
reintegrates oriented 180° from the original orientation. There are two types
a. Pericentric inversions include the centromere.
b. Paracentric inversions do not include the centromere.
Figure 8: types of inversions.
Translocation: is a change in location of a chromosome segment is a
translocation. No DNA is lost or gained. Simple translocations are of two types:
a. Intrachromosomal, with a change of position within the same chromosome.
b. Interchromosomal, with transfer of the segment to a nonhomologous
chromosome.
1. If a segment is transferred from one chromosome to another, it is
nonreciprocal.
Figure 9:types of Translocations.
3 .pdf (p.14-23)
4.pdf (p.24-33)
5.pdf (p.34-41)
67.pdf (p.42-46)
8 .pdf (p.47-60)

introductory lecture - csw.uobaghdad.edu.iq

Documents