Ch2 chromosome structure

Copyright © 2009 Pearson Education, Inc.
2.0 Chromosome structure
Prepared by Pratheep Sandrasaigaran
Lecturer at Manipal International University

By the end of this chapter you
should be able to:
• Define the basis of “Central Dogma”
• Chromosome Structure and DNA packaging
• Compare the nuclear DNA with
• Mitochondrial DNA
• Chloroplast DNA
• Cell cycle
• Mitosis and meiosis (Task)
Diagram from Internet source

2.1 The Central Dogma

The “Central Dogma”
• DNA functions primarily by directing the production
of proteins.
• Each DNA molecule can carry thousands of genes
which in return plan for building a particular protein,
or part of a particular protein.
• The type of produced decides everything about a cell
and eventually the human body as a whole:
• The color of the hair and skin
• Propensity to certain diseases
• Unique ability
• Fat, thin, tall, short, bold, hairy, even for the
matter of ‘long or short’….

The “Central Dogma”
• The “Central dogma” describes the flow of genetic
information from DNA to protein.
• DNA makes ribonucleic acid (RNA), which
coordinate polypeptide/ protein synthesis.
• This involves two main stages
a. Transcription (mRNA)
b. Translation (Polypeptide)

Transcription
• The genetic information, the nucleotide
sequence carried by one strand of the DNA
helix is transcribed onto an mRNA (messenger
RNA).
• The process of ‘making’ RNA from DNA

Transcription
• The double helix become detached from
each other and exposes the genes
(sequences of bases)
• Just one of the strands serves as a
template to produce the RNA strand.
• RNA polymerase binds to the DNA and
moves along it, attaching free nucleotides
making strand of mRNA.
• What is the sequence of mRNA that you
expect?
Diagram adopted from
The Facts On File Illustrated Guide to the Human Body: Cells and Genetics

Transcription
• The mRNA consists of a single chain of
nucleotides with that the base uracil
(U) occurs instead of thymine (T).
• mRNA carries the genetic code, in the
form of base triplets, or codons.
• What happen to the other strand of
DNA?
• They are not transcribed

Translation
• The base sequence of each mRNA molecule is
“read” by a ribosome.
• What is Ribosome?
• A third type of RNA, called transfer RNA (tRNA),
brings amino acids to the assembly site.
• As the mRNA molecule feeds through the
ribosome, amino acids are added to the end of the
growing polypeptide chain.

Translation
• Each type of tRNA bears an anticodon,
which complements that of the mRNA
codon currently inside the ribosome.
• Because of this, the amino acids are
incorporated into the polypeptide chain
in the correct order.
• What is the linkage that hold amino
acids together?
Crash course: Cell Biology and Genetics, 4th
ED

Summery of
‘central dogma’

TEST YOUR KNOWLEDGE 1

Define the process of transcription. Where does this
process fit into the central dogma of molecular
genetics (DNA makes RNA makes protein)?

What are the similarities and differences between
transcription and DNA replication?

2.2 Chromosome Structure and
DNA packaging

Introduction
• A gene provides each cell in the body with
instructions for making (synthesizing) a particular
protein (or part of a protein).
• Each protein, either directly or indirectly, determines
a particular measurable characteristic or cell
function.
• Proteins are formed either as enzymes or structural
proteins.
• What is the function of enzyme and structural
protein?

Where and when genes are
active?
• Except for sex cells, all human cells contain a
set of about 30,000 genes.
• Which genes manufacture proteins depends on
where in the body a cell is situated.
• Where is the gene is located in the body and
how does such vast information can be
coordinated?

Basic structure of a chromosome
• Genes are organized into structures called
chromosomes, which serve as vehicles for
transmitting genetic information.
• In eukaryotes, nuclear chromosomes are
packaged by proteins into a condensed structure
called chromatin.
• This allows the very long DNA molecules to fit
into the cell nucleus.

Basic structure of a chromosome
• Chromosomes are usually diffuse, threadlike
structures, not easily distinguishable from each
other within the nucleus.
• Just before and during cell division the
chromosomes condense (become shorter and
fatter), so that their different shapes become
visible under a microscope.
• The chromosome also copies itself, making two
identical chromatids that meet at a narrow
point called the centromere.
Chromosome
sex
Autosomal

Sex chromosomes
• These chromosomes determine gender.
• Human cells contain two sex chromosomes.
• If you’re female, you have two X chromosomes,
and if you’re male, you have an X and a Y
chromosome.

Autosomal chromosomes
• Autosomal simply refers to non-sex
chromosomes.
• So, sticking with the human example, do the
math, and you can see that humans have 44
autosomal chromosomes.
• In humans, chromosomes come in pairs.
• How many pairs of chromosome that you will
find in your cells?

Diagram adopted from Genetics for Dummies, Tara. R. R
The 46 Human chromosomes

DNA packaging in the
chromosomes
• In the nucleus of a normal human cell, there are
46 chromosomes each containing 48–240 million
bases of DNA.
• Watson and Crick’s double helix model predicts
that each chromosome would have a contour
length of 1.6–8.2 cm
• While the total length of the DNA would be
about 3 m.

Diagram from Internet source
DNA packaging in the
chromosomes
• However, the average nucleus has a
diameter of approximately 5 mm.
• How it is possible?
• A high degree of organization is
needed to fit this amount of DNA into
the nucleus…!

The different levels of DNA condensation,
from DNA double helix to mitotic
chromosome
ED
Three higher order of
chromatin structure
DNA winds onto nucleosome spools
The nucleosome chain coils into a
solenoid
The solenoid forms loops, which attach
to a central scaffold
The scaffold plus loops arrange into a
giant supercoil

First order: The chromatin
• Chromatin is the collective name for the long
strands of DNA, RNA and their associated
nucleoproteins.
• During interphase of the cell cycle, chromatin is
dispersed throughout the nucleus, becoming
more compact during mitosis or meiosis
• Two types of chromatin can be seen with
electron microscopy.
• Heterochromatin
• Euchromatin

Heterochromatin
• Is an electron dense and distributed around the
periphery of the nucleus and in discrete masses
within the nucleus.
• The DNA is in close association with
nucleoproteins, and it is not active in RNA
synthesis.
• Serves as structural purpose during the
chromosomal stages.

Euchromatin
• Is an electron lucent and represents DNA that is
actually or potentially active in RNA synthesis.
• Example, the protein coding gene region

Nucleosomes
• A nucleosome is formed by 146 bp of DNA
wound twice around an octamer (Eight) of
histone proteins.
• The octamer consists of two copies each of the
histone proteins H2A, H2B, H3, and H4.
• Histone proteins are conserved throughout
eukaryotic evolution.
• They contain a high proportion of positively
charged amino-acid residues that can form ionic
bonds with the negatively charged DNA.

Nucleosomes
• This interaction does not depend on DNA
sequence and theoretically histones can bind
with any piece of DNA.
• However, in vivo, the position of histone binding
is influenced by:
• AT content (bends more easily than GC)
• The presence of other tightly bound proteins.
• Nucleosome bound regions of DNA are
separated by a region of linker DNA that varies
from 0–80 bp in length.

ED
Chromatin fibre
organization.
A. The nucleosome core particle is composed
of pairs of histones. 146 bp of DNA wind
around each nucleosome. Linker DNA
consisting of 8–114 base pairs runs between
one nucleosome and the next.
B. Chromatin consists of nucleosomes bound
together through their H1 proteins (not
shown in this part of the figure).
C. Bound nucleosomes form a solenoid, with
six nucleosomes per turn.

Second order: Solenoid formation
• The second level of DNA packing is mediated by
histone HI, binding together adjacent
nucleosomes to condense DNA into the
supercoiled 30-nm fibre.
• This fibre is also known as the solenoid.
• The solenoid exhibits six to eight nucleosomes
per turn of the spiral, corresponding to
heterochromatin.

Third order: Giant supercoil
• The third level of organization is thought to
involve the formation of transcriptional units of
DNA loops radiating from a central scaffold of
non-histone proteins…. WHY?
• Histone binding protects DNA from degradation
with DNaseI (endonuclease that breaks the
internal phosphodiester bonds in DNA
irrespective of its base sequence).
• If there is histone bind to DNA, no transcription.

Chromosome
•What is chromosome?
•At metaphase, chromatin is maximally condensed
and forms 1400-nm fibres.
•After cell staining these structures are visible as
chromosomes under light microscopy.

Copyright © 2009 Pearson Education, Inc. Figure 2.13
Diagram adopted from Concepts of Genetics, Klug.W.S., 10th
ED
Chromatin fibers Metaphase chromosomes
Metaphase chromosomes

Centromeres
• Each metaphase chromosome is composed of
two identical sister chromatids.
• Chromatids are connected at a central region
called the centromere
• Centromeres consist of hundreds of kilobases of
repetitive DNA and are responsible for the
movement of chromosomes at cell division.
• Each centromere divides the chromosome into
short (p) and long (q) arms.

Anatomy of a chromosome
showing the three shapes
Diagram adopted from Crash course: Cell Biology and Genetics, 4th
ED

Copyright © 2009 Pearson Education, Inc. Figure 2.3
Diagram adopted from Concepts of Genetics, Klug.W.S., 10th
ED
Centromere locations and
designations of chromosomes

kinetochore
• An organelle located at the
centromere region
• It acts as a microtubule organizing
centre.
• It also facilitates spindle formation
by polymerization of tubulin dimers
to form microtubules early in
mitosis.
ED

Telomeres
• The ends of chromosomes are
protected by DNA structures called
telomeres.
• Telomeres are tandem repeats of the
hexameric sequence ‘TTAGGG’ and
loops back on itself to form the T-loop.
ED

Telomeres
• Telomeres have several functions in
preserving chromosome stability:
• Preventing abnormal end-to-end fusion of
chromosomes
• Protecting the ends of chromosomes from
degradation
• Ensuring complete DNA replication
• Having a role in chromosome pairing
during meiosis.

Chromosome structure- Summary
Diagram adopted from Genetics for Dummies, Tara. R. R

1. Look at the following Karyotype; is
this organism male or female?
2. How many chromosomes are found
in the somatic cells of this organism?
3. How many chromosomes are found
in sperm cells from this organism?
4. How many pairs of chromosomes
does this organism’s karyotype
contain?
5. How many chromosomes would be
found in this organism’s skin cells?
6. How many chromosomes would be
found in this organism’s egg cells?
Karyotype Analysis

Define these terms
• Gene
A discrete unit of hereditary information consisting of
a specific nucleotide sequence in DNA (or RNA, in
some viruses)
• Locus
A specific place along the length of a chromosome
where a given gene is located
• Gamete
A haploid reproductive cell, such as an egg or sperm.
Gametes unite during sexual reproduction to
produce a diploid zygote.

Define these terms
• Male gamete
Sperm
• Female gamete
Eggs
• Asexual reproduction
The generation of offspring from a single parent
that occurs without the fusion of gametes (by
budding, division of a single cell, or division of
the entire organism into two or more parts). In
most cases, the offspring are genetically
identical to the parent.

1. What is a somatic cell? Give examples of two human
somatic cell types
A somatic cell is any cell in a multicellular organism except
a sperm or egg or their precursors. Examples may vary but
could include bone cells, skin cells, blood cells, etc.
2. How does a somatic cell compare to a gamete in terms of
chromosome number?
Unlike somatic cells, gametes contain a single set of
chromosomes. Such cells are called haploid cells, and each
has a haploid number of chromosomes (n). For humans,
the haploid number is 23.

2.3 Compare the nuclear DNA
The Mitochondrial DNA

Mitochondrial DNA and the
genetic code
• Mitochondria contain their own unique DNA,
which in humans consists of 16 kb of circular
dsDNA
• This makes 37 essential genes
• Mitochondrial DNA code for:
• 22 mitochondrial (mt) tRNAs
• Two mt rRNAs
• 13 proteins synthesized by the mitochondrion’s
machinery; subunits of the oxidative
phosphorylation pathway.

• Codon/anticodon pairings show more ‘wobble’ pairings than in the
process originating in the nucleus due to unusual mt tRNA sequences
Nuclear DNA vs Mitochondrial DNA
Diagram adopted from Crash course: Cell Biology and Genetics, 4th
ED

Mitochondrial inheritance
• Mitochondrial DNA (mtDNA) is only
maternally inherited
• Sperm mtDNA (mid-piece) normally will be
degraded after fertilization.
• Hence, affected males cannot transmit the
disease to their offspring, single ancestral
lineage
• Used to track back the evolutionary history
of human
ED

Mitochondrial inherited disease
• Leber hereditary optic neuropathy- an
inherited form of vision loss
• Mitochondrial encephalomyopathy, lactic
acidosis and stroke-like syndrome (MELAS)
• Myoclonus with epilepsy and with ragged
red fibres (MERRF).

2.3 Compare the nuclear DNA
The Chloroplast DNA

Chloroplast DNA and the genetic
code
• Chloroplast DNA (cpDNA) has between 100 and
225 kb in length.
• It is circular and double stranded.
• The size of cpDNA is much larger than that of
mtDNA, hence account for a larger number of
genes.
• Most cpDNA are non coding and duplications of
same DNA sequences

Chloroplast DNA and the genetic
code
• Numerous gene products encoded by chloroplast
DNA function during translation within the
organelle.
• Genes specific to the photosynthetic function have
also been identified.
• Mutations in these genes may inactivate
photosynthesis.

Ribulose-1-5-bisphosphate
carboxylase
• Also known as Rubisco
• This enzyme has its small subunit
encoded by a nuclear gene,
whereas the large subunit is
encoded by cpDNA

2.4 Cell cycle

Interphase and cell division
• Interphase- The time when a cell is
not dividing.
• It has three sub-phases
• Growth1 (G1)- Gap1
• Synthetic (S)
• Growth2 (G2)- Gap2

Centrioles
Growth1 (G1)
• A rapid growth for the cell occurs.
• Centrioles (small rod-shaped structures) begin to
make copies of themselves
• Cells spend a varying amount of time at this stage
depending on their function, age, and the
surrounding temperature.
• For cells that divide rapidly,G1 may only last a few
minutes while for others, it can last for months or
even years.

Synthetic (or S)
• During this phase, strands of
deoxyribonucleic acid (DNA), which make
up the bar-shaped chromosomes, duplicate
themselves.
• This ensures that future copies of the cell
will receive the same genes (inheritable
coded units of DNA).

Growth2 (G2)
• The final preparations for cell division are
made.
• The centrioles finish replicating, and each
cell now has two pairs.

Cell division,
M Phase

Controlling the cell cycle
• Breakdown in the control mechanisms can lead to
• Abnormal mitosis and cell division
• Uncontrolled proliferation of cells
• Produces cancerous tumors
• What control the mechanism?
• Control is exerted by a small group of enzymes
called cyclin-dependent kinases (Cdks)

Controlling the cell cycle
• G1 phase- Cdk-cyclin (CdkC)
complexes activates transcription
factors that copy the genes that
encode enzymes needed for protein
synthesis.
• S phase- CdkCs activate the enzymes
that perform DNA replication.
• G2 phase- Mitotic CdkCs are
synthesized in an inactive form

Cell cycle checkpoints

Checkpoint 1
•Damage to DNA causes G1 arrest and allows cell to
replace damaged or lost DNA nucleotides before they
are copied during S phase.
Checkpoint 2
•The presence of unreplicated DNA causes S arrest and
allows cell to complete DNA replication before
mitosis.

Checkpoint 3
•Damaged DNA causes G2 arrest, enabling the cell
to repair double strand breaks in DNA that
otherwise.
Checkpoint 4
•Delayed or faulty assembly of the mitotic spindle
causes M arrest
•Mitosis is delayed, and chromosomes remain in a
condensed state.
•This prevents abnormal segregation of
chromosomes.

Cell cycle Answers
G2
S resulted in the duplication of each chromatid. Since
there is only one centromere on the sister chromatids,
we still call them one chromosome. When completed,
the cells are in G2 and preparing for M
Kinases
kinases add phosphate to molecules, and the
modification can serve as a "switch" to turn events in
the cell on or off. Cdk or cyclin dependent kinases
regulate the cell cycle.
G1 to S to G2 to Mto cytokinesis
G1 as a preparation for S and G2 as the time between
the completion of S and entry into M. Cytokinesis occurs
after the other stages to create two daughter cells.
Which stage of the cell cycle where the cell is
preparing to begin DNA replication is called? G1 cells are preparing for S
Histones
histones form structural complexes with DNA. In the
electron microscope, these can take the appearance of
beads on a string
Which stage of the cell cycle where each
chromosome is composed of two chromatids in
preparation for mitosis?
Which class of enzymes that are involved in
triggering events in the cell cycle are called?
Which sequence of the cell cycle is common to
eukaryotes?
The proteins which complex with DNA producing
the "beads on a string" or nucleosomes are called

Cell cycle Answers
Cytokinesis
the animal cell can pinch into two by a ring of
microfilaments. The plant cell with a rigid wall
synthesizes a new cell plate. In both cases, the spindle
fibers play a role in determining the site where the cell
is split
Sister chromatids
The replication of the chromosome begins with the
production of sister chromatids. The complex is
considered to be one chromosome since there is only
one centromere
Prophase
At the beginning of prophase, the chromosomes
condense into structures visible in the light microscope
The formation of a cell plate in the cytoplasm
The spindle fibers are used to bring in vesicles that line
up along the cell plate and produce a new cell wall
Which of the following features of cell division are
very different for animal and plant cells?
Prior to cell division, each chromosome replicates
or duplicates its genetic material. The products are
connected by a centromere and are called as?
The first stage of mitosis when chromosomes start
becoming visible in the microscope is called?
Cytokinesis in a plant cell is characterized by

Mitosis and Meiosis

Ch2 chromosome structure

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