DNA is made of a double helix structure with two strands held together by hydrogen bonds between complementary nucleotide base pairs. In eukaryotes, DNA is organized into linear chromosomes in the nucleus and circular DNA molecules in mitochondria and chloroplasts. DNA can be denatured by increasing temperature to separate the strands, and will renature when cooled by reformation of hydrogen bonds between complementary bases.
Chromatin is the complex combination of DNA and proteins that makes up chromosomes. It can be made visible by staining with specific techniques and stain (thus the name chromatin which literally means colored material). The major proteins involved in chromatin are histone proteins; although many other chromosomal proteins have prominent roles too. The functions of chromatin is to package DNA into smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and to serve as a mechanism to control gene expression and DNA replication.
Genetic material
Anant Mohan Sharma
All cell have the capability to give rise to the cell and
the encoded information in living cell is passed from
one generation to another. The information encoded
material is the genetic material or hereditary material
of the cell.
The genetic material is long sequence of nucleic
acids that contain the genetic instruction. Nucleic
acid are macromolecules in the form of DNA or
RNA.
Experimental evidences
Griffith’s experiment
Avery, MacLeod &McCarty experiment
Hershey & Chase experiment
RNA as genetic material
DNA structure
Z- DNA
V. Sasisekharan RL model
Types of RNA
Chromatin is the complex combination of DNA and proteins that makes up chromosomes. It can be made visible by staining with specific techniques and stain (thus the name chromatin which literally means colored material). The major proteins involved in chromatin are histone proteins; although many other chromosomal proteins have prominent roles too. The functions of chromatin is to package DNA into smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and to serve as a mechanism to control gene expression and DNA replication.
Genetic material
Anant Mohan Sharma
All cell have the capability to give rise to the cell and
the encoded information in living cell is passed from
one generation to another. The information encoded
material is the genetic material or hereditary material
of the cell.
The genetic material is long sequence of nucleic
acids that contain the genetic instruction. Nucleic
acid are macromolecules in the form of DNA or
RNA.
Experimental evidences
Griffith’s experiment
Avery, MacLeod &McCarty experiment
Hershey & Chase experiment
RNA as genetic material
DNA structure
Z- DNA
V. Sasisekharan RL model
Types of RNA
DNA is tightly packed in the nucleus of every cell. DNA wraps around special proteins called histones, which form loops of DNA called nucleosomes. These nucleosomes coil and stack together to form fibers called chromatin. Chromatin in turn forms larger loops and coils to form chromosomes.
DNA packaging is crucial because it makes sure that those excessive DNA are able to fit nicely in a cell that is many times smaller.
The DNA in bacterial cells are either circular or linear. To accommodate the size of bacterial cell, supercoiled DNA are folded into loops with each loop resembles shape of bead-like packets containing small basic proteins that is analogous to histone found in Eukaryotes.
Nuclear Genomes(Short Answers and questions)Zohaib HUSSAIN
1. What did researchers find when they sequenced the centromeres of Arabidopsis? Why was this finding surprising?
Ans: Before the Arabidopsis sequences were obtained it was thought that these repeat sequences were by far the principal component of centromeric DNA. However, Arabidopsis centromeres also contain multiple copies of genome-wide repeats, along with a few genes, the latter at a density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions of Arabidopsis chromosomes. The discovery that centromeric DNA contains genes was a big surprise because it was thought that these regions were genetically inactive.
2. What differences in gene distribution and repetitive DNA content are seen when yeast and human chromosomes are compared?
Ans. A typical region of a human chromosome will have few genes (most of which will contain introns), several repeated sequences, and a large amount of nonrepetitive, nongenic DNA. Yeast chromosomes have higher gene densities, with very few genes containing introns, and have few repeated sequences and much less nongenic DNA.
3. The human genome contains about 50,000 fewer genes than was predicted by many researchers. Why were these initial predictions so high?
Ans. These early estimates were high because they were based on the supposition that, in most cases, a single gene specifies a single mRNA and a single protein. According to this model, the number of genes in the human genome should be similar to the number of proteins in human cells, leading to the estimates of 80,000–100,000. The discovery that the number of genes is much lower than this indicates that alternative splicing, the process by which exons from a pre-mRNA are assembled in different combinations so that more than one protein can be coded by a single gene is more prevalent than was originally appreciated.
4. What are the different methods used to catalog genes? What are the advantages or disadvantages of these methods?
Ans. Gene catalogs can be based on the known functions of genes, but such catalogs are incomplete because in most genomes many genes have unknown functions. Gene catalogs that are based on the identities of protein domains coded by genes are more comprehensive as these include many genes whose specific functions are unknown.
5. What is the function of the different genes in the human globin gene families?
Ans. The globins are the blood proteins that combine to make hemoglobin, each molecule of hemoglobin being made up of two a-type and two b-type globins.The a-globin cluster is located on chromosome 16 and the b-cluster on chromosome 11. Both clusters contain genes that are expressed at different developmental stages and each includes at least one pseudogene. Note that expression of the a-type gene x2 begins in the embryo and continues during the fetal stage; there is no fetal-specific a-type globin. The q pseudogene is expressed but its protein product is inactive. None of the other p
Facts about DNA
Eukaryotic chromosomes
Chemical composition of eukaryotic chromosomes
Histones
Non-histone chromosomal protein
Scaffold proteins
Folded fibre model
Nucleosome model
H1 proteins
Histone modification
Chromatosome
Higher order of chromatin structure
Mechanism of DNA packaging
Conclusion
DNA is tightly packed in the nucleus of every cell. DNA wraps around special proteins called histones, which form loops of DNA called nucleosomes. These nucleosomes coil and stack together to form fibers called chromatin. Chromatin in turn forms larger loops and coils to form chromosomes.
DNA packaging is crucial because it makes sure that those excessive DNA are able to fit nicely in a cell that is many times smaller.
The DNA in bacterial cells are either circular or linear. To accommodate the size of bacterial cell, supercoiled DNA are folded into loops with each loop resembles shape of bead-like packets containing small basic proteins that is analogous to histone found in Eukaryotes.
Nuclear Genomes(Short Answers and questions)Zohaib HUSSAIN
1. What did researchers find when they sequenced the centromeres of Arabidopsis? Why was this finding surprising?
Ans: Before the Arabidopsis sequences were obtained it was thought that these repeat sequences were by far the principal component of centromeric DNA. However, Arabidopsis centromeres also contain multiple copies of genome-wide repeats, along with a few genes, the latter at a density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions of Arabidopsis chromosomes. The discovery that centromeric DNA contains genes was a big surprise because it was thought that these regions were genetically inactive.
2. What differences in gene distribution and repetitive DNA content are seen when yeast and human chromosomes are compared?
Ans. A typical region of a human chromosome will have few genes (most of which will contain introns), several repeated sequences, and a large amount of nonrepetitive, nongenic DNA. Yeast chromosomes have higher gene densities, with very few genes containing introns, and have few repeated sequences and much less nongenic DNA.
3. The human genome contains about 50,000 fewer genes than was predicted by many researchers. Why were these initial predictions so high?
Ans. These early estimates were high because they were based on the supposition that, in most cases, a single gene specifies a single mRNA and a single protein. According to this model, the number of genes in the human genome should be similar to the number of proteins in human cells, leading to the estimates of 80,000–100,000. The discovery that the number of genes is much lower than this indicates that alternative splicing, the process by which exons from a pre-mRNA are assembled in different combinations so that more than one protein can be coded by a single gene is more prevalent than was originally appreciated.
4. What are the different methods used to catalog genes? What are the advantages or disadvantages of these methods?
Ans. Gene catalogs can be based on the known functions of genes, but such catalogs are incomplete because in most genomes many genes have unknown functions. Gene catalogs that are based on the identities of protein domains coded by genes are more comprehensive as these include many genes whose specific functions are unknown.
5. What is the function of the different genes in the human globin gene families?
Ans. The globins are the blood proteins that combine to make hemoglobin, each molecule of hemoglobin being made up of two a-type and two b-type globins.The a-globin cluster is located on chromosome 16 and the b-cluster on chromosome 11. Both clusters contain genes that are expressed at different developmental stages and each includes at least one pseudogene. Note that expression of the a-type gene x2 begins in the embryo and continues during the fetal stage; there is no fetal-specific a-type globin. The q pseudogene is expressed but its protein product is inactive. None of the other p
Facts about DNA
Eukaryotic chromosomes
Chemical composition of eukaryotic chromosomes
Histones
Non-histone chromosomal protein
Scaffold proteins
Folded fibre model
Nucleosome model
H1 proteins
Histone modification
Chromatosome
Higher order of chromatin structure
Mechanism of DNA packaging
Conclusion
This lecture covers some nice stories about the origins of the words "genome" and the derived word "genomics". the lecture also introduces viral, bacterial, and eukaryotic genomes.
Basics of Undergraduate/university fellows
Nucleosome model of chromosome is proposed by ROGER KORNBERG (son of Arthur
Kornberg) in 1974.
It was confirmed and crystalised by P. Oudet et al., (1975).
Nucleosome is the lowest level of Chromosome organization in eukaryotic cells.
Nucleosome model is a scientific model which explains the organization of DNA and
associated proteins in the chromosomes.
Nucleosome model also explains the exact mechanism of the folding of DNA in
thenucleus.
It is the most accepted model of chromatin organization.
Polytene chromosome with respect to historical basis, occurrence, structural organisation, bands and inter bands, puff are briefly stated for basic idea.
You may find this interesting understand the reason behind the gaint structure of these chromosomes.
This study material is a compilation of various sources such as text books, website etc...
Enjoy the process of Learning
Thank you
This is a comprehensive account of the structure of eukaryotic chromosomes. It deals with the morphology, formation, and types of chromosomes present in eukaryotic cells. The main point of interest is the folding and packaging of DNA and proteins to make chromatin.
Chromosome structure and packaging of dnaDIPTI NARWAL
Chromosome structure : classification based upon centromere position, autosomes and allosomes
Morphology of chromosome: chromatids, chromomeres, telomeres, sister chromatids
packaging of DNA: nucleosome model
functions of Chromosomes
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and
offering a wide range of dental certified courses in different formats.for more details please visit
www.indiandentalacademy.com
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and
offering a wide range of dental certified courses in different formats.for more details please visit
www.indiandentalacademy.com
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by chaperone proteins, bind to and condense the DNA molecule to maintain its integrity.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
Accelerate your Kubernetes clusters with Varnish CachingThijs Feryn
A presentation about the usage and availability of Varnish on Kubernetes. This talk explores the capabilities of Varnish caching and shows how to use the Varnish Helm chart to deploy it to Kubernetes.
This presentation was delivered at K8SUG Singapore. See https://feryn.eu/presentations/accelerate-your-kubernetes-clusters-with-varnish-caching-k8sug-singapore-28-2024 for more details.
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
FIDO Alliance Osaka Seminar: The WebAuthn API and Discoverable Credentials.pdf
Manipulatingproteins 111109090227-phpapp01
1.
2. DNA is the stuff our genes are made of…
The organization of total sum of genetic information
(or genome) of an organism is in the form of double-
stranded DNA, except that viruses may have single-
stranded DNA, single-stranded RNA or double-
stranded RNA genomes.
In many viruses and prokaryotes, the genome is a
single linear or circular molecule.
In eukaryotes, the nuclear genome consists of linear
chromosomes (usually as a diploid set) and the
mitochondrial and chloroplast (in plants) genomes
are small circular DNA molecules.
In 1952, Watson and Crick proposed that DNA is a
double helix which is known to have alternative
forms.
3.
4. (a) The B form of DNA
has ≈10.5 base pairs per helical turn. Adjacent stacked base pairs
are 0.36 nm apart. (b) The more compact A form of DNA has 11
base pairs per turn and exhibits a large tilt of the base pairs with
respect to the helix axis. (c) Z DNA is a left-handed double helix.
5. DNA supercoils can be removed by
cleavage of one strand. (a) EM of SV40
viral DNA. When the SV40 circular
DNA is isolated, the DNA duplex is
underwound and assumes the
supercoiled configuration. (b) If a
supercoiled DNA is nicked, the strands
can rewind, leading to loss of a
supercoil. Topoisomerase I catalyzes
this reaction and also reseals the
broken ends. All the supercoils in
isolated SV40 DNA can be removed by
the sequential action of this enzyme,
producing the relaxed-circle
conformation.
6.
7. In general,
genome
size
increases
with the
complexity
of
organism.
8. 1. Base stacking interactions - hydrophobic interactions resulting from
the individual base pairs’ stacking on top of each other in the nonpolar
interior of the double helix, electrostatic forces between nearest-
neighbor base pairs, and from van der Waals forces between the
bases.
2. Deoxyribose sugar- this is less reactive because of C-H bonds.
Consequently, DNA has smaller grooves which hinder attachment of
damaging enzymes that attack DNA.
3. Hydrogen bonds- the sum of all the H-bonds between the paired bases
leads to a stabilizing "zipper effect.“
4. Protective "twisting" of the DNA helix and flexibility of the two strands
- although the bases cannot rotate freely about the axis of their bonds
with each other, they are able to rotate around their bonds with the
sugars. This area of rotation is like a joint on a human arm. In
DNA, there are several flexible bonds:
a. bonds between oxygen and phosphorus in phosphate groups
b. bonds linking the phosphate groups to the sugar rings
c. bonds which link the sugar rings to the aromatic bases
5. Interaction with histones- chains of DNA become even more stable, as
they entwine with histones. DNA ribbons coil around histones for
protection, like a string on a spool.
9. The bacterial chromosome is
localized in the nucleoid
region of the cell (no nucleus)
and is looped into negative
coils.
The loops are 50,000 to
100,000 bps in length (similar
to eukaryotic chromosomes)
which are held in place by
RNA and small basic (histone-
like) proteins.
Plasmids, small negatively
supercoiled circular DNA
molecules, carry usually non-
essential genes (often drug
resistance).
10. A chromosome is formed from a single,
enormously long DNA molecule that contains a
linear array of many genes.
The human genome contains 3.2 × 109 DNA
nucleotide pairs, divided between 22 different
autosomes and 2 sex chromosomes.
11. Chromosomal banding patterns and multicolor FISH are
used to analyze human anomalies
Characteristic chromosomal translocations are associated with
certain genetic disorders and specific types of cancers. In nearly
all patients with chronic myelogenous leukemia, the leukemic
cells contain the Philadelphia chromosome, a shortened
chromosome 22 [der (22)], and an abnormally long chromosome
9 [der (9)]. These result from a translocation between normal
chromosomes 9 and 22.
12. Comparative studies reveal that human genomes contain genes in
the same order as another mammal, a feature called conserved
synteny. Using chromosome banding/ painting, the phylogenetic
history of our own chromosomes maybe reconstructed by
comparing them with those from other mammals.
13. DNA in a eukaryotic chromosome contains genes, many
replication origins, one centromere, and two telomeres.
These sequences ensure that the chromosome can be
replicated efficiently and passed on to daughter cells.
14. If each nucleotide pair
is drawn as 1 mm as in
(A), then the human
genome would extend
3200 km (approximately
2000 miles), far enough
to stretch across the
center of Africa, the site
of our human origins
(red line in B). At this
scale, there would
be, on average, a
protein-coding gene
every 300 m. An average
gene would extend for
30 m, but the coding
Human DNA, if fully extended, would have a
total length of 1.7 m. If you unwrap all the sequences in this gene
DNA you have in all your cells, you could would add up to only
reach the moon ...6000 times! just over a meter.
17. Interphase chromosomes contain both condensed
and more extended forms of chromatin
Constitutive heterochromatin - found in the
centromere, nucleolar organizers (found in human
chromosomes 13,14,15,21, and 22), repetitive or
satellite DNA
Facultative heterochromatin- one of the
homologues become heterochromatic, e.g. X
chromosome becomes Barr body
Euchromatin – loosely packed, actively
transcribed regions of the chromosome.
Chromatin structure is dynamic: by temporarily
altering its structure by using chromatin remodeling
complexes and enzymes that modify histone tail, the
cell can ensure that proteins involved in gene
expression, replication, and repair have
rapid, localized access to the necessary DNA
18. Different
chromatin
remodeling
complexes disrupt
and reform
nucleosomes. The
same complex
might catalyze both
reactions. The
DNA-binding
proteins could be
involved in gene
expression, DNA
replication, or DNA
repair.
19. Each histone can be
modified by the covalent attachment of different molecules.
Histone H3, for example, can receive an acetyl group (Ac), a
methyl group (Me), or a phosphate (P). Note that some positions
(e.g., lysine 9 and 27) can be modified in more than one way.
20. Different combinations of histone tail modifications may
constitute a type of “histone code.” Each marking conveys a
specific meaning to the stretch of chromatin on which it occurs.
Only a few of the meanings of the modifications are known.
21. Contains
alpha
satellite
sequences
(5,000-
15,000
copies of
171 base
pair
sequences).
Position of
centromere
P and q
arms
22. Within the centromere
region, the actual location
where the attachment of
chromosomes to spindle
fibers occurs is called the
kinetochore and is
composed of both DNA and
a protein called CEN DNA.
It can be moved from one
chromosome to another
and still provide the
chromosome with the
ability to segregate. CEN
DNA consists of several
sub-domains, CDE-I, CDE-II
and CDE-III. Additional
analyses of the DNA and
protein components of the
centromere are necessary
to fully understand the
mechanics of chromosome
segregation.
23. Telomeres are non-sticky
regions that prevent fusion of
chromosomes and DNAse from
degrading their ends.
They facilitate replication
without loss of material.
Most species have telomeric
3’G overhangs that form G-
quartets (Hoogstein base-
pairing)
Contain tandem repeats which
are highly conserved
(TTAGGGG in man)
These 500-3,000 repeats in
normal cells shorten with age
(biological fortune-tellers?)
24.
25.
26. The stability of the T-
loop is largely
dependent on the
integrity of associated
telomere-specific
proteins called the
shelterin complex.
TRF (telomeric repeat-binding factor) 1 and TRF2 bind to the
double-stranded segment of telomeric DNA. POT1 (protein
protection of telomeres 1) binds directly to the single-stranded
telomeric DNA and interacts directly with TPP1 (tripeptidyl
peptidase 1). Rap1 (repressor activator protein 1) binds TRF2, and
TIN2 (TRF1-interacting nuclear factor 2) is a central component of
the complex interacting with TRF1, TRF2 and TPP1.
27. TERRA (Telomeric
repeat-containing
RNA)
Biogenesis, telomere
association and
displacement from
telomeres. TERRA
forms telomeric
heterochromatin
which may have
roles (?) in
telomerase
regulation and in
orchestrating
chromatin
remodelling
throughout
development and
cellular
differentiation.
TERRA dysfunction
leads to RF collapse.
28. Most human cells lack
telomerase. In normal
cells that still produce
functional p53 and have
their cell-cycle
checkpoints intact, this
triggers cell death. But a
cell that has acquired a
p53 mutation may ignore
this signal and cause
massive chromosomal
damage. Some cells
reactivate telomerase,
which restores enough
chromosomal stability for
cell survival. These
damaged cells can then
go on to accumulate the
additional mutations
needed to produce a
cancer.
29. The mitochondria and chloroplasts also have a DNA genome
(or chromosome). These resemble procaryotic genomes
(likely due to the endosymbiotic origin of these organelles)
but are much smaller.
The mitochondrial genome varies in size among eukaryotes
(mammals =16.5 kb & 37 genes, yeast and plants are greater
than 5X this).
Chloroplasts are ~120
kb and have ~120 genes.
DNA in ORGANELLES
30. DNA Can Undergo Reversible Strand Separation
Denaturation or “melting,”(unwinding and separation
of DNA strands), can be induced by increasing the
temperature of a solution of DNA.
Denaturation and renaturation of DNA are the basis
of nucleic acid hybridization.
Loss of the multiple weak interactions holding the
strands together along the entire length of the DNA
molecules lead to an abrupt change in the
absorption of ultraviolet (UV) light.
The melting temperature (Tm ) at which DNA strands
will separate depends on several factors:
a. When the ion concentration is low, shielding of
negatively charged phosphate groups in the two
strands by positively charged ions is
decreased, thus increasing the repulsive forces
between the strands and reducing the Tm.
31. b. A greater proportion of G-C pairs require higher
temperatures to denature.
c. pH extremes denature DNA at low temperature. At low
pH, the bases become positively charged, repelling each
other. At high pH, the bases become negatively charged,
again repelling each other because of the similar charge.
d. Agents that destabilize hydrogen bonds, such as
formamide or urea, also lower the Tm.
32. Through the analysis of DNA renaturation studies, the large sizes
of eukaryotic genomes reveal large amounts of repeated DNA.
These undergo a complex pattern of re-annealing which reveals
a large amount of repeated DNA sequences (fast annealing) and
unique, non-repeated DNA (slow annealing).
Editor's Notes
A NUCLEOSOME(11 nm fiber) is composed of histoneoctamer (2 each of H2A, H2B, H3, H4) around which is wound 176 DNA base pairs; nucleosomes are linked to each other by H1Larger fibers made of nucleosome groups are called SOLENOIDS (30 nm fiber)