Mitul Vakani Assistant professor, - PowerPoint Presentation

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Mitul VakaniAssistant professor,Neotech College of applied Science and Research, Neotech Technical Campus (NTC), Virod, Vadodara, Gujarat

Basic Concept of

Molecular Biology,

Unit:1

[B.Sc. Bio-chemistry, sem-III, paper code BSCOC

307 A, Title

of paper :

Molecular Biology

]

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Central Dogma of Life

(Genes XII by Lewin)

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RNA (Identical to other strand of DNA)

(Gene)

What is

GENE

?

A gene is a sequence of DNA that directly produces a single strand of another nucleic acid, RNA, with a sequence that is (at least initially) identical to one of the two

polynucleotide strands of DNA.

(Genes XII by Lewin)

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OR

(Integrated into Ribosome or Non-Coding RNA or Regulatory RNA)

(Genes XII by Lewin)

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GENE

Genes dictate the inherent properties of a species. The products of

most genes are specific proteins.

Proteins are the main macro-molecules of an organism.One

gene can exist in several forms that differ from one another, generally in small ways. These forms of a gene are called alleles. Allelic variation causes hereditary variation within a species. At the protein level, allelic variation becomes

protein variation

.

Alleles

 are different forms of the same gene.

An 

example of alleles

 for flower color in pea plants are the dominant purple 

allele

, and the recessive white 

allele

; for height they are the dominant tall 

allele

 and recessive short 

allele

; for pea color, they are the dominant yellow 

allele

 and recessive green 

allele.

An Introduction to Genetic Analysis

Eighth Edition Anthony J.F. Griffiths

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Nature of GENE

Replication. Hereditary molecules must be capable of being copied at two key stages of the life cycle The first stage is the production of the cell type that will ensure the continuation of a species from one generation to the next. The other stage is when the first cell of a new organism undergoes multiple rounds of division to produce a multicellular organism.

Generation of form.

The working structures that make up an organism can be thought of as form or substance, and DNA has the essential “information”

needed to create form.Mutation. A gene that has changed from one allelic form into another has undergone mutation—an event that happens rarely but regularly. Mutation is not only a basis for variation within a species, but also, over the long term, the raw material for

evolution.

An Introduction to Genetic Analysis

Eighth Edition Anthony J.F. Griffiths

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GENE

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Deoxyribonucleicacid (DNA)

DNA is that it is usually composed of two polynucleotide chains twisted around each other in the form of a double helix.

One turn of the helix (34 A˚ or 3.4

nm) spans 10.5

bp. Space between two base pair ~3.4 A° .DNA consist of 3 ComponentSugar (

deoxy

Ribose)

Phosphate Group

Base (A,T,G,C)

Minor Groove

Major

Groove

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Structure of DNA

1. SugarDNA

RNA

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2. Base

IN RNA Thymine is replaced by Uracil(Genes XII by Lewin)

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COMPONENT OF DNA1

23

1

(Genes XII by Lewin)

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Nucleotide Oligomerisation

Nucleotide oligomerisation of DNA from (5’ to 3’)

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Types of DNANormal DNA

Voet and Voet

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Syn and Anti nucleotide

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Difference in DNA typesVoet and

Voet

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Eukaryotic Genome size : Plant Genome size:- ~100GbpMammal Genome size:- 3.3Gbp

DNA 1bp distance 3.4A° * 3.3 Gbp (3.3 *

)= 11.12*

11.12*

= 1.12 meter/cell

 

HOW this long DNA can be fit into micro meter cell????

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Packaging of DNA in different Organism

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For bacteria or eukaryotic cell compartments, the discrepancy is hard to calculate exactly, because the DNA is contained in a compact area that occupies only part of the compartment. The genetic material is seen in the form of the

nucleoid in bacteria, and as the mass of chromatin

in eukaryotic nuclei at interphase (between divisions), or as maximally condensed chromosomes

during mitosis.The density of DNA in these compartments is high. In a bacterium it is approximately 10 mg/mL, in a eukaryotic nucleus it is approximately 100 mg/mL, and in the phage T4 head it is more

than 500 mg/mL.

Packaging of DNA in different Organism

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Packaging RATIO

The overall compression of the DNA can be described by the packing ratio, which is the length of the DNA divided by the length of the unit that contains it.

For example, the smallest human chromosome contains approximately 4.6 × 10 base pairs (

bp) of DNA (about 10 times the genome size of the bacterium Escherichia coli

). This is equivalent to 14,000 μm (= 1.4 cm) of extended DNA. At the point of maximal condensation during mitosis, the chromosome is approximately 2 μm

long. Thus, the packing ratio of DNA in the chromosome can be as great as 7,000.

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Packaging of DNA

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DNA During Mitosis (Replicated and Condensed)Condensations of DNA occurs starting of Mitosis (Forms Chromosome like structure)

Different gene responsible for different phenotype

CHROMOSOME

(Made up of two sister chromatids)

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Structure of ChromosomeChromosome are the physical carrier of the gene and consist of DNA and its associated protein.

Bacteria has one circular chromosome and eukaryotes has linear Chromosome with wide range of size and number of chromosome.It is consist of two sister chromatids attached with centromere.

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Chromosomes are not visible in the cell’s nucleus—not even under a microscope—when the cell is not dividing. However, the DNA that makes up chromosomes becomes more tightly packed during cell division and is then visible under a microscope. Most of what researchers know about chromosomes was learned by observing chromosomes during cell division.

Each chromosome has a constriction point called the centromere, which divides the chromosome into two sections, or “arms.” The short arm of the chromosome is labeled the “p arm.” The long arm of the chromosome is labeled the “q arm.” 

Chromosome

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ChromosomeHuman has 23pair of Chromosomes.

22 Pair autosomal Chromosome1 pair Sex Chromosomes

In Male X ,Y sex chromosome

In Female X, X sex Chromosome.

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Types of ChromosomeMetacentric Chromosomes

Metacentric chromosomes have the centromere in the center, such that both sections are of equal length. Human chromosome 1 and 3 are metacentric.Submetacentric Chromosomes

Submetacentric chromosomes have the centromere slightly offset from the center leading to a slight asymmetry in the length of the two sections. Human chromosomes 4 through 12 are submetacentric.

Acrocentric ChromosomesAcrocentric chromosomes have a centromere which is severely offset from the center leading to one very long and one very short section. Human chromosomes 13,15, 21, and 22 are acrocentric.

Telocentric ChromosomesTelocentric chromosomes have the centromere at the very end of the chromosome. Humans do not possess telocentric chromosomes but they are found in other species such as mice.

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Types of Chromosome

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ChromatinChromatin has a compact organization in which most DNA sequences are structurally inaccessible and functionally inactive.

Within this mass is the minority of active sequences.It is Mad up of DNA + Protein structure.Basic Unit of Chromatin is

Nucleosome.

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NucleosomeNucleosome is fundamental unit of the Chromatin.

The nucleosome contains about 200 base pairs (bp) of DNA, organized by an octamer of small, basic proteins into a beadlike structure.

The protein components are histones.

DNA wrapped around the Protein (Histone)

HISTONE PROTEIN

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They form an interior core; the DNA lies on the surface of the particle. Additional regions of the histones, known as the histone tails, extend from the surface.Nucleosomes are an invariant component of euchromatin

and heterochromatin in the interphase nucleus And of mitotic chromosomes.

Nucleosome

Euchromatin is a lightly packed form of chromatin that is enriched in genes , and is often (but not always) under active transcription . Heterochromatin is densely packed form of chromatin.

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NucleosomeThe nucleosome provides the

first level of organization, compacting the DNA about 6-fold over the length of naked DNA, resulting in a “beads-on-a-string” fiber of approximately 10 nm in diameter.

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The secondary level of organization involves interactions between nucleosomes of the 10-nm fiber, leading to more condensed chromatin

fibers.Biochemical studies have shown that nucleosomes can assemble into helical arrays that form a fiber of approximately 30 nm in diameter. The structure of this fiber requires the histone tails and is stabilized by linker histones.

Nucleosome

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The final, tertiary level of chromatin organization requires the further folding and compacting of chromatin fibers into the 3D structures of interphase chromatin or mitotic chromosomes.

Nucleosome

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Nucleosomal DNA

Nucleosomal DNA divided into 2 typesCore DNA

Linker DNA

Core DNA has a length of 145–147 bp

, the length of DNA needed to form a stable monomeric nucleosome, and is relatively resistant to digestion by nucleases.Linker DNA comprises the rest of the repeating unit. Its length varies from as little as 7 bp

to as many as 115

bp

per

nucleosome.

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Nucleosomal DNA

Department of BiologyMemorial University of Newfoundland

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Nucleosome Structure

The nucleosome contains about 200 bp

of DNA associated with a histone octamer

that consists of two copies each of histones H2A, H2B, H3, and H4. These are known as the core histones.

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The nucleosome consists of approximately equal masses of DNA and histones (including H1). The predicted mass of a nucleosome that contains H1 is 262 kD

.

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Histone Protein

The histones are small, basic proteins (rich in arginine and lysine residues), resulting in a high affinity for DNA. Histones H3 and H4 are among the most conserved proteins known

, and the core histones are responsible for DNA packaging in all eukaryotes.

H2A and H2B are also conserved among eukaryotes, but show appreciable species-specific variation in sequence, particularly in the histone tails. The core regions of the histones are even conserved in archaea and appear to play a similar role in

compaction of archaeal DNA.

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The shape of the nucleosome corresponds to a flat disk or cylinder of diameter 11 nm and height 6 nm. The length of the DNA is roughly twice the 34-nm circumference of the particle. The DNA follows a symmetrical path around the octamer

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The height of the cylinder is 6 nm, of which 4 nm are occupied by the two turns of DNA (each of diameter 2 nm). The pattern of the two turns has a possible functional consequence. One turn around the nucleosome takes about 80 bp

of DNA, so 2 points separated by 80 bp in the free double helix can actually be close on the nucleosome surface

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Histone Modification

All of the histones are subject to numerous covalent modifications, most of which occur in the histone tails.

The histone tails can be

acetylated, methylated, phosphorylated, and ubiquitylated

at numerous sites. Not all possible modifications are shown.

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Lysines in the histone tails are the most common targets of modification. Acetylation, methylation,

ubiquitylation, and

sumoylation all occur on the free epsilon (ε) amino group of lysine.

The positive charge on lysine is neutralized upon acetylation, whereas methylated lysine and arginine retain their positive charges.

Lysine Modification

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Arginine and Serine Modification

Arginine retain their

positive charges in methyl modification. Serine or threonine phosphorylation results in a negative charge.

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All of these modifications are reversible, and a given modification might exist only transiently, or can be maintained stably through multiple cell divisions. Some modifications change the charge of the protein molecule, and, as a result, they are potentially able to change the functional properties of the octamers.

For example, extensive lysine acetylation reduces the overall positive charge of the tails, leading to release of the tails from interactions with DNA on their own or other nucleosomes

.

Modification of histones is associated with structural changes that occur in chromatin at replication and transcription, and specific modifications also

facilitate DNA repair.Modifications at specific

positions on

specific

histones can define different functional states of chromatin.

Histone Modification

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Newly synthesized core histones carry specific patterns of acetylation that are removed after the histones are assembled into chromatin

Acetylation associated with gene activation occurs by directly modifying specific sites on histones that are already incorporated into nucleosomes.

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Histone Modification

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Histone Modification

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Viral Genome Packaging

A virus particle is deceptively simple in its superficial appearance The nucleic acid genome is contained within a capsid, which is a symmetrical or

quasisymmetrical structure assembled from one or only a few proteins. Attached to the capsid (or incorporated into it) are other structures; these structures are assembled from distinct proteins and are necessary for infection of the host cell.

The rules

for assembly of identical subunits into closed structures restrict the capsid to one of two types. For the first type, the protein subunits stack sequentially in a helical array to form a

filamentous

or

rodlike

shape.

For the second type, they form a

pseudospherical

shell—a type of structure that conforms to a polyhedron with icosahedral

symmetry.

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Viral Genome Packaging

There are two general solutions to the problem of how to construct a capsid that contains nucleic acid: The protein shell can be assembled around the nucleic acid, thereby condensing the DNA or RNA by protein–nucleic acid interactions during the process of assembly.

The capsid can be constructed from its component(s) in the form of an empty shell, into which the nucleic acid must be inserted, being condensed as it enters

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A helical path for TMV RNA is created by the stacking of protein subunits in the virion

(the entire virus particle).

Tobacco mosaic virus (TMV). Assembly begins at a duplex hairpin that lies within the RNA sequence.

From this nucleation center

, assembly proceeds bi-directionally long the RNA until it reaches the ends.. TMV RNA packaging

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The disk is a circular structure, which forms a helix as it interacts with the RNA. At the nucleation center, the RNA hairpin inserts into the central hole in the disk, and the disk changes conformation into a helical structure that surrounds the RNA.

Additional disks are added, with each new disk pulling a new stretch of RNA into its central hole. The RNA becomes coiled in a helical array on the inside of the protein shell.

TMV RNA packaging

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Assembly of lambda

Maturation of phage lambda passes through several stages. The empty head changes shape and expands when it becomes filled with DNA, diagrammed on the left.

The electron micrographs on the right show the particles at the beginning (top) and the end (bottom) of the maturation pathway.

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Inserting DNA into a phage head involves two types of reaction:translocation

condensation. Both are energetically

unfavorable.

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Translocation is an active process in which the DNA is driven into the head by an ATP-dependent mechanism. A common mechanism for translocation is used for many viruses that replicate by a rolling circle mechanism to generate long tails that contain multimers

of the viral genome.

Translocation

1

23

4

Terminase

protein binds to specific sites on a

multimer

of virus genomes generated by rolling circle replication. It cuts the DNA and binds to an empty virus capsid, and then uses energy from hydrolysis of ATP to insert the DNA into the capsid.

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Less is known about the mechanism(s) of condensation into an empty capsid, except that capsids typically contain “internal proteins” as well as DNA. Such internal proteins might provide some sort of scaffolding onto which the DNA condenses.

This would be similar to the use of the proteins of the shell in the plant RNA viruses (e.g., TMV)

Condensation

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Sources :

https://ib.bioninja.com.au/standard-level/topic-3-genetics/32-chromosomes/genome-size.htmlGenome Size comparison

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Source: http://jetnewh2biology.blogspot.com/p/chapter-4-organisation-and-control-of_22.html

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Sources :https://www.differencebetween.com/difference-between-prokaryotic-and-vs-eukaryotic-genome/

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References

Image Courtesy:

1.”Prokaryote cell

diagram”By

Mariana Ruiz

LadyofHats

– Own work (Public Domain) via 

Commons Wikimedia

2.”Eukaryote DNA-

en”By

LadyofHats

(Mariana Ruiz) 

(CC BY-SA 3.0)

 via 

Commons Wikimedia