Genetics

Introduction to Genetics:

Genetics is the science of heredity (inheritance) that deals with the mechanism of transmission of character from parents to off spring.

• The term Genetics was introduced by W. Bateson in 1906.
• So, Genetic is a science that deals with heredity & Variation.
• Father of Genetics is Gregor Johann Mendel.

Genetic Material

The substance which stores biological information in a coded form & transfer it to next generation & cause its expression in the offspring is called Genetic material.

Essential requirement of Genetic materials:

The genetic materials should have the following characteristics.

1. It should be present in every cell.
2. It should be able to duplicate itself, forming its Carbon Copy.
3. It should be able to faithfully pass its copies into the progeny.
4. It should be able to occasionally develop inheritable change (mutation) to allow adaptation & evolution to occur in organ.
5. It should be able to express its information in the progeny.

Hereditary:

The tendancy of an individual to resemble with parent is called hereditary.
Heredity may be defined as transmission of character from parents to offspring i.e. through egg & sperm.

Inheritance:

It is a process by which the characters are passed on from the parent to the progeny. It is the basis of heredity.

Variation:

Acutally children only resembles their parents they are not identical. These difference shown by the individual of species are termed as Variation.
Variation means the differences that exist in the individual of Species i.e. the degree by which progeny differs from parents.

Significance of Variations:

1. It develops variations of Species.
2. It brings changes in the individual and help them to adapt the new environment.
3. It may causes evolution.

Chromosome

A thread like structure of nucleic acid & protein found in the nucleus of most living cell, carrying genetic information in the form of gene.

Gene:

A gene is a sequence of nucleotides acid (DNA) which codes for a particular character.

Properties of Gene:

• Each gene occupies a fix positive in a specific chromosomes. The position of gene is called locus of gene.
• Genes which moves from one locus to another locus is called transportional mobile gene / Jumping gene.
• Genes are arranged in linear position.
• Each gene has atleast two forms known as alleles.
• Alleles must have similar locus in homologous chromosome. Genes present on different chromosome are called non-alleles.
• Few genes have more than two alleles called multiple alleles.
  Example: Blood group (three).
• Genes are capable of being copied which is also called replication.
• Genes can undergo modification to form a new gene with different character that process is called mutation.

Function of Gene:

• Gene code for Special protein which determine the various character of cell so character of Organism is determined by Gene.
• They are responsible for the passage of characters from parent to offspring.

Some important terms

1. Cistron :-

It's the functional unit of DNA. It is a gene consisting of number of nucleotides & which is capable of synthesizing a polypeptide chain. S. Benzer coined the term.

2. Muton

It's the smallest unit of DNA which can under goes mutation. It represent change in pair of nucleotides.

3. Recon :-

It's the smallest unit of DNA that can undergo recombination & crossing over. It can be as small as one nucleotide pair of DNA.

Central Dogma of Molecular Genetics

Central Dogma is "Unidirectional Flow of genetic information from DNA to protein via RNA".

DNA (Replication) → DNA (Transcription) → RNA (Translation) → Protein

Reverse Central Dogma

Here genetic information get transferred from RNA to DNA then to protein through mRNA formation. Done by retroviruses.

RNA (Reverse transcription) → DNA (Transcription) → mRNA (Translation) → Protein

DNA is Genetic materials (Griffith experiment of Bacterial transformation)

• The experiment performal by Frederick Griffith in 1928 provided the evidence that DNA is a heriditary materials.
• Bacteriologist Griffith conducted an experiment with Streptococcus pneumoniae a bacterium that causes pneumonia in mammal also in human & commonly called pneumococcus.
• Griffith found 2 strains of Pneumococcus:
  1. Non-capsulated or non-virulent strain (R-type): It's non-pathogenic bacteria without capsule & cannot cause infection. These bacteria produce "rough" colony so called R-type 'R' stand for rough.
  2. Capsulated or virulent strain (S-type): It's pathogenic bacteria & causes infection when injected to mice. These bacteria produces Smooth colony (Polysaccharide) in culture media so called S-type 'S' stand for smooth.

So he injected live rough bacteria into mice, the mice didn't die. Then the mice was injected with live smooth bacteria, the mice died.

But when the mice was injected with heat-killed Smooth bacteria survived. Finally he then injected mice with a mixture of live rough bacteria & heat killed smooth bacteria. As these bacteria alone are harmless but their mixture called Pneumonia & killed the mice. He found live smooth bacteria in the blood of dead mice.

So, he concluded that some transforming principle (a chemical substance) from the dead smooth bacteria had entered the living rough bacteria & is transformed later into smooth bacteria. Thus transformation was a permanent genetic changes i.e. the evidence that DNA is the only genetic material in Organism.

Types :-

There are two types of nucleic acid.

1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)

a. Deoxyribonucleic acid (DNA)

DNA is the polymer of deoxyribonucleotide that contains many deoxyribonucleotide covalenty linked by phosphodiester bonds. DNA is generally double structured except in certain viruses where Single stranded DNA is Present ex: Parvovirus.

DNA is the genetic material & forms molecular basis of heredity in all organism. In certain viruses such as Tobacco mosaic virus (TMV), RNA is the genetic material.
In Prokaryotes, DNA occurs in cytoplasm whereas in eukaryotic cells, DNA is largely Confined to nucleus & is main Compound of chromosome hence called nuclear DNA.

• DNA molecule shows Primary, Secondary & tertiary structure like a Protein molecule being coiled in three Order for accomodation in small space.
• The DNA shows polarity (direction) one end of each DNA strand is called 5' end & other end is 3' end.
• DNA molecules are of 2 types: linear & circular. Linear DNA is found in the nuclei of eukaryotic cell. It is associated with protein in about 1:1 ratio. Circular DNA is found in many viruses, prokaryotic, mitochondria & chloroplast of eukaryotic & has little proteins.

Base pair:

The term 'base pair' refers to two bases one in each chain of DNA molecule joined together by hydrogen bonds. Each base pair consist of one 2-ringed purine & one 1-ringed pyrimidine. Therefore all the base pair have equal width & DNA helix has Constant diameter.

Anti parallel direction:

The two chains of DNA molecule run in opposite or antiparallel direction. Thus the two chains are parallel but their 5 prime - symbol (5') & 3 direction are opposite. This is analogous to a 2-lane road where the lane run parallel but carry traffic in opp. direction.

Chargaff's rule:

In 1950 E.E Chargaff formulated important generalization about DNA structure. These generalization are called chargaff's rule in his honour. They are summerized as below:

1. The DNA molecule irrespective of its source always has the A-T base pair equal in no to the G-C base pair.
2. The purine & pyrimidines are always in equal amount ie. A+G = T+C.
3. The amount of adenine is always equal to that of thymine & the amount of guanine is always equal to cytosine ie A=T & G=C.
4. The base ratio A+T / G+C may vary from one Species to another, but it's constant for a given Species. This ratio can be used to identify the Source of DNA & also help in classification.
5. The deoxyribose Sugar & phosphate component occurs in equal proportions.

Denaturation & Renaturation:

If DNA molecules is exposed to high temperature or titration with an acid or an alkali the two strands unwind & separate by breakdown of hydrogen bonds between the base pair. This process is called denaturation & Renaturation (melting).
When denatured DNA is incubated at a low temperature the two seperated strands reassociate to form a DNA duplex Called as renaturation.

Physical structure:

Astbury, Wilkins & Franklin have suggested 3-dimensional, helical configuration for DNA molecule by x-ray diffraction studies. So their investigation helped Watson & Crick to design model of DNA molecule.

Watson & Crick model of DNA:

Watson & Crick (1953) proposed the possible model for the deoxyribonucleic acid (DNA) known as "double helix structure". They were awarded by Nobel prize in 1962.

1. DNA molecule consist of two polynucleotide chains (strands).
2. These chains forms a double helix like a spiral staircase.
3. The sugar phosphate units forms the back bone & base forms the centres.
4. Both the strands are joined together by weak hydrogen bonds.
5. The two strands are antiparallel ie if one runs in 3'-5' direction, the other in 5'-3' direction.
6. The width of the DNA molecule is 20 A°.
7. The helix takes a complete turn after 34 A° long.
8. There are ten (3.4 A° for each) base pair in a complex turn (34 A°).
9. One chain can have any sequence of base but the other has to be Complementary. If there is a purine base on one helix, it has to be Pyrimidine on the other. This is called base paring. It is very specific & the only pattern follows is
   A = T (2 hydrogen bonds)
   C ≡ G (3 hydrogen bonds)
10. The nucleotides in a helix are joined together by phosphodiester bonds.
11. The two chains role spirally coiled around a common axis to form regular, right handed double helix.
12. The helix has a major groove & a minor groove alternately.

[Diagram: Watson-Crick model of DNA molecule showing P-S-A=T-S-P backbone, 34nM pitch, 0.34nm rise per base pair, 20A diameter]

Types of DNA:

DNA double helix model proposed by Watson & Crick is B-DNA. B-DNA has 10 base pair per turn & it is right handed helix.

Other forms of DNA:

1. A-DNA: Double helix DNA having 11 base pair per complete turn is called A-DNA. It is not found in normal physiological condition.
2. C-DNA: This type of DNA have 9 base pair per complete turns of right handed double helical form.
3. D-DNA: This type of DNA has 8 base pair per complete turn of right handed double helical form.
4. Z-DNA: A left-handed double helical form of DNA which has 12 base pairs per complete turn is known as Z-DNA.

Function of DNA:

1. It is the genetic materials & carries hereditary character from parents to young ones. This is achieved through its unique property of replication.
2. It enables the cell to maintain grow & divide by directing the synthesis of structural proteins.
3. It controls metabolism in the cell by directing the formation of necessary enzymatic protein.
4. Its produces RNAs by transcription for use in protein synthesis.
5. It creates variety in population by causing recombination through crossing over.
6. It contributes to the evolution of the organs by undergoing gene mutation (change in base pair).
7. It brings about differentiation of cells during development.
8. DNA has autocatalytic function directs the synthesis of its own carbon copy.
9. It controls the postnatal development through adulthood to death by its "internal clock". Thus DNA is the very basis of life.

b. Ribonucleic Acid (RNA):

• RNA is a polymers of ribonucleotides of adenine, uracil, thymine & Guanine which are joined together by phosphodiester bond. In Prokaryotic Cell, whole RNA is found in cytoplasm as there is no nucleus. In Eukaryotic cell most of RNA occurs in Cytoplasm confined to ribosomes & a small amount in nucleus.
• It is a single stranded long chain macromolecule of the ribonucleotides.
• RNA is a non-genetic materials except some viruses. Eg TMV, HIV etc.

Types of RNA:

On the basis of molecule size & function, there are three major types of RNA.

1. Ribosomal RNA (r-RNA)
2. Messenger RNA (m-RNA)
3. Transfer RNA (t-RNA)

i) Ribosomal RNA (r-RNA)

• It is the most abundant & stable type of RNA.
• It constitute about 70-80% of total RNA.
• r-RNA is present in ribosomes.
• r-RNA combines with ribosomal protein to form complete functional ribosome & plays a important role in the binding of mRNA to ribosome during translation.
• r-RNA is Synthesized from the DNA.

ii) Messenger RNA (m-RNA)

• It is most heterogenous in size & stability.
• It consitute about 5 to 10% of total RNA.
• It is also called nuclear RNA.
• It brings message from DNA ie it carries gentic information specifying the aminoacid sequence in protein to ribosome.
• m-RNA is the only RNA that is translated into protein.

iii) Transfer RNA (t-RNA): (Clover leaf structure)

• It is the second most stable type of RNA & Soluble RNA.
• It constitute of 10-15% of total RNA.
• It is the smallest RNA out of three RNA.
• It helps to transfer aminoacid to make protein chain.
• It is Single stranded structure but has a clover-leaf like structure which is folded to consist of 5 arms in which four arms are recognition steps.

[Diagram: t-RNA structure with Enzyme Site, Aminoacyl-tRNA synthetase loop, Extra loop (variable loop)]

Function of RNA:

RNA plays a multiple role in a cell.

1. It brings about protein synthesis in a cell. All the 3 types of RNA play a role in this process.
2. RNA is the genetic material of certain Viruses Ex HIV.
3. The rRNA is a component of ribosomes, the site of protein synthesis.
4. Some RNA is associated with chromatin fibres during interphase. It initiates replication of DNA.
5. Certain RNAs acts as enzymes Ex Ribonuclease.
6. RNA primer is essential for starting replication of DNA.

Difference between DNA & RNA

Replication : Synthesis of DNA

The unique process of making an identical copy of a double stranded DNA, using existing DNA as a tempelate for the synthesis of new DNA strand is called DNA replication.

Chemical necessary for DNA synthesis:

These chemical are listed as below:

a) Building block: The building blocks of DNA is deoxyribonucleotide which are located in nucleoplasm. There are four type of nucleotide dAMP, dGMP, dCMP & dTMP. These nucleotides are activated into dATP, dGTP, dCTP & dTTP through phosphorylation & in presence of enzyme phosphorylase.

b) Enzymes: There are different enzymes such as

1. DNA helicase: It opens the helix (unwind the helix by breaking H-bonds).
2. DNA gyrases / Topoisomerase: It release tension by cutting, rotating & resealing the strands.
3. Single strand binding Protein (SSBP): stabilizing. After unwinding DNA strand, SSBP bind with Single stranded of DNA & prevents the strand from rewinding. It makes the stable strand.
4. DNA ligase: When topoisomerase cut the strand they are joined by ligases (joining of DNA fragments).
5. DNA polymerase I: It helps in removing primer (DNA segment) obstructing in the way of growing DNA.
6. DNA polymerase II: It's actually participating in replication.
7. Primases: It is an enzymes help in the synthesis of RNA primer & that guides the process of replication (as segment of RNA).

Types of Replication

Replication is of three types:

1. Conservative replication: In this replication, two strands of Parental DNA do not seperate, but they are conserve in one daughter DNA where as another daughter DNA consist of two new strands.
2. Dispersive replication: The replication two strands of parental DNA. The replication in which the Original DNA strands break & synthesis their complementant part and recombines in a random fashion so that each strands have old and new part.
3. Semi Conservation mode of DNA replication: Watson and Crick suggested that the two strand of DNA molecule uncoil and seperate and each strand serves as a template for the synthesis of a new Complementary strand. The template and its Complement for a new DNA double strand that is identical to Original DNA molecule. Each daughter DNA molecule consist of one parent strands one new strand. Since only one parent strand is Conserved in each daughter molecule so this mode of replication is called Semi-Conservative.

Procedure for DNA replication:

It is a Complex multistep process requiring the services of many enzyme protein factors and metal ions.

a. Activation of deoxyribonucleotide:
Four types of deoxyribonucleotide monophosphate are found floating free in the nucleoplasm and serve as the raw materials in DNA synthesis. For incorporation into DNA nucleotide are activated by ATP. This reaction is called phosphorylation and is catalysed by an enzyme phosphorylase. The nucleoplasm has inactive deoxyribonucleotide (DAMP, DGMP, DCMP and DTMP) with the help of phosphorylase enzyme the inactivated deoxyribonucleotide are activated (DATP, DGTP, DCTP and DTTP).

b. Unwinding of Parental DNA:
Replication starts at specific point of DNA known as Origin or site of replication (ori).
DNA helicase lies at ori and moves forward so that hydrogen bond and nitrogen base are broken. It develops Y-shaped structure called as replication fork. When DNA helicase continues to work the helicase move apart and each helix is called templates. The separated helix are stabilize by SSBP. So unwinding create a problem of Supercoiling which is stoped i relaxed by DNA gyrase.

c. Formation of RNA primer:
A short chain of RNA is formed on the DNA template at the 5' end. This is called as RNA primer. The enzymes primase catalyzed the polymerization of RNA building blocks (A, U, G, C) into primer. The primers are latter removed and the gaps left are filled with deoxyribonucleotide to make DNA strands Continuous.

d. Base pairing:
The deoxyribonucleoside triphosphate get joined by hydrogen bond to the appropriate nitrogen base of the both single DNA chain according to the base pair rule of Watson & Crick.
i.e. A-T, T-A, C-C and G-C.

e. Conversion of Deoxyribonucleotide monophosphate:
The deoxyribonucleoside triphosphate joined to each single DNA chain break off their inner higher energy bonds and set free pyrophosphate (P~P) molecule.
P~P + H2O Pyrophosphatase → 2Pi + Energy
This energy is used to desire the polymerization of Nucleosides to form DNA.

f. Formation of New DNA chain / chain elongation:
As helix gets unwounded, RNA primer initiates DNA synthesis. After aligning RNA primer to DNA template DNA polymerase III begins to add deoxyribonucleotides or primer only in 5' to 3' direction. So RNA primer move forward deoxyribonucleotides continue to add on growing DNA strand.

This process produces two double DNA chains which are identical to each other as well as to the Orginal "mother chain". In this way, the genetic code is faithfull transmitted from one DNA "generation" to the next.

The DNA polymerase can polymerise that deoxyribonucleotides in the 5'-3' direction. The two DNA strand are antiparallel. So one new strand is formed in a continuous stretch in the 5'-3' direction & called leading strand.
On the other parent strand, short DNA segement are formed starting from RNA primer. These DNA segments are called okazaki fragments which are joined together by DNA Ligase after replacing RNA primer with Deoxyribonucleotide. Such discontinuous strand is called lagging strand.

g. Editing (Proof reading) & DNA repair:
The specificit of base-pairing ensures accurate replication. However sometimes wrong bases do get in. These are noted & remove by DNA polymerase.
The abnormal region of DNA resulting from mutation are splitted by enzyme called nuclease. DNA polymerase resynthesis the missing segment of DNA strand. The DNA ligase reseals the strand under repair. Thu made the damaged DNA strand normal.

h. Helix Formation:
Each daughter double DNA molecular became esp. spirally coiled to form a double helix.

Significance of DNA replication:

• DNA replication is necessary for cell division.
• DNA replication helps to maintain genetic make up of an Organism.
• DNA replication essential for the transmission of parental character to offspring.

Genetic Code

The cells are enabled to synthesize their specific protein by the informating flowering from the DNA this information exist as the particular sequences of base in the DNA strand & is called genetic code.
So genetic code is defined as "the Sequence of base triplets in DNA molecules".

Nature of Genetic Code:

There are twenty kinds of aminoacid & only four types of nucleotides. If a sequence of three bases coded for one aminoacid, the four bases would specify 64 (4x4x4) aminoacid. So sequence of three bases are called the triplet code And this code was first suggested by George Gamow in 1954.
When reading the cods the cell begins at a fixed point called a state codon (AUG) & ends at codons such as (UAA, UAG, UGA).

Characteristics of Genetic code:

These are listed as below:

1. Triplet nature: The genetic code is a triplet code. Three adjacent bases are called as Codon & specify one aa.
2. No overlapping: The adjacent codon do not overlap. three do not share any base. Each single base is a part of only one codon ie once used arent used again to.
   Ex: The Sequence CCUCAG is read only as CCU, CAG not as CCU, CUC, UCA, CAG.
3. No punctuation: The genetic code is commaless, there is no punctuation marks "(gaps) between the coding triplets. So reading of code begins at a fixed point & Continue three nucleotide at a time without a Pause till the termina for Codon marks the end of message.
4. Universality: The genetic code is Universal ie a given codon in the DNA & mRNA is Same in all living Organ i.e from bacteria to man.
5. Degeneracy (Redundancy): The genetic code is degenerate. It lacks specificity & one aminoacid of few has more than one Code triplet.
   Only methionine & tryptophan have single triplet codon. Phenylalanine has two codons such as UUU & UUC. Where as other aas are Specified by 2-6 base triplet such as CGU, CGC, CGA, CGG, AGA & AGG.
6. Non ambiguity of codons: Each codon codes for only one aas none for more than one. Ex the Codon GAA & GAG both specify glutamic acid, neither of them specifies any other aas.
7. "Nonsense" or terminator codons: Three of the 64 codons namely UAA, UAG & UGA donot specify any aas but signal the end of message they are called nonsense. Thus only 61 of the 64 codons code for aas.
8. Initiation or start codon: The codon AUG is called initiation or start codon as it begins the synthesis a polypeptide chain.
9. Collinearity: DNA is a linear polynucleotides & a protein is a linear polypeptide chain. The sequence of aas in a polypeptide chain corresponds the sequence of nucleotide bases in the gene (DNA the codes for it).