Molecular Genetics

The Genetic/Molecular Basis of Inheritance

DNA
Polymer containing chains of nucleotide monomers i.e., Polynucleotide

Nucleotide
sugar + base + phosphate

Sugar
2 deoxyribose i.e., -OH group on carbon 2 of ribose replaced by H 5 carbon ring Base attached to the 1 carbon of the deoxyribose

Base
Purines : two carbon-nitrogen rings Adenine Guanine Nitrogen at position 9 of the ring Pyrimidines : single carbon nitrogen ring Thymine Uracil Cytosine

Nucleoside
A sugar + Base

Phosphate group
Nucleotide has 1 or 2 or 3 phosphate groups (PO4 ) attached to the 5 carbon of the sugar

Nucleotides

Nucleotides occur as individual molecule or polymerized as DNA or RNA

DNA Polynucleotide
Nucleotide triphosphate Two phosphates are lost during polymerization Nucleotides joined by remaining phophate

DNA Polynucleotide
Phosphodiester bond between 5phosphate of one nucleotide and 3 hydroxyl of the next nucleotide Therefore, polynucleotide has a free 5 phosphate at one end (5 end) and a free 3OH (3end) at the other end

The Double Helix

Two polynucleotide strands wrapped around each other to form double helix
Sugar phosphate part of molecule forms a backbone Base face inwards and stacked on top of each other Two polynucleotide chains run in opposite direction

The Double Helix

Right Handed Executes a turn every 10 bases

Major groove interacts with proteins

Variant DNA structure identified including Z DNA having left handed helix

The Double Helix

Complementary base pairing Hydrogen bonds between bases on the two DNA strands stabilize the double helix Purine always with pyrimidine

Therefore, A with T or U and G with C

The Double Helix

Advantages of Complementary base pairing Allows genetic information to be preserved during replication of DNA and expression of genes Separation of two strands by heat or chemicals or action of enzymes

RNA Structure
Thymine replaced by Uracil 2deoxyribose replaced by ribose

Exists as a single polynucleotide strand

Gene
A unit of information Corresponds to a discrete segment of DNA that encodes the amino acid sequence of a polypeptide In humans about 30,000 genes arranged on 23 chromosomes

Gene

Dispersed and separated by noncoding intergenic DNA In humans genes sequence account for less than about 30% of the total DNA

Gene
Information encoded on the template strand or antisense strand or noncoding strand which directs the synthesis of an RNA molecule The other strand is called nontemplate strand or sense strand or coding strand
Both DNA strands can act as the template strand

Gene

Genes vary greatly in size from less than 100 bases pairs to several million base pairs

Gene families
Most genes spread out randomly along chromosomes

Some organized into groups or clusters

Operons in bacteria and multigene families in higher organism

Gene families
Lac operon in E.coli Codes for enzymes required by the bacterium to break down lactose Allows to be switched on or off at the same time allowing the organism to use its resources efficiently

Multigene families
Genes are identical or very similar Not regulated coordinately

Probably reflects a requirement for multiple copies of that gene fulfilled by evolution
May exist as separate clusters on different chromosomes

Multigene families
May be simple or complex
Simple multigene families have identical genes e.g., gene for the 56 ribosomal RNA, there are about 2000 clustered copies of this gene Complex multigene families contain genes that are very similar but not identical e.g., Genes that encode protein chains found in hemoglobins

Gene expression

Transcription Process of transfer of information by DNA directing the synthesis of mRNA molecule of complementary sequence

Gene expression
Translation Process of mRNA directing the synthesis of a poly peptide bases on base sequence of the mRNA The amino acid sequence of the protein determines its three dimensional structure which in turn dictates its function

The Central Dogma

The transfer of information can only occur in one direction from DNA to RNA to protein and cannot occur in reverse Exception reverse transcriptase enzyme found in retroviruses which can copy RNA into DNA

Gene
Structural features of a typical human gene

Gene promoters
Gene enhancers Gene silencers

Locus controlled regions

Gene promoters

Expression of genes is regulated by a segment of DNA sequence present upstream of the coding sequence is known as promoter

Gene promoters
DNA sequence gene in promoters are conserved

Recognized and bound by the RNA polymerase and other associated proteins called transcription factors that bring about the synthesis of an RNA transcript of the gene

Introns and Exons

Exons : Coding segments of DNA of a gene Introns : Interspersed noncoding segments of DNA of a gene Before the biological information in a gene can be used to synthesise a protein, the introns must be removed from RNA molecules by splicing leaving only the coding information of exons in continuity

Pseudogenes
Copies of some genes which contain sequence errors acquired during evolution whereby rendering them non functional are known as pseudogenes.
Represent evolutionary relics of original genes Examples : Several globin pseudogenes present in the globin gene clusters

Gene Expression

Genetic information coded in the base sequences of DNA molecules as a series of genes Gene expression term describes how cells decode the information to synthesize proteins required for cellular function

Gene Expression
It involves the synthesis of a complementary RNA molecule whose sequence specifies the amino acid sequence of a protein For every gene the DNA sequence is collinear with the amino acid sequence of the polypeptide it encodes

Gene Expression

5 -3 base sequence of the coding strand specifies the amino acid sequence of the encoded polypeptide from the amino to carboxy terminus

Genetic Code
It describes how base sequences are converted into amino acid sequences during protein synthesis DNA sequence of a gene divided into a series of units of three bases

Codon
Each set of three bases is called is called a codon
It specifies a particular amino acid The four bases in DNA and RNA can combine as a total of 4 = 64 codons
3

They specify the 20 amino acids found in proteins

Codon
Degeneracy or the redundancy of the genetic code

Amino acid having more than one codon

Exception : Methionine and tryptophan

Codon
Synonyms : Codons which specify the same amino acids and tend to be similar

Variations between synonyms tend to occur at the third position of the codon, known as the wobble position
This minimizes the effects of mutations

Codon

Of the 64 possible codons, 61 code for amino acids

The remaining three, UAG, UGA, and UAA act as signals for protein synthesis to stop : Termination codons or stop codons

Codon

AUG the codon for methionine, is the signal for protein synthesis to start : initiation codon

All polypeptides start with methionine, may be removed subsequently

Reading Frames
Each set of codons is known as a reading frame

Depending on which base is chosen as the start codon, three possible sets of codons may be read from any base sequence

Reading Frames
The initiation codon determines the reading frame of a protein coding sequence

Usually other reading frames tend to contain stop codons and are not used for protein synthesis An open reading frame is a sequence of codons bounded by start and stop codons

Universality of the code

The genetic code applies universally with all organisms using the same codons for each amino acid Exception : Mitochondrial genomes and some unicellular organisms For example in mitochondria, UGA, a termination codon, codes for tryptophan

DNA replication
Copy of DNA produced prior to division of cell DNA is copied 5 3 by DNA polymerase using single stranded DNA as a template Replication semiconservative

In E. coli, DNA polymerases I and III have 3 5 exonuclease activity proofread sequences ensuring a very low error rate

The replication fork

DNA synthesis occurs at the replicaton fork A helicase separates the double helix

A single strand binding (SSB) protein keeps strand separate

DNA synthesized continuously on the leading strand

The replication fork

Discontinuously as segments (Okazaki fragments) on the lagging strand
DNA polymerase alpha initiates DNA synthesis DNA polymerase delta and alpha synthesize respectively leading and lagging strand DNA ligase joins the Okazaki fragments by a phosphodiester bond

DNA Replication
Chromosomes replicated from multiple origins
Replication bubbles form and merge eventually Transcriptionally active regions replicated first Repication requires DNA to be unwound from nucleosomes

DNA Replication

Special mechanisms required to replicate the ends of chromosomes Telomerase adds noncoding sequence that allows replication of chromosome ends