Gene Expression

Central dogma

The central dogma of molecular biology was first articulated by Francis Crick in 1958[1] and re-

stated in a Nature paper published in 1970:[2]

Information flow in biological systems

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of

sequential information. It states that information cannot be transferred back from protein to either

protein or nucleic acid.

In other words, once information gets into protein, it can't flow back to nucleic acid.

The dogma is a framework for understanding the transfer of sequence information between

sequential information-carrying biopolymers, in the most common or general case, in living

organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and

protein. There are 3×3 = 9 conceivable direct transfers of information that can occur between

these. The dogma classes these into 3 groups of 3: 3 general transfers (believed to occur normally in

most cells), 3 special transfers (known to occur, but only under specific conditions in case of some

viruses or in a laboratory), and 3 unknown transfers (believed never to occur). The general transfers

describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA

information can be copied into mRNA, (transcription), and proteins can be synthesized using the

information in mRNA as a template (translation).

Biological sequence information

The biopolymers DNA, RNA and proteins, are linear polymers (i.e.: each monomer is connected to at

most two other monomers). The sequence of their monomers effectively encodes information. The

transfers of information described by the central dogma are faithful, deterministic transfers, wherein

one biopolymer's sequence is used as a template for the construction of another biopolymer with a

sequence that is entirely dependent on the original biopolymer's sequence.

[edit] General transfers of biological sequential information

Cdmb.svg

Table of the 3 classes of information transfer suggested by the dogma

General Special Unknown

DNA → DNA RNA → DNA protein → DNA

DNA → RNA RNA → RNA protein → RNA

DNA replication

As the final step in the Central Dogma, to transmit the genetic information between parents and

progeny, the DNA must be replicated faithfully. Replication is carried out by a complex group of

proteins that unwind the superhelix, unwind the double-stranded DNA helix, and, using DNA

polymerase and its associated proteins, copy or replicate the master template itself so the cycle can

repeat DNA → RNA → protein in a new generation of cells or organisms.

Transcription

is the process by which the information contained in a section of DNA is transferred to a newly

assembled piece of messenger RNA (mRNA). It is facilitated by RNA polymerase and transcription

factors. In eukaryote cells the primary transcript (pre-mRNA) is often processed further via

alternative splicing. In this process, blocks of mRNA are cut out and rearranged, to produce different

arrangements of the original sequence.

Translation

Eventually, this mature mRNA finds its way to a ribosome, where it is translated. In prokaryotic cells,

which have no nuclear compartment, the process of transcription and translation may be linked

together. In eukaryotic cells, the site of transcription (the cell nucleus) is usually separated from the

site of translation (the cytoplasm), so the mRNA must be transported out of the nucleus into the

cytoplasm, where it can be bound by ribosomes. The mRNA is read by the ribosome as triplet

codons, usually beginning with an AUG, or initiator methionine codon downstream of the ribosome

binding site. Complexes of initiation factors and elongation factors bring aminoacylated transfer

RNAs (tRNAs) into the ribosome-mRNA complex, matching the codon in the mRNA to the anti-codon

in the tRNA, thereby adding the correct amino acid in the sequence encoding the gene. As the

amino acids are linked into the growing peptide chain, they begin folding into the correct

conformation. This folding continues until the nascent polypeptide chains are released from the

ribosome as a mature protein. In some cases the new polypeptide chain requires additional

processing to make a mature protein. The correct folding process is quite complex and may require

other proteins, called chaperone proteins. Occasionally, proteins themselves can be further spliced;

when this happens, the inside "discarded" section is known as an intein.

[edit] Special transfers of biological sequential information

Reverse transcription
Reverse transcription is the transfer of information from RNA to DNA (the reverse of normal

transcription). This is known to occur in the case of retroviruses, such as HIV, as well as in

eukaryotes, in the case of retrotransposons and telomere synthesis.

RNA replication

RNA replication is the copying of one RNA to another. Many viruses replicate this way. The enzymes

that copy RNA to new RNA, called RNA-dependent RNA polymerases, are also found in many

eukaryotes where they are involved in RNA silencing.[3]

Direct translation from DNA to protein

Direct translation from DNA to protein has been demonstrated in a cell-free system (i.e. in a test

tube), using extracts from E. coli that contained ribosomes, but not intact cells. These cell fragments

could express proteins from foreign DNA templates, and neomycin was found to enhance this effect.

[4][5]

Methylation

Variation in methylation states of DNA can alter gene expression levels significantly. Methylation

variation usually occurs through the action of DNA methylases. When the change is heritable, it is

considered epigenetic. When the change in information status is not heritable, it would be a somatic

epitype. The effective information content has been changed by means of the actions of a protein or

proteins on DNA, but the primary DNA sequence is not altered.

Promoter Sequence

a promoter is a region of DNA that facilitates the transcription of a particular gene. Promoters are

typically located near the genes they regulate, on the same strand and upstream (towards the 5'

region of the sense strand).

Overview

In order for the transcription to take place, the enzyme that synthesizes RNA, known as RNA

polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences and

response elements which provide a secure initial binding site for RNA polymerase and for proteins

called transcription factors that recruit RNA polymerase. These transcription factors have specific

activator or repressor sequences of corresponding nucleotides that attach to specific promoters and

regulate gene expressions.

In bacteria
 the promoter is recognized by RNA polymerase and an associated sigma factor, which in turn are

often brought to the promoter DNA by an activator protein binding to its own DNA binding site

nearby.

In eukaryotes

the process is more complicated, and at least seven different factors are necessary for the

binding of an RNA polymerase II to the promoter.

Promoters represent critical elements that can work in concert with other regulatory regions

(enhancers, silencers, boundary elements/insulators) to direct the level of transcription of a given

gene.

Identification of relative location

As promoters are typically immediately adjacent to the gene in question, positions in the promoter

are designated relative to the transcriptional start site, where transcription of RNA begins for a

particular gene (i.e., positions upstream are negative numbers counting back from -1, for example

-100 is a position 100 base pairs upstream).

Promoter elements

* Core promoter - the minimal portion of the promoter required to properly initiate transcription

o Transcription Start Site (TSS)

o Approximately -34 bp upstream of the start site

o A binding site for RNA polymerase

+ RNA polymerase I: transcribes genes encoding ribosomal RNA

+ RNA polymerase II: transcribes genes encoding messenger RNA and certain small

nuclear RNAs

+ RNA polymerase III: transcribes genes encoding tRNAs and other small RNAs

o General transcription factor binding sites

* Proximal promoter - the proximal sequence upstream of the gene that tends to contain

primary regulatory elements

o Approximately -250 bp upstream of the start site

o Specific transcription factor binding sites

* Distal promoter - the distal sequence upstream of the gene that may contain additional

regulatory elements, often with a weaker influence than the proximal promoter

o Anything further upstream (but not an enhancer or other regulatory region whose influence

is positional/orientation independent)

o Specific transcription factor binding sites

Genes hold the information and help to transfer from one generation to the other. These genes

contain DNA. The DNA transcripts to RNA and then to proteins. This process is known as “Gene

Expression” .

‘Operon’ is a ‘cluster of genes’ that is been operated by a single promoter. An operon is a unit of

genetic material that functions in a co-ordinated manner by the help of an operator, a promoter and

structural genes that are transcribed together. The operons are mostly seen in prokaryotes like

E.coli. A good example is Lactose operon, which helps in utilization of lactose accordingly.

Important Regions of an Operon

Operator: A specific region of the DNA at the initial end of a gene, where the repressor protein

binds and blocks mRNA synthesis

Repressor: A protein that binds to an operator, blocking transcription of an operon.

Promoter: The region of an operon that acts as the initial binding site for RNA polymerase.

Structural genes: A gene that determines the amino acid sequence of a protein

types of operon

Inducible Operon

This is a type of operon which is switched on when a chemical, called inducer, is present. The

inducer is almost always a substrate. This operon has following components.

Repressible Operon

Another type of operon system is the repressible operon which is regulated by a chemical substance

called co-repressor. It is almost always the end product of a metabolic reaction. The operon is

switched off when the co-repressor, is present.

Summary

* Protein synthesis is a controlled process in which a given protein is synthesised in the cell only

when it is necessary.
 * When a particular protein is to be synthesised the specific gene has to express and initiate

transcription.

* The mechanism that stimulates the expression of certain genes and inhibits the others is called

gene regulation.

* The mechanism of gene regulation has been extensively studied in bacterial cells.

* In 1961 two scientists Jacob and Monad proposed the operon concept to explain the mechanism

of gene regulation.

* There are two types of operon systems inducible and repressible

* Inducible operon system consists of structural genes (cistrons), operator gene can either switch

on or switch off the structural genes by allowing or not allowing RNA polymerase molecules found

attached to promoter gene.

* The role of the operator gene is decided by a repressor protein synthesised by the regulate

gene.

* The repressor protein binds with the operate gene, RNA polymerase cannot be allowed and

hence structural genes get switched off.

* The repressor protein is kept in an active state by the inducer which is usually the substrate

molecule.

* The repressible operon has the same components as in inducible operon.

* The repressor is here activated by a chemical substance called co-repressor, which is usually the

end product.

* In eukaryotes gene regulation involves both inducible and repressible operons.

* The genes that code for enzymes of a given metabolic pathway may be even found on different

chromosomes.
 * Some genes in eukaryotic genes are always in a state of expression since the products that they

code are constantly required for the survival of the cell. Such genes are called constitutive genes or

housekeeping genes.