2 nd lecture: Gene structure - PowerPoint Presentation

Slide1

2

nd

lecture:

Gene

structure

by

Dr. Susan A. Ibrahim

What is a gene

?

A

gene is a sequence of nucleotides in DNA

that

codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

Central dogma

is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA and RNA makes protein

This

states that once 'information' has passed into 

protein

 it cannot get out again. In more detail, the transfer of information from 

nucleic acid

 to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.

Gene structure in general

The structure of a gene consists of many elements of which the actual protein coding sequence is often only a small part. These

include:

DNA regions that are not transcribed as well as

untranslated

regions of the RNA.

Flanking the open reading frame, genes contain a regulatory sequence that is required for their expression. First, genes require a promoter sequence. The promoter is recognized and bound by transcription factors that recruit and help RNA polymerase bind to the region to initiate transcription. The recognition typically occurs as a consensus sequence like the TATA box.

Additionally, genes can have regulatory regions many kilo-bases upstream or downstream of the open reading frame that alter expression. These act by binding to transcription factors which then cause the DNA to loop so that the regulatory sequence (and bound transcription factor) become close to the RNA polymerase binding site. For example, enhancers increase transcription by binding an activator protein which then helps to recruit the RNA polymerase to the promoter; conversely silencers bind repressor proteins and make the DNA less available for RNA polymerase.

The transcribed pre-mRNA contains

untranslated

regions at both ends which contain a ribosome binding site, terminator and start and stop codons.

In

addition, most eukaryotic open reading frames contain

untranslated

introns which are removed before the exons are translated. The sequences at the ends of the introns dictate the splice sites to generate the final mature mRNA which encodes the protein or RNA product

.

Eukaryotic gene

The cap and the poly(A)tail mentioned in the image are added to the mRNA to prevent the mRNA from being degraded by enzymes in the cell.

Many prokaryotic genes are organized into operons, with multiple protein-coding sequences that are transcribed as a unit. The genes in an operon are transcribed as a continuous messenger RNA, referred to as a

polycistronic

mRNA

. The term

cistron

in this context is equivalent to gene. The transcription of an operon's mRNA is often controlled by a

repressor

that can occur in an active or inactive state depending on the presence of specific metabolites. When active, the repressor binds to a DNA sequence at the beginning of the operon, called the operator region, and represses transcription of the operon; when the repressor is inactive transcription of the operon can occur (e.g. Lac operon). The products of operon genes typically have related functions and are involved in the same regulatory network.

Operons

Bacterial operons are

polycistronic

transcripts that are able to produce multiple proteins from one mRNA transcript. In this case, when lactose is required as a sugar source for the bacterium, the three genes of the lac operon can be expressed and their subsequent proteins translated:

lacZ

,

lacY

, and

lacA

. The gene product of

lacZ

is β-galactosidase which cleaves lactose, a disaccharide, into glucose and galactose.

lacY

encodes Beta-

galactoside

permease, a protein which becomes embedded in the cytoplasmic membrane to enable transport of lactose into the cell

.

Finally,

lacA

encodes β-

galactoside

transacetylase

.

The

lac operon uses a

two-part control mechanism

to ensure that the cell expends energy producing the enzymes encoded by the lac operon

only when necessary

.

In

the absence of lactose

, the lac repressor,

lacI

, halts production of the enzymes encoded by the lac

operon

.

The

lac

repressor is always expressed

unless a co-inducer binds to it

. In other words, it is transcribed only in the presence of small molecule co-inducer.

In

the presence of glucose

, the catabolite activator protein (CAP), required for production of the enzymes, remains inactive, and

EIIA

Glc

shuts down lactose permease to prevent transport of lactose into the cell. This dual control mechanism causes the sequential utilization of glucose and lactose in two distinct growth phases, known as

diauxic growth

.

Operon( lac gene structure)

1: RNA Polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6:

lacZ

, 7:

lacY

, 8:

lacA

.

Top:

The gene is essentially turned off.

There is no lactose to

inhibit the repressor, so the repressor binds to the operator, which obstructs the RNA polymerase from binding to the promoter and making lactase.

Bottom:

The gene is turned on.

Lactose is inhibiting the repressor

, allowing the RNA polymerase to bind with the promoter, and express the genes, which synthesize lactase. Eventually, the lactase will digest all of the lactose, until there is none to bind to the repressor. The repressor will then bind to the operator, stopping the manufacture of lactase.

The

trp

operon is

a

group of genes that is used, or transcribed,

together. The operon

codes for the components for production of tryptophan. The

trp

operon is present in many bacteria, but was first characterized in

Escherichia coli

. The operon is regulated so that when tryptophan is present in the environment, the genes for tryptophan synthesis are not expressed.

The

lac operon can be activated by a chemical (

allolactose

), the tryptophan (

Trp

) operon is inhibited by a chemical (tryptophan)

.

This

operon contains five structural genes

:

trp

E,

trp

D,

trp C, trp B, and trp A, which encode tryptophan synthetase. It also contains a repressive regulator gene called trp R.- trp R has a promoter where RNA polymerase binds and synthesizes mRNA for a regulatory protein. The protein that is synthesized by trp R then binds to the operator which then causes the transcription to be blocked. In the lac operon, allolactose binds to the repressor protein, allowing gene transcription, while in the trp operon, tryptophan binds to the repressor protein effectively blocking gene transcription. allowing transcription).

Tryptophan operon (

trp

operon

)

Also

unlike the lac operon, the

trp

operon contains a leader peptide and an attenuator sequence which allows for graded regulation.

It is an example of repressible negative regulation of gene expression. Within the operon's regulatory sequence, the operator is blocked by the repressor protein in the presence of tryptophan (thereby preventing transcription) and is liberated in tryptophan's absence (thereby thereby allowing transcription). The process of attenuation

complements

this regulatory action.

Trp

operon