DNA-Part2

RNA.

Mechanism of protein synthesis.

Identification of genetic code.

Messenger RNA.

Ribosome RNA.

Transfer RNA.

Protein synthesis.

Gene summary.

RNA.

RNA stands for ribonucleic acid.

The basic chemical structure of RNA, is very similar to that of DNA.

Both RNA and DNA, have

A phosphate group,

A sugar,

and a base.

The sugar in RNA is ribose.

The sugar in DNA is deoxyribose.

There is however, some very significant differences, between RNA and DNA.

DNA is a biomolecule, with a long double helix structure.

RNA is a shorter, single strand, biomolecule.

This difference dramatically differentiates, the functions of RNA and DNA.

DNA is the repository of all genetic information.

RNA is a carrier of instructions, from one gene to the cell.

DNA is resident inside the nucleus.

The DNA molecule is so big, that it cannot exit, from the nucleus.

The RNA molecules, however, can exit from the nucleus,

through the nuclear pore, to the cell, because they are much smaller.

There is another difference, between RNA and DNA.

DNA has the bases, A, T, C, and G.

RNA has the base, Uracil, instead of Thymine.

Uracil is denoted by the alphabet “U”.

So, RNA has the bases A, U, C, and G.

Adenine and Uracil are complementary.

Adenine always combines with Uracil.

DNA is a double stranded, long helix, of billions of nucleotides.

RNA is a single stranded, short string of nucleotides.

RNA carries instructions and information,

from the DNA inside the nucleus,

to the cell, outside the nucleus.

RNA transcribes the code present in DNA.

It faithfully, transcribes the code, present in the gene,

which is part of the DNA.

Gene transcription.

Let us consider the example of the DNA code, discussed earlier.

The DNA code was:

A, T, T,. A, G, G,. T, A, C,. G, T, A,. T, G, T,. G, A, T,.

RNA will faithfully transcribe this code.

It will only replace “T” with “U”.

The RNA code, which corresponds, to this DNA code will be:

A, U, U,. A, G, G,. U, A, C,. G, U, A,. U, G, U,. G, A, U,.

We note that RNA, precisely carries the information of the DNA.

Just like DNA, RNA comprises of three character codons.

These codons represent the same amino acid, that the DNA codons represent.

For example,

A, U, U,. corresponds to the amino acid: i,l,e : which is called Isoleucine.

A, G, G,. corresponds to the amino acid: A,r,g : which is called Arginine.

U, A, C,. corresponds to the amino acid: T,y,r : which is called Tyrosine.

G, U, A,. corresponds to the amino acid: V,a,l : which is called Valine.

U, G, U,. corresponds to the amino acid: C,y,s : which is called Cysteine.

G, A, U,. corresponds to the amino acid: A,s,p : which is called Aspartic acid.

Scientist often use RNA sequences, to identify genes.

We can do this, because RNA sequences,

faithfully represent DNA sequences.

A typical RNA string, will transcribe the code, of ‘one’ gene.

DNA, comprises of thousands of genes.

A typical RNA string, will correspond to ‘one’ gene.

Summary of RNA.

It is called Ribonucleic acid.

It has only a single strand.

It has the base, Uracil, instead of Thymine.

It is a relatively short single strand, biomolecule.

It faithfully represents the code of a gene, in the DNA.

It carries instructions and information from the DNA within the nucleus,

to the cell, outside the nucleus.

Mechanism of protein synthesis.

The genes in the DNA, have the code to synthesise proteins.

DNA is resident inside the nucleus.

DNA is a large bio molecule.

It cannot escape from the nucleus.

Typically a gene, will have the code, to synthesise a protein.

The machinery for synthesising proteins is present in the cytoplasm,

outside the cell.

Somehow the instructions inside the nucleus, has to be communicated,

to the cell outside the nucleus.

This very important communication, is achieved using RNA strands.

The code of the gene, is transcribed into RNA strands.

This process is called transcription.

RNA strands, can exit the nucleus, through tiny pores.

This way it reaches the cell cytoplasm.

Ribosomes are present in the cytoplasm.

Ribosomes are the actual bio chemical machinery,

which translate the code, into a physical protein molecule.

This process is called translation.

We consume proteins in our food.

The proteins are broken down, by the digestive system.

The proteins that we consume, are broken down into amino acids.

These amino acids, are present in the cytoplasm.

These free amino acids, are the raw material, for synthesising protein.

It is interesting to note, that the proteins the body synthesises,

is different from the proteins we consume.

Ribosomes take the instructions, from the RNA,

and amino acids, in the cytoplasm,

and synthesise the required protein.

To construct a protein, DNA sends out instructions, in RNA.

RNA exits the nucleus, and carries the instructions,

to the molecular machines, in the cytoplasm.

DNA sends out 3 types of RNA.

Messenger RNA, or m RNA.

Ribosome RNA, or r RNA.

Transfer RNA, or t RNA.

Using an interesting mechanism,

with these 3 instructions, the cell is able to synthesise a specific protein,

using the amino acids, in the cytoplasm of the cell.

We note that DNA, is the origin of the instructions,

and RNA are carriers of the instructions.

The central dogma of molecular biology,

is that information is transferred from DNA to RNA,

and then from RNA to protein.

The stable long term information, is located in the DNA,

gets transcribed to create a temporary messenger RNA.

The messenger RNA, moves out of the nucleus.

The ribosome, reads the code in the RNA,

translates it, and synthesises, a protein.

Identification of genetic code.

There are vast areas, in the genetic code, that are not used.

That is the current belief of scientists.

They even call the unused portion, as junk DNA.

By very rough estimates, they currently believe, that 10% of the DNA,

is used to code proteins, and other regulatory functions.

A gene is a long string of nucleotides, A, T, C, and G.

We have thousands of genes, in the DNA code.

How do we identify, where a code for a gene starts and stops.

DNA uses markers to identify, where the gene code starts.

The markers, which indicate the start, are called ‘TATA’ boxes.

RNA strands carry the code for a gene.

RNA codes have start and stop markers.

These start and stop markers, are also codons.

For example, the codons:

U, A, A.

U, A, G.

U, G, A.

There are also code sequences before the gene code,

which act as switches and regulators, for the gene.

A gene can be switched on and off or regulated by biochemical mechanisms.

Messenger RNA.

DNA creates, the messenger RNA, using the code sequence of the gene.

The gene is present in the DNA, as a double helix structure.

The bases A and T, are linked with hydrogen bonds.

The bases C and G, are linked with hydrogen bonds.

When RNA has to be formed, these bonds, in a gene, are temporarily broken.

Each of the strands, has a string of nucleotides, A, T, C and G.

Inside the nucleus, there are uncombined ribonucleotide molecules,

each containing 3 phosphate groups.

They are:

Adenine triphosphate, or ATP.

Uracil triphosphate, or UTP.

Guanine triphosphate, or GTP.

Cytosine triphosphate, or CTP.

When a segment, corresponding to a gene, is opened up,

there is a string of exposed nucleotides.

This string of exposed nucleotides, have the bases, A, T, C, and G.

The exposed nucleotides, pair up, with the free nucleotide triphosphates,

UTP, ATP, GTP, and CTP.

As expected :

”A” pairs with “U”.

”T” pairs with “A”.

”C” pairs with “G”.

”G” pairs with “C”.

The exposed nucleotide, in the gene, acts like a template.

A new messenger RNA molecule, is eventually synthesised.

The messenger RNA molecule, now has the template, to synthesise a specific protein.

The messenger RNA molecule, has a series of codons.

In the first step, all the codons, in the gene, creates a complimentary codon,

in the messenger RNA.

All the codons are not used, to code a protein.

Only selected portions, of the messenger RNA, are used for protein synthesis.

The segments that are used are called Exons.

The segments that are not used, are called Introns.

Initially the messenger RNA, has a long string,

of useful Exons,

and intermediate strings, of non useable Introns.

Messenger RNA, goes through a process of RNA processing.

In this process, the unusable Introns, are removed,

and the useful Exons, are stitched together.

After RNA processing, the messenger RNA, becomes much much shorter.

It has only useful codons.

Each codon, has 3 bases, and corresponds to, an amino acid.

A long string of codons will correspond to a long string of amino acids.

A protein, is a long string of amino acids.

This condensed messenger RNA, exits, via the pores in the nucleus,

to the cytoplasm of the cell.

This completes, one part of the process, to synthesise proteins.

Ribosome RNA.

Ribosomes are small granules, present in the cytoplasm.

Ribosomes are the site for, protein synthesis.

Ribosomal RNA, or r RNA is synthesised in the nucleus.

It has two subunits.

One is called as the 40S, subunit.

The other is called as the 60S, subunit.

The messenger RNA, binds with the Ribosomal RNA, in the cytoplasm.

The messenger RNA, now resides in a groove,

between the 60S subunit, and the 40S subunit.

This completes the second stage, of protein synthesis.

Transfer RNA.

Transfer RNA, or t RNA, is also synthesised in the nucleus.

Transfer RNA helps to identify, a specific codon, and link it to,

a corresponding, free amino acid.

Free amino acids are available, in the cytoplasm.

Free amino acids, are derived from digested proteins.

The key feature of transfer RNA, is that it can bind,

with both a specific amino acid,

and a codon, in the messenger RNA, specific for that amino acid.

A transfer RNA, attaches itself to a specific amino acid.

Alanine is an example, of an amino acid.

It corresponds to the codon G, C, A.

This binds with a transfer RNA, of Alanine.

Transfer RNA, has a clover shape.

At one end, is attached the Alanine amino acid.

The other end, has an anti codon.

The anti codon, is complementary to the codon.

Alanine corresponds to the codon G, C, A.

Alanine transfer RNA, has the anti codon C, G, U.

As we can see, C, G, U, is complementary to G, C, A.

Using its anti codon, Alanine transfer RNA, can identify,

the codon G, C, A, in the messenger RNA.

When there is a match, it can release, the amino acid, Alanine.

Now we have a messenger RNA, with a codon,

and many transfer RNAs, to identify each codon.

This completes the 3rd stage, for protein synthesis.

Protein synthesis.

Protein synthesis, is the process of binding together, a long string,

of amino acids.

It uses the messenger RNA, to identify each amino acid,

and the sequence of amino acids.

The Ribosome RNA has two binding sites, for transfer RNA.

It acts like a stitching machine.

One end holds the string of already stitched amino acids.

Another end holds the next amino acid, to be stitched.

The ribosomal RNA, facilitates the bonding of the new amino acid,

with the string of bonded amino acids.

This process is repeated, one amino acid at a time.

The ribosome starts the process, at the beginning, of the messenger RNA.

It proceeds along the messenger RNA, one codon at a time.

After each step, the string of amino acids, get longer and longer.

When it reaches the end of the messenger RNA, the complete protein is assembled.

The assembled protein, is released.

What started out as a set of instructions,

has now been successfully translated, into a complete protein.

Protein synthesis, is now complete.

All the proteins required by the cell, and the body, is synthesised by this process.

A specific type of cell, will synthesise, a specific set of proteins.

Different type of cells, will synthesise, different set of proteins.

The master DNA is the same, in all cells.

The way it expresses itself, is unique to a particular type of cell.

Gene summary.

Genes comprises of 3 character codons.

A gene typically contains the code, to synthesise a protein.

Proteins are the molecular machinery of life.

These proteins are being continuously synthesised, in our cells.

The proteins that we consume as food, is broken down to amino acids.

These amino acids, are the raw material, to synthesise proteins.

The code for synthesising proteins, is provided by the genes.

A very significant portion of cell metabolism, is achieved by genes and proteins.