Sunday, 29 January 2017

BIOLOGY NOTES: CENTRAL DOGMA: AN OVERVIEW

BIOLOGY NOTES: CENTRAL DOGMA: AN OVERVIEW: central Dogma is the  relationship between DNA, RNA and proteins. It was  proposed by CRICK  in 1958. Crick proposed that the in...

Thursday, 26 January 2017

BIOLOGY NOTES: CENTRAL DOGMA: AN OVERVIEW

BIOLOGY NOTES: CENTRAL DOGMA: AN OVERVIEW: central Dogma is the  relationship between DNA, RNA and proteins. It was  proposed by CRICK  in 1958. Crick proposed that the in...

Wednesday, 25 January 2017

BIOLOGY NOTES: CENTRAL DOGMA: AN OVERVIEW

BIOLOGY NOTES: CENTRAL DOGMA: AN OVERVIEW: central Dogma is the  relationship between DNA, RNA and proteins. It was  proposed by CRICK  in 1958. Crick proposed that the in...

CENTRAL DOGMA: AN OVERVIEW

central Dogma is the relationship between DNA, RNA and proteins.

It was proposed by CRICK in 1958.






Crick proposed that the information present in DNA is transferred to DNA via replication and to RNA via transciprtion. Transciprtion leads to the production of tRNA, mRNA, rRNA. Now, mRNA undergoes translation to form proteins. 

This relationship between RNA, DNA and protein is known as central dogma in which information flows from DNA RNA PROTEIN and never in reverse.


Following is a basic idea of all these three processes.

DNA Replication is the process of making 2 identical copies of DNA from one original DNA copy. 
Essentially the DNA “unzips” and each of the original strands acts as a template for the new strands. 
DNA is synthesized in a 5’–>3’ direction during the S phase of the cell cycle.

Transcription is when template DNA strand is converted to complementary RNA. 
The RNA is very similar to DNA, except that it has Uracil (U) in place of Thymine (T) and it is single stranded.
RNA is synthesized in a 5 –> 3 direction as the RNA Polymerase moves along the DNA in a 3–> 5 Direction.

Post-Transcriptional Modification (RNA Processing) is the process of converting immature RNA to mature RNA that is ready to be translated.  5'- capping, 3'- tailing, splicing are carried out.

Translation is the process by which a RNA sequence is converted into a set of amino acids (AKA a protein) using tRNA, ribosomes and translation factors.

NOTE:The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes code for proteins, and that proteins fulfill most structural and catalytic and also most of the regulatory functions, in all cells, from microbes to mammals. 
However, the latter may not be the case in complex organisms.


This is because the concept of central dogma is just a simple interpretation of the exchange of genetic information going inside the cell; and, a simple interpretation often ignores many complications just to make things simple or easy to understand. 
central dogma was proposed in 1950s and many other parts and processes related to DNA, RNA and proteins known then and the one which are continuously discovered today are not included.



e.g. The presence of non-coding RNA (ncRNA), Alternative splicing, reverse transcriptase, introns, junk DNA, epigenetics, RNA viruses, trans-splicing, transposons, prions, epigenetics, and gene rearrangements are ignored to simplify things.

Exceptions also exist in the form of RETROVIRUSES. They carry out reverse transciption and RNA dependent RNA replication.
e.g. in TMV (tobacco mosaic virus),
ΦR17, ΦMS2 etc. the viral RNA is able to replicate itself and carry out RNA to RNA change with the help of RNA replicase.
similarly, RSV (ross sarcoma virus) can change RNA to DNA using reverse transcriptase. This process is called reverse transcription.


Reverse transcription and RNA dependent RNA replication and other above mentioned parts and processes doesn't form a part of central dogma.

Only DNA replication, transcription, and translation forms a part of it.

A number of startling observations and phenomena suggests that the traditional view of genetic regulatory systems in animals and plants may be incorrect.

It will take years, perhaps decades, to construct a detailed theory that explains how DNA, RNA and the epigenetic machinery all fit into an interlocking, self- regulating system.
But there is no longer any doubt that a new theory is needed to replace the central dogma that has been the foundation of molecular genetics and biotechnology since the 1950s.
The central dogma, as usually stated, is quite simple: DNA makes RNA, RNA makes protein, and proteins do almost all of the work of biology.

Friday, 20 January 2017

TUMOUR SUPRESSOR GENES

TUMOUR SUPRESSOR GENES
It suppresses cell division and growth. It is a loss of function mutation and a recessive one too because both alleles of a TSG needs to be deactivated for tumorigenesis to take place. But, some dominant loss of function mutations are also known.

The two best characterized Tumor Suppressed Genes are:
 1)RB  2) p53.

RB locus:
The gene RB is located in band q14 of human chromosome 13. It encodes RB protein .
The loss or inactivation of RB locus is mainly involved in retinoblastoma alongwith other type of cancer such as osteosarcomas  and small cell lung cancer.


During the M-to-G1 transition,
 pRb is dephosphorylated by PP1, to its growth-suppressive hypophosphorylated state Rb ; so that no growth takes place now.

E2F is actually  a group of transcription factor and forms E2F-DP complex with dimerization partner (DP) protein . This dimer activates genes whose products are necessary to push a cell into S phase.

                                                      But, When Rb is bound to E2F of E2F-DP complex, the complex acts as a growth suppressor and prevents progression through the cell cycle.
The Rb-E2F/DP complex also attracts a histone deacetylase (HDAC) protein to the chromatin, reducing transcription of S phase promoting factors.


When it is time for a cell to enter S phase,
complexes of CDK and cyclins phosphorylate Rb to pRb, inhibiting its activity.The initial phosphorylation is performed by Cyclin D/CDK4/CDK6 and followed by additional phosphorylation by Cyclin E/CDK2. pRb remains phosphorylated throughout S, G2 and M phase.


Phosphorylation of Rb allows E2F-DP to dissociate from pRb and become active.When E2F is free it activates factors like cyclins (e.g. Cyclin E and A), which push the cell through the cell cycle by activating cyclin-dependent kinases, and a molecule called proliferating cell nuclear antigen, or PCNA, which speeds DNA replication and repair by helping to attach polymerase to DNA.

Similarly, p16,  p21 and p27  ensure that CDK-4 and 6 remains inactive and thus contribute to tumour supression.

HOW CANCER TAKES PLACE:If both alleles of RB are inactivated; then it leads to absence of RB protein and absence of inhibition of E2F leading to continuous cell division.
 Similarly,  SV40 T Antigen and E1A protein of adenovirus binds with  unphosphorylated  RB and deter it from binding to E2F. As a result; E2F remains ever active and contribute to uncontrolled cell division.

p53 genep53 is the most important Tumor Suppressor Genes. It is involved in more than half of all cancers.
Initially, p53  was identified as an oncogene but later recognized as a dominant negative mutant.
Wild type p53 controls cell proliferation.

Protein p53 has different domains which help it perform  different  functions :

It's central domain binds the DNA by recognizing a 10 bp motif in it. SV40 binds to this central domain to deter it from binding DNA.

Now N terminal domian of p53  interacts with TBP to activate transcription of those genes ;whose promoter region contain 10 bp motif to which central domian of p53 has bound.
E1B protein of adenovirus binds with this N terminal domain to block p53 from functioning.

C terminal domain- it works during DNA damage.
If DNA damage is recognized during  G1 phase;then p53 binds to the single stranded DNA. Now DNA damage is repaired first and then only cell may enter S phase.
But, if the cell has already committed to division;  then p53 triggers apoptosis.

Functional p53 is a tetramer and C terminal domain works to oligomerize it.
It also has a signalling domain which binds to SH3 domain.

p53 as a transcription factor has the following 3 roles: 
1) Apoptosis,  
2) Cell cycle arrest in G1, 
3) Prevention of genomic instability.

CELL CYCLE ARREST IN G1 - Protein p53 binds to single stranded region and to mismatches produced by deletion or addition of 1-3 bases. Thus binding activates the DNA binding and transcription activation domain of p53 and now it leaves the site of damage and activates the target gene.
Transcription of p21 is activated and it prevents the action of CDK4,6-cyclin D and CDK2-cyclin E action, which prevents the onset of S phase.

APOPTOSIS - Protein p53 following it's activation by damaged DNA activates genes leading to apoptosis.

PREVENTION OF GENOMIC INSTABILITY - Level of p53 is regulated by interaction between p53 and cellular oncoprotein Mdm2. An increase in p53 level induces transcription  of Mdm2. Increase in Mdm2 level now inhibits p53 activity. This interaction maintains a low level of both proteins in normal cells.

Transcription activation by p53 requires the coactivators p300/CBP; .  p300 binds the transcription  activation domain of p53; thus helps Mdm2 to bind to p53. Binding of Mdm2 to p53 makes it an easy tsrget for degradation and thus helps to inhibit transcription activation by p53.

Protein p53 is modified in response to environmental signals thst influence cell growth. Signals like ionizing and UV  irradiation  cause acetylation of lysine, phosphorylation and dephosphorylation of serine at specific position of  p53. These changes maty affect the stability,  DNA binding  ,oligomerization,, and binding to other proteins.  Thus, p53 acts as a sensor that integrates information from many pathways that affect cell division.
NOTE- Both p53 and RB are activated by multiple pathways. Locus INK4A-ARF affects the function of both RB and p53. This locus produces p16 and p29. p16 prevents both assembly and activity of CDK-4,6-cyclin D ; as a result, RB remains active.
Similarly,  p19 inactivates  Mdm2 and this retains p53 active.

Thursday, 19 January 2017

BIOLOGY NOTES: ENZYMES INVOLVED IN DNA REPLICATION

BIOLOGY NOTES: ENZYMES INVOLVED IN DNA REPLICATION: ENZYMES INVOLVED IN DNA REPLICATION •Variety of enzymes help in DNA replication. •They can be listed as below: a) DNA Polymerase b) L...

Sunday, 15 January 2017