Thursday, March 12, 2009

Some Important Links of Cell Biology

I think understanding bioinformatics depends on the concepts of cell biology (cell anatomy, cell function, chromosome structure, etc.. ). So, here i provide some important links from where you can get the concept of cell biology :

If anyone interested on "Origins of Life on Earth"

Future i will discuss the hot topics of cell biology which need to understand Basic Bioinformatics.

Wednesday, March 11, 2009

Domain: a compact local semi-independent folding unit presumed to have arisen by gene fusion & gene duplication events.Domains are not formed from contiguous region of amino acid sequence.They may be discrete entities joined by a flexible linking region of the gene & may also exchange chains with domain neighbours.The combination of domains within a protein determines its overall functions & stable structure.

Analogues: non-homologus proteins that have similar folding site which are believed to have arisen through converges evolution.

ORF: Open Reading Frame.A series of DNA codon including a 5' initiation codon & a 3' termination codon that encodes a putative( known) gene.A DNA sequence must contain a translation start codon(usually ATG) & not exhibit any of the stop codons (usually TAA,TAG,TGA) in phase with the ATG for quite some length(at least 300 nuclotides seperate the start & stop codon).

The ORFing protocols can probably correctly identify 85% of the protein coding regions.There are a variety of situations that frequently occur where a more sophisticated approach need to use.One such approach is taken by GenMark which include
  • finding very short proteins,
  • resolving ambiguous cases where overlapping ORFs are predicted in different reading frames.
  • to pinpoint the exact start codon(most distal ATG is not always the correct one).
Six Frame Translation: Translation of a stretch of DNA taking into account three forward translations and three reverse translations arising from three possible reading frames of an uncharacterised stretch of DNA.
Destination of Proteins:

Proteins have to reach right destination in the organism or within the cell to correctly accomplish their functions.As protein is translated,the peptide chain may expose to a variety of highly specific sequence signals.
One such signal is "ZIP code" which is used by the cell to direct the protein to the appropriate compartment (in or out of the cell).This process always involves the transport of the protein across one or several membranes & is also referred to as translocation.The activity or destination of a protein-
  • getting attached to the cell membrane,
  • being secreted outside the cell,
  • being transported into the periplasm (incase of bacteria),
  • being transported to the mitochondria or any other organelle,
  • being transported into the cell nucleus.
So it is important to know the final compartment of a protein where it ends up to understand its function.This proven/predicted information is recorded in protein databases like swiss-Prot,PDB etc.

A newly synthesized peptide chain is converted into a functional protein by the folding of this chain into a compact & stable 3-D structure.The final structure of a protein generally consists of several relative independent domains.

Most natural proteins are made of combination of 1 to 10 domains picked from a set of a few thousands.The domains are identifiable by their scaffold sequence signatures (the motif in the protein means amino acid texts that remain recognisable despite a zillion years of divergent evolution).The domain architecture underlying a particular protein sequence provides hints about the possible 3-D structure of it & its potential biochemical or cellular functions.

The recognition & definition of protein domains is a major research topic of Bio-informatics.

Tuesday, March 10, 2009

Steps of Producing matured Proteins:

  • Replication- Formation of Single strand of DNA from double strands of DNA.
  • Transcription- Formation of primary transcript from single strand of DNA.
Primary transcripts consist of introns (non-coding regions of DNA sequences which contains prediction of promoter regions,regulatory elements and protein binding sites) and exons (coding regions of DNA sequences which are usually small-150 bp long on average and here the sequence of their splice sites are available).
  • Splicing- Formation of mRNA from primary transcript by removing introns.
  • Translation- Native/nascent protein is formed from mRNA through this process.
  • Post translational modification- matured proteins are formed.
Protein maturation/post translation modification include any combination of the following stages:
- cuts within the amino acid chain,
- removal of fragment of the amino acid chain (eg. insulin),
- chemical modification of specific amino acids (eg. methylation),
-addition of lipid molecules (eg. myristoylation),
- addition of glycosidic(sugar) molecules (eg. glycosylation).