DNA replication

This is a good animation that gives detail info about Dna replication.http://sites.fas.harvard.edu/~biotext/animations/replication1.html

dna animations link

http://www.dnalc.org/resources/3d/12-transcription-basic.html

how mitochondria powers cell

peek into cell

 a wonderful video where you can peek the dynamics inside  the cell.

chromosome

 When I ask my under graduating students to define chromosome, they invariably answer – it is a vehicle of inheritance that contains Genetic Material or DNA or Genes.  
When asked further, how it appears or looks like in the cell?  Can you draw a picture of the chromosome? 
They draw the typical picture showing two chromatids joint at centromere.

There is a big flaw in defining the chromosome. There is no text available that can snapshot the in depth true picture of the CHROMOSOME.

       The term CHROMOSOME has been misused. There should have been some restriction on using the term at wrong place. With rare exceptions most of the authors use the term CHROMOSOME very liberally. 
       That causes confusion among the young learners.  I can give many examples of mishandling of the term chromosome but that is not our purpose at the moment.

Le t we start with one example, what biology online says about Chromosome.

Biology online

Definition

noun, plural: chromosomes

A structure within the cell that bears the genetic material as a threadlike linear strand of DNA bonded to various proteins in the nucleus of eukaryotic cells, or as a circular strand of DNA (or RNA in some viruses) in the cytoplasm of prokaryotes and in the mitochondrion and chloroplast of certain eukaryotes.

Supplement

In eukaryotes, the chromosomes appear as threadlike strand that condense into thicker structures and aligns on the metaphase plate during mitosis. Humans normally have 23 pairs of chromosomes, each with a characteristic length and banding pattern. Chromosomes occur in pairs (in most somatic cells) since one member of each pair comes from the mother and the other from the father. In most prokaryotes, the chromosome is usually a circular strand of DNA; hence, the entire genome is carried on only one chromosome. In viruses, the chromosome may appear as short linear or circular structure containing the DNA or RNA molecule often lacking any structural proteins.

Word origin: from the Greek chroma = color + soma = body.

Now look at biology online basic definition (without supplement)

Definition

noun, plural: chromosomes

A structure within the cell that bears the genetic material as a threadlike linear strand of DNA bonded to various proteins in the nucleus of eukaryotic cells, or as a circular strand of DNA (or RNA in some viruses) in the cytoplasm of prokaryotes and in the mitochondrion and chloroplast of certain eukaryotes

Let we scrutinize it:

 Chromosome in eukaryotic cell:

It is a structure in the nucleus.

It is a structure that bears genetic material.

The structure bears the genetic material as a thread like linear strand of DNA bonded to various proteins.

Chromosome -In prokaryotic cell:

It is a structure in the cytoplasm.

It is a structure that bears genetic material.

The structure bears the genetic material as a circular strand of DNA.

Chromosome In some viruses-

-As a strand of RNA (of course in other viruses as a strand of DNA)

Chromosome In mitochondrion and chloroplast of certain Eukaryotes-

- As a circular strand of DNA.

Adding supplement to definition serves nothing but further supplements the confusion.

All this makes the chromosome definition a blurry thing. It neither fixes its structure nor the chemical composition.So chromosome is a very vague term used by biologist. Bear in mind it has different meaning at different places.

Is there any solution to clear this mess?

Yes, I have been working hard to make it simple and clear.

But I wish to know, how many people are interested?

If anyone happens to visit this blog and feels that confusion must be cleared, please comment. 
 I will write further in detail.

The Valuable Antisense

The particular terminology with respect to Gene Expression is quite confusing for beginners. at least i have faced this problem during my student life.

the sense strand ( DNA)

the nonsense or antisense strand( DNA)

here antisense or nonsense strand is the active strand that participates in transcription.

whereas

the sense strand just opposite complimentary strand.

So according to this definition - The ANTI-SENSE is VALUABLE

But this makes things complicated. And it is further complicated by Using Additional terminology

coding and non- coding strand.

here again interestingly coding strand is actually not participating strand.

and it is non-coding strand that undergoes transcription.

So say anti- sense or non- coding, it points to same strand - that undergoes transcription.

what beginner in molecular biology may think that 
in DNA helix which consist of double strand, out of the these  two strands
 one strand is sense strand and the other is antisense strand.

But this is not true if we scrutinize this definition.

why?

Because-

1) in reality particular transcription occurs only in very short stretch of DNA strand with respect to full length of DNA. ( particular gene - from promoter region to terminator region)

2) since Genes are present on both the strands, same strand of DNA may become antisense for one gene and sense strand for another gene. see in fig. gene1 and gene2 carefully template strand in two genes are not the same.

So I prefer simple and unambiguous terminology and snuggest students to follow this and keep things simple.-template strand and non- template strand for a specific gene.

Template Strand- is that stretch of DNA which acts as template for transcription. (mind it, only stretch DNA from specific promoter to terminator not full length DNA)

and

Non- Template Strand- is just a H- bonded opposite complimentary stretch of the DNA strand.

So be sensible, do not heed much to nonsense things.

GENE

It is by convention,

when a DNA sequence associated with a gene is specified,

it is the sequence of the non-template strand that is given,

and it is written in the 5'-to-3' direction.

This convention is adopted

because the sequence of the non-template strand corresponds to the sequence of the RNA that is made. (except T is replaced by U)