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Q: The hierarchy of cells, chromosomes, genes, and DNA ( Answered 5 out of 5 stars,   3 Comments )
Question  
Subject: The hierarchy of cells, chromosomes, genes, and DNA
Category: Science > Biology
Asked by: rambler-ga
List Price: $25.00
Posted: 29 Jul 2005 11:48 PDT
Expires: 28 Aug 2005 11:48 PDT
Question ID: 549516
TV programs give the impression that DNA is one long continuous molecule.
But I always thought that there was a hierarchy:
(a) Cells contain chromosomes.
(b) Chromosomes contain genes.
(c) Genes contain DNA.

So, I have a couple of questions:
(1) Which is it? Is DNA one long continuous molecule, or is it divided into genes?
(2) Chromosomes are visible under a strong microscope as distinct entities.
But how are distinct GENES identified? What marks the beginning and end
of a particular gene?
(3) Is there a website that gives a visual representation of the hierarchy
of cells, chromosomes, genes, and DNA?
Answer  
Subject: Re: The hierarchy of cells, chromosomes, genes, and DNA
Answered By: richard-ga on 29 Jul 2005 19:41 PDT
Rated:5 out of 5 stars
 
Hello and thank you for your question.

As you probably know, the 'gene' was defined experimentally before the
function of DNA was understood or even known.

Your question is addressed fully in an article that appeared in
Science Magazine in April, 2003.
Genomics. Defining genes in the genomics era. 
M Snyder, M Gerstein (2003) Science 300: 258-60. 
http://papers.gersteinlab.org/e-print/whatisgene/all.pdf
http://papers.gersteinlab.org/e-print/whatisgene/reprint.html

The article is only a bit over 2 pages long, and is worth careful reading.
Here are the first two paragraphs [citations omitted]:
"A genome is defined as the entire collection of genes encoded by a
particular organism. But what is a gene? Historically, the term gene,
attributed to Johansson, first appeared in the early 1900s as an
abstract concept to explain the hereditary basis of traits. Phenotypic
traits were ascribed to hereditary factors even though the physical
basis of those factors was not known. Subsequently, early genetic
studies by Morgan and others associated heritable traits with specific
chromosomal regions. In the 1930s, Beadle introduced the concept of
'one gene, one enzyme,' which later became 'one gene, one
polypeptide.'
"With the advent of recombinant DNA and gene cloning, it became
possible to combine the assignment of a gene to a specific segment of
DNA and the production of a gene product. Although it was originally
presumed that the final product was a protein, the discovery that RNA
has structural, catalytic, and even regulatory properties made it
evident that the end product could be a nucleic acid. Thus, we now
define a gene in molecular terms as "a complete chromosomal segment
responsible for making a functional product." This definition has
several logical components: the expression of a gene product, the
requirement that it be functional, and the inclusion of both coding
and regulatory regions. According to this definition, it should be
possible to use straightforward criteria to identify genes in the DNA
sequence of a genome. Five such criteria are in common use, but their
application is not straightforward."

According to the article, the five criteria for identifying a gene are:
*Open reading frames 
*Sequence features
*Sequence conservation
*Evidence for transcription
*Gene inactivation

I won't quote or paraphrase the article any further, but as the first
paragraph indicates, in the most basic terms:  As a matter of
hindsight (now that we know a good deal about the function of DNA and
RNA), what Mendel and his successors observed in their
genetics/heredity experiments was the action of sections of
chromosomes, called genes, in which a stip of DNA provided the coding
whereby RNA could read out the recipe so that units inside the cell
(ribosomes, golgi, etc.) could manufacture the particular proteins and
other molecules that made this pea smooth, that pea wrinkled, and so
forth.
TUTORIAL ON DNA STRUCTURE, REPLICATION, TRANSCRIPTION, AND PROTEIN SYNTHESIS
http://www.ncc.gmu.edu/dna/

To answer your questions more specifically,
(1) (a) Is DNA one long continuous molecule? 
For prokaryotes (bacteria) the answer is yes;
"The nucleoid of prokaryotes is one long, single molecule of double
stranded, helical, supercoiled DNA"
http://www.cat.cc.md.us/biotutorials/dna/dna.html
 for eukaryotes (plants and animals) the answer is more complicated:
"The DNA in eukaryotic cells is packaged in a highly organized way. It
consists of a basic unit called a nucleosome (def), a beadlike
structure 11 nm in diameter that consists of 146 base pairs of DNA
wrapped around eight histone molecules. The nucleosomes are linked to
one another by a segment of DNA approximately 60 base pairs long
called linker DNA (see Fig. 10). Another histone associated with the
linker DNA then packages adjacent nucleotides together to form a
nucleosome thread 30nm in diameter. Finally, these packaged nucleosome
threads form large coiled loops that are held together by nonhistone
scaffolding proteins. These coiled loops on the scaffolding proteins
interact to form the condensed chromatin seen in chromosomes during
mitosis."
Ibid

  (b)is it divided into genes?
Also yes, but as indicated above genes are more logical than physical units.


(2) Chromosomes are visible under a strong microscope as distinct entities.
But how are distinct GENES identified? What marks the beginning and end
of a particular gene?
As the "Defining genes in the genomics era" article indicates, the
definition of a particular gene is more one of function (that's what
the 5 criteria are about) than physical form.
But there is an alternative way of answering this question too - -
research has shown where in the chromosome many genetic traits and
mistakes are found--and these can also be called genes.  For example,
http://www.ncbi.nlm.nih.gov/Omim/getmap.cgi
http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi
http://www.ncbi.nlm.nih.gov/genome/guide/human/
In this last reference, you can click on one of the chromosomes shown
in the left section of the page and gene maps of that area will
appear.  But again, these aren't physical structures - - they're the
sections of DNA that have been associated with particular heritable
functions.


(3) Is there a website that gives a visual representation of the hierarchy
of cells, chromosomes, genes, and DNA?
The best sources are the one cited above:
http://www.ncbi.nlm.nih.gov/genome/guide/human/
and also
http://wsrv.clas.virginia.edu/~rjh9u/dnaprot.html
and its many links.

Search terms used:
"what is a gene
eukaryotic dna "single molecule"

Thanks again for bringing us your question

Google Answers Researcher
Richard-ga

Request for Answer Clarification by rambler-ga on 29 Jul 2005 20:45 PDT
Am I correct in saying that:
(1) Every cell nucleus contains physically separate chromosomes.
(2) Each chromosome contains a long continuous molecule of DNA (i.e.
each cell contains several molecules of DNA, one for each chromosome).
(3) Each molecule of DNA contains logically separate genes that are
identified by their function.

I realize that I am oversimplifying an extremely complicated subject,
but am I on the right track?

Clarification of Answer by richard-ga on 30 Jul 2005 06:47 PDT
(1) Every cell nucleus contains physically separate chromosomes.
Yes, but it's only during certain phases of mitosis (nucleus and cell
division) that the chromosomes 'condense' and become visible:
"Prophase is the first stage of mitosis in which the nuclear membrane
breaks down and the chromosomes become short and thick. By late
prophase, individual chromosomes are visible, appearing as two
parallel threads attached at a constriction point called the
centromere."
http://www2.mcdaniel.edu/Biology/PGclass/mitosis/pg3bd.htm
[good micrographs and illustrations on this page]

(2) Each chromosome contains a long continuous molecule of DNA (i.e.
each cell contains several molecules of DNA, one for each chromosome).
Generally, yes
http://staff.jccc.net/pdecell/celldivision/cellcycle.html

(3) Each molecule of DNA contains logically separate genes that are
identified by their function.
Yes
http://www.massgeneral.org/pubaffairs/releases/110299Li_study.htm
http://www.jcb.org/cgi/content/abstract/124/4/475
http://godot.ncgr.org/servlets/TairObject?type=locus&id=128952

I think you've got it!
-R
rambler-ga rated this answer:5 out of 5 stars and gave an additional tip of: $5.00
Thank you for clearing up my misconceptions.
DNA is a fascinating, but obviously very complex, subject.

Comments  
Subject: Re: The hierarchy of cells, chromosomes, genes, and DNA
From: dops-ga on 29 Jul 2005 14:25 PDT
 
Here's the short answer:

DNA is one long double stranded molecule that is packaged together
with proteins to produce structures called chromosomes that can be
stained or tagged and visualized microscopically. The relationship
between DNA, Chromosome and Gene is very simply explained on this
site:http://www.accessexcellence.org/AE/AEPC/WWC/1993/a_spool.html

One cannot visualize genes per se, but in Drosohila salivary glands
there are things called polytene chromosomes
(http://opbs.okstate.edu/~melcher/MG/MGW1/MG1133.html), in which one
can visualize areas of euchromatin where actively transcribed genes
tend to reside.

In the simplest terms a gene is composed of both the cDNA (coding
sequence) and non-coding sequences. The non-coding sequences include a
promoter, which regulated the spatial and temporal expression of the
transcript, 5' and 3' untranslated sequences and introns. So something
is said to be a gene based upon sequence organization. There are many
complicated programs designed to search through DNA sequences and
determine which stretches are likely to be genes. Here's an
example:http://nema.cap.ed.ac.uk/Caenorhabditis/C_elegans_genome/acedb.html
Subject: Re: The hierarchy of cells, chromosomes, genes, and DNA
From: hfshaw-ga on 29 Jul 2005 14:35 PDT
 
Cells contain chromosomes, which are composed of strands of DNA. 

The DNA in a cell is not one cotinuous strand.  

Different species have different numbers of chromosomes.  

DNA is made up of nucleotides (the molecules adenine, guanine,
cytosine, and thymine).

Genes are the sequences of nucleotides that code for specific proteins. 

Proteins are composed of strands of amino acids (which fold up into
complicated shapes), and sets of three nucleotide pairs (called
codons) code for individual amino acids (see
<http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html#The_DNA_Codons>.

The sequence of codons that specifies a protein is called a gene.  

DNA also contains "start" (adenine-thymine-guanine, or ATG) and "stop"
codons (thymine-adenine-adenine, thymine-adenine-guanine, or
thymine-guanine-adenine, -- TAA, TAG, or TGA) that tell the molecular
machinery of the cell where the coding for a protein starts and stops.

Check out:
<http://gslc.genetics.utah.edu/units/basics/tour/>
<http://gslc.genetics.utah.edu/units/basics/>
<http://www.population.health.wa.gov.au/Genomics/Genetics/htmls/basicgenetics.html>
Subject: Re: The hierarchy of cells, chromosomes, genes, and DNA
From: drmendel-ga on 30 Jul 2005 22:55 PDT
 
Clarification to point number two is incorrect.

With the only exception of some viruses, chromosomes contain TWO long
continuous molecules of DNA. These molecules are complementary and
make DNA double stranded.

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