Review of Chromosome Architecture

Chromatin is double stranded DNA wound around histone octamers to form nucleosomes held together by linker DNA.  During Interphase (G1, S, G2) chromatin is not condensed.  As the cell  goes into mitosis or meiosis however, the nucleosomes are packed together to form chromosomes. Chromosomes are first visible in Prophase and become increasingly condensed until metaphase.  Fully condensed metaphase chromosomes have a centromere which divides the chromosome into a p arm (short) and a q arm (long).

    QUESTION:  What is the difference between chromatin and a chromosome?
 

Homologous chromosomes are usually seen as dyads with two identical chromatids.  This is the result of  DNA replication and chromosome duplication during S phase of the cell cycle.

    QUESTION:  What is the difference homology and identity?
 
 

Each gene has a locus, or location, on a DNA molecule.  Therefore, when the DNA molecule is packaged into nucleosomes, which are packaged into chromosomes - each gene has a locus on the chromosome.  The loci of the genes on a chromosome can be indicated on an idiogram of a chromosome (click on the image for an enlargement).
 

A technique called FISH (fluorescent in situ hybridization)  allows a single gene to be visualized (click on the image for an enlargement)..  A copy of the gene is made, and then labeled with fluorescent dye.  Since the DNA in the copy is complementary to the DNA of the same gene in a chromosome, it will hybridize to the chromosome at the locus of the gene.  When this is viewed under a microscope, using uv light instead of visible light,  the dye fluoresces yellow and shows the locus of the gene.  In this image the human gene encoding the enzyme muscle glycogen phosphorylase is seen as a yellow fluorescent spot close to the centromere of each sister chromatid of two homologous dyads of chromosome 11.
 
 

Karyotypes

A karyotype is a representation of all the chromosomes in a cell.  A typical photographic karyotype is shown here.  To begin with, actively dividing mitotic cells are treated with colchicine or colcemid.  These drugs inhibit the polymerization of spindle fibers, so the chromatids cannot separate as they normally would in Anaphase.  Instead cells, which are arrested in metaphase, accumulate.  These cells can be swollen by osmosis in a hypotonic solution.  If they are then dropped from a height onto a glass slide, many of the cells and nuclei burst, and the chromosomes splash apart.  A "chromosome spread" from a single nucleus is shown on the right of the image.  These spreads are then stained, usually with Giemsa stain (see below) or with a fluorescent dye and viewed under the microscope.  Photomicrographs are taken.  Each chromosome is then cut out of the photo, matched with its homologous partner, and pasted onto a piece of paper to produce the karyotype on the left of the image above.
 
 

Chromosome morphology

As you know most organisms are diploid - that is they have 2 sets of chromosomes.  BUT  how can we tell the homologous pairs of chromosomes apart?   As shown in the figure, there are 3 ways:
 
 

	CLICK on the image for an enlargement!   Size:   some chromosomes are large; some small; some in between.   Centromere position:  some centromeres are in the middle (metacentrics), and divide the chromosome into 2 equal arms;  some centromeres are offset to one end ( sub-metacentrics and acrocentrics) so there is a p arm and a q arm.  Some centromeres are placed at the end of the chromosome (telocentrics).
	Banding pattern:  mammalian chromosomes do not naturally exhibit bands.  However if they are stained with Giemsa stain, using a special techniques called G-banding, bands can be made to appear.  The value of banding is plain by looking at the smaller sub-metacentrics (6 - 12).  In the karyotype above the size and position of the centromeres is very similar.  However if you look carefully, each of these can be readily distinguished by a different pattern of G bands. The dark bands are thought to be heterochromatin and the lighter bands are thought to be euchromatin. QUESTION:  What is the difference euchromatin and heterochromatin?
	CLICK on the image for an enlargement! Each of the bands on a chromosome is distinguished by a numerical code. This is a cytogenetic map.   NOTE:  the numerical code is not simply linear. On the long (q) arm of chromosome 7, there are 3 major segments.  Within segment 3 there are 6 subdivisions.   The subdivisions themselves may be further subdivided - for example section 21.1 contains 3 subdivisions. The gene which is defective in Cystic Fibrosis is located at 7q31.2. This does not mean the locus of the CF gene is in the thirty-first band!  It means the locus is in the second subdivision of the first subdivision of region three of the long arm of chromosome 7.

X chromosome morhphology

The X chromosome carries hundreds of genes but few, if any, of these have anything to do directly with sex. However, the inheritance of these genes follows special rules. These arise because:

• males have only a single X chromosome
• almost all the genes on the X have no counterpart on the Y; thus
• any gene on the X, even if recessive in females, will be expressed in males.

An idiogram of the human X chromosome showing the G bands.  Also shown are the locations of some 'markers' or 'signposts' which are used for mapping. CLICK on the image for an enlargement!

An idiogram of the human X chromosome showing the G bands.  Also shown are the locations of several genes in which mutant alleles result in disease phenotypes!   Note the difference in size between the X and Y chromosome.   CLICK on the image for an enlargement!