Chromosome Structure - BIO 321 Genetics PDF

BIO 321 : Genetics CHROMOSOME STRUCTURE Chapter 2 The Problem DNA is a long thin molecule. As mentioned before, the DNA in an average human chromosome is 3.4 cm long, containing 100 million bp, and as we'll see there are 46 such molecules in a cell. These must be packaged into a...

BIO 321 : Genetics CHROMOSOME STRUCTURE Chapter 2 The Problem DNA is a long thin molecule. As mentioned before, the DNA in an average human chromosome is 3.4 cm long, containing 100 million bp, and as we'll see there are 46 such molecules in a cell. These must be packaged into a cell's nucleus which may be only a few microns in diameter, 1/10,000 the length of the DNA. At one level this may not appear to be a big problem, because although its long, the DNA molecule is very narrow and so can be folded over on itself. However, the backbone of the DNA consists of the negatively charged phosphates which repel each other making the DNA rather stiff. Thus, in order to package the DNA, the cell must somehow neutralize this backbone. Also, there has to be some order in the folding to avoid tangling all the molecules Nucleosome Structure DNA in eukaryotic cells is packaged into chromosomes that, at least during cell division, are so densely packed with DNA and protein that they are visible in the light microscope. Let's start with a DNA molecule and see how it is assembled into a chromosome. The most basic structure of the chromosome is the nucleosome comprised of four proteins called histones and DNA.  The histone proteins are: H1, H2a, H2b, H3, and H4. Two copies each of histones H2a and b, H3 and H4 assemble into the a short, cylindrical particle 110 A in diameter and 57 A high. DNA is wound around the circumference of the cylinder 1 3/4 times. This represents 146 bp of DNA. This basic unit is the nucleosome. If DNA is isolated from cells using appropriate procedures, this unit can be observed under the electron microscope. The structure looks like beads on a string. Fig 10-14.  There is about 50 to 100 bp between nucleosomes; this amount varies in different species and in different cell-types in the same species. The histone H1 attaches to the DNA at its juncture with the nucleosome, but is not an integral member of the particle and is not associated with all nucleosomes in a cell or in all cells. Archaebacteria are thought to possess histones but not eubacteria (actually archae are thought to be evolutionary closer to eukaryotes) Most histones are very highly conserved throughout eukaryotes (why?) Condensation of Nucleosomes In most cells not in the process of cell division, different regions of the DNA molecule exist in varying states of condensation. This reflects the fact that in any given cell, some genes are expressed while others are not. It is the spectrum of genes that are being expressed in a particular cell that gives that cell is characteristic properties. Thus, a muscle cell expresses one set of genes, including the genes encoding the actin and myosin proteins that make up muscle fibers, while liver cells express a different set of genes that encode detoxification and metabolic functions. In genes that are readily accessible for expression, the DNA is in an uncondensed state with the nucleosomes bound, but not associated with each other. These structures are referred to as euchromatin.  For DNA that is not accessible, the nucleosomes associate to take on a higher order, more condensed structure called heterochromatin. Heterochromatin consists of nucleosomes associated into helical fibers 30 nm (solenoid structure) across that themselves are anchored in loops to a chromosome scaffold. Associated with this packaging are a large number of poorly defined proteins, comprising part of the chromatin that are termed non- histone chromosomal proteins.  Two types of heterochromatin actually: 1) Constitutive: Always tightly packed, no gene expression, mainly structural (centromeres, telomeres). 2) Facultative: shifts between heterochromatin and euchromatin (Bar body for example) IMP to note that the issue here is not just an issue of packaging DNA to fit in a cell. There is another equally important issue which is regulation of gene Expression: DNA that is “open” (euchromatin) is accessible to the transcription Machinery and can be expressed (activation) DNA that is tightly packed (heterochromatin) is not accessible and thus not transcribed (repression) That’s why even if all cells have exactly same DNA they do not express same proteins: differentiation, tissues, organs… Also Temporal and spatial patterns of expression (assume you and chimp have exact same gene for hair, even if genotype same, phenotype is not) Can go from one state to another (dynamic) through: Acetylation/deacetylation, methylation, CRC etc… Epigenetics: “changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself”.) (More about all that LATER) Chromosomes During Cell Division During cell division, the entire DNA molecule condenses into heterochromatin, comprising the visible chromosomes which have several distinctive features. There are two copies of the DNA molecule in them, because, before condensation, the DNA molecule had been replicated so that each new cell can receive a copy. Consequently, a single chromosome at the beginning of cell division appears as a doublet. Each member of the doublet is a sister chromatid. Fig 1.13  The sister chromatids are attached at one point called the centromere. Each of the chromatids have a centromeric structure. The ends of the chromosomes are called telomeres. The positioning of the telomeres and the centromeres with respect to each other is fixed for a given chromosome and defines that chromosome as metacentric (centromere in the middle), submetacentric (centromere off center) acrocentric (centromere near the telomere), and telocentric (centromere at the end). Fig 1.7  Using a variety of different stains, the chromosomes show banding patterns that are distinctive for each chromosome, called a karyotype. Fig 10.5. To perform a karyotype you extract blood, (lymphocytes), add growth factors to the culture inducing cell division, then add a drug (colcemide) that disrupts the spindle fiber and prevents the completion of mitosis. You thus have a lot of cells stuck in metaphase. Add a hypotonic solution that makes the nuclei and chromosomes swell, followed by a dye and observe under light microscopic. Banding patterns are visible on the chromosomes that are due to the selective dye binding.  In humans, this karotyping can identify chromosomal abnormalities such as Down's syndrome, in which there is an extra chromosome 21, or sex since females have a pair of the X chromosome, but males have one X chromosome and one Y. Thus for a given species, chromosomes can be identified by their size, the location of the centromere, and their staining patterns. Ploidy Cell ploidy refers to the number of copies of each chromosome each cell has. Haploid cells have one copy, diploid cells have two, triploid cells have three, etc. The cells of most higher organisms are diploid. For each chromosome pair, one comes from one parent and the other from the other parent. The two chromosomes of the pair carry the same genes, although as we will see, not necessarily the same form of the gene. Both might code for eye color, but one might code for brown and the other blue. This is different than the sister chromatids which are identical because they arose from semi-conservative replication. The chromosome pair is referred to as a homologue, or homologous chromosomes. DNA Content and Chromosome Number There is a great variation in the DNA content from species to species, and also a great variation in chromosome number. While there is some correlation of DNA complexity with organism complexity, it is not strong and reflects the fact that, especially in higher organisms, a lot of the DNA has no specific function and only a small percentage encodes genes. (especially in plants) There is obviously no correlation of chromosome number with amount of DNA.  For example: E. Coli : 4.5 million bases, 4400 genes Humans: 3.3 billion bases, around 20000 genes !!!!! E. Coli much more “compact” very few non coding regions IF the human genome had the same gene density as E. coli it would have around 3 million genes!  n Numbers slightly off since older slide, but concept still relevant  Purpose of non coding DNA (95-98% of human genome)? Introns Various non mRNAs Regulatory elements (modulate transcription) Former genes (pseudogenes)? Blueprint for future gene evolution? Protect coding genes from random mutations? Repeat elements/transposons/retrotransposons (are they truly non coding? ENCODE project)