What is a Chromosome?

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While "DNA" is an almost magically powerful term in everyday language, featuring prominently in matters ranging from casual remarks about inheritance to the conviction or exoneration of criminals, "chromosome" is not. This is something of a curiosity given that chromosomes are really nothing more than very large amounts of deoxyribonucleic acid (DNA) with some proteins and other substances mixed in.

Humans have about 2 meters' worth of DNA in every cell. That means that if all of the genes in a single one of your cells were lined up end to end, it would very likely be taller than you. Yet each one of your trillions of cells is only a few millionths of a meter wide. Clearly, evolution has allowed organisms to develop a filing system that rivals that of the most powerful computer hard-disk drives in existence. That system, broadly speaking, consists of chromosomes, which are distinct sets of a nucleic acid-protein mishmash known as chromatin.

Chromosome Basics

Chromosomes are found in the nuclei of animal and plant cells; other organisms have DNA, but it is arranged differently within their cells. You may think of chromosomes as "thread-like," complete with the capacity to become tightly coiled, like thread, as well as as diffuse, not unlike a hairball. The word "chromosome" comes from the Greek words for "color" and "body."

Chromosomes are fundamentally responsible for the development and growth of organisms. While the DNA they carry is essential in the reproduction of organisms as a whole, chromosomes direct the division of individual cells in addition to contributing genetic information to these cells. This allows for the replacement of old, worn-out cells. If chromosomes did nothing other than sit within cells waiting for the parent organism to reproduce, that organism would cease to function altogether.

Chromosomes cannot be easily seen within the nucleus even by powerful microscopes unless they are dividing. During cell division, the DNA within chromosomes becomes tightly and characteristically bunched, making them visible with the use of sensitive instruments. Most of what cell biologists have learned about chromosomes has, accordingly, been when they have been examining dividing cells.

Humans have 46 pairs of chromosomes in each cell except for gametes (sex cells), which have one copy of each chromosome – 22 somatic chromosomes (autosomes) numbered 1 through 22 and one sex chromosome (either an X-chromosome or a Y-chromosome). Gametes have only one copy of each chromosome because gametes are the cells that fuse during reproduction to create a cell with 46 chromosomes that can then develop into a new person. Females have two X-chromosome, while males have an X-chromosome and a Y-chromosome. Because everyone gets one sex chromosome from each parent, it is clear that the father's contribution ultimately determines the sex of the offspring, since females must contribute an X-chromosome. Each new baby thus has equal odds of being male or being female. In the early 1900s, the researcher Thomas Hunt Morgan identified the X-chromosome as carrying heritable traits in his studies of fruit flies.

Chromosome Structure

In eukaryotes, each chromosome consists of a single very long molecule of DNA along with a great deal of protein. Prokaryotes (e.g., bacteria) do not have nuclei, so their DNA, which is usually in the form of a single ring-shaped chromosome, sits in the cell cytoplasm.

As noted, chromosomes are simply divisions of the substance into which DNA is packed within cells, called chromatin. Chromatin consists of DNA and proteins that serve to compress and relax the overall structure of chromosomes depending on the cell's state of division. Most of these proteins are called histones, which are octamers of eight subunits, each of which is paired with another subunit. The four histone units are named H2A, H2B, H3 and H4. Histones carry a positive electrical charge, while DNA molecules are negatively charged, so these two molecules bond readily to one another. DNA wraps itself around the histone octamer complex a little over twice, like thread being wound around the spool. The amount of DNA that is included in one complex varies, but on average, it is approximately 150 base pairs, or 150 consecutive nucleotides. The single circular chromosome a prokaryotic cell contains, with rare exceptions, does not contain any histones, reflecting prokaryotes' smaller genomes and therefore a less urgent need to compress all of the organism's DNA to make it fit within a single cell.

Like DNA itself, chromosomes are divided into repeating units. In DNA, these are called nucleotides, whereas in chromosomes they are called nucleosomes. A nucleosome is a histone-DNA complex. These were discovered when scientists used caustic materials to dissolve the outer proteins from chromosomes, leaving behind chromatin containing only histones and DNA. Chromatin offers a "beads on a string" appearance on microscopic examination.

Again in eukaryotes only, each chromosome has a centromere, a constricted region of the chromosome at which sister chromatids are joined. Sister chromatids are identical copies of a chromosome that has replicated itself in preparation for cell division. In addition to separating the sister chromatids along the long axis of the chromosomes, the centromere separates the chromosome into arms. The centromere, its name notwithstanding, is not usually found in the middle of the chromosome, but toward one end. This gives a replicated chromosome the appearance of an asymmetrical letter X. (The centromere of a Y-chromosome is so close to one end that the chromosome looks like its name suggests it should.) On this view, each side of the X is a sister chromatid, while the top includes two paired arms and the bottom includes another pair of arms. The shorter arm of any chromosome is called the p-arm, while the longer arm is known as the q-arm. The position of the centromere is helpful in identifying the location of specific genes on the chromosome, especially now that the Human Genome Project of the early 21st century has allowed for the mapping of all of the genes on every chromosome. A gene is a length of DNA that contains the instructions for making a specific protein.

It can be easy to confuse chromosome vs. chromatid vs. chromatin. Remember that a chromosome is nothing more than chromatin divided into chunks called chromosomes, each of which consists of two identical chromatids once the chromosome has replicated.

Chromosome Regulation and Tasks

When chromosomes are in their "relaxed" and more diffuse state, they are not merely dormant and awaiting the time when they draw into tight linear shapes again for purposes of cell division. On the contrary, this relaxation affords the physical space for processes such as replication (DNA making a copy of itself), transcription (messenger RNA being synthesized from a DNA template) and DNA repair to occur. Just as you may need to take apart a household appliance to repair a problem or replace a part, the loosened structure of chromosomes in the interphase (i.e., between cell divisions) state allows enzymes, which help chemical reactions such as replication and transcription along, to find their way to where they are needed along the DNA molecule. Regions of chromosomes that are participating in transcription (messenger RNA synthesis) and are therefore more relaxed are called euchromatin, whereas more compressed regions in which the chromosome is not being transcribed is known as heterochromatin.

The "beads on a string" appearance of nucleosomes under a microscope belies what chromosomes normally look like. In addition to the winding of the DNA around the histone proteins within a nucleosome, the nucleosomes are, in living cells, compressed very tightly together in multiple levels of packaging. The first level creates a structure about 30 nanometers wide – only 30 one-billionths of a meter. These are wound into geometrically articulate but well-studied arrays that fold back in on themselves.

This tight packing not only allows the genetic material in a cell to occupy a very tiny physical space, but also serves functional roles as well. For example, the multiple levels of folding and coiling bring parts of a chromosome together that would be very far apart, relatively speaking, were the DNA strictly linear. This can influence gene expression; in recent decades, scientists have learned that it is not only what is in a gene that determines that gene's behavior, but also the nature of other DNA in the vicinity of that gene. Genes, in this sense, have purpose, but they also have advisors and supervisors on hand, largely thanks to the specific structure of chromosomes.

Chromosome Abnormalities

Chromosomes and the DNA within them, along with the proteins that coordinate their activities, do their jobs with a remarkable level of accuracy. If they didn't, you would probably not be here to read this. Nevertheless, errors do occur. This can happen because of damage to individual chromosomes or because the wrong number of correctly formed chromosomes wind up in the genome of an organism in a nonlethal, but harmful, way.

Chromosome 18 in humans is an example of a chromosome with well-known genetic defects associated with specific aberrations in the chromosome. This chromosome is about 78 million base pairs long and makes up 2.4 percent of human DNA. (This makes it smaller than average; based on human chromosome number, a typical chromosome would have about 1/23rd of all DNA, about 4.3 percent.) An abnormality called distal 18q deletion syndrome results in delayed development, learning disabilities, short height, weak muscle tones, foot problems and a host of other issues. In this disorder, part of the far end of the long arm of chromosome 18 is missing. ("Distal" means "farther away from a reference point"; its counterpart, "proximal," means "closer to the reference point," in this case the centromere.) Another malady resulting from a chromosome 18 problem, one with similar features, is proximal 18q deletion syndrome, in which a different set of genes is absent.

Chromosome 21 is the smallest human chromosome, containing about 48 million base pairs, or roughly 1.5 to 2 percent of the human genome. In a condition called trisomy 21, usually, three copies of chromosome 21 are produced in each cell, resulting in what is commonly known as Down syndrome. (This is very commonly written incorrectly as "Down's syndrome.") Less commonly, this can result from a translocation of part of chromosome 21 to a different chromosome. In this condition, individuals have two copies of chromosome 21, but the portion that wandered off early in embryonic development continues to function in its new location in a detrimental way. People with Down syndrome have intellectual disability and a characteristic facial appearance. The presence of a third copy of chromosome 21 in affected individuals is believed to contribute to a range of health problems typically experienced by those with Down syndrome.

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