Genes and the Genome

A submicroscopic virus able to infect and kill bacteria. Many bacteriophages have DNA inside a protective protein coat. Like plasmids, bacteriophage are used to insert genes into bacteria.

base pair

The linkage of two bases in DNA, with the two bases being on opposite strands of the DNA double helix.

Adenine always pairs with thymine, and cytosine, always pairs with guanine.

Caenorhabditis elegans (a small roundworm) has 97 million base pairs in its genome.

C

carcinogen

A chemical that causes cancer, usually by modifying the DNA.

cell

The smallest unit of living matter that can reproduce. A membrane separates the inside of the cell from the environment. Its basic function is to make protein. Cells contain DNA (which store information), ribosomes (which make proteins), and mechanisms for converting energy to fuel protein construction.

80% water; 15% protein; 3% lipids; 1% carbohydrates; 1% nucleic acids and minerals.

centimorgan

A unit of measurement for linkage maps; 1 centimorgan equals a 1% chance of separation, for two DNA segments during crossing over.

chromosome

The chromosome is divided into genes. Each chromosome contains thousands of genes. (Okay, maybe the Y (the guy gene) is wimpier.)

codon

A 3-letter word in DNA that specifies a particular amino acid.

crossing over

Exchange of DNA between a pair of chromosomes.

cytoplasm

Protoplasm of the cell less the nucleus.

cytosine

A base on a strand of the DNA double helix. Always pairs with guanine.

D

diploid number

The total number of different chromosomes.

Humans have a diploid number of 46.

diploid species

Has two sets of chromosomes (each parent contributing one set at the time of conception).

Has a haploid number (number of chromosomes (one set) ) and diploid number (number of chromosomes (two sets) ).

DNA

Deoxyribonucleic acid. A 2-stranded molecule in the shape of the long double-helix chain. The molecule that carries the basis of genetic inheritance of all organisms, and encodes the information for a cell to make protein.

Often hundreds or thousands of times longer than the cell that contains it, and tightly wrapped to fit inside.

DNA ligase

A protein molecule that can seal breaks in DNA and join together separate DNA molecules.

DNA polymerase

A protein that makes new DNA.

E

endoplasmic reticulum

Layers of flattened vesicles (bladders); protein in various stages of being constructed; rough (studied with ribosome) and smooth (estrogen, cortisol, and other production of steroid molecules).

enzyme

A protein (or sometimes RNA molecule. It can catalyze a chemical reaction (i.e., speed it up without being consumed).

eukaryote

An organism whose genetic material is localized in a membrane-bound nucleus.

exon

Protein-coding region of the gene. About 10% of genetic material, the rest being intron.

F

G

gene

A unit of inheritable material.

A specific sequence of nucleotides in a specific region of DNA.

A gene contains DNA, which describes (encodes) information on the construction of one protein molecule, or (sometimes) for the construction of RNA. In effect, a gene leads to a visible, physical result by providing the code for the construction of a particular protein.

A gene may contain more than one exon (region of genetic code). If so, the gene is interrupted by introns (RNA removes the introns during formation of mRNA.)

How big is a gene? It varies. It can be on the order of thousands or millions of nucleotides long.

genetic code

Some call it "the almost universal" genetic code. The nucleotides are the alphabet of DNA. The amino acids. are the alphabet of protein.

Four nucleotides taken in threes give 64 combinations, each triplet being a codon. Of those combinations:

Three of the codons signify termination of a sequence, while each of the other combinations codes for an amino acid.
For 8 sets of first-and-second nucleotides in a triplet, the third letter is ignored in the determination of the generated amino acid.
Two codons each lead to a unique amino acid.
None of the other codons are unique in the amino acid they generate.

genetic map

A map of DNA in which the relative position of each region has been found from the frequency of genetic recombinations between observable traits.

gene therapy

Altering the genes of a living person, by adding DNA to cells, to avoid the consequences of a defective gene.

genetic recombination

Exchange of DNA between a pair of chromosomes.

genome

The genetic information of an organism (or of a virus). It include the genes and any other DNA of an organism.

The instructions for building and maintaining an organism, and for passing on instructions to the next generation of the organism.

The genome is divided into chromosomes.

For an organism like a human, which has two pairs of each chromosome, the genome is the information in a single set.

The human genome contains about 30,000 genes, and about 3 billion pairs of bases (adenine, cytosine, guanine, and thymine). The order of those bases determines the species of an organism and the organism-specific attributes of each organism.

The fruit fly genome is 165 million base pairs; the human genome is more than 10 times larger.

Each species has its own genome: the dolphin genome, the redwood (Sequoia sempervirens) genome, the Escherichia coli genome, etc.

Within a species, each individual (except for identical twins or other clones) has a unique genome.

genome map

A genome map is a less detailed picture of a genome than a genome sequence. It identifies a series of "landmarks" in the genome. A landmark may be a DNA sequence.

Such a map may not tell you about the sequence of the genome.

genome sequence

A sequence spells out the order of every DNA base in the genome. To make a genome sequence, you determine the order of DNA nucleotides (bases) in a genome. That is, you discover the order of As (adenine), Cs (cytosines), Gs (guanines), and Ts (thymine) in an organism's DNA.

A genome sequence is a more detailed picture of a genome than a genome map.

A sequence may not tell you about the genome map.

guanine

A base on a strand of the DNA double helix. Always pairs with cytosine.

H

haploid number

The number of different chromosomes present (expressed as the number of pairs).

Humans have a haploid number of 23.

heredity

Transmission of traits from parents to children via genes.

hormone

A protein that regulates biological functions such as growth and reproduction.

I

intron

Non-protein-coding region of the gene. About 90% of genetic material, the rest being exon.

A region that RNA removes in the splicing step; thus it cannot contribute directions for protein formation.

J

jumping genes

Also called retrotransposons. Sequences of DNA that are readily copied from one location in the genome and inserted somewhere else, such as in developing eggs.

They do not always insert themselves cleanly into the DNA. In practice, about a tenth of the insertions remove a long piece of the chromosome.

Nearly half of the human genome is composed of transposable elements or jumping DNA. Dr. Barbara McClintock (in the 1940's) first discovered jumping DNA, where stretches of DNA can move on and between chromosomes.

Such transposons may be linked to genetic disorders including hemophilia, leukemia, and breast cancer.

junk DNA

Most of the genome retrotransposons. Sequences of DNA that are readily copied from one location in the genome and inserted somewhere else, such as in developing eggs.

They do not always insert themselves cleanly into the DNA. In practice, about a tenth of the insertions remove a long piece of the chromosome.

K

karyotype

The set of chromosomes characteristic of a given species. The number of chromosomes varies with species, being:

46 (23 pairs) in humans.
12 in kangaroos.

L

linkage map

The distance between genes is measured in terms of probability! (This is a great deal easier to measure than physical distance/) The units are centimorgans, a measure of the likelihood that 2 DNA segments will separate during meiosis. The order of the genes is the same as on a physical genetic map, but the distances between the genes signifies different things on the two maps, and does not correspond directly.

lysosome

Cellular garbage collector.

A membrane-enclosed structure that can break down biological substances such as protein.

M

meiosis

A type of cell division, that produces gametes (egg and sperm cells) containing half the typical number of chromosomes. Occurs in two stages:

Chromosomes in the parent cell pair up and exchange genetic material in the "crossing over" process. This is also called "genetic recombination."
Cell division leads to individual cells with only one of the 23 (crossed over) chromosomes from each pair. Union of such egg and sperm cells can lead to the full freight of chromosomes - 23 pairs.

mosaic (genetic)

A creature whose body is a mixture of cells of two or more different genotypes. In mammals, this can be caused by various methods, most commonly the fusion of two different zygotes. (The resulting animal is called a "chimera".)

However, in each female mammal, one of their two X chromosome is randomly inactivated in all their somatic cells. Thus every female is a mosaic (and hence a chimera) for the genes on the X chromosome.

mutation

Error in DNA, commonly caused during DNA replication. Causes an incorrect amino acid sequence.

N

nucleotide

Composed of a base, a sugar, and a phosphate.

A building block of nucleic acid.

A link (or base) in a DNA molecule. There are four types of links: (adenine, cytosine, guanine, and thymine).

The specific order of the nucleotides stores genetic information.

The nucleotide sequence for the bacterium Hemophilus contains 1.8 million nucleotide pairs.

nucleus

Spherical body in a cell; supervises cell activity; contains DNA (protein-coated hereditary material) in

The condensed chromosomes form and the dipersed chromatin form.

O

oncogene

A gene whose resulting protein leads to malignant growth through the loss of cellular control over division. An oncogene inserted into a normal cell transforms that cell into a tumor cell.

organelle

A working component of a cell.

P

peptides

Molecule of two or more amino acid molecules joined by a peptide bond (circular enough for you?). A peptide bond links the acid group of one amino acid to the amino group of the other.

physical map

The distance between genes is based on physical distance and is measured in nucleotide base pairs. (Contrast this with the frequency of frequency of genetic recombination.) The order of the genes is the same as on a genetic linkage map, but the distances between the genes does not correspond.

plasmid

A small and circular DNA molecule that infects a bacterial cell. It reproduces every time the host cell reproduces. It often gives antibiotic resistance to its host cell. Plasmids are used to insert genes into bacteria. Compare with bacteriophage.

ploidy

The number of sets of chromosomes present in a species. Most higher organisms are diploid species, having two sets of chromosomes (each parent contributes one set at conception).

protein

A long molecule composed of amino acids. Many proteins control chemical reactions in the cells.

protoplasm

Essential living matter; ground substance of life.

Q

R

repressor

A protein that binds to a particular location on DNA, where it prevents RNA synthesis from a particular gene.

restriction enzyme

A bacterial enzyme that breaks a DNA chain in two at a particular point. This is a fundamental tool in genetic engineering.

retrotransposon

See jumping gene. Sequences of DNA that are readily copied from one location in the genome and inserted somewhere else, such as in developing eggs.

Such a gene must be transcribed into RNA before it can "jump".

Roughly, the older (in terms of the species ancestors) a retrotransposon element, the shorter (and possibly more corrupted) is its "tail" of repeated adenines. Meanwhile it seems that later insertions have longer and purer adenine tails.

ribosome

A large structure (in the cell) where proteins are made by linking protein subunits. Composed of ribosomal RNA and ribosome-specific proteins.

retrovirus

A virus in which the genetic information is converted from RNA to DNA. during infection of cells. Then the inserted viral DNA directs the synthesis of viral RNA and proteins, which proliferate the virus.

One retrovirus causes AIDS, others cancer. They are also used in cloning.

RNA

Ribonucleic acid.

Single-stranded molecule, formed from DNA by transcription. Used in translating the genetic material of DNA into protein.

In the retroviruses, RNA is also the hereditary material.

Like DNA, RNA uses a 4-letter alphabet to store information.

Messenger RNA (mRNA) is a template for protein synthesis (translation). Transmits information from a gene on DNA to a ribosome, where the information is used in making protein.
Transfer RNA (tRNA) helps to position amino acids correctly during protein synthesis. Small molecules, about 80 nucleotides long.

RNA polymerase

A protein that makes new RNA.

S

T

thymine

A base on a strand of the DNA double helix. Always pairs with adenine.

X-chromosome inactivation

A process that causes one of the two X chromosomes of a female mammal unable to express is genes.

A fertilized egg.

The Human Genome Project: Cracking the Code Within Us by Elizabeth Marshall. An easy introduction.
Genome: The Autobiography of a Species in 23 Chapters by Matt Ridley (2000). Interesting and well written. A populist text.
Understanding DNA and Gene Cloning: A Guide for the Curious (4th edition is just out in 2003) by Karl Drlica. Lots of detail and diagrams. The science behind the chattiness of Ridley.
Bioinformatics: Sequence and Genome Analysis by David W. Mount (2001). Get down! The math, the assumptions, the models, the Greek letters. Enough detail to snow your friends and relations.
List of the best of the 100 books I read in 2002.
Check our new Log of Books, with recommendations and warnings.