- One of the alternative forms of a single gene (that is, a particular nucleotide sequence occurring at a given locus on a chromosome)
- amino acids:
The building blocks of proteins. There are 20 common amino acids found in proteins.
- A nitrogen-containing ring structure which is part of nucleotides forming DNA.
In DNA, four different bases are found:
1. two purines, called adenine (A) and guanine (G)
2. two pyrimidines, called thymine (T) and cytosine (C)
- Base Pairs:
- Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak hydrogen bonds that form the rungs of the twisted ladder sturcture of DNA.
- class of biochemical compounds which includes sugars, starch, chitin, and steroids.
- Fundamental structural unit of all life. The cell consists primarily of an outer plasma membrane, which separates it from the environment; the genetic material (DNA), which encodes heritable information for the maintainance of life; and the cytoplasm, a heterogeneous assemblage of ions, molecules, and fluid.
- Linear piece of eukaryotic (Plant and Animal) DNA, often bound by specialized proteins known as histones. Contained in the nucleus of cells.
MT - Mitochondria
||Chrosomes are frequently illustrated in an X shape, which is what they look like as they are replicated during the cell division process (mitosis), when they condense into short (~ 5 µm) structures which can be stained and easily observed under the light microscope. They are normally too elongated and tenuous to be seen under a microscope.
Human cells have 46 chromosomes arranged in 23 pairs. Except egg and sperm cells which have 23 single chrosomes, not pairs.
Men have and X and a Y; Women have two X chromosomes.
|1 ||2,776 ||247
|2 ||1,866 ||243
|3 ||1,473 ||200
|4 ||1,164 ||191
|5 ||1,281 ||181
|6 ||1,528 ||171
|7 ||1,474 ||159
|8 ||1,025 ||146
|9 ||1,207 ||140
|10 ||1,094 ||135
|11 ||1,841 ||134
|12 ||1,355 ||132
|13 ||556 ||114
|14 ||1,220 ||106
|15 ||961 ||100
|16 ||1,108 ||89
|17 ||1,442 ||79
|18 ||438 ||76
|19 ||1,624 ||64
|20 ||717 ||62
|21 ||367 ||47
|22 ||756 ||50
|X ||1,344 ||155
|Y ||322 ||58
|MT ||37 ||.016
|Total ||28,976 ||3.1
Sources: Number of genes above is from the International Human Genome Sequencing Consortium database Build 36, Version 1 Statistics (Fall, 2005) and Genome View at The National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH).
Note: The number of genes are determined by computer programs which identify base pair sequences which look like genes, and the numbers keep changing as the analysis gets more sophisticated. The function of most of them is still unknown. See genes below.
The number of chromosomes is not proportional to the number of base pairs or genes; e.g. butterflies have 380 chromosomes.
Chromosomes for the Hominidae Family (humans and the great apes; orangutan, gorilla, and chimpanzee):
Humans have 23 pairs the others have 24, most likely two chromosomes from an ancestor were fused into one in humans.
Chromosomes 6, 13, 19, 21, 22, and X have identical banding patterns in all four species. The others have some differences in one or more of the species. Most of the chromosomal differences among the four species involve inversions - localities on the chromosome that have been inverted, or swapped end for end. Other types of rearrangements include a few translocations (parts swapped among the chromosomes).
Humans and chimpanzees share 97.5 % of their DNA.
See: Human and Ape chrosomes.
- A sequence of 3 base pairs. 3 base pairs define an amino-acid, a basic component of proteins. The sequence of amino acids in a polypeptide is dictated by the codons in the messenger RNA (mRNA) molecules from which the polypeptide was translated.
a codon (three-base-pair-long word) in one organism (say, bacteria) codes for the same amino acid it codes for in another organism. There can be from 1 to 6 cocons which code for the same amino-acid.
61 of the 64 possible permutations code for amino acids and 3 are stop codons (Signal to stop production of a protein.)
Note: You will see U (Uracil) used in place of T (Thymine) because Uracil is in RNA where Thymine is in DNA.
See RNA codon Table
Source: June 2003, Science and Technology from Lawrence Livermore National Laboratory
Source: Owensboro College
"DeoxyriboNucleic Acid". The nucleic acid which carries the genetic code of an organism. It is the primary component of chromosomes. DNA molecules have a unique double-helical structure and a four-letter informational code.
The DNA molecule as proposed by Watson and Crick in 1953 resembled a gently-twisted ladder. The rails of the ladder are composed of alternating units of deoxyribose sugar and phosphate held together by strong covalent bonds. The rungs of the helical ladder are composed of a pair of nucleotides (base pairs), held together by weak hydrogen bonds. The nucleotides
Adenine always pairs with thymine and cytosine always with quinine. So DNA can be coded as a sequence of pairs e.g. GC TA CG AT AT ...
There are 3.5 billion base pairs in humans. Only about 3% of them are in genes, the function of the rest is not understood.
Bacteria have several million base pairs.
Eukaryotic (organism composed of cells with nucleus') DNA ranges for sever tens of millions of base pairs in fungi to several hundred billion in some flowering plants.
See: Introduction to Nucleic Acids at Rutgers.
Glossary at the UC Berkeley Museum of Paleontology.
Talking Glossary at genome.gov
A Glossary Of Terms Commonly Used In Molecular Biology at med.unc.edu
- A complex protein which helps to speed biochemical reactions. Enzymes are important in the construction and degradation of other molecules. Hemoglobin on the surface of red blood cells is a type of enzyme.
See Enzymes at HowStuffWorks
- gene :
- Genes, which are units of information, are "encoded" in the DNA. A sequence of consecutive base pairs (or Nucleotides) along the DNA. Provides a specific function to an organism by:
Although the human genome was decoded in 2003 this only listed the base pair sequences in each chromosome, only a fraction of these represent genes and many of the genes have not been identified yet.
Estimates are that humans have around 25,000 genes (see Human Genome Project below). Each gene is defined by 300 - 3,000 base pairs starting with a sequence of base pairs called a promoter and ending with a stop codon (3 base pairs). They control everything from the formation of protein macromolecules, to the regulation of metabolism and synthesis.
- Coding (via transcription into messenger RNA) for a polypeptide chain ("cistron") in a protein.
- Being transcribed into a sequence of ribonucleotides used as ribosomal RNA or transfer RNA
- Possessing recognition sites for protein attachment (for example, see Enhancers, Promoters) that regulate processes such as replication and transcription of other genes
Bacteria have thousands of genes.
We still don't know exactly how many genes there are in the Human Genome.
There are computer programs which go thru the human genome database and identify sequences which look like genes, but many are "pseudo genes", which have very similar sequences to actual
genes but never are expressed.
In "The Initial sequencing and analysis of the human genome". Nature 409:860-921 (Feb., 2001) they estimated there were 30,000 to 40,000 protein-coding genes. Another study published in Cell in August 2001 predicted a total of 42,000 genes.
The latest estimates as of June 2006 from Build 36, Version 1 (2005) of the database were 29,919 genes from International Human Genome Sequencing Consortium and 29,134 at Celera.
In 2002 there were 8,965 entries in the OMIM (Online Mendelian Inheritance in Man) database, but many only have guesses as to what they do.
See How Many Genes Are in the Human Genome? at the Oak Ridge national Laboratory.
Genes compose only 2-5% of the human DNA the rest has been referred to as "junk-DNA" or Introns, intragenic regions. Much of it (50%) is repeated sequences. Studies in 2004 has suggested that this junk DNA may have some function afterall. Other species have less junk DNA. Genes account for about 30% of the DNA in the Japanese pufferfish and 50-60% of the DNA in Arabidopsis thaliana, a small weed in the mustard family, a common laboratory plant for botanists.
Genes define protiens produced by the body.
We can make many more proteins than the number of genes because some genes are able to "encode" multiple different proteins.
Most individual genes are made up of multiple coding regions called exons and multiple noncoding regions called introns.
The smallest cells (Mycoplasmas) have less than 500
Mice have 20 pairs of chromosomes and about 28,620 genes (in build 36); in the nematode (C. elegans), the number is around 19,000; in yeast (S. cerevisiae) there are approximately 6,000 genes; and the microbe responsible for tuberculosis has around 4000.
Most bacteria have from 1,000-4,000 genes
Human DNA is 98 per cent identical to chimpanzees.
"We share 99 percent of our genes with mice," says Jane Rogers of the Wellcome Trust Sanger Institute in Cambridge, England, "and we even have the genes that could make a tail." In fact, only about 300 genes are unique to either organism. (Scientific American Dec. 2002)
99.9% of the nucleotides are the same in all people.
The 0.1 per cent that makes us individual rather than identical clones - is likely to be just as interesting and important as the main 'meat' of the sequence. Much of this variation is due to single nucleotide polymorphisms (SNPs), which occur about once every 1000 bases.
"What is a Gene", Journal of Nature 441, 398-401 (25 May 2006)
- Genomics :
- The science of determining what the genes actually do.
- A chemical messenger that binds to receptors on target cells, which leads to some change in that cells physiologic state. Hormones are produced by various glands e.g. Pancreas (Insulin, glucagon, ..), Thyroid (Thyroxine, triiodothyronine and calcitonin), Adranal (Cortisol, Aldosterone, ...), Testes (testosterone), ovaries (estrogen, progesterone), Adrenal (cortisol, aldosterone, epinephrine also called adrenaline, norepinephrine).
- Human Genome Project (HGP):
- Begun in 1990, the Human Genome Project was a 15-year effort to map the human genome. Although 16 institutions participate in the HGP, most sequencing takes place at 5 locations. These are the DOE Joint Genome Institute (JGI) (1997), Washington University (St. Louis), Sanger Center (U.K.) (1992), Baylor College of Medicine, and The Whitehead Institute at MIT. The effort was coordinated by the Department of Energy and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH). Their data for humans.
In May 1998, Craig Venter, announces a new company, Celera, and declares that it will sequence the human genome within 3 years for $300 million. In Feb. 2001 the International Human Genome Mapping Consortium of 19 centers around the world, including the US JGI, Sanger Center and others, published a working draft of their results in Nature and Celera published their working draft in Science. The race was declared a tie.
See Summary at the Whitehead Institute at MIT.
The HGP identified base pairs, but not all base pairs are associated with genes. See Gene above. The draft indicated there were between 30,000 and 40,000 genes, however in 2004 a consortium of scientists published an article in Nature saying analysis of the "gold standard" version of the genome, published in 2003, showed the human genome contains only 20,000 to 25,000 genes.
To make the map, the researchers used bacterial artificial chromosomes (BACs) - Large segments of DNA (about 175,000 base pairs long) that are cloned into bacteria. Once human DNA is cloned into bacteria, it can be copied and analyzed. Developed by Mel Simon and colleagues at Caltech .
THe DNA sequenced same from 12 anonymous volunteers. (There was a story that Venter used his own DNA in the Celera project.)
See a History of the Human Genome Project in the Feb. 2001 issue of Science.
Stanford course on the HGP
As of Nov. 2005 they were up to build 36 of the database.
- The process of nuclear division in eukaryotes. It is one step in cytokinesis, or cellular division. See Cell Reproduction at ebiomedia.com
- Creation of egg and sperm cells each with only a single chrosome of each type instead of a pair in normal cells. Through a sequence of steps, the replicated genetic material in a parent cell is distributed to four daughter cells. Each of the resulting daughter cells has one half of the number of chromosomes as the parent cell. In a process of "crossing over", some genes can move from the paternal homologue (Chromosome) to the maternal. Each resulting cell can have any of the 223 combinations of paternal or maternal chrosomes plus variations because of crossing over.
See illustration at UC Davis and meiosis at contexo.info.
- Unit from which nucleic acids are constructed. In addition to one of the 4 bases, it contains a phosphate molecule and a sugar molecule (deoxyribose in DNA, and ribose in the other nucleic acid, RNA). See DNA above. The phosphate molecule can be mono- (1 phosphate), DAMP for Adenine, di- (2 phosphates), dADP, or triphospaate (3 phospates), dATP. <
See Nucleotides at Kimball's Biology Pages and theFreeDictionary.
- Polymerase Chain Reaction (PCR):
- A technique to attain large amounts of DNA from situations where only a small amount of DNA may be available making DNA analysis much easier. Kary Mullis won the Nobel Prize for this discovery.
- This is the "outward, physical manifestation" of the organism, e.g. eye or hair color. These are the physical parts, the sum of the atoms, molecules, macromolecules, cells, structures, metabolism, energy utilization, tissues, organs, reflexes and behaviors. It is determined by "genotype", the "internally coded, inheritable information" carried by all living organisms and the environment.
- Chains of amino acids. Proteins are made up of one or more polypeptide molecules. See Polypeptides at Kimball's Biology Pages.
- A class of biochemical compounds constructed from amino acids.
Structural proteins make up such things as hair and cartilage.
Reactive proteins, such as hormones, enzymes, and antibodies react with other molecules in various life functions.
Humans have more than 100,000 kinds of proteins.
- An enzyme that reads messenger RNA, produced from the DNA, and converts it into amino-acid chains.
- ribose nucleic acid. Messanger RNA (mRNA) and Transfer RNA (tRNA) play a key role in protein synthesis. Another very interesting type of RNA is called a ribozyme, which is an RNA that has catalytic activity. See Introduction to Nucleic Acids at Rutgers.
- any of several small carbohydrates, such as glucose, which are "sweet" to the taste.
- Segments of (jumping) DNA that can move around to different positions in the genome of a single cell. In the process, they may cause mutations or ncrease (or decrease) the amount of DNA in the genome.
- Transcription is the copying of genetic code from a gene in DNA onto mRNA. Translation is the assembly of a polypeptide from the genetic code on the mRNA.
3 nucleotides (a codon) determine a peptide; A gene defines a sequence of peptides which combine to form a popypeptide and ultimatly a protein.
See Making Enzymes: DNA at howstuffworks.
The sequence start is indicated by promoters. The basal or core promoter is found in all protein-coding genes. It contains a sequence of 7 bases (TATAAAA).
Glossaries at ucmp.berkeley.edu: Cell Biology,
Glossary List at NCBI Resource Guide
Birgid Schlindwein's Hypermedia Glossary Of Genetic Terms
Glossary of Terms for the Creation/Evolution Debate at EvC Forum
Miscelaneous Notes which need to be organized:
During the formation of reducing the number of chromosomes (diploid number) to one half (haploid) in a process of sex cell formation of sperm and egg, homologous pairs of chromosomes undergo synapsis (form tetrads). The process of splitting the number of chromosomes is called meiosis. Sometimes there is an exchange of segments between chromatids (individual chromosomes) of a tetrad. In such an exchange of parts, some of the parts of the chromosomes exchange places. This is called crossingover and it is because of the new linkage that we have variety in life.
it is estimated that each of us carriers at least four to eight harmful hidden genes that we may pass on to our children or grandchildren.
the gene, controls the production if a polypeptide chain
Most human cells are roughly 20 µm; across, with nuclei about 10 µm; in diameter. A human egg is 100 µm, A neuron can be up to 1.5 m long.
Red blood cells are about 7-9 µm. See size.
(Red Cell size in diagnostic tests is measured by MCV (mean corpuscular volume) [Normal size is 86 - 98 femtoliters (10-15 liter]
A DNA molecule is 2.5 nm in diameter and 5.7 µm long, but if streched out would be 1.8 meters long.
Amino acids are about 0.8 nm.