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Glossary

Others A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Others

1,3-bisphosphoglycerate

One of the intermediate products in the glycolysis. It is produced from glyceraldehyde triphosphate by removing an hydrogen and adding phosphate with the catalysis of glyceraldehyde triphosphate dehydrogenase.

1,3-BPG

See "1,3-bisphosphoglycerate".

2.2_7 ribbon

A kind of right-handed helical structure of polypeptide chains, in which every amino acid residue forms a hydrogen bond to the two residues earlier amino acid. In practice, this structure has never been observed, because of the steric hindrance. The general expression is 2.2_7 helix, which means it proceeds 2.2 residues per helical turn and the number of atoms in the ring that is closed by the hydrogen bond is seven.

2PG

See "2-phosphoglycerate".

2-phosphoglycerate

3_10 helix

A kind of right-handed helical structure of polypeptide chains, in which every amino acid residue forms a hydrogen bond to the three residues earlier amino acid. This structure has a little steric hindrance and then has rarely observed at the end of alpha helices. The general expression is 3_10 helix, which means it proceeds three residues per helical turn and the number of atoms in the ring that is closed by the hydrogen bond is ten.

3PG

See "3-phosphoglycerate".

3-phosphoglycerate

A

abscisic acid

acatalasemia

See "acatalasia".

acatalasia

A congenital disease which caused by the lack of catalase gene. The symptom is progressive gangrenous oral ulcer. It also called acatalasia or Takahara's disease.

acetohydroxyacid synthase

A enzyme involving in amino acid synthesis. Its EC number is 2.2.1.6. The inhibitor of this enzyme such as sulfonylurea is used for herbicide.

acetylcholine

A acetyl ester of coline which is one of the neurotransmitter. In animals, it is released from the end of the neuron at the synapse, which exists between two neurons, or at the endplate, which between neuron and muscle fiber, to stimulate the parasympathetic nerve, and then it causes the physiological action such as falling in blood pressure, muscle contraction, and so on. In vivo, it is synthesized from a coline and an acetyl CoA by catalyzing of acetyltransferase.

acetyl-CoA

An acetyl derivative of coenzyme a. It acts as acetyl group donor and is involved in various metabolic reaction, such as glycolysis, citric acid cycle, biosynthesis of acetylcholine, beta oxidation of lipid, and so on.

aciclovir

A therapeutic drug for herpesvirus infection. It inhibits the function of virus DNA polymerase. The IUPAC name is 2-amino-9-((2-hydroxyethoxy)methyl)-1H-purin-6(9H)-one.

acquired immune deficiency syndrome

See "acquired immunodeficiency syndrome".

acquired immunity

See "adaptive immunity".

acquired immunodeficiency syndrome

A infectious disease caused by the Human Immunodeficiency Virus (HIV). The immune system is destroyed to present various opportunistic infections such as Pneumocystis infection, and Kaposi's sarcoma etc.

ACTH

See "adrenocorticotropic hormone".

actin

Protein that forms actin filaments in all eukaryotic cells. The globular monomer and the filamentous polymer are sometimes called G-actin and F-actin, respectively. In muscle, forms actomyosin together with myosin filament and plays a major role in muscle

Actinobacteria

A group of gram-positive bacteria belonging in Actinomycetales. It's name is from the radial morphology of mycelia. But some actinomycetes don't have such morphology and excluded from it. There are various actinomycete, such as antibiotic producing, nitrogen fixation, pathogen, and so on.

actinomycete

See "Actinobacteria".

actin-specific ADP-ribosylating toxin

A kind of exotoxin which destroys cytoskeletons to kill cells. It is produced by bacteria causing diarrhea related antibiotics.

adaptive immunity

One of the immune systems which is found only in the vertebrates. At first, it acts slower than innate immunity. But it memorize the antigen and acts faster to the specific target after the next time. There are two types of adaptive immunity, cell-mediated immunity and humoral immunity.

adenosine diphosphate

A nucleotide which consists of ribose, a kind of furanose, adenine, a kind of base, and two phosphates. It often means the Adenosine 5'-DiPhosphate which is the adenosine bound to a pyrophosphate at the 5' position and abbreviate as ADP. Derived from ATP by hydrolysis of terminal phosphate. Turns to ATP again by oxidative phosphorylation.

adenovirus

Virus belonging in the I group, Adenoviridae family, which have their genome in double strand DNA (dsDNA). It has an icosahedral capsid. In this group, it is known about fifty kinds of viruses with pathogenicity for human such as pneumonia, pharyngoconjunctival fever, and epidemic keratoconjunctivitis.

adjuvant

ADP

See "adenosine diphosphate".

ADPRT

See "actin-specific ADP-ribosylating toxin".

adrenal cortex

A endocrine organ which composes the outer part of the adrenal gland. It secretes several kinds of adrenal cortex hormone.

adrenal cortex hormone

A general term of steroid hormone produced in the adrenal cortex. It can be classified into glucocorticoid and mineralocorticoid.

adrenal corticoid

See "adrenal cortex hormone".

adrenal gland

A endocrine organ which exists beside of the kidney of vertebrate. It consist of two parts, adrenal medulla composing the inner part and adrenal cortex composing the outer part.

adrenal medulla

A tissue which constitutes the core part of adrenal gland. It secrets adrenaline or noradrenaline by the stimulation of autonomic nerve.

adrenaline

"Material which is secreted from the adrenal medulla. It also secrets from the adrenergic neuron and acts as neurotransmitter. It induces the excited state such as the heart rate raising, blood pressure raising, blood glucose level raising. and pupillary dilatation etc. The IUPAC name is the 4-(2-Amino-1-hydroxyethyl) benzene-1,2-diol."

adrenergic receptor

A protein which exists at the surface of cells and accepts the adrenaline, a kind of neurotransmitter. As binding to the adrenaline, it directs for each part of inside of the cell to prepare for defence, according to the function of the cell. This molecule is introduced in the 100th article of Molecule of the Month.

adrenocortical hormone

See "corticosteroid".

adrenocorticotropic hormone

A hormone which acts on adrenal cortex to secret the adrenal cortex hormone. It secrets from anterior pituitary, and the corticotropin-releasing hormone promotes the secretion of this hormone.

Aequipecten irradians

See "bay scallop".

Aequorea

Jellyfish belonging in the Cnidaria phylum, Hydrozoa class, Leptomedusae order, and Aequoreidae family. If it is stimulated, Its gonad emits bluish white light by the act of green fluorescent protein (GFP).

aequorin

Luminescent protein found in the Aequorea, a kind of luminescent jellyfish. It emits blue light by the raising of Ca2+ concentration.

aflatoxin

African clawed frog

An South African aquatic flog of Pipidae, Xenopus genus. It is studied as a model organism. The scientific name is Xenopus laevis.

African sleeping sickness

A infectious disease caused by African sleeping sickness protozoa Trypanosoma brucei which transmitted by the tsetse fly. The first symptoms are high fever and headaches etc. The invasion into the central nervous system causes coma and sleeping.

agonist

A agent which has affinity to a specific cell receptor and similar effects such as neurotransmitter or hormone.

AIDS

See "acquired immunodeficiency syndrome".

AIDS virus

See "HIV virus".

alanine

One of the twenty amino acids composing proteins. It has methyl group in its sidechain. The abbreviates are Ala or A.

albumin

A general term of proteins which exists in cells and body fluid. The name derives from albumen (egg white) which is mainly composed of this proteins. There are several kinds of albumin, such as serum albumin in blood serum besides egg albumin. It plays roles such as osmotic pressure regulation and material transportation etc.

aldehyde

Organic compound containing aldehyde group (-CHO). Can be oxidized to an acid or reduced to an alcohol.

aldose

allergy

An excessive immune reaction against an antigen.

allosteric effect

A regulation of protein function by binding an other molecule (called effector molecule) to the other site of protein's functional site (called allosteric site). The binding causes the conformational change to the protein to regulate it's function. It also called to allosteric regulation. The enzyme regulated by this method is called the allosteric enzyme.

allosteric enzyme

See "allosteric effect".

allosteric regulation

See "allosteric effect".

alpha helix

A kind of right-handed helical structure of polypeptide chains, in which every amino acid residue forms a hydrogen bond to the four residues earlier amino acid. The hydrogen bonds of it exist inner side of the backbone to be stabilized. Moreover, it has steric favourable structure, resulting that it is an often observed secondary structure in proteins. The general expression is 3.6_13 helix, which means it proceeds 3.6 residues per helical turn and the number of atoms in the ring that is closed by the hydrogen bond is thirteen.

alpha-latrotoxin

ALS

1) See "amyotrophic lateral sclerosis". 2) See "acetohydroxyacid synthase".

Alzheimer's disease

A kind of dementia with symptoms of lower cognition ability etc. In pathology, senile plaques are found in the cerebral cortex. The plaques are derived from deposition of beta amyloid. The ICD-10 ID is G30.

amine

Organic compound or functional group that contains nitrogen as the core atom. Derived from ammonia (NH3) in which one or more hydrogen atoms are replaced by organic substituents. Monovalent amine is called amino group.

amino acid

A kind of organic compound which includes both an amino group (-NH2) and carboxyl group (-COOH) in its molecule. Most of amino acids are alpha amino acids, of which amino group and carboxyl group bind to the same carbon atom, and each of them links by the peptide bonds to form proteins or peptide chains. Generally, proteins consist of twenty kinds of amino acids, including proline, an imino acid.

amino group

Weakly basic functional group derived from ammonia (NH3) in which one or more hydrogen atoms are replaced by organic substituent. In aqueous solution it can accept a proton and carry a positive charge.

amino terminal

One end of a polypeptide chain that carries a free alpha-amino group. Also called N terminal (terminus). The amino acid sequence (primary structure) of a protein is described from amino terminal.

amino terminus

See "amino terminal".

AMP

Abbreviation of Adenosine 5'-MonoPhosphate. One of the four nucleotides in an RNA molecule.

amphioxus

See "lancelets".

amylase

A general term of enzymes which catalyse the hydrolysis of glycoside bonds of starch to produce oligosaccharide or monosaccharide. It includes several enzymes such as alpha-amylase (EC 3.2.1.1), beta-amylase (EC 3.2.1.2), glucoamylase (EC 3.2.1.3) etc.

amyloid

A kind of insoluble fibrous protein which tends to aggregation. The deposition to organs causes the amyloidosis etc.

amylopectin

A kind of starch consisting of glucose units. The units bind with alpha-1,4 glycoside bonds and with alpha-1,6 glycoside bonds which make branches in the molecule.

amylose

A kind of starch consisting of glucose units. The units bind with alpha-1,4 glycoside bonds sequentially.

amyotrophic lateral sclerosis

This is a neurodegenerative disease caused by the degeneration of motor neurons, which causes muscle weakness and atrophy throughout the body. In Japan, it is assigned to an intractable disease. It is also called to Lou Gehrig's disease, which is named for the namesake famous person. The cause of it has been unidentifiable. though the genomic disorder of SuperOxide Dismutase (SOD) is involved in it for a part of patients. The ID of ICD-10 is G12.2.

anabolic steroid

anaphylaxis

Acute systemic irritable reaction caused by IgE antibody.

androgen

A general term of steroid hormone that stimulates or controls the development and maintenance of masculine characteristics in vertebrates.

androstenedione

anisogamy

A type of sexual reproduction that the size of gametes is different each other. It can be found in animals and so on.

annealing

To make two single nucleic strand into one double strand. It is indispensable for making double strands that the sequences of each single strand are complementary, and such feature makes it possible to measure the complementation.

Anopheles

A genus of insect belonging to the Diptera order, Culicidae family. It includes species which mediate malaria.

anthrax

1) See "Bacillus anthracis" for the bacterial name. 2) A fatal disease which caused by Bacillus anthracis. It may by caught from animals, such as cattle, pigs, and sheep and has high

antibiotic

Substance that inhibits or abolishes the growth of microorganisms. Usually a product of a particular microorganism or plant. penicillin or streptomycin is known.

antiparallel

One relative orientation of the two strands. The polarity of one strand is oriented in the opposite direction to that of the other. Seen in the double helix of DNA, and secondary structure of proteins.

apoptosis

Form of controlled cell death shown in multicellular organism. It is also called "programmed cell death". A "suicide" program is activated within the cell, leading to fragmentation of the DNA, shrinkage of the cytoplasm, membrane changes and cell death without lysis or damage to neighboring cells.

appendicitis

aquaporin

A transmembrane protein which selectively conducts water molecules in and out of the cell.

archaea

A organism group included in prokaryote. Compose one of three organism domains together with eubacteria and eukaryote. The "archaea (archea)" is a plural form, while the singular form is "archaeon (archeon)".

arginine

One of the twenty amino acids composing proteins. It is classified into the basic polar sidechain amino acid. The abbreviates are Arg or R.

argonaute

A protein which has mRNA cleaving activity. It is indispensable for RNAi and forms the active site of catalyzing in RISC (RNA-Induced Silencing Complex）

asparagine

One of the twenty amino acids composing proteins. It is classified into the neutral polar sidechain amino acid. The side chain is -CH2-CONH2. The abbreviates are Asn or N.

aspartic acid

One of the twenty amino acids composing proteins. It is classified into the acidic polar sidechain amino acid. The side chain is -CH2-CONH2. The abbreviates are Asp or D.

astrocyte

A kind of glia cell exists in central nervous system. Its name is derived from its shape with rich protrusions.

astroglia

See "astrocyte".

asymmetric center

A central atom (usually carbon) which covalently bound four kinds of atoms or functional group that are different each other. It causes the chirality of the molecule.

ATP

A chemical component derived from a ribose, a kind of sugar, bound to adenine, a kind of purine base, at the 1' position, and bound to three sequenced phosphate groups at the 5' position. It often utilizes as energy carrier in various organisms. The phosphodiester bond is unstable and easily serves free energy by bond hydrolysis or transferring. It is the acronym of Adenosine 5'-TriPhosphate.

autosome

Chromosome with no involvement in sexuality decision. Any chromosome except for sex chromosomes.

auxin

avian flu

See "avian influenza".

avian influenza

A infectious disease which occurs among birds caused by the infection of type A influenza viruses.

axonin

A kind of glycoprotein which is specifically secreted from nerve cells. It is involved in the development of nerve system.

B

B cell

Type of lymphocyte that produces antibodies. Plays an central role in humoral immunity, a kind of acquired immunity.

bacillus

See "rod-shaped bacteria".

Bacillus anthracis

A gram-positive, facultatively anaerobic, rod-shaped bacterium which causes the anthrax disease. It is often found in soil, coated with capsule, and lack of flagella or cilia. When the circumstance gets worse, it makes endospore to endure.

Bacillus cereus

A kind of eubacteria belonging in the Bacillus genus. It is facultative aerobic gram-positive and causes food poisoning.

Bacillus influenzae

A gram-negative rod-shaped bacteria belonging the Haemophilus genus. It is not directly involved in the influenza disease. Although there are various kind of it, the type b is most common and causes meningitis and pneumonia to infant children.

Bacillus subtilis

A gram-positive obligate aerobe eubacteria which is commonly found in nature. The Bacillus subtilis natto utilized for the natto production is a kind of subspecies.

backbone

The core part of linear molecules such as proteins and nucleic acids. It means the part consisting of alpha carbon atoms and peptide bonds in proteins, and sugar and phosphate in nucleic acids.

backpackers diarrhea

See "giardiasis".

bacteriophage

A kind of virus which parasitizes bacteria as hosts and grow in them.

Baltimore classification

A virus classification proposed by David Baltimore, who is a molecular biologist of America. By the classification, viruses are classified into seven groups. The current virus classification governed by the International Committee on Taxonomy of Viruses (ICTV) is based on it. The seven classifications are described below: I.dsDNA (double strand DNA), II.ssDNA (single strand DNA), III.dsRNA (double strand RNA), IV.(+)ssRNA (single strand (+) sense RNA (mRNA)), V.(-)ssRNA (single strand (-) sense RNA (template RNA)), VI.ssRNA-RT (reverse transcribing single strand (+) sense RNA), and VII.dsDNA-RT (reverse transcribing double strand DNA).

basal lamina

Thin membrane exist between the epithelia and connective tissue.

base

A general term of chemical compounds which accept protons or donate electrons. Nucleobases such as purine bases and pyrimidine bases are sometimes referred to simply as bases.

basement membrane

See "basal lamina".

Basic Local Alignment Search Tool

See "BLAST".

bay scallop

A shellfish belonging to the Mollusca phylum, the Bivalvia class, and Pectinidae family. It is edible.

beaver fever

See "giardiasis".

beta barrel

A kind of partial structure of proteins, which consists of several beta sheets, forming cylindrical structure. It is often found in molecule transporting proteins such as porins.

beta hairpin

beta sheet

A secondary structure of protein. The different sections of the peptide chain align parallel and are bound by hydrogen bonds each other.

bioluminescence

A luminescent phenomena by organisms. A type of energy form with light emission.

black porgy

See "black sea bream".

black sea bream

A kind of teleost belonging to the Perciformes order, Sparidae family. It habitat the east Asia coast, and is edible. It is also called chinu.

BLAST

An algorithm comparing two DNA base sequences or protein amino acid sequences to know local sequence homology. Programs with the algorithm are also called with same name. It can be used at various sites such as NCBI Website.

blood

A kind of body fluids of animals. It plays roles such as supplying oxygen and nutrients to each cell of the body, retrieving carbon dioxide and waste products, immunity, and so on. It consists of red blood cells, white blood cells, platelets, blood plasma etc.

blood cell

A general term of free cells which found in blood. It includes two types, erythrocyte with respiratory pigment, and leukocyte without respiratory pigment.

blood coagulation factor

A general term of compounds which is involved in the blood coagulation, such as fibrinogen and prothrombin.

blood fluke

blood plasma

The liquid component of the blood. In vertebrate, It is equivalent to the blood which removed the solid components.

BMRB

A structure database of biological macro molecules determined by means of NMR. It is a member of world wide Protein Data Bank (wwPDB) whose name is the acronym of Biological Magnetic Resonance data Bank. It is managed by BioMagResBank at University of Wisconsin-Madison.

Bordetella pertussis

A Gram-negative eubacteria belonging to Beta Proteobacteria class, Burkholderiales order, and Alcaligenaceae family. It causes pertussis.

Bovine spongeiform encephalopathy

A type of Transmissible Spongiform Encephalopathy (TSE), which causes the formation of cavity in brain. In Japan, it is assigned to a domestic animal's disease in the law. It is suggested the abnormally structured prion proteins will cause it.

BSE

See "Bovine sponge-form encephalopathy".

bZIP protein

See "leucine zipper".

C

C reactive protein

Protein appears in blood according to the inflammation or tissue damage. It's name is derived from its feature of binding to the C polysaccharide of pneumococci.

C terminal

See "carboxyl terminal".

C terminus

See "C terminal".

C3 plant

A plant which only has the Calvin cycle for carbon fixation pathway of photosynthesis.

C4 plant

A plant which has two steps of pathways for carbon fixation pathway of photosynthesis. The one is the Calvin cycle, and the other is the C4 pathway for concentration of carbon dioxide.

cadherin

A member of family of proteins which mediates cell-cell adhesion in animal tissues. The function depends on calcium ion (Ca2+), therefore it's name. This molecule is introduced in the 99th article of Molecule of the Month.

Caenorhabditis elegans

A invertebrate organism belonging in the Nematoda phylum, Secernentea class, Rhabditida order, and Caenorhabditis genus. It is used as a model organism.

caffeine

Alkaloid included in coffee, tea, and so on. It has effects of awake and diuretic.

calmodulin

A family of calcium-binding protein controlled by intracellular calcium ion (Ca2+) concentration. It is ubiquitous and modifies the activity of target enzymes and membrane transport proteins.

Calvin cycle

A part of photosynthesis pathway. During this cycle, sugar is made from carbon dioxide by utilizing NADPH and ATP produced in light pathway.

Calvin-Benson cycle

See "Calvin cycle".

CAM

See "cell adhesion molecule".

CAM plant

A plant which has two steps of pathways for carbon fixation pathway of photosynthesis. The one is the Calvin cycle, and the other is the CAM pathway. In night stomas are opened to uptake carbon dioxide and water. Whereas in day, the carbon fixation runs not opening stomas but using stored carbon components. This type of plant has strong tolerance for drying.

cAMP

See "cyclic AMP".

cancer

Spontaneously growing low-differentiated epithelial cell clusters (tumors), which is derived from autologous cells, and has expanding feature such as invasion and metastasis. It causes gene damage and so on.

cane sugar

See "sucrose".

capsid

Protein shell enveloping genetic materials of a virus. Often form helical or icosahedral structure. Consists of several protein subunits.

carboxyl terminal

One end of a polypeptide chain that carries a free alpha-carboxyl group. Also called C terminal (terminus). Locates in the end of amino acid sequence (primary structure) of a protein.

carboxyl terminus

See "carboxyl terminal".

carp

Fish belonging in the Cyprinidae family, and the Cyprinus genus. It's scientific name is Cyprinus carpio.

catalase

A enzyme which catalyzes the reaction converting a hydrogen peroxide into water and oxygen gas. It contributes to removing harmful active oxygen. The EC number is 1.11.1.6. The gene CAT encoding this enzyme located on the p13 of 11th chromosome.

cataracta

Disease of eyes lens opacity, and lost transparency. There are some types, congenital and a posterior etc.

catechin

catenin

catenin

CATH

A database which classified proteins based on their structural feature. It's name is the acronym of the major four classification hierarchies, Class, Architecture, Topology, and Homologous superfamily. It is managed by University College London (UCL) in UK. http://www.cathdb.info/

CD

An abbreviation of the Cluster of Differentiation or the Cluster of Determination. It is a classification of monoclonal antibodies by its properties to various antigens on the surface of cells (mainly blood cells).

Cdk

See "cyclin-dependent kinase".

cDNA

See "circular DNA".

cell adhesion molecule

Protein on the surface of an animal cell that mediates binding between cell and cell or between cell and extracellular matrix. Abbreviates as CAM.

cell cycle

Reproductive cycle of a cell. The orderly sequence of events by which a cell duplicates its contents and divides into two. It is also called cell-division cycle.

cell division

Phenomenon that a mother cell separates into two or more daughter cells. In eukaryotic cells, the division of the nucleus (mitosis) followed by the division of the cytoplasm (cytokinesis).

cell junction

Specialized region of connection between two cells or between a cell and the extracellular matrix.

cell wall

Extracellular matrix exists on outer surface of cell membrane. Works as structural enhancement of cell. Found in plants, bacteria, archaea, fungi, and algae cells, whereas not found in animal and protists cells.

cell-mediated immunity

A kind of adaptive immunity. Immunity effect that activates antigen specific T cells which kill infected cells and tumor cells, activate macrophages and natural killer cells (NK cells) destroying intracellular pathogens, and so on.

cellulase

Enzyme that catalyze the hydrolysis of cellulose. Produced chiefly by fungi, bacteria, and protozoan. The EC number is 3.2.1.4. Related entry: xPSSS:1JS4.

cellulose

Polysaccharide consisting of linear sequenced glucose connected with beta 1,4-glycosidic bonds. Main component of cell wall of plant cell, and serves the cell structure enhancement.

ceramide

A compound of sphingoid bound to a fatty acid by acid amid bond. A kind of sphingolipid.

chaperone

Protein that assists folding of other proteins. Prevents misfolding in order not to produce inactive or aggregated polypeptides.

chaperonin

chemokine

A kind of cytokine involved in move inducing of cells. In many case, it contains four cysteine residues forming disulfide bonds.

chickenpox

See "varicella".

chiral center

See "asymmetric center".

chirality

A molecular feature that there is its enantiomer.

chlorophyll

A kind of photosynthetic pigment included in the chloroplasts of plants and cyanobacteria. It has one magnesium atom at the center of tetrapyrrol ring. There are several types with the different type of tetrapyrrol ring or binding of long chain alcohol (phytol) etc.

chloroplast

Organelle found in green algae and plant cells that contains chlorophyll and conducts photosynthesis. It is a class of organelle known as a plastid.

cholera

cholesterol

choline

chromatin

Complex of DNA and proteins such as histones. Exists in nucleus of eukaryotic cell and in nucleoid of prokaryotic cell. Before M (mitotic) phase of the cell division, packed up into a more compact structure.

chromosome

A rod like structure composed of DNA molecule and associated proteins (histone). Especially evident in plant and animal cells undergoing mitosis or meiosis.

chymotrypsin

circadian rhythm

circular DNA

A DNA strand whose both ends are joined to form cyclic shape. It is found in prokaryote and plasmids.

citrate synthase

citric acid cycle

A part of metabolic pathway of aerobic organisms for obtaining energy. In the cycle, acetyl group derived from organic compounds of intaken foods is oxdized, resulting to produce energy and by-product, such as carbon dioxide and water. In eukaryote cells it occurs in the mitochondria.

CJD

See "Creutzfeldt-Jakob disease".

class

1) See "class (structural classification)". 2) See "class (taxonomy)".

class (structural classification)

A classification layer of protein structural classification in the SCOP.

class (taxonomy)

A hierarchy of biological taxonomy. It is the upper layer of order and the lower layer of phylum or division.

clathrin

Protein which is involved in endocytosis (uptaking materials from outside to inside of a cell). Consists of two kind of subunits, H chain and L chain. Three H chains and three L chains aggregate to form a three-legged structure (triskelion) and then they assemble the surface of inner side of cell membrane to form basketlike convex structure.

clathrin coated vesicle

A intracellular vesicle formed by proteins such as clathrin. Formed in the process of uptaking materials into a cell by endocytosis. It becomes into an endosome by removing clathrins.

Clostridium botulinum

cluster of differentiation

See "CD".

Cnidaria

coccus

A kind of bacteria whose shape is globose. The plural form is "cocci".

code

The role of gene to direct the amino acid sequence of proteins. That is, the gene codes the protein.

codon

Three sequenced nucleotides each of which direct an amino acid of proteins. It is included in DNA or mRNA. The relation between codon and amino acid is common in almost all organisms.

Coelenterata

coiled-coil

A kind of structural domain (super secondary structure) of proteins. More than one alpha helices twist each other to form coiled coil formation.

colchicine

Alkaloid included in the seed and rhizome of meadow saffron of Liliaceae family. It is used not only as therapeutic drug of rheumatoid and gout, but also breed improvement and production of seedless watermelon, utilizing the property of inducing chromosome doubling in cell division. It also has strong toxicity. These effects are derived from the inhibiting act to the tubulin, major protein component of the microtubule.

collagen

Protein often seen in extracellular matrix and connective tissues. Rich in glycine and proline. Often constructs left-handed helix and three of it coil around each other and turn into right-handed triple-stranded helical rod, called tropocollagen.

colon bacillus

See "Escherichia coli".

common cold virus

See "rhinovirus".

cone snail

congenital immunity

See "innate immunity".

connective tissue

A general term of tissue which lies between other tissue, to fill the intercellular space, to maintain the structure, and so on. Cells in it contain rich extracellular matrix. It includes bone, cartilage, blood, and so on.

conotoxin

conservation

Conus

See "cone snail".

corpuscle

See "blood cell".

corticosteroid

See "adrenal cortex hormone".

corticotropin-releasing hormone

Hormone secreted from the hypothalamus, and acts to the anterior lobe of hypothalamohypophyseal to prompt the release of adrenocorticotropic hormone (ACTH).

cortisone

"A kind of the glucocorticoid. The IUPAC name is 17,21-dihydroxypregn -4-ene-3,11,20-trione."

crambin

creatine

creatine kinase

Creutzfeldt-Jakob disease

CRF

See "Corticotropin-releasing hormone".

CRH

See "corticotropin-releasing hormone".

CRP

See "C reactive protein".

cryo electron microscope

CryoEM

See "cryo electron microscope".

cryptobiosis

State of organisms with almost no metabolism. They take it to tolerant severe circumstance by storing trehalose in their body. The well known organism to do it is the water bear.

crystallin

A structural protein which forms the primary component of the eye lens.

CTL

See "cytotoxic T lymphocyte".

Culex tritaeniorhynchus

Insect belonging in the Diptera order, Culicidae family, and Culex genus. It is a mosquito mediating the Japanese encephalitis virus.

Cushing's syndrome

A disease caused by the excessive secretion of glucocorticoid, one of the adrenal cortex hormone. The major symptoms are obesity, muscle weakness, hypertension, diabetes similar symptom, osteoporosis. It is induced by the abnormality of the adrenal gland or the pituitary gland.

Cycas revoluta

A kind of gymnosperm belonging in the Cycadaceae family, Cycas genus.

cyclic AMP

Nucleotide generated from ATP by adenylyl cyclase. Stimulation to cell-surface receptors activate its producing. Act as intracellular signalling molecule.

cyclin

Protein family controlling cell cycle progression. Complexed with cyclin-dependent protein kinase (Cdk) to activate its function proceeding one stage of the cell cycle to the next. Different cyclin acts each cell cycle step.

cyclin-dependent kinase

See "cyclin".

Cyprinus carpio

See "carp".

cyst

cysteine

A hydrophobic amino acid including a sulfur atom in the side chain. It contributes the protein stabilization by forming disulfide bonds between two molecules of it. The abbreviation is Cys, or C.

cytochrome

Redox active protein that is colored, included heme iron at the core, Exists in many organisms, and carries electrons in electron transport chain such as aerobic respiration and photosynthesis.

cytokine

Extracellular signalling protein between cells. Although there are many types of them, most are involved in immunity or inflammation.

cytokinesis

Division process of cytoplasm following the division of nucleus in eukaryotic cell division.

cytokinin

cytoskeleton

System which contributes to maintain the cell shape and to move. Exists in cytoplasm, and consists of filament proteins such as actin filaments, intermediate filaments, microtubules, and so on. Formerly, it was thought that only the eukaryotes have it. But it has shown that the prokaryotes also have it. PubMed:16959967

cytotoxic T lymphocyte

It also called killer T cell or CTL. It recognizes class I MHC on the target cell mediated the specific T cell antigen receptor (TCR) and kills the target. It has CD8 as the cell surface antigen.

D

DALI

Dalton

A unit of molecular mass. Approximately equal to the mass of a hydrogen atom (1.66 x 10-24 g).

dark reaction

A part of photosynthesis pathway of carbon fixation. It utilizes electrons and ATP produced in the light reaction.

DCT

See "distal convoluted tubule".

dementia

dementia with lewy body

dengue fever

An infectious disease which mainly found in the tropical region. The major symptoms of it is headache, fever, and blooding.

Dengue virus

Virus belonging in the IV group (+ssRNA), Flaviviridae family, and Flavivirus genus. It causes the dengue fever.

deoxyribonucleic acid

See "DNA".

deoxyribose

Sugar which is composed of five carbon atoms and forms DNA molecules.

depression

A psychiatric disorder which is accompanied by depression. For treatment, secreting stimulating medicine of neurotrarnsmitter is used.

dextrin

DHAP

See "dihydroxyaceton phosphate".

dicer

In the RNA interference (RNAi), it is a protein which cleaves the foreign double strand RNA such as viruses to produces the small Interfering RNA (siRNA).

dihydroxyaceton phosphate

diphtheria

diploid

1) An organism which has two pairs of homologous genomes. In life cycle, it indicates the organism in diploid generation. 2) An organism which has two pairs of hetero genomes. It's number of chromosomes is two times many as the base number.

distal convoluted tubule

disulfide bond

Covalent bond formed between two thiol groups (-SH) on cysteines. It contributes the conformational stability of proteins.

division

See "phylum".

DNA

Abbreviation of DeoxyriboNucleic Acid. It acts as the store of hereditary information within a cell and the carrier of this information from generation to generation. Consists of a kind of sugar 2'-deoxyribose bound to a phosphate at 3' position and a ba

DNA ligase

DNA polymerase

Enzyme that synthesizes a new DNA strand by joining nucleotides together using a DNA template strand as a guide.

domain

1) See "domain (protein)" for the partial structure of protein molecules. 2) See "domain (taxonomy)" for the highest taxonomic group.

domain (biological classification)

In biological taxonomy, this is the new highest hierarchy which is higher than kingdom, formerly highest hierarchy, and proposed in the Carl Woese's three-domain system (1990). In this system, there are three domains, Archaea, Bacteria, and Eukaryota.

dopamine

double fertilization

Fertilization form which is specific to angiosperm. It means the phenomenon that one of two sperm cells at the head of pollen tube fertilizes an egg cell and the other does an central cell. After fertilizing, one sperm nucleus coalesces to egg nucleus, and the other sperm nucleus coalesces two polar nuclei. The former is called reproductive fertilization, and the latter is called nutritional fertilization.

Drosophila melanogaster

A small fly that belongs to Diptera order, Drosophilidae family, and Drosophila genus. The scientific name is Drosophila melanogaster. The number of chromosomes is 8. The sex-determination pattern is type XY. Feed fruit and so on. Used as model organism in various area of biology

dysentery bacillus

E

EBI

See "Europian Bioinformatics Institute".

EC number

Numerical classification for enzymes with four hierarchies, based on chemical reactions they catalyze. It is established by Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB).

ecdysone

egg

See "ovum".

elastase

elastin

A hydrophobic protein that forms extracellular extensible fibers (elastic fibers). It acts on tissues to enhance their stretchability and resilience.

electron microscope

electron transport chain

EM

See "electron microscope".

enantiomer

A kind of stereoisomer which are mirror image each other.

encephalitis

endocytosis

Process to uptaking of material into a cell by an invagination of the cell membrane. Related word: clathrin

endoplasmic reticulum

A labyrinthine membrane-enclosed organelle in the cytoplasm of eukaryotic cells. Involved in synthesis and intracellular transportation of materials such as proteins and phospholipids.

endosome

A membrane-enclosed organelle included in most of eukaryotic cell. Carries materials uptaken by endocytosis. Related words: clathrin, lysosome

endotoxin

enolase

enterobacter

entropy

envelop

epidermophytosis

See "tinea".

epigenetics

epinephrine

See "adrenaline".

epithelial tissue

ER

See "endoplasmic reticulum".

erythroblast

erythrocyte

A kind of blood cell (hemocyte, . It plays a role to carry oxygen for each cell in body of organisms.

erythropoietin

Hormone synthesized and secreted by the kidney, which stimulates production of erythrocytes (red blood cells).

Escherichia coli

A species of gram-negative bacteria whose shape are rodlike. They often utilize to biological studies, and to produce various chemical compounds by genetic introduction. This name is the scientific name of colon bacillus.

essential amino acid

Amino acids which can't synthesize by itself and need to intake from foods. In human, they consists of nine kinds of amino acids, Val, Leu, Ile, Met, Phe, Trp, Thr, Lys, and His.

estrogen

ethylene

eukaryote

Organism which consists of one or more cells with a distinct nucleus and cytoplasm. Includes all kind of life except viruses and prokaryotes (bacteria and archaea). In three-domain system of organism classification, it composes one of the three domain , and includes four kingdom, Animalia, Fungi, Plantae, and Protista.

European rabbit

Europian Bioinformatics Institute

http://www.ebi.ac.uk/

exocytosis

A method to secret　molecules in eukaryotic cells. Membrane-bounded vesicles included molecules fuse with the cell membrane and release their contents to outside.

exon

A segment consists of a sequence of nucleotides that will be finally expressed to translate into protein . Usually exists adjacent to a noncoding DNA segment called an intron.

exotoxin

expression

Production of an observable phenotype by gene. It is often directed by protein synthesis.

extracellular matrix

A general term which means outer side cellular structures created by cell secretion materials such as polysaccharide and protein. It includes cell wall of bacteria and plants, cuticle of insects, shell of mollusk, and so on.

F

F6P

See "fructose-6-phosphate".

family

1) See "family (taxonomy)". 2) See "family (protein)".

family (protein)

A concept of group which includes similar proteins in function or structure.

family (taxonomy)

A hierarchy of biological taxonomy. It is the upper layer of genus and the lower layer of order.

fatty acid synthase

FBP

See "fructose-1,6-bisphosphate".

FBPase

See "fructose-1,6-bisphosphatase".

ferredoxin

fibrin

fibrinogen

filamin

filterable microorganism

See "virus".

first category infectious disease

flagella

See "flagellum".

flagellum

A long, whiplike structure protruded from cell. It drives the cell by moving undulately. The eukaryotic flagella are longer form of cilia, whereas the prokaryotic flagella have different construction and mechanism of action. The term "flagella" is the plural form.

flavivirus

FMDV

See "foot-and-mouth disease virus".

fold

foot-and-mouth disease

foot-and-mouth disease virus

fructose

fructose-1,6-bisphosphatase

fructose-1,6-bisphosphate

fructose-6-phosphate

fruit fly

A generic name of a small fly that belongs to the Diptera order, Drosophilidae family. It often means yellow fruit fly (Drosophila melanogaster), a species of it, which often used in genetic research.

fruit sugar

See "fructose".

FSSP

A database of protein structural similarity. It is managed by EBI, European Bioinformatics Institute, using DALI algorithm. The URL is http://www.sander.ebi.ac.uk/dali/fssp/

fungi

A organism group consisting of a kingdom in biological taxonomy. It is a heterotrophic eukaryotic organism, which has chitinous cell wall. It includes yeast, mushroom, mold, and so on. The singular form is fungus.

fungus

See "fungi".

furanose

G

G protein

See "GTP binding protein".

G6P

See "glucose-6-phosphate".

gamete

A haploid cell specialized for producing zygote by fertilization or mating. It can classify into two types, anisogamy and isogamy. Animals have anisogamy, and the larger and immotile one is called female gamete (ovum, egg), whereas the smaller and motile one is called male gamete (spermatozoon, sperm).

gametocyte

A cell which is divided into gametocyte (ovum or spermatocyte) by meiosis. Derived from gametogonium by mitosis.

gametogonium

A cell which is divided into gametocytes by mitosis. Included in germline.

ganglioside

A glycolipid bound one or more sialic acid. It is one of the component of cell membranes, and is especially rich in the cell membrane of nerve cell.

GAP

See "glyceraldehyde-3-phosphate".

GAP

See "GTPase activating protein".

garden pea

GEF

See "guanine nucleotide exchange factor".

gene ontology

A thesaurus database for unifying terms of genetic products. It is managed with the Gene Ontology consortium which consists of many organism's databases. Terms are classified into three structured categories, biological processes, cellular components and molecular functions. http://www.geneontology.org/

gene silencing

A process to repress the gene expression. There are two types, in transcription and in post-transcription.

genus

A hierarchy of biological taxonomy. It is the upper layer of species and the lower layer of family.

germ cell

A cell produced from gametocyte (oocyte and spermatocyte) by meiosis. This cell turns to a gamete (egg and sperm).

germline

A general term which refers to cells involving reproduction in organisms. Genetic mutations in these cells will be passed to next generations. The other cells are called somatic cells.

GFP

See "green fluorescent protein".

ghrelin

Giardia lamblia

giardiasis

gibberellin

glaucoma

glia cell

See "glial cell".

gliacyte

See "glial cell".

glial cell

A general term which means all the cells except for nerve cells. It plays various roles such as fixation and insulation of nerve cells. There are various types such as oligodendroglia cell, astrocyte, microglia cell, schwann cell and so on.

gliocyte

See "gliacyte".

globulin

glucagon

glucan

A general term of polysaccharide whose monosaccharide unit is glucose. There are many types of glucans according to the difference of their bond type. For example, the amylose bound with alpha-1,4 bonds, the glycogen bound with alpha-1,4 and alpha-1,6 bonds, and the cellulose bound with beta-1,4 bonds.

glucocorticoid

A adrenal cortex hormone which secreted from the adrenal cortex. It is a kind of steroid hormone which acts on the facilitation of proteins and lipids degradation, antiinflammation, stress response, and so on.

glucose

Monosaccharide with six carbons which plays a major role in the metabolism of living cells. Stored in polymeric form as glycogen in animal cells and as starch in plant cells.

glucose-6-phosphate

glucose-6-phosphate isomerase

glutamic acid

One of the twenty amino acids composing proteins. It classified into the acidic polar sidechain amino acid. The abbreviates are Glu or G.

glutamine

One of the twenty amino acids composing proteins. It classified into the neutral polar sidechain amino acid. The abbreviates are Gln or Q.

glyceraldehyde-3-phosphate

glyceraldehyde-3-phosphate dehydrogenase

glycine

One of the twenty amino acids composing proteins. It is the only amino acid which has no asymmetric carbon. The abbreviates are Gly or G.

glycogen

Polysaccharide which is utilized to energy store in animals. Sugar chain which composed of D-glucose units linked by alpha-1,4 glycosidic bonds also makes alpha-1.6 bonds every about ten glucose residues. It results many blanched structure.

glycolipid

A lipid molecule bound to sugar residues or sugar chain at the polar headgroup. Exist in the surface of biological membranes and is involved in various functions.

glycolysis

A metabolic pathway to get energy by degrading glucoses. Most of all organisms utilize it in the cytosol. The degradation of this pathway is incomplete, and the other oxidative pathway (citric acid cycle and electron transport chain) is necessary to derive more energy

glycoprotein

A protein complexed with one or more oligosaccharide chains covalently linked to amino-acid side chains. Most secreted proteins and most proteins exposed on the outer surface of the cell membrane are glycoproteins.

glycosidic bond

glycosylation

The process of adding one or more sugars to a lipid or a protein molecule.

GO

See "gene ontology".

Golgi apparatus

See "golgi body".

golgi body

A organelle found in eukaryotic cells. It is composed of membrane-bounded sacs. It processes and sorts proteins and lipids transported from the endoplasmic reticulum.

gout

gouty arthritis

GPCR

See "G-protein-coupled receptor".

G-protein-coupled receptor

grain rot

Gram-negative bacteria

Gram-positive bacteria

Gram-staining

Greek key motif

green fluorescent protein

Fluorescent protein found in luminescent organ of Aequorea victoria (a kind of jellyfish). It is often used to mark various compounds such as proteins, cells, and intracellular organella, because the marking with it makes easy to chase compounds.

GTP

A chemical compound of guanosine, which is one of the nucleoside, bound to three linear sequenced phosphates at the 5' position. Same as ATP, it releases large energy by hydrolytic cleavage of the end phosphate. It plays various physiological roles, such as material of RNA, aggregation of microtubule, protein synthesis, cell signalling.

GTP binding protein

A general term of protein with GTPase activity which hydrolysis a guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and phosphate. It is involved in control various intercellular signal transmission by activate or inactivate other proteins.

GTPase

See "GTP binding protein".

GTPase activating protein

A protein which binds to a GTP binding protein and inactivates it. It stimulates the GTPase activity of GTP binding protein to hydrolyze its bound GTP to GDP. On the contrary, the guanine nucleotide exchange factor (GEF) activates the GTP binding protein.

guanine nucleotide exchange factor

A protein which binds to a GTP binding protein and activates it. It releases the GDP molecule bound to the GTP binding protein to allow it to bind GTP in its place. On the contrary, the GTPase activating protein (GAP) inactivates the GTP binding protein.

guanosine 5'-triphosphate

See "GTP".

guide RNA

H

H antigen

habu snake

Haemophilus influenzae

See "Bacillus influenzae".

Hansen’s bacillus

See "Mycobacterium leprae".

Hansen's disease

haploid

An organism which has only one chromosome pair to maintain life. Most of animals, only the gametes are haploid.

heat shock protein

A protein whose amount of production increases when cells, tissues, or individual of organisms suffer form temperature higher than normal circumstance. Other stresses such as heave metal, ethanol, and oxygen deficiency also induce its production to avoid the damage.

HeLa cell

helicase

Enzyme that unwinds a double helix shaped nucleotide strand into two single strands.

helix

helix-loop-helix motif

A structural motif that often seen in gene regulating proteins.

helix-turn-helix motif

helper T cell

hemagglutinin

hematopoietic stem cell

heme

A porphyrin divalent iron complex. It is the pigment of hemoglobin. It play roles of carrying oxygen in hemoglobin and carrying electron in cytochromes.

hemocyanin

Respiratory pigment included in the blood of crustaceans and molluscs, containing copper atoms. It isn't included in blood cells but is solved in hemolymph, playing a role of oxygen transferring. The color without oxygen state (pentavalent copper) is colorless, whereas the color with oxygen state (divalent copper) is blue.

hemocyte

See "blood cell".

hemoglobin

The main protein contained in red blood cells of vertebrate and some kinds of other organisms. It transports oxygen from the lung to the whole body and is tetramer consists of two alpha subunits and two beta subunits. Each subunit contains heme, one porphyrin complex with divalent iron atom, which bound to oxygen. The normal hemoglobin (hemoglobin A) will change by the mutation in the sixth residue of beta subunit from glutamate to valine, to hemoglobin S causing sickle cell disease.

heparin

heparin

A kind of glucosaminoglycan produced by animal mast cells. It is a negative charged electrolyte polymer which is rich in the sulfate group and carboxyl group. It can found in liver as the blood coagulation inhibitor.

hepatitis virus

A general term of viruses which cause hepatitis, liver inflammation.

Herpesviridae

A family of DNA virus, belonging to the Ist group (double strand DNA (dsDNA)). It includes three subfamily, Alphaherpesvirinae, Betaherpesvirinae, Gammaherpesvirinae, and others.

heterochromatin

heterogamy

See "anisogamy".

heterozygote

hexokinase

hexose

HHV-3

See "varicella zoster virus".

hippocampi

See "hippocampus".

hippocampus

histamine

Chemical component secreted from mast cells and basophils. The IUPAC name is 1H-imidazole-4-ethanamine. It is synthesized from a histidine amino acid by catalizing of histidine decarboxylase. It stimulates vasodilation, blood pressure reduction, and smooth muscle contraction etc. The over secretion causes allergic symptom.

histidine

One of the twenty amino acids composing proteins. It is classified into the basic polar sidechain amino acid, and has a imidazole ring in its sidechain. It is one of the human essential amino acid. The abbreviates are His or H.

histone

HIV virus

A reverse transcribing virus belonging to Retroviridae family, Lentifirus genus.

hives

See "urticaria".

HK

See "hexokinase".

homeobox

homeobox gene

homeodomain

homeodomain protein

homeosis

homeotic gene

homogamy

See "isogamy".

homozygote

Hoogsteen base pair

house mouse

See "mouse".

HSP

See "heat shock protein".

Human herpesvirus 3

See "varicella zoster virus".

humoral immunity

Huntington's disease

hyaluronic acid

hybridoma

hydrogen bond

A noncovalent bond which joins between a positive charged hydrogen atom and two negative charged atoms. It is stronger than the van der Waals force, weaker than the covalent bond and ion bond. It contributes the structural stability of molecules.

hydrolase

A general term of enzymes which catalyze the hydrolysis of a chemical bond. It is classified into the EC 3 group.

hydrophilic residue

hydrophobic residue

hydroxyproline

hypercortisolism

See "Cushing's syndrome".

hyperuricemia

hypothalamus

I

ICD

See "International Statistical Classification of Diseases and Related Health Problems".

IL

See "interleukin".

imidazolinone

immediate hypersensitivity reaction

See "anaphylaxis".

immune

A system to exclude exogenous or endogenous foreign bodies for maintaining the homeostasis of host animal. It can classify innate immunity and acquired immunity.

immunoglobulin

A kind of antibody molecule abbreviated Ig. In higher bertebrates, there are five kinds , IgA, IgD, IgE, IgG, and IgM. Each of Ig has different roles in the immune response.

induced pluripotent stem cell

See "iPS cell".

infection

influenza

A infectious disease caused by influenza virus. The symptoms of it is high fever, myalgia (muscular pain), respiratory disorder, and so on.

influenza virus

A sense-negative single strand RNA virus belonging in Orthomyxoviridae family. There are three types, A, B, and C. It causes the influenza disease.

innate immunity

A general term of immune biological defending system except for adoptive immunity in a wide sense. This immune system is found in various organisms, and its antigen is non-specific.

insulin

integrin

integron

intein

interferon

interleukin

International Statistical Classification of Diseases and Related Health Problems

A classification of death causes of and disease made by World Health Organization (WHO). It intends to record the data of death and disease systematically, which is from distinctive country, region at distinctive period, in order to analysis, interpret, and compare. The latest version is ICD-10, consists of 22nd of categories. The URL is http://www.who.int/classifications/ .

intron

iPS cell

A cell which is produced by inducing some genes to a body cell and has same pluripotent ability as embryonic stem cell (ES cell). It was first produced by Shinya Yamanaka's team at Kyoto University. It can settle the ethical problem by disrupting the blastcyst stage cells and is expected to help regenerative therapy. It is the abbreviation of the induced pluripotent stem cell.

iron-sulfur cluster

islets of Langerhans

isoenzyme

See "isozyme".

isoform

See "protein isoform".

isogamy

A type of sexual reproduction that the size of gametes is same. It can be found protists, fungi, algae, and so on.

isoleucine

One of the twenty amino acids composing proteins. It is hydrophobic and the essential amino acid for human as being unable to synthesize by itself. The abbreviates are Ile or I.

isomerase

A general term of enzymes which catalyze geometric or structural changes within a molecule to form a single product. It is classified into the EC 5 group.

isozyme

A variation of a enzyme with the same activity and with small difference of amino acid sequence. This is a term of protein isoform used for only enzymes.

J

Japanese encephalitis

Japanese encephalitis virus

JH

See "juvenile hormone".

Jmol

A java-based open source software visualizing molecular structures. It is developed for replacement of obsolete same software Xmol, because the maintenance of the Xmol finished. The URL is http://www.jmol.org/

juvenile hormone

jV

A software of the macromolecule structure viewer, developed as part of activity of the Protein Data Bank Japan (PDBj). It can read the molecule structural data with XML format files (PDBMLs) and the text format files (PDB format files), and visualize and operate the molecule structural images interactively, It can also display non-molecular polygon information. Utilizing the feature , the electrostatic surface information from the eF-site database can be display. It requires a Java available circumstance. The URL is http://www.pdbj.org/jV/TOP.html

K

KEGG

See "Kyoto Encyclopedia of Genes and Genomes".

keratin

ketose

kidney

killer T cell

See "cytotoxic T lymphocyte".

kinase

kingdom

Krebs cycle

See "citric acid cycle".

Kyoto Encyclopedia of Genes and Genomes

L

lactamase

A enzyme which catalyzes the degrading reaction of the penicillin, a kind of antibiotic.

lactic acid

lactic acid fermentation

lagging strand

Lamblia intestinalis

See "Giardia lamblia".

laminin

A kind of glycoprotein which is the main component of basal laminae.

lancelets

Latrodectus hasseltii

See "redback spider".

leading strand

Leishmania

leishmaniasis

leucine

One of the twenty amino acids composing proteins. It is hydrophobic and the essential amino acid for human as being unable to synthesize by itself. It is contained in almost all proteins. The abbreviates are Leu or L.

leucine zipper

A protein domain which includes several leucine every seven residue of alpha helices. It includes protruded regions consist of hydrophobic leucine residues every two rotations, and two domains may form a dimer by engaging each leucine residue as zipper . The transcription regulating factors include this domain have basic amino acid near by the zipper region, which is the DNA binding site and then the factors are also called basic ZIP (bZIP) proteins.

leukemia

General term of disease with the tumorigenesis and growth of hematopoietic cells. Tumor cells often have chromosomal abnormality. It may be caused such as radioactivity, oncogenic chemicals, and viruses.

leukocyte

A general term of blood cell which has no respiratory pigment.

Lewy body

ligand

Small molecule which specifically binds to proteins etc. It includes various molecules such as substrates and coenzymes of the enzyme, and receptor binding molecules such as antigens, antibody, hormones, and neurotransmitter.

ligase

A general term of enzymes which are coupled with exergonic reaction. It is also called synthetase, and is classified into the EC 6 group.

light reaction

lipase

lipid raft

A micro structure exists in cell membranes. It is abundant in sphingolipids and cholesterols, and is thought to help the function of transmembrane proteins.

lipocalin

A family of proteins which transport hydrophobic molecules. Members of the family have common beta barrel structure.

lipopolysaccharide

luciferase

A general term of enzyme which catalyzes the reaction of oxidation in biological luminescence.

luciferin

A general term of light emitting material in chemical luminescence of biology.

lyase

A general term of enzymes which catalyze the reaction which cleave a various chemical bond except for hydrolysis and oxidation. It is classified into the EC 4 group.

lymphocyte

lymphoma

General term of disease with the tumorigenesis and grouth of lymphatic cells.

lymphoma

See "malignant lymphoma".

lysine

One of the twenty amino acids composing proteins. It classified into the basic polar side chain amino acid. It is one of the human essential amino acids. It is rich in bean, dairy products, and fish etc. The abbreviation is Lys and K.

M

macrophage

mad cow disease

See "Bovine spongeiform encephalopathy".

magnetic resonance imaging

mainchain

See "backbone".

major histocompatibility complex

malaria

malignant neoplasm

See "cancer".

malignant tumor

See "cancer".

maltose

marmoset

mast cell

mastocyte

See "mast cell".

mathylation

measles

measles virus

meiosis

melioidosis

MeSH

A thesaurus database for managing the information of books and journals collected by National Library of Medicine (NLM) in U.S. It is mainly constructed by structured descriptors which is classified into 16 categories. It's name is from the acronym of Medical Subject Headings. http://www.nlm.nih.gov/mesh/

messenger RNA

See "mRNA".

Metazoa

methanogen

methionine

One of the twenty amino acids composing proteins. It is a hydrophobic and sulfur containing amino acid. It is the essential amino acid for human as being unable to synthesize by itself. The abbreviates are Met or M.

MHC

See "major histocompatibility complex".

microsporidia

microtuble

mineral corticoid

See "mineralocorticoid".

mineralocorticoid

A adrenal cortex hormone which secreted from the adrenal cortex. It is involved in the regulation of water and mineral metabolism. It acts on the distal convoluted tubule (DCT) of kidney nephron to facilitate the reabsorption of sodium ion and water and the excretion of potassium ion.

mitochondria

Membrane-enclosed organelle found in most eukaryotic cells. It carries out oxidative phosphorylation, produces ATP, and supply energy to cells. It is the plural form, and the singular form is "mitochondrion".

mitosis

molting hormone

See "ecdysone".

monoclonal antibody

mouse

A general term of small mouse belonging in Muridae family, and Mus genus. Usually the mouse means the house mouse (scientific name is Mus musculus) which often used as the model organism.

MRI

See "magnetic resonance imaging".

mRNA

RNA molecule that specifies the amino acid sequence of a protein. In eukaryotes, a RNA precursor (pre-mRNA) made as a complementary copy of DNA undergoes RNA splicing and becomes mRNA.

muscle tissue

mutase

A kind of isomerase which catalyzes the transferring reaction of a functional group from one position to another within the same molecule. It is classified into the EC number 5.4.

Mycobacterium leprae

Mycobacterium tuberculosis

myelin sheath

myosin

N

N terminal

See "amino terminal".

N terminus

See "N terminal".

NAD

See "nicotineamide adeninedinucleotide".

NADP

See "nicotineamide adeninedinucleotide phosphate".

National Center for Biotechnology Information

http://www.ncbi.nlm.nih.gov/

National Institutes of Health

The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the primary Federal agency for conducting and supporting medical research. It founded in 1887. The head office is at Bethesda, Maryland. It is composed of 27 institutes and centers. The URL is http://www.nih.gov/ .

natural immunity

See "innate immunity".

natural killer cell

NCBI

See "National Center for Biotechnology Information".

nematode

See "Caenorhabditis elegans".

neoplasm

See "tumor".

nephron

nerve cell

See "neuron".

nerve tissue

neuron

A cell composed the nervous system. It consists of a cell body and protrusions from it. There are two type of protrusions, the short is dendrite and the long is axon. The latter composes the nerve fiber. The direction of neurotransmission is from the dendrite, through the cell body, and to the axon. Then transmits to the adjacent neuron via synapse.

nicotine

nicotineamide

nicotineamide adeninedinucleotide

nicotineamide adeninedinucleotide phosphate

NIH

See "National Institutes of Health".

NK cell

See "natural killer cell".

NMR

A acronym of Nuclear Magnetic Resonance.

noradrenaline

"Material which is secreted from the adrenal medulla and the end of sympathetic nerve. The chemical component is same as the adrenaline without a methyl group. It acts as neurotransmitter, and induces the contraction of peripheral artery and rising of blood pressure. It also arises the fighting or avoidance behavior. The IUPAC name is the 4-(2-Amino-1-hydroxyethyl) benzene-1,2-diol."

norepinephrine

See "noradrenaline".

nuclear phase

nucleobase

A component of nucleic acid such as DNA and RNA. It is classified into the purine base and pyrimidine base according to its structure. The former includes adenine (A) and guanine (G), the latter includes cytosine (C), thymine (T), and uracil (U). The bases of A, T, G, and C are utilized in DNA, whereas A, U, G, C are utilized in RNA. A and T join to make base pair by hydrogen bond. G and C join as same.

nucleocapsid

The Structure of viruses, which consists of genomic material and covering capsule called capsid. In case of viruses without outer capsule called envelop, it is equal to the virion which is the functional unit of viruses.

nucleoside

nucleosome

A globular structure found in chromatin of eukaryotic cells. It is composed of a short length of DNA wrapped around a core of histone proteins, and is the basic structural unit of chromatin.

nucleotide

Chemical compound that consists of a base, a sugar, and one or more phosphates. It is the structural units of nucleic acid, such as DNA and RNA, the component of coenzyme, and so on.

O

O antigen

Okazaki fragment

Short lengths of DNA strand produced near by the replication point. As the direction of nucleotide polymerization is only from 5' end to 3' end, at the replication of lagging strand, which is need to replicate to reverse direction, it is produced at first, and then joined by DNA ligase to form a continuous DNA strand.

oligodendrocyte

omega loop

oocyst

oocyte

Female gametocyte. It produced one ovum and three polar bodies.

oogonium

Female gametogonium. It is divided into oocytes by mitosis. Derived from oogonium by mitosis.

open reading frame

Opisthokonta

opportunistic infection

opsin

order

A hierarchy of biological taxonomy. It is the upper layer of family and the lower layer of class.

ORF

See "open reading frame".

Oryctolagus cuniculus

See "European rabbit".

osteoporosis

ovum

Female gamete.

oxydoreductase

A general term of enzymes which catalyze the reaction to transfer electrons from one molecule to another. It is classified into the EC 1 group.

P

p53 tumor suppressor

palmitic acid

papain

papilloma

parallel beta sheet

Parkinson's disease

pathogen

Organism which invades a host organism, disrupts its homeostasis, causes disease to it.

PCT

See "proximal convoluted tubule".

PDB

See "Protein Data Bank".

penicillin

penicillinase

See "lactamase".

penicillin-binding protein

PEP

See "phosphoenolpyruvate".

pepsin

peptideglycan

periplasm

pertussis

A infectious disease caused by the Bordetella pertussis. The symptom of it is the characteristic convulsive cough seizure. In Japan, it is assigned as the fifth group infectious disease in the enforcement regulation of Law Concerning the Prevention of Infections and Medical Care for Patients with Infections, and vaccinated together with diphtheria and tetanus.

PGI

pharyngoconjunctival fever

phenylalanine

One of the twenty amino acids composing proteins. It is classified into the neutral hydrophobic sidechain amino acid, and one of the human essential amino acid. The abbreviates are Phe and F.

phosphaatase

phosphoenolpyruvate

phosphofructokinase

phosphoglucose isomerase

phosphoglycerate kinase

phosphoglycerate mutase

phospholipid

A lipid molecule bound to phosphate which found in various organisms. It is one of the important component of biological membranes and is involved in their various functions.

phosphotransferase

See "kinase".

photosynthesis

phylum

A hierarchy of biological taxonomy. It is the upper layer of class and the lower layer of kingdom. It is called "phylum" (the plural form is "phyla") in animals, while is called "division" in plants.

Physeter macrocephalus

See "sperm whale".

pie helix

piked dogfish

See "spiny dogfish".

PIR

See "Protein Information Resource".

Pisum sativum

See "garden pea".

pituitary gland

placebo

plasmid

plasmodia

See "plasmodium".

plasmodium

platelet

A kind of blood cell which is derived from the megakaryocyte in bone marrow by torn off its cytoplasm. It is involved in blood coagulation.

poliomyelitis

poliovirus

A virus species which belongs to the IVth group (positive single strand RNA, +ss RNA), Picornaviridae family, Enterovirus genus. It causes poliomyelitis.

polypeptide

A kind of linear polymer which is joined amino acids by peptide bonds.

prion

progesterone

prokaryote

proline

One of the twenty amino acids composing proteins. It is classified into the neutral hydrophobic sidechain amino acid. It is the only imino acid in the protein composing amino acid, which has a covalent bond between sidechain and amino group of main chain. The abbreviates are Pro and P.

prostaglandin

prostate gland

Protein Data Bank

protein family

See "family (protein)".

Protein Globe

Protein Information Resource

http://pir.georgetown.edu/

protein isoform

A variation of a protein with the same function and with small difference of amino acid sequence.

protein kinase

See "protein phosphorylation enzyme".

protein phosphorylation enzyme

proximal convoluted tubule

Pseudomonas aeruginosa

pseudouridine

purine

purine body

PyMOL

An open source software visualizing molecular structures. It is available on various platforms such as Windows, MacOS, and Linux etc. The URL is http://pymol.sourceforge.net/

pyranose

pyrimidine

pyruvate dehydrogenase

A enzyme which catalyzes the reaction from a pyruvic acid to an acetyl CoA, the last step of glycolysis. In acting, it forms a complex with other enzymes. The EC number is 1.2.4.1。

pyruvate kinase

In glycolysis, it catalyzes the reaction to transfer a phosphate group from a phosphoenolpyruvate to an ADP, and then produce a pyruvic acid and an ATP. The EC number is 2.7.1.40。

pyruvic acid

A kind of alpha-keto acid which is metabolic intermediate products found in various organisms. The final product of glycolysis.

Q

quinone

R

RA

See "rheumatoid arthritis".

Ramachandran diagram

See "Ramachandran plot".

Ramachandran map

See "Ramachandran plot".

Ramachandran plot

A diagram indicating allowed torsion angles of bonds between residues of linear macromolecules such as polypeptides or polysaccharides. It is calculated from van der Waals radii of each atom. It suggests the available structures of polypeptide chains or polysaccharides.

Rasmol

A software which visualizes molecule structures. The URL is http://www.rasmol.org/

RCSB

See "Research Collaboratory for Structural Bioinformatics".

recombination

Process in which DNA molecules broken and then rejoined in new combination. Can occur during meiosis as chromosomal crossover.

red blood cell

See "erythrocyte".

redback spider

redback widow spider

See "redback spider".

repair

replication

repressor element 1 silencing transcription factor

See "REST".

Research Collaboratory for Structural Bioinformatics

A member of worldwide Protein Data Bank (wwPDB) which is the depository of information about the three-dimensional structures of large biological molecules. The URL is http://www.pdb.org/pdb/home/home.do

REST

A transcription factor which is specifically found in neuron.

restriction enzyme

retinal

A compound derived from retinol (vitamin A1) replaced the terminal alcohol group to the aldehyde. It consists of two parts, the ring part (trimethyl cyclohexene ring) and the sidechain. There are 16 types of isomers by the difference of sidechain type, the double bond, trans, or cis. The 11-cis type acts as the chromophore of visual pigment.

retinol

See "vitamin A".

retrovirus

A family of viruses of which genome is made from single strand RNA and is transcribed to the DNA before growth and gene expression. It is a part of the sixth group (ssRNA-RT) of Baltimore classification. It includes human immunodeficiency virus (HIV) etc. This word is sometimes used as the meaning all of the ssRNA-RT viruses.

reverse transcriptase

A enzyme which catalyzes the DNA producing reaction from RNA. It is used by virus which has its genome as RNA. The EC number is 2.7.7.49.

rheumatoid arthritis

rhinovirus

rhizobia

rhodopsin

A visual pigment contained in photoreceptor cells which distinguishes between light and dark. It consists of opsin protein bound to chromophore 11-cis-retinal. It is a typical G-protein coupled receptor protein, which has seven alpha helices.

ribonuclease

ribonucleic acid

See "RNA".

ribose

ribosome

ribosome RNA

See "rRNA".

ribulose 1,5-bisphosphate carboxylase/oxygenase

See "RubisCO".

ringworm

See "tinea".

RISC

See "RNA-induced silencing complex".

RMSD

A indication value of the protein structural similarity. When comparing structures of two protein molecules, it is defined to be the square-root of average of the square of the distance between each corresponding alpha carbon atom.

RNA

Abbreviation of RiboNucleic Acid. Consists of a kind of sugar ribose bound to a phosphate at 3' position and a base at 1' position. Utilizes in gene expression process and so on. See also nucleobase, mRNA, tRNA, and rRNA.

RNA interference

Selective intracellular degradation of RNA to remove foreign RNAs, such as those of viruses. Utilized to the technique of silencing the expression of selected genes.

RNA splicing

A reaction series which removes the gene non-coding region (intron) from a precursor mRNA (pre-mRNA) and then links the gene coding region (exon).

RNAi

See "RNA interference".

RNA-induced silencing complex

rod-shaped bacteria

A kind of bacteria with rod-shape. The plural form is "bacilli".

root nodule bacteria

See "rhizobia".

rRNA

rubeola

See "measles".

RubisCO

A enzyme in the Calvin cycle which catalyzes the reaction from a ribulose 1,5-bisphosphate and a carbon dioxide to two 3-phosphoglycerate.

S

Salmonella typhi

sarcoma

sarcoplasmic reticulum

satellite

Sav1866

SCA

See "sickle cell anemia".

scanning electron microscope

SCD

See "sickle cell disease".

SCN

See "suprachiasmic (suprachiasmatic) nucleus".

SCOP

A database which classified proteins based on their structural feature. It's name is the acronym of "Structural Classification Of Protein". It is managed by Centre for Protein Engineering (CPE) at Cambridge University in UK. http://scop.mrc-lmb.cam.ac.uk/scop/

scrapie

sea hare

sea slug

second category infectious disease

selectase

self-splicing

SEM

See "scanning electron microscope".

sepsis

sequence alignment

serine

One of the twenty amino acids composing proteins. It is classified into the neutral polar amino acid. The abbreviates are Ser and S.

serine protease

serotonin

Monoamine neurotransmitter synthesized from the triptophan. 5-hydroxytryptamine. It often found in the enterochromaffin cell (EC cell) in the mucosa of small intestine, and also found in hypothalamus and platelet etc. It stimulate the peristaltic movement of small intestine and capillary vessel contraction. It is also included in the synaptic vesicle and acts as neurotransmitter.

serum

serum albumin

sex chromosome

Chromosomes involving in decision of sex. Other chromosomes are called autosomes.

sex determining ｒegion Y gene

See "SRY gene".

sheet

Shiga-like toxin

See "verotoxin".

shpingoglycolipid

A general term of glycolipid which is a ceramide bound to sugar compounds at 1' position hydroxyl group. A kind of sphingolipid.

SIB

See "Swiss Institute of Bioinformatics".

sickle cell anemia

See "sickle cell disease".

sickle cell disease

sidechain

simian virus

siRNA

See "small interfering RNA".

small interfering RNA

In the RNA interference (RNAi), it is a small RNA strand which is consist of about 21 base pair, and is produced from foreign double strand RNA such as viruses cleaved by the dicer protein. Then the argonaute protein takes in it to utilize the template for detection of the same kind of foreign RNA strand. This molecule is introduced in the 98th article of Molecule of the Month.

smallpox

An infectious disease which caused by the smallpox virus. The symptoms of this disease are high fever, eczema, and respiratory distress. The smallpox vaccine eliminates it and WHO decelerates the extermination in 1980.

SOD

See "superoxide Dismutase".

somatic cell

A cell in organisms which is not involved in reproduction. It includes all the cells except for germline cells. Genetic mutations in these cells will not be passed to next generations.

sperm

See "spermatozoon".

sperm whale

A species of toothed whales belonging to the Cetartiodactyla order, Cetacea order (suborder), and Physeteridae family. The first protein of which structure was determined by the X-ray crystallographic analysis is a myoglobin from this species.

spermatocyte

Male gametocyte. It produced four spermatids. Derived from spermatogonium by mitosis.

spermatogonium

Male gametogonium. It is divided into spermatocytes by mitosis.

spermatozoon

Male gamete. Produced from spermatid by spermiogenesis.

sphingolipid

A kind of complex lipid including ceramides and their derivatives bound to sugar or phosphocholine at the 1' position hydroxyl group. The sugar bound one is called sphingoglycolipid and the phosphoric compound bound one is called sphingophospholipid. It is abundantly found in cell membranes, and is thought to assist functions of membrane proteins,

sphingomyelin

A primary sphingophospholipid. It is often found in brain tissue, nerve tissue, red blood cells (erythrocytes), and so on of the higher animals.

sphingophospholipid

A general term of phospholipid which is a ceramide bound to phosphoric compounds at 1' position hydroxyl group. A kind of sphingolipid.

sphingosine

A long chain 18-carbon amino alcohol with one unsaturated bond. A kind of sphingoid which is a component of sphingolipid. 2-amino-4-octadecene-1,3-diol.

spiny dogfish

A kind of elasmobranch belonging to the Squalidae family. It is used for foods. The scientific name is the Squalus acanthias.

spirillum

A helix-shape bacteria. The plural form is "spirilla". The many spiral one is called spirochete.

spleen

An organ involved in the blood storage and degradation, hematopoiesis (blood forming), and immunity.

squalene

SRY gene

starch

Polysaccharide which is utilized to energy store in plants.

stem cell

structural domain (protein)

In tertiary structure (conformation) of protein molecule, conformational group region. Large protein molecules often consist of several domains. Each domain is linked with flexible polypeptide chains.

structural motif

In the protein structure, it means the partial structure unit composed of secondary structures. It is also called super secondary structure.

sucrose

sulfonylurea

summer type hypersensitivity pneumonitis

A kind of pneumonia caused by a kind of fungus Trichosporon cutaneum. Inhaling the spores of it causes allergic reaction and cough. It onsets mainly in summer.

superfamily

1) A classification layer of SCOP, protein structural classification. 2)A taxonomical layer, upper of the family, lower of the order or suborder.

superoxide Dismutase

suprachiasmic (suprachiasmatic) nucleus

Swiss Institute of Bioinformatics

http://www.isb-sib.ch/

Swiss-Prot

See "UniProt".

synapse

The terminal part of the nerve cell closed to the next cell. It secrets neurotransmitter, and deliver signals to the next cell.

synthase

See "lyase".

synthesizing enzyme

A general term of enzymes which catalyze the synthesizing reaction of a chemical compounds. There are two types of enzymes, synthetases which require coupling of a exergonic reaction (EC 6 group), and synthases which are not accompanied by coupling reaction (EC 4 group).

synthetase

See "ligase".

T

T cell

T cell receptor

T lymphocyte

See "T cell".

T4

See "thyroxin".

Takahara's disease

See "acatalasia".

talin

Tardigrade

See "water bear".

TATA box

TBSV

See "Tomato bushy stunt virus".

TCA cycle

See "citric acid cycle".

TCR

See "T cell receptor".

telomerase

Enzyme to extend the telomera, which get shoter by each cell division.

telomere

Structure exists at the end of chromosome of eukaryotic cells. It is composed of specific base sequences and proteins, and protects from unintended DNA repair and degradation. It gradually shorten by cell division. When it is completely lost, the cell division stops. Then it is thought to be involved in the age of cell.

TEM

See "transmission electron microscope".

testosterone

A kind of androgen (mele hormone).

tetanus

tetrodotoxin

Alkaloid with highly toxicity known as fugu toxin. It is thought to be produced by some kind of bacteria, and concentrated to fugu by the process of food chain.

thele cress

An annual plant which belongs to Brassicaceae family. Often use in genetic studies as model organisms. The scientific name is Arabidopsis thaliana. The number of chromosomes (2n) is 10.

thermophile

third category infectious disease

three semicircular canal

Organ exists in the inner ear, controlling the equilibrium.

threonine

One of the twenty amino acids composing proteins. It is classified into the neutral polar sidechain amino acid, and one of the human essential amino acid. The abbreviates are Thr and T.

thrombin

thrombocyte

See "platelet".

thymine dimer

thyroid

thyroid hormone

thyroxin

A kind of the thyroid hormone.

TIM barrel

A basic structural unit (motif) of the protein, which is also called (beta/alpha) 8 barrel. It is found in many kinds of proteins, and most of them has catalytic activity. The name of TIM is the acronym of triose phosphate isomerase.

tinea

TMV

See "tobacco mosaic virus".

tobacco mosaic virus

TolC

Toll-like receptor

Tomato bushy stunt virus

toxoplasma

Protozoan belonging in the Apicomplexa phylum, Coccidiasina subclass, Sarcocystidae family, and Toxoplasma genus. It causes the toxoplasmosis.

Toxoplasma gondii

See "toxoplasma".

toxoplasmosis

An infectious disease which caused by the toxoplasma protozoan. Usually, no symptom will be onset, except for fetuses, infants, and immunocompromised persons. Though it lays its oocysts (eggs) only to the Felidae animals, it may infect from soil or other animals since the oocysts are released via excreted fecalith.

transcription

Replication of one strand of DNA into a complementary sequenced RNA by the enzyme RNA polymerase.

transfer RNA

See "tRNA".

transfer RNA

See "tRNA".

transferase

A general term of enzymes which catalyze the reaction to transfer a functional group from one molecule to another. It is classified into the EC 2 group.

transferrin

translation

The synthetic reaction from the messenger RNA which includes gene information to the peptide chain.

transmissible sponge-form encephalopathy

transmission electron microscope

transposon

Base sequences which can move between inside of cell genome. In narrow sense, they only mean DNA sequences which directory move their position, whereas in wide sense, they include retro transposons which are translated to RNA and then reverse translated to another position of genome. They are thought to stimulate the genome change and to be involved in biological evolution.

trehalose

TrEMBL

See "UniProt".

tricarboxylic acid cycle

See "citric acid cycle".

Trichophyton

The general term of fungi which cause tinea (epidermophytosis).

trichophytosis

See "tinea".

Trichosporon cutaneum

A kind of fungi which causes the summer type hypersensitivity pneumonitis. It breeds in the damp place, such as bathroom, kitchen, and inside of air conditioner.

Trimeresurus flavoviridis

See "habu snake".

triose phosphate isomerase

tRNA

It is also called "transfer RNA".

tropomyosin

troponin

trypanosome

A protozoan which parasitizes human, horse etc to cause the African sleeping disease. It is a kind of protozoa with flagella and infects by mediation of tsetse fly.

trypsin

A kind of protease which degrades proteins. It is a type of the endopeptidase cleaving the middle of polypeptide chains at the carboxyl side of lysine and arginine residues. It acts as activating the other enzyme precursor as well as the digestive enzyme. The EC number is 3.4.21.4。

tryptophan

One of the twenty amino acids composing proteins. It is classified into the neutral hydrophobic sidechain amino acid and the aromatic amino acid as it has indole ring in its sidechain. It is one of the human essential amino acid. The abbreviates are Trp and W.

TSE

See "transmissible sponge-form encephalopathy".

tsetse fly

A hematophagous fly mediating trypanosomes which cause the African sleeping disease. It is a general term of insects included in Diptera order, Glossinidae family.

TTX

See "tetrodotoxin".

tumor

Cell population which is derived from own cell of the organism, and grows autonomously. It can be classified into the benign tumor, which is well differentiated and grows slowly, and malignant tumor, which is less differentiated and grows fast. And more, the latter can be classified into epithelial carcinomas and non-epithelial sarcomas etc.

typhlitis

See "appendicitis".

typhtoid fever

An infectious disease which caused by the Salmonella typhi. In Japan, it is designated as the category II infectious disease by the law.

tyrosine

One of the twenty amino acids composing proteins. It is classified into the neutral hydrophobic sidechain amino acid and the aromatic amino acid as it has a phenol group in its sidechain. The abbreviates are Tyr and Y.

U

ubiqutin

A small highly conserved protein which is ubiquitous in eukaryotic cells. It binds to lysines of other proteins and mark them as the target to degradation. The ubiqutin bound protein is degraded by the proteasome.

ultraviolet light

A kind of electromagnetic ray. The wavelength is shorter than optical light, and is longer then X-ray. The range of wavelength is about between 380nm and 10nm. It has strongly act on chemical reaction. The good examples are sterilizing, vitamin D synthesis, and metabolism facilitation, whereas it may harmful to skin, eye, and immunity.

UniProt

A integrated database of protein primary structure (amino acid sequence) and its related information. It consists of two kinds of data, TrEMBL whose data is automatically generated, and Swiss-Prot whose data is manually annotated. It is managed by EBI, SIB, and PIR. Its URL is http://www.uniprot.org/

urinary bladder

A extensible hollow organ of urinary system, which temporarily stores urine transported from the kidney via ureter.

urticaria

A kind of acute dermatitis.

V

vaccine

A general term of antigen used for prevention and treatment of infectious disease. It is made from attenuated pathogen (live vaccine), inactivated pathogen, metabolite from pathogen, and so on. The name is derived from smallpox vaccine.

valine

One of the twenty amino acids composing proteins. It is hydrophobic and the essential amino acid for human as being unable to synthesize by itself. The abbreviates are Val or V.

varicella

A infectious disease caused by varicella zoster virus. The major symptom is blister. In Japan, this disease is assigned to the fifth category infectious disease in Enforcement Regulation of Law of Infectious disease prevention.

varicella zoster virus

A virus species which belongs to the Ist group (double strand DNA, dsDNA), Herpesviridae family, Alphaherpesvirinae subfamily, Varicellovirus genus. It causes varicella.

verotoxin

A toxin which is similar to the shiga toxin produced by dysentery bacillus. It is a exotoxin protein which produced by the O157:H7, one of the enterohemorrhagic Escherichia coli (EHEC), and others, and causes the hemorrhagic diarrhea etc.

virion

A basic unit of viruses with particulate structure and infectivity. Viruses exist in this form at the outside of the host cell.

viroid

A kind of viruses. Its RNA genome is bare, without the capsule (capsid). The gene does not encodes proteins, depends on its host.

virus

A submicroscopic structure which has no cellular structure and energy production system. It can propagate only in infection host cell. It has its genome either DNA or RNA and is classified into seven groups according to the types of genome, called Baltimore classification.

vitamin A

A kind of lipid soluble vitamin. The deficiency of it causes the nyctalophia, skin disorder, growth inhibition etc. On the contrary, the excess causes organ disorder and abnormality etc, they are called hypervitaminosis A.

W

water bear

Organism belonging to the Tardigrade phylum. It has high ability to tolerate severe circumstances such as dry, hot, cold, high pressure, and radiation by entering into a quiescent state (also called cryptobiosis) with no metabolism.

water channel

See "aquaporin".

West Nile fever

Infectious disease caused by the West Nile virus. About only 20 percent of infected patients affect. The symptom of it is similar to that of influenza, such as fever, headache, and myalgia. Typically, it is not so serious, but as virus infects the brain, it may cause fatal encephalopathy. As there is no vaccine for human now, the cure is limited for symptomatic treatment. It typically recover for between a few day and a week. The epidemic area is Africa, West Asia, Middle East, Europe, and North America. In Japan, it is assigned as the group 4 infectious disease.

West Nile virus

Virus belonging in the group IV (positive single strand RNA, +ssRNA), Flaviviridae family, and Flavivirus genus. It causes the West Nile fever. It growth in the birds, and infects other animals by mediation of mosquitoes.

white blood cell

See "leukocyte".

whooping cough

See "pertussis".

Worldwide Protein Data Bank

A organization to maintain the Protein Data Bank (PDB), a single worldwide resource of macromolecular structural data. It consists of four member of groups, the Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular Structure Database (MSD) group at the European Bioinformatics Institute (EBI), the Protein Data Bank Japan (PDBj) group at the Institute for Protein Research in Osaka University, and Biological Magnetic Resonance data Bank (BMRB) group at the University of Wisconsin-Madison. The URL is http://www.wwpdb.org/ .

wwPDB

See "Worldwide Protein Data Bank".

X

X ray

Electromagnetic ray whose wavelength is about between 10nm and 1pm. It is generated by the transient of electron orbit of atom. It is discovered by Roentgen, German physical scientist. It is utilized for various purpose such as medical diagnosis (roentgen and CT examination etc.), material examination (non-destructive inspection), and crystal structural analysis.

Xenopus laevis

See "African clawed frog".

X-ray crystal structural analysis

Method to decide the atom arrangement in the crystal lattice by utilizing X-ray diffraction phenomenon.

Y

yeast

Originally, it is used as the general term of unicellular fungi. But it often means only the baker's yeast Saccharomyces cerevisiae utilized for bread production.

yellow fever

Infectious disease caused by the yellow fever virus. It mainly prevails in the tropical area of Latin America and Africa. It mediated by mosquitoes such as Stegomyia (Aedes) aegypti. As infected, the liver was affected to develop jaundice.

yellow fever virus

Virus belonging in the group IV (positive single strand RNA, +ssRNA), Flaviviridae family, and Flavivirus genus. It causes the yellow fever.

yellow fruit fly

See "Drosophila melanogaster".

Z

zebra fish

A species of fish which belongs to Cyprinidae family. It's about 3.2cm long, and often used as model organisms. The scientific name is Zebra danio. The number of chromosomes (2n) is 50.

zinc finger

A kind of partial structure (motif) which is found in the nucleotide binding proteins. It includes zinc atom to coordinate four cysteine or two cysteine and two histidine, and has a finger like region between the second cysteine and third cysteine/histidine.

zygote

A cell derived from fusion of two gametes.