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Compiled by Amit Yadav.
amityadav8@gmail.com
 Last Updated on 30
th
July 2008
.
THE GLOSSARY OFGEETICS, CELL & MOLECULAR BIOLOGY
 
3' end/5' end:
A nucleic acid strand is inherently directional,and the "5 prime end" has a free hydroxyl (or phosphate) on a5' carbon and the "3 prime end" has a free hydroxyl (or  phosphate) on a 3' carbon (carbon atoms in the sugar ring arenumbered from 1' to 5'. That's simple enough for an RNAstrand or for single-stranded (ss) DNA. However, for double-stranded (ds) DNA it's not so obvious - each strand has a 5'end and a 3' end, and the 5' end of one strand is paired with the3' end of the other strand (it is "antiparallel". One would talk about the 5' end of ds DNA only if there was some reason toemphasize one strand over the other - for example if onestrand is the sense strand of a gene. In that case, theorientation of the sense strand establishes the direction.
3' flanking region:
A region of DNA which is NOT copiedinto the mature mRNA, but which is present adjacent to 3' endof the gene. It was originally thought that the 3' flanking DNAwas not transcribed at all, but it was discovered to betranscribed into RNA, but quickly removed during processingof the primary transcript to form the mature mRNA. The 3'flanking region often contains sequences that affect theformation of the 3' end of the message. It may also containenhancers or other sites to which proteins may bind.
3' untranslated region:
A region of the DNA which IStranscribed into mRNA and becomes the 3' end or themessage, but which does not contain protein coding sequence.Everything between the stop codon and the polyA tail isconsidered to be 3' untranslated. The 3' untranslated regionmay affect the translation efficiency of the mRNA or thestability of the mRNA. It also has sequences which arerequired for the addition of the poly (A) tail to the message(including one known as the "hexanucleotide", AAUAAA).
3’ end:
The end of a DNA or RNA strand with a free 3’hydroxyl group corresponding to the end of transcription (seealso five-prime end).
5' flanking region:
A region of DNA which is NOTtranscribed into RNA, but rather is adjacent to 5' end of thegene. The 5'-flanking region contains the promoter, and mayalso contain enhancers or other protein binding sites.
5' or 3' end
The nucleoside residues which form nucleic acidsare joined by phosphodiester linkages between the 3' C atomof one ribose moiety and the 5' C atom of the next. Thereforeeach strand of DNA or RNA has a free 3' C at one end and afree 5' C at the other. The free 3' C normally carries a - OHgroup and the 5' C a phosphate group.
 5' untranslated region:
A region of a gene which IStranscribed into mRNA, becoming the 5' end of the message, butwhich does not contain protein coding sequence. The 5'-untranslated region is the portion of the DNA starting from thecap site and extending to the base just before the ATGtranslation initiation codon. While not itself translated, thisregion may have sequences which alter the translation efficiencyof the mRNA, or which affect the stability of the mRNA. # Theshort sequence between the transcription initiation site and thestart of translation that is retained in mRNA but not translated. Itcontains the ribosomal binding site (leader sequence) and signalsequence.
5’ end:
The end of a DNA or RNA strand with a free 5’ phosphate group corresponding to the transcription initiation(see also three-prime end).
A
 A form
. A duplex DNA structure with right-handed twisting inwhich the planes of the base pairs are tilted about 70° withrespect tothe helix axis.
A site:
holds the incoming tRNA molecule charged with thenext amino acid; the tRNA are held so that the anticodons form base pairs with adjacent complementary codons of the mRNAmoving through the ribosome.
Abdomen
-- region of the body furthest from the mouth. Ininsects, the third body region behind the head and thorax.
Abiotic stress.
Outside (nonliving) factors which can causeharmful effects to plants, such as soil conditions, drought, andextreme temperatures.
Ablation experiment:
An experiment designed to produce ananimal deficient in one or a few cell types, in order to study celllineage or cell function. The idea is to make a transgenic mousewith a toxin gene (often diphtheria toxin) under control of aspecialized promoter which activates only in the target cell type.When embryo development progresses to the point where itstarts to form the target tissue, the toxin gene is activated, andthat specific tissue dies. Other tissues are unaffected.
Absorption
- the taking in of water and dissolved minerals andnutrients across cell membranes. Contrast with
ingestion
.
Abyssal plain
-- the ocean floor offshore from the continentalmargin, usually very flat with a slight slope.
Abzyme.
See Catalytic antibody.
Acentric fragment:
a portion of a chromatid or chromosomethat lacks a centromere.
Acetal
. The product formed by the successive condensation of two alcohols with a single aldehyde. It contains two ether-linkedoxygen attached to a central carbon atom.
Acetyl-CoA
. Acetyl-coenzyme A, a high-energy ester of aceticacid that is important both in the tricarboxylic acid cycle and infatty acid biosynthesis.
 
 
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Acrocentric chromosome
: A chromosome with itscentromere towards one end. Human chromosomes13,14,15,21,22 are Acrocentric.
Acrylamide gels:
A polymer gel used for electrophoresis of DNA or protein to measure their sizes (in daltons for proteins,or in base pairs for DNA). See "Gel Electrophoresis".Acrylamide gels are especially useful for high-resolutionseparations of DNA in the range of tens to hundreds of nucleotides in length.
Actin
. A protein found in combination with myosin in muscleand also found as filaments constituting an important part of the cytoskeleton in many eukaryotic cells.
Actinomycin D pulse experiments
The application of actinomycin D to actively metabolizing cells results in thecessation of new RNA transcription. Consequently, serialdeterminations of specific RNA levels will allow one tocalculate the mRNA half-life. Should this vary betweencontrol and stimulated conditions, evidence is garnered that agene of interest is regulated at the level of mRNA stability.
Actinomycin D
. An antibiotic that binds to DNA and inhibitsRNA chain elongation.
Activated complex
. The highest free energy state of acomplex in going from reactants to products.
Active site
. The region of an enzyme molecule that containsthe substrate binding site and the catalytic site for convertingthe substrate(s) into product(s).
Active transport
. The energy-dependent transport of asubstance across a membrane.
Adaptation
change in a organism resulting from naturalselection; a structure which is the result of such selection. #Adjustment to environmental demands through the long-term process of natural selection acting on genotypes.
Adaptive immunity
: A collective term for the long-lastingand specific response of lymphocytes to antigens. Requires theMHC, T-cell receptors (TCR) and immunoglobulins (Ig) aswell as enzymes with a recombinase activity (for therearrangements at TCR and Ig gene loci). Present in allvertebrates except jawless fish (see innate immunity).
Adaptive radiation
. The evolution of new species or subspecies to fill unoccupied ecological niches.
Additive and non-additive components
: In studies of heredity, the portions of the genetic component that are passedand not passed to offspring, respectively.
Additive genetic variance:
genetic variance atributed to theaverage effects of substituting one allele for another at a ivenlocus, or at the multiple loci governing a polygenic trait.
Adenine
. A purine base found in DNA or RNA.
Adenosine Triphosphate ATP:
Adenosine 5'- (tetrahydrogentriphosphate). An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition toits crucial roles in metabolism adenosine triphosphate is aneurotransmitter. [MeSH] # The nucleotide formed by addinga pyrophosphate group to the 5'-OH group of adenosine.
Adenosine
. A purine nucleoside found in DNA, RNA, andmany cofactors.
Adenylate cyclase
. The enzyme that catalyzes the formationof cyclic 3',5' adenosine monophosphate (cAMP) from ATP.
Adipocyte
. A specialized cell that functions as a storage depotfor lipid.
Adult
- the mature stage of an organism, usually recognized by the organism's attaining the ability to reproduce.
Advanced (synonym: derived; opposite: primitive):
In phylogenic studies, an organism or character further removedfrom an evolutionary divergence than a more primitive one.
Aerobe
. A microorganism that grows in the presence of oxygen. See Anaerobe.
Aerobic
-- aerobic organisms require oxygen for their life processes.
Affinity Chromatography
This separation method depends onusing any molecule that can preferentially bind to a protein of interest. Typical methodologies include using lectins (such aswheat germ or concanavalin A) to bind glycoproteins or usingcovalently coupled monoclonal antibodies to bind specific protein ligands.
#
A column chromatographic technique thatemploys attached functional groups that have a specific affinityfor sites on particular proteins.
Agarose Gel Electrophoresis
- A method for separating nucleicacids (DNA or RNA) within a gel made of agarose in a suitable buffer under the influence of an electrical field. Suitable for separation of large fragments of nucleic acid, separation is based primarily upon the size of the nucleic acid. # A matrixcomposed of a highly purified form of agar that is used toseparate larger DNA and RNA molecules ranging 20,000nucleotides. (See Electrophoresis.)
Agarose gels:
A polysaccharide gel used to measure the size of nucleic acids (in bases or base pairs). See "Gel Electrophoresis".This is the gel of choice for DNA or RNA in the range of thousands of bases in length, or even up to 1 megabase if youare using pulsed field gel electrophoresis.
Agnatha (means jawless):
The Class Agnatha represents themost primitive ‘jawless’ vertebrates. MHC genes have beencloned from all vertebrate classes except Agnatha.
 Agrobacterium tumefaciens
: A soil bacterium that causes acancer-like plant disease (crown gall) in dicotyledenous plants(all agricultural crops except cereals). It contains the Ti plasmid.The tumor induction ability of the bacterium spreads toneighboring cells via the plasmid.
a-helix:
Common secondary structure of proteins in which thelinear sequence of amino acids is folded into a spiral that isstabilized by hydrogen bonds between the carboxyl oxygen of each peptide bond.
Alcohol
. A molecule with a hydroxyl group attached to a carbonatom.
Aldehyde
. A molecule containing a doubly bonded oxygen anda hydrogen attached to the same carbon atom.
Algae
: A heterogeneous group of aquatic, unicellular, colonialor multicellular, eukaryotic and photosynthetic organisms. They belong to the Kingdom Protista and include the multicellular red(rhodophyte), green and brown (kelp) algae. They are not plants but all land plants evolved from the green algae (see alsoChromista).
Alginate
-- component of the cell walls of many rhodophytesand kelps. Alginates have an affinity for water, and so help toslow dessication when the algae are exposed to the air; they arecommercially important in the production of paper, toothpaste, beer, and frozen foods.
Alkaline
-- term pertaining to a highly basic, as opposed toacidic, subtance. For example, hydroxide or carbonate of sodium or potassium.
Allee effect
: The benefit individuals gain from the presence of conspecifics. Link to a brief explanation of Allee effect.
Allele
- One of two or more alternative forms of a gene that mayoccupy the same locus on a particular chromosome #Alternate
 
 
33
 
forms of a gene or DNA sequence, which occur on either of two homologous chromosomes in a diploid organism. (SeeDNA polymorphism.) # A known variation (version) of a particular gene. Formerly called allelomorph. # One of a seriesof possible alternative forms of a given gene, differing inDNA sequence and affecting the functioning of a single product (RNA or protein
Allele frequencies (or gene frequencies)
- the proportions of different alleles present at a particular locus in a population of organisms. # The percentage of all alleles at a given locus in a population gene pool represented by a particular allele.
Allele-specific hybridization
If the nucleotide basis for aspecific genetic abnormality is known, oligonucleotidesspecific for wild type and for mutant sequence can bedesigned and used to probe Southern blots of an individual’sgenomic DNA. The pattern of hybridization thus givesspecific information regarding which alleles are present. In a polymorphic disease such as thalassemia (in whichmultiple mutations can give rise to the same disease phenotype), multiple probes might be required to detect all possible causes. In addition, new mutations causing the samedisease would be missed. However, should a specific probe prove useful for one population group or be positive in onefamily member, that probe becomes very useful for theindividual under study.
Allele-specific PCR 
By using generic PCR primers flankingthe immunoglobulin or T cell receptor genes, the preciserearranged gene characteristic of a B or T cell neoplasm can be amplified and sequenced. Once so obtained, new PCR  primers can then be designed that are unique to the patient’stumor. Such allele-specific PCR can then be used to detect blood cell contamination by tumor and to detect minimalresidual disease following therapy.
Allelic
 
exclusion
: Expression of only one of the twohomologous alleles at a locus in the case of heterozygosity.This usually occurs at loci such as immunoglobulin or T cellreceptor (TCR) genes where a functional rearrangementamong genes takes place. One of the alleles is either non-functionally or incompletely rearranged and not expressed.This way, each T-cell expresses only one set of TCR genes.
Allelopathy
: The influence exerted by a living plant on other  plants nearby or microorganisms through production of achemical.
Allen’s Rule
: Within species of warm-blooded animals (birds+ mammals) those populations living in colder environmentswill tend to have shorter appendages than populations inwarmer areas.
Alliance for Cellular Signaling AfCS:
The overall goal of the Alliance for Cellular Signaling is to understand ascompletely as possible the relationships between sets of inputsand outputs in signaling cells that vary both temporally andspatially. The same goal, stated from a slightly different perspective, is to understand fully how cells interpret signalsin a context-dependent manner. This will involveidentification of all the proteins that comprise the varioussignaling systems, the assessment of time- dependentinformation flow through the systems in both normal and pathological states, and finally the reduction of the mass of detailed data into a set of interacting theoretical models thatdescribe cellular signaling. http://www.afcs.org/
Allochthonous
refers to something formed elswhere than its present location. Antonym of autochthonous.
Allogeneic
: Two genetically dissimilar individuals of the samespecies like any two human beings except monozygotic twins.
Allometry
Equation: Most lines of relative growth conform to y= bxa where y and x are the two variates being compared, b anda are constants. The value of a, the allometric exponent, is 1 onethe growth is isometric; allometry is said to be positive whena>1 and negative when a<1.
Allophenic
: Chimeric, i.e., composed of cells of two differentgenotypes (also called hybrid).
Allopolyploidy:
the combination of genetically distinctchromosome sets that results in a polyploid organism.
Allorecognition
: Recognition by T cells of the MHC moleculeson an allogeneic individual’s antigen-presenting cells whichresults in allograft rejection in vivo and mixed lymphocytereaction (MLR) in vitro.
Allosteric enzyme
. An enzyme whose active site can be altered by the binding of a small molecule at a nonoverlapping site.
Allosteric protein:
a protein that may change its shape as aconsequence of interaction with another molecule.
Allozygosity:
having two homologous genes at one locus thatare of independent origin, as far as can be determined from a pedigree.
Allozymes
- Alternative enzyme forms found in a population,encoded by different alleles at the same locus.
Altered self 
: A term used to describe the MHC moleculeassociated with a peptide rather than in its native form. Thus, anative MHC molecule does not induce an immune reactionexcept when it is presenting a peptide.
Alternation of generations
: An alternation of sexual (haploid)and asexual (diploid) form of generations in a life cycle(example: aphids). The relative dominance of each phase isvariable in each organism (mosses have a dominant haploid phase whereas angiosperms have a dominant diploid phase).Besides aphids, Daphnia (water flea), rotifers, Hydra havealternation of generations in response to environmentalconditions. # Life cycle in which
haploid
and
diploid
 generations alternate with each other.
Alternative mRA splicing.
The inclusion or exclusion of different exons to form different mRNA transcripts. (SeeRNA.)
Alternative splicing
: Formation of diverse mRNAs throughdifferential splicing of the same RNA precursor.
Altruism
: Helping others without direct benefit, and sometimesharm, to oneself.
Ambulacra
-- row of tube feet of an echinoderm.
Amino acid
. unit molecule from which proteins are constructed by polymerization. # Any of 20 basic building blocks of proteinscomposed of a free amino (NH2) end, a free carboxyl (COOH)end, and a side group (R). # The 20 basic building blocks of  proteins, consisting of the basic formula NH2-CHR-COOH,where "R" is the side chain which defines the amino acid:
Amino Terminus
- Refers to the NH2 end of a
 peptide
chain.
Amino-acyl trna synthetase:
an enzyme that activates aminoacids and attaches each activated amino acid to its own speciesof tRNA.
Amp resistance:
See "Antibiotic resistance".
Amphiesma
-- the outer covering of a dinoflagellate, consistingof several membrane layers.
Amphipathic
: A molecule that has both a hydrophobic and ahydrophilic part.
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