C

C-Banding:

It is a technique for generating stained regions around centromeres.

C-Value:

It is the total amont of DNA in a haploid genome.

Calibrator:

A single reference sample used as the basis for relative-fold increase in expression studies (assuming constant reaction efficiency). This calibrator should be included in each assay.

Cap:

All eukaryotes have at the 5' end of their messages a structure called a "cap", consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of the mRNA. It is added post-transcriptionally, and is not encoded in the DNA.

Cap Site:

In eukaryotes, the cap site is the position in the gene at which transcription starts, and really should be called the "transcription initiation site". The first nucleotide is transcribed from this site to start the nascent RNA chain. That nucleotide becomes the 5' end of the chain, and thus the nucleotide to which the cap structure is attached.

Capsid:

It is the external protein coat of a virus particle.

CAT Assay:

An enzyme assay. CAT stands for chloramphenicol acetyl transferase, a bacterial enzyme which inactivates chloramphenicol by acetylating it. CAT assays are often performed to test the function of a promoter. The gene coding for CAT is linked onto a promoter (transcription control region) from another gene, and the construct is "transfected" into cultured cells. The amount of CAT enzyme produced is taken to indicate the transcriptional activity of the promoter (relative to other promoters which must be tested in parallel). It is easier to perform a CAT assay than it is to do a Northern blot, so CAT assays were a common method for testing the effects of sequence changes on promoter function. Largely supplanted by the reporter gene luciferase.

CCAAT Box:

(CAT box, CAAT box, other variants) A sequence found in the 5' flanking region of certain genes which is necessary for efficient expression. A transcription factor (CCAAT-binding protein, CBP) binds to this site.

cDNA Clone:

"complementary DNA"; a piece of DNA copied from an mRNA. The term "clone" indicates that this cDNA has been spliced into a plasmid or other vector in order to propagate it.

Central Dogma:

A phrase that refers to the concept of information flow proceeding only from DNA to RNA to protein.

Centromere:

A specialized constricted region of a chromosome to which spindle fibers attach during cell division at which two sister chromatids are joined, and which attach to the spindle during cell division.

Chaperone Proteins:

A series of proteins present in the endoplasmic reticulum which prevent proteins from folding prematurely and guide the proper folding of secreted proteins through a complex series of binding and release reactions.

Chemical Complexity:

It is the amount of a DNA component measured by chemical assay.

Chromatid:

A single, continuous double stranded DNA molecule with its unique, complete grouping of genetic information, associated proteins, higher-order structures, and centromeric and telomeric regions necessary for separation and maintenance after replication.

Chromatin Immunoprecipitation:

This is a method for isolating and characterizing the specific pieces of DNA out of an entire genome, to which is bound a protein of interest. The protein of interest could for example be a transcription factor, or a specific modified histone, or any other DNA binding protein.

Chromosomes:

A condensed, fibrillar, self- replicating genetic structures of cells containing the cellular DNA that bears in its nucleotide sequence the linear array of genes. In prokaryotes, chromosomal DNA is circular, and the entire genome is carried on one chromosome. Eukaryotic genomes consist of a number of chromosomes whose DNA is associated with different kinds of proteins.

Chromosome Jumping:

A technique whereby one starts with a piece of DNA from one region of a chromosome, and obtains clones from nearby regions without cloning everything in between (as in chromosome walking; see below). One round of jumping yields new clones at distances of several tens of kb away from the starting point. In practice, this method is used when classical genetics proves that a known piece of DNA is located on the chromosome close to a gene you would like to clone (such as a human disease gene). By cloning fragments some distance away in both directions from the known fragment, one might obtain (1) fragments further from the desired gene (which are discarded); (2) fragments even more closely linked to the desired gene (in which case one goes for another round of jumping); or (3) fragments from within the desired gene - the optimal result.

Chromosome Walking:

A technique for cloning everything in the genome around a known piece of DNA. You screen a genomic library for all clones hybridizing with the probe, and then figure out which one extends furthest into the surrounding DNA. The most distal piece of this most distal clone is then used as a probe, so that ever more distal regions can be cloned. This has been used to move as much as 200 kb away from a given starting point (an immense undertaking). Typically used to "walk" from a starting point towards some nearby gene in order to clone that gene. Also used to obtain the remainder of a gene when you have isolated a part of it.

Cis:

An interaction between two sites which are located within the same molecule. However, a cis-acting protein can either be one which acts only on the molecule of DNA from which it was expressed, or a protein which acts on itself.

Cistron:

A nucleic acid segment corresponding to a polypeptide chain, including the relevant translational start (initiation) and stop (termination) codons.

Clones:

A group of cells derived from a single ancestor.

Cloning:

The process of generating sufficient copies of a particular piece of DNA or asexually producing a group of cells (clones), all genetically identical, from a single ancestor. In recombinant DNA technology, the use of DNA manipulation procedures to produce multiple copies of a single gene or segment of DNA is referred to as cloning DNA.

Cloning Vector:

DNA molecule originating from a virus, a plasmid, or the cell of a higher organism into which another DNA fragment of appropriate size can be integrated without loss of the vectors capacity for self- replication; vectors introduce foreign DNA into host cells, where it can be reproduced in large quantities. Examples are plasmids, cosmids, bacterial artificial chromosomes (BAC) and yeast artificial chromosomes (YAC); vectors are often recombinant molecules containing DNA sequences from several sources.

Closed Reading Frames:

It contains termination codons that prevent its translation into proteins.

Coding Sequence:

The portion of a gene or an mRNA which actually codes for a protein. Introns are not coding sequences; The coding sequence in a cDNA or mature mRNA includes everything from the AUG (or ATG) initiation codon through to the stop codon.

Coding Strand:

an ambiguous term intended to refer to one specific strand in a double-stranded gene.

Codon:

A group of three consecutive nucleotides within messenger RNA (mRNA) that encodes a message to initiate translation, to incorporate a specific amino acid into the growing polypeptide chain, or to stop translation. The sequence of codons in the mRNA unambiguously defines the primary structure of the final protein. Of course, the codons in the mRNA were also present in the genomic DNA, but the sequence may be interrupted by introns.

Codon Bias:

The tendency for an organism or virus to use certain codons more than others to encode a particular amino acid. An important determinant of codon bias is the guanosine-cytosine (GC) content of the genome. An organism that has a relatively low G+C content of 30% will be less likely to have a G or C at the third position of a codon (wobble position) than a A or T to specify an amino acid that can be represented by more than one codon.

Coefficient of Variation (CV):

Used as a measure of experimental variation. It is important that a linear value is used to calculate the CV (but not Ct values which are logarithmic).

Co-linearity:

Refers to an exact correspondence between information encoded in DNA and the polypeptide product ultimately translated from transcripts made from the DNA. Most prokaryotic genes are co-linear with their products; eukaryotic genes often are not.

Competent:

Bacterial cells which are capable of accepting foreign extra-chromosomal DNA.

Complementary DNA (cDNA):

A DNA sequence synthesized from a messenger RNA molecule, using reverse transcriptase enzyme. cDNAs can be used experimentally to determine the sequence of messenger RNAs after their introns (non-protein-coding sections) have been spliced out. The single- stranded form is often used as a probe in physical mapping.

Complementary Sequences:

Nucleic acid base sequences that can form a double- stranded structure by matching base pairs; the complementary sequence to G- T- A- C is C- A- T- G.

Composite Transposons:

They have a central region flnked on each side by insertion sequences, either or both of which may enable the entire element to transpose.

Concatemer:

Tandem arrays of monomeric DNA molecules with complementary ends. Intra-molecular reassociation of such molecules leads to circularisation while inter-molecular reaction produces concatemers.

Conformational Epitope:

Also called a "global epitope". An epitope comprised of contiguous but physically discontinuous components of the immunogenic molecule. In a proteinaceous antigen this could be sequences from different stretches within a polypeptide, or even from different polypeptide subunits.

Conjugation:

Physical contact with the establishment of plasma bridges between two different bacterial cells allowing directed transfer of DNA.

Consensus Sequence:

A term that refers to sequences common to different genes within an organism, or to the same gene among different organisms, that encode a specific function. This term may be applied to either nucleic acids or proteins, since the protein sequence is completely dependent upon the nucleic acid sequence.

Conservation:

Identical parts of genes that are present in two distinct organisms are said to be conserved. Conservation can be detected by measuring the similarity of the two sequences at the base (RNA or DNA) or amino-acid (protein) level.

Conserved Sequence:

A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained essentially unchanged throughout evolution. The more similarities there are, the more highly conserved the two sequences.

Conservative Substitution:

A nucleotide mutation which alters the amino acid sequence of the protein, but which causes the substitution of one amino acid with another which has a side chain with similar charge/polarity characteristics.

Complementary Sequences:

Nucleic acid base sequences that can form a double- stranded structure by matching base pairs; the complementary sequence to G- T- A- C is C- A- T- G.

Concatemer:

Tandem arrays of monomeric DNA molecules with complementary ends. Intra-molecular reassociation of such molecules leads to circularisation while inter-molecular reaction produces concatemers.

Conformation:

The 3-dimensional structure of a molecule.

Conjugation:

Physical contact with the establishment of plasma bridges between two different bacterial cells allowing directed transfer of DNA.

Conservation:

Identical parts of genes that are present in two distinct organisms are said to be conserved. Conservation can be detected by measuring the similarity of the two sequences at the base (RNA or DNA) or amino-acid (protein) level.

Constitutive Expression:

Constantly expressed at some appreciable level.

Constitutive Genes:

These are expressed as a function of the interaction of RNA polymerase with the promoter without additional promoter.

Contig:

A 'contig' may refer to a map showing placement of a set of clones that completely, contiguously cover some segment of DNA. More often, the term 'contig' is used to refer to the final product of a shotgun sequencing project. When individual lanes of sequence information are merged to infer the sequence of the larger DNA piece, the product consensus sequence is called a 'contig'.

Contig Map:

A map depicting the relative order of a linked library of small overlapping clones representing a complete chromosomal segment.

Cosmid:

A type of artificially constructed vector used for cloning 35-45 kb of DNA. These are plasmids carrying a phage l cos site, an origin of replication and an antibiotic resistance gene. A plasmid of 40 kb is very difficult to put into bacteria, but can replicate once there. Cosmids, however, have a cos site, and thus can be packaged into l phage heads to allow efficient introduction into bacteria.

Crossing Over:

The breaking during meiosis of one maternal and one paternal chromosome, the exchange of corresponding sections of DNA, and the rejoining of the chromosomes. This process can result in an exchange of alleles between chromosomes.

Cyclins:

These are the proteins that accumulate continously throughout the life cycle and are then destroyed by proteolysis during meiosis.

Cytosine (C):

One of the pyrimidine bases found in DNA and RNA (4-amino-2-hydroxypyrimidine). one member of the base pair G-C (guanine and cytosine).

Cytoplasmic Inheritance:

It is a property of genes located in a mitochondria or chloroplasts .

Ct (threshold cycle):

Threshold cycle reflects the cycle number at which the fluorescence generated within a reaction crosses the threshold. It is inversely correlated to the logarithm of the initial copy number. The Ct value assigned to a particular well thus reflects the point during the reaction at which a sufficient number of amplicons have accumulated. Also called crossing point (Cp) in LightCycler terminology.

Cytosol:

It describes the geenral volume of cytoplasm in which organelles are located.