Cell cycle Stages in the life cycle of replicating eukaryotic cells. After cell division (mitosis), a cell goes through the resting G1/Go phase prior to DNA replication in the S phase. Completion of duplication of cellular materials in the G2 phase occurs prior to mitosis (M phase).
Chromatin Cellular genome as nucleoprotein which contains DNA, histones, and a variety of nonhistone chromosomal proteins.
Chromatin remodeling Alteration in the structure of segment of chromatin which is brought about by hi-stone acetylation/deacetylation and/or mediated by interaction with large protein complexes as a prerequisite for modulation of transcription activity.
Chromosomes Discrete and microscopically visible segments of the eukaryotic genome complexed with proteins and capped by telomeres; each normally contains thousands of genes.
Cis element Short, specific DNA sequences, usually in the promoter, that bind cognate trans-acting factors.
Deoxyribonucleotides Monomeric units of DNA, including deoxyadenylic (dAMP), deoxyguanylic (dGMP), deoxycytidylic (dCMP), and deoxythymidylic (dTMP) acids.
DNA Deoxyribonucleic acid: linear copolymers of mo-nomeric deoxyribonucleotides normally present as a two-stranded intertwined helix; the deoxyribose sugar moiety lacks
DNA helicase An enzyme which unwinds the double helical DNA using energy provided by ATP hydrolysis.
DNA ligase The enzyme which catalyzes joining of the 5′ and 3′ termini of two single-stranded DNA fragments in a double-stranded DNA by forming a phosphodiester bond.
DNA repair Enzymatic process that maintains sequence integrity by removing both endogenously and exoge-nously induced DNA damage. Such lesions could be mutagenic because of misreplication at the damage site. Replication errors are also corrected by DNA repair. Repair involves removal of the DNA damage site in duplex DNA, followed by resynthesis of the damaged strand using the unaffected complementary strand as the template.
Enhancer elements DNA sequences which activate the expression of genes in an orientation- and position-independent fashion.
Episome Small extrachromosomal and sometimes self-replicating DNA molecules, including infecting viral DNA, founded in both prokaryotes and eukaryotes.
Error-bypass DNA polymerases A new class of recently discovered DNA polymerases in both prokaryotes and eukaryotes which are more tolerant of improper base pairing and may function in maintaining genomic continuity when damaged DNA bases have not been repaired.
Function The intrinsic 3′ exonuclease activity of replica-tive DNA polymerase or polymerase complexes needed to excise incorrect deoxynucleotides inserted at the terminus of a growing DNA chain.
Gene Basic functional unit in the genome which is transcribed to produce messenger RNA, which in turn is translated into protein. (Some genes, e.g., those for ri-bosomal and transfer RNAs, are only transcribed and not translated.)
Genome Complete genetic information stored in the nu-cleotide sequence (usually DNA) of an organism, or-ganelle, or episome.
HMG proteins High mobility group (based on gel elec-trophoresis) proteins which are associated with chro-matin; a subset of nonhistone chromosomal (NHC) proteins.
Lagging strand Nascent DNA strand synthesized dis-continuously by replication of the 5′ ^ 3′ template strand.
Leading strand Nascent DNA synthesized by continuous replication of the 3′ ^ 5′ template strand.
Mitochondrial genome Multiple copies of the circular DNA duplex molecule in eukaryotic mitochondria. Believed to be a vestigial prokaryotic genome, it is replicated by a special DNA polymerase (Pol y ) which, along with other proteins required for mitochondrial DNA replication, is encoded by the nuclear genome.
Mutation Change in the genome sequence via the process of mutagenesis, which can occur either spontaneously due to endogenous reactions or after exposure to external mutagens, including radiation and chemicals. Mutations include large-scale sequence alterations, including deletion or insertion of thousands of DNA base pairs and genomic rearrangement which could involve translocation of one chromosomal segment to another. Mutations could also be subtle, including changes of a single base (known as point mutation), which include loss or addition of a single base.
Nontranscribed strand The complementary strand (5′-3′) of DNA with the same sequence as the RNA transcribed from the other (transcribed or template) strand.
Nucleosome Smallest repeat unit of chromatin nucleo-protein, containing 145 bp of DNA wrapped around a histone octamer core (2 subunits each of histone H2A, H2B, H3, and H4) along with linker DNA of variable length. Mild treatment of chromatin with DNase digests the linker and generates nucleosome fragments of different repeat lengths ("ladder").
Okazaki fragments Nascent DNA fragments generated by discontinuous synthesis of the lagging (5′ ^ 3′) strand in all organisms.
Operator A small, specific, and often palindromic DNA sequence or its repeats cognate to regulated bacterial genes. A repressor (or activator) binds the operators to prevent (or activate) transcription.
Ori (origin) Origin of replication in the genome. These are unique sequences which bind the replication initiation complex as a prerequisite for primer synthesis.
PCR Polymerase chain reaction.
Plasmid Extrachromosomal DNA molecule, usually much smaller than the cell genome. Plasmids are autonomously replicated in the cell, utilizing the cellular replication machinery.
Pol DNA or RNA polymerase.
Primase Enzyme (sometimes with other accessory proteins) which is a component of the DNA replication machinery and is needed for synthesis of an oligori-bonucleotide primer.
Promoter Specific DNA sequence usually found at the beginning of a gene, which binds the transcriptional machinery as a prerequisite to transcription initiation from the gene.
Replicon Unit of DNA replication in the genome, containing one ori site. Small genomes of bacteria, plas-mids, and viruses have single replicons, while larger eukaryotic genomes have hundreds or thousands of replicons which could be simultaneously or sequentially fired for synthesis of different segments of the genome. This is necessary to reduce the overall replication time of a genome which is 103 times larger than a bacterial genome.
Repressor Proteins which bind to specific operators and thus negatively regulate gene expression by inhibiting transcription.
Reverse transcriptase (RT) Specialized DNA poly-merase encoded by retroviruses, including the AIDS virus (HIV), which utilizes both RNA and DNA template. It is responsible for propagation of retroviruses via synthesis of a proviral DNA intermediate.
Ribonucleotides Monomeric units of RNA, namely, adenylic (AMP), guanylic (GMP), cytidylic (CMP), and uridylic (UMP); the ribose sugar moiety of each contains a 2′-OH.
Ribosome Protein synthesis factory consisting of two differently sized subunits of ribonucleoprotein complexes with several active centers. It travels along mRNA and reads triplet codons for individual amino acids which are brought in by transfer RNAs via base pairing with cognate anticodon sequences in these RNAs. Protein synthesis occurs on the ribosome to which the growing polypeptide chain remains attached.
RNA Ribonucleic acid: linear copolymers usually of four ribonucleotides. Three major types of RNA are synthesized in the cell: ribosomal RNA (rRNA), the major component of ribosomes; transfer RNA (tRNA), the adaptor for protein synthesis; and messenger RNA (mRNA), which is required for information transfer. Other small RNAs with specialized functions are also synthesized in small amounts in both prokaryotic and eukaryotic cells.
RTPCR Reverse transcript polymerase chain reaction. Modification of the PCR method to amplify RNA, which involves generation of a complementary DNA molecule from RNA (by reverse transcriptase) which is then used in PCR.
Telomerase A special eukaryotic DNA polymerase that adds a repeat sequence to chromosome termini without a template.
Telomere Terminal region of a linear chromosome, containing partial single-stranded DNA and repeat sequences of short oligonucleotides. Its loss could cause chromosome fusion and rearrangement.
Template-independent poly(A) polymerase A template-independent RNA polymerase which catalyzes formation of AMP containing homopolymers up to several hundred monomers at the 3′ termini of nascent RNA molecules. The poly(A) tail promotes transport of mRNA from the nucleus, enhances its stability, and is necessary for translation.
Terminator Specific sequence found at the end of genes for termination of transcription due to release of RNA and RNA polymerase.
Topoisomerase Enzymes which alter topologically constrained DNA, including circular DNA, by changing the linking number. Topoisomerase I changes the linking number one at a time and does not require an external energy source. Topoisomerase II changes the linking number two at a time and generally requires ATP. The linking number is changed by transient breakage and rejoining, with an enzyme-DNA covalent bond intermediate. The enzyme acts as a swivel for rotating DNA strands around each other. Trans-acting factors Proteins that bind to specific DNA sequences (cis elements) in genes and regulate transcription positively or negatively. Transcribed strand The 3′ ^ 5′ DNA strand utilized by RNA polymerase as its transcriptional template. Transcriptional activator Trans-acting proteins which enhance transcription and, thus, the level of specific proteins.
Transcription unit Discrete segment of DNA, corresponding to one or more genes, which is utilized as a template by RNA polymerase. In prokaryotes, the transcription unit is called an operon. Translation Synthesis of a protein, directed by mRNA molecules on ribosome.
