Ap Bio-Information B

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bacteriophage

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A virus that infects bacteria; also called a phage.

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DNA ligase

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A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3’ end of a new DNA fragment to the 5’ end of a growing chain.

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DNA polymerase

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An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain.

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double helix

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The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.

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helicase

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An enzyme that untwists the double helix of DNA at the replication forks.

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lagging strand

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A discontinuously synthesized DNA strand that elongates in a direction away from the replication fork.

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leading strand

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The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5’ ( 3’ direction.

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mismatch repair

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The cellular process that uses special enzymes to fix incorrectly paired nucleotides.

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nuclease

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An enzyme that hydrolyzes DNA and RNA into their component nucleotides.

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nucleotide excision repair

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The process of removing and then correctly replacing a damaged segment of DNA using the undamaged strand as a guide.

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Okazaki fragment

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A short segment of DNA synthesized on a template strand during DNA replication. Make up the lagging strand of newly synthesized DNA.

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origin of replication

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Site where the replication of a DNA molecule begins.

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phage

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A virus that infects bacteria; also called a bacteriophage.

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primase

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An enzyme that joins RNA nucleotides to make the primer.

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replication fork

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A Y-shaped region on a replicating DNA molecule where new strands are growing.

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semiconservative model

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Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand.

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single-strand binding protein

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During DNA replication, molecules that line up along the unpaired DNA strands, holding them apart while the DNA strands serve as templates for the synthesis of complementary strands of DNA.

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telomerase

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An enzyme that catalyzes the lengthening of telomeres. The enzyme includes a molecule of RNA that serves as a template for new telomere segments.

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telomere

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The protective structure at each end of a eukaryotic chromosome. Specifically, the tandemly repetitive DNA at the end of the chromosome’s DNA molecule. See also repetitive DNA.

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topoisomerase

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A protein that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.

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transformation

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(1) The conversion of a normal animal cell to a cancerous cell. (2) A change in genotype and phenotype due to the assimilation of external DNA by a cell.

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5’ cap

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The 5’ end of a pre-mRNA molecule modified by the addition of a cap of guanine nucleotide.

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A site

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One of a ribosome’s three binding sites for tRNA during translation. It holds the tRNA carrying the next amino acid to be added to the polypeptide chain. (_ stands for aminoacyl tRNA.)

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alternative RNA splicing

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A type of regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

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aminoacyl-tRNA synthetase

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An enzyme that joins each amino acid to the correct tRNA.

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anticodon

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A specialized base triplet at one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule.

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base-pair substitution

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A type of point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides.

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codon

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A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

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deletion

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1) A deficiency in a chromosome resulting from the loss of a fragment through breakage. (2) A mutational loss of one or more nucleotide pairs from a gene.

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domain

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An independently folding part of a protein.

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E site

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One of a ribosome’s three binding sites for tRNA during translation. It is the place where discharged tRNAs leave the ribosome.

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exon

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A coding region of a eukaryotic gene. They are separated from each other by introns.

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frameshift mutation

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A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the following nucleotides into codons.

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insertion

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A mutation involving the addition of one or more nucleotide pairs to a gene.

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intron

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A noncoding, intervening sequence within a eukaryotic gene.

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messenger RNA (mRNA)

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A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

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missense mutation

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The most common type of mutation, a base-pair substitution in which the new codon makes sense in that it still codes for an amino acid.

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mutagen

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A chemical or physical agent that interacts with DNA and causes a mutation.

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nonsense mutation

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A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

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one gene–one polypeptide hypothesis

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The premise that a gene is a segment of DNA that codes for one polypeptide.

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P site

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One of a ribosome’s three binding sites for tRNA during translation. It holds the tRNA carrying the growing polypeptide chain.

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point mutation

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A change in a gene at a single nucleotide pair.

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poly-A tail

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The modified end of the 3’ end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.

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polyribosome (polysome)

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An aggregation of several ribosomes attached to one messenger RNA molecule.

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primary transcript

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An initial RNA transcript; also called pre-mRNA when transcribed from a protein-coding gene.

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promoter

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A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.

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reading frame

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The way a cell’s mRNA-translating machinery groups the mRNA nucleotides into codons.

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ribosomal RNA (rRNA)

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The most abundant type of RNA, which together with proteins forms the structure of ribosomes. Ribosomes coordinate the sequential coupling of tRNA molecules to mRNA codons.

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ribosome

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A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits.

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ribozyme

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An enzymatic RNA molecule that catalyzes reactions during RNA splicing.

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RNA polymerase

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An enzyme that links together the growing chain of ribonucleotides during transcription.

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RNA processing

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Modification of RNA before it leaves the nucleus, a process unique to eukaryotes.

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RNA splicing

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The removal of noncoding portions (introns) of the RNA molecule after initial synthesis.

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signal peptide

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A stretch of amino acids on a polypeptide that targets the protein to a specific destination in a eukaryotic cell.

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signal-recognition particle (SRP)

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A protein-RNA complex that recognizes a signal peptide as it emerges from the ribosome.

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spliceosome

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A complex assembly that interacts with the ends of an RNA intron in splicing RNA, releasing the intron and joining the two adjacent exons.

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TATA box

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A promoter DNA sequence crucial in forming the transcription initiation complex.

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template strand

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The DNA strand that provides the template for ordering the sequence of nucleotides in an RNA transcript.

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terminator

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In prokaryotes, a special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene.

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transcription

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The synthesis of RNA on a DNA template.

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transcription factor

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A regulatory protein that binds to DNA and stimulates transcription of specific genes.

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transcription initiation complex

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The completed assembly of transcription factors and RNA polymerase bound to the promoter.

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transcription unit

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A region of a DNA molecule that is transcribed into an RNA molecule.

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transfer RNA (tRNA)

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An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA.

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translation

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The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of languagefrom nucleotides to amino acids.

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triplet code

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A set of three-nucleotide-long words that specify the amino acids for polypeptide chains.

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wobble

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A violation of the base-pairing rules in that the third nucleotide (5’ end) of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3’ end) of a codon.

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activator

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A protein that binds to DNA and stimulates transcription of a specific gene.

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AIDS (acquired immunodeficiency syndrome)

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The name of the late stages of HIV infection, defined by a specified reduction of T cells and the appearance of characteristic secondary infections.

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bacteriophage

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A virus that infects bacteria; also called a phage.

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capsid

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The protein shell that encloses a viral genome. It may be rod-shaped, polyhedral, or more complex in shape.

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conjugation

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In prokaryotes, the direct transfer of DNA between two cells that are temporarily joined. In ciliates, a sexual process in which two cells exchange haploid micronuclei.

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corepressor

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A small molecule that cooperates with a repressor protein to switch on operon off.

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cyclic AMP (cAMP)

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Cyclic adenosine monophosphate, a ring-shaped molecule made from ATP that is a common intracellular signaling molecule (second messenger) in eukaryotic cells (for example, in vertebrate endocrine cells). It is also a regulator of some bacterial operons.

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episome

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A genetic element that can exist either as a plasmid or as part of the bacterial chromosome.

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F factor

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A fertility factor in bacteria; a DNA segment that confers the ability to form pili for conjugation and associated functions required for the transfer of DNA from donor to recipient. It may exist as a plasmid or be integrated into the bacterial chromosome.

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F plasmid

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The plasmid form of the F factor.

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HIV (human immunodeficiency virus)

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The infectious agent that causes AIDS

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host range

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The limited range of host cells that each type of virus can infect and parasitize.

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inducer

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A specific small molecule that inactivates the repressor in an operon.

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insertion sequence

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The simplest kind of transposable element, consisting of inverted repeats of DNA flanking a gene for transposase, the enzyme that catalyzes transposition.

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lysogenic cycle

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A phage replication cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage and does not kill the host.

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lytic cycle

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A type of viral (phage) replication cycle resulting in the release of new phages by lysis (and death) of the host cell.

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nucleoid

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A dense region of DNA in a prokaryotic cell.

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operator

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In prokaryotic DNA, a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon.

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operon

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A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions.

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phage

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A virus that infects bacteria; also called a bacteriophage.

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plasmid

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A small ring of DNA that carries accessory genes separate from those of a bacterial chromosome; also found in some eukaryotes, such as yeast.

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prion

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An infectious form of protein that may increase in number by converting related proteins to more of itself.

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prophage

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A phage genome that has been inserted into a specific site on the bacterial chromosome.

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provirus

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Viral DNA that inserts into a host genome.

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R plasmid

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A bacterial plasmid carrying genes that confer resistance to certain antibiotics.

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regulatory gene

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A gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes.

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repressor

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A protein that suppresses the transcription of a gene.

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retrovirus

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An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.

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reverse transcriptase

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An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.

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temperate phage

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A phage that is capable of reproducing by either the lytic or lysogenic cycle.

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transduction

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A DNA transfer process in which phages carry bacterial genes from one host cell to another.

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transformation

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A change in genotype and phenotype due to the assimilation of external DNA by a cell. Also, the conversion of a normal animal cell to a cancerous cell.

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transposable genetic element

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A segment of DNA that can move within the genome of a cell by means of a DNA or RNA intermediate; also called a transposable element.

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transposon

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A transposable genetic element that moves within a genome by means of a DNA intermediate.

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vaccine

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A harmless variant or derivative of a pathogen that stimulates a host’s immune system to mount defenses against the pathogen.

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viral envelope

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A membrane that cloaks the capsid that in turn encloses a viral genome.

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viroid

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A plant pathogen composed of molecules of naked circular RNA only several hundred nucleotides long.

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virulent phage

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A phage that reproduces only by a lytic cycle.

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activator

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A protein that binds to DNA and stimulates transcription of a specific gene.

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alternative RNA splicing

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A type of regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

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cell differentiation

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The structural and functional divergence of cells as they become specialized during a multicellular organism’s development; dependent on the control of gene expression.

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chromatin

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The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing, it exists as a mass of very long, thin fibers that are not visible with a light microscope.

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control element

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A segment of noncoding DNA that helps regulate transcription of a gene by binding proteins called transcription factors.

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differential gene expression

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The expression of different sets of genes by cells with the same genome.

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enhancer

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A DNA segment containing multiple control elements that may be located far away from the gene it regulates.

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epigenetic inheritance

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Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.

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euchromatin

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The more open, unraveled form of eukaryotic chromatin that is available for transcription.

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genomic imprinting

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Phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent.

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heterochromatin

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Nontranscribed eukaryotic chromatin that is so highly compacted that it is visible with a light microscope during interphase.

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histone

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A small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in its chromatin structure.

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histone acetylation

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The attachment of acetyl groups to certain amino acids of histone proteins.

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micro-RNA (miRNA)

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A small, single-stranded RNA molecule that binds to a complementary sequence in mRNA molecules and directs associated proteins to degrade or prevent translation of the target mRNA.

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multigene family

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A collection of genes with similar or identical sequences, presumably of common origin.

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nucleosome

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The basic, bead-like unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each of four types of histone.

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oncogene

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A gene found in viruses or as part of the normal genome that is involved in triggering cancerous characteristics.

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p53 gene

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A gene that is expressed when a cell’s DNA is damaged. Its product functions as a transcription factor for several genes.

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proteasome

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A giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin.

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proto-oncogene

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A normal cellular gene corresponding to an oncogene; a gene with a potential to cause cancer but that requires some alteration to become an oncogene.

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pseudogene

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A DNA segment very similar to a real gene but which does not yield a functional product; a gene that has become inactivated in a particular species because of mutation.

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Ras gene

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A gene that codes for Ras protein, a G protein that relays a growth signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases that ultimately results in the stimulation of the cell cycle. Many ras oncogenes have a point mutation that leads to a hyperactive version of the Ras protein that can lead to excessive cell division.

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repetitive DNA

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Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome. The repeated units may be short and arranged tandemly (in series) or long and dispersed in the genome.

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repressor

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A protein that suppresses the transcription of a gene.

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retrotransposon

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A transposable element that moves within a genome by means of an RNA intermediate, a transcript of the ______ DNA.

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RNA interference (RNAi)

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A technique to silence the expression of selected genes in nonmammalian organisms. The method uses synthetic double-stranded RNA molecules matching the sequence of a particular gene to trigger the breakdown of the gene’s messenger RNA.

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transcription factor

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A regulatory protein that binds to DNA and stimulates transcription of specific genes.

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transposon

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A transposable genetic element that moves within a genome by means of a DNA intermediate.

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tumor-suppressor gene

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A gene whose protein products inhibit cell division, thereby preventing uncontrolled cell growth (cancer).