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Glossary

Acceptor Site - the 3 ' end of an intron. See Donor Site.

Adenine - a purine base found in DNA and RNA. See figure.

Allele - one of several different forms of a gene at a particular place on a chromosome. Alleles are located on opposite pairs of chromosomes, but in the same relative place.

Amino Acid - The building blocks of proteins are called amino acids. Amino acids contain an ammonia group (amino) as well as a carboxyl group (acid). Example amino acids include alanine, glycine, lysine, glutamic acid, arginine.

Anaphase - fourth part of the cell cycle during which chromosomes are pulled toward the poles of the cell.

Antibodies - proteins (four chains) produced by lymphocytes having a very distinctive shape that enables them to bind tightly to molecules that "fit" into the shape (like a lock fits a key). The molecule bound by an antibody is referred to as an antigen.

Anti-codon - portion of a tRNA that pairs with a codon during translation.

Antigen - molecule bound by an antibody. Antigens are capably of stimulating an immune response - resulting in the production of antibodies.

Bacteriophage - a bacteriophage is a virus that infects bacteria. T4 is a well known bacteriphage.

Branch point - pyrimidine-rich sequence near the 3' end of an intron to which the 5' end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.

Catalysis - word used to describe the speeding up of a chemical reaction. Enzymes act as catalysts of chemical reactions because they speed them up many times faster than they would occur naturally.

cDNA - complementary DNA made by using reverse transcriptase on RNA. Usually the term is used to refer to the DNA made from mRNA, but cDNA can be made from any RNA with reverse transcriptase and dNTPs. See cDNA library.

Cell - fundamental unit of life.

Cell Cycle - The orderly visible sequence of events through which dividing cells pass. Can be broken into interphase and mitosis. Mitosis can be further broken into prophase, metaphase, anaphase, telophase, cytokinesis.

Centromere - specialized structure on a chromosome to which the mitotic spindle (fiber like structure) attaches during mitosis. It is visible as a constriction in the chromosome.

Chloroplast - plant organelle containing apparatus for synthesis of sugar from the energy of light (photosynthesis).

Chromosomes - structures composed of DNA and proteins found in the nucleus of eukaryotic cells. Chromosomes carry the genetic material.

Codon - a sequence of three nucleotides that is a signal to the translation machinery. A codon specifies either an amino acid or a stop translation signal. See genetic code.

Cytokinesis - the last part of the mitotic cycle during which the two daughter cells separate. Technically cytokinesis is the division of the cytoplasm.

Cytosine - a pyrimidine base found in DNA and RNA. See picture.

Deoxyribonucleotides - the fundamental building blocks of DNA. The four monomeric deoxyribonucleotides in DNA are abbreviated dAMP, dGMP, dCMP, and dTMP. A mixture of the deoxyribonucleotides is generically called dNTPs. Deoxyribonucleotides (in DNA) differ from ribonucleotides (in RNA)in the usage of the base thymine instead of uracil and in the use of deoxyribose as the sugar instead of ribose. See also nucleotides.

Deoxyribose - the sugar present in deoxyribonucleotides. (See figure)

Dideoxynucleotide - a nucleotide lacking an oxygen at both positions two and three of the sugar ring. See figure.

Diploid - Cells containing two complete sets of chromosomes. Most of the cells of our body are diploid. The germ cells are haploid.

DNA - An acronym for deoxyribonucleic acid. DNA is the genetic material, or "blueprint" of the cell. Chromosomes contain DNA (proteins too). DNA carries information to make all of the proteins of a cell. DNA is composed of two chains of polynucleotides intertwined with each other (figure) in a very specific way. Each polynucleotide chain contains sufficient information to replicate the other strand under proper conditions.

DNA Polymerase - an enzyme that catalyzes the incorporation of deoxyribonucleotides in a DNA template.

DNA Replication - the process by which DNA is duplicated. Prior to mitosis, the DNA in a cell must be copied so each of the daughter cells has a complete copy of the DNA that the parent had.

Donor Site - the 5 ' end of an intron. Donor sites usually have the sequence GU at their 5' most end (See Acceptor Site)

Downstream - molecular biology lingo meaning 3' to a defined point. The termination site of transcription might be described as downstream of the initiation site. See upstream.

Endoplasmic Reticulum - cellular organelle where protein synthesis can occur.

Enhancer - a eukaryotic DNA sequence that can affect the transcription of a gene. Enhancers are different from promoters in their ability to be located long distances away from the gene (over 1000 nucleotides, in some cases) and their location - upstream or downstream of a gene.

Enzymes - Proteins made by the cell that catalyze chemical reactions.

Eukaryotic cells - cells containing distinct organelles having specific functions. Usually multicellular, but some (yeast, for example) are unicellular. Includes plants and animals.

Exons - the individual "pieces" of a gene that are put together by splicing. Exons are separated by introns. (See figure)

Exonuclease - an enzymatic activity responsible for removing nucleotides from an existing strand of nucleic acid. Works counter to DNA (or RNA) polymerase activity.

Expression vector - for our purposes, we will define an expression vector as a plasmid containing an E. coli replication origin, a selectable marker (such as antibiotic resistance), and an E. coli promoter upstream of the region where the protein coding sequence is placed.

Gel electrophoresis - laboratory process for separating macromolecules on the basis of size.

Gene - The fundamental unit of inheritance. A part of the cellular "blueprint" which provides the necessary information for making a protein. (Note - biotechnologists also use the term gene in a broader sense to include the parts of DNA that are transcribed into rRNA and tRNA as well.) The cellular blueprint, of course, is DNA.

Genetic Code - the "language" of heredity. The genetic code defines sequence of nucleotides in DNA which ultimately (via mRNA) specifies a sequence of amino acids in a protein. The "letters" of the language are referred to as codons. Proteins in such a scheme may be thought to be "words" (that is - composed of a specific sequence of letters). (See Figure). Though there are slight variations of the genetic code that have been found, we think of the code as being "universal" - that is, the same from one organism to another.

Genetic Material - The "blueprint" for all of the proteins needed for a cell. DNA is the genetic material in all cells and most viruses. DNA is a component of chromosomes.

Genome - word used to describe all of the genetic material of an organism.

Genotype - the genetic makeup of a cell. The term is usually used to describe one gene or a set of genes, as opposed to the makeup of all the genes in a cell. See phenotype.

Golgi Apparatus - cellular organelle involved in modifying proteins in preparation for secretion.

Guanine - a purine base found in DNA and RNA. See picture.

Haploid - cells containing only a single set of chromosomes. Our germ cells are haploid. The rest of our cells are diploid.

Heterozygous - word used to describe the situation where an individual has genes for different traits (such as brown and blue eyes) at the same chromosomal locus of their paired chromosomes. Opposite of homozygous.

Histones - Small positively charged proteins that interact with DNA non-specifically. The structures they form in complex with DNA (DNA is "rolled" around the histones) are referred to as nucleosomes, and the effect of their wrapping in this manner is to reduce the effective length of DNA in the cell. See Picture.

Homozygous - word used to describe the situation where an individual has the same gene coding for the same trait (such as brown and brown eyes) at the same place on a chromosomal pair. Opposite of heterozygous.

Intron - an intervening sequence of nucleic acid present within a gene before splicing. Introns are removed by splicing before translation occurs. See exon. See figure.

Labeling - to attach a an identifying marker of some sort to a nucleic acid or protein. Usually the marker is a radioactive element, such as 32P, but non-radioactive markers are also available.

Lagging Strand Synthesis - In DNA synthesis, polymerization occurs both in the direction of the nearest replication fork and away from it. Polymerization away from the nearest replication fork occurs with fits and starts and is referred to as lagging strand synthesis. The short fragments produced in lagging strand synthesis are called Okazaki fragments. (See also leading strand synthesis and figure).

Leading Strand Synthesis - In DNA synthesis, polymerization occurs both in the direction of the nearest replication fork and away from it. Polymerization towards the nearest replication fork is called leading strand synthesis and produces newly synthesized segments of DNA longer than those produced in lagging strand synthesis. (See figure).

Library - A collection of all the sequences of an organism (genomic library) or its genes (cDNA library). Though a solution of genomic DNA would technically be a library by this definition, the term is usually applied only when the sequences are all contained in (ligated to) a cloning vector (plasmid).

Lipid Bilayer - A double layer of phospholipids serving as the boundary between the cell and its environment. The phospholipids are oriented such that the "polar" portion (containing phosphate) is oriented outwards and the non-polar portion is oriented inwards.

Locus - term used to describe a specific site on a chromosome. We speak of a gene as being located at a specific chromosomal locus.

Lymphocytes - white blood cells that produce antibodies.

Macromolecule - large molecules of a cell are called macromolecules. Typically they are a polymer (molecule containing hundreds, thousands, or millions of common building block molecules linked end-to-end). The individual building blocks of a polymer are called monomers. Starch is a polymer of units of the sugar glucose. Proteins are macromolecules that are polymers of amino acids. DNA and RNA are polymers of nucleotide units. The sequence with which the amino acids of a protein are linked together give the protein its characteristic activity. The sequence of the nucleotides in DNA and RNA ultimately determines the sequence of the amino acids in a protein.

Meiosis - A type of cell division in which cells divide without replication of the chromosomes. Consequently, diploid cells (2 complete sets of chromosomes) become haploid (1 complete set of chromosomes). Gametes (sperm and egg) go through meiosis. Upon fertilization, the fertilized egg contains two complete sets of chromosomes and is diploid.

Metaphase - third part of the mitotic cycle in which the chromosomes are aligned at the metaphase plate in preparation for anaphase.

Mitochondrion - cellular organelle involved in energy production/regulation in the cell. (Plural = mitochondria).

Mitosis - a term used generally to refer to the process of cell division. Technically the term is used to describe the division of the nucleus. Chromosomes are duplicated during mitosis and the cell divides in half, each half obtaining a complete set (copy) of the chromosome(s). The pair of cells produced by mitosis are called daughter cells.

Monomer - individual unit of a polymer. For examply, AMP is a monomer of RNA, which is a polymer of nucleotides.

mRNA - messenger RNA. This is the RNA translated by the ribosomes into protein.

Mutation - any alteration of the sequence of nucleotides in a DNA molecule is described as a mutation. Since the sequence of nucleotides in a DNA may specify the sequence of amino acids in a protein, mutations in DNA can give rise to mutant proteins, which may have aberrant (often undesired) activities from their unmutated forms.

Northern blotting - technique for detecting and identifying trace quantities of RNA after they have been separated by gel electrophoresis. See Southern blotting and Western blotting.

Nucleic Acids - a term is used to refer to DNA and RNA in general. Technically the term refers to a polymer of nucleotides.

Nucleoside - a base linked to a sugar. The difference between a nucleotide and a nucleoside is that a nucleotide is a base plus a sugar plus one or more phosphates. A nucleoside has no phosphate. Please note that the base names are changed when they are linked to a sugar. Guanine becomes guanosine. Adenine becomes adenosine. Thymine becomes thymidine. Cytosine becomes cytidine. Uracil becomes uridine.

Nucleotide - the building blocks of nucleic acids are called nucleotides. Deoxyribonucleotides are the building blocks of DNA whereas ribonucleotides are the building blocks of RNA. The term nucleotide shall be used generically in this class to indicate either deoxyribonucleotides or ribonucleotides. Nucleotides are composed of a sugar, phosphate(s), and a base (adenine, guanine, thymine (DNA only), uracil (RNA only), or cytosine).

Nucleus - cellular organelle in eukaryotes that houses the genetic material.

Okazaki Fragments - relatively short newly synthesized fragments of DNA produced in lagging strand DNA synthesis.

Oligonucleotide - a short polymer of nucleic acid. Typically under 100 bases long. May be either RNA or DNA.

Oncogene - a gene capable of causing cancer. Oncogenes are mutated forms of normal cellular genes called proto-oncogenes.

Operon - a unit containing a group of bacterial genes and control elements which are recognized and controlled by regulator genes.

Organelle - a structure of a cell that performs a specialized function. For example, the mitochondrion is an organelle designed to produce energy for the cell. See cell organelles.

Origin of Replication - a site within a chromosome at which DNA replication events begin. Origins have specific DNA sequences that are recognized by the proteins involved in initiating replication. E. coli has a single replication origin on its circular chromosome called oriC. Binding of dnaA protein is an important first step in initiation of E. coli replication. Replication proceeds in both directions (bidirectionally) from oriC.

PCR - an acronym for the Polymerase Chain Reaction, a technique for specifically amplifying a desired sequence apart from all the other sequences surrounding it.

Peptide bonds - the fundamental covalent linkage between adjacent amino acids in a protein. Peptide bonds are formed by the joining of the carboxyl group of one amino acid to the alpha amino group of another amino acid.

Phenotype - the physical characteristics of a cell or an organism that arise from its genetic make-up (genotype). For example, blond hair is a phentoype.

Plasma Membrane - The outer boundary of an animal cell is a plasma membrane. Membranes protect the cell from the outside environment. Membranes are composed of lipid bilayers. Plant cells have a rigid cell wall outside of the plasma membrane.

Plasmid - A piece of DNA capable of replicating independently of the chromosomal DNA. Plasmids must contain a replication origin. Numerous plasmids (both linear and circular) from many species are known. Most commonly the plasmids employed by biotechnologists are small (under 7,000 base pairs), circular ones capable of replicating in E. coli.

Ploidy - word used to describe the number of copies of the chromosomes a cell contains. Cells in multicellular organisms are often diploid - they have two complete sets of chromosomes. Human cells have 23 pairs (that is, 2 complete sets of 23) of chromosomes. Haploid cells contain only a single copy of the chromosome(s). Gametes (sperm and egg cells) are haploid because they have gone through meiosis.

Poly-A tail - sequence of about 100 nucleotides of A at the 3' end of eukaryotic mRNAs. The signal for the tail is the sequence AAUAAA approximately 11-30 nucleotides 5' to the poly-A site. Poly-A tails appear to play a role in stability of mRNAs. Though the majority of eukaryotic mRNAs get a poly-A tail, not all do.

Primer - an essential template requirement for DNA polymerases. Consists of an oligonucleotide hybridized to a duplex DNA. The oligonucleotide must have a free 3' end from which DNA polymerase initiates replication. Primers are very useful for
defining sites of initiating DNA replication for processes such as the Polymerase Chain Reaction (PCR). (See RNA Primer).

Primosome - a complex of enzymes present at DNA replication forks that helps synthesize RNA primers for lagging strand synthesis and also helps to unwind DNA strands for leading strand synthesis.

Probe - a radioactively labeled fragment of nucleic acid (usually DNA) of a desired sequence. Probes can be used in blotting techniques to identify desired sequences by the fact that they are complementary to them.

Processivity - a term used to describe the tendency of an enzyme to act on DNA without falling off. The more processive an enzyme is, the longer it will act on DNA before falling off. Subunit Beta helps the DNA Pol III holoenzyme to be more processive.

Prokaryotic cells - single cell life forms lacking a nucleus. Often thought of as primitive. Prokaryotic cells are generally much smaller than eukaryotic cells. Bacteria are prokaryotes.

Promoter - DNA sequence bound by RNA polymerase. The promoter defines the region where transcription will begin.

Prophase - First part of the cycle of mitosis during which the chromosomes become apparent. Prior to this they are not very visible.

Prometaphase - Second part of the mitotic cycle during which the nucleus has dissolved, and the paired sister chromatids become linked to spindle fibers.

Proteins - macromolecules composed of polymer(s) of amino acids that perform the "work" of a cell. Some proteins function as enzymes and catalyze the chemical reactions in a cell. Other proteins provide structural integrity to the cell. Still others exert their effects by "turning on" or "turning off" the synthesis of other proteins. The amino acids in a protein are linked together by what are called "peptide bonds". Proteins are often called peptides or polypeptides.

Proto-oncogene - cellular gene that, when mutated, can cause a cell to become cancerous. See oncogene.

Purines - the bases adenine and guanine are referred to as purines. (See pyrimidines)

Pyrimidine - the bases cytosine, uracil and thymine are referred to as pyrimidines. (See purines)

Reading frame - proteins are translated from mRNA sequence using the genetic code. The context in which the three bases making up the codons are read is referred to as the reading frame. (see example)

Recombination - In nature, a process whereby DNA sequences in chromosomes are rearranged. (In the laboratory, scientists cause recombination with restriction enzymes and DNA ligase). Recombination in nature usually involves migration of a DNA sequence from one site on a chromosome to another where a similar sequence resides. Such a recombination is referred to as homologous recombination.

Restriction enzyme - an enzyme often employed in biotechnology. It acts to cleave DNA at a specific sequence called a recognition site. EcoRI is one such restriction enzyme.

Restriction fragments - pieces of DNA created by cutting with a restriction enzyme.

Restriction map - a circular or linear "map" for a DNA showing the location of restriction enzyme recognition sites on it. Restriction maps are assembled using information from multiple cuts of DNA with different enzymes. The size of the DNA fragments from such cuts are analyzed by gel electrophoresis, and the location of sites in the parental DNA are inferred by comparing the pattern generated by cutting with a single enzyme compared to cutting it with pairs of enzymes.

Retrotransposon - a type of transposon that passes through an RNA intermediate. Retrotransposons require reverse transcriptase in their cycle of reproduction.

Retrovirus - a relatively small RNA virus that typically codes for at least three common genes (called GAG, POL, and ENV). The POL gene is a reverse transcriptase that enables the viral RNA to be converted to DNA upon infection of a cell. The DNA can invade the cell's chromosomes and produce many copies of more viral RNA. HIV is a retrovirus.

Reverse Transcriptase - an enzyme that can use RNA as a template and can make DNA in the presence of dNTPs.

RFLPs - an acronym for Restriction Fragment Length Polymorphisms. RFLPs refer to different sizes of restriction fragments in the same area of the genome in two different DNAs. RFLPs are evidence of mutation/modification of DNA sequence occurring at a particular site of a chromosome.

Ribonucleotides - the fundamental building blocks of RNA. The four ribonucleotides found in RNA are abbreviated AMP, GMP, CMP, and UMP. Ribonucleotides differ from deoxyribonucleotides in the usage of the base U instead of T and in the use of ribose as the sugar instead of deoxyribose. See also nucleotides.

Ribose - the sugar present in ribonucleotides. See figure.

Ribosomes - Macromolecular structures composed of proteins and RNA that translate mRNAs to protein.

Ribozyme - an RNA that can catalyze a reaction. The first known ribozymes were the self-splicing RNAs.

RNA - an acronym for RiboNucleic Acid, a type of nucleic acid related to DNA and which is made from DNA in a process called transcription. RNA is a polymer of ribonucleotides, which are so named because they contain the sugar ribose. Primary RNAs in the cell include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA).

RNA Polymerase - an enzyme that makes RNA from a DNA template using ribonucleotides

RNA Primers - in many DNA replication systems, the primer for replication is actually a short polymer of RNA. Such RNA primers are created by an enzyme called Primase.

rRNA - ribosomal RNA. A class of three (prokaryotes) or four (eukaryotes) molecules of RNA bound in the ribosomes and used in translation.

snRNAs - an acronym for small nuclear RNAs, snRNAs are components of snRNPs - ribonucleic acid-protein complexes involved in splicing RNAs in the nucleus of eukaryotic cells. snRNAs include U1, U2, U5, and U4/U6.

snRNPs - a complex of (usually) a single snRNA and several (about 10) nuclear proteins. snRNPs bind to the RNA that is to be spliced and catalyze the excision of the introns and covalent joining of the exons. The resulting intron structure from this reaction is in the form of a lariat. snRNPs are named for the snRNA(s) they contain.

Southern blotting - technique for detecting and identifying trace quantities of DNA after they have been separated by gel electrophoresis. See Northern blotting and Western blotting.

Spliceosome - a protein/RNA structure (composed of RNAs to be spliced and snRNPs) where introns are removed from RNAs and the exons are joined together.

Splicing - a process occurring almost exclusively on eukaryotic genes in which introns are removed from RNAs and exons are put together to make a gene sequence ready for translation. Splicing occurs in the nucleus of eukaryotic cells.

Supercoiling - word used to describe alterations of a DNA helix that underwind (negative supercoiling) or overwind (positive supercoiling) the most relaxed form of the DNA. See topoisomerases.

TATA Box - a region rich in the sequence A-T found about 25 base pairs before the startpoint of eukaryotic transcription start point or about 10 base pairs before the startpoint of a prokaryotic transcription start point.

Telomere - structure found a t the end of a eukaryotic chromosome. Has a distinct repetitious sequence within the DNA.

Telophase - fifth part of the cell cycle during which chromosomes reach the poles of a cell.

Template - strand of nucleic acid copied by a polymerase.

Thymine - a pyrimidine base found in DNA and RNA (rarely). See picture.

Thymine Dimers - when DNA is exposed to ultraviolet (UV) light, adjacent thymine residues can become covalently lined together. (See picture)

Transcription - the process by which RNA is copied from DNA.

Transcription Factors - proteins that bind to DNA promoter sequences, facilitating binding of RNA polymerase. Eukaryotic RNA polymerases do not bind to promoters on "naked" DNA.

Translation - The process by which information in DNA is ultimately converted to make a protein. Information is initially passed from DNA to mRNA. Ribosomes "read" the sequence of bases in mRNA and sequentially attach amino acids (via peptide bonds) corresponding to what they read.

Transposon - a "mobile genetic element". Transposons are pieces of DNA that are capable of moving from one chromosomal location to another, or from a chromosome in one cell to a chromosome in another cell.

tRNA - transfer RNA. Small RNA molecules containing an anti-codon loop at one end (for pairing with codons during translation) and an amino acid covalently linked to the 3' end of the strand at the other end. Amino acids are specific to the anti-codon on the tRNA.

Upstream - molecular biology lingo meaning 5' to a defined point. The initiation site of transcription might be described as upstream of the termination site. See downstream.

Uracil - a pyrimidine base found in RNA. See picture.

Vacuole - cellular structure that performs functions of storage and/or degradation of materials. Vacuoles are very prominent in plant cells.

Western blotting - technique for detecting and identifying trace quantities of protein after they have been separated by gel electrophoresis. See Southern blotting and Northern blotting.

Wild Type - DNAs that have been mutated are described as mutated or mutant. Unmutated DNAs are called wild type. The terms wild type and mutant are also used to describe proteins or cells resulting from these mutations.



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