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Biology Definitions

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D SegmentAntibodies are created by the stochastic (random) splicing of three different gene sequences: a V Segment, a J Segment, and a D Segement. In this way, the immune system can create many different antibodies. Note that the joining of the V, J, and D segment is somewhat sloppy, resulting in even more mutations and variations in antibodies.Antibody, Antigen
dATPA deoxynucleotide with Adenine (A) as its organic base. A purine nucleotide used as a monomer to create DNA polymers. The "TP" stands for Triphosphate.Deoxynucleotide, Purine, Monomer, Polymer
dCTPA deoxynucleotide with Cytosine (C) as its organic base. A pyrimidine used as a monomer to create DNA polymers. The "TP" stands for Triphosphate.Deoxynucleotide, Pyrimidine, Monomer, Polymer
Dehydration ReactionA chemical reaction in which two molecules are joined together and a water molecule (H20) is released. Also known as a condensation reaction.Esterification, Condensation Reaction, Peptide Bond, Polymer
DenatureTo change the structure of a molecule with heat, alkali, acid or some other means. Examples include separating the strands of a DNA molecule, and changing the structure of a protein to prevent it from performing its function. Protein, DNA, Alkali, Acid
DendriteDendrites are branch-like projections from a neuron that receive electrical signals from other neurons. These electrical signals are then transferred to the cell body of the neuron, changing the electrical potential of the cell-wall, and sometimes causing an Action PotentialNeuron, Hillock, Action Potential
Dendritic CellA type of immune cell used in the regulation and activation of the immune system. Dendritic cells engulf molecules and microbes that they encounter, break them up into small pieces (oligopeptides), and present these pieces (antigens) on their surface. A Dendritic cell can bind to a T Helper Cell which has the same antigen on its surface, and thus activate the T Helper Cell, initiating an immune response. Although similar to Macrophages, Dendritic cells tend to inhabit the Lymph Nodes, whereas Macrophages are found throughout the body and tissues.Immune System, Antigen, MHC class II, T Helper Cell, B Cell, MHC Class II
DeoxynucleotideNucleotides which are used to create strands of DNA. The term "nucleotide" describes both RNA and DNA monomers, but the term "Deoxynucleotide" describes a monomer that can only be used to create a polymer of DNA.Nucleotide, DNA, Monomer, Polymer
dGTPA deoxynucleotide with Guanine (G) as its organic base. A purine nucleotide used as a monomer to create DNA polymers. The "TP" stands for Triphosphate. Deoxynucleotide, Purine, Monomer, Polymer
Differentiated CellsCells in the body are called "differentiated" if they have specialized, for example, turned into neurons or liver cells. Very often, differentiated cells are also postmitotic cells.Cell Cycle, Post Mitotic
DiploidA cell is diploid if it has a pair of each type of chromosome. Somatic cells are diploid.Haploid, Chromosome, Somatic, Diploid
Directed MutagenesisA method of gene sequence analysis which follows variations on the following procedure: 1.). A scientist takes a sequence of DNA, and mutates it in-vitro, by changing one of its bases, deleting one or more of its bases, or adding a new segment of DNA. 2.) The scientist then replaces the organism's gene with the new gene (perhaps by injecting it into a newly fertilized egg) 3.) The scientist then checks the phenotype of the individuals with the known changes (or deletions) in their genome.In Vitro
DNADNA is a macromolecule which contains the instructions which tell the cell how to produce proteins. It can be replicated so that the cell's hereditary information can be passed on to two daughter cells. It can be transcribed into RNA, which can then be translated into proteins. A DNA monomer is comprised of a sugar (2' Deoxyribose), a base (Adenine, Guanine, Cytosine, or Thymine), and a Triphosphate. The energy of the Triphosphate is used to form the DNA into a polymer. The order of the bases (A, T, C, and G) in the resulting DNA polymer determine the order of the amino acids in the proteins that are produced by the cell.RNA, Base Pairing
DNA CloningScientists who wish to "purify" (separate out) all the genetic sequences in a genome utilize variations on the following DNA cloning procedure: 1.) Cut DNA into fragments at defined sites. 2.) Paste (ligate) each fragment of DNA into a bacterial DNA vector which is capable of replicating within a bacterial cell. 3.) Put ("Transform") DNA into a bacterial host cell 4.) Plate transformed bacterial cells, and "select" only those that have been "transformed" . Note that the usual biochemistry purification techniques cannot be used to isolate genes because the genes in a genome are too similar to each other in terms of weight, charge, etc.Recombinant DNA, Gene, Genome, Transform, Library, Restriction Enzymes, Episome
DNA PolymeraseOnce a primer has initiated DNA Replication, the enzyme DNA Polymerase is used to add nucleotides onto the 3' end of the new DNA strand. DNA Polymerize adds a DNA Adenine (A) to the new strand when it sees a Thymine (T) on the old strand. Similarly when it "sees" a Thymine (T) it adds an Adenine (A), when it detects a Guanine (G) it adds Cytosine (C), and a Cytosine (C) on the original strand results in a Guanine on the new strand. The Triphosphate of the nucleotide is broken down in a dehydration reaction (losing 2 phosphates), and giving its energy to the polymerization reaction (creating a covalent bond between a sugar and phosphate, forming the backbone of the DNA strand). Because DNA Polymerase occasionally makes a mistake, adding an incorrect base which does not complement the parent strand, it performs a DNA Proofreading activity, in which it continuously removes bases (exonuclease activity) it has just added, removing incorrect bases more often than it removes correct bases. DNA Polymerase can process about 2000 nucleotides per second.DNA, Polymerase, Primer, Enzyme, Nucleotide, Triphosphate, DNA Polymerase
DNA Polymerase 1DNA Polymerase 1 was originally believed to be the enzyme which polymerized entire DNA chromosomes. It was later found to be a Repair Enzyme which is used to fill in gaps. DNA Polymerase 3 was discovered to be the main DNA polymerization catalyst.Detect and Repair Enzyme, DNA, Replication, Polymerase
DNA ProofreadingDuring DNA Replication, DNA Polymerase is supposed to add a complementary base (A->T, T->A, C->G, G->C) to the new DNA strand. Occasionally, it will make a mistake. For example, it might "read" an Adenine (A) on the parent strand, but then place a Guanine (G) instead of a Thymine (T) on the new strand. Proof reading mechanisms then try to correct this to avoid mutations. DNA Polymerase has an Exonuclation Actvity which performs proofreading, and there are also Detect and Repair Enzymes that can find and fix mutations.DNA, Replication, Exonuclease Activity. Mismatch Detection and Repair Enzymes
DNA RearrangementOne of the rarer forms of Gene Regulation, DNA Rearrangement involves the rearrangement of sections of DNA. For example, some immune system cells rearrange DNA into new sequences, and some bacteria actually "flip" sequences in their chromosome to turn genes on or off.Gene Regulation
DNA Sequence AnalysisA scientist with a DNA sequence is confronted with a number of problems when trying to analyze the sequence for genes. When looking at long sequences of DNA letters, the scientist does not know in advance which of the two complementary strands the gene is coded on, and which of three possible reading frames (for a given strand) that the gene resides on. The scientist may try looking for start codons (ATG), The scientist may also try to solve this problem by looking for long sequences that do not contain a stop codon (there are three, which can appear randomly in approximate every 20 base pairs of a non-coding sections). The scientist may also compare the genomic sequence to cDNAs. When analyzing human DNA, the scientist may take into account that human genes appear to prefer certain stop codons, and may also compare the human genome to the mouse genome, knowing that exon sequences are generally preserved between species while intron sequences generally are not.DNA Cloning, Shotgun Sequencing, Start Codon, Stop Codon, cDNA
DNA SequencingScientists who wish to determine the sequence of a DNA strand utilize variations on the following DNA sequencing procedure: 1.) Heat up the DNA to break the hydrogen bonds between the two strands, thus separating them. 2.) Add primer, DNA Polymerase, and nucleotides (dATP, cCTP, dGTP, and dTTP) to the solution. 3.) Choose a nuclelotide (e.g. dATP), and add additional "defective" versions of this molecule to the solution. For example, removing a hydroxyl group from a nucleotide will make it "defective", causing DNA Polymerase to stop the polymerization process after adding the defective nucleotide to the strand. 4.) Use Gel Electrophoresis to measure the lengths of the strands. 5.) Repeat the process 3 more times, but using defective dCTP, then defective dGTP, and finally defective dTTP. By comparing the results of the Gel Electrophoresis, the scientist can read out the locations of the bases. To make it easier to read the gel, you can use radioactive labeled primer, or use dNTPs which have flourescent dyes attached. Sanger won a Nobel prize for inventing this technique.DNA Cloning
dNTPDeoxynucleoside Triphosphate (note that we say "nucleoside" and not "nucleotide" because we are explicitly mentioning the triphosphate). dNTP is used to describe any one of the following: dATP, dCTP, dGTP, dTTPdATP, dCTP, dGTP, dTTP, Nucleoside, Nucleotide
Double-Stranded DNA VirusA virus that uses a double-stranded DNA genome as its genetic material. 22 families of virus use double-stranded DNA, including Poxvirus, Adenoviruses, Herpes Virus, Papillomavirus, Polyoma Viruses. Some of these use linear DNA (Poxvirus, Adenovirus), and some use circular DNA (Polyoma Viruses, Papillomavirus)Baltimore Scheme, Viral Genome
Double-Stranded Gapped DNA VirusA type of virus that uses double-stranded DNA, but some of the DNA is missing ("gaps"), so that some of the DNA is single-stranded. Hepatitis B virus has a double-stranded, gapped DNA genomic structure (additionally, it includes a protein attached to the DNA, and also a small piece of single-stranded, plus-polarity RNA). When the virus enters the cell, it begins its replication cycle by filling in the missing DNA in the "gap", and then creating mRNA from the now complete double-stranded DNA. Note that RNA polymerases require a double-stranded DNA in order to transcribe mRNA.Double-Stranded DNA Virus. Baltimore Scheme, Viral Genomes
Double-Stranded RNA virusA type of virus that has a double-stranded RNA genome. Note that double-stranded RNA cannot be translated (only single-stranded RNA can be used to create mRNA). Instead, the virus carries in an enzyme that can create single-stranded, plus-polarity RNA from the double-stranded template. Rotavirus is an example of a double-stranded RNA virus.Baltimore Scheme, Viral Genomes
dTTPA deoxynucleotide with Thymidine (T) as its organic base. A pyrimidine used as a monomer to create DNA polymers. The "TP" stands for Triphosphate.Deoxynucleotide, Pyrimidine, Monomer, Polymer

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