Biology Flash Cards

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Biology Definitions

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Partial DigestionsA scientist engaged in a DNA Cloning procedure is presented with the following problem. The restriction enzyme used may cleave the middle of a given gene (because it contains the target sequence of the restriction enzyme). Because the scientist wants the final "library" to contain full copies of all genes, the scientist can ensure that the part of the cloning procedure that uses restriction enzymes is not allowed to run to completion, and thus some DNA sequences will not be cleaved at the restriction point, allowing all possible DNA sequences to appear in the final DNA library. This is known as "Partial Digestion", and is also referred to as one of many "cooking tips" used in DNA Cloning.DNA Cloning
PathogenesisThe study of how a disease is caused.Virus, Bacteria, Parasite, Transform, Cancer Cells
PathogenicCapable of causing disease. For example, the wild-type Polio Virus can cause severe disease, but "attenuated" polio virus does not cause disease, and can be used as a vaccine. 
PCRPolymerase Chain Reaction; a techique that allows scientists to re-sequence a gene. That is, having the genomic sequence for a given individual of a species, PCR allows scientist to sequence the gene from another individual without all the work of creating an entire Library of Clones for the second individual. By just using a short, known sequence of the primer of the gene, the scientist is able to "amplify" the genetic sequence from another individual, allowing her to study differences (alleles) in the gene between individuals. The PCR procedure consists of variations on the following steps: 1.) Heat up a strand of DNA (to about 97 degrees celsius), to denature it, breaking apart the hydrogen bonds that hold the two complementary strands together. 2.) Determine which primer precedes the gene of interest (from the previously sequenced genome, typically about 20 bases). 3.) Synthesize (or order from a catalog!) two primers, one which matches that found in Step 2, and one which is complementary to that sequence. 4.) Add DNA Polymerase and dNTPs to the solution. 5.) Allow DNA Polymerase to create new strands from each of the primers and original DNA strands. At this point, you have doubled the number of copies of your gene. 6.) Repeat steps 1-5, again doubling the number of copies of the gene. Continue this process until you have enough copies of the gene for analysis.DNA Cloning, Denature, Polymerase, dNTP, Primer, Thermus Aquaticus
PCR ApplicationsPCR can be used for many real-world applications, including: 1.) Re-sequence a gene, 2.) Checking for a virus in a blood sample. 3.) Single Sperm Typing (amplying one gene from a single sperm) 4.) Embryo Typing (In Vitro Fertilization clinics use the technique to grow a fertilized egg to 8 or 16 cells, and then use one of the cells to check for genetic diseases using PCR. 5.) Surveillance for low quantities of cancer cells (with known mutations), particularly after a cancer patient has undergone treatment. 6.) Forensics applications which can distinguish people based on various known genetic variations.PCR
PDGFPlatelet Derived Growth Factor. When Platelets form clots, they give off Growth Factors which "tell" the surrounding cells that they should grow and divide, and thus repair the wound. PDGF is dimeric (it has two parts), and it can thus bind to two PDGF receptors on a cell. When two trans-membrane PDGF receptors are brought together (because they are both bound to the same PDGF ligand), they create a growth signal within the cell. The growth signal is initiated when the Tyrosine Kinase domains of the two PDGF receptors are brought together, and the two molecules phosphoralate each other. The many phosphoralted Tyrosines then act as docking sites for other signalling proteins.Platelet, Serum, Tyrosine Kinase, Ligand
PedigreeA chart of an individual's ancestors which shows which members of an extended family have or had a given disease or phenotype. Used by geneticists to analyze a mutataion and determine if it is recessive or dominant, sex-linked or sex-limited, incompletely dominant, etc.Genetics, Recessive, Dominant, Sex-Linked, Sex-Limited
PelletThe settled precipitate at the bottom of a tube after a substance has been centrifuged. Centrifuge, Supernatent
PeptideA molecule consisting of 2 or more amino acids. The carboxyl group of one amino acid links to the amino group of another amino acid.Polypeptide, Amino Acid, Carboxyl Group, Amino Group, Protein
Peptide BondThe chemical bond that binds amino acids together to form a protein. The Peptide bond links the carboxyl group (COOH) of one amino acid to the amino group (NH2) of another amino acid, creating the bond (CONH) and releasing a water (H2O). This bond is formed via a condensation (a.k.a dehydration) reaction.Peptide, Protein, Amino Acid, Carboxyl Group
PeriplasmThe region between the outer cellular membrane and inner cellular membrane of a bacterial cell.Prokaryotes, Bacteria
Phage"Phage" is a shortened version of the word "Bacteriophage". "Phage" means "to eat". Another name for a virus that attacks bacteria.Bacteriophage, Virus
Phagocytic CellA cell that is able to digest other things (other cells, waste materials, etc.). Macrophages are an example of phagocytic cells.Cellular Immunity, Macrophage.
PhenotypeAn observable, measurable characteristic of an organism. The physical manifestation of the genotype as a particular trait. For example, some peas can have a phenotype of roundness while others have a phenotype of roughness. Genotype
PhosphataseAn enzyme that removes phosphate groups from another molecule. Typically, a protein phosphatase enables or disables a biochemical pathway by removing a phosphate group from a protein in that pathway; by removing the phosphate group, that section of the protein can become a binding site for other molecules, or, in other cases, the lack of a phosphate will prevent binding.Kinase, Enzyme, Protein
PhosphotyrosineA tyrosine that has been phosphoralated (had a Phosphate group added to it). A PDGF molecule can bind to two PDGF receptors, bringing them near each other, and allowing their Tyrosine Kinase domains to phosphorolate each other, and the Phosphotyrosine's create docking sites for other signalling proteins, thus enabling the biochemical pathway that causes the cell to grow and divide.PDGF, Tyrosine Kinase, Cell Cycle
Pinocytosis"Cell-drinking". A type of Endocytosis which imports small molecules into the cell via small vesicles which are subsequently sent to lysosomes which break down ("hydrolyze") the imported particles. Pinocytosis requires a lot energy in the form of ATP,Endocytosis, ATP
PlaqueWhen a scientist plates out bacteria on a petri dish, the empty sections of the "lawn" (perhaps containing bacterialphage which have killed the bacterial cells) are called plaques. Lawn
Plasma CellA subset of B Cells which secrete antibodies into serum (plasma). Each plasma cell is responsible for producing and secreting one particular kind of antibody. Plasma cells are produced after a parent B Cell is exposed to its matching antigen.B Cell, Serum, Antigen
Plasma MembraneThe cell's outer membrane which separates the cell's contents from the outer environment. It is made up of lipids and proteins, and regulates what can enter and exit the cells. In Eukaryotes, it is the outermost covering of the cell. In plants, fungi, and some bacteria, there is an additional outer cell wall. Also called the "Cell Membrane".Prokaryotes, Eukaryotes, Cell Wall
PlasmidLinear or circular double-stranded DNA that is separate from a cell's chromosomes, and is able to replicate autonomously. Usually found in Prokaryotes, and often used for recombinant DNA. A type of Episome.DNA, Chromosome, Bacteria, Episome
PlateletesFragments of anucleated (having no nucleus) bone marrow cells found in the blood that prevent bleeding by forming clots. As the platelets form a clot, they also release growth factors (platelete derived Growth Factor, PDGF) which are used to notify cells in the damaged area that they need to grow and divide in order to repair the damage.Serum
Plus Polarity (a.k.a. "Plus Strand)An mRNA has "plus polarity" if it can be directly translated by the host ribosome. The complementary strand of a "plus polarity" mRNA molecule is said to have "negative polarity". A DNA molecule has "plus polarity" if it can be transcribed into mRNA. Note that the complement of a plus strand DNA molecule has "negative polarity". Note that the polarity of a DNA or RNA strand has nothing to do with its electrical characteristics.Virus, Viral Genomes, Baltimore Scheme
Polio VirusVirus with a single-stranded, polyadenylated (poly-A tail, which allows it to serve as messenger RNA), plus-polarity (can be translated immediately) RNA genome, encapsidated in a proteinaceous coat made up of viral proteins. Polio virus creates its own polymerase which converts the single-stranded RNA into double-stranded RNA, and the new strand of RNA is then used to make more progeny RNA. Since no DNA is involved, Polio Virus can even grow in a cell that has been deprived of its nucleus. The virus invades the gastrointestinal track, causing mild diarrhea. In 1 out of 100 persons, the virus escapes from the GI track, and invades the central nervous system, causing paralysis. Polio Virus is a highly cytopathic virus.Virus, Polymerase, Immunology
Poly (A) TailIn Eukaryotic cells, a sequence of nucleotide A's is added to the end of the messenger RNA before it exits the nucleus. The length of the Poly (A) Tail appears to regulate degradation of mRNA. mRNA's with shorter tails are degraded much more rapidly. Knowing that A binds to T, biochemists sometimes use Poly (T) tails to purify messenger RNA from cell solutions. Biochemists can also use a sequence like this TTTTT as a primer when using reverse transcriptase to clone the RNA into DNA (e.g. to turn a human gene, such as the gene for insulin, into a gene that can be transcribed by bacteria, since bacteria cannot do RNA splicing).Cap, Transcription, Messenger RNA
Polycistronic MessageIn Prokaryotes, a single messenger RNA (mRNA) can contain the code for multiple proteins. Different sections of the mRNA are translated by different ribosomes into different proteins. This type of mRNA is called "Polycistronic". Often, these messages contains the code for multiple proteins in the same biochemical pathway, giving the bacteria efficiencies in the regulation of said pathway.Operon, mRNA, Translation, Prokaryote, Ribosome
PolymerA complex molecule made up of many small, simple, repeated units (monomers) which are linked together. For example, DNA is a polymer, and it's monomer units are nucleotides.Monomer, DNA, RNA, Carbohydrate, Protein, Nucleotide
PolymeraseAn enzyme that adds monomers to a polymer. For example, DNA Polymerase adds DNA monomers to a strand of DNA.DNA, Enzyme, Monomer, Polymer
PolypeptideA peptide containing many amino acids. Polypeptide typically have at least 10 amino acids. Proteins are polypeptides.Peptide, Protein, Amino Acid
Post-Translational RegulationA type of Gene Regulation that happens after the Protein has been Translated. For example, a protein may be completely inactive until another protein has added a Phosphate to it (conversely, a protein may be inactive until a Phosphate group has been removed). By preventing this phosphoralation, the cell can regulate (turn on or off) the function of this protein.Gene Regulation
PostmitoticA cell is "postmitotic" if it has exited the Cell Cycle and thus can no longer grow and divideCell Cycle, G0 Phase
Primary StructureThe linear sequence of sub-molecules in a macromolecule, without regard to the 3-D structure of the macromolecule. For example, the linear sequence of amino acids in a protein, or the sequence of nucleotides in a DNA molecule.Secondary Structure, Tertiary Structure, Quaternary Structure, Protein, DNA, RNA, amino acid, Nucleotide, Macromolecule
PrimaseThe enzyme which makes a primer (short complementary strand of DNA) which is used to initiate DNA replication. Once DNA replication is started, DNA Polymerase is used to complete the DNA strand.Primer, DNA, Replication, DNA Polymerase
PrimerA short, complementary strand of DNA which is used to initiate the replication of a DNA strand. Primer is created by the enzyme Primase.Replication
PrionA misfolded protein which aggregates with other misfolded proteins into tightly packed sheets which are extremely stable and resistent to denaturation. These sheets of prions act as an infectious agent, causing other proteins to misfold via mechanisms which are not currently understood. Prions are believed to cause mad cow disease, scrapie, and other degenerative diseases. Protein, Denature
ProbandWhen a geneticist creates a pedigree (family tree) to study the inheritance of a particular disease (phenotype), the "proband" is the person for whom the pedigree is being created. The person who came to clinical attention. Also known as the "Index Case"Genetics, Pedigree, Phenotype
ProkaryoteSingle celled organisms that do not have a distinct, membrane-bound nucleus or organelles. Their DNA is not organized into chromosomes. Bacteria and Archaea are Prokaryotes. Prokaryotes typically have double-stranded, circular DNA. Prokaryotes typically have much smaller genomes than do Eukaryotes.Eukaryote, nucleus, nucleoid, organelle, DNA, Bacteria, Archaea
PromoterA section of DNA that tells the RNA Polymerase where the transcription of a particular gene should begin.Transcription
Promoter SiteA site on a gene which determines where RNA Polymerase can begin transcribing an RNA MoleculeTranscribe, RNA, DNA, RNA Polymerase
Proofreading MechanismsDNA Polymerase makes a mistake in about 1 in 10^5 bases. The cell has proofreading mechanisms which repair mistakes in DNA replication, resulting in an error rate of approximately 1 in 10^9 bases. A human cell contains approximately 3 x 10^9 bases, so each replication produces approximately 3 errors.DNA Polymerase, Replication
ProphaseA sub-stage of Mitosis in which the chromosomes condense, becoming visible, the nuclear membrane breaks down, and spindles form on opposites ends of the cellMitosis, Cell Cycle Phases, Interphase
ProteaseA protein (enzyme) that breaks down other proteins into peptides or amino acids.Protein, Enzyme, Amino Acid, Peptide
Protein Shell"Protein Shell" is the third type of virus structural classification (helical symmetry and enveloped being the first two). Many viruses have nucleic acid, surrounded by a protein shell which exhibits Icosehedral Symmetry (20 sided polygon, with equilateral triangles for each face of the polygon). Virus Structure, Viral Envelope, Helical Symmetry, Icosehedral Symmetry
Proto-OncogeneA gene which acts as a precursor to an oncogene (cancer causing gene). A normal gene which can be transformed in a cancer-causing gene. An example would be the proto-oncogene SRC which is present in many eukaryotes, and can be used by Rous Sarcoma Virus (SRV) to transform a cell (make the cell cancerous).Oncogene, SRC
PrototrophAn organism that can grow on minimal media, having the ability to create its own amino acids and other important biomolecules. Geneticists often compare prototrophs (wild type) with mutants (auxotrophs that require compounds not found in minimal media) as a means of studying biochemical pathways. Yeast is a good candidate for these types of experiments.Genetics, Auxotroph, Yeast, Minimal Media
ProtozoaSingle-celled, Eukaryotic organisms, such as amoebas and flagellates; some protozoa are mobileEukaryote
ProvirusRNA Viruses carry an RNA genome and reverse transcriptase into an infected cell. The reverse transcriptase produces DNA from the RNA genome. The DNA produced is called a "provirus". This DNA is integrated with the host cells chromosomes, so that it can produce mRNA (to create viral proteins) and also more viral RNA genome.Virus
Pulse LabelTo add a radioactive atom to a protein or molecule in order to "trace" what happens to the molecule as it reacts with other molecules and moves. This technique can be used to study the transport and export of proteins within the cells via Radiactive Amino Acids.Protein, Amino Acid
PurineAdenine (A) and Guanine (G) are Purines. Purines are slightly larger than pyrimidines.DNA, Pyrimidine, Chargaff's Rules
PyrimidineCytosine (C) and Thymine (T) are pyrimidines. Pyrimidines are slightly smaller than purines.Purine, DNA, Chargaff's Rules

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