Molecular Biology for Computer Scientists,
Mathematicians and Engineers
BIO 5099 (3 credits)
CU Denver/Auraria Library 004 (Directions)
Tuesdays and Thursdays, 4:00-5:15pm
TA office hours Tuesdays 1:30-2:30pm (Directions)
Available by video links on other campuses
Prof. Larry Hunter
Office: SoM #2817b
Office phone: 303-315-1094
E-mail: Larry.Hunter@ucdenver.edu
http://compbio.ucdenver.edu/Hunter/
Home Syllabus Glossary Lecture Notes Homework Project/Exam

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These terms are linked to the Oxford Dictionary of Biology when possible. Other sources include the National Human Genome Research Institute's Talking Glossary (including pronunciations!) and the DoE Human Genome Project Glossary. When no official source is available, you get our definition.

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Acid
Acid Hydrolytic Enzyme
Actin
Activation Energy
Activator
Active Site
Activity (In Chemical Sense)
Adaptation
Adenine
Adenosine Triphosphate (ATP)
Adiabatic
Advantageous mutation
A mutation that increases the reproductive fitness of the organism carrying it.
Affinity (Enzyme)
Allele
Allosteric
Allosteric Regulation
Alpha Carbon (Amino Acid)
Alpha Helix
Alpha-Ketoglutarate
An intermediate in the Krebs cycle. Interconversion between this molecule and the amino acid glutamate is the gateway for nitrogen incorporation in the cell. See, e.g. http://www.orst.edu/instruction/bb450/winter2002/ch14/akglut.htm
Amino Acid
Anabolic Metabolism
Angiosperms
Anhydrous
Aqueous Solution
Archaea
Aromatic
Assortive mating
Non-random selection of mating partners with respect to one or more traits; it is positive when like phenotypes mate more frequently than would be expected by chance and is negative when the reverse occurs. [Source: GrowFAQ]
Atom
ATP Synthase
The enzyme which exploits a proton gradient to phosphorylate ADP to ATP, creating usable energy for the cell. Its mechanism involves circular motion. See, e.g. http://www.csun.edu/~hcchm001/wwwatp2.htm
Attenuation
Autosomal
Any chromosome that is not involved in determining an organism's sex. Humans have 22 pairs of autosomal chromosomes in each cell. [Source: PhRMA Genomics Lexicon]
Autotroph
Balanced polymorphism
Base
Beta-Oxidation
Bilateria
Taxon containing all organisms with bilateral symmetry.
Binary Fission
Biochemistry
Bond Energy
Budding
Carbon
Carbon Chain
A series of bonded carbon atoms in an organic compound. Compounds can involve straight chains (each carbon atom is bonded to one or two others) or branched chains (at least one carbon atom is bonded to three or more other carbons).
Catabolic Metabolism
Cell Cycle
Cell membrane
Cell Wall
Cenancestor
See Universal Ancestor
Central Dogma
Centromere
(Membrane) Channel
Charge
Chemical Bond
Chemical Properties
Things such as reactivity, oxidation states, flammability, and corrosiveness. [Source: Chemical Glossary]
Chemical Reaction
Chemoautotroph
Chemotaxis
Chirality
Chloroplast
Chloroplasts
Chordata
Chromatid
Chromatin
Chromosome
Cisternae
Cladistics
Coding Region
Portions of a DNA molecule that encode a protein or functional RNA.
Coenzyme
Coevolution
Commensalism
Committed Step
The first irreversible reaction in an enzymatic pathway
Competition
Compound
Concentration
Conformation
Constitutive
Genes which are always expressed in a cell. Compare inducible expression.
Covalent Bond
Cristae
Cytochrome
Cytokinesis
Cytoplasm
Cytoplasmic Dynein
Cytosine
Cytoskeleton
Cytosol
Deleterious mutation
A mutation that decreases the reproductive fitness of the organism carrying it.
Dinitrogen Heterocycle
a heterocyclic compound with two nitrogen atoms in the ring.
Diploid
Directional selection
Diversifying selection
The natural selection strategy by which multiple phenotypes in a population are favored in different environments. Diversifying selection results in an overall increase in genetic diversity. [Source: about.com]
DNA Gyrase
DNA Helicase
A class of enzymes which unwind DNA, e.g. for replication.
DNA Ligase
DNA Polymerase
DNA Primase
DNA Sequence
Dominant
Dynamic Equilibrium


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Efficiency (Enzyme)
Kcat/Km (constant part of Vmax/Km) from Michaelis-Menton kinetics. Intuitively, the rate at which an enzyme converts a bound substrate into product. Compare affinity.
Electron
Electron Transport Chain
Electrostatics
Element
Elongation Factor (Ribosome)
Endomembrane System
Endothermic
Entropy
Enzyme
Equilibrium Constant
Escalation
A kind of preditor/prey coevolution in which attacks and defenses become increasingly effective. Controversial because it implies evolutionary progress over time
Essential Amino Acids
Euchromatin
Eukaryotes
Evolution
Exaptation
Exonuclease
Exothermic
Expression (Of A Gene)
Extremophiles
Feedback Inhibition
Fermentation
Fitness
Fitness landscape
A surface in genotype space indicating the fitness of each genotype.
Flagellum
Fluorescent In Situ Hybridization (FISH)
A process by which specific molecules are tagged with fluorescent markers while still active in a cell. Used for visualizating the location (or change in location) of molecules in a cell.
Founder Effect
Function
The role or activity of a biological entity. Ultimately connected with reproductive fitness (although often quite indirectly).
Functional Group
Fungi
Gene
Gene flow
Genetic Bottleneck
An extreme examples of genetic drift due to a population passing through a generation with a small number of individuals
Genetic Drift
Genetic Recombination
Genome
Genotype
Gibbs Free Energy
Gluconeogenesis
Glutamine
Glycine
Glycogen
Glycolysis
Golgi Complex
Green algae
Guanine
Hardy-Weinberg Equations
Heterochromatin
Heterocyclic
Heterotroph
Heterozygotic
Hexose
Histone
Homologous Recombination
The exchange of very similar regions from two different DNA molecules. Compare to Transpositional and Site-Specific recombination.
Homozygotic
Horizontal (Or Lateral) Transmission
The transmission of genes among organisms other than parent to offspring. For example, from a virus to host.
Hydrogen Bonds
Hydrolase
Hydrolysis
Hydrophilic
Hydrophobic
Hydrophobic Core (Protein)
the central (not surface) region of a protein. Generally a compact, non-dynamic region that is not solvent accessible.
Hydrophobic Effect
The tendency of nonpolar groups to cluster so as to shield themselves from contact with an aqueous environment. [Source: Glossary of Organic Chemistry Terms]
Inbred strain
A stock of organisms that are essentially identical as a result of the crossing of closely related plants within a species. [Source: Agricultural Genome Information System, USDA]
Inbreeding
Inducible
Genes which are expressed intermittantly in a cell. The timing and extent of expression is controlled by transcription factors.
Inheritance
Initiation Factor (Ribosome)
Intermediate Filaments
Intermediates (Metabolic)
Intermolecular Forces
Internal Energy
Ion
Ion Product Constant
The product of concentrations of hydrogen and hydroxide ions in a solution. [OH-][H+] = 10-14
Ionic Bond
Isomer
Isomerase
Isotope
Karyotype
Kinetochore
Km
Krebs Cycle


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Lagging Strand
Lamarckian Inheritance
An erroneous theory, perpetuated by Jean- Baptiste, Chevalier de Lamarck, stating that, if an individual strives in a certain direction, any resulting change will be passed on to the next generation. A giraffe, for example, that is constantly reaching for higher leaves, will lengthen its neck. This longer neck would then be passed to the giraffešs offspring. Of course, such acquired characteristics do not translate into genetic change, and therefore arenšt subject to heredity. [Source: After Darwin Glossary]
Leading Strand
Lewis Diagram
Ligase
Linkage
Linkage map
Linnean name
The official (Latin) naming of an organism by its genus and species.
Lipid
Lipid Bilayer
Lyase
Lysosome
Macroevolution
Macromolecule
Mass Extinction Event
A mass extinction is a relatively sudden, global decrease in the diversity of life forms. [Source : Paleontology and Geology Glossary]
Matter
Meiosis
Membrane
Mendelian Inheritance
The mode of inheritance of nulear genes, in contrast to "non-Mendelian" or "extra-nuclear" inheritance which is controlled by cytoplasmic heredity determinants. [Source: Agricultural Genome Information System, USDA]
Metabolic Pathway
Metabolism
Metabolite
Metazoa
Methylation
Michaelis-Menton Kinetics
Microevolution
Microfilaments
Microtubule
Mitochondria
Mitosis
Mixture
Mole
Molecule
Monogenic
Controlled by a single gene.
Mutation
Mutation (DNA)
Mutualism
Myosin
Natural Selection
Network Autocatalytic
A mechanism of self-replication that involves a series of reactions which recreates itself. For example, the substrates in the Krebs cycle. Compare to Template autocatalytic
Neutral Lipid
Lipids which at cellular pH, they bear no charged groups. Generally, they are completely nonpolar, with no affinity for water.
Neutral Mutation
A mutation that has no effect on the Darwinian fitness of its carriers, or a mutation that has no phenotypic effect. [Source: Genetics Glossary]
Neutron
Niche
Nicotinamide Adenine Dinucleotide (NAD / NADH)
Nuclear Envelope
Nuclear Matrix
Nuclear Membrane
Nuclear Pore
Nuclear Scaffold
The skeleton of the nucleus which provides structure for the chromosomes and the protein complexes involved with the replication and transcription of DNA. Regions of DNA called scaffold-attached regions (SARs) are AT-rich sequences that bind to the nuclear scaffold.
Nucleic Acid
Nucleolus
Nucleosome
Nucleotide
Nucleotide Excision Repair
A process of DNA repair by which a defective base pair is removed from a newly replicated strand DNA.
Nucleus
Offspring
Okazaki Fragments
Operon
Orbital
Organelle
Osmotic Lysis
Oxidation
Oxidation State
Oxidative Phosphorylation
Oxidoreductase
Parasitism
Parent
Pathogen
Pedigree
Peptide Bond
Peptidoglycan
Perinuclear Space
Periodic Table Of The Elements
Peroxisome
pH
Phage
Phenotype
Phi Angle
The dihedral angle defined by the alpha carbon and the carboxy carbon of one amino acid with the amino nitrogen of an amino acid bonded to it by a peptide bond.
Phosphofructokinase
Phosphoglyceride
Phospholipid
Phosphorylation
Phosphotidyl Choline
Photoautotroph
Photosynthesis
Phylum
Physical Properties
Things such things color, density, hardness, ductility, malleability, solubility, heat conduction, electrical properties, melting and boiling point. Compare chemical properties
Plasmids
Pleiotropy
Polar Covalent Bond
Polygenic
Polymer
Polymorphism
Polypeptide
Polyploidy
Population
Population Genetics
Primary Structure (Protein)
Processivity
The effectiveness of a DNA polymerase. A polymerase which creates new DNA strands at a high rate is said to have high processivity.
Products
In a chemical reaction, the componds produced.
Prokaryotes
Promoter
Protein
Protist
Protist
Proton
Proton Motive Force
The force exerted by a proton gradient across a membrane.
Psi Angle
The dihedral angle defined by the carboxy carbon in one amino acid and the amino nitrogen and alpha carbon of an amino acid bonded to it by a peptide bond.
Punnett Square
Pure
A substance that cannot be physically separated into fractions with different chemical properties.
Purine
Pyrimidine
Pyruvate


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Quaternary Structure
Random Coil
The name for a region of a protein with no (other) recognizable secondary structure.
Rate Limiting Step
Reactants
Recessive
Redox Reaction
Reduction
Replication Fork
Replication Initiation Complex
The collection of DNA-bound proteins necessary to begin replication of the DNA molecule.
Replication Initiation Site
Replicon
Repressor
Respiration
Reversable Reaction
Ribosomal Large Unit
Ribosomal Small Unit
Ribosome
RNA Secondary Structure
Watson-Crick pairing within an RNA molecule, creating stem and loop structures.
Rough Endoplasmic Reticulum
rRNA
Saturated
Saturated (Enzyme)
Secondary Structure (Protein)
Selection
See Natural Selection
Self-replication
Creating a (perhaps imperfect) copy of one's self.
Semi-Conservative Replication
Sequence
Side Chain
Signal Recognition Complex
Signal Transduction
Site-Specific Recombination
Exchange of regions from two different DNA molecules by means of enzymes which recognize particular short sequences. The recognition sequences are the sites of recombination.
Small Molecule
A molecule of relatively low weight, perhaps less than 100 atoms; the opposite of a macromolecule.
Smooth Endoplasmic Reticulum
Solute
Solution
Solvent
Speciation
Species
Species (Chemical)
A pure chemical substance, such a molecule, ion or atom
Stabilizing selection
Stegocephalians
A taxon of terrestrial vertebrates and other vertebrates that bear limbs with digits rather than fins. [Source: Tree of Life]
Stoichiometric Coefficients
Structure
Subatomic Particle
Substrate
Supercoiling
Symbiosis
Taxis
Taxon
Taxonomy
Telomerase
Telomere
Template Autocatalytic
A mechanism of self-replication that involves a polymerization reaction that is organized by an existing (template) polymer. For example, the replication of DNA. Compare to Network Autocatalytic.
Termination Factor (Ribosome)
A set of enzymes that frees a newly synthesized protein from the ribosomal substrate on which it was created.
Tertiary Structure
Thermodynamic Feasibility (of a reaction)
A reaction with negative delta-G is said to be thermodynamically feasible. Intuitively, the reaction can take place without an additional input of energy. Not all thermodynamically feasible reactions occur spontaneously; see activation energy.
Thermodynamics
Thymine
Topoisomerase
Trait
An inheritable characteristic.
Transamination
Transcription
Transcription Factor
Transcription Factor Binding Site
A DNA sequence that is specifically recognized by a transcription factor.
Transferase
Translation
Transmembrane Region
A portion of a protein that passes through a bilipid membrane. These regions are typically extended and contain hydrophobic amino acids.
Transpositional Recombination
A process that inserts a mobile genetic element into a region of DNA. Mobile genetic elements include transposons, which are operons containing DNA splicing enzymes.
Transposons
Triose
Tubulin
Ubiquinone
Universal Ancestor
The most recent common ancestor of all extant life forms. Also known as the cenancestor.
Vacuole
Valence
Van Der Waals Force
Variation
Vesicle
Virus
Vmax
Water
Watson-Crick Base Complementarity
Yeast

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Home Syllabus Glossary Lecture Notes Homework Project/Exam

This document last modified 08/09/10 13:08.