CZ:Biology Workgroup/concepts

Basic biochemistry concepts

• Major categories of bio-compounds:
  • Carbohydrates : sugar -- disaccharide -- polysaccharide -- starch -- glycogen
  • Lipids : fatty acid -- fats -- essential oils -- oils -- waxes -- cholesterol
  • Nucleic acids : DNA -- RNA -- mRNA -- tRNA -- rRNA -- codon -- adenosine -- cytosine -- guanine -- thymine -- uracil
  • Proteins :
    • amino acid -- glycine -- arginine -- lysine
    • peptide -- primary structure -- secondary structure -- tertiary structure -- conformation -- protein folding
• Chemical properties:
  • molecular bond -- covalent bond -- ionic bond -- hydrogen bond -- ester -- ethyl
  • molecular charge -- hydrophilic -- hydrophobic -- polar
  • pH -- acid -- alkaline -- base
  • oxidation -- reduction -- hydrolysis
• Structural compounds:
  • In cells: flagellin -- peptidoglycan -- myelin -- actin -- myosin
  • In animals: chitin -- keratin -- collagen -- silk
  • In plants: cellulose -- lignin -- cell wall
• Enzymes and enzyme activity:
  • enzyme kinetics -- enzyme inhibition
  • proteolysis -- ubiquitin -- proteasome
  • kinase -- dehydrogenase
• Membranes : fluid mosaic model -- diffusion -- osmosis
  • phospholipids -- glycolipid -- glycocalyx -- antigen -- isoprene
  • ion channel -- proton pump -- electron transport -- ion gradient -- antiporter -- symporter -- quinone -- riboflavin
• Energy pathways :
  • pigments : chlorophyll -- carotenoids -- xanthophyll -- cytochrome -- phycobilin -- bacteriorhodopsin -- hemoglobin -- myoglobin -- absorption spectrum -- action spectrum -- fluorescence
  • Photosynthesis : light reaction -- dark reaction
  • Fermentation : Acetyl-CoA -- lactic acid
  • Cellular respiration : Adenosine triphosphate (ATP) -- NADH -- pyruvate -- oxalate -- citrate
  • Chemosynthesis
• Regulation
  • hormones : auxin
  • signal transduction -- growth factor -- transcription factor -- protein kinase -- SH3 domain
  • Malfunctions : tumor -- oncogene -- tumor suppressor gene
  • Receptors : Integrin -- transmembrane receptor -- ion channel
• Techniques : electrophoresis -- chromatography -- mass spectrometry -- x-ray diffraction -- Southern blot -- fractionation -- Gram stain

Subdisciplines of biology

Acarology -- Anatomy -- Arachnology -- Biochemistry -- Bioinformatics -- Biomechanics -- Bionomics -- Biophysics -- Biotechnology -- Botany -- Cell biology -- Ecology -- Entomology -- Evolution -- Genetics -- Gerontology -- Herpetology -- Histology -- Ichnology -- Ichthyology -- Immunology -- Limnology -- Marine biology -- Microbiology -- Molecular biology -- Mycology -- Myrmecology -- Neurobiology -- Ornithology -- Paleontology -- Palynology -- Parasitology -- Photobiology -- Phycology -- Physiology -- Plant physiology -- Biological psychology-- Radiobiology -- Sociobiology -- Structural biology -- Taxonomy -- Virology -- Zoology

Basic biology concepts

Ecology & evolution

• Life: origin of life -- Miller-Urey experiment
• Ecology:
  • Autecology: autotroph -- heterotroph -- acclimatization -- endotherm -- ectotherm -- hibernation -- homeostasis -- behavior -- circadian rhythm
  • Population ecology: population -- competition -- mating -- biological dispersal -- endemism -- niche -- growth curve -- carrying capacity
  • Community ecology: community -- keystone species -- mimicry -- symbiosis -- pollination -- mutualism -- commensalism -- parasitism -- predation -- invasive species -- environmental heterogeneity -- edge effect
  • Ecosystems: biodiversity -- biome -- habitat -- plankton -- thermocline -- carbon cycle -- water cycle -- nitrogen cycle -- food web -- trophic level -- saprobe -- decomposition
• Evolutionary biology (evolution)
  • Microevolution: species -- speciation -- adaptation -- selection -- natural selection -- directional selection -- sexual selection -- genetic drift -- sexual reproduction -- asexual reproduction -- colony -- allele frequency -- neutral theory of molecular evolution -- population genetics -- Hardy-Weinberg principle
  • Macroevolution: adaptive radiation -- convergent evolution -- extinction -- mass extinction -- fossil -- taphonomy -- geologic time -- plate tectonics -- continental drift -- vicariance -- Gondwana -- Pangaea -- endosymbiosis
  • Systematics: taxon -- taxonomy -- scientific classification -- phylogeny -- evolutionary tree -- cladistics -- synapomorphy -- homology -- molecular clock

Organismal biology

• Groups of living organisms
  • viruses : DNA viruses -- RNA viruses -- retroviruses
  • Single-cell organisms:
    • prokaryotes : microbe -- bacteria -- archaebacteria -- eubacteria
    • eukaryotes: fungi -- algae -- protozoa -- protista
  • Multicellular organisms:
    • plantae -- plants -- bryophytes -- pteridophytes -- seed plants
    • animalia -- animals -- metazoa -- insects -- molluscs -- vertebrates
    • fungi -- lichen -- mycorrhizae
• Developmental biology : gamete -- spermatid -- ovum -- zygote -- embryo -- cellular differentiation -- morphogenesis --homeobox
  • Animal development: stem cell -- blastula -- gastrula -- egg (biology) -- fetus -- placenta
  • Plant development: seed -- cotyledon -- meristem -- apical meristem -- vascular cambium -- cork cambium
• Morphology, Anatomy, & Physiology:
  • Techniques: electrophysiology -- electron microscopy
  • tissues -- organ -- senescence
  • Plant systems: root -- shoot -- stem -- leaf -- flower
    • vascular tissue -- Casparian strip -- turgor pressure -- xylem -- phloem -- transpiration -- wood
    • alternation of generations -- gametophyte -- antheridium -- archegonium -- sporophyte -- spore -- sporangium
    • tropism -- taxis
  • Animal systems: skin cell
    • skeleton -- bone -- cartilage -- joint -- muscle -- tendon -- actin -- myosin -- reflex
    • circulatory system -- respiration -- lung -- heart -- artery -- vein -- capillary -- blood -- blood cell
    • digestive system -- stomach -- intestine -- liver -- nutrition -- primary nutritional groups metabolism -- kidney -- excretion
    • nervous system: limbic system -- vestibular system -- neuron -- axon -- dendrite -- brain -- eye -- vision -- audition -- proprioception -- olfaction -- memory
    • nerve signaling: action potential -- signal transduction -- synapse -- receptor
    • endocrine system -- hormone
    • reproductive system -- testes -- ovary -- pregnancy
• Medicine:
  • Diseases: cancer -- diabetes -- obesity -- hereditary disease -- communicable disease
  • immune system: antibody -- host -- vaccine -- immune cell -- AIDS -- T-cell -- leucocyte
  • Drugs: antibiotic -- barbiturate -- SSRI
  • Techniques: MRI -- Computed axial tomography -- blood count

Cell & molecular biology

• Cell biology: the cell
  • Techniques: culture -- microscope -- SEM -- TEM
  • cell components:
    • organelles: Golgi apparatus -- nucleus -- cytoplasm -- vacuole -- vesicle -- lysosome -- peroxisome -- mitochondrion -- plastid -- chloroplast
    • membranes: plasma membrane -- endomembrane system -- endoplasmic reticulum -- mitochondrial membrane -- chloroplast membrane
    • Other subcellular features: cell wall -- pseudopod -- cytoskeleton -- mitotic spindle -- flagellum -- cilium
  • cell processes:
    • diffusion -- osmosis -- isotonic -- active transport -- phagocytosis
    • energy pathways: fermentation -- glycolysis -- cellular respiration -- citric acid cycle -- photosynthesis -- Calvin cycle
    • protein biosynthesis -- ribosomes
    • cellular reproduction: cytokinesis -- centromere -- meiosis
    • nuclear reproduction: mitosis -- interphase -- prophase -- metaphase -- anaphase -- telophase
    • programmed cell death -- apoptosis -- cell senescence
• Biochemistry :
  • Biomolecules:
    • Small: amino acids -- Adenosine triphosphate (ATP) -- fats -- lipids -- oil -- phospholipid -- prion -- sugar -- vitamins -- neurotransmitter -- wax
    • Medium-sized:
      • pigments: chlorophyll -- carotenoid -- xanthophyll -- melanin
    • Biopolymers/macromolecules
      • proteins: primary structure -- secondary structure -- tertiary structure -- conformation -- native state -- protein folding -- enzyme -- receptor -- transmembrane receptor -- ion channel -- membrane transporter-- collagen -- silk
      • DNA -- RNA
      • polysaccharide: cellulose -- carbohydrate -- chitin -- glycogen -- starch
  • Biochemical mechanisms: proteolysis -- cooperativity
  • Techniques: electrophoresis -- His tag --affinity chromatography -- x-ray diffraction -- Proteomics -- mass spectrometry
• Molecular biology:
  • genetic structure: DNA -- DNA replication -- nucleosome -- genetic code -- codon -- transcription factor -- transcription -- translation -- RNA -- histone -- telomere
  • gene expression -- heterochromatin -- promoter -- enhancer -- operon
  • mutation -- point mutation -- crossover -- recombination --plasmid -- transposon
  • molecular genetics: DNA fingerprinting -- genetic fingerprint -- microsatellite -- gene knockout-- imprinting -- RNA interference
  • Genomics: computational biology -- bioinformatics
  • Molecular Techniques: gel electrophoresis -- transformation -- PCR -- PCR mutagenesis -- primer -- chromosome walking -- RFLP -- restriction enzyme -- sequencing -- shotgun sequencing -- cloning -- culture -- DNA microarray
• Genetics (classical genetics) :
  • heredity -- Mendelian inheritance -- gene -- locus -- trait -- allele -- polymorphism -- homozygote -- heterozygote -- hybrid -- hybridization -- dihybrid cross -- Punnett square
  • genotype-phenotype distinction -- genotype -- phenotype -- dominant gene -- recessive gene
  • genetic interactions -- Mendel's law of segregation -- genetic mosaic -- maternal effect -- penetrance -- complementation -- suppression -- epistasis -- genetic linkage
  • chromosomal effects: chromosome -- haploid -- diploid -- polyploidy -- dosage effect -- inbreeding
  • Model organisms: Drosophila -- Arabidopsis -- Caenorhabditis elegans -- mouse -- Saccharomyces cerevisiae -- Escherichia coli -- Lambda phage -- Xenopus
  • Techniques: genetic screen -- paternity test -- linkage map -- genetic map

Influential biologists

Charles Robert Darwin -- Alfred Russel Wallace -- Jean-Baptiste Lamarck -- Sir Charles Lyell -- Alfred Wegener -- Alexander Fleming -- Andrew Huxley -- Robert Koch -- Konrad Lorenz -- Ernst Haeckel -- Theodor Bilharz -- Marcello Malpighi -- Antoni van Leeuwenhoek -- Konrad Lorenz -- Thomas Malthus -- Edward Jenner -- Carolus Linnaeus -- Sewall Wright -- Louis Pasteur -- Gregor Mendel -- Barbara McClintock -- James D. Watson -- Francis Crick -- Kary Mullis -- Rosalind Franklin -- Steven Jay Gould -- Lynn Margulis -- Carl Woese -- Jane Goodall