Outline of biology

History of biology

• History of anatomy
• History of biochemistry
• History of biotechnology
• History of botany
• History of ecology
• History of genetics
• History of evolutionary thought:
• *Darwinism
• *Eclipse of Darwinism
• *Modern synthesis
• *History of molecular evolution
• *History of speciation
• History of marine biology
• History of medicine
• History of model organisms
• History of molecular biology
• Natural history
• History of neuroscience
• History of plant systematics
• History of pathology
• History of virology
• History of zoology

  Overview

• Biology
• *Science
• *Life
• **Properties: Adaptation – Energy processing – Growth – Order – Regulation – Reproduction – Response to environment
• *Biological organization: atom – molecule – cell – tissue – organ – organ system – organism – population – community – ecosystem – biosphere
• **Approach: Reductionism – emergent property – mechanistic
• Biology as a science:
• *Natural science
• *Scientific method: observation – research question – hypothesis – testability – prediction – experiment – data – statistics
• *Scientific theory – scientific law
• Research method
• *List of research methods in biology
• Scientific literature
• *List of biology journals: peer review

  Chemical basis

• Atoms and molecules
• *matter – element – atom – proton – neutron – electron– Bohr model – isotope – chemical bond – ionic bond – ions – covalent bond – hydrogen bond – molecule
• Water:
• *properties of water – solvent – cohesion – adhesion – surface tension – pH
• Organic compounds:
• *carbon – carbon-carbon bonds – hydrocarbon – monosaccharide – amino acids – nucleotide – functional group – monomer – adenosine triphosphate – lipids – oil – sugar – vitamins – neurotransmitter – wax
• Macromolecules:
• *polysaccharide: cellulose – carbohydrate – chitin – glycogen – starch
• *proteins: primary structure – secondary structure – tertiary structure – conformation – native state – protein folding – enzyme – receptor – transmembrane receptor – ion channel – membrane transporter – collagen – pigments: chlorophyll – carotenoid – xanthophyll – melanin – prion
• *lipids: cell membrane – fats – phospholipids
• *nucleic acids: DNA – RNA

  Cells

• Cell structure:
• *Cell coined by Robert Hooke
• *Techniques: cell culture – flow cytometry – microscope – light microscope – electron microscopy – SEM – TEM – live cell imaging
• * Organelles: Cytoplasm – Vacuole – Peroxisome – Plastid
• ** Cell nucleus
• *** Nucleoplasm – Nucleolus – Chromatin – Chromosome
• ** Endomembrane system
• *** Nuclear envelope – Endoplasmic reticulum – Golgi apparatus – Vesicles – Lysosome
• ** Energy creators: Mitochondrion and Chloroplast
• *Biological membranes:
• ** Plasma membrane – Mitochondrial membrane – Chloroplast membrane
• *Other subcellular features: Cell wall – pseudopod – cytoskeleton – mitotic spindle – flagellum – cilium
• ** Cell transport: Diffusion – Osmosis – isotonic – active transport – phagocytosis
• **Cellular reproduction: cytokinesis – centromere – meiosis
• **Nuclear reproduction: mitosis – interphase – prophase – metaphase – anaphase – telophase
• **programmed cell death – apoptosis – cell senescence
• Metabolism:
• **enzyme - activation energy - proteolysis – cooperativity
• Cellular respiration
• ** Glycolysis – Pyruvate dehydrogenase complex – Citric acid cycle – electron transport chain – fermentation
• Photosynthesis
• ** light-dependent reactions – Calvin cycle
• Cell cycle
• *mitosis – chromosome – haploid – diploid – polyploidy – prophase – metaphase – anaphase – telophase – cytokinesis – meiosis

  Genetics

• Inheritance
• *heredity – Mendelian inheritance – gene – locus – trait – allele – polymorphism – homozygote – heterozygote – hybrid – hybridization – dihybrid cross – Punnett square – inbreeding
• *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
• *Model organisms: Drosophila – Arabidopsis – Caenorhabditis elegans – mouse – Saccharomyces cerevisiae – Escherichia coli – Lambda phage – Xenopus – chicken – zebrafish – Ciona intestinalis – amphioxus
• *Techniques: genetic screen – linkage map – genetic map
• DNA
• *Nucleic acid double helix
• *Nucleobase: adenine – cytosine – guanine – thymine – uracil
• *DNA replication – mutation – mutation rate – proofreading – DNA mismatch repair – point mutation – crossover – recombination – plasmid – transposon
• Gene expression
• *Central dogma of molecular biology: nucleosome – genetic code – codon – transcription factor – transcription – translation – RNA – histone – telomere
• *heterochromatin – promoter – RNA polymerase
• *Protein biosynthesis – ribosomes
• Gene regulation
• *operon – activator – repressor – corepressor – enhancer – alternative splicing
• Genomes
• *DNA sequencing – high throughput sequencing – bioinformatics
• *Proteome – proteomics – metabolome – metabolomics
• *DNA paternity testing
• Biotechnology :
• *DNA fingerprinting – genetic fingerprint – microsatellite – gene knockout – imprinting – RNA interference Genomics – computational biology – bioinformatics – gel electrophoresis – transformation – PCR – PCR mutagenesis – primer – chromosome walking – RFLP – restriction enzyme – sequencing – shotgun sequencing – cloning – culture – DNA microarray – electrophoresis – protein tag – affinity chromatography – x-ray diffraction – proteomics – mass spectrometry – CRISPR – gene therapy
• Genes, development, and evolution
• *Apoptosis
• *French flag model
• *Pattern formation
• *Evo-devo gene toolkit
• *Transcription factor

  Evolution

• Evolutionary processes
• *evolution
• *microevolution: 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
• Speciation
• *Species
• Phylogeny
• *Lineage – evolutionary tree – cladistics – species – taxon – clade – monophyletic – polyphyly – paraphyly – heredity – phenotypic trait – nucleic acid sequence – synapomorphy – homology – molecular clock – outgroup – maximum parsimony – Computational phylogenetics
• *Linnaean taxonomy: Carl Linnaeus – domain – kingdom – phylum – class – order – family – genus – species
• *Three-domain system: archaea – bacteria – eukaryote – protist – fungi – plant – animal
• *Binomial nomenclature: scientific classification – Homo sapiens
• History of life
• *Origin of life – hierarchy of life – Miller–Urey experiment
• *Macroevolution: adaptive radiation – convergent evolution – extinction – mass extinction – fossil – taphonomy – geologic time – plate tectonics – continental drift – vicariance – Gondwana – Pangaea – endosymbiosis

  Life

• Bacteria and Archaea
• Protists
• Plant diversity
• * Green algae
• ** Chlorophyta
• ** Charophyta
• * Bryophytes
• ** Marchantiophyta
• ** Anthocerotophyta
• ** Moss
• * Pteridophytes
• ** Lycopodiophyta
• ** Polypodiophyta
• * Seed plants
• ** Cycadophyta
• ** Ginkgophyta
• ** Pinophyta
• ** Gnetophyta
• ** Magnoliophyta
• Fungi
• *Yeast – mold – mushroom
• Animal diversity
• *Invertebrates:
• **sponge – cnidarian – coral – jellyfish – Hydra – sea anemone
• **flatworms – nematodes
• **arthropods: crustacean – chelicerata – myriapoda – arachnids – insects – annelids – molluscs
• *Vertebrates:
• **fishes: – agnatha – chondrichthyes – osteichthyes
• **Tiktaalik
• **tetrapods
• ***amphibians
• ***reptiles
• ***birds
• ****flightless birds – Neognathae – dinosaurs
• ***mammals
• ****placental: primates
• ****marsupial
• ****monotreme
• Viruses
• *DNA viruses – RNA viruses – retroviruses

  Plant form and function

• Plant body
• *Organ systems: root – shoot – stem – leaf – flower
• Plant nutrition and transport
• *Vascular tissue – bark – Casparian strip – turgor pressure – xylem – phloem – transpiration – wood – trunk
• Plant development
• *tropism – taxis
• *seed – cotyledon – meristem – apical meristem – vascular cambium – cork cambium
• *alternation of generations – gametophyte – antheridium – archegonium – sporophyte – spore – sporangium
• Plant reproduction
• *angiosperms – flower – reproduction – sperm – pollination – self-pollination – cross-pollination – nectar – pollen
• Plant responses
• *Plant hormone – ripening – fruit – Ethylene as a plant hormone – toxin – pollinator – phototropism – skototropism – phototropin – phytochrome – auxin – photoperiodism – gravity

  Animal form and function

• General features: morphology – anatomy – physiology – biological tissues – organ – organ systems
• Water and salt balance
• *Body fluids: osmotic pressure – ionic composition – volume
• **Diffusion – osmosis) – Tonicity – sodium – potassium – calcium – chloride
• *Excretion
• Nutrition and digestion
• *Digestive system: stomach – intestine – liver – nutrition – primary nutritional groups metabolism – kidney – excretion
• Breathing
• *Respiratory system: lungs
• Circulation
• *Circulatory system: heart – artery – vein – capillary – Blood – blood cell
• *Lymphatic system: lymph node
• Muscle and movement
• *Skeletal system: bone – cartilage – joint – tendon
• *Muscular system: muscle – actin – myosin – reflex
• Nervous system
• *Neuron – dendrite – axon – nerve – electrochemical gradient – electrophysiology – action potential – signal transduction – synapse – receptor –
• *Central nervous system: brain – spinal cord
• **limbic system – memory – vestibular system
• *Peripheral nervous system
• *Sensory nervous system: eye – vision – audition – proprioception – olfaction –
• Integumentary system: skin cell
• Hormonal control
• *Endocrine system: hormone
• Animal reproduction
• *Reproductive system: testes – ovary – pregnancy
• **Fish#Reproductive system
• **Mammalian reproductive system
• ***Human reproductive system
• ***Mammalian penis
• ****Os penis
• ****Penile spines
• ***Genitalia of bottlenose dolphins
• ***Genitalia of marsupials
• ***Equine reproductive system
• ***Even-toed ungulate#Genitourinary system
• ***Bull#Reproductive anatomy
• ***Carnivora#Reproductive system
• ****Fossa #External genitalia
• ****Female genitalia of spotted hyenas
• ****Cat anatomy#Genitalia
• ****Genitalia of dogs
• *****Canine penis
• ******Bulbus glandis
• Animal development
• *stem cell – blastula – gastrula – egg – fetus – placenta - gamete – spermatid – ovum – zygote – embryo – cellular differentiation – morphogenesis – homeobox
• Immune system
• *antibody – host – vaccine – immune cell – AIDS – T cell – leucocyte
• Animal behavior
• *Behavior: mating – animal communication – seek shelter – migration
• *Fixed action pattern
• *Altruism