Biology

Biology

1. Biodiversity

   • Prokaryotes
     • Bacteria and Archaea
       • the prokaryotic domains of microscopic organisms so critical to the cycling of carbon and other elements essential to life
     • Peptidoglycan
       • a complex polymer of sugars and amino acids; makes up the cell wall that supports bacteria
     • Carbon Cycle
       • describes the path of carbon as it moves between organisms, the atmosphere, rocks, soil, and the ocean
     • Plasmids
       • small circles of DNA that replicate independently of the cell's circular chromosomes
     • Horizontal Gene Transfer
       • major source of genetic ancestry in bacteria
     • Conjugation
       • transfers plasmids from one cell to another, spreading novel genes throughout a population
     • Transformation
       • genes can be transferred from one cell to another without any direct bridge between cells.  DNA released to the environment by cell breakdown can be taken up by other cells
     • Transduction
       • horizontal gene transfer by means of viruses; common in nature and is also widely used in the laboratory to introduce novel genes into bacteria for medical research
     • Oxygenic
       • all photosynthetic eukaryotes, the photosynthetic reaction is oxygen producing
     • Aerobic
       • all respiration in eukaryotic cells is oxygen using
     • Anoxygenic
       • bacteria that doesn't produce oxygen
     • Bacteriochlorophyll
       • a light-harvesting pigment that is closely related to the chlorophyll found in plants, algae, and cyanobacteria
     • Fermentation
       • involves the partial oxidation of carbon compounds to molecules that are less oxidized than CO2
     • Photoheterotrophs
       • plants rely on organic molecules obtained from the environment as their source of Carbon
     • Chemoautotrophs
       • microorganisms that oxidize molecules and ions such as H2, H2S, and Fe2+ to generate the ATP and reducing power required to incorporate CO2 into organic molecules
     • Primary Producers
       • the organisms that reduce CO2 to form carbohydrates, fulfill this role
     • Assimilation
       • plants take up sulfate (SO4^2-) ions from the soil and reduce them within their cells to hydrogen sulfide (H2S) that can be incorporated into cysteine and other biomolecules
     • Nitrogen Fixation
       • the process of converting N2 into a biologically useful form such as ammonia and it is one of the most important reactions ever evolved
     • Nitrification
       • Ammonia can be taken up by primary producers, but more commonly it is oxidized to nitrate (NO3-) by chemoautotrophic bacteria
     • Denitrification
       • some bacteria can use nitrate as an electron acceptor in respiration
     • Anammox
       • Ammonium ion is oxidized to nitrogen gas, and nitrite is reduced to nitrogen gas; water is produced by a by-product
     • Periodic Selection
       • genetic diversity in laboratory cultures gradually increases through time and then rapidly decreases with the emergence of a successful variant that out competes the rest
     • Proteobacteria
       • far and away the most diverse of all bacterial groups
     • Gram-Positive Bacteria
       • bacteria that retain the dye and dorm a well-defined branch of the bacterial tree
     • Cyanobacteria
       • all bacteria capable of oxygenic photosynthesis form a single branch of the bacterial tree; can be found in environments that range from deserts to the open ocean
     • Hyperthermophiles
       • Archaeons that branch from lower nodes of the archaeal tree exhibit a remarkable ability to grow and reproduce at temperatures of 80 C or more
     • Methanogens
       • Euryarchaeotes include Earth's only biological source of natural gas, or methane (CH4); they generate methane by fermenting acetate (CH3COO-) or by chemoautotrophic pathways in which hydrogen gas (H2) reduces CO2 to CH4
     • Coevolution
       • when prokaryotic organisms and eukaryotes evolve together
   • Eukaryotes
     • Plantae
     • Animalia
   • Multicellularity

2. Microevolution

   • Population genetics
   • Phylogenetics

3. Organisms

   • Water and Temperature Regularity
   • Nutrient Acquisition
   • Reproduction

4. Population Ecology

   • Communities of interacting populations
   • Ecosystems

5. Natural Selection

   • Balancing selection
     • acts to maintain two or more alleles in a population
   • Stabilizing selection
     • maintains the status quo and acts against extremes
   • Directional selection
     • leads to a change in a trait over time
   • Artificial selection
     • analogous to natural selection, but the competitive element is removed
   • Disruptive selection
     • operates in favor of extremes and against intermediate forms
   • Sexual selection
     • promotes traits that increase an individual's access to reproductive opportunities
     • Intrasexual selection
       • members of one sex compete with one another for access to the other sex
     • Intersexual selection
       • females choose their mates; interaction between opposite sex
   • Bottleneck
     • occurs when an originally large population is reduced to just a few individuals
   • Founder Event
     • when a few individuals start a new population
   • Gene Flow
     • the movement of alleles from one population to another
   • Inbreeding Depression
     • a reduction in the child's fitness caused by homozygosity of deterious recessive mutations
   • Molecular Evolution
     • populations have diverged genetically
   • Molecular Clock
     • correlation between the time for which two species have been evolutionary separated and the amount of genetic divergence between them
   • Pseudogene
     • an extreme case of a fast molecular clock; a gene that is no longer functional
   • Heterozygote Advantage
     • balancing selection occurs when the heterozygote's fitness is higher than that of either of the homozygotes, resulting in selection that ensures both alleles remain in the population at intermediate frequencies
   • Modern Synthesis
     • combines Mendelian genetics and Darwinian evolution
   • Fitness
     • a measure of the extent to which the individual's genotype is represented in the next generation
   • Allele Frequency
     • the raw information for this comes from the rates of occurrence of alleles in populations
   • Genotype Frequency
     • the proportion in a population of each genotype at a particular gene or set of genes
   • Hardy-Weinberg Equilibrium
     • allele and genotype frequencies change over time only if specific forces act on the population; describes the situation in which evolution does not occur. IN the absence of evolutionary forces (such as natural selection), allele and genotype frequencies do not change
     • 1
       • there is no difference in the survival and reproductive success of individuals
     • 2
       • the population is sufficiently large to prevent sampling errors
     • 3
       • populations are not added to or subtracted from by migration
     • 4
       • there is no mutation
     • 5
       • individuals mate at random
     • Allelic frequencies
       • p + q = 1
     • Genotypic frequencies
       • p2 + 2pq + q2 = 1
   • Genetic Drift
     • a change in the frequency of an allele due to the random effects of small population size
   • Nonrandom Mating
     • occurs when individuals do not mate randomly
   • Gene Pool
     • consists of all the alleles present in all of the individuals in the species
   • Mutations
     • Somatic Mutations
       • occur in the body's tissues in nonreproductive cells; affects only the cells descended from the one cell in which the mutation originally arose, so it affects only that one individual
     • Germ-Line Mutation
       • occurs in the reproductive cells, passed on to the next generation, so, from an evolutionary standpoint, these are our primary focus

6. Evolution

   • Species and Speciation
     • the process that produces new and distinct forms of life
     • Biological Species Concept (BSC)
       • species are groups of actually or potentially interbreeding populations that are reproductively isolated from other such groups
     • Ecological Species Concept (ESC)
       • the idea that there is a one-to-one correspondence between a species and its niche
     • Phylogenetic Species Concept (PSC)
       • emphasizes that members of a species all share a common ancestry and a common fate
     • Morphospecies Concept
       • holds that members of the same species usually look alike
     • Hybrid Offspring
       • when two different species reproduce and form a single species
     • Hybridization
       • different forms of a species are considered on large species because they are able to reproduce and produce fertile offspring
     • Pre-zygotic
       • isolating factors act before the fertilization of an egg
     • Post-zygotic
       • isolating factors come into play after fertilization
     • Behaviorally Isolated
       • individuals mate only with other individuals based on specific courtship rituals, songs, or other behaviors
     • Gametic Isolation
       • incompatibilities between the gametes of two different species
     • Mechanical Incompatibility
       • when the genitalia of one species is not configured to the genitalia of another species
     • Temporal Isolation
       • both plants and animals may also be pre-zygotically isolated in time
     • Geographic/Ecological Isolation
       • plants and animals can also be isolated in space
     • Genetic Incompatibility
       • post-zygotic isolating factors involve mechanisms that come into play after fertilization of the egg
     • Partially Reproductively Isolated
       • two species are not truly separate species, but the genetic differences between them are extensive enough that the hybrid offspring they produce have reduced fertility or viability compared to offspring produced by crosses between individuals within each population
     • Allopatric
       • populations which are geographically separated from each other
     • Subspecies
       • genetic distinctness is sometimes recognized by taxonomists
     • Dispersal
       • individuals colonize a distant place, such as an island, far from the main source population
     • Vicariance
       • a geographic barrier arises within a single population, separating it into two or more isolated populations
     • Peripatric Speciation
       • dispersal is important in a specific kind of allopatric speciation
     • Mainland Population
       • central population of a species
     • Island Population
     • Adaptive Radiation
       • a bout of unusually rapid evolutionary diversification in which natural selection accelerates the rates of both speciation and adaptation
     • Co-speciation
       • a process in which two groups of organisms speciate in response to each other and at the same time
     • Sympatric
       • term used to describe populations that are in the same geographic location
     • Instaneous Speciation
       • caused by hybridization between two species in which the offspring are reproductively isolated from both parents