biology 1108 exam 1

Evolution: a change in allele frequency in a population over time

Population: a group of individuals of the same species

Alleles: variants of genes

Adaptations: heritable traits that help individuals survive and reproduce in their current environment

Natural selection: increases the frequency of the advantageous traits in the population over time (mechanism of evolution)

Fitness: an individual’s ability to survive and reproduce

Stabilizing selection: favors survival of individuals with intermediate phenotypes

Directional selection: favors individuals at one extreme of a phenotypic range

Disruptive selection: two or more extreme phenotypes are favored

Genetic drift: changes in allele frequency due to random chance events (bottleneck, founder)

Gene flow: involves the movement of genes into or out of a population

Mutation: creation of new alleles, original source of all genetic variation

Speciation: the formation of 2 species from an ancestral species. The same evolutionary processes that produce changes in populations also contribute to speciation

Biological species concept: a species is one whose organisms can actually or potentially reproduce viable fertile offspring (reproductively isolated)

Morphological species concept: a species as one whose members have similar morphology (physical structure). Widely applicable for fossil and extant species

Phylogenetic species concept: a species is the smallest tip on a phylogenetic tree, or the smallest set of organisms that share a single common ancestor and certain shared traits (evolutionary history and genetic similarity) 

Reproductively isolated species: organisms that can breed within their own group but not outside of it

Prezygotic mechanisms: those that prevent the formation of a zygote (temporal, habitat, behavior)

Postzygotic isolating mechanisms: a zygote is formed but may not develop properly (hybrid inviability) or organism produced may be sterile (hybrid sterility) (often due to mismatch of chromosomes between species)

Allopatric speciation: reproductive isolation due to a geographic barrier. Populations are physically separated from each other (allo: other; patric: homeland)

Dispersal: some individuals disperse and colonize a new habitat that is geographically isolated from the original

Vicariance: a physical barrier forms to separate populations

·       Sympatric speciation: populations become reproductively isolated without physical separation (sym: same)

Polyploidy: having more than 2 sets of chromosomes

Autopolyploidy: diploid plant reproduces diploid gametes due to an error in meiosis instead of its normal haploid gametes

·       If the tetraploid plants survive and reproduce, they will make diploid gametes

·       If mating occurs between new tetraploid and original diploid plants, triploid zygotes will be produced (typically non-viable or sterile)

·       The new tetraploid population is reproductively isolated from the original diploid population (postzygotic isolation)

Allopolyploidy: chromosomal changes that result in when gametes from 2 different species combined to form a hybrid 

 Phylogeny: the evolutionary history and relationships of a (group) of organisms

Phylogenetic trees: type of diagram used to depict evolutionary history and relationships

·       Tips, the group of interest

·       Branches, each lineage through time

·       Nodes/branch points, speciation events where one lineage splits into two or more

·       Root, the single common ancestor of all organisms on the tree

Monophyletic group (clade): a group includes a common ancestor and all descendants of that ancestor

Paraphyletic group: includes a common ancestor and some descendants

Synapomorphies: shared derived characters of monophyletic groups, can be displayed in phylogenetic trees

Homologous traits: those that are similar due to common ancestry

Analogous traits: those that are similar but were not inherited from a common ancestor

Convergent evolution: evolution that is independent but displays the same or similar features

Maximum parsimony: the grouping in taxa in ways that minimize the number of evolutionary changes that had to have occurred

Sister groups: descendants that split from the same node; closest relatives to each other

Outgroup: a taxon that is outside the groups of interest; often included to help construct a phylogeny 

 Taxonomy: the science of classifying organisms

·       Classification groups called taxa or taxon (singular)

Binomial nomenclature: the two-word convention of naming species (Genus species)

Domain: the broadest taxonomic group

·       Bacteria

o   Prokaryotes: cells that lack a membrane-bound nucleus, have little to no organelles, use via binary fission, and have a peptidoglycan cell wall

·       Archaea

o    Prokaryotes: distinct cell membrane chemistry, no peptidoglycan, use binary fission, and can live in extreme environments.

·       Eukarya

o   Eukaryotes: contain a membrane-bound nucleus, internal organelles, can be multicellular, reproduce by mitosis and cytokinesis, and sexual and asexual reproduction occur

Adaptive Radiation: the rapid speciation of an ancestral lineage into many descendants, with the newly formed lineages adapted to diverse niches

·       Can be triggered by new opportunities/lack of competition or new adaptations that allow exploitation

Niche: a species’ role within the environment (space it occupies, resources used, behavior, etc.)

Mass Extinction: events that wipe out most species within a relatively short period

·       Five mass extinctions have occurred within the past 500 million years

Prokaryotes: Oldest, structurally simplest, and most abundant forms of life, 90 to 99% are unknown and undescribed, Less than 1% cause disease, Fall into two domains: Bacteria and Archaea

Tracing the lineages: The ancestor to modern archaea is believed to have given rise to Eukarya.

Binary Fission: the genomic DNA is replicated and divided, along with the cytoplasmic contents, resulting in 2 identical daughter cells

 Plasma membrane: Bacterial lipids are unbranched and use ester bonds, Archaean membranes are formed on glycerol skeleton with either linkage (not ester), Hydrocarbons may be branched or have rings, tetraether polymer allows extremophiles to withstand high temperatures

Glycocalyces: gelatinous sticky substance surrounding outside of the cell. Composed of polysaccharides, polypeptides, or both. 2 types:

Glycocalyces Capsule: composed of organized repeating units of organic chemicals, firmly attached to cell surface, and may prevent bacteria from being recognized by host

Glycocalyces Slime layer: loosely attached to cell surface, water-soluble, sticky layer allows prokaryotes to attach to surfaces

S-layer (surface layer): rigid protein or glycoprotein layer found in some bacteria and archaea, outside of peptidoglycan or outer membrane layers in bacteria, and provides protection, structural support, and adhesion

Capsule: gelatinous layer found in some bacteria, aids in attachment, and protects from the immune system

Flagella: slender, rigid helical structures, composed of the protein flagellin, and involved in locomotion- spins like propeller

Pilus (pili): short, hairlike structures, found in gram-negative bacteria, and aid in attachment and conjugation

Prokaryotic morphology: cocci (spherical), bacilli (rod), spirilla (spiral)

Endospores: develop a thick wall around their genome and a small portion of the cytoplasm., From inside bacterial cells when exposed to environmental stress, Are highly resistant to environmental stress, especially heat, When conditions improve, they can germinate and return to normal cell division, Cause tetanus, botulism, and anthrax.

Symbiosis: ecological relationship between different species that live in direct contact with each other

Mutualism: both parties benefit

 Commensalism: one organism benefits and the other is unaffected

Parasitism: one organism benefits and the other is harmed

Bacterial Cell Walls: provide structure, shape, and protect cell from osmotic forces, assist some in attaching to other cells or in resisting antimicrobial drugs, can target cell wall of bacteria with antibiotics

Peptidoglycan: forms rigid network in bacterial cell wall, maintains shape and withstands hypotonic environments, archaean cell walls have diverse structures but do not contain peptidoglycan

Gram stain: stains bacteria purple or pink based on cell wall characteristics

Gram-positive: have a thicker peptidoglycan wall and stain a purple color, contain unique chemicals called teichoic acids and lipoteichoic acids

Gram-negative: contain less peptidoglycan and stain pink, many impede the treatment of disease bilayer membrane outside the peptidoglycan contains phospholipids, proteins, and lipopolysaccharide (LPS)

Extremophiles: organisms that love and thrive in extreme environments. Found in oceans, hot springs, polar regions, deserts, deep earth, harsh chemical, and high radiation environments.

Halobacteria: salt-loving bacteria

Microbial nutrient utilization: organisms use a variety of nutrients for their energy needs and to build organic molecules and cellular structures. Most common nutrients contain necessary elements (C, O, N, H). Obtain nutrients from a variety of sources

Autotrophs, Heterotrophs: Two groups of organisms based on source of carbon:

Chemotrophs, Phototrophs: Two groups of organisms based on source of energy

Horizontal gene transfer among prokaryotes: prokaryotes divide by binary fission, do not reproduce sexually but genetic variation is still important.

Griffith’s bacterial transformation experiment: Late 1920s, Frederick Griffith was interested in Streptococcus pnemoniae virulence (disease severity)

Lederberg and Tatum’s work with E. coli: demonstrated genetic transfer between bacteria: stains of E. coli have different nutritional requirements, due to genetic differences between strains

Bernard Davis’s U-tube experiment: demonstrated that direct cell-to-cell contact is required for bacterial conjugation

Transformation: the cell takes up prokaryotic DNA directly from the environment. May remain separate as plasmid DNA or be incorporated host genome

Transduction: a bacteriophage injects DNA into the cell that contains a small fragment of DNA from a different prokaryote

Conjugation: DNA is transferred from one cell to another via a pilus that connects the cells

Natural transformation occurs in many bacterial species

  Artificial transformation can be accomplished in lab using

Bacterial conjugation: plasmids may encode advantageous information

Antoni van Leeuwenhoek and the early years of microbiology: What does life really look like? Began making and using simple microscopes, Often made a new microscope for each specimen,  Examined water and visualized tiny animals, fungi, algae, and a single-celled protozoa; “animalcules”

·       End of 19^th century, they were now called microorganisms

Louis Pasteur’s Swan-Neck Flask Experiment: Does microbial life spontaneously generate? Preformed experiments with “swan-necked” flasks,  When the flasks remained upright, no microbial growth appeared, When the flask was tilted, dust from the bend in the neck seeped back into the flask and made the infusion cloudy with microbes within a day

Robert Koch: studied anthrax and proposed 4 postulates to prove a causal relationship between a microorganism and an individual

What causes Disease? Koch’s Postulates: Suspected causative agent must be found in every case of disease and be absent from healthy hosts, Agent must be isolated and grown outside host, When agent is introduced to a healthy, susceptible host, the host must get the disease, Same agent must be found in the diseased experimental host

Pathogens: parasitic microbes that cause disease symptoms

Beneficial prokaryotes: only a small % of bacteria are pathogenic, bacteria are vital to the environment for carbon and nitrogen cycles, produce nutrients in animal digestive tracts, used in the production of human foods, decomposers release atoms to the environment

Element Fixation: conversion of elements forms the environment into biologically usable forms

Biofactories: produce various chemicals, including insulin and antibiotics

Bioremediation: remove pollutants from water, air, soil (Exxon Valdez oil spill)

Biostimulation/Bioenhancement: add nutrients to encourage growth of naturally occurring microbes

Process of primary endosymbiosis: host eukaryotic cell engulfs a cyanobacterium, enter a symbiotic relationship, bacterium loses independent function, its genetic material transfers to the nuclear genome and evolves into an organelle.

Process of secondary endosymbiosis: a protist (the host) engulfs another prokaryotic cell that has already undergone primary endosymbiosis, engulfed cell loses its original structure, genes are transferred to host’s nuclear genome. (ex: red algae and green algae)

Evidence of primary endosymbiosis: DNA found in mitochondria and chloroplasts, organelles have double membranes, highly folded inner membranes, ETC and ATP synthase

Evidence of secondary endosymbiosis: Some posits have 3 membranes around plastids instead of the usual 4 (ex: brown algae, diatoms, euglena, and dinoflagellates)

Morphological forms: unicellular, colonial, filaments, or multicellular

Motility: cilia, pseudopod, flagellum, secrete mucilage, sessile(float)

Photosynthetic protists: green algae, red algae, brown algae

Heterotrophic via ingestion: paramecium

heterotrophic via absorption: downy mildew, oomycetes

Photosynthetic: all have chlorophyll, many have carotenoids and other accessory pigments

Predators: Surround and engulf prey item

Decomposers and parasites: absorb nutrients form the environment

Archaeplastida: plants, red algae, green algae (primary endosymbiosis)

Opisthokonta: fungi and animals (no endosymbiosis)

Chromalveolata: dinoflagellates and diatoms (secondary endosymbiosis)

Amoeba: freshwater, pseudopodia, cytoplasmic streaming, contractile vacuole, some parasitic, some produce cells

Euglena: one flagellum, pellicle strips, eye spot, contractile vacuole, some heterotrophic

Dinoflagellates: cellulose plates, some bioluminescent, some mutualism within protistan hosts

Ciliates: fresh and salt water, cilia, contractive vacuole, oral groove

Brown algae: all multicellular, mostly marine, photosynthetic

Diatoms: phytoplankton, fresh and salt water, unicellular, photosynthetic, cell walls contain silica (separated by raphe), diatomaceous earth (mined and use as an abrasive)

Red algae: multicellular, common in deep clear tropical waters

Green algae: diverse forms and life cycles, fresh and salt water, chlorophytes and charophytes

Positive impacts of protists: photosynthesis, phytoplankton, nutrition

Ecological impacts of protists: blooms of dinoflagellates (red tides)

Phytophthora infesting: crop disease that caused the Irish potato famine

Giardia intestinalis: infective cyst that when ingested cause beaver fever

Apicomplexans: non-photosynthetic plastid, all parasitic, form infectious spores, protist that causes malaria

Trypanosoma: injected through Tsetse fly, affects nervous system, causes sleeping sickness

Conjugation: formation of cytoplasmic bridge

Haploid dominant: haploid becomes adult, mitosis results in gametes (most green algae, apicomplexans, most fungi)

Diploid dominant: diploid becomes adult, meiosis results in gametes (some brown and green algae

Alternation of generations: meiosis produces haploid spores, and mitosis produces gametes (some green algae, all red algae)