biol1030 (copy)

Biodiversity

considering all the different ways to be alive in the world

Classification

taxonomic levels

Domain

most inclusive level of classification

Kingdom

the highest category in taxonomic classification

Phylum (-a)

taxonomic rank below kingdom and above class

Class

a set or category of things having some property or attribute in common and differentiated from others by kind, type, or quality

Order

comprised of families sharing a set of similar nature or character

Family

a group of elements with similar properties

Genus (-era)

a taxonomic group covering more than one species

Species

is one of the basic units of biological classification and a taxonomic rank

Phylogeny

evolutionary history of an organism

Taxonomy

science of naming organisms

Taxon

named group of organisms - species, domain, phylum

Competing Philosophies

how we name groups of evolutionary organisms

Homologous

structures that are similar based on shared common ancestry

Analogous

look similar due to individual evolutionary events

Homoplasy

when things appear to be homologous but are not - occurs within the finer scale - close related organisms

Convergent Evolution

when things evolve multiple times through similarity in habitats, functionality - similar habitat most commonly
- used to describe an analogous structure

Parallel Evolution

same traits evolving multiple times in a relatively small lineage - not based on shared common ancestry

Cladistics

group of organisms that share a common ancestor

Monophyletic

a single common ancestor (base of tree)

Holophyletic

includes all descendants of the single common ancestor

Paraphyletic

on the side of - doesn't include all of the descendants from a single common ancestor - includes most but not all
• Applied to organisms themselves, but also to the traits of the organisms

Polyphyletic

evolved more than once

Morphology

the branch of biology that deals with the form of living organisms, and with relationships between their structures

Plesiomorphic

refers to the ancestral trait state, usually in reference to a derived trait state. A symplesiomorphic trait is also shared with other taxa that have an earlier last common ancestor with the taxa under consideration

Apomorphic

novel evolutionary trait that is unique to a particular species and all its descendants and which can be used as a defining character for a species or group in phylogenetic terms

Symplesiomorphic

an ancestral character or trait state shared by two or more taxa

Synapomorphic

a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants

Autapomorphic

a distinctive anatomical feature, known as a derived trait, that is unique to a given taxon

Types of Phylogenic Trees

Phylogram, Dendrogram, Cladogram

Phylogram

a phylogenetic tree that has branch spans proportional to the amount of character change

Dendrogram

a tree diagram, especially one showing taxonomic relationships.

Cladogram

a branching diagram showing the cladistic relationship between a number of species

Horotely

biological evolution at rates within the range or rate distribution usual for a given group of plants or animals

Tachtyely

of or relating to evolution at a rate faster than the standard for a given group of plants or animals.

Bradytely

of or relating to evolution at a rate faster than the standard for a given group of plants or animals.

Tribe

a taxonomic category that ranks above genus and below family or subfamily, usually ending in -ini

Sub-

under, beneath, behind; division of taxonomic groups

Super-

above, on the upper side , upon, over

Infra-

below, lower than

3 domains

1. Archaea
2. Bacteria
3. Eukarya

6 kingdoms

1. Archaebacteria
2. Eubacteria
3. Protista
4. Fungi
5. Plantae
6. Animalia

Prokaryotes

cells that lack nuclei
o Taxonomic clades are best defined using Synapomorphies
o Lacking nucleus is a symplesiomorphy
o Prokaryotes, which share the ancestral characteristic of lacking a nucleus are NOT a recognized biological taxon
o Share characteristic but it doesn't mean they are related to each other

Prokaryote Domains (2)

Bacteria and Archaea

Dr. Carl Woese

(1928-2912) proposed splitting the prokaryotes into two novel taxonomic groups about the kingdom level

Archaebacteria

"ancient ones'
most are found in extreme environments reminiscent of the ancient earth

Archaea and Eukarya

form a monophyletic clade that is distinct from Bacteria

Colonial

a collective life form comprising associations of individual organisms that are incompletely separated, as corals and moss animals

Multicellular

made of many cells

Shape/Cell Morphology

Spherical --\> coccus (-i)
Rod-shaped --\> bacillus (-i)
Spiral --\> spirilla

Staphlylo-

"cluster of grapes"

Strepto-

'twisted chain'

Cell Wall

a rigid layer of polysaccharides lying outside the plasma membrane of the cells of plants, fungi, and bacteria

Archeans

gram-negative and the peptidoglycan layer are stuck between membranes and it doesn't pick up the gram-stains

Capsule

outside of the cell wall of bacteria - DNA of dead smooth bacteria

Fimbriae (-ae)

latin for fringe; anchors bacteria to a substrate/host
• Look like cilia - but bacteria don't have cilia
• Griffith: rough and smooth bacteria

Pilus (-i)

helps with gene transfer (sex pilus)
• Hollow - like a straw

Motility

The ability to move actively and on instinct, usually consuming energy in the process

Flagella

Long, slender, threadlike, whiplike extension of certain cells or unicellular organisms used mainly for movements

Taxis

the movement of an organism in response to a stimulus such as light or the presence of food

Positive phototaxis

A direct response in response to the presence of light in organism, where a positive effect sees the organism move towards the light and a negative one away from the light.

Negative chemotaxis

movement by a cell or organism in reaction to a chemical stimulus

Genome

the complete set of genes or genetic material present in a cell or organism

Genomic Arrangement

A graphic representation of the arrangement of a gene or a DNA sequence on a chromosome

No nucleus

no membrane enclosing the genetic information

Single cellular

chromosome single circular chromosome like headphones

Plasmids

smaller loops of DNA that aren't part of the nucleoid

Reproductions

biological process by which new individual organisms - "offspring" - are produced from their "parents"

Binary fission

a kind of asexual reproduction. It is the most common form of reproduction in prokaryotes and occurs in some single-celled eukaryotes. After replicating its genetic material, the cell divides into two nearly equal sized daughter cells

Horizontal gene transfer

genetic information passed from one cell to another

Transformation

genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material (exogenous DNA) from its surroundings through the cell membrane

Transduction

process by which genetic material, e.g. DNA or siRNA, is inserted into a cell by a virus

Conjugation

the direct transfer of DNA from one bacterial cell to another bacterial cell. The transferred DNA is a plasmid, a circle of DNA that is distinct from the main bacterial chromosome

Endospores

resistant forms of bacteria

Autoclave

an apparatus in which special conditions (as high or low pressure or temperature) can be established for a variety of applications
- especially an apparatus (as for sterilizing) using steam under high pressure

Nutritional Modes

how food is obtained

Heterotroph

an organism deriving its nutritional requirements from complex organic substances

Autotroph

an organism that produces complex organic compounds from simple substances present in its surroundings, generally using energy from light or inorganic chemical reactions

Photoautotroph

produce food by photo bust synthesis

Photoheterotroph

get ATP from sunlight but they cannot fix the carbon from the atmosphere - have to eat it from an outside source

Chemoautotroph

eat chemicals produced by other organisms, some organisms exclusively prokaryotes that are chemoautotrophic

Chemoautotrophic

take forms of energy and produce ATP

Thermal Vents

earths chemical energy stored in magma/earth's core - whole communities are dependent on bacteria that take the earth's chemical energy and turn it into a source of energy/nutrients for other organisms

Aerobic

require oxygen that is in the air, then use it as an electron acceptor

Anaerobic

does not require oxygen - many different alternative terminal electron acceptors (other than oxygen) in prokaryotes

Obligate

have to have oxygen to live

Facultative

can go both ways (anaerobic or aerobic)

Fermentation

is a metabolic process that converts sugar to acids, gases or alcohol. It occurs in yeast and bacteria, and also in oxygen-starved muscle cells, as in the case of lactic acid fermentation

Ecological Relationships

the relationship between organisms in an ecosystem

Pathogenic Bacteria

disease causing bacteria

Free-Living Bacteria

Living independently of another organism; not part of a parasitic or symbiotic relationship

Mutualistic

provides benefit to host and host provides benefits to the host

Decomposers

important and necessary in aiding decomposition - cycle nutrients atmosphere

Nitrogen

used in amino acids, nucleic acids, nitrogenous bases - need biologically available nitrogen → prokaryotes take it from the atmosphere and make it available

Biofilms

species of bacteria that are working together - lots of little bacteria come together to form a super bacteria → use other's waste to create their own products

Endosymbiotic Origin of Eukaryotic Organelles

- The mitochondria of eukaryotes evolved from aerobic bacteria (probably related to the rickettsias) living within their host cell.
- The chloroplasts of red algae, green algae, and plants evolved from endosymbiotic cyanobacteria.

Alphaproteobacteria

similar function to mitochondria

Cyanobacteria

similar function to chloroplasts; the true bacteria
- Oscillatoria

Metagenomic Prospecting

faster, better way to resolve sequences