3.G: Unit 3 Glossary

Unit 3.2

basal taxon

A lineage on a phylogenetic tree that evolved early from the root and remains unbranched over time

binomial nomenclature

a system of two-part scientific names for an organism, which includes genus and species names

branch point

see: node

cladogram

one of most common representations of phylogeny; based in cladistics

clades

groups of organisms that descended from a single ancestor

cladistics

comparison of homologous and analogous traits of various organisms

class

the category in the taxonomic classification system that falls within phylum and includes orders

common ancestor

a single branch point at the bottom of many phylogenetic trees, indicating a common origin species from which all others derive

domain

the highest level category in the classification system and that includes all taxonomic classifications below it; it is the most inclusive taxon

family

the category in the taxonomic classification system that falls within order and includes genera

genus

the category in the taxonomic classification system that falls within family and includes species; the first part of the scientific name

ingroup

in cladistics, the group of taxa being analyzed

kingdom

the category in the taxonomic classification system that falls within domain and includes phyla

maximum parsimony

the likeliest order of events in phylogeny is probably the simplest shortest path

molecular characters

includes differences in the amino-acid sequence of a protein, shapes of a protein, RNA, location of a gene, differences in the individual nucleotide sequence of a gene, or differences in the arrangements of genes

molecular systematics

describes the use of information on the molecular level including DNA sequencing

monophyletic group

a single clade including all descendants from a branch point

node

a point on a phylogenetic tree where a single lineage splits to distinct new ones

order

the category in the taxonomic classification system that falls within class and includes families

outgroup

in cladistics, a species or group of species that diverged before the lineage containing the group(s) of interest

phylogenetic tree

diagram used to reflect the evolutionary relationships between organisms or groups of organisms

phylogeny

evolutionary history and relationship of an organism or group of organisms

phylum

the category in the taxonomic classification system that falls within kingdom and includes classes

polytomy

a node with more than two lineages

rooted

describing a phylogenetic tree with a single ancestral lineage to which all organisms represented in the diagram relate

scientific name

the genus and species name of an organism, italicized

sister taxa

two lineages that diverged from the same branch point

shared ancestral character

trait shared by all species of a group

shared derived character

trait shared by only some species within a group

species

the most specific category of classification

systematics

the science of determining the evolutionary relationships of organisms

taxon

a single level in the taxonomic classification system

taxonomy

the science of classifying organisms

Unit 3.3

accessory pigments

chlorophyll a and a range of other pigments capable of harvesting energy from light

acidophile

acid-loving prokaryotes

aerobic respiration

cellular respiration in the presence of oxygen

ages

smallest unit of geologic time

alkilophile

alkaline-loving prokaryotes

alpha-proteobacteria

a group of bacteria that were likely the LCA of the endosymbiont that became mitochondria

Alvarez Hypothesis

a giant asteroid or comet striking the Earth 66 million years ago caused the massive die-off at the end of the Cretaceous Period

Anthropocene

proposed epoch to include the impact of humans on Earth

biofilm

a microbial mat comprised of colonies of organisms along with and extracellular matrix

chloroplasts

photosynthetic plastids of plants

continental drift

the theory that the continents of the Earth have moved over geologic time

Domain Archaea

comprises all archaeans

Domain Bacteria

comprises all eubacteria

Domain Eukarya

comprises all eukaryotes including protists, fungi, animals, and plants

eon

the broadest category of geological time

endosymbiosis

engulfment of one cell within another such that the engulfed cell survives, and both cells benefit; the process responsible for the evolution of mitochondria and chloroplasts in eukaryotes

endosymbiotic theory

theory that states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such

epochs

subdivisions of periods in geologic time

era

second longest unit of geologic time

extant

species that are currently living

extinct

no longer existing species

extracellular matrix

proteins and carbohydrates which help affix the organisms in a biofilm to each other and to a surface

extremophiles

organisms that have adapted to life in extreme conditions not suitable for most forms of life

geologic time scale

a reference and communication system for comparing rocks and fossils from throughout the world and important in identifying the milestones in the history of life

Gondwanaland

southern continent that formed when Pangaea broke apart

Great Oxygenation Event (GOE)

about 2 billion years ago geological evidence shows that oxygen built up to higher concentrations in the atmosphere due to the evolution of cyanobacteria

halophile

salt-loving prokaryotes

hydrothermal vent

a fissure in the Earth’s surface that releases geothermally-heated water and chemicals leached from rocks in the Earth’s interior

hypersaline

concentrated saltwater

K-Pg boundary

the interface between the rocks of the Cretaceous and those of the Paleogene Epoch

Laurasia

northern continent that formed when Pangaea broke apart

mass extinctions

when large numbers of species go extinct all within a very short period of geologic time

mitochondria

a eukaryotic organelle capable of generating ATP from organic molecules

Pangaea

a single, massive landmass composed of all modern continents that existed during the Mesozoic era

period

subdivision of eras in geologic time

Phanerozoic

the current eon; comprised of the Paleozoic, Mesozoic, and Cenozoic eras

photosynthesis

use of energy from sunlight to power the formation of organic compounds

Precambrian

the Hadean, Archean, and Proterozoic eons combined

prokaryote

single-celled organisms without a nucleus or membrane-bound organelles that were the first inhabitants on Earth

ribozymes

certain RNA molecules have enzymatic activity on their own

RNA World Hypothesis

ribozyme (RNA) molecules have enzymatic activity, can store information, and may have been able to synthesize the proteins that life needed

Stanley Miller

created an apparatus that mimicked the Earth’s early conditions and atmosphere and proposed a hypothesis for the origin of life

stromatolite

a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat

Unit 3.4

Unit 3.4.1

acellular

biological entities without a cellular structure

apoptosis

programmed cell death

bacteriophages

viruses that infect bacteria

Baltimore classification

groups viruses according to how the mRNA is produced during the replicative cycle of the virus

budding

viral reproductive process where virions leave the cell individually

capsid

a protective layer of proteins on the external surface of a virus

cytopathic

causes cell damage

lysis

cell bursting

pathogen

agent with the ability to cause disease

permissive

cells that a virus may use to replicate

prion

infectious particle that consists of proteins that replicate without DNA or RNA

progressive hypothesis

hypothesis that viruses originated from RNA and DNA molecules that escaped from a host cell

regressive hypothesis

hypothesis that viruses evolved from free-living cells that progressively lost the ability to reproduce and metabolize on their own

segments

pieces of genetic material in some viruses (versus a single nucleic acid)

viral receptor

for a cell to be permissive, this surface molecule must be found on the host cell surface for the virus to attach

virions

single virus particles outside of the cell

viroid

plant pathogen that produces only a single, specific RNA

virus

acellular parasitic entities that are not classified within any domain or kingdom

virus core

contains total genome of the virus

virus molecular systematics

field of study which aims to determine whether the progressive or regressive hypothesis is correct through comparisons of sequenced genetic material

Unit 3.4.2

ammonification

process by which ammonia is released during the decomposition of nitrogen-containing organic compounds

autotroph

organisms that can fix inorganic carbon into organic molecules

bacilli

bacteria that are rod-shaped

binary fission

replication of the prokaryotic chromosome and separation of the bacterial cell into two identical copies

capsule (prokaryotes)

external structure that enables a prokaryote to attach to surfaces and protects it from dehydration

cell wall (prokaryotes)

a protective layer that surrounds some cells and gives them shape and rigidity; contains peptidoglycan; chemical composition varies between Archaea and Bacteria and between bacterial species

chemoautotrophs

obtain their energy from chemical compounds

chemolitotrophs

chemoautotrophs that use inorganic compounds as energy sources

chemoorganotrophs

chemoautotrophs that can use organic compounds as energy sources

cocci

bacteria that are spherically-shaped

conjugation

process by which prokaryotes move DNA from one individual to another using a pilus

denitrification

the reduction of nitrate from the soils to gaseous compounds such as N₂O, NO, and N₂

fix

transforming nitrogen gas (N₂) into a form useable for other life forms

Gram-negative

bacterium whose cell wall contains little peptidoglycan but has an outer membrane

Gram-positive

bacterium that contains mainly peptidoglycan in its cell walls

heterotroph

obtain carbon from organic compounds

nitrification

conversion of ammonium to nitrite and nitrate

peptidoglycan

polysaccharide chains cross-linked by peptides

pilus

surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes

photoautotrophs

obtain their energy from sunlight

pseudopeptidoglycan

component of archaea cell walls that is similar to peptidoglycan in morphology but contains different sugars

S-layer

surface-layer protein present on the outside of cell walls of archaea and bacteria

spirilli

bacteria that are spiral-shaped

teichoic acid

polymer associated with the cell wall of Gram-positive bacteria

transduction

process by which a bacteriophage moves DNA from one prokaryote to another

transformation

process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes

Unit 3.4.3

cyst (protist)

a protective, resting stage of the life cycle

mixotroph

obtaining nutrition by photoautotrophic or heterotrophic routes, depending on whether sunlight or organic nutrients are available

paraphyletic group

a taxonomic group that does not contain all descendants of its common ancestor

pellicle

interlocking protein strips that function like a flexible coat of armor, preventing tearing or piercing

phagocytosis

when the cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous sac

phototaxis

movement toward light

Protista

a paraphyletic group of diverse eukaryotes

pseudopodia

cytoplasmic extensions which allow movement

saprobe

organism that derives nutrients from decaying organic matter; also saprophyte

supergroup

taxonomic divisions of the Domain Eukaryota that are hypothesized to be monophyletic

Unit 3.4.4

ascocarp

fruiting body of ascomycetes, composed of millions of asci

asci

spore-forming sacs of Ascomycota

Ascomycota

(also, sac fungi) phylum of fungi that store spores in a sac called ascus

basidiocarp

fruiting body that protrudes from the ground and bears the basidia

Basidiomycota

(also, club fungi) phylum of fungi that produce club-shaped structures (basidia) that contain spores

basidium

club-shaped fruiting body of basidiomycetes; many fuse together into basidiocarp

Chytridiomycota

(also, chytrids) primitive phylum of fungi that live in water and produce gametes with flagella

coenocytic hypha

single hypha that lacks septa and contains many nuclei

conidiospores

unicellular or multicellular spores that are released directly from the tip or side of the hypha

decomposer

organism that carries out the decomposition of dead organisms

Eucomycota

true fungi belonging to the Kingdom Fungi

exoenzymes

enzymes transported by the hyphae into the environment for external digestion

faculative anaerobes

organisms that can perform both aerobic and anaerobic respiration and can survive in oxygen-rich and oxygen-poor environment

fungus

comes from the Latin word for mushrooms

Glomeromycota

phylum of fungi that form symbiotic relationships with the roots of trees

heterothallic

describes when only one mating type is present in an individual mycelium

homothallic

describes when both mating types are present in mycelium

hypha

fungal filament composed of one or more cells

imperfect fungi

reproduce asexually

karyogamy

fusion of nuclei

lichen

close association of a fungus with a photosynthetic alga or bacterium that benefits both partners

mycelium

mass of fungal hyphae

mycology

scientific study of fungi

mycorrhizae

a mutualistic relationship between a plant and a fungus; are connections between fungal hyphae, which provide soil minerals to the plant, and plant roots, which provide carbohydrates to the fungus

obligate aerobes

organisms that require oxygen to survive

obligate anaerobes

organisms that only use anaerobic respiration because oxygen will disrupt their metabolism

oenology

science of wine-making

perfect fungi

reproduce sexually and asexually

polycyclic aromatic hydrocarbons (PAHs)

toxic chemicals that are a byproduct of some industrial processes

plasmogamy

fusion of cytoplasm

rhizoid

underground organ

septa

cell wall division between hyphae

sessile

seemingly immobile

sporangiospores

produced in a sporangium

sporangium

reproductive sac that contains spores

spore

a haploid cell that can undergo mitosis to form a multicellular, haploid individual

symbiosis

ecological interaction between two organisms that live together

thallus

vegetative body of a fungus

yeast

general term used to describe unicellular fungi

Zygomycota

(also, conjugated fungi) phylum of fungi that form a zygote contained in a zygospore

zygospore

structure with thick cell wall that contains the zygote in zygomycetes

zoospore

asexual spores of chytrids

Unit 3.4.5

animal

eukaryotic, heterotrophic, motile (at least at certain life stages), multicellular organisms, with differentiated and specialized tissues; require a source of food and perform internal digestion

body plan

morphology or constant shape of an organism

Cambrian explosion

time during the Cambrian period (542–488 million years ago) when most of the animal phyla in existence today evolvedni

Cryogenian period

geologic period (850–630 million years ago) characterized by a very cold global climate

Ediacaran biota

oldest definite multicellular organisms with tissues that evolved geological period (630–542 million years ago)

Eumetazoa

group of animals with true differentiated tissues

Metazoa

group containing all animals

niche

an organisms's role within an ecosystem

Parazoa

group of animals without true differentiated tissues

Unit 3.4.6

acoelomate

animal without a body cavity

asymmetry

unique feature of Parazoa

bilateral symmetry

type of symmetry in which there is only one plane of symmetry, so the left and right halves of an animal are mirror images

blastopore

indentation formed during gastrulation, evident in the gastrula stage

coelom

lined body cavity

deuterostome

blastopore develops into the anus, with the second opening developing into the mouth

diploblast

animal that develops from two germ layers

eucoelomate

animal with a body cavity completely lined with mesodermal tissue

gamete

haploid reproductive cells produced through meiosis

gastrulation

stage of animal development characterized by the formation of the digestive cavity

germ cell

collection of cells formed during embryogenesis that will give rise to future body tissues, more pronounced in vertebrate embryogenesis

Hox gene

(also, homeobox gene) master control gene that can turn on or off large numbers of other genes during embryogenesis

parthenogenesis

unfertilized eggs can develop into new offspring

protostome

blastopore develops into the mouth of protostomes, with the second opening developing into the anus

pseudocoelomate

animal with a body cavity located between the mesoderm and endoderm

radial symmetry

type of symmetry with multiple planes of symmetry, with body parts (rays) arranged around a central disk

somatic

diploid body cells produced through mitosis

triploblast

animal that develops from three germ layers

Unit 3.4.7

angiosperm

flowering plants

Anthocerotophyta

the hornworts

Anthophyta

division to which angiosperms belong

basal angiosperms

a group of plants that probably branched off before the separation of monocots and eudicots

bryophytes

seedless, non-vascular plants; liverworts, hornworts, and mosses

Bryophyta

the mosses

charophyte

other term for green algae; considered the closest relative of land plants

club mosses

earliest group of seedless vascular plants

Coniferophyta

dominant division of gymnosperms with the most variety of trees

cotyledon

primitive leaf that develop in the zygote; monocots have one cotyledon, and dicots have two cotyledons

cupule

enclose and protect the ovule in gymnosperms

Cycadophyta

gymnosperm that grows in tropical climates and resembles a palm tree

Division

taxonomic category of plants used in place of phyla

eudicot

related group of angiosperms whose embryos possess two cotyledons

fern

seedless vascular plant that produces large fronds; the most advanced group of seedless vascular plants

flower

helps to facilitate pollination

fruit

functions in seed protection, dispersal, and germination

gametophyte

haploid portion of the plant

Gingkophyta

gymnosperm with one extant species, the Gingko biloba; a tree with fan-shaped leaves

Gnetophyta

gymnosperm shrub with varied morphological features that produces vessel elements in its woody tissues; the division includes the genera Ephedra, Gnetum and Welwitschia

gymnosperm

seed plant with naked seeds (seeds exposed on modified leaves or in cones)

hornworts

group of non-vascular plants in which stomata appear

horsetail

seedless vascular plant characterized by joints

liverworts

most primitive group of the non-vascular plants

lycophyte

club moss

Lycopodiophyta

the club mosses

Marchantiophyta

the liverworts

monocot

related group of angiosperms that produce embryos with one cotyledon and pollen with a single ridge

mosses

group of bryophytes in which a primitive conductive system appears

non-vascular plant

plant that lacks vascular tissue, which is formed of specialized cells for the transport of water and nutrients

ovary

chamber that contains and protects the ovule or female megasporangium

ovule

the female gametophyte

Plantae

the Kingdom of plants including all organisms that are eukaryotic, multicellular with differentiated tissues, and photosynthetic; mosses, ferns, conifers, and flowering plants are all members of the plant kingdom

pollination

the process of genetic recombination through sexual reproduction in some plants

Pteridophyta

the ferns, horseetails, and whisk ferns

pterophyte

seedless, vascular plants; ferns, horsetails, and whisk ferns

secondary cambium

cells that generate the vascular system of the trunk or stem and are partially specialized for water transportation

seedless vascular plant

plant that does not produce seeds; club mosses, ferns, horsetails, and whisk ferns

spermatophytes

seed-bearing plants

sporangium

reproductive sac that contains spores

sporophyll

leaf modified structurally to bear sporangia

sporophyte

diploid portion of the plant

strobili

cone-like structures that contain the sporangia

strobilus

plant structure with a tight arrangement of sporophylls around a central stalk, as seen in cones or flowers; the male strobilus produces pollen, and the female strobilus produces eggs

tracheid

xylem cells specialized for forming conduits inside the plant to conduct water

tracheophyte

vascular plant

vascular plant

plant containing a network of cells that conducts water and solutes through the organism

whisk fern

seedless vascular plant that lost roots and leaves by reduction

Unit 3.4.8

alternation of generations

a life cycle in which an organism has both haploid and diploid multicellular stages; haplodiplodonitc

antheridium

male gametangium

anther

sac-like structure at the tip of the stamen in which pollen grains are produced

apical meristem

tissue that increases the length of shoots and roots through rapid cell division

archegonium

female gametangium

calyx

whorl of sepals

carpel

single unit of the pistil

corolla

collection of petals

cuticle

protects the leaves and stems from desiccation

dioecious

describes a species in which the male and female reproductive organs are carried on separate specimens

diplontic

a lifecycle in which the diploid is the dominant life stage

embryo

a diploid structure that germinates into a sporophyte; contained within a protective coat making it a seed

embryophyte

other name for land plant; embryo is protected and nourished by the sporophyte

filament

thin stalk that links the anther to the base of the flower

gametangium

structure on the gametophyte in which gametes are produced

gynoecium

(also, carpel) structure that constitute the female reproductive organ

haplodiplodontic

a life cycle in which haploid and diploid stages alternate; alternation of generations

haplontic

a lifecycle in which the haploid stage is the dominant stage

herbaceous

grass-like plant noticeable by the absence of woody tissue

homosporous

refers to the one type of spore produced by the seedless, non-vascular plants

lateral meristem

tissue that produces cells that increase the diameter of tree trunks

lignin

complex polymer impermeable to water

megaspore

female spore

megasporocyte

megaspore mother cell; larger spore that germinates into a female gametophyte in a heterosporous plant

microspore

male spore

microsporocyte

smaller spore that produces a male gametophyte in a heterosporous plant

monoecious

describes a species in which the male and female reproductive organs are on the same plant

paleobotanist

traces the evolution of plants by following the modifications in plant morphology

perianth

part of the plant consisting of the calyx (sepals) and corolla (petals)

petal

modified leaf interior to the sepals; colorful petals attract animal pollinators

phloem

tissue responsible for transport of sugars, proteins, and other solutes

pistil

fused group of carpels

pollen

male gametophytes

rhizoids

thin filaments that anchor the plant to the substrate

secondary metabolites

complex organic molecules such as alkaloids, whose noxious smells and unpleasant taste deter animals

seed

contains the embryo protected by a coat

sepal

modified leaf that encloses the bud; outermost structure of a flower

stamen

structure that contains the male reproductive organs

stigma

uppermost structure of the carpel where pollen is deposited

stomata

pores that open and close to regulate gases and water vapor

style

long, thin structure that links the stigma to the ovary

xylem

tissue responsible for long-distance transport of water and nutrients