BIOL 111 Midterm Exam

natural selection

the process through which populations of living organisms adapt and change

direct selection

-selection moving in one direction

-overall distribution of traits shifts

-mean trait changes

disruptive selection

-selection takes away from mean group

-mean trait doesn’t necessarily change

stabilizing selection

-selection reinforces mean character trait

genetic drift

-random changes in allele frequency

-has greater effect on small populations

-still a type of evolution, just not natural selection

sexual selection

-type of natural selection where members of a sex compete for access to mates based on specific traits

-can oppose other forms of natural selection and result in fitness costs

-(think male peacock example)

continuous variation

trait changes gradually over a wide range of values

• NO distinct categories

• ex: height, skin color

discontinuous/discrete variation

variation falls into distinct, separate categories

• ex: blood groups

biogeography

the scientific study of the geographic distribution of species, organisms, and ecosystems across geographic/geological space and time

heritability

the proportion of variation in a genetic trait within a specific population that is due to genetic differences between individuals, rather than environmental factorsnic

niche

all of the interactions of a species with the other members of its community,

speciation

-the formation of new and distinct species in the course of evolution

-the splitting of a single evolutionary lineage into two or more genetically independent lineages.

sister taxa

groups that share an immediate common ancestor, making them each other's closest relatives on a phylogenetic tree

outgroup

more distantly related species on phylogenetic tree

node (on phylogeny)

points at the ends of branches which represent sequences or hypothetical sequences at various points in evolutionary history. 

branch (on phylogeny)

-path of transmission of genetic information from one generation to the next

-branch lengths indicate genetic change i.e. the longer the branch, the more genetic change has occurred. 

common ancestor

an ancestral group of organisms or individual species from which two or more descendant lineages evolved

extant

species, genus, or family still living on Earth

polyploidy

-a condition where a cell or organism has three or more complete sets of chromosomes instead of the usual two sets

-can lead to nearly instant speciation

phenology

the study of the timing of recurring biological life cycle events and how they are influenced by seasonal weather and climate.

(phenotypic) plasticity

different phenotypes emerging from a single genotype

range shift

a change in the geographic distribution of a species or population over time

artificial selection

the human-driven process of intentionally choosing and breeding specific plants or animals to amplify desired traits in future generations

microbe

A single-celled, microscopic organism, including bacteria, archaea, viruses, and some eurkaryotes.

spontaneous generation

the theory that living cells emerge spontaneously from non-living matter

symbiosis

-two or more organisms of different species living together in close proximity

-can include beneficial, neutral or harmful (e.g. parasitism) relationships.

cell

an individual biological unit capable or metabolism and reproduction

-bound by a plasma membrane and containing a genome

genome

-the entire genetic content of a cell, including the chromosome and any extra-chromosomal elements like plasmids

-can be made up of DNA or RNA

transcription

the process of synthesizing a single-stranded mRNA molecule from a coding sequence of DNA (a gene) in the genome

ribosome

a complex of RNA and protein that translates mRNA into protein

translation

the process of synthesizing a protein as a specific sequence of amino acids specified by codons in mRNA

mRNA (messenger RNA)

a long RNA molecule transcribed from DNA, consisting of codons.

codon

a specific sequence of 3 consecutive nucleotides that encode a specific amino acid or the ‘start’ or ‘end’ of translation

protein

a string of specific amino acids that fold into a specific 3-dimensional structure that determines its biological function (e.g enzyme, structural, etc).

horizontal gene transfer

the transfer of genetic material between organisms rather than from parent to offspring

-primarily occurs in microbes

Pasteur’s spontaneous generation experiment

-pasteur determined that microbes do not arise from spontaneous fermentation, they come from other microorganisms in environment

-only breaking the neck of the flask allowed the microbes into the broth, previously they would be unable to swim through the steep neck of the flask

autotroph

an organism that uses an inorganic carbon source (like carbon dioxide)

heterotroph

an organism that uses organic carbon (like carbohydrates and sugar)

phototroph

an organisms that gets its energy from light (rather than chemical energy)

oxidation

loss of electrons by a molecule.

reduction

gain of electrons by a molecule

redox

the coupling of oxidation and reduction ‘half reactions’ into a single chemical reaction, releasing energ

respiration

The process of oxidizing organic compounds using a terminal electron acceptor
such as oxygen (in the case of aerobic respiration), sulphate or nitrate (in the case of
anaerobic respiration).

LUCA

most recent common ancestor of all life living on Earth today

ribozyme

an RNA molecule that catalyses a chemical reaction

RNA World Theory (1960s)

-RNA formed first, eventually leading to DNA/protein formation

-RNA can store replication info, replicate itself, act as an enzyme (ribozyme), could have catalyzed reactions before DNA/protein evolution

-But… RNA isn’t stable in water (gets broken down through hydrolysis)

Primordial Soup Theory (1871)

-Early earth environment had many compounds that are abundant in life: C, H, H₂O, NH_3. Early earth had chemically reducing atmosphere (very low levels of O₂ gas)

-the atmosphere produced simple organic compounds from energy sources

-compounds accumulated in a “soup” concentrated at various locations.

-concentration led to eventual formation of complex organic molecules

• life eventually rose from complex polymers

• early cells then broke down polymers to generate ATP (heterotrophy)

Deep Sea Hydrothermal Vent Theory (2010)

-Alkaline water from vents combines with acidic ocean water to create natural proton gradient

-hydrothermal vent structures produced by chemical reactions between rock and water

-chimney structures are porous and can act as a semi-permeable membrane (energy generated with movement of proton gradient)

-Once energy was reliably generated, formation of organic monomers, polymers, DNA, RNA, and proteins would follow

stromatolite

macroscopic structures formed through the activity of microbial mats, either fossilized or living.

microbial mat

layered community of microorganisms growing together on a surface

biosignature

evidence that may indicate the presence of past or present life

molecular biomarker

an organic molecule preserved in rocks or sediments that can provide evidence about past life

anoxygenic photosynthesis

photosynthesis that does not produce O₂ and uses electron donors other than water

cyanobacteria

bacteria capable of oxygenic photosynthesis

Great Oxidation Event

-the interval when O₂ first accumulated substantially in Earth’s atmosphere

-occurred 2.4-2.1 billion years ago

-caused by cyanobacteria that performed oxygenic photosynthesis

prokaryote

an organism whose cells lack a membrane bound nucleus

eukaryote

-organism whose cells contain DNA within a membrane-bound nucleus and other membrane-bound organelles

-a domain of life on Earth

endosymbiosis

-a relationship in which one organism lives inside another

-central to the origin of mitochondria and chloroplasts

eukaryogenesis

-the evolutionary process that gave rise to the eukaryotic cell and lineage

-merging of asgard archaea and alphaproteobacteria (evolved into the mitochondria)

archaea

single-celled microorganisms that are evolutionarily distinct from bacteria

asgard archaea

a group of archaea that are the closest known archaeal relatives of eukaryotes

metagenomics

sequencing of DNA directly from an environmental sample without first culturing the organisms

Horizontal Gene Transfer (HGT)

movement of genetic material between organisms rather than from parent to offspring

vertical inheritance

transmission of genetic material form parent to offspring

species tree

a phylogenetic tree showing the evolutionary relationships among organisms

gene tree

a phylogenetic tree showing the evolutionary history of a particular gene

virus

genetic material enclosed in a protein coat that requires a host cell to replicate

phage

a virus that infects bacteria or archaea

polytomy

a node on an evolutionary tree where more than two descendant lineages split from a single ancestral group

yeasts

singe-celled funghi

hypha/hyphae

-long, thin, branching filaments that form the main body (mycelium) of a fungus

-can absorb a ton of nutrients

mycelium/mycelia

the vegetative body of a fungus that is made up of hyphae

chitin

tough, natural sugar polymer that forms the cell wall of a fungus

septum/septa

internal dividers that split hyphae into cellular compartments

saprophyte/saprophytic

an organism that obtains nutrients from dead/rotting plant or animal material

symbiont

-an organism that lives in long-term association with an organism of a different species

-typically refers to the smaller of the two partners (the larger=host)

-does NOT imply a mutually beneficial association

conidia

asexual, non-motile spores produced by some fungi for reproduction and dispersal

conidiophore

specialized branch of a fungus that produces conidia

Dikaryotic stage

-fungi reproductive stage where each cell contains 2 separate, genetically distinct haploid nuclei (but one cytoplasm) from different parents

plasmogamy

1st stage of fungi sexual reproduction where cytoplasm of 2 parent cells fuse without the fusion of their nuclei

karyogamy

final step in fungi sexual reproduction where 2 haploid cell nuclei fuse to forma single diploid nucleus

monophyletic

a biological grouping that consists of a single common ancestor and ALL of it’s descendants

protist

any eukaryotic organism that is not a plant, animal, or fungus

plantae

taxonomic kingdom consisting of multicellular, eukaryotic, and mostly autotrophic organisms that photosynthesize

archaeplastids

a group of living things including land plants, green/red algae, and glaucophytes

opisthokonts

a broad group of eukaryotes, including both the animal and fungus kingdoms

chloroplasts

structure within the cells of plants and green algae that is the site of photosynthesis

secondary endosymbiosis

a non-photosynthetic eukaryote engulfs another photosynthetic eukaryotic cell (such as red/green algae), that has already undergone primary endosymbiosis

thallus

a vegetative body (such as algae, fungi…) that lacks true roots, stems, leaves, and vascular tissue

trophic cascade

-adding or removing top predators triggers a domino effect of dramatic changes down through the lower levels of a food web

-ex: local sea otter extinction led to surplus of sea urchins that consumed kelp, which resulted in the destruction of kelp forests

alternation of generations

-unique to plants

-life cycle where an organism switches between multicellular haploid stage (1 set of chromosomes) and multicellular diploid phase (2 sets of chromosomes

• haploid=gametophyte: produces gametes through mitosis

• diploid=sporophyte: produces spores through meiosis

-(spores = haploid!)

sporophyte

the diploid, spore-producing phase in the life cycle of plants and some algae

gametophyte

the haploid phase in the life cycle of plants and some algae that produces gametes (sperm+eggs)