Bio 111 Midterm Vocab

Bio 111 Midterm Vocab

Ecology and Evolution

Phylogeny: A branching tree depicting evolutionary relationships among a group of organisms with a common ancestor. Shows ancestor and descendents.

Insects: ½ of all species on Earth.

Evolution: Changes in allele frequencies across generations.

Key Mechanisms of Evolution: Mutation, genetic drift, natural selection, sexual selection, and gene flow.

Mendelian study of evolutionary change: The study of how genes in individuals are inherited from parents.

Quantitative study of evolutionary change: Looking at populations and seeing how multiple genes are favored for survival.

Allele Frequencies: Count up the total number of one type of allele and divide by the total number of alleles.

Genetic drift: Within small populations, frequency of existing gene variants changes due to random chance. Causes random changes in allele frequencies.

Sexual Selection: Can be intra-sexual = male-male competition, or inter-sexual = female choice of mate.

Gene flow: Migration or Immigration between populations. That causes allele frequencies to change.

Maladaptation: When a species is not appropriately adjusting to their environment (may be a new environment due to climate change) and can lead to extinction or extirpation.

Ecological Traps: When organisms make poor habitat choices based on cues that correlated formerly with habitat quality.

Evolutionary Traps: Dissociation between cues that organisms use to make any behavioral or life-history decision and outcomes normally associated with that decision.

Range changes: The change in distribution (where a species is located in the world).

Elevational shifts: As species (like birds) get pushed up or down the mountain, their habitat space may run out.

Latitudinal shift: When a species is pushed north or south of its original habitat, this may lead to habitat space running out.

Microbes

Symbiosis: Interaction between two organisms living in close proximity, typically a mutual advantage however could be a disadvantage or no effect. “Living together”. Played a big role in the evolution of life.

Microbiome: Community of microorganisms existing in a particular environment. Most plants and animals have microbes living in and on them.

Microbe: Within the invisible world, about 100 nm to 1um. Microbes reproduce very quickly due to small surface area. Because they are small cells, they can absorb more nutrients per unit volume, thus needing less energy and nutrients to survive and reproduce.

Plasma Membrane: Boundary of all cells made up of a phospholipid bilayer. This is made up of hydrophobic (fear of water) tails on the inside, which consist of lipids, and a hydrophilic head group (phosphorus) on the inside and outside of the lipids.

Function of plasma membrane: To transport, allow specific molecules and ions to enter the cell. To signal, receptors bind and can change cell behavior. Perform adhesion, adhesion proteins hold cells together. The membrane holds all the reactants in the cell needed to perform cellular respiration. The membrane holds all the information (DNA) within the cell.

Plasmids: Small DNA molecules in bacteria that are picked up from the environment that help them survive adverse conditions or harm the bacteria like a parasite. They replicate at the same time as chromosomes, not always passed down to daughter cells. Some plasmids code for conjugation between two cells.

DNA polymerase: An enzyme that makes up a replisome, aids in bringing in new nucleotides during replication to complete both single strands of the DNA that was split and creates two double strands of DNA.

Replisome: Consists of DNA polymerase that aids in bringing new nucleotides during replication to complete both single strands of the DNA that was split and creates two double strands of DNA.

Photoautotroph: An organism that makes its own energy using sunlight and carbon dioxide via photosynthesis.

Heterotroph: An organism that cannot produce its own energy, getting carbon from other organic sources like plant or animal matter.

Ribosome: Consists of ribosomal RNA and proteins, where mRNA is translated into proteins.

Special Creation: The belief that a higher power created life on Earth.

Panspermia: Undirected - dispersal of microbes from planet to planet. Directed - deliberate seeding of planets by aliens. Misdirected - galactic pollution by spacecraft (meteors)

Spontaneous generation: The theory that life spontaneously and randomly appeared. There are two subtheories, either that complex organisms such as bacteria arose spontaneously, or that there was a continuous series of entities linking the unambiguously chemical with the living.

Electron transport chain: Happens in the mitochondria of eukaryotes, when electrons are passed from more electropositive to more electronegative molecules and in the process energy is released.

Glycolysis: Initial stage of energy production where a 6-carbon molecule of glucose is broken down into two 3-carbon molecules of pyruvate. This generates energy (ATP) and reduces power (NADH). NADH is an electron donor at the top of the electron transport chain.

Fermentation: If oxygen is not available, pyruvate is the final electron acceptor. NADH must be re-oxidized (loss of electron) to NAD⁺ as the electron carrier necessary for a fresh round of glycolysis. This process doesn’t generate energy.

Phylogenetic Methods: Start with a sequence alignment, identify changes at homologous sites, choose either distanced based approach (compute a distance matrix between each pair of sequences and join the two most similar sequences) or parsimony (choose the phylogenetic tree that minimizes the total number of mutations.

Domains: Bacteria, Eukarya, Archaea.

Monophyletic: Sharing a common ancestor that excludes other groups.

Relatedness: When two species share a common ancestor. The more recent that common ancestor is, the more related they are.

LUCA: Last Universal Common Ancestor known as “LUCA” gave rise to two daughter cells, one was the ancestor of all living Eubacteria, the other was the ancestor to all living Archaea.

Endosymbiotic theory: A horizontal process (Horizontal Gene Transfer) across a phylogenetic tree in which prokaryote engulfed another prokaryote

Evolutionary Trade Off: A key concept in evolution, adapting to one thing will include trade offs of being less good at something else. One virus can’t be good at everything, so specializing in a certain species may make the virus less effective with other species.

Phage: A virus that infects bacteria or archaea, highly diverse, linear double stranded DNA. Phages are a vector of horizontal gene transfer, injecting itself into a cell, copying its genome and cutting the cell's genome up, packaging new phages (some have phage DNA and some have cell DNA). The phages can now inject other cells with phage or the first cell DNA. This is how DNA from the first cell is transferred to a new cell. Phages and bacteria are in a cycle of coevolution (mutually imposed selective pressure). The phage puts a selective pressure on the bacteria to either learn how to resist a phage or it dies. The bacteria will become resistant to phages and so there is selective pressure on the phage to adapt and learn how to reinfect the new resistant bacteria.

Fungi

Features of fungi: Fungi are single celled or multicellular (made of filaments that are thread like cells). They have cell walls that are made of chitin (similar to some animals that use chitin to make up exoskeletons, like crustaceans, crabs, shrimp, insects). This is different from plant cell walls that are made of cellulose. Fungi don’t have a complex transport system like animals and plants do with a vascular system, instead they are made of hyphae. Fungi are heterotrophs, they absorb food directly from surroundings. Fungi reproduce both sexually and asexually. Fungi produce spores for dispersal which are tough and can tolerate dry conditions. They are saprophytes meaning they eat dead stuff. Fungi are also symbionts meaning they get fed by others, not always intentionally. They are one of the few organisms that can break down cellulose and plant matter. They often have symbiosis with other organisms like algae, cyanobacteria, and many other plants, 80% of vascular plants partner with fungi to get nutrients from soil.

Mycelia: Network of hyphae underground that allows the mushroom to absorb nutrients from their surroundings.

Hyphae: Cells that make up Fungi, they are long and thin, creating a large surface area which leads to high absorption. Hyphae are separated by septa (cross walls) and have large pores allowing for the passage of nutrients. Hyphae are 80-90% water.

Fungi Reproduction: They reproduce sexually and asexually, and sometimes during both haploid and diploid phases. When reproducing asexually they either break apart (fragmentation) or reproduce during the haploid phase, creating vegetative spores (1n).

Plasmogamy: Sexual reproduction in fungi when two compatible individuals (haploid nuclei 1n) fuse their mycelia together to initiate sexual cycle creating one cell with two nuclei (dikaryotic). The resulting dikaryotic cell can stay in this stage for decades.

Karyogamy: When a dikaryotic cell fuses their two 1n haploid nuclei, creating a cell with 1 2n nuclei. This cell with a 2n nucleus can then split into two cells through meiosis, creating 1n spores.

Saprophytes: Fungi are saprophytes meaning they eat dead stuff, decomposers.

Yeast: A single celled fungus that reproduces by budding and is able to ferment sugars, used in beer, wine, and bread making.

Mycorrhizae: Through symbiosis of plant and fungi, mycorrhizae are created. Vascular plants partner with fungi to increase the area of the root system for absorption.

Plants

Monophyletic: A group that evolved from a common ancestor and includes all descendants.

Sister Groups: Two groups that split from a common node (evolved from a common ancestor).

Archaeplastida/Plantae/Plants: Single or multicellular organisms, plantae is monophyletic with most organisms performing photosynthesis (however not all). It is important to note that photosynthesis is not monophyletic.

Chloroplast: An organelle where photosynthesis takes place. Eukaryotes acquired chloroplast through endosymbiosis with a cyanobacteria. Through secondary endosymbiosis photosynthesis was able to spread within eukaryotes.

Endosymbiosis Theory: The theory that photosynthetic eukaryotes evolved from cyanobacteria when a single celled eukaryote engulfed a cyanobacteria, and the cyanobacteria became the organelle chloroplast in the eukaryote. This is also the theory for the origin of mitochondria in eukaryotes. It is thought that a bacteria had mitochondria-like properties, and a single celled eukaryote engulfed the bacteria, the bacteria evolved into the organelle mitochondria in eukaryotes. The endosymbiont theory of mitochondria must have come first because all eukaryotes have a mitochondria, but not all have a chloroplast.

Secondary Endosymbiosis: When an organism engulfs a cell that has previously undergone endosymbiosis. Photosynthesis arose due to first endosymbiosis once in eukaryotes. Photosynthesis was able to spread to many different species in eukaryotes due to secondary endosymbiosis. A predatory eukaryote engulfed a photosynthetic eukaryote, now that the photosynthetic eukaryote is in the predatory eukaryote, the nucleus of the photosynthetic eukaryote is lost and the predatory eukaryote now has a chloroplast.

Phytoplankton: Single celled photosynthetic organism ,made up of either photosynthetic bacteria or photosynthetic eukaryotes. The base of almost every ocean food web.

Trophic Cascade: Ecological change when a predator (key stone species) is removed from the food pyramid. The removal of a carnivore at the top of the pyramid affects prey animals and vegetation.

Carotenoid: Pigment used in photosynthesis, colors both brown and red algae. It is also a pigment found all over biology for uv protection, coloration, and photosynthesis. Carotid is important to red algae because the pigment helps absorb blue light, allowing them to live at great depths where not much light reaches.

Viridiplantae: “Green plants”, monophyletic, key innovations are the chloroplast, UV-absorbing compounds, a cuticle, and reproduction methods. Red Algae→ Green Algae→ Land plants→ Vascular Plants→ Seed Plants (Gymnosperm or Angiosperm). They reproduce and create spores or gametes (made in complex multicellular structures. In land plants, zygotes begin development on the parent plant and form multicellular embryos that remain attached to the parent plant. Embryo retention is a key innovation of land plants. As land plants became more complex, sporophytes became dominant. The gametophyte dominant life-cycle evolved first and then came the sporophyte dominant life-cycle.

Non Vascular Plants: These plants evolved first before vascular. They lack vascular tissue, they absorb water and nutrients from their surroundings at their surface through diffusion. An example would be bryophytes and green algae.

Desiccation Resistant Spores: Spores are tough and strong, able to resist dying, drying out, survive for long periods, and be dispersed.

Bryophytes: Non vascular, the ancestors of the first land plant, no true roots, absorbs nutrients and water through their leaves. Leaves surrounded by a cuticle, little to no stomata. They are slow growing as they are limited by diffusion. They undergo alternation of generations with the gametophyte phase being more dominant, and can be unisexual or bisexual. They need water for reproduction, the thin layer on plants allows sperm to move between gametophytes.

Cuticle: A cuticle is a watertight sealant coving aboveground plant parts (leaves). It is produced by epidermal cells and is made of hydrocarbons, lipids, and wax. It prevents water loss and limits gas exchange. Present in vascular plants, early non-vascular plants have rudimentary cuticles (no stomata)

Spore: A product of reproduction (1n), they are encased in a tough outer shell. This tough coating allows them to resist drying, survive for long periods of time, and be dispersed by wind.

Alternative Generations: Phases added into the reproduction cycle of a plant that reproduces sexually, where they can be multicellular in 1n and 2n stages. 1n spores will undergo mitosis, creating a multicellular organism called a gametophyte. Eventually the 1n cells from this gametophyte will break off, two 1n cells will fuse together, creating a zygote. This zygote will mature into a multicellular organism called a sporophyte. This sporophyte will undergo meiosis to create spores.

Gametophyte: A multicellular organism in a stage in alternative generations when the cells are 1n. Gametophyte cells (1n) will fuse together to create a zygote (2n).

Sporophyte: A multicellular organism in a stage in alternative generations when the cells are 2n. A sporophyte will undergo meiosis to create 1n spores.

Sphagnum: A type of moss, piled together creates peat lands, a highly efficient carbon sink. Sphagnum is a keystone species that creates massive carbon sinks. They grow very slowly