EFB 101 Exam 2

Phylogeny

Evolutionary history of a species or group of species.

Apomorphy

a derived character state.

Synapomorphy

shared derived character (i have a spine and birds have a spine because our shared ancestor has a spine)

Homology

shared trait resulting from common ancestry (same as synapomorphy)

Homoplasy

A similar (analogous) structure or molecular sequence that has evolved independently in two species. Aka convergent evolution.

Autapomorphy

A derived character state that is unique to a single taxon; e.g. only humans have opposable thumbs

Monophyly

the condition that a taxon or other group of organisms contains the most recent common ancestor of the group and all of its descendants

Polyphyly

a group that does not uniquely share a common ancestor - undesirable classification

Paraphyly

a group with an ancestor and only some of its descendants - undesirable classification

node

a point where one taxon diverges from another - where a common ancestor occurs

polytomy

a branch from which more than one taxon emerges due to lack of info

Taxon

group or level of organization into which organisms are classified

basal taxon

the most common ancestor

secondary loss

reversion to ancestral condition; a reason for homoplasy

Plesiomorphy

ancestral character state (plesiomorphic erin) (based)

parsimony

the least possible evolutionary steps; most parsimonious is preferred

outgroup

a group of organisms not belonging to the group whose evolutionary relationships are being investigated. must be included in a phylogeny. They have all plesiomorphic traits

molecular clock

Supposed constant rate of change for evolutionary mutations. High error margin due to the following: (1)Some genes evolve in irregular bursts
(2)Even clocklike genes have deviations from AROC
(3)Some genes evolve at different rates in different organisms
(4)Some genes evolve faster than others even in the same organism
(5)Some mutations are selectively neutral and have little to no effect on fitness. These mutate faster.
(6)Estimates of evolutionary divergences predating the fossil record have a high degree of uncertainty

Virus

A tiny, nonliving (debated), infectious particle that invades and then reproduces inside a living cell. Consisting of genetic material (either dna or rna, NOT both), obligate intracellular parasites.

three taxonomic domains

Bacteria, Archaea, Eukarya

obligate intracellular parasites

cannot multiply unless they invade a specific host cell and instruct its genetic and metabolic machinery to make and release new viruses. Host ribosomes are used to translate mRNA.

host range

The limited range of host cells that each type of virus can infect and parasitize.

tissue tropism

the range of tissue types that a virus can infect

lytic cycle

A type of viral (phage) replication cycle resulting in the release of new phages by lysis (and death) of the host cell. we just need to know it kills the host.

lysogenic cycle

a viral reproductive cycle in which the viral DNA is added to the host cell's DNA and is copied along with the host cell's DNA

Induction

switch from lytic to lysogenic cycles

phage conversion

alteration of the phenotype of a host cell by a lysogenization

Interferons

Antiviral proteins secreted by T cells; interfere with viral gene replication

Rendesivir

an antiviral that inhibits transcription

Ritonavir

an antiviral that inhibits protein synthesis

Hydroxychloroquine

an antiviral that inhibits viruses entering host cells

Antigen

A protein on a virus that triggers the production of an antibody

genetic recombination

The regrouping of genes in an offspring that results in a genetic makeup that is different from that of the parents.

Bacteriophage

A virus that infects bacteria, good for antibiotic resistant bacteria

How much of our genome is viral?

8%

Endosymbiosis

A theorized process in which early eukaryotic cells were formed from simpler prokaryotes.

What organelles does endosymbiosis concern?

Mitochondria and chloroplasts

Prokaryote

A unicellular organism that lacks a nucleus and membrane bound organelles

How many prokaryotic cells do we carry in comparison to our own cells?

10x more

Microbiome

all of the microorganisms that live in a particular environment, such as a human body

Symbiotic functions of prokaryotes living on us

Extract energy from food, produce vitamins, prevent disease

Microbiome delivery methods - horizontal

Environment to person

Microbiome delivery methods - vertical

Parent to child

Other microbiome delivery methods

Diet, pets

Mitochondria

Powerhouse of the cell

What kinds of conditions do prokaryotes love?

Harsh (hot, salty, cold, etc)

What two domains are prokaryotes?

Archaea and Bacteria

How is prokaryotic genetic material stored?

Single circular chromosomes

Bacillus

Of a bacterium, rod shapes

Coccus

Hahahahhahahahahahahahahahahah
a spherical bacterium

Strepto-

chains of bacteria

Staphylo-

grape-like clusters of bacteria

Taxis

Of a bacterium, movement towards or away from a stimulus

Flagellum

Tail that helps with movement; homoplasious

Three components of a flagellum

Motor, hook, filament

tumble and run

Describes the movement of prokaryotic organisms. Tumbles in counterclockwise flagellum rotation and then runs in clockwise

Bacteria functions

Producers, decomposes, disease-causers, nutrient cyclers

peptidoglycan

A protein-carbohydrate compound that makes the cell walls of bacteria rigid

Gram-positive bacteria

Bacteria with a thick peptidoglycan layer, affected by antibiotics

Gram-negative bacteria

Bacteria that have complex cell walls with less peptidoglycan but with lipopolysaccharides (we just need to know it's an extra layer). Antibiotic resistant.

Commensalist bacteria

Skin bacteria

Mutualist prokaryotes

Gut microbiome, some fungi

nitrogen-fixing bacteria

bacteria that can use nitrogen in soil to make nitrogen compounds

parasitic bacteria

The bad guys. Cause disease by releasing endotoxins

Endotoxins

Toxin released only when bacteria die and their cell walls break down

Exotoxins

toxic substances that bacteria secrete into their environment

Bacterial organization is...

Simple!

(T/F) bacteria usually have circular chromosomes

True

(T/F) bacteria have a nucleus

False

R plasmid

A bacterial plasmid carrying genes that confer resistance to certain antibiotics.

binary fission

A form of asexual reproduction in single-celled organisms by which one cell divides into two cells of the same size

Antibiotic types - bacteriostatic

An antibiotic that halts bacteria reproduction

Antibiotic types - bactericidal

Kills bacteria

What makes a good antibiotic?

selective toxicity - targets stuff bacteria have that we don't

Methods of antibiotic resistance? (There are 4)

adjusting membrane permeability, breaking down with enzymes, using lysosomes to dispose of them, changing activation sites

Transformation

A change in genotype and phenotype due to the assimilation of external DNA by a cell. More common than once believed

Transduction

Bacteriophages (recall) carry genes from one host cell to another

Conjugation

In gram-negative bacteria, the direct transfer of DNA between two cells that are temporarily joined via pilus; requires set of up to 25 genes that create the pilus

Final electron donor in electron transport chain - aerobes

O2

Obligate aerobes

Require oxygen

Facultative aerobes

Choose to use O2

Phototroph

an organism that gets its energy from sunlight

Autotroph

An organism that makes its own food

Heterotroph

An organism that cannot make its own food.

Chemotroph

organisms that gain energy from chemical compounds

Chemolithotroph

an organism that obtains its energy from inorganic compounds

Chemoorganotroph

an organism that obtains its energy from organic compounds

Where do autotrophs get carbon?

CO2, HCO3+, etc

where do heterotrophs get their carbon?

organic compounds in things they eat

Anaerobic phototroph

Oxidize organic molecules, don't produce O2

Aerobic phototroph

Cyanobacteria, use water to get electrons, supply O2 and N

Endospore

A thick-walled protective spore that forms inside a bacterial cell and resists harsh conditions.

Eukaryote characteristics

Membrane-bound nucleus and organelles, larger

Genome

the complete instructions for making an organism, consisting of all the genetic material in that organism's chromosomes

Prokaryotic vs. Eukaryotic genome

Eukaryotic is much larger and therefore error prone, prokaryotes have mostly coding dna while eukaryotes have only a little

Why do cells have folds in the membrane.

To increase area we increasing volume

Mitochondria have their own circular dna and are self replicating.

Idk how to make that a flash card but it's important lol. Also supports the theory of endosymbiosis (recall)

Why are chloroplasts supportive to endosymbiosis?

They have similar bacterial characteristics to mitochondria. They are self replicating. Some have peptidoglycans also found in cyanobacteria cell walls.

(T/F) some prokaryotes can reproduce sexually.

False!

Disadvantages of sexual reproduction

Gene dilution (also an advantage if your genes are shit tho)
Decreases fitness, chance for maladaption during recombination, STDs.