Exam 1

a. Miller/ Urey experiments-recreated reducing atmosphere- synthesized amino

            acids

            b. Hydrothermal vents-reducing atmospheres exist

            life around vents relies on sulfur for energy instead                                                                         of the sun. 

            c. Extraterrestrial origins- large proportion of dust in universe has amino acids

            which are raining down on us on a regular basis

First cells appear ~3.5BYA

The first photoautotrophs (rely on sun)

            Stromatolites (3.5 BYA)-rock-like structures comprised of photosynthetic bacteria (cyanobacteria) and sediment, rare now but used to be common on Earth

-oldest known fossils that formed 3.5 BYA

Oxygen is the waste product of photosynthesis. Stromatolites create an oxygen rich atmosphere

Metabolic waste O2 saturates oceans, precipitation iron oxides-O2 then seeped into the atmosphere.

Oxygen toxic to most existing prokaryotes (they are anaerobic). 

                        -Aerobic metabolism spreads, creating new evolutionary possibilities

                        (Aerobic metabolism generates ALOT more ATP than anaerobic metabolism)

Formation of heterotrophy- Prok autotrophs open new ecological niche: the consumer is formed (heterotrophic)

            Evolution of Euk due to development of hetertrophs

-The Endosymbiotic model (Lynn Margulis) :

Heterotroph ate another cell and did not digest it well (phagocytosis)

This eventually forms a symbiotic relationship- host and endocytosed become single organism

- organelles have same biochem as Prok

        -  orgenelle replicates through binary fission

single cells began aggregating into colonies (pays to group together in harsh conditions and specialize)

-Evolves multiple times (ind in plants, fungi, and animals)

Phanerozoic

Paleozoic, Cenozoic, Mesozoic

Eons > Eras >  Periods >  Epochs

Pangea (Paleozoic)- one giant land mass

Gondwana (Mesozoic)- breaking up of giant land mass

Laurasia (Mesozoic)

Cenozoic - modern establishment of continents

colonization of land >>>plants>>>invertebrates>>>vertebrates

specific location of a gene / DNA sequence on a chromosome

- Migration -gene (allele) flow

        - Mutation - error in replication leads to shift in allele freq- could inc or dec alleles

        - Genetic drift - random change in allele frequency in a pop. over time-  ALL pop drift but drift is most effective in small populations

        - Selection - mechanism that adaptively shape traits via differential reproductive success amongst different genotypes. 

stabilizing- select against all extremes

disruptive - select for the most extreme phenotypes

directional- alleles at one extreme or another selected for or against

Sexual selection - selection in direct relation to competition for mates or fertilizations- non-random mating aka assortative mating

Hardy-Weinberg equilibrium theorem

allele / genotype frequencies remain constant from generation to generation unless acted on by one (or more) of the mechanisms of evolution

p² + 2pq + q²  = 1

Mutation

a.      Substitution

b.      Insertion / deletion

Meiosis

Crossing over

            Random fertilization of gametes

Nonsense mutations, Silent Mutations, Missense mutations

silent- code for the same amino acid

missense- code for a different amino acid

nonsense- code for a stop and can truncate the protein

Pre-zygotic barriers -barriers before the zygote is formed

            i. Premating

a. Habitat isolation-live in diff but adjacent habitats

                        b. Temporal Isolation- mate in diff seasons

                        c. Behavioral Isolation- variation in sexual signals (auditory and visual)

ii. Postmating prezygotic- barriers before an offspring is made but after mating has occured (or otherwise been attempted)

                        a. mechanical isolation- variation in genital morphology among species

                        b. gametic isolation -sperm is selectively used from an organisms own species

-Post-zygotic barriers

            i. Reduced hybrid viability

            ii. reduced hybrid fertility

                        iii. hybrid breakdown

BIOLOGICAL SPECIES CONCEPT- species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups

.)-asexual organisms

-fossils

-organisms where little is known about reproduction

-even some well defined species have the potential to interbreed

Allopatric- geographic seperation restricts gene flow

Anagenesis- gradual transition of one sp into another

versus cladogenesis- branching of one or more new species from a parent species

Normally evolution does not occur in one generation

-Gradualism -contention exists because fossil record is largely incomplete

a.      Gaps in fossil record prevents assessment of speciation rate in many lineages

          -Punctuated equilibrium - suggests that gaps in fossil record not actually gaps; but very rapid evolution not captured as fossils.

          i.            Wrong environment

            ii.            Soft bodies

            iii.          Episodic /local fossilization

            iv.          Fossils lost

Microevolution – evolution within a population or species; generational timescale.  Covers new breeding population to new species realm

Macroevolution – evolution across species; geological timescale

synapomorphies- shared derived traits

i. Radiometric analysis of surrounding rocks-unstable radioactive element that gives off beta or alpha particles -decays into another element- the half life of that element is the time it takes to lose a half of that parent element.  Look at ration of parent vs daughter element and can determine age of a rock based on its radioactive signature.

igneous – (cooled magma) provides absolute age

b. sedimentary – (sediments deposited in aged layers, most fossils)provides relative age

c.  metamorphic - (altered ignaceous and sedimentary rock) often not useful

ii. Index fossils (correlation analysis)- compares unknown with known

a. e.g Ammonite fossil- global distribution- makes good index fossils

iii. Magnetism- lava has a high iron conten

-aligns with magnetic poles as it cools

-potassium/argon dating indicates that poles reverse ~500,000 YRS

Homology- structures that have shared evoltionary history.

homoplasy aka analogous-structures that appear similiar but do not share a common evoltionary origin

Synapomorphy (shared derived traits-new) versus Plesiomorphy (shared ancestral traits-old)

autapomorphy- derived but not shared by any other lineage.  only synapomorphies are useful in constructing phylogenies

Outgroup – taxon outside a closely related group (clade)

-used as a reference to help infer an evolutionary relationship within a more closely related group

-outgroup will not have synapomorphic traits

how do we build a phylogeny?

- choose outgroup

- id synapomorphies

- collect data on synapomorphies

- create phylogeny

Follow the rule of parsimony-the hypothesis requiring least number of evolutionary events is likely correct

Cladograms – branch length arbitrary- shows basic grouping of taxa and how they are related

            Phylogram – branch length indicates number of differences (diversity)

            Ultrametric – branch length indicates time since divergence- always has a timeline below it

- Monophyletic – group consisting of last common ancestor and ALL descendants -can count clades by counting all of the nodes but you must include all of the descendents

            - Paraphyletic – group consisting of ancestor and MOST descendants

Technique used to relate molecular differences between two lineages to their absolute time since divergence

Reveal changes not captured by the fossil record

Resolve evolutionary hypotheses

Identify illegal activity

            Track the origins and spread of infectious disease

Tobacco Mosaic Virus (TMV) – first virus isolated

determined that TMV waas a dz caused by bio agent - that agent was contained in sap and that agent was likely bacteria

-filters sap- finds dz caused by bacterial toxin (not actual bacteria)

-realizes that a dz caused by a tiny replacationg agent (unusually small bacteria) - deduces this because he filters sap once- infect plant and filters this sap again and reinfects a plant which means there is some kind of self-replicating mechanism- rules out toxin idea

-tried to culture and would not culture- realizes it is not a bacterial agent and it needs a host to replicate

Capsid – outer shell of virus

            Capsomer – functional unit of capsid

            Membrane – host derived cell-membrane

            Surface proteins

contains a capsid and capsomers and RNA (two functional pieces RNA and Protein (capsid))

takes a pc of host cell membrane and wraps it self in it to avoid detection from the hosts' immune system

-virus enters cell- capsid breaks apart inside host cell

                        - host cell replicates viral genome

                        -viral genes transcribed

                        - viral proteins / genes self-assemble

                        - Completed virus departs cell

same as general with addition of the following:

                        - Completed virus takes host membrane upon departure

transcriptase – enzyme that transcribes viral RNA to DNA

            integrase – enzyme that randomly inserts new DNA into cell genome

Lytic (virulent; cell death via lysis eminent)

            Lysogenic (temperate; cell death via lysis eventual)- viral genome incorporated -non-virulent for many cell cycles

viroids and prions

Viroids-

-small circular ss RNA

-no protein coat

-makes no proteins

-cause plant dz by interfering with gene transcription

-delta-viruses are viral parasites

-Can be parasites of other viruses

Prions -

- Misfolded proteins (no nucleic acids)

cause degenerative neural dz -forms plaques in the brain

resistant to heat and other sterilization methods

long incubation periods (10yrs)

-Replicate by touching other normal proteins-prion touches normal protein and changes normal protein conformation to prion conformation (zombiesim)

-bovine spongiform encephalopathy (aka mad cow) is an example of a dz caused by a prion

archaea and bacteria

no membrane / organelles , no mitosis / meiosis, often flagellated, unicellular

Cocci (spherical), Bacilli (rod), Spirullum (spiral)

- peptidoglycan wall (bacteria only)

                        - RNA polymerase (bacteria has only one type)

                        - introns (archaea only)

                        - Histones (archaea only)

                        - pathogenicity (bacteria only)

                        - antibiotic susceptibility  (bacteria only)

                        - extreme environments (archaea only)

-Transformation – uptake of foreign DNA

- Transduction – Horizontal gene transfer btw bacteria via phage virus

- Conjugation – one way transfer of genes (plasmid or chromosome); F

factor needed for pilus formation 

heterocysts

natural process by which nitrogen in the atmosphere (N2) is converted to ammonia (NH3).  This process is essential for life because nitrogen is needed to form the basic building blocks of life.

Resistant bacteria are selected for when there is selective pressure against bacteria that are susceptible to antibiotics.  The resistant bacteria have increased room to grow and food to eat when the other bacteria are dead.  This is thrown out of balance with the overuse of antibiotics (unneeded perscription, animals, etc)

multiple branches extending from one node- do not understand their evolutionary relationship

Eukaryotic heterotrophy engulfs photosynthetic cyanobacterium (primary endosymbiosis).

-Bacterium membrane lost, forms organelle (i.e. chloroplast). New organism known as algae- two algae lineages arise (red and green algae lineage)

-Eukaryotic heterotrophy engulfs algae (secondary endosymbiosis)

        A. Excavata

            1. Unifying traits

                        a. Highly modified mitochondrira, multiple flagella, 'excavated'                                                 feeding groove (why they have the Excavata name)

B. Chromalveolata

            1. Derived from secondary endosymbiosis of red algae

C. Rhizaria

            1. Amoeba like; thread-like pseudopodia           

D. Archaeplastida- gave rise to the green algae (which have plant like chloroplasts)

            1. Main groups include red algae, green algae and land plants           

E. Unikonta- one of these lineages eventually give rise to animals

chaonoflagellates -closest protist relative to animals

            1. Amoebazoans; tube-like pseudopodia