How long ago did the sun and planets form?
4 steps to get to evolution of basic cells:
A. abiotic synthesis of small organic molecules-
Three ideas on how this could have happened include: extraterrestrial origins, deep sea vents, reducing atmosphere
B. single molecules (monomers) join with other molecules to produce polymers- clay lattice
C. self replication- RNA evolved before DNA- DNA was selected due to its stability
D. polymers and monomers packed into protobionts
What is the evidence supporting each hypothesis of the abiotic synthesis of organic molecules?
a. Miller/ Urey experiments-recreated reducing atmosphere- synthesized amino
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
What is the evidence that supports RNA being the original unit of heredity?
When did the first cells appear?
First cells appear ~3.5BYA
Describe the first Prokaryotes
The first chemoautotrophs
- Sulfur derived ( find in hydrothermal vents)
- Methane derived (find in cold seeps)
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.
Direct consequences of the Oxygen Revolution
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)
How did evolution of Eukaryotes occur?
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
What is the evidence that supports the endosymbiotic model?
- organelles have same biochem as Prok
- orgenelle replicates through binary fission- organelles possess their own DNA!
What are the domains of life?
How did evolution of multicellular organisms occur?
single cells began aggregating into colonies (pays to group together in harsh conditions and specialize)
-Evolves multiple times (ind in plants, fungi, and animals)-Allows for the evolution of cellular specialization (i.e. tissues)
What were the pre-Cambrian eons?
What eon did the Cambrian explosion occur in?
Paleozoic, Cenozoic, Mesozoic
What era and period did the Cambrian explosion occur in?
What is the hierarchy (most inclusive to least inclusive) of geologic time?
Eons > Eras > Periods > Epochs
Pangea (Paleozoic)- one giant land mass
Gondwana (Mesozoic)- breaking up of giant land mass
Cenozoic - modern establishment of continents
colonization of land >>>plants>>>invertebrates>>>vertebrates
specific location of a gene / DNA sequence on a chromosome
Define gene pool
What are the mechanisms that cause a change in allele frequency within a population?
- 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.
What are the ways that selection can modify phenotypes; describe each type.
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
Give an example of how natural selection and sexual selection can oppose one another.
Hardy-Weinberg equilibrium theorem
What does the answer to number 35 state?
allele / genotype frequencies remain constant from generation to generation unless acted on by one (or more) of the mechanisms of evolution
How can you calculate genotype frequencies?
p2 + 2pq + q2 = 1
b. Insertion / deletion
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
What is adaptive radiation?
Barrier to gene flow can exist premating, postmating, or post-zygotic
Pre-zygotic barriers -barriers before the zygote is formed
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
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
What are the problems associated with the biological species concept?
-organisms where little is known about reproduction
-even some well defined species have the potential to interbreed
Allopatric- geographic seperation restricts gene flowsympatric - biological factors reduce gene flow (evolution of species not developed from geographical barriers)
What are the patterns of evolutionary change (resulting from speciation)?
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.
Why is it possible that the fossil record is incomplete?
i. Wrong environment
ii. Soft bodies
iii. Episodic /local fossilization
iv. Fossils lost
What are the possible scales of evolution?
Microevolution – evolution within a population or species; generational timescale. Covers new breeding population to new species realm
Macroevolution – evolution across species; geological timescale
All evolution whether micro or macro are products of four different processes that cause evolution.
What are systematics?
Systematics – study of biological diversity and its origins / history via phylogenetics
Goal of systematics: reconstruct evolutionary history of life
Problems when dealing with systematics and how can these be overcome?
Problem: cannot observe evolutionary histroy (cannot directly be seen, must be worked out through inferences)
Solution: Infer history using deductive logic using phylogenetic analysis
What is a phylogeny?
What is an extant species?
What does the closeness of two branches extending from the same node indicate?
nothing- nodes can swivel and thus their relative distance is arbitrary
What are phylogenies based on?
synapomorphies- shared derived traits
What are synapomorphies based on?
1. Fossil record
2. morphology -
3. molecular / genetic data -
4. behavior - how do they act
5. Ecological- where do things live
How is the fossil record dated?(#1)
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
Differences between homology and homoplasy
Homology- structures that have shared evoltionary history.
homoplasy aka analogous-structures that appear similiar but do not share a common evoltionary origin
What is convergent evolution and what kind of traits are typically evolved in response to convergent evolution?
Distinguish the differences between synapomorphy, plesiomorphy, and autamorphy. Are they all useful when constructing a phylogeny?
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
What is an outgroup?
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
What are the steps to constructing a phylogeny?
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
What are monophyletic groups aka?
What are molecular clocks used for?
Technique used to relate molecular differences between two lineages to their absolute time since divergence
What does a molecular clock assume?
What are some modern uses of phylogenies?
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-called this pathogen a virus
What are the possible components of viral structure?
Capsid – outer shell of virus
Capsomer – functional unit of capsid
Membrane – host derived cell-membrane
contains a capsid and capsomers and RNA (two functional pieces RNA and Protein (capsid))
What are the icosohedral virus characteristics?
What are the enveloped virus characteristics?
takes a pc of host cell membrane and wraps it self in it to avoid detection from the hosts' immune system
What is the general virus life cycle?
-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
What is the enveloped virus life cycle?
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
-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
- 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
What are the characteristics of prokaryotes?
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)
Where is DNA found in bacteria?
What is bacteria's method of asexual reproduction?
Why is number 91 analogous to mitosis?
-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
What are the specialized cells in bacteria that fix nitrogen called?
What is nitrogen fixation?
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.
What is antibiotic resistance caused by?
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
Describe the process for secondary endosymbiosis to occur.
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)
Five supergroups of Protists and their respective traits.(#1)
1. Unifying traits
a. Highly modified mitochondrira, multiple flagella, 'excavated' feeding groove (why they have the Excavata name)
1. Derived from secondary endosymbiosis of red algae
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