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ancestor (evolution tweaks development leading to different adult forms tails, etc.)
3. Homology: similarity of structure due to common ancestors despite differences in
function (wings/fins/arms/legs). 4. Biogeography: species colonized new habitats and
divided by geographic barriers, took on distributions they have today. 5. Fossils:
Fossils showed transitional forms and Darwin hypothesized that modern day animals
evolved from land dwelling ancestors.
15. Two sources of genetic variation: See answer for question 7.
Can be applied to asexual organisms and fossil records. (Problems are that it relies on
subjective criteria and does not always match DNA sequences). Ecological Species
Concept: Classified based on food source and habitat. (Problems: Organisms can occupy
similar ecological niches and not produce viable offspring). Phylogenic Species
Concept: Classified as the smallest group of organisms which share a common ancestor.
Compare appearance, DNA sequences, and metabolism pathways (Problems: How many
differences define a different species?). Mate Recognition Species Concept:
Recognition of mates (Problems: Cannot apply to fossil record).
3. Reproductive isolation is the key to the BSC. Prezygotic barriers: Habitat isolation
(geography separates them Ex. Snakes who live in water/land), temporal isolation
(different breeding times Ex. Two types of skunks who breed in late winter/late
summer), behavioral isolation (courtship rituals Ex. Blue foot boobies who do a high
step to show off their blue feet), mechanical isolation (morphological differences prevent
successful completion of mating Ex. Snails with opposite genital opening direction),
gametic isolation (Sperm cannot fertilize eggs of another species Ex. Sea urchins,
proteins on surfaces of sperm eggs make them bind poorly in difference species).
Postzygotic barriers: Reduced hybrid viability (impair hybrid development or survival
Ex. Frail hybrid salamanders), reduced hybrid fertility (hybrids who are sterile Ex.
Male donkey/female horse = mule), hybrid breakdown (1st generation viable but
following offspring not Ex. Strains of cultivated rice).
4. BSC is more useful in theory than in practice. Problems are interpretation of fossil record,
asexual reproduction, and species who appear different from one another but can mate
and produce viable offspring.
5. BSC does not apply to asexual or extinct organisms.
6. Hybridization complicates the BSC. Example are female horses who can mate with male
donkeys and produce mules. Another example are ligers and tigons (between lions and
tigers).
7. Prezygotic barriers: Habitat isolation (geography separates them Ex. Snakes who live in
water/land), temporal isolation (different breeding times Ex. Two types of skunks who
breed in late winter/late summer), behavioral isolation (courtship rituals Ex. Blue foot
boobies who do a high step to show off their blue feet), mechanical isolation
(morphological differences prevent successful completion of mating Ex. Snails with
opposite genital opening direction), gametic isolation (Sperm cannot fertilize eggs of
another species Ex. Sea urchins, proteins on surfaces of sperm eggs make them bind
poorly in difference species).
8. Postzygotic barriers: Reduced hybrid viability (impair hybrid development or survival
Ex. Frail hybrid salamanders), reduced hybrid fertility (hybrids who are sterile Ex.
Male donkey/female horse = mule), hybrid breakdown (1st generation viable but
following offspring not Ex. Strains of cultivated rice).
9. Reproductive barriers: See definition for reproductive barriers.
10. Mechanisms responsible for speciation: See definitions for allopatric and sympatric
speciation.
11. How can speciation occur with or without natural selection: Mutations, hybridization,
allopatric speciation, and sympatric speciation.
12. How can natural selection enhance reproductive isolation? Through genetic variation, this
can prevent gene flow between species due to variation in the gene pool.
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(magnetic shield protection from solar and cosmic radiation. Later on the ozone layer
emerged from free oxygen produced by living organisms.
Four sequential stages of the origin of life from non-living matter: 1. Synthesis of small
organic molecules (amino acids/nucleotides) by non-living processes organic molecules
created from lightning and UV radiation / deep sea alkaline vents with high pH, warmth,
and amino acids with ammonia / volcanos produced sponge-like minerals (zeolites)
organic compounds / meteorites contained amino acids, lipids, simple sugars, and uracil.
2. Joining organic molecules into polymers (proteins and nucleic acids) such as heated
monomers will form cross-linked polymers on hot sand, clay, and rock. 3. Packaging
molecules into protocells with lipid membranes (can absorb molecules and replicate
metabolism and replication are key properties of life). 4. Origin of self-replicating
molecules required for inheritance (short RNA molecules can form from monomers and a
complementary strand can give rise to double stranded RNA gave template to more
stable DNA).
How rock and fossil records can be analyzed in order to decipher evolutionary time and
evolutionary events: Succession of fossils through strata / radiometric dating can be used.
Limitation of using fossil record: It is an incomplete record because some fossils are
destroyed, few individuals are fossilized, few fossils are discovered, and only shows
abundant/long lived/widespread/had hard body parts/lived and died in certain
environments.
Evidence to support endosymbiotic theory: 1. Plasma membrane of prokaryotes similar to
inner membranes of chloroplasts and mitochondria. Eukaryotes have organelles that seem
to have an independent origin of life. 2. Mitochondria, chloroplasts, and prokaryotes
replicate by binary fission, have circular DNA, can transcribe mRNA and translate
protein, and they have similar ribosome size/sequence.
Major events in Earths history which lead to changes in life on Earth: Explosion of
animals occurs during Cambrian explosion (first predators appear). Colonization of land
started with plants and fungi. Mass extinctions: Permian Extinction (possibly by volcanic
activity), Cretaceous Extinction: (meteor). Adaptive radiation followed mass extinction
allowed for new habitats to be exploited by survivors and the potential for rapid
speciation.
Continental drift and mass extinctions stimulated speciation: allopatric speciation /
adaptive radiation. Different environments / different level of competition / exploitation
of new habitats / adaptation to new environments / natural selection.
Three scenarios in which adaptive radiation likely to occur: 1. Extinction events (less
competition / exploitation of new environments by survivors / adaptation). 2. Evolution
of new character which is novel (super competitive). Natural selection can increase
frequency of the trait. 3. Migration into a new environment.
Process of speciation is not goal directed, can reverse itself, and is not a straight line but a
branching tree.
6. A node is a branching point on a tree and can be rotated without changing evolutionary
relationships.
7. A tree is built on the basis of shared derived characteristics rather than primitive traits
because nodes (branching) can be created based on derived traits and compared to other
species who may or may not have the derived trait. Therefore, we have more data to
hypothesize the relationships of species/groups.
8. Only shared derived (synapomorphic) characters are useful in constructing a phylogenetic
tree.
9. Morphological and molecular data provide a wealth of characters for tree building.
10. The concept of parsimony in tree building is the concept in which trees require the fewest
evolutionary events invoked to explain traits in the studied groups. This affects tree
building because it minimizes the number of independent origins of that character state
(makes it less complicated).
III.
SCENARIOS
1. Human-Chimpanzee-Bonobo-Gorilla phylogeny Humans form a sister group with the
chimp/bonobo group (are more closely related to each other than either is to the gorilla).
However, chimps and bonobos look more similar to gorillas. However, chimp/bonobo
molecular data is more similar to humans.
Virus Lacking the structures and metabolic machinery found in a cell, a virus is an
infectious particle consisting of little more than genes packaged in a protein coat. They may
contain either DNA or RNA.
Viron Complete, fully developed, infectious viral particle with a nucleic acid surrounded
by a protein coat. Viruses are classified by differences in the structure of the protein coat.
Capsid The protein shell enclosing the virus genome. The capsid may be rod-shaped,
polyhedral, or more complex in shape.
Virus morphology Virus morphology is a way to classify viruses based on their capsid
structure. 1. Helical: Resemble long helical rods with the nucleic acid in the hollow center
(Ebola, rabies viruses). 2. Polyhedral: Many sided virus with each face forming an equilateral
triangle (Polio virus). 3. Enveloped: Capsid (helical or polyhedral) covered by a roughly
spherical envelope (Influenza, herpes simplex viruses). 4. Complex: Have capsids with
additional structures attached (bacteriophages).
Host Range The spectrum of host cells the virus can infect. Determined by the viruses
specific attachment to the surface of the host cell. This could be the cell wall, fimbriae, or
flagella in bacteria or plasma membrane in animal cells. The host range can be broad or
narrow.
Bacteriophages Viruses which infect bacteria (also called phages).
Lytic Cycle One of the mechanisms of bacteriophage multiplication. The phage attaches to
a host cell and injects DNA and the phage DNA circularizes. Then either lytic cycle induced
or lysogenic cycle entered. If lytic cycle induced, new phage DNA and proteins are
synthesized and self-assemble into phages. Then, the cell lyses and the phages are released.
The lytic cycle culminates in the death of the host cell. A virulent phage only uses the lytic
cycle for replication.
Lysogenic Cycle If lysogenic cycle is entered, phage DNA integrates into the bacterial
chromosome, becoming a prophage. The bacterium reproduces normally, copying the
prophage and transmitting it to daughter cells. Many cell divisions produce a large population
of bacteria infected with the prophage (prophage is viral DNA through the lysogenic cycle).
Occasionally, the prophage exits the bacterial chromosome and initiates a lytic cycle.
Vaccine A harmless form, derivative, or segment of pathogen which stimulates the immune
system to acquire long term defenses against the harmful pathogen. Some viruses which pose
greater health risks can be prevented through the use of vaccines.
Emerging Virus Viruses which suddenly become important to human public health.
Viruses emerge through: 1. High mutation rate of replicating virus. 2. Increase in human
contact due to travel, blood transfusions, etc. 3. Increase transmission from animals (act as a
reservoir for virus).
II.
CONCEPTS
1. Unique characteristics of prokaryotes - Cell wall: made of peptidoglycan structure of
the cell wall can be identified by gram stain (gram positive have simpler walls with large
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amount of peptidoglycan / gram negative have less peptidoglycan and more complex with
outer membrane that contains lipopolysaccharides). Endospore: original cell produces
copy of its chromosome and surrounds it with tough multilayered structure. Water is
removed and original cell lyses, releasing the endospore. Therefore, it can withstand
harsh environments. Capsule: Cell wall surrounded by capsule (sticky layer of
polysaccharide or protein protects against dehydration and attacks from immune system
/ helps them adhere to substrates or colonies). Fimbriae: Hair-like appendages used to
stick to substrate or one another (shorter and more numerous than pili). DNA: Have
circular chromosomes associated with fewer proteins than in eukaryotes. They do not
have a nucleus. Prokaryotes have a nucleoid which is a region of cytoplasm not enclosed
in membrane where DNA is located. Prokaryotes also have plasmids (smaller rings of
independently replicating DNA molecules rings). Size and Shape: Diameters ranging
from 0.5 to 5 micrometers. They have a variety of shapes, including spherical (cocci),
rod-shaped (bacilli), and spiral (spirilla).
Mechanisms of prokaryotes that contribute to their variation and diversity: Rapid
reproduction by binary fission / horizontal gene transfer / transformation / transduction /
conjugation / mutations.
Energy source and carbon source Energy source for metabolism: phototrophs (use light
energy) / chemotrophs (use chemical energy). Carbon source (needed for protein
building): autotrophs (need CO2 for carbon) / heterotrophs (need organic compounds for
carbon).
Characteristics of viruses: see virus morphology, lytic cycle, lysogenic cycle, and
definitions for virus.
Structural components of viruses - Nucleic acid: DNA or RNA can either be single or
double stranded. Nucleic acid can be linear of circular. Can have 3-1000 genes. Capsids:
Genome protected by protein shell called capsid made up of subunits called capsomeres
(helical, polyhedral, enveloped, or complex). Envelope contains lipids and proteins from
host along with viral protein-carbohydrate spikes which are used to attach to host ells.
Lytic and lysogenic cycle - Lytic Cycle: 1. Attachment 2. Entry of phage DNA and
degradation of host DNA 3. Synthesis of viral genomes and proteins 4. Self-assembly 5.
Release. Lysogenic Cycle: See definition.
Main structural feature of animal viruses which make them different from phages and
how are they used during the replication cycle? Nearly all animal viruses with RNA
genome have an envelope as do some with DNA genomes. It uses the envelope to enter
the host cell. There are viral glycoproteins that protrude from the envelope that bind to
specific receptor molecules on the surface of the host cell. In this cycle, the digestion of
the capsid by cellular enzymes releases the viral genome. Complementary strands are
made of RNA and new copies of viral genome RNA are made using the complementary
strands as template. Complementary RNA also function as mRNA, which is translated
into both capsid proteins and glycoproteins for the viral envelope. Vesicles transport
envelope glycoproteins to the plasma membrane. A capsid assembles around each viral
genome molecule. Each new virus (capsid) buds from the cell wrapped in membrane and
its envelope is studded with viral glycoproteins embedded in membrane derived from the
host cell.
8. Emerging Viruses Emerging viruses are viruses which suddenly become important to
human public health. These viruses emerge from 1. High mutation rate of replicating
virus RNA/DNA. 2. Increase in human contact due to travel, blood transfusions, etc. 3.
Increase transmission from animals who act as a reservoir for virus. Epidemic:
widespread outbreak. Pandemic: Global widespread outbreak.
III.
THOUGHT QUESTIONS
1. Features of prokaryotes which enable them to survive environments that are too harsh for
humans: Their ability to rapidly reproduce combined with mutation allowed them to
adapt to different environments. Their different sources of nutrition and different modes
of metabolism (also their ability to colonize and form symbiotic relationships).
2. Is virus a living organism? They have genetic information (DNA or RNA) and have
protein coat that surround the nucleic acid. They have the ability to replicate through cell
machinery. They synthesis specialized structures that can transfer viral nucleic acid to
other cells (sophisticated adaptations).
3. What viral traits suggest they are not living? No modes of metabolism. They lack
enzymes for protein synthesis and ATP generation.
4. What features suggest viruses are simple organism? They are simply composed simply of
nucleic acid surrounded by protein coat.
5. What features of viruses suggest they are complex? Their capsid structure (helical,
polyhedral, enveloped, and complex). Their modes of replication (lytic and lysogenic
cycles / replication of animal viruses).
6. In what ways are bacteria and viruses alike? How do they differ? They are both
pathogenic (bacteria releases exotoxins poison / endotoxins released when bacteria
die and cell wall breaks down.. viruses use cells as hosts for replication and can
destroy the cell). They both have genetic material that is not organized in a nucleus. They
differ because bacteria have modes of metabolism and viruses do not. Bacteria can also
self-replicate through binary fission while viruses need a host cell to replicate.
7. Scientists know less about archaea organism because they can live in very extreme
environments (I.e. Hypothermal vents underwater, under ice, etc.)
8. What aspects of bacteria and archaea biology lead to rapid evolution? Rapid reproduction
by binary fission / horizontal gene transfer / transformation / transduction / conjugation /
mutations.