English Revolution
* Childless Queen Elizabeth of the Tudor dynasty died in 1603 and King James VI of Scotland ( aka James I) of the Stuart dynasty took over.
James I
- Believed strongly in the divine right of kings
~ This alienated the Parliament which, during the Tudor's rule, worked along with the King.
- Strongly defended the Anglican (Catholic) church
~ Most of England's gentry and significant part of Parliament were puritans.  They weren't happy with this.

Charles I (son of James I)
- Also believed in divine-right monarchy
- Tried to impose more catholic rituals
~ Puritans are mad!

* Grievances mounted until England slipped into civil war (1642 - 1648)

Oliver Cromwell
-> created New Model Army composed of extreme Puritans who believed they fought for God
-> won the war due to well trained soldiers and new military tactics
-> In 1649, Parliament abolished monarch and House of Lords and proclaimed England a commonwealth
-> Oliver, unable to work with Parliament, dispersed it by force and established a military dictatorship
-> He died in 1658 and army restored monarchy under Charles II

Charles II (Son of Charles I) 1660 - 1685
- sympathetic to Catholicisim
- issued Declaration of Indulgence that suspended laws that Parliament had passed against Catholics and Puritans
- Parliament forced king to suspend the declaration

James II 1685 - 1688
-> As an open and devout catholic, he named Catholics to high positions in Government.
-> Parliament didn't rebel since he was an old man and his successors were his Protestant daughters.
-> However, as soon as a son was born to his Catholic wife, a group of prominent Englishmen invited William (husband of James' daughter Mary) to invade.
-> William and Mary invaded while James fled and England underwent its Glorious Revolution with barely any bloodshed.

42. Briefly describe the formation of Earth.
A: It is proposed that the solar system was formed by a condensing nebula which is a cloud of gas and dust in space.  Over time, most of the material in the nebula pulled together due to gravity and materials that remained in the nebula's disk circled the newly formed sun.

Repeated collision of this space debris over time built up into planets of our solar system.  Many asteroids struck the planet Earth releasing enormous amount of heat which kept materials making up Earth in a molten state which eventually separated into different layers.

Hydrogen, carbon monoxide, and nitrogen were released from the interior which combined to form an atmosphere.  Oxygen only formed after the first forms of life had begun to evolve.  As impacts became less frequent, Earth cooled don, continents formed, and water vapor condensed as rain and got collected into large bodies of water.

43. What is the Miller-Urey experiment?
A: It suggests that organic compounds could be formed from inorganic materials by passing an electrical current, representing lightning, through a mixture of gases.

44. What are the two main early cell structure hypotheses?
A: - Iron-sulfide bubble hypothesis: when warm sodium sulfide is injected into cool iron-rich solution, they form a chimney-like structure.  These structures could have acted as the first cell membranes.

- Lipid membrane hypothesis: lipid membranes could form membrane-enclosed spheres or liposomes which could form around a variety of organic molecules.

45. List a few reasons that support the hypothesis that RNA, rather than DNA, was the genetic material that stored information in living things on early Earth.
A: - RNA can copy itself and chop itself into pieces without enzymes.

- Since RNA could fold into different shapes, it can perform more functions that DNA.

46. What is the theory of Endosymbiosis?
A: It is a relationship where one organism lives within the body of another and both benefit from the relationship.  The theory suggests that early mitochondria and chloroplasts were once simple prokaryotic cells that were taken up by larger prokaryotes.  The large cell got energy from mitochondria while the mitochondria found a stable environment and nutrients.

36. What are several ways in which fossils are formed?
A: - Permineralization: occurs when minerals carried by water are deposited around a hard structure.

- Natural casts: occurs whens water removes all original fossils and minerals fill in and recreate the original shape.

- Trace fossils: records the activity of an organism (Ex. footprints)

- Amber-preserved fossils: organisms trapped in tree resin that hardens into amber.

- Preserved remains: forms when an entire organism becomes encased in material such as ice.

37. What is relative dating?
A: It estimates the time during which an organism lived by comparing placement of fossils of that organism with placement of fossils in other layers of rock.  This does not provide the actual ages.

38. How is the actual age of a fossil determined?
A: Radiometric dating can be used which uses natural decay rate of unstable isotopes found in materials in order to calculate the age of that material.  A half-life is the amount of time it takes for half of the isotope to decay into a different element.

39. What are index fossils?
A: They are fossils of organisms that existed only during specific spans of time over large geographic areas.

40. What are the three basic units that make up the geologic time scale?
A: - Eras: lasts hundreds of millions of years

- Periods: lasts tens of millions of years and is associated with particular type of rock system

- Epochs: lasts several million years

Mass extinction events often define the boundaries between many geologic periods.

41. List and describe the three main eras from oldest to youngest.
A: - Palezoic era: existing animal phyla developed through Cambrian Explosion.  Marine invertebrates evolved and earliest land plants arose.  Later, fish diversified and modern pine trees appeared.

- Mesozoic Era: dinosaurs evolved after the largest mass extinction and they diversified.  As they became extinct, birds survived.

- Cenozoic Era: mammals, flowering plants, and birds diversified while primates evolved.  This period includes all modern forms of life and still continues today.

33. What sources did the evidence for evolution come from during Darwin's time?
A: -Fossils: pointed out Earth was way more than 6000 years old.

- Geography: when organisms get separated by various landforms, they adopt and develop new traits essential for survival in the new environment.

- Embryology: similar features of embryos in very different organisms suggest evolution from a distant common ancestor.

- Anatomy: homologous structures were formed in organisms which are features that are similar in structures but appear in different organisms and have different functions.  This suggests that those animals share  a common ancestor.
Whereas, analogous structures are structures that perform a similar function but are not similar in origin.

34. What are vestigial structures?
A: They are remnants of organs or structures that had a function in an early ancestor but no longer used by the current organism.

35. How does molecular and genetic evidence support fossil and anatomical evidence?
A: The comparison of DNA or protein sequences can be used to show probable evolutionary relationship between species.  The more related two organisms are, the more similar their DNA will be.  Molecular fingerprinting can be used to reveal similarities in proteins of an organism.  Other ways are Pseudogenes and Homeobox genes.

20. What is the scientific definition of evolution?
A: It is the process of biological change by which descendants come to differ from their ancestors.

21. What is a species?
A: It is a group of organisms so similar to one another that they can reproduce and have a fertile offspring.

22. Name the early scientists who contributed to evolution and describe their contributions.
A: - Carolus Linnaeus: developed a classification system for organisms where he grouped them by their similarity.  He proposed that some organisms must have arose through hybridization.

- George Buffon: proposed species shared ancestors and suggested Earth was much older than 6000 years

- Erasmus Darwin: all living things descended from a common ancestor and more complex forms of life arose from less complex forms.

- Jean-Baptiste Lamarck: all organisms evolved toward perfection and complexity.  Reasoned that organisms evolved into different forms.

Lamarck's Proposal: Proposed that changes in environment caused organism's behavior to change, leading to greater use or disuse of a structure or organ.  The structure would become larger or smaller as a result. The organism would pass on these changes to its offspring which is known as the inheritance of acquired traits.

- George Cuvier: thought that organisms couldn't change but become extinct based open observing fossils.  He proposed the theory of catastrophism which states that natural disasters such as floods and volcanic eruptions have happened often before.

- James Hutton: changes he observed in land forms resulted from slow changes over a long period of time which came to be know as gradualism.

- Charles Lyell: produced the theory of uniformitarism which states that geologic forces that shape Earth are uniform through time.

23. What is variation?
A: It is the difference in the physical traits of an individual from those of other individuals in the group to which it belongs.

- Interspecific variation: among different species
- Intraspecific variation: among same species

24. What is an adaptation?
A: An adaptation is a feature that allows an organism to better survive in its environment which leads to genetic change.

25. What were a few other things that Darwin noticed on Galapagos Islands?
A: He noticed the differences between species on different islands well suites to the animals' environment.  Also, he found fossil evidence of species changing over time which made him believe that the Earth must be much more than 6000 years old.

26. What is artificial selection?
A: Artificial selection is when humans change a species by breeding it for certain traits. Darwin explored this by breeding pigeons.

27. What is heritability?
A: It is the ability of a trait to be passed down from one generation to next.

28. What is natural selection?
A: It is the mechanism by which individuals that have inherited beneficial adaptations produce more offspring on average than do other individuals.

29. What did Thomas Malthus proposed and how did Darwin expand it?
A: Thomas Malthus proposed that resources such as food, water, and shelter are natural limits to population growth.  Darwin reasoned that organisms have more offspring than could ever survive.

30. What is a population?
A: It includes all the individuals of a species that live in an area.

31. Describe four main principles to the theory of natural selection.
A: - Variation: variations are the basis for natural section

- Overproduction: having many offspring raises both the chances that some will survive and would result in competition.

- Adaptation: certain variation allows an individual to survive better.

- Descent with modification: natural selection would result in well adapted species and reproduction of that species increases.

32. How is the term "fitness" used in Biology?
A: It is the measure of the ability to survive and produce more offspring relative to other members of the population.

p = frequency of dominant allele
q = frequency of recessive allele

11. What are the five factors that led to evolution?
A: -Genetic Drift: allele frequencies can change due to chance alone

- Gene flow: movement of allele from one population to another changes allele frequencies in each population

- Mutation: new alleles form through mutation  creating genetic variation

- Sexual selection: certain traits improve mating success and alleles for these traits increase in frequency.

- Natural selection: certain traits may be an advantage for survival and alleles for these traits increase in frequency.

12. What is speciation?
A: It is the rise of two or more species from one existing species.

13. What are 4 ways in which populations get isolated?
A: -Behavioral isolation:  differences in courtship or mating behaviors

- Geographic isolation: physical barriers that divide a population

- Temporal isolation: timing prevents reproduction between populations

- Reproductive isolation: members of different population can successfully mate with each other

14. What is "random" and what is "chance" in science?
A: Mutations and genetic drifts are random resulting in genetic variation while natural selection is when individuals with favorable traits have a better "chance" of survival.

15. What is the difference between convergent and divergent evolution?
A: Evolution toward similar characteristics in unrelated species is called convergent evolution while divergent evolution is when closely related species evolve in different directions.

16. Briefly describe co-evolution and evolutionary arms races.
A: -Coevolution: two or more species respond to change in each other
 
- Evolutionary arms races: each species responds to pressure from other through better adaptations over many generations

17. What are two types of extinction?
A: -Background extinctions: elimination of a species occurring at a continuous but low rate

-Mass extinction: results in destruction of many species suddenly due to catastrophic event

18. What is punctuated equilibrium?
A: They are bursts of evolutionary activity followed by long periods of stability.

19. What is adaptive radiation?
A: It is the diversification of one ancestral species into many descendent species.

1. How does genetic variation in a population increases the chance that some individuals will survive?

A: A population with a lot of genetic variation has a wide range of phenotypes.  Genetic variation is stored in a  population's gene pool which is the combined alleles of all individuals in a population.  When organisms mate and have offspring, different combinations occur and some might be very advantageous for the organism.

2. What are two main sources of genetic variation?

A: -Mutation - a random change in the DNA of a gene
-Recombination: new allele combinations form in offspring, mostly during meiosis.

3. What is normal distribution?

A: When frequency is high near mean value and decreases to both ends.

4. What is microevolution?

A: It is the observable change in allele frequencies of a population over time.

5. What are the tree way in which natural selection change the distribution of a trait?

A: -Directional selection - phenotype at one extreme of a trait's range is preferred.  A trait that once was rare becomes more common.

- Stabilizing selection - when intermediate phenotype is favored

- Disruptive selection - when both extreme phenotypes are favored while intermediate phenotypes are selected against by something in nature.

6. What is an example of a gene flow?

A: When individuals move between populations, it increases genetic variation of receiving population which is gene flow.  The less the gene flow, the more different two populations become.

7. Genetic drift is the change in allele frequencies due to chance.  What are two types of genetic drifts and what impacts do they have?

A: -The bottleneck effect is when the size of population is greatly reduced due to some event

- Founder effect is when a small number of individuals colonize a new area.

Genetic drift causes the population to lose genetic variation.

8. What are two types of sexual selection?

A: -Intrasexual selection - competition among males for females

- Intersexual selection - certain traits in males attract females