Examination One: Due Friday 11 February at 1:00 pm California Time
Notes: Although there is a minimum word count of 2,000 words for this exam, you will find that it is likely going to require more than
the minimum to fully answer the question. You may not copy or quote from any source. All information must be re-written in your
own words. Answer all questions. Read the course Style Guide for detailed instructions of structure and
format.
Do not include the question(s) on your essays and exams.
Question 1: Origin of Elements (25 points)
Describe the structure of atoms and their origins in the hearts of stars. Include in your answer:
a. the particles involved in atomic structure,
b. the nature of electron orbitals of atoms with different numbers of protons,
c. a description of why heavy elements are rare in Universe,
d. a definition of electronegativity
Question 2: Distribution of Earth’s Heat (25 points)
Describe the distribution of Earth’s heat by air and water movemens. Include in your answer: Include in your answer:
a. a description of differential insolation by latitude that causes global air movement
b. a description of the Coriolis effect and the creation oceanic currents and gyres
c. a description of how Earth’s heat and plate tectonics have partitioned the distribution of plants and animals
Question 3: Color as Electromagnetic Radiation (25 points)
Describe (1) the nature of light as wave and particle and how it is absorbed and emitted by matter, (2) the production of pigmentary
color by differential absorption and production of structural colors by reflection, diffraction and refraction, and (3) the function of
color and color change in animals. Consider the following when creating your essay:
a. a description of the interaction of matter and light to cause gasses to glow with different colors and the ability to use an
emission and absorption spectrum to determine the atomic/molecular composition of a fluid or gas
b. a description of how light waves can cancel and be additive and how these properties are used in the coloration of the Gold
Beetle (Metriona bicolor) and how scattering can produce the blue of the Blue Dasher (Pachydiplax longipennis) and a
description of how sunlight and the atmosphere create a blue sky.
c. a description of the nature of color and color change in the Opalescent Squid (Loligo opalescens) and, in particular, the
process by which iridocytes can “tune in” a particular color to match ambient light.
Question 4: Physical Evidence of Earth’s Earliest Life and Atmospheric Changes (25 points)
Describe the sequence of early life that is preserved in the fossil record that provides evidence for the early evolution of life and
Earth’s atmosphere. Include in your answer:
a. a description of LUCA and a general description of life’s hereditary information
b. a description of horizontal gene transfer, endosymbiosis and the roles of each in the diversification of early life
c. the physical evidence in the fossil record for the origin and evolution of oxygenic photoautotrophs and the changes in Earth’s
atmosphere culminating in the increase in atmospheric oxygen
References
Immediately following the essay, two lines below the last line of your essay, list all sources used in writing your essay to answer the
question. Do not use in-text citations and do not use footnotes. Simply list your sources in this “References” section. You must have
a References section with at least five references which you have used in preparing your answers: the course textbook, and at least
four additional sources. If you do not include a References section, you will lose 10 points (2 points for each missing source). Be sure
to include the References section with your submission to Turnitin. If you forget, you are able to re-submit until the deadline, but not
after.
Exam Page Format
First Two Lines
Line 1: Assignment and Number, for example, Exam 1
Line 2: Your full name, your course animal code, and your course email address
Follow the header form below precisely but with your name, course animal code, and email address. You will lose 2 points if these first two lines are missing or do not follow this form exactly.
Exam 1
Jonathan Smith aardvark (jonathan.smith@gmail.com)
Body
Number each answer but do not include the questions as part of the exam. Add each answer as a series of paragraphs with each paragraph separated by a vertical space between paragraphs. Use single spacing; do not double-space your answers to the questions. Do not use footnotes. Do not include illustrations or graphs. Do not include quotations. Your answers are to be narrative only and re-written in your own words. List all sources for all answers at the end of the exam; do not list sources at the end of each question, and do not use in-text citations.
The top of the first page of an exam will look something like this . . .
Exam 1
Jonathan Smith aardvark (jonathan.smith@gmail.com)
Question 1
Charles Darwin (1809-1882) is perhaps one of the most influential scientists of our time. All of his life he worked toward understanding the reason why species are so diverse and how animals and their ancestors developed over time. His theory of evolution was formed during his trip to the Galapagos Islands while aboard the ship the HMS Beagle.
Darwin studied animal husbandry upon returning to England. He was intersted in the selection of animals to improve the breed. He wondered whether the same selection by natural forces could lead to modification of animals in nature. If so, he hypothesized, the ancestors of the Galapagos finches could have, by chance, arrived on the islands and each island’s characteristics, being different from the others, acted somehow to modify future generations of finches as does artificial selection act to improve a breed of domesticated animals. More . . . et cetera
Question 2
DNA structure comprises sequences of nucleotides, Adenine (A), Thymine (T), Guanine (G) and Cytosine (C), in two strands that wrap about one another in a helix. The two strands are held together by the attractions between nucleotides forming “base pairs”: between A and T and between G and C. Changing these AT and GC base pairs is one type of mutation that can occur. Mutations include changes to individual nucleotides, duplicating or deleting regions of DNA, and changing the locations of regions of DNA.
Mutations can occur by a number of different processes. Radioactive minerals of Earth emit particles as those minerals decay over time. Some of these particles are harmless, not even able to penetrate the outer layers of skin. Other particles are able to pass through our bodies and as they do may strike our DNA molecules causing physical damage. High frequency, high energy electromagnetic radiation such as ultraviolet, X-ray and gamma-ray radiation can cause chemical changes as they are absorbed by DNA, making the DNA more chemically reactive. And, of course, DNA itself is a molecule that can react with other molecules and by so doing be changed in the course of the reaction. Radiation and chemicals that can cause damage to DNA are referred to as mutagens More . . . et cetera
References Style Guide
List five and only five sources in the References section: the textbook and an additional four resources that were most useful to you in constructing your answers to the exam questions. Alphabetize your references by the first author’s last name.
Enter your References section two lines directly below the last answer of the examination.
Note: Do not include common, basic sources such as dictionaries. For encyclopedic sites such as Wikipedia or Encyclopedia Britannica, cite only once regardless of the number of pages or topics used. It is best to use sources from scholarly journals.
References
Brusca, Richard C., Wendy Moore and Stephen M. Shuster. 2016. Invertebrates, 3/e. Sinauer Associates.
Friesen, Larry Jon. 2022. Natural Science. NatureJournal.
Internet: www.110biology.net/spring/
Humphreys, Ian R., et al. 2021. Computed structures of core eukaryotic protein complexes. Science. Vol 374, Issue 6573
Internet: www.science.org/doi/10.1126/science.abm4805
Rousset, Vincent, et al. 2006. A molecular phylogeny of annelids. Blackwell Publishing.
Internet: www.amnh.org/content/download/43569/660971
Schmidt-Nielsen, Knut. 1972. How Animals Work. Cambridge University Press.
Citation Formats
Use the following simplified formats for listing your sources.
If it is a book: List by author’s last name. Additional authors are listed first name last name. If there are more than three authors, list only the first author followed by “et al.” as with Humphreys (below). All primary words of a book title are capitalized. If the source was accessed via the Internet, list the URL indented below the source with “Internet:” before the URL as with Humphreys (below)
Author’s last name, Author’s first name. Date. Title of Book. Publisher.
Brusca, Richard C., Wendy Moore and Stephen M. Shuster. 2016. Invertebrates, 3/e. Sinauer Associates.
If it is an article in a periodical: use the same format as above except (a) series and periodical titles are listed with an initial capital of the first word only and (b) the journal name (instead of publisher) is used and should include volume and issue numbers if available.
Author’s last name, Author’s first name. Date. Title of article. Title of periodical. Volume (if available).
Humphreys, Ian R., et al. 2021. Computed structures of core eukaryotic protein complexes. Science. Vol 374, Issue 6573
Internet: www.science.org/doi/10.1126/science.abm4805
If it is an Internet site: Do not use only the URL. Use the book or periodical format and, if no author is listed, use the institution’s name that hosts the website. If no author is listed, use the parent organization name as the author as with the NASA website listed below. If a publication year is not listed, use the current year with a lead of “Accessed:” as shown below.
Author’s last name, author’s first name. Date. Title of Internet site. URL for the home page of the Internet site.
NASA. Accessed 2021. Moon to Mars. NASA
Internet: www.nasa.gov/topics/moon-to-mars
Submission of Completed Examinations
Your examinations will be submitted through Turnitin.com looking something like the form that follows. The sample format below is about 700 words. The minimum word count for each exam is 2,000 words (about 500 words per question).
Exam 1
Jonathan Smith aardvark (jonathan.smith@gmail.com)
Question 1
Charles Darwin (1809-1882) is perhaps one of the most influential scientists of our time. All of his life he worked toward understanding the reason why species are so diverse and how animals and their ancestors developed over time. His theory of evolution was formed during his trip to the Galapagos Islands while aboard the ship the HMS Beagle.
Darwin studied animal husbandry upon returning to England. He was intersted in the selection of animals to improve the breed. He wondered whether the same selection by natural forces could lead to modification of animals in nature. If so, he hypothesized, the ancestors of the Galapagos finches could have, by chance, arrived on the islands and each island’s characteristics, being different from the others, acted somehow to modify future generations of finches as does artificial selection act to improve a breed of domesticated animals. More . . . et cetera
Question 2
DNA structure comprises sequences of nucleotides, Adenine (A), Thymine (T), Guanine (G) and Cytosine (C), in two strands that wrap about one another in a helix. The two strands are held together by the attractions between nucleotides forming “base pairs”: between A and T and between G and C. Changing these AT and GC base pairs is one type of mutation that can occur. Mutations include changes to individual nucleotides, duplicating or deleting regions of DNA, and changing the locations of regions of DNA.
Mutations can occur by a number of different processes. Radioactive minerals of Earth emit particles as those minerals decay over time. Some of these particles are harmless, not even able to penetrate the outer layers of skin. Other particles are able to pass through our bodies and as they do may strike our DNA molecules causing physical damage. High frequency, high energy electromagnetic radiation such as ultraviolet, X-ray and gamma-ray radiation can cause chemical changes as they are absorbed by DNA, making the DNA more chemically reactive. And, of course, DNA itself is a molecule that can react with other molecules and by so doing be changed in the course of the reaction. Radiation and chemicals that can cause damage to DNA are referred to as mutagens. More . . . et cetera
Question 3
The differences in electronegativity between hydrogen (2.1) and oxygen (3.5) causes the bonding electrons of the hydrogens to be drawn more strongly toward the oxygen nucleus (with an 8+ charge) than to the single proton (with a 1+ charge) that is the hydrogen nucleus.
Because of these polar covalent bonds between oxygen and hydrogen, the hydrogen poles of the molecule have a partial positive charge (d+) and the two filled orbitals of oxygen have partial negative (d-) charges. Water molecules thus behave as magnets with two positive poles and two negative poles and will be attracted to anything polar or with a charge . . . hydrogens attracted to negative areas, and oxygen’s orbitals filled with electrons attracted to positive areas. More . . . et cetera
Question 4
Enzymes are fragile. Proteins have complex structures dependent on weak interactions between their various parts to become folded into very specific shapes. These shapes are essential to an enzyme’s function because the various surfaces of the enzyme are important in recognizing the molecules on which they act and are reactive, participating in the chemical reactions with the substrate (the molecule on which an enzyme acts). Any change in shape influences the activity of the enzyme and a permanent change in shape and the destruction of enzyme activity can be due to temperatures which are too high. A permanent change in enzyme shape that inhibits its activity is called “denaturation”. A good analogy is the heating of the protein white of an egg and its “denaturation” from a clear, viscous fluid to an opaque, white rubbery solid. This denaturation is irreversible . . . you cannot reverse this reaction to regain the fluid egg white. Over-heating causes denaturation of proteins and, in particular, the class of proteins that are enzymes are most sensitive. Therefore, during heat stoke the denaturation of structural proteins and enzymes is irreversible and even if normal temperatures are regained, the damage has been done. More . . . et cetera
References
Brusca, Richard C., Wendy Moore and Stephen M. Shuster. 2016. Invertebrates, 3/e. Sinauer Associates.
Friesen, Larry Jon. 2022. Natural Science. NatureJournal.
Internet: www.110biology.net/spring/
Humphreys, Ian R., et al. 2021. Computed structures of core eukaryotic protein complexes. Science. Vol 374, Issue 6573
Internet: www.science.org/doi/10.1126/science.abm4805
Schmidt-Nielsen, Knut. 1972. How Animals Work. Cambridge University Press.
Rousset, Vincent, et al. 2006. A molecular phylogeny of annelids. Blackwell Publishing.
Internet: www.amnh.org/content/download/43569/660971
It is your responsibility to assure that your exams have been submitted successfully. Once you have submitted an assignment, return to the Turnitin website to be sure that your assignment has uploaded successfully. Occasionally, a student does not realize that submission is a two-step process. Once the submit button is clicked you are directed to a page that asks that you confirm the file that you have chosen and to click submit again. If you skip this last step, your file is not uploaded.
Formatting Point Deductions
Missing or improperly formatted first two lines (-2 points)
Missing or incorrect References header (-2 points)
Missing or incomplete References section (-2 points for each missing source)
Website sources in References section formatted as URLs only (-5 points)
Including question(s) in your exam (-5 points)