Intro Biology - Test Essay Questions

Please formulate an answer, in outline format where possible, to the following questions using the
material presented in lecture, lab and the assigned readings.

1) Describe the three inferences based on five observations of the theory of evolution as formulated by
Charles Darwin and analyzed by Ernst Mayr. Identify the most relevant data available today that confirm
the theory. What did other individuals contribute to the process of the formulation of this theory?

2) Describe the scientific method and describe how the method was applied in the paper, Natural
Selection of Darwins Finches, using the concepts of hypothesis, rationale for formulation of an
hypothesis, data collection and testing of hypotheses, refinement of hypotheses based on test results.

3) Toads and professors appear in many respects to be different. Biologists assert that toads and
professors are a consequence of evolution and that both types of organisms developed from fertilized
eggs following instructions carried in their genes. Explain the molecular basis for the theory of evolution,
including the precise reasons why genotype (or nucleotide sequences in DNA) determines phenotype.

4) Describe the structure of the atom and the relationship between this structure and covalent, ionic and
hydrogen bonds.

5) Water was one of the most common molecules on the surface of the earth as the earth's crust cooled
and life evolved. Due to its prevalence, water was in an optimal position to become the biological
solvent. What is it about the structure of water that both facilitated its role as solvent and how did this
structure influence the evolution/selection of the other specific groups of molecules, such as proteins,
lipids, carbohydrates, and ions, that contribute to the structure and function of cells and organisms?

6) Compare in detail, using specific molecular diagrams, the molecular structure of proteins,
carbohydrates and lipids, indicating in detail how these structures result in their respective functions in
biological systems.

7) What are the functions of a plasma membrane (cell surface membrane) and what aspects of its
molecular structure promote these functions?

8) Define the mechanisms by which molecules move into and out of cells in detail, including the energy
requirements of such processes and how this energy is provided.

9) Describe the structure of an enzyme at the molecular level and precisely how it mediates a chemical
reaction and how enzyme activity is regulated. Please include a description of free energy and energy of
activation as they relate to enzyme mediated reactions. Precisely how do enzymes reduce the energy of
activation.

10) Moving from the nucleus through the extracellular matrix, discuss the roles of specific proteins in
determining cell and tissue shape. Include specialized types of cell junctions.

11) Starting with a molecule of glucose, trace the process by which energy within the bonds between the
six carbon atoms is removed. Include glycolysis (in the presence and absence of oxygen), the Krebs
Cycle and oxidative phosphorylation. Draw the complete structure of glucose, pyruvate and lactate.
12) Identify the central elements associated with the ethical analysis of the providing health care
to individuals in general and in the United States more specifically.

13) Trace in detail the diverse processes by which extracellular signals regulate cell function via
second messengers, kinases, phosphatases and the different classes of target proteins.

14) Oncogenes and tumor suppressor genes play central roles in the transformation of normal
cells to cancer cells. Review how members of these two different classes of genes contribute to
cancer. How do they relate to the following: induction of cancer by radiation; induction of cancer
by viruses; induction of cancer by environmental chemicals; heritability of cancer.

Radiation: causes mutation proto uncogens ** to mutated uncogenes

Gene which is isolated from a particular gene to another.
Makes a cell divide without control.
Many of the proto uncogenes control protein kinase. They are all normal, and we hope
that none of them change into mutated uncogenes.
Tumor suppressor gene. Initiating cell death when there is something wrong with the cell.
Also when cell is dividing inappropriately. Mutation in these genes are bad. leads to
prostate removal
Viruses can pick up genes from cells. And drop it in the other cells. Moves genes between
cells.
Chemicals: causes mutations; mutagenic chemicals
Viruses: human tumors that are associated with viruses.

15) Using experimental single and two character test crosses between pea plants, demonstrate
how you might obtain data which would permit you to formulate hypotheses regarding:
1) Segregation of alleles and 2) Independent Assortment of alleles. Describe the design of an
additional experiment (one per hypothesis) that might prove these two hypotheses. Within your
answer use the terms alleles, phenotype, genotype, dominant and recessive.

16) Describe the experiment and data that lead to the conclusion one gene produces its effect via
one protein as well as the experiment and data that permitted the genetic code to be determined.

17) Draw in general terms the structure of the double helix of DNA indicating the differences
between the 5 end and the 3 end. Your answer/structure should reflect the concept that the two
strands of DNA are complimentary and antiparallel. What are the implications for this antiparallel
design for the enzymes that mediate DNA replication and transcription?

18) One gene produces two different proteins in two different types of muscle cells of the fruit fly.
Explain how this can occur in the context of the complete sequence of events that transpire as the
gene is translated and transcribed.

19) Regulation of operon expression in bacteria provides a significant model for understanding the
regulation of the transcription and ultimately the translation of genes. Using three cartoons,
contrast the different mechanisms for regulation of transcription of the trp and lac operons.
Suppose that a bacterium had no source of tryptophan in its environment. What would be the
immediate and ultimate consequence if a bacteria were presented with a drug that had a structure
that was so similar to the structure of tryptophan that the drug activated the tryp repressor?

20) By providing detailed information about HIV, defend the statement that the structure, gene
expression and life cycle of HIV promote its success as a parasite. What is the basis of diagnosis
of HIV infection? What are the mechanisms of two main classes of drugs that are used to treat
HIV infection?

21) As a research scientist, you wish to determine the amino acid sequence of a liver protein for
which you know the function but have no sequence information. Two related methods are
available to you. Based on your detailed description of both methods, explain why you would
select one over the other. Which method would ultimately give your more information about the
gene itself and why? From the sequence of the DNA how does one get the protein sequence.
Include in your answer how you would quickly [within a few hours] get information about the
entire gene by knowing sequence information obtained from your method of choice.

22) As a research scientist, you wish to determine if a cancer cell is producing different types or
quantities of specific proteins than are produced by non-cancer cells of the same type from a
patient in a clinical trial. You are given both types of cells from that patient. Describe the method
that you would used to achieve this.

23) An entire organism develops from a single fertilized egg that contains one complete genome.
Write an essay in which you propose mechanisms involving gene expression by which cells
expressing different structures and functions, such as lymphocytes, muscle, nerve and liver, are
derived from a single egg cell. Complete this essay by providing examples of such processes in the
development of Drosophila.

24) Given a limited number of genes available to direct the synthesis of proteins, how is it that the
mammalian immune system can respond to a nearly infinite number of structurally different
antigens, including some that may never have appeared on this planet during the course of
evolution.

25) If an antigen is defined as "non-self," what cellular processes permit cells of the immune
system to determine what is an antigen and what is not?

26) Jenner immunized his patient with cowpox and this resulted in immunity to smallpox. Write
an essay outline that would have explained to Jenner the details of the cellular processes that
transpired beginning with the cowpox vaccination ("encowment") and ending with production of
antibodies that recognized smallpox antigens.

27) Using your knowledge of the regulation of the mammalian reproductive systems and two
other substantive endocrine systems, defend the hypothesis that the nervous system controls many
aspects of the endocrine system function via feedback processes.

28) Using the mammalian female reproductive system as an example, explain the role of the
hypothalamus in regulation of hormone expression and target tissue response. Include in your
answer the events associated with implantation of a fertilized egg in the uterus.

29) Using your knowledge of the structure and function of the nephron, explain how your kidneys
can selectively excrete some small molecules while retaining others, like amino acids and at the
same time contribute to the pH an osmolarity of your tissues.

30) Digestion of carbohydrates, proteins and lipids in our diets is a highly regulated process
starting with salivary enzymes in the mouth and ending in the small intestine. In digestion, what
would be the consequences of loss of liver function? Loss of pancreas function?

31) Describe the cellular events which are responsible for the membrane potential in a nerve cell
and defend with your detailed knowledge of nerve cell function the assertion that the membrane
potential is the central element in information movement within and between neurons.
32) On what basis might one conclude that the functions of the mind are attributable the functions
of the cells known as brain? What data on brain structure and function support the hypothesis
that the brain has the capacity to execute the complex functions ascribed to mind.

33) In outline format, review chemical neurotransmitters, their receptors and their actions.
Explain precisely how these transmitters contribute to: a) diverse types of communication among
nerve cells; b) integration of information from diverse sources; c) rapid decision making based on
that integration; d) transient signals in target cells; e) long lasting changes in cells receiving and in
cells delivering information within a circuit particularly as it relates to cellular processes that
underlie memory.

34) Odor is a highly sophisticated sense in mammals. In terms of receptors on olfactory

epithelium and nerve cell circuits, how are mammals able to distinguish among such a wide variety
of novel odors. How does the design of this sensory system permit one to integrate information
on several different odorant molecules that may be found in one scent, for example the smell of a
rose, and that together contribute to ones perception of a complex scent.