Study Guide for Ecology
Ecology
This is a study of animal and plant populations, the mechanisms of their distribution and regulation, energy relationships, adaptation, community organization, and succession.
Course Objectives:
- Students will be able to describe ecological processes as they apply to individuals, populations, habitats, landscapes and global level issues; this would include:
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o Soil CEC and Field Capacity
o Tolerance, transpiration, and PAR
o Homeothermy, mineral balance, and water balance
Students will be able to explain the ecological relation between populations and communities
o Population characteristics, rates of increase (r and K)
o Population regulation, mortality, reproductive strategies
o Symbiosis, niche concept, Lotka-Volterra model, Rosenzweig-MacArthur model
o Functional responses, searching-handling time, food preference and prey switching
o Predation and optimal foraging
Students will be able to identify and contrast patterns in landscape ecology and large-scale events, including extinction, natural disturbance and human impact
o Metapopulations
o Biogeography, including island biogeography
o Patterns of species distribution
o Successional dynamics
Students will be able to apply ecological approaches to an environmental problem Concepts
The organism in its environment
Using a north temperate mammal such as a raccoon as an example, explain how it obtains its energy (autotroph? heterotroph? decomposer?). Describe mechanisms by which an individual raccoon adjusts its physiology and behavior to varying temperature and food availability throughout a year. Discuss how the individual animal's adjustment to the cold in one winter contrasts with how a whole population would adapt to a cooling trend in climate that occurs over the course of many generations.
Population dynamics
Some species experience dramatic changes in population growth rate, experiencing periods of rapid growth and catastrophic crashes (e.g., some northern rodents and rabbits). Others show a steadier, stable population level over time (e.g., elephants). Discuss some of the external factors that affect population growth rates, and also some of the internal factors--for example, those that depend on the species' reproductive characteristics. For each factor, explain whether it is density dependent or density-independent.
Species interactions
Foxes and bobcats are two small predators of similar size who share their range. If you want to know whether they engage in significant interspecific competition, what information and evidence would you look for? What sorts of experiments could you do? If you observe an insect species living exclusively on one plant species, what sorts of evidence would tell you whether this is an instance of parasitism, mutualism, or symbiosis?
Community assembly and stability
After a landscape has undergone a major disturbance (a major volcanic eruption, for instance), would you expect the area to gradually regain a biological community that is essentially the same as before the impact? What stages would you expect to see during recovery, and what factors would influence the assembly and stability of the new biological community?
Energy and nutrients in ecosystems
Energy and nutrients are critical to all ecosystems, but the flow of energy and the cycling of nutrients vary depending on how a particular ecosystem works. Compare a tropical forest and an Arctic tundra with respect to available solar energy; how energy is stored; available nutrients; and how nutrients are recycled. If the tundra warms up due to climate change, how might this affect its pattern of energy flow and nutrient cycling?
Course objectives:
Introduce you to the basic biology and taxonomy of birds
Familiarize you with the identification of the local avifauna
Introduce you to techniques used to study birds
Learn why birds are important to humans and ecosystems
These are good questions just to make sure you have the basic background of what was discussed in class. Make sure you review the discussion questions you answered during class and the essays.
Understand the adaptations that have allowed birds to develop flight. What physics principles are used to allow flight?
Why do birds migrate? What physiological changes occur to prepare for the arduous task of migration?
How do birds migrate? What are the relationships between habitat stopover points and what they use to migrate?
Using your knowledge of the basic features of birds, how would you explain to someone else how to identify birds in the field? What are the basic features of some of the bird Orders?
What is the relationship of habitat, and bird form and function?
Why did birds develop so many mating systems? What are they and what are the good features of each and the challenging features of each?
What are the pros and cons of the theories of the origin of birds?
- Objectives
Biology 510 covers topics including but not limited to:
1. cellular structure and cellular function,
2. organelle physiology,
3. regulation of the cell cycle,
4. cytoskeleton,
5. cellular transport, and
6. cellular communication.
The goal is to have students:
7. demonstrate an understanding of the internal functioning of eukaryotic (and to a much lesser extent, prokaryotic cells) and
8. the interaction between cells in a multicellular organism.
Biology 510 Cell Biology
Biology 510 Cell Biology
Describe proteins. Many proteins contain one or more motifs built from particular combinations of secondary structure. Describe the three common structural motifs discussed in this course. Describe some of the general functions of protein domains on the extracellular membrane surface, within the membrane, or on the cytosolic face of the membrane. The biological activities of proteins are affected by chemical modifications. Describe the different types of chemical modifications discussed in this course.
Compare and contrast the processes of transcription and translation. Be sure to include the different molecules involved.
Discuss the different types of DNA damage that can promote cancer. Be sure to discuss the effects of this damage on the cells and how the cancer cells begin to grow. Discuss how different physical agents (such as chemicals or radiation) cause DNA damage that contribute to cancer.
The nucleus is the largest of the eukaryotic organelles and contains the genome of the organism. A) Please describe the proteins and process of nuclear import and export. B) Please describe, in general terms, an experiment that could be conducted to show that there are specific signals for nuclear import or export. Please remember that this question is asking about import and export and not about the nuclear pore complex.
The cytoskeleton is a vital part of a eukaryotic cell. A) Please describe the 3 major components of the cytoskeletal system including the proteins that comprise the different members. B) Please describe, in detail, only one of the following connections: Desmosome; hemidesmosome; gap junction; tight junction. You must include the cytoskeletal components and include any accessory proteins, where they can be found and how they help a multicellular organism.
Mitosis is only a small part of the entire cell cycle. A) Please discuss the complete cell cycle in a human cell, not just mitosis (but mitosis must explained in your answer), and, in general, the regulatory components (i.e. the proteins associated with cellular checkpoints) of the cell cycle. You do not need to be extremely specific, but you need to give the major players of the cell cycle regulation. B) Tumor growth results when the cell cycle checkpoints are ignored. Please give a general example of how tumor growth could result from either a loss-of-function or a gain-of-function mutation.
The chloroplast and mitochondrion both contain their own genomes. However, a number of genes encoding mitochondrial or chloroplastic proteins are found in the nuclear genome. A) Please explain one mechanism for how a nuclear encoded protein is targeted to the inner membrane of the mitochondrion. B) Please explain the mechanism for how a nuclear encoded protein is targeted to the thylakoid membrane. C) Please describe, in general, an experiment that could be conducted to show that there is a targeting system for a nuclear encoded protein that ultimately finds its way to a specific organelle.
A) Please explain how a glycoprotein, that is ultimately found on the outer surface of the plasma membrane, is translated, modified and ultimately transported to the outer plasma membrane. Be sure to explain the migration of the protein from the beginning of translation to placement in the cellular membrane. B) Please describe an experiment that might be conducted to determine if any specific signal is necessary for the proper targeting to the ER or the plasma membrane.
There are a number of different proteins that can be found in/on the plasma membrane. Please describe the 3 major types of proteins that can be found at the plasma membrane and give examples of each type of protein and the function that each plays in the functioning of the cell.
Myosin, kinesin and dynein are considered motor proteins. A) Please explain the structure of dynein and kinesin and how their structures aid in organelle movement within a eukaryotic cell. B) Please explain the structure of a muscle fiber and how the two proteins, actin and myosin, function together to produce movement.
All living cells are surrounded by some type of plasma membrane. While all cells have a plasma membrane, plasma membranes can be highly dynamic and asymmetrical even within a multicellular organism like a human. Please describe the basic components of a plasma membrane and explain in detail the asymmetry that occurs in a red blood cell in terms of the membrane and the associated proteins.
- Objectives
Upon successful completion of this course, the student should be able to:
- Understand basic concepts of pharmacodynamics and pharmacokinetics
- Understand and describe mechanisms of action of major drug classes
- Understand the pathophysiology of different human systems and the mechanism of drugs used to treat disease
- Develop ability to explain pharmacology concepts in online oral presentations.
Biology 515 Pharmacology
Absorption, Distribution, Metabolism, and Excretion
Routes of drug administration and factors that influence choice
Mechanisms of drug movement across biological membranes and factors that influence drug solubility and membrane permeability
Factors that influence drug bioavailability
Factors influencing drug binding to plasma proteins and tissue reservoirs
Distribution of drugs into special body compartments, e.g. role of blood-brain barrier, placenta
Relationship of drug metabolism to excretion of drugs and termination of drug effects
Metabolism as a determinant of bioavailability: the first-pass effect
Pathways of drug metabolism: phase I (oxidation, reduction, hydrolysis) and phase II (glucuronidation, sulfation, acetylation, methylation, glutathione conjugation)
Enzyme multiplicity and broad substrate selectivity of drug-metabolizing enzymes, with the cytochromes P450 as a prime example
Role of drug metabolism in adverse drug reactions: factors that control the balance between drug bioactivation and detoxification
Drug-metabolizing enzymes as key sites for drug-drug interactions: inhibition and induction of drug metabolism
Major sites of drug elimination: liver and biliary excretion, kidney, lungs
Zero-order and first-order kinetics of drug elimination
Rational dosing to achieve a target steady-state drug concentration: loading dose, maintenance dose, the plateau principle
Principles of Pharmacodynamics
Drug-Receptor Interactions
Nature and properties of biological drug receptors/targets (e.g. G-protein coupled receptors, DNA, enzymes, ion channels, receptor tyrosine kinases, etc.)
Classification of drugs based on their effects on receptors: full agonist, partial agonist, inverse agonist, antagonist (competitive, non-competitive, etc.)
Analysis of log-dose-response curves to gain understanding of the following drug properties: median effective concentration or dose, median lethal concentration or dose, therapeutic index, potency, efficacy
Regulation of receptors: homologous and heterologous receptor desensitization, receptor internalization and trafficking, receptor down-regulation
In addition to understanding the basic concepts outlined above, you should review the use of pharmacological therapies in the following specific disease processes.
I. Antibiotics
-Define the terms bacteriostatic and bacteriocidal
- Mechanism of action of beta-lactam antibiotics
- Mechanisms of resistance to beta-lactam antibiotics
- Mechanism of action for one antibiotic effective against methicillin-
resistant S. aureus (MRSA).
II. Human Immunodeficiency virus (HIV)
- HAART Therapy- rationale and mechanisms of action of: NRTIs, NNRTIs, Protease inhibitors
III. Chemotherapy
- Mechanism of action of cisplatin and alkylating agents, why are these drugs effective at killing cancerous cells?
- Mechanisms of resistance
IV. Treatment of depressive and anxiety disorders
- Compare and contrast the mechanisms of action and side effects for tricyclic antidepressants (TCAs), selective serotonin reuptake inhibitors (SSRIs), and MAO inhibitors
- Mechanism of action of benzodiazepines
V. Treatment of stroke
- Compare and contrast hemorrhagic and ischemic stroke
- Understand the mechanism of action and indications for warfarin, heparin, tPA, and aspirin
VI. Treatment of Hyperlipidemia
- Understand the metabolism of lipoproteins
- Mechanism of action for HMG coAreductase inhibitors and the effects on lipoprotein levels
VII. Treatment of angina and myocardial infarction
- Review the etiology and associated pathophysiology
- Mechanism of action for ??blockers (you should be able to describe this pathway from the receptor to the cellular action)
- Use of nitrates and mechanism of action
VIII. Treatment of congestive heart failure and hypertension
- Mechanism of action and major side effects of loop diuretics, ACE inhibitors, blockers, Ca2+ channel blockers
IX. Cyclooxygenase (COX) Inhibitors
- Understand prostaglandin synthesis
- Mechanism of action for COX inhibitors
- Compare and contrast COX-1 versus COX-2 selective inhibitors
X. Neuromuscular blockers (NMBs)
- Mechanism of action of depolarizing and nondepolarizing NMBs
XI. Treatment of peptic ulcer disease
- Understand the process of H+ secretion from parietal cells including the various ligands and receptors that can stimulate secretion.
- Mechanism of action for proton pump inhibitors (PPIs)
- Understand the role of H. pylori
XII. Treatment of Diabetes
- Compare and contrast the pathophysiology and treatment of type I versus type II diabetes
- Biology 516 Toxicology
You have been invited on a trip of a lifetime. A group of scientists sponsored by a grant from the U.S. National Academy of Sciences are going to Antarctica to attempt to determine the extent of pollution from human activities in the ecosystem. Biologists, divers with dredging equipment, all manner of collection equipment, etc. will be made available to you. Transportation anywhere in Antarctica and with scientific justification, anywhere else in the world is at your request. The team leader wants you to state a hypothesis and some brief idea of what you might do to assess pollution by measuring biotransformation reactions or capability.
Describe the different ways a toxic compound can be metabolized and eliminated from the body. Be sure to include why types of pathways are available, the types of enzymes that are involved, what types of compounds are metabolized in which manner and what is the desired and actual outcome of the metabolism.
Describe in detail the different modes of absorption and distribution of toxicants in the body. Be sure to give specific examples.
Imagine that the average age for a female child to reach puberty in your family is 12 years old. However, your niece Cynthia begins menstruating and developing mature female sexual characteristics at 10 years of age. When consulting with her parents you learn that she was fed soy milk as a child. Explain how this might occur, applying your knowledge of reproductive and developmental toxicology and endocrine disrupting chemicals. Be sure to include a description of the potential mechanisms (molecular, cellular and physiological) that would explain her precocious puberty.
Imagine that you are a regulatory scientist at the Environmental Protection Agency. You are concerned that the level of lead in drinking water has reached potentially harmful levels in certain regions of the country. How would you go about testing what concentrations of lead would be safe for consumption? Include at least one approach from the following 4 categories: in vitro assay, cell-based test, rodent bioassay, toxicogenomic approach. For the rodent bioassay, include mock results in a dose-response curve format and indicate/illustrate how you would determine the NOAEL and LOAEL values for lead in your bioassay.
One of the fathers of toxicology, Paracelsus, is famous for saying that "all substances are poisons; there is none which is not a poison. The right dose differentiates a poison from a remedy." Explain what he meant by this statement. Illustrate your point using a graded dose-response curve. Explain why some agents such as iron may display both beneficial and harmful effects. Given this view, why so some xenobiotics toxicants display a hormesis-type dose-response, whereas others show a more classical logarithmic dose-response curve? What does this reveal about their different mechanisms of action? Give an example of how a xenobiotic could differ in its molecular and physiological mechanisms of action depending on the dose
Objectives
Course Description and Objectives.
This course introduces concepts of Toxicology, topics including metabolism, types of toxicity, classes of chemicals, risk assessment, and diagnosis and treatment.
Upon completion of this course, the successful student will be able to:
1. Demonstrate the relationship between chemical risk factors and disease.
2. Determine causal events for certain diseases and methods of exposure.
3. Predict possible toxic exposures arising from characteristics of the population such as new technologies used over time (cell phones, new curative creams, medications, etc).
- Course Objectives: By the end of this course, students will understand:
1. the proximate control, organization, and development of animal behavior;
2. the ultimate ecological and evolutionary mechanisms underlying animal behavior; and
3. both foundational and contemporary theories and application of animal behavior.
By the end of this course, students will be able to:
4. integrate major concepts in animal behavior with evidence supporting these concepts;
5. compare proximate and ultimate explanations for animal behaviors;
6. apply major concepts in animal behavior to conservation biology and to understanding human behavior;
7. integrate behavioral concepts with the process of scientific inquiry; and
8. understand and critically evaluate articles from the primary literature.
Study Guide for Biology 517 Animal Behavior
Biology 517 Animal Behavior
In preparing for questions from Animal Behavior, students should understand social structure among populations of animals and its determinants, particularly in the establishment of dominance hierarchies and communication within the group. Students should also understand the inheritance of behavioral traits and mechanisms of exhibiting these "hard-wired" behaviors.
Some representative questions:
Contrast the following two ideas about the evolution of communication systems in animals: (a) Displays evolve so as to maximize information transfer from sender to receiver; (b) Displays evolve so as to maximize manipulation of the receiver by the sender.
Discuss the relationship between the distribution of food resources and social organization in animals.
Males typically compete for access to females and often obtain more than one mate, while females are particular about whom they mate with. In some species, however, the male supplies the female with large "gifts" in the form of captured prey or large, protein-rich sperm packets. What differences might you expect to see in the reproductive behavior of such species when compared with the typical pattern?
How is it possible that a trait might evolve that predisposes an organism to help a relative rather than produce its own offspring? In what situations would a trait predispose an organism not to help a relative?
Discuss the concept of IRMs in reference to the following observation: when chickens are sitting on a next, a nearby egg will be drawn into the clutch; however, when an egg is found in the yard, it is attacked by pecking until broken, at which point it is consumed.
Biology 519 Cancer Biology
To prepare for questions from Biol 519 (the Biology of cancer) on the comprehensive exam I recommend you be able to answer each of these five questions drawn from the objectives of the course.
- Describe the processes of cellular signaling and metabolism that are altered during the transformation of a cell.
- Interpret the role oncogenes and tumor suppressors play in transformation.
- Illustrate cancer cell types and understand the differentiation process that occurs during cancer development.
- Identify the key steps of transformation, tumorigenesis and metastasis on a cellular and tissue level.
- Analyze the roles DNA repair, cell cycle control and the immune system play in cancer development.
- Evaluate current literature focused on tumorigenesis, cancer progression, and cancer treatments.
Explain why p53 is mutated in the vast majority of human cancers.
Compare and contrast tumor suppressor genes to oncogenes
Describe the five hallmarks of tumor cells and explain how each is required for transformation.
Explain how cancer cells change and evolve during the development of cancer.
Explain the roles DNA repair, cell cycle control and inflammation play in the transformation process
Discuss the link between the exponential growth of tumors and tumor metastasis and how these are influenced by cancer chemotherapy.
Discuss how growth factors influence cell signaling and proliferation that leads to cancer induction, progression and metastasis. Be sure to include the involvement of apoptosis and angiogenesis.
Describe how different chemicals and radiation can be involved in the development of cancer. Then, describe how chemicals and radiation can be used to treat a patient with cancer.
- Objectives
Biology 590-01 covers topics including but not limited to:
- describing the main components used by cells in their communications,
- cellular signaling pathways, as well as
- discussing how molecular "signal" proteins interact.
My goal is to have my students demonstrate an understanding of the
- intricate molecular network of cellular signaling and
- pathways that play important roles in development, growth, and apoptosis.
Types of distal and local signaling including autocrine paracrine endocrine and electrical /neurosynaptic signaling.
Hormone signaling including estrogen and testosterone signaling from production, secretion, receptor binding, receptor modification, and intracellular signaling, to the triggering of cellular proliferation.
Receptor/protein phosphorylation and its role in cellular signaling and metabolism
G protein signaling and its effect on metabolism, and cellular viability/proliferation.
Insulin -like Growth Factor (IGF) signaling and its effect on metabolism.
IGF receptor binding and its result on intracellular signaling.
- Biology 531 Proteonomics
1. What two major sequencing technologies were used to reveal the entire human genome sequence?
2. Explain automated sequencing using the terms - genomic DNA, subclones, library, contigs, and BACs.
3. How are Mass Spectroscopy and Microarray technologies used to examine protein function?
4. Can the DNA sequence tell a scientist about the structural properties of proteins?
5. Describe in detail your 3 favorite classes of proteins. Be sure to provide structural and functional details for each class and a specific example for each.
6. What is a genome wide association study? How is this important for translational medicine/science?
Objectives
This course will examine the newly emerging field of proteomics, the study ofthe proteome, by
- considering the link between proteomics and genomics,
- the relationship between protein conformation and biological activity,
- the role of proteins insignaling pathways, and
- the contributions of specific proteins to human physiology andpathology.