2014-2015
AP Biology Topic Outline and Class Discussion
Questions.
Introduction
Course Introduction
1. Evolution
1.1. Introduction to Evolutionary Biology
1.2. Evolutionary Forces
1.3. Evidence of Evolution
1.4. Measuring evolution
1.5. Classification
1.6. Speciation
1.7. Origin of Life
2. Matter
2.1.1. Chemistry Review
2.1.2. Water
2.1.3. Carbon
2.2.1 Biological Molecules 1 (Carbs/Lipids)
2.2.2 Biological Molecules 2 (Proteins/Nucleic Acids)
2.3. Structure and support
2.4. Transport
2.5. Domains & Prokaryote Cellular Anatomy
2.6. Eukaryote Cellular Anatomy & Endomembrane System
2.7. Matter & Energy Processing
3. Energy
3.1.1 Energetics- Theory
3.1.2 Energetics- Practice
3.2.1 Photoautotrophic Nutrition- The Light Reactions
3.2.2 Photoautotrophic Nutrition- Calvin Cycle and Control
3.3.1 Chemoheterotrophic Nutrition- Introduction &
Glycolysis/Fermentation
3.2.2 Chemoheterotrophic Nutrition- Aerobic Cellular Respiration
4. Information
4.1. Introduction to DNA Structure
4.2.1 Central Dogma 1- Replication
4.2.2 Central Dogma 2- Transcription
4.2.3 Central Dogma 3- Translation
4.3.1 Biotechnology Tools & Techniques:
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4.3.2 Biotechnology Applications
4.3.3 Biotechnology 4: Ethics
Agree/Disagree Statements:
4.4. Viruses
4.5. Mitosis
4.6. Cell Cycle Control
4.7. Meiosis
4.8. Chromosomal Abnormalities
4.9. Introduction to Mendelian Genetics
4.10.1 Extensions to mendelian ratios
4.10.2 Part 2: Non-Mendelian Ratios
4.11. Human Genetic Conditions
4.12.1 Prokaryotic Genome Regulation
4.12.2 Eukaryotic Genome Regulation
5. Regulation
5.1.1 Genomics
5.1.2 Developmental Genetics
5.2 Development
5.3 Osmoregulation
5.5 Transport and Gas Exchange
5.6 Immunity
5.7 Responses
6. Communication
6.1 Cellular Communication
6.2 Hormonal Control
6.3. Behavior
6.4- Neurons
6.5- Nervous Systems
7. Interactions
7.1 Organism Organization
7.2 Reproduction
7.3. Community Interactions
7.4 Population Dynamics
7.5. Ecosystem Structure
7.6. Conservation Biology
Introduction
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Course Introduction
1. What is the difference between science as a process and science as
a body of knowledge?
2. Does the “scientific method” really exist?
3. Can things ever be proven in science? Why is falsifiability so
important to scientific inquiry?
4. What does a good hypothesis look like?
5. What makes something a theory?
6. Are there any biological “laws”?
7. How does scientific thinking differ from other ways of thinking?
8. What is “reductionism”? How does it work?
9. Are there any problems with a reductionist way of analyzing the
world?
10.
What is a “system”?
11.
How does feedback work?
12.
How can systems have properties that the parts of that system
don’t have individually?
13.
Why is it hard to analyze complex systems?
14.
What are the major properties of living systems? (put up 4 big
ideas and place properties of life under each one as a group).
1. Evolution
1.1. Introduction to Evolutionary Biology
1. Did Darwin develop his theory all by himself?
2. What were the major contributions of scientists that informed
Darwin’s theory of natural selection?
3. How is the idea of Uniformitarianism demonstrated in Darwin’s
work?
4. How are Lamarckian ideas of evolution different from Darwinian
ideas?
5. What is the theory of natural selection?
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a. Why is variation present in all organisms?
b. What is the “struggle for existence”? Why does it occur?
c. What does it mean to be “fit”, evolutionarily?
6. How does evolution support the idea of a very old Earth?
7. How does evolution support the idea of common ancestry
among all living organisms?
8. Why do we tend to show evolutionary relationships in tree
diagrams?
9. Why is the theory of evolution so controversial among certain
groups of people?
1.2. Evolutionary Forces
1. How is the modern theory of evolution different from Darwin’s
conception?
2. Why is it appropriate to define evolution as “change in gene
frequencies in a population over time?”
3. How does natural selection change gene frequencies?
4. How does natural selection affect a population?
5. What are some examples of how natural selection has affected
populations?
6. How does genetic drift change gene frequencies?
7. How does genetic drift affect a population?
8. What are some examples of how genetic drift has affected
populations?
9. How does gene flow change gene frequencies?
10.
How does sexual selection change gene frequencies?
11.
How does sexual selection affect a population?
12.
What are some examples of how sexual selection has
affected populations?
13.
How can evolution affect the distribution of a particular
variation in a population?
14.
What are similar among all modes of evolution?
15.
What is different in each mode of evolution?
16.
When can evolution not affect the distribution of a
particular variation in a population?
1.3. Evidence of Evolution
1. How are we able to make scientific conclusions about events
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and processes that we are not able to directly witness?
2. How does the fossil record support evolutionary theory?
3. How does morphological analysis of organisms support
evolutionary theory?
4. What are homologous structures?
5. What are analogous structures?
6. What are vestigial structures?
7. Why do embryos of different species possess morphological
similarities?
8. How does molecular analysis of DNA and protein sequences
support evolutionary theory?
9. What is the relationship between molecular similarity and
evolutionary relatedness among species?
10.
How does biogeography support evolutionary theory?
11.
How does artificial selection support evolutionary theory?
12.
How is artificial selection different from natural selection?
13.
Why is is a misconception of evolutionary theory to think
that the evolution of life demonstrates a progression towards
increasing complexity, or a purpose, or that evolution would require
an “intelligent designer”?
1.4. Measuring evolution
1. We can define evolution as “differential reproductive success”.
What does this mean? Why is reproductive success not uniform?
2. Where do variations come from?
3. Why are sexually reproducing organisms more varied than
asexually reproducing ones?
4. Explain each of the following terms:
a. Gene
b. Allele
c. Dominant
d. Recessive
e. Homozygous
f. Heterozygous
g. Population
h. Gene Pool
5. If we define evolution as “change in allele frequencies in a
population over time”, how does this lead to differential reproductive
success?
5
6. How does each of the following lead to evolution in a
population?
a. Mutation
b. Gene Flow
c. Non-Random Mating
d. Genetic Drift
e. Natural Selection
7. What would a population need to look like in order for it to not
evolve?
8. How does the Hardy-Weinberg Equation work?
9. Is any population actually in HW Equilibrium? Why is HW
Equilibrium useful?
10.
How do we solve HW problems?
11.
What is the square root of .25? Why?
12.
How can we use the HW equilibrium to investigate realworld instances of evolution?
13.
What is the “heterozygote advantage”?
1.5. Classification
1. How were organisms originally classified?
2. What is the basis of the Linnaean Hierarchy?
3. What is the basis of Binomial Nomenclature?
4. How are organism’s scientific names written?
5. What are the major problems associated with traditional
classification schemes?
6. How are organism’s classified now?
7. Why are modern modes of classification more accurate than
traditional modes?
8. What is the relationship between DNA sequences and
evolutionary relationships? Why does this relationship exist?
9. How is a cladogram constructed?
10.
What is the rule of “maximum parsimony”? What is the
rule of “maximum likelihood”? Why are these scientifically sound
concepts to use when constructing a cladogram?
11.
Is a cladogram always indicative of evolutionary
relationships?
12.
What characteristics are most useful for constructing an
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evolutionarily accurate cladogram?
13.
What are the differences between monophyletic,
paraphyletic, and polyphyletic groups in a phylogenetic tree?
14.
Why are computers used to compare DNA sequences for
homology?
1.6. Speciation
1. How do we define a species? Why is the biological species
definition sometimes less than useful?
2. How does speciation happen allopatrically? How does it
happen sympatrically?
3. Does isolation always lead to speciation?
4. What are the major prezygotic barriers that contribute to
speciation? What are the major postzygotic barriers?
5. What are some of the major, researched, speciation examples?
6. What is the idea of gradualism? How does it compare to the
idea of punctuated Equilibrium?
1.7. Origin of Life
1. How can we know anything about the history of life if we were
not around to directly observe it?
2. What are the approximate dates of the following “milestones” of
life’s history:
a. Creation of the earth
b. Origin of life
c. Origin of photosynthesis
d. Evolution of eukaryotes/endosymbiosis
e. Origin of multicellularity
f. Origin of plants
g. Origin of land vertebrates
h. Origin of dinosaurs
i. Origin of mammals
j. Origin of humans
3. Why has the diversity of life increased over time?
4. What patterns do we see in the history of life (mass extinctions/
adaptive radiations)?
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5. How has the evolution of humans affected terrestrial life?
6. How have recent research into the genetics of development
illustrated how diversity of organisms can increase?
2. Matter
2.1.1. Chemistry Review
1. Where do atoms come from?
2. Is there anything interesting about the atoms that living things are
made from?
3. How does energy interact with atoms?
4. How do atoms bond with each other?
5. What is the difference between an ionic bond and a covalent bond?
6. What is the difference between a polar molecule and a non-polar
molecule?
7. What are hydrogen bonds?
8. Explain the relationship between the bonds in a molecule and the
shape of that molecule.
9. Explain the significance of molecular shape in biology.
10.
What is the relationship between energy, atoms, and bonds?
11.
How do compounds demonstrate the concept of emergence?
12.
What is radioactivity?
13.
How is radioactivity used in biological
investigations/medicine/etc?
2.1.2. Water
1.
2.
3.
4.
How is water necessary for living systems?
Why is water a polar substance?
How does water’s polarity contribute to hydrogen bonds?
How does the polarity of water lead to:
a. adhesion/cohesion
b. high specific heat
c. ice being less dense than liquid water
8
d. water acting as a good biological solvent
e. water dissociating easily
5. How do these properties of water affect biological systems?
6. What is the mathematical relationship between [H+] and [OH-] in a
particular aqueous solution?
2.1.3. Carbon
1.
2.
3.
4.
5.
Why is the carbon atom so versatile?
Why is the carbon atom the foundation of biological molecules?
What is an isomer?
What is a functional group?
How do functional groups modify the chemical properties of a
molecule?
6. How do functional groups modify the biological properties of a
molecule?
2.2.1 Biological Molecules 1 (Carbs/Lipids)
1. What does it mean when we say that biological molecules are
“polymers”?
2. What are the monomers and polymers of carbohydrates? proteins?
Nucleic acids?
3. How are biological molecules built (“synthesized”)?
4. How are biological molecules (“hydrolyzed”)?
5. What are the roles of carbohydrates in a biological system?
6. How can we recognize carbohydrate molecules?
7. How does the structure of cellulose differ from the structure of starch?
How does this affect the function of these two molecules?
8. What are the roles of lipids in a biological system?
9. How can we recognize lipid molecules?
10.
How does the structure of a triglyceride relate to its function?
11.
How do the structural differences between saturated and
unsaturated fat molecules affect their functions?
12.
How does the structure of a phospholipid relate to its function?
13.
How does the structure of a steroid relate to its function?
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2.2.2 Biological Molecules 2 (Proteins/Nucleic Acids)
1. What are the roles of proteins in biological systems?
2. How does the structure of an amino acid influence its chemical
properties?
3. How can we recognize the following landmarks in a chain of amino
acids (a “polypeptide”)?
a. the N and C terminus?
b. The R-groups?
c. The peptide bonds?
4. What aspects of a polypeptide/protein’s structure contribute to the
four levels of protein structure?
5. How is it possible that proteins can have such highly unique, specific
shapes?
6. How does the structure of a protein molecule relate to its function?
7. What happens if the structure of a protein is altered? What types of
conditions alter protein structure? How do changes in these
conditions affect protein structure? How do changes in these
conditions affect protein function?
8. What are the roles of nucleic acids in biological systems?
9. How does the structure of a nucleotide influence its chemical
properties?
10.
What are the major structural differences between DNA and
RNA?
11.
How can we recognize the following landmarks in a nucleic
acid?
a. The 3’ and 5’ end
b. Complementary base-pairs
c. Phosphodiester bonds
12.
What happens if the structure of a nucleic acid is altered?
What types of events alter nucleic acid structure?
2.3. Structure and support
1.
2.
3.
4.
5.
6.
Why do cells need support and structure?
How is the cytoskeleton used by cells?
How does the structure of the cytoskeleton allow for its functions?
How is the cell membrane used by cells?
How does the structure of the cell membrane allow for its functions?
What determines the permeability of the cell membrane?
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7. How do the structures of particular membrane proteins allow for their
functions?
8. What is the role of cholesterol in the cell membrane?
9. How is the cell wall used by cells?
10.
How does the structure of the cell wall allow for its functions?
11.
How does the extracellular matrix function for cells?
12.
How does the structure of the extracellular matrix function for
cells?
13.
How do the various types of junctions between cells function in
cellular and organismal physiology?
2.4. Transport
1. Why does material move from high concentration to low
concentration without the input of energy?
2. Why is energy required to move material from low concentration to
high concentration?
3. What are the similarities and differences between:
a. passive transport and active transport
b. simple diffusion and facilitated diffusion
c. pump proteins and co-transporters
4. What are the roles of proteins in cellular transport?
5. How is energy used by pump proteins in active transport?
6. How are tonicity relationships used to predict the direction of
transport and effects on cellular physiology?
7. What are the major modes of bulk transport in cells?
2.5. Domains & Prokaryote Cellular Anatomy
1. Why has life been classified into three domains? How are the
domains differentiated?
2. How do prokaryotes differ from eukaryotes?
3. What cellular anatomy is found in prokaryotic cells?
4. How do prokaryotes generate genetic variation?
5. Why do prokaryotes evolve rapidly?
6. What are the scientific hypotheses regarding the evolution of
eukaryotes from prokaryotes?
2.6. Eukaryote Cellular Anatomy & Endomembrane
System
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1. What had to happen for cells to be discovered?
2. What is the cell theory?
3. How do microscopes work?
a. Advantages and disadvantages of light microscopy and
electron microscopy
4. Are there other ways to study cells other than microscopy?
5. Why are there no giant cells?
6. Does anything prevent cells from getting too small?
7. What is the major difference between prokaryotic and eukaryotic
cells?
8. How does compartmentalization lead to increased complexity in
eukaryotic cells?
9. What do cells need to do to remain alive?
10.
How does the endomembrane system allow cells to process
matter?
11.
Explain the structure and function of each of the following:
a. nucleus
b. ribosomes (free vs. bound)
c. endoplasmic reticulum (rough vs. smooth)
d. vesicles
e. golgi apparatus
2.7. Matter & Energy Processing
1. Why do cells need to process energy and matter?
2. Where do cells get energy from? What do cells use energy for?
3. How are the mitochondria and chloroplasts used by cells to process
energy and matter?
4. How do cells dispose of waste/digest material?
5. How is the structure of a lysosome useful for its functions?
6. What are some of the consequences of non-functional lysosomes?
7. How do cells store material?
8. How is the structure of a vacuole useful for its functions?
9. How do vacuoles differ in plant-like and animal-like cells?
10.
How is the structure of a mitochondrion involved in its
functions?
11.
How is the structure of a chloroplast involved in its functions?
12.
What are the similarities and differences in
chloroplast/mitochondria structure and function?
13.
What is the evidence that suggests mitochondria and
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chloroplasts are the result of endosymbiotic events?
14.
How common is endosymbiosis in the eukarya?
3. Energy
3.1.1 Energetics - Theory
1. What is the first law of thermodynamics?
2. What consequences does the first law of thermodynamics have for
biological systems?
3. How do living systems process energy to do work?
4. What determines if a reaction happens spontaneously or not?
5. How are exergonic reactions and endergonic reactions linked in
biological systems?
6. What is the second law of thermodynamics?
7. What consequences does the second law of thermodynamics have
for biological systems?
8. Why do living systems need to be open?
9. Why do living systems need to exist at a point away from equilibrium?
10.
How does ATP function in cellular energetic systems?
11.
What processes produce ATP?
12.
What processes use ATP?
13.
What is cellular metabolism?
14.
How does the coupling of endergonic reactions and exergonic
reactions increase cellular efficiency and metabolic complexity?
15.
Why are catalysts needed in biological systems??
3.1.2 Energetics - Practice
1.
2.
3.
4.
How do enzymes function to catalyze biological reactions?
What are co-factors?
How do cells regulate the enzymatically controlled reactions?
How are competitive and noncompetitive regulation similar? How do
they differ?
5. How does compartmentalization increase cellular efficiency?
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6. How does the local environment affect enzymatic activity?
7. How do cellular metabolic pathways utilize feedback loops for
regulation?
3.2.1 Photoautotrophic Nutrition - The Light Reactions
1. How does chlorophyll convert electromagnetic radiation into electrical
energy?
2. What will be oxidized in photoautotrophic nutrition? What will be
reduced?
3. Where do the light reactions occur in plants?
4. How do the electrons produced by chlorophyll contribute to ATP
production?
5. Where do the electrons produced by chlorophyll during the light
reactions end up at the end of the light reactions?
6. What are the inputs and outputs of the light reactions?
3.2.2 Photoautotrophic Nutrition - Calvin Cycle and
Control
1. How do the end products of the light reactions contribute to the Calvin
cycle?
2. What happens during the Calvin cycle?
3. What are the inputs and outputs of the Calvin cycle?
4. How does the Calvin cycle produce sugars?
5. How does the behavior of rubisco require adaptations in some plant
species?
6. How important is photosynthesis for biological systems?
3.3.1 Chemoheterotrophic Nutrition - Introduction &
Glycolysis/Fermentation
1. What is the relationship between chemoheterotrophic nutrition and
photoautotrophic nutrition?
2. Why are enzymes needed to regulate respiratory processes?
3. What is a redox reaction?
4. Why are biological energetic reactions redox reactions?
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5. What is the role of electron shuttles in biological energetic reactions?
6. What will ultimately be oxidized in chemoheterotrophic nutrition?
What will be reduced?
7. What happens during glycolysis?
8. What are the inputs and outputs of glycolysis?
9. Why is it hypothesized that glycolysis is the most ancient metabolic
pathway?
10.
Why is fermentation required for anaerobic respiration? What
happens to the end products of glycolysis in fermentation?
3.2.2 Chemoheterotrophic Nutrition- Aerobic Cellular
Respiration
1. What happens during aerobic cellular respiration?
2. What happens to the end products of glycolysis in aerobic cellular
respiration?
3. What happens during the acetyl-coA cycle?
4. What are the inputs and outputs of the acetyl-coA cycle?
5. Where does the acetyl-coA cycle occur?
6. What happens during the citric acid cycle?
7. What are the inputs and outputs of the citric acid cycle?
8. Where does the citric acid cycle occur?
9. What happens during oxidative phosphorylation?
10.
What are the inputs and outputs of oxidative phosphorylation?
11.
What happens during chemiosmosis?
12.
How does chemiosmosis produce ATP?
13.
Where does oxidative phosphorylation occur?
14.
How do aerobic and anaerobic cellular respiration compare?
15.
How efficient is respiration?
16.
How does a cell respire molecules other than glucose?
17.
How is cellular respiration controlled in a cell?
4. Information
15
4.1. Introduction to DNA Structure
1. How was it determined that the DNA contained the genetic code?
2. Why did folks think that protein might have contained the genetic
code?
3. How did Griffith’s transformation experiment illustrate the molecular
nature of inheritance?
4. How did the work of Avery, McCarty, and McCleod expand upon the
work of Griffith?
5. How did the work of Hershey and Chase expand upon the work of
Avery, McCarty and McCleod?
6. What contribution did Erwin Chargaff make to the determination of
the structure of DNA?
7. How did Watson and Crick determine the structure of DNA?
8. What contribution to the determination of DNA Structure was made
by Franklin and Wilkins?
4.2.1 Central Dogma 1 - Replication
1. How does the information in DNA move through the cell?
2. How does the information in DNA move through successive
generations?
3. How does the structure of a DNA molecule inform us about how it is
replicated?
4. How did the Meselson/Stahl experiment demonstrate evidence to
support the hypothesis of semi-conservative replication?
5. What needs to happen to replicate a strand of DNA?
6. What needs to occur in each of the following phases of DNA
replication?
a. Initiation
i. What needs to happen?
ii. Where does replication begin?
iii. How does each of the following enzymes contribute?
1. helicase
2. single strand binding proteins
3. primase
b. Elongation
i. What needs to happen?
ii. How does the antiparallel structure of a DNA molecule
complicate things?
iii. How does each of the following enzymes contribute?
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1. DNA polymerase
a. How do are new nucleotides incorporated into
a DNA molecule?
2. Topoisomerase
3. ligase
c. Termination
i. What needs to happen?
ii. How do the ends of eukaryotic chromosomes complicate
things?
iii. How does each of the following enzymes contribute?
1. telomerase
7. What is the meaning of the term “replisome”?
8. How are errors in DNA replication detected and repaired?
9. What is the error rate in replication?
10.
What are the major differences in replication between
prokaryotes and eukaryotes?
4.2.2 Central Dogma 2 - Transcription
1. What is transcription?
2. Where does transcription occur?
3. What needs to occur in each of the following phases of transcription?
a. Initiation
i. What needs to happen?
ii. How is the beginning of a gene identified on a DNA
molecule?
iii. How is initiation of transcription different in prokaryotes
and eukaryotes?
iv. What is the role of RNA polymerase?
v. How does RNA polymerase work?
b. Elongation
i. What needs to happen?
ii. What is the relationship between the “template” and the
“coding” strand of a DNA molecule? How can they be
identified?
c. Termination
i. What needs to happen?
ii. How does it happen?
4. What happens to the RNA molecules that are transcribed?
5. What happens to eukaryotic mRNA in each of the following
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“processing” steps?
a. 5’ capping
b. polyadenylation
c. exon splicing/intron excision
6. What are the major differences in transcription between prokaryotes
and eukaryotes?
4.2.3 Central Dogma 3 - Translation
1. What is translation?
2. Where does translation occur?
a. What is the role of the ribosome?
i. How is ribosomal structure related to its function?
b. What is the role of tRNA molecule
i. How is tRNA structure related to its function?
3. How is the genetic code interpreted in the cell?
4. What are the implications of the universality of the genetic code
among all lineages?
5. What needs to occur in each of the following phases of translation?
a. Initiation
i. What needs to happen?
6.
7.
8.
9.
ii. How is the beginning of a gene identified by the
ribosome?
iii. How do tRNA molecules align to the transcript?
b. Elongation
i. What needs to happen?
c. Termination
i. What needs to happen?
ii. What happens to the end products of translation following
termination?
What are the major differences in translation between prokaryotes
and eukaryotes?
a. What is transcription/translation “coupling”? Why is it only
possible in prokaryotes?
b. How are polypeptides that need to be produced at the ER
identified in eukaryotic cells?
What is a gene?
How were genes identified?
How can DNA-level mutations affect the structure of proteins?
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a.
b.
c.
d.
silent
neutral
missense
nonsense
10.
What are the major differences between in/del and substitution
mutations?
4.3.1 Biotechnology Tools & Techniques:
1. What do restriction enzymes do? What purpose do they serve for the
organisms that have them? What do we use them for in the lab?
2. What are vectors? What purpose do they serve for the organisms
that have them? What do we use them for in the lab?
3. What is cDNA? Why is it needed? How is it made?
4. What is gel electrophoresis? How does it work? Why is it useful?
5. Why is it necessary to label genetic sequences? How is it
accomplished?
6. What is PCR? How does it work? Why is it useful?
7. What is a genetic library? Why are they useful?
8. How are DNA molecules sequenced?
9. How are microarrays used? Why are they useful?
4.3.2 Biotechnology Applications
1. What is genetic engineering? How is it accomplished?
2. How are successfully engineered organisms identified?
3. How is the engineering of eukaryotes different from the engineering
of prokaryotes?
4. What are the goals of gene therapy?
5. What are the challenges involved in engineering complex traits? How
are they being approached?
6. What is genetic testing? How is it accomplished?
7. Why do individuals have detectable differences in DNA sequences?
How are those sequences detected?
8. How is genetic testing used to establish identity? How is it used in
health fields? How is it used in research?
9. What is meant by cloning?
10.
How is cloning accomplished?
11.
What are the aims of reproductive cloning? Therapeutic
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cloning?
12.
What are the ethical issues associated with cloning?
4.3.3 Biotechnology 4: Ethics
1. What are the ethical issues related to consent associated with
biotechnology?
2. What are the ethical issues related to ownership associated with
biotechnology?
3. What are the ethical issues related to conceptions of “life” associated
with biotechnology?
4. How can we approach all of these ethical issues in ways that are
constructive and respectful?
5. What are the ethical issues associated with genetic testing?
Agree/Disagree Statements:
● Humans should be allowed to genetically engineer other species.
● Humans should be allowed to genetically engineer other humans without
their consent.
● Humans should be allowed to genetically engineer themselves (or elect to be
genetically engineered by someone else).
● Genetically modified food should be labeled.
● Insurance companies should be able to use my DNA sequences to determine
the cost of my insurance.
● Companies should be allowed to patent genes that they discover.
● Companies should be allowed to patent genetic constructs that they create
(ex. artificial combinations of existing genes).
● Companies should be allowed to patent organisms that they genetically
engineer.
● Research that involves the engineering of human organs should be allowed.
● Stem cell research that is focused on improving human health, and involves
the creation of embryos that will not be brought to term should be allowed
● Humans should be able to select the gender of their child.
● Humans should be able to select traits other than gender in their child.
● Humans should be able to reproductively clone themselves.
4.4. Viruses
1. What is a virus, and how does it differ from traditional definitions of
life?
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2.
3.
4.
5.
6.
7.
8.
How do viruses cause disease?
What is the lytic bacteriophage life-cycle?
What is the lysogenic bacteriophage life-cycle?
How do eukaryotic viruses differ from prokaryotic viruses?
Why might phages be useful in controlling bacterial infections?
Why are RNA viral genomes only seen in eukaryotic viruses?
Why do viral polymerases demonstrate a greater error rate than
cellular polymerases?
9. How does HIV cause AIDS?
10.
What is the function of reverse transcriptase?
11.
Why is it difficult/impossible to cure viruses?
12.
How do viruses compare to viroids and prions?
4.5. Mitosis
1. Why do cells need to divide?
2. What has to happen when cells divide in order for life to continue?
3. What has to happen before a cell divides to produce two functional
daughter cells?
4. How is prokaryotic cell division different from eukaryotic cell division?
5. Why does DNA condense into chromosomes prior to eukaryotic cell
division?
6. What is the difference between a diploid cell and a haploid cell?
7. What are the major events in a diploid cell in each of the following
stages of the cell cycle:
a. Interphase
i. G1
ii. S
iii. G2
b. Prophase
c. Metaphase
d. Anaphase
e. Telophase
f. Cytokinesis
8. What are the major differences between cell division in plant-like cells
and animal-like cells?
4.6. Cell Cycle Control
21
1.
2.
3.
4.
Why does the cell cycle need to be controlled?
What happens if a cell divides when it shouldn’t?
Why do most cells in a multicellular organism stop dividing?
What are the major types of internal and external controls on cell
division?
a. How does the CdK/cyclin/mpf system work?
b. Why do cells stop dividing when they are surrounded by other
cells?
5. How does cancer develop at the molecular level?
6. What are the functions of proto-oncogenes and tumor suppressor
genes?
7. Why does cancer require multiple mutations to develop?
8. Why are some folks genetically predisposed to develop cancer?
9. After it develops, how does cancer cause disease?
10.
How is cancer treated?
4.7. Meiosis
1. What is sex?
2. How are the sexual life cycles of animals, plants and fungi similar?
How do they differ?
3. Why are haploid gametes needed for sexual reproduction to function?
4. How does meiosis produce haploid gametes?
5. How does meiosis differ from mitosis?
6. What happens during the following stages of meiosis:
a. prophase I
b. Metaphase I
How do these events increase genetic variation in gametes?
7. Why is DNA not replicated between meiosis I and meiosis II?
8. How do we quantify the increased amount of genetic variation
introduced during meiosis and sexual reproduction:
a. Number of possible gametes
b. Random nature of fertilization
c. Number of permutations from crossing over
4.8. Chromosomal Abnormalities
1. What happens during a nondisjunction event?
2. How can these events affect the physiology of the organism?
22
3. What happens during the following chromosomal rearrangements:
a. deletion
b. duplication
c. inversion
d. translocation
4. How can these event affect the physiology of the organism?
5. Why do chromosomal abnormalities have to occur in germ-line cells
to affect future generations of organisms?
6. Explain what happens and the effects of each of the following:
a. Down’s Syndrome
b. Turner’s Syndrome
c. Klinefelter's Syndrome
7. Why are multiple Y chromosomes not a problem for the organism?
8. Explain what happens during X-inactivation, and how it affects the
physiology of the organism?
9. Explain what happens during a polyploidy mutation, and why these
mutations are mostly tolerated by plants.
10.
How can chromosomal abnormalities be detected?
4.9. Introduction to Mendelian Genetics
1.
2.
3.
4.
5.
6.
7.
8.
9.
Prior to Mendel, how did folks think traits were inherited?
What was Mendel’s experimental method?
Why are pea plants a good model organism for genetic studies?
What did Mendel’s data show?
How does Mendel’s work support the notion of 2 alleles in diploid
organisms?
How does Mendel’s work support the notion of dominance and
recessiveness in alleles?
How does Mendel’s work support the notion of segregation of alleles
during meiosis?
How does Mendel’s work support the notion of independent
assortment of alleles during meiosis?
How do we use probability to solve mendelian genetics problems?
4.10.1 Extensions to Mendelian ratios
23
1. What does dominance really mean in the sense of genetics?
2. How do incomplete dominance and codominance extend our
understanding of genetics? How do they alter offspring ratios?
3. How do multiple alleles extend our understanding of genetics? How
do they alter offspring ratios?
4. How do polygenic traits extend our understanding of genetics? How
do they alter offspring ratios?
5. How do pleiotropy and epistasis extend our understanding of
genetics? How do they alter offspring ratios?
4.10.2 Part 2: Non-Mendelian Ratios
6.
7.
8.
9.
How was gene linkage discovered?
Explain the experimental method of TH Morgan and his students.
Why are fruit flies a good model organism for genetics?
How does sex linkage extend our understanding of genetics? How
does it alter offspring ratios?
10.
How does autosomal gene linkage extend our understanding of
genetics? How does it alter offspring ratios?
11.
How are recombinant offspring produced when they inherit
linked genes?
12.
How can we use linkage data to determine the relative
distances between linked genes?
13.
How do non-nuclear genes extend our understanding of
genetics?
14.
How can we use non-nuclear genes to investigate heredity and
evolution?
15.
How do epistatic interactions extend our understanding of
genetics?
16.
What are some of the major epistatic interactions in the
genome?
17.
How do the environment and the genome interact to determine
an organism’s phenotype?
4.11. Human Genetic Conditions
1. How do we use pedigrees to investigate the transmission of genes
and traits throughout generations?
2. What do the transmission of autosomal/sex-
24
linked/dominant/recessive traits look like in pedigrees?
3. Why is inbreeding a bad idea, from a genetic perspective?
4. Why are some traits evolutionarily favorable, but unfavorable in
particular environments?
5. Explain the modes of transmission, genetic causes, and phenotypic
effects of each of the following:
a. Achondroplasia
b. Acromegaly
c. Huntington’s Chorea
d. Albinism
e. Phenylketonuria
f. Cystic Fibrosis
g. Duchenne Muscular Dystrophy
h. Hemophilia
i. Red-Green color blindness
4.12.1 Prokaryotic Genome Regulation
1. Why can prokaryotes couple transcription and translation?
2. How does the coupling of both phases of protein synthesis allow for
increased efficiency of gene expression?
3. How does the coupling of both phases of protein synthesis restrict
control points for gene expression?
4. How is an operon organized? What are the functions of each region?
5. What types of metabolic pathways are controlled by inducible
operons?
6. What types of metabolic pathways are controlled by repressible
operons?
7. What type of feedback is utilized to control operon function?
8. What is the purpose of upregulation? Why is cAMP a useful signaling
molecule for upregulation?
4.12.2 Eukaryotic Genome Regulation
1. How does the decoupling of transcription and translation increase the
number of control points in eukaryotic protein synthesis?
2. How is it possible that cells that have different functional roles in a
eukaryotic organism all have the same genome?
3. How is access to DNA controlled in eukaryotic cells? How is this
used to regulate gene expression?
25
4. How are “upstream regulatory elements” used by eukaryotic cells to
control gene expression? Why do we liken these elements to
“switches”?
5. How are regulatory elements involved in controlling differentiation of
eukaryotic cells?
6. How do post-transcriptional processing mechanisms allow for control
of gene expression in eukaryotes?
7. How do post-transcriptional processing mechanisms increase the
total number of gene products available in a eukaryotic cell?
8. What roles to RNA molecules play in the regulation of gene
expression in eukaryotic cells?
9. How does RNAi function to control gene expression in eukaryotic
cells?
10.
How do post-translational mechanisms like ubiquitin control
gene expression in eukaryotic cells?
5. Regulation
5.1.1 Genomics
1. How is a genome sequenced?
2. Why are computers needed to analyze genome sequence
information?
3. What are the major trends in genome organization in prokaryotes and
eukaryotes?
4. What are the major types of sequences found in the human genome?
a. Repetitive sequences
i. transposable elements
1. What prevents transposable elements from “taking
over” a genome?
b. Large segment duplications
c. Unique non-coding DNA
i. pseudogenes
1. Where do pseudogenes come from?
d. Regulatory elements
i. What do regulatory elements regulate?
26
ii. Why do we say that regulatory elements are like
“switches”?
e. introns
f. coding sequences
5. How can we use genomic information to investigate the evolutionary
history of a species?
6. What is a gene “family”? How do they evolve?
7. How do alterations in chromosome numbers evolve? Why can they
lead to speciation events?
8. How is genetic evidence combined with fossil evidence to help us
study evolution?
9. Why does duplication of genetic information typically precede
divergence of genetic sequences?
10.
How can duplication lead to the evolution of new phenotypes?
5.1.2 Developmental Genetics
1. How do cells in a eukaryotic organism differentiate into different
structural and functional roles?
2. Compare the roles played by induction and cytoplasmic determinants
in differentiation.
3. Why does determination have to precede differentiation?
4. Generally speaking, how do regulatory genes regulate gene
expression?
5. Why is pattern formation crucial for development?
6. How does a cell determine its position in a developing organism?
7. How is bicoid used to determine the anterior/posterior axis in animal
embryos?
8. What are homeotic (aka homeobox aka hox) genes?
9. How do hox genes contribute to the development of structures in
animals?
10.
What is the significance of the highly conserved sequence of
hox genes?
5.2 Development
No questions
5.3 Osmoregulation
27
No questions
5.4 Nutrition
No questions
5.5 Transport and Gas Exchange
No questions
5.6 Immunity
1. How do multicellular organisms defend themselves from threats to
their health?
2. What is the difference between a specific and a non-specific immune
system? Who has which?
3. Mammalian Immune Systems:
a. What is the difference between the cell mediated and the
humoral immune system?
b. How does the cell-mediated immune system function?
c. How does the humoral immune system function?
d. How is a specific immune response generated?
e. Why does the mammalian immune system demonstrate a
memory function for previously encountered infections?
f. How do immune system cells communicate with each other?
g. How does a vaccine work?
h. How do disruptions of the immune system affect the health of
the organism?
5.7 Responses
No questions
6. Communication
6.1 Cellular Communication
1. Why do cells need to communicate?
28
2. How do cells communicate?
3. What are the similarities and differences between major modes of
cellular communication?
4. How do differences in steroid and protein ligand affect the way that
their signals are received?
5. What happens once a ligand binds to a receptor?
6. How is a cellular message relayed inside a cell?
7. What is the purpose of a second messenger?
8. How can the same signal ligand evoke different responses in different
cells?
9. How is a cellular signal amplified in a signaling pathway?
10.
Why are signaling pathways able to increase in complexity
inside a cell?
11.
How are signaling pathways used in:
a. adrenaline signaling
b. quorum sensing
c. yeast mating
d. apoptosis
6.2 Hormonal Control
1.
2.
3.
4.
5.
6.
7.
8.
How is endocrine signaling accomplished?
How are the endocrine and nervous systems related?
How do the endocrine and nervous systems differ?
Why do all multi-cellular organisms have hormonal signaling
systems?
How are cellular signaling mechanisms utilized by the endocrine
system?
What are the glands, organs, and responses associated with:
a. Digestion
b. Growth
c. Metabolism
d. Circulation
e. Excretion
f. Reproduction and Development
How do disruptions to the endocrine system affect the organism?
Why are endocrine glands a major target for medical drugs?
6.3. Behavior
29
1. What is behavior?
2. Why do organisms behave in particular ways?
3. What is the relationship between proximate and ultimate explanations
for organismal behaviors?
4. Why does behavior require communication?
5. How do organisms communicate?
6. What is the relationship between innate and learned behavior?
7. What are the common features of innate behaviors?
8. What are the major features of Fixed Action Patterns?
9. How complex can innate behaviors be?
10.
What are the common features of learned behaviors?
11.
What are the major features of
a. imprinting?
b. spatial learning?
c. cognition?
d. associative learning?
e. social learning?
12.
How do particular behaviors evolve?
13.
What is the role of genetics in behavior?
14.
What is the role of the environment in behavior?
15.
How does behavior influence fitness?
16.
What hypotheses explain the evolution of altruistic behaviors?
6.4- Neurons
1.
2.
3.
4.
5.
6.
7.
Why are neurons only found in animals?
How is a neuron’s structure related to it’s function?
How does a neuron generate an action potential?
How does an action potential propagate through a neuron?
How do neurons communicate with other neurons?
How do different neurotransmitters affect neurons?
How do disruptions to the functioning of neurons affect the
homeostasis of the organism?
8. How are nervous signals interpreted by afferent neurons? How are
they interpreted by the organism?
6.5- Nervous Systems
30
1. What is the relationship between the:
a. Peripheral and central nervous system?
b. Voluntary and autonomic nervous system?
c. Sympathetic and parasympathetic divisions?
2. How does the brain work?
3. How does complexity of thought develop in the brain?
4. How do disruptions to the nervous system affect the organism?
5. How are feedback mechanisms used to regulate the nervous
system?
7. Interactions
7.1 Organism Organization
No questions
7.2 Reproduction
No questions
7.3. Community Interactions
1. What’s a community? How can species interact with each other in an
ecosystem?
2. What’s a niche? Why would species with overlapping niches
compete with each other more?
3. How can competition affect a species?
4. How can predation affect a species?
5. What is symbiosis? How does it work?
a. Examples
6. What does it mean to facilitate? How can a species facilitate other
species in the environment?
7. Why is diversity important in a community?
8. How can diversity be characterized?
31
9. What is the difference between a food chain and a food web?
10.
Are all organisms equally “important” in determining the trophic
structure of a community?
11.
Why is some level of disturbance a feature of all communities?
12.
How does disturbance affect the structure of a community?
13.
What happens to the structure of a community over time?
14.
How does the geography and climate of an environment affect
the structure of the community?
7.4 Population Dynamics
1. What’s a population?
2. Does a population have emergent properties that the individuals that
make up that population don’t have? Examples?
3. What factors contribute to the size of a population?
4. How can we model a population’s growth rate or decline?
a. Exponential model
b. Logistic model
5. How can you measure a population’s size?
6. How can you classify the distribution of individuals in a population?
7. What are demographics? Why are they useful for studying
populations?
8. What is survivorship?
9. How closely do real populations follow the model equations?
10.
How can evolutionary adaptations affect the structure of a
population?
11.
How can the environment affect the structure of a population?
12.
How can we classify the human population? Historically?
Globally? Locally?
13.
Why do industrialized nations have lower growth rates?
7.5. Ecosystem Structure
1. What’s an ecosystem?
2. What is the relationship between an ecosystem and a biome?
32
3. Why does the Earth have seasons?
4. What is climate?
5. How does the landscape influence the climate?
6. What factors determine terrestrial biomes?
7. What factors determine aquatic biomes?
8. How does matter move through an ecosystem?
9. How does energy move through an ecosystem?
10.
Why does the productivity of an ecosystem determine the
structure of the community?
11.
What factors limit productivity in ecosystems? Are they the
same in aquatic and terrestrial ecosystems?
12.
How is energy transferred between trophic levels in an
ecosystem?
13.
How does the transfer of energy between trophic levels affect
the structure of the community?
14.
What are the common features of nutrient cycles?
15.
What are the major features of the water, carbon/oxygen,
nitrogen, and phosphorous cycles?
7.6. Conservation Biology
1.
2.
3.
4.
5.
6.
7.
Why conserve resources?
What are some benefits of conservation?
What are some benefits of a high level of biodiversity?
What are some of the services that ecosystems provide for us?
Explain the relationship between conservation and environmentalism.
Where do the major issues related to conservation come from?
How does a decreasing biodiversity lead to an increased risk of
extinction?
8. What is an interaction network?
9. Why is it impossible to completely predict the effects of a disruption
on an interaction network?
10.
What are “edge effects”?
11.
What happens during each stage of the conservation process:
a. monitoring
b. planning
c. action
12.
What are some of the goals of restoration ecology?
33