Download Chapter 7: Photosynthesis

BI 112 Course Objectives - Chapters 1-6, 8-11, (some of 7, 13)
The course objectives are designed to give students a summary of the important
concepts they will need to understand and remember for BI 112. The course
objectives should be used to guide your study and help you to organize the topics.
They are intended as a guide, not a substitute for attending lectures. Therefore it is
critical that you come to lecture and not rely solely on the course objectives. Many
students find it very helpful to write out the information that each
objective covers and discussing them with study partners as we progress
through each chapter.
Chapter 1: Biology: Exploring Life
1. What is life from a biological perspective? Describe and explain the key
characteristics of life.
2. Explain the relationship between structure and function.
3. Diagram and describe the levels of biological organization (starting from
atoms to organisms and from organisms to the biosphere).
4. Describe the flow of energy through organisms and the cycling of nutrients.
5. Biologists say that life has unity and diversity. What do they mean by this?
6. Describe the classification system used by biologists today. In your
description list and distinguish between the three domains and between the
four eukaryotic kingdoms.
7. Distinguish between prokaryotes and eukaryotes.
8. Explain the evolutionary view of diversity including the concepts of random
mutation and the mechanism of natural selection.
9. List the key points of natural selection
10.
Describe the scientific approach to studying nature.
11.
Describe how scientific experiments are designed by giving an example
of an experiment. In you describe correctly use and explain the following
terms: observation, hypothesis, prediction, variable (dependent and
independent), controlled (standardized) variables, control group,
experimental or test group, and conclusion.
12.
What does the term theory mean to scientists?
13.
What are the limits of science? What is the value of science?
Chapter 2: The Chemical Basis of Life
1. Explain the importance of chemistry to the study of life.
2. What are the four elements that are most abundant in living organisms?
3. Know the symbols for the following elements: potassium, sodium, carbon,
oxygen, hydrogen, calcium, nitrogen, sulfur, phosphorus, and chlorine.
4. Distinguish between elements and atoms.
5. Distinguish between electrons, neutrons and protons, atomic number and
mass number, and atomic weight and mass number.
6. How can the atomic number and mass number of an atom be used to
determine the number of neutrons?
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7. What are the major differences between atoms of different elements, e.g.,
carbon and hydrogen?
8. Define the term isotope and give two biological applications that use
radioactive isotopes.
9. What are orbitals and shells? How are they related to the energy level of the
electron(s) that occupy them?
10. What are valence electrons and how are they related to the bonding
behavior of atoms?
11. Describe, draw and label a simplified model of an atom, such as carbon,
hydrogen, nitrogen, oxygen, phosphorus, or sulfur given its atomic number
and atomic mass.
12. Distinguish between molecules, compounds, and mixtures.
13. Use a molecular formula to determine the number and types of atoms.
14. Explain and draw an example of each of the four main types of bonds.
(ionic, nonpolar covalent, polar covalent, and hydrogen bonds).
15. What is the relative strength of the four main bond types?
16. Why do organisms need both strong and weak bonds?
17. Diagram and explain the polarity of water molecules.
18. Distinguish between hydrophobic and hydrophilic interactions and give an
example of each
19. Explain the characteristics of water that result from hydrogen binding
including specific heat, cohesion, adhesion, surface tension, heat of
vaporization, and density of water.
20. What are a solute, a solvent, and a solution?
21. Explain pH. Define acid and base. Give examples of some acids and
bases.
22. How are acids and bases capable of changing the hydrogen concentration
of a solution?
23. Explain how buffers work using the example of the bicarbonate buffer
system described in your text.
24. What are salts?
Chapter 3: Molecules of Cells
1. What are organic compounds?
2. Explain why carbon is such an important part of the structure of organic
compounds.
3. Distinguish between monomers and polymers.
4. Name, recognize and describe the basic structure of the seven major
functional groups found in organic molecules and identify the chemical
properties associated with each functional group.
5. Describe the five categories of reactions.
6. Explain condensation and hydrolysis reactions. Include in your explanation
the role of water in these reactions.
7. What is the general formula for a carbohydrate? How do cells use
carbohydrates?
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8. Describe the structure and functions of simple sugars, short-chain
carbohydrates, and complex carbohydrates.
9. Differentiate between monosaccharides, disaccharides, oligosaccharides, and
polysaccharides and describe their structures and functions.
10.Describe the structure and biological importance of fats, phospholipids,
steroids, and waxes.
11.What makes lipids hydrophobic?
12.Explain the difference between a saturated fat and an unsaturated fat and
how saturation affects their physical properties?
13.Describe the structure of an amino acid. What is the significance of an amino
acid’s R group?
14.How do the various R groups differ?
15.What is the name of the bond that joins two amino acids? What kind of a
bond is it?
16.What is meant by primary, secondary, tertiary, and quaternary protein
structure? What types of bonds are involved in each level of structure?
17.Why is protein structure important?
18.Explain what it means when we say that a protein is denatured? Identify
some conditions under which denaturation can occur.
19.List the different ways that cells can use various nucleotides.
20.What are the three main parts of a nucleotide?
21.Briefly describe the three-dimensional structure of DNA, making note of the
kinds of bonds that hold its structure together
22.To review macromolecules, for each of the four major groups of organic
molecules, identify the basic structural features, the subgroups, and their
related functions and be able to give an example of each subgroup.
Chapter 4: A Tour of the Cell
1. Identify the main concepts of cell theory
2. What is a cell?
3. What components are common to all cells?
4. Compare and contrast prokaryotic cells and eukaryotic cells.
5. Briefly describe the structure and function of cell membrane (also called the
plasma membrane)? What is the cytoplasm of a cell?
6. Explain why the surface area:volume ratio ensures that cells are almost
always microscopic.
7. Describe the structures and associated functions of the components of
prokaryotic cells (keeping in mind that not all prokaryotic cells possess all
possible structures).
8. What are organelles?
9. Be able to identify and describe the structure and function of the nucleus and
the following components of the nucleus: nuclear envelop, nucleoplasm,
nucleolus, chromosomes, and chromatin.
10.
Be able to identify and describe the structure and function of
the following components of the endomembrane system: endoplasmic
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reticulum (smooth and rough), ribosomes, Golgi bodies, vesicles, lysosomes,
and peroxisomes.
11.
Be able to identify and describe the structure and function of
mitochondria (including cristae, inner and outer membranes and inner and
outer compartments)
12.Explain what the theory of endosymbiosis suggests about the origin of
mitochondria and chloroplasts. What evidence supports this theory?
13.Be able to identify and describe the structure and essential function of
chloroplasts, plant cell walls, and the central vacuole of plant cells.
14.Describe the functions of the cytoskeleton.
15.What are cilia, flagella and pseudopods and how do they function?
Chapter 5: The Working Cell
1. Define metabolism.
2. Define energy. Distinguish between kinetic energy and potential energy and
be able to provide a real example of each.
3. Explain the first and second laws of thermodynamics in your own words. Be
sure to define entropy. Explain why highly ordered living organisms do not
violate the second law of thermodynamics.
4. Explain the role of activation energy in a chemical reaction.
5. Distinguish between exergonic and endergonic reactions. Give an example of
each.
6. Describe the structure and function of ATP and explain how it is used to
couple exergonic and endergonic reactions.
7. Describe the function of enzymes (as catalysts) in biological systems.
8. Define the following terms: substrate, active site, intermediate, product,
cofactor and coenzyme.
9. What is the transition state? Describe the transition state.
10.
Explain the relationship between enzyme structure and specificity.
11.
Describe some mechanisms by which enzymes lower activation energy.
12.
Explain the induced fit model of enzyme function.
13.
Predict the effects of enzyme and substrate concentrations on the rate
of the reaction.
14.
Describe enzyme regulation in terms of: synthesis, protein modification,
feedback inhibition, allosteric control, and competitive inhibition.
15.
Predict and explain the effects of pH, salinity, and temperature on
enzyme activity.
16.
Describe a lipid bilayer.
17.
What is the fluid mosaic model? How can proteins be positioned within
the membrane?
18.
List the functional types of membrane proteins and describe their
function.
19.
What is a selectively permeable membrane?
20.
What substances can freely cross cell membranes? What substances
are not able to freely cross cell membranes?
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21.
Describe diffusion using the example of the drop of dye entering a bowl
of water. In your description explain the concept of concentration gradient.
22.
Explain the relationship between the concentration gradient of a
substance across a membrane and potential energy.
23.
What factors affect the rate of diffusion?
24.
Compare and contrast passive and active transport.
25.
Explain the process of osmosis and be able to predict the direction of
water movement based on differences in solute concentrations.
26.
Distinguish among hypertonic, hypotonic, and isotonic solutions.
27.
Describe how cells are able take in or expel large molecules or particles.
28.
How are cell membranes recyled?
29.
Explain how signals can be transmitted across a lipid bilayer even when
no molecules are moving in or out of the cell.
Chapter 6: How Cells Harvest Chemical Energy
1. Describe metabolic pathways. Explain the difference between anabolic and
catabolic pathways.
2. Explain oxidation-reduction reactions.
3. Explain why cells obtain energy via electron transport chains rather than
through the instantaneous breakdown of glucose.
4. Define aerobic respiration.
5. Briefly describe the overall summary equation for aerobic respiration. Write
the specific chemical equation for the degradation of glucose.
6. Describe the role of ATP in aerobic respiration.
7. Describe the role of NAD+ and FAD in aerobic respiration.
8. Give an overview of the main stages in aerobic respiration and briefly
describe what happens in each stage and where each stage occurs within the
cell.
9. List the products of glycolysis including the energy carrying molecules.
10.
Describe where pyruvate is oxidized to acetyl CoA, list the molecules
produced, and how this process links glycolysis to the Krebs Cycle.
11.
List the products formed during the Krebs cycle form one molecule of
glucose (Remember: 2 molecules of pyruvate are formed from one glucose
molecule).
12.
Distinguish between substrate-level phosphorylation and electron
transfer (oxidative) phosphorylation.
13.
Explain what NADH and FADH2 do with the electrons they carry in the
final stage of aerobic respiration.
14.
Describe how a H+ gradient is formed as electrons move along the
electron transport chain.
15.
Describe how the formation of a H+ gradient is coupled to the synthesis
of ATP.
16.
What is the role of oxygen in aerobic respiration? Describe the role of
oxygen in aerobic respiration.
17.
Summarize the net ATP yield from the oxidation of a glucose molecule.
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18.
Describe how anaerobic metabolic pathways differ from aerobic
respiration.
19.
Compare the fate of pyruvate in alcohol fermentation and in lactic acid
fermentation.
20.
Compare the yield of ATP, per molecule of glucose, generated by
fermentation with that produced by aerobic respiration.
21.
Briefly describe the anaerobic electron transfers seen in some bacteria
and archeans.
22.
Describe how food molecules other than glucose (including lipids,
proteins, and other carbohydrates) can be oxidized to make ATP.
Chapter 7 (NOT in book): Photosynthesis
1. Provide the summary equation for photosynthesis.
2. State the importance of sunlight in photosynthesis.
Chapter 8: Cell Division
1. Describe the reasons why cell divide.
2. Differentiate between prokaryotic and eukaryotic cell division
3. Describe the structure of a eukaryotic chromosome. In your description,
explain the following terms: sister chromatid, homologous chromosome,
histone, nucleosome, and centromere.
4. Name, put in correct order, and describe what is occurring in each of the
stages of interphase.
5. Describe the role of microtubules in mitosis.
6. Name, put in correct order, and describe what is occurring in each of the
stages of mitosis.
7. Sketch a typical animal cell at each phase of mitosis. With each diagram,
name the phase (or subphase) and describe the main events that occur
during that phase. Be sure that you can recognize the phases/subphases from
diagrams or micrographs.
8. Distinguish between chromosome number and diploid number.
9. Compare cytokinesis in animal and plant cells.
10.
Distinguish between sexual and asexual reproduction.
11.
Define gene. Describe the relationship between the term "gene" and the
term "allele". Define gene locus.
12.
Distinguish between homologous chromosomes and sister chromatids.
Apply an analogy (cookbook, instructions for building a house, or something
similar) to explain the difference between these terms.
13.
What is the function of meiosis? What is a gamete? Explain how haploid
and diploid cell differ.
14.
Distinguish between germ cells (gametes) and somatic cells.
15.
List in correct order and briefly describe the phases of meiosis: pay
particular attention to the number of chromosomes and chromatids in each
step, when DNA replication occurs, and which cells are haploid vs. diploid.
Know which steps involve the separation of homologous chromosomes and
which involve the separation of sister chromatids.
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16.
Briefly describe crossing-over during prophase 1 and explain how
genetic recombination can result in new combinations of alleles.
17.
Explain the significance of alignment and separation in meiosis 1.
(independent assortment)
18.
Compare and contrast mitosis and meiosis with respect to process and
outcomes.
19.
When is the diploid number of chromosomes restored?
20.
Explain how crossing-over, independent assortment, and random
fertilization contribute to genetic variation in sexually reproducing organisms.
21.
Discuss the advantages and disadvantages of sexual reproduction as
compared with asexual reproduction for species survival.
22.
Distinguish between sex chromosomes and autosomes.
23.
Describe the process of karyotyping.
24.
Define aneuploidy and explain the possible consequences of
nondisjunction.
25.
Distinguish between trisomy and triploidy (polyploidy).
26.
Give some examples of disorders that are a result of changes in
chromosome number in both autosomal cells and sex cells and describe
chromosomal alterations that give rise to each of these disorders.
Chapter 9: Patterns of Inheritance
1. Describe how alleles of a gene relate to the gene product (protein).
2. Describe what is meant by the terms dominant and recessive, as they apply
to alleles.
3. Explain what it means to be heterozygous or homozygous for a given trait.
4. Distinguish between genotype and phenotype.
5. Use a Punnett square to predict the results of a monohybrid cross and state
the phenotypic and genotypic ratios of the F1 and F2 generations.
6. Describe the inheritance patterns of autosomal recessive disorders and
provide an example of this type of disorder.
7. Describe the inheritance patterns of autosomal dominant disorders and
provide an example of this type of disorder.
8. Explain the phenotypic condition of various possible genotypes (heterozygous,
homozygous dominant, homozygous recessive). What does it mean to be a
carrier?
9. Explain how a test-cross can be used to determine whether a dominant
phenotype if homozygous or heterozygous.
10.
In your own words, describe Mendel's Theory of Segregation of alleles
and Theory of Independent Assortment.
11.
Use a Punnett square to predict the results of a dihybrid cross and state
the phenotypic and genotypic rations of the F1 and F2 generations.
12.
Explain why it is important that Mendel used large sample sizes in his
studies.
13.
Compare and contrast the notion of independent assortment with gene
linkage. How are these phenomena related to the gene locus?
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14.
What is the importance of crossing-over and how does it relate to gene
linkage?
15.
What does it mean when we say that a gene has multiple alleles?
16.
What does it mean when we say that a given allele has pleiotropic
effects?
17.
Describe polygenic inheritance and explain why some characteristics
(such as eye color or height in humans) can show such complex patterns of
variation in a population.
18.
Distinguish between dominance, incomplete dominance, and codominance.
19.
Describe the co-dominant inheritance associated with the ABO blood
typing system. What two alleles, in this multi-allele system are co-dominant?
20.
Predict the results of a monohybrid cross involving dominant, codominant, and incomplete dominant traits.
21.
Explain how phenotypes arise through epistatis.
22.
Explain how some traits can be subject to environmental conditions,
and provide an example.
23.
Describe how sex is determined in humans.
24.
Differentiate between linked genes and sex-linked genes.
25.
Explain why sex-linked diseases are more common in human males.
26.
Describe the inheritance of sex-linked disorders. Provide an example of
a sex-linked disorder.
27.
Describe the main categories of heritable changes in chromosome
structure including duplication, deletion, inversion, and translocation.
28.
Describe how geneticists use pedigrees and be able to analyze and
interpret a pedigree.
Chapter 10: DNA Structure and Function
1. Explain why researchers originally thought that protein was the key molecule
directing inheritance.
2. Summarize experiments that provided compelling evidence that DNA is the
molecule responsible for inheritance (Avery, Hershey/Chase).
3. What was Chargaff’s key insight about the amount of each of the nucleotide
bases in DNA, and how does that relate to the DNA structure?
4. Briefly describe the roles of Rosalind Franklin and Watson and Crick in
deducing the structure of DNA
5. Draw a diagram of a nucleotide; label each of the three key parts.
6. Diagram the structure of DNA, using an “S” for the sugar, a “P” for the
phosphate, and G, A T and C for each of the 4 bases on one strand, bonded to
the complementary bases on the opposite strand. Use solid lines to indicate
covalent bonds between the key groups, and dotted lines for each of the
hydrogen bonds. Circle a base pair.
7. Explain what is meant by “semi-conservative replication”. Why is this an
important feature of DNA?
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8. Describe the process of DNA replication, including the roles played by:
Helicase, DNA Polymerase and Ligase.
9. Explain why continuous synthesis of both DNA strands is not possible during
DNA replication.
10.
What happens if an incorrect nucleotide is inserted during replication?
11.
What is the fundamental function of DNA?
12.
Name the two major steps in the process by which DNA information is
used to make proteins
13.
Compare and contrast the structure of DNA and RNA
14.
Name and describe the function of the three classes of RNA molecule.
15.
Compare and contrast transcription and replication
16.
Describe the process of transcription, including the roles of RNA
polymerase and the promoter.
17.
Describe some of the modifications that must be made to an mRNA
molecule (in eukaryotic cells) before it leaves the nucleus.
18.
Explain the relationship between the sequence of bases in the RNA and
the sequence of amino acids in proteins.
19.
Given a DNA sequence, determine the sequence of the RNA transcript,
identify the codons, and using the genetic code, predict the amino acid
sequence that would result. (You need not memorize the genetic code – a
table will be provided)
20.
Although the “t” in tRNA stands for transfer, it can also be considered
the essential translator molecule in translation. Explain.
21.
What is an “anticodon” and where is it found?
22.
Identify the kinds of macromolecules that make up a ribosome
23.
Describe the three stages of translation. What is occurring at each
stage?
24.
Explain how ribosomal structure facilitates creation of a peptide bond
between two amino acids.
25.
Explain how a mutation that is a base pair substitution in DNA can
cause a change in protein primary structure. Why does it not always have this
effect? What kinds of single base pair substitutions can result in a shortened
polypeptide chain?
26.
Explain how an insertion or deletion of only a few nucleotides can cause
a change in primary protein structure. Why do some insertions or deletions
cause a “frame shift”, while others do not?
27.
Describe how mutations (changes) can be introduced into DNA.
Chapter 11: Control of Gene Expression
1. What is meant by gene expression?
2. Identify and describe six points along the process from DNA to active protein
at which gene expression can be controlled.
3. Identify chemical modifications of RNA that affect transcription and the effect
of these modifications.
4. Describe three mechanisms of control by transcript processing.
5. Explain what is meant by cell differentiation, and how it comes about.
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6. Explain how X chromosome inactivation results in a mosaic of certain traits in
an organism.
7. What is thought to be the benefit of X-chromosome inactivation in mammals?
8. Describe the mechanism which allow bacteria (E.coli in particular) to control
the production of proteins to break down lactose (your answer should include
a description of the operon, the role of the operator, the promoter, the
repressor protein, lactose (or allolactose), RNA polymerase and the genes for
the three enzymes.
9. Why is control of gene expression important?
Chapter 13: How Populations Change (From online readings, not in text)
1. Populations change mainly thru two main forces, selection and genetic drift.
2. Two minor forces that also change populations include mutation and gene
flow.
3. Mutation is too rare to change a population much and gene flow tends to
make two populations more similar which is why they are minor forces.
4. Selection –organisms with favorable traits are more likely to survive and
reproduce.
5. Genetic drift –differences in reproduction or survival that are due to random
chance.
6. Mutation creates all new genetic variation (new genes), selection, genetic
drift, and gene flow then act on this genetic variation to change a population.
7. Genetic drift and selection tend to make two populations diverge, gene flow
tends to make two populations converge.
8. Adaptation –a characteristic that improves the survival of a population. Only
natural selection better adapts a population to its environment.
9. Adaptations are not perfect for a number of reasons, so a population never
reaches perfect adaptation to an environment.
10. Walking Sticks are a species that is adapting to two environments, the Wild
Lilac and the Chemise bush.
11. The solid green Walking Sticks are adapting to the Wild Lilac, the striped
Walking Sticks are adapting to the Chemise bush.
12. Each form of Walking Sticks is better at surviving and reproducing on its
preferred plant. Their coloration allows them to hide better on their preferred
plant, but they also have different enzymes to better digest the different pulp,
fiber, chemical contents, and plant toxins of the leaves of the two plants.
13. Walking Sticks prefer to mate with others of the same color pattern probably
because “hybrid” offspring are less well adapted than single form offspring.
14. This is causing the Walking Stick population to diverge.
15. When the two forms loose the ability to interbreed, they will become by
definition two species.
16. Speciation -When one species splits to form two species.
17. Evolution –When the allele frequencies are changing in a population.
18. Only populations can evolve, individuals cannot.
19. An example of macroevolution is what has been done in dogs to make all
the different breeds of dogs.
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