General Botany- Cellular and Molecular aspects
 
Dr. Ralph Seelke
McCaskill 119A
Office hours, Fall 2003: 11-12 MWF, or by appointment

Phone: 394-8320; E-mail: rseelke@uwsuper.edu

Homepage: http://www2.uwsuper.edu/rseelke/index.htm
 
I will be teaching the middle six weeks/third of the course, which consists of the cellular and
molecular topics of botany. These topics go beyond botany, and are important in zoology,
microbiology,and cell biology as well.
 

My web page has information about my part of this course. It contains links to my course notes, my learning objectives, and an example of one of my exams.

 
The course notes are pretty much what I use to lecture from.
 
The learning objectives are an attempt on my part to summarize those parts of the lecture and the text that are important. They are presented in the form of questions or statements about what you should be able to do or know after you have studied this material. A good use of these learning objectives is to make up practice questions for an exam. I will use these learning objectives in preparing my exams.
 
The sample exam gives you a good idea of what my exam is like.
 
If you have had little chemistry, or did not have a good experience with high school chemistry, I
would STRONGLY RECOMMEND that you also read Appendix A. We will be going over a
number of chemical structures, and this section will help you understand the structures and
reactions that we will be talking about in later chapters.


 BIOLOGY 111- GENERAL BOTANY
 LEARNING OBJECTIVES
 
 Chapter 1: Introduction to Botany
 
 These learning objectives are an attempt on my part to summarize those parts of the lecture and the text that are
important. They are presented in the form of questions or statements about what you should be able to do or know after you have studied this material. A good use of these learning objectives is to make up practice questions for an exam. I will use these learning objectives in preparing my exams.
 
1. What types of organisms are studied in botany? What are the
features that distinguish them from one another? 
 
2. Be able to define and give examples of:
 
eukaryotic and prokaryotic organisms
 
autotrophs and heterotrophs
 
3. What are the components of a typical plant? In particular, be able to define: (fig 1-10)
roots, shoots, meristem, xylem phloem, vascular system.
 
4. What subdivisions are found in botany? 
 
 Chapter 2: Molecular Composition of Cells
 
1. What is an organic molecule? Be able to describe the function and components of the four major classes of organic molecules in cells (Summary Table)
2. Be able to recognize the structure of mono- di- and polysaccharides; What is the difference in the structure and
 function of cellulose and starch? What is a dehydration synthesis?
3. Be able to recognize the structure of a fat and phospholipid.
 Where are phospholipids found? What is the difference between a saturated and unsaturated fatty acid?
4. Be able to recognize the structure of a typical amino acid, and the structure of a peptide bond. What is meant by the primary, secondary, tertiary, and quaternary structure of a protein? What are enzymes?
5. What are the subunits that compose DNA and RNA? What is the function of DNA and RNA in the cell? 
6. What is a secondary metabolite? What are some of their botanical functions? Be able to place morphine, caffeine,
rubber, lignin, and salicylic acid in the category of alkaloids, terpenoids, or phenolics.
 
 Chapter 3: Introduction to the Plant Cell
 
1. Be able to identify the following structures on a drawing of a cell, and give its function(s). Be able to answer the
questions associated with each structure (see summary table) 
cell membrane : what is its main function? 
nucleus and nucleolus; what is meant by haploid and diploid
numbers of chromosomes? 
plastids: what are the functions of chloroplasts, eoplasts,
chromoplasts, and leucoplasts?
mitochondria; what does the theory of endosymbiosis say about
the origins of plastids and mitochondria?
cytosol or ground substance
endoplasmic reticulum, both smooth and rough
Golgi apparatus or dictyosome; what is meant by the endomembrane
system?
vacuole, tonoplast, and cell sap
cytoskeleton, including the major structural proteins,
microtubules and actin
cell wall: what are some of the components of the primary and
secondary walls, and middle lamella? Where might lignin be
found? What types of cells have secondary walls?
 
 
 GENERAL BOTANY 111 - LEARNING OBJECTIVES 
  Chapter 4
 
 Membrane Structure and Function
 
1. Be able to describe the structure of a typical cellular membrane. What is meant by the fluid mosaic model, and what are the roles of the two major components? What are transmembrane and peripheral proteins?
 
2. What is meant by water potential? By substances moving up or down a
gradient? By bulk flow? 
 
3. Be able to define the following:
 
Simple diffusion; what moves by this method in and out of a cell?
 
osmosis
 
hypo, hyper, and isotonic solutions
 
osmotic pressure
 
tugor pressure
 
plasmolysis
 
4. Be able to define and recognize examples of:
 
facilitated diffusion
Active transport, both primary and secondary
uniport, symport, antiport
cotransport
phagocytosis
pinocytosis
receptor-mediated endocytosis
exocytosis
symplastic and apoplastic transport
 
What is meant by signal transduction?
 
 LEARNING OBJECTIVES: CHAPTERS 5-7
Chapter 5
 
1. What are the first and second laws of thermodynamics, and how do they
relate to the flow of energy in plants?
 
2. What is meant by oxidation and reduction? Given an oxidation -reduction reaction, be able to tell which components are oxidized and which are reduced. 
 
3. Be able to define metabolism, anabolism, and catabolism, and the relationship between anabolic and catabolic reactions. What is meant by an endergonic and exergonic reaction?
 
4. What are enzymes, and how are they involved in generating energy?
 
5. What is the role of ATP and NAD(P)H in the cell?
 
Chapter 6
 
1. Be able to describe how ATP is produced in both fermentation and
respiration. What are the 3 stages of respiration?
 
2. Be able to give the overall reaction that occurs in glycolysis, including initial substrates and final products. What is meant by substrate-level phosphorylation? Where does glycolysis occur in the cell? 
Be able to recognize a substrate-level phosphorylation reaction.
 
3. Be able to recognize the reaction that prepares pyruvate for oxidation in the Krebs cycle, and the initial reaction of the Krebs cycle that brings acetyl CoA into the cycle. What are the energy rich products of the Krebs
cycle? In what form is the carbon released from the Krebs cycle? 
 
4. Electron Transport: Be able to describe how the energy of NADH and/or FADH2 is used to produce ATP. Be able to recognize the compounds used as electron carriers. Where does electron transport occur? What is
meant by chemiosmotic coupling? What is the final electron acceptor in electron transport? What is the theoretical yield of ATP in respiration, and how does that yield compare to the yield in fermentation? 
 
5. What are the final electron acceptors in lactate and alcoholic fermentations?
 
Chapter 7: Photosynthesis
 
1. What is the overall reaction in photosynthesis?
 
2. How do the light-dependent reactions result in the production of ATP and NADPH? What are the roles of chlorophylls a and b, carotenoids, and phycobilins in the light reactions? Which are accessory pigments? What is
meant by a reaction center complex and antenna complex in photosynthesis? 
 
3. How does the chemiosmotic-coupling model explain the production of ATP in photosynthesis? Be able to distinguish between cyclic and non-cyclic photophosphorylation.
 
4. What is the first reaction in the Calvin cycle? What is the overall equation for the production of glucose by the Calvin cycle? 
 
5. How does carbon fixation occur in C4 and CAM plants?
  Chapters 8&9
 
1. The cell cycle: 
a. What are the four phases of the cell cycle? Which are included in "interphase"? In which does DNA replication occur? 
b. Be able to describe mitosis, including the events occuring in each phase.
c. Be able to define cytokinesis, and describe the process as it occurs in plant cells, including the role of the phragmoplast and cell plate.
 
2. Meiosis and sexual reproduction: Be able to describe the process of
meiosis. In particular know:
 a. the results of meiosis, in terms of number of gametes produced and the number of chromosomes in each.
 b. the events that occur in prophase, metaphase, anaphase, and telophase in both meiosis I and II. In what phase is the chromosome number reduced in half, and what phases result in genetic variation in the
resulting gametes?
 c. how are meiosis and mitosis similar, and how are they different? 
 d. be able to define chromatid, synapsis, homologous chromosome, diploid, and haploid. 
 e. STRANGE SEX: be able to define zygotic meiosis, gametic meiosis, and sporic meiosis, sporophyte and gametophyte.
 
 Chapters 10-12: Heredity, Genetics, and Evolution
HEREDITY AND DNA REPLICATION:
1. What is meant by segregation and independent assortment of genes? Given a monohybrid or dihybrid cross, be able to predict the offspring that would be produced from the F2 generation of each type of cross.
 
2. Be able to define and use:
genotype
phenotype
dominant, recessive, and incompletely dominant traits
linkage
 
3.  What is the structure of DNA? What aspects of its structure make it suitable to serve as genetic material? Given a sequence of either DNA or RNA, be able to give the complementary sequence.
 
5. DNA replication: what is meant by semiconservative replication? What is a DNA polymerase? An origin of replication?
 
GENE EXPRESSION:
6. Transcription: Where does transcription start and stop? What enzyme(s) is (are) responsible for transcription? How does the initial transcript differ from the one that is translated? 
 
7. Translation: Be able to describe the process of initiation, elogation, and termination. In particular:
 
a. What is meant by the genetic code, and that the code is degenerate? 
What is a stop, or termination, codon?
b. What are the roles of rRNA, tRNA and mRNA? What is a charged tRNA? 
From which end of the mRNA does translation begin?
c. What is the amino acid that starts protein synthesis? What are the A and P sites? How are amino acids added to the peptide chain? 
d. How is translation terminated?
 
8.(MAYBE-OPTIONAL QUESTIONS) How is transcription regulated? Using the lac operon as a model, be able to describe the roles of the promoter, operator, structural genes, regulator genes, repressor, and inducer molecules in
regulating transcription.
 
  EVOLUTION
 
What are the assumptions that are the basis for the current theories on evolution and the origins of life?
 
What events are thought to have occurred in the early earth that led to life? Why is RNA considered a key molecule in the origins of life, and what are some of the evidences for such a role?
 
What are the roles of mutation and selection in the process of evolution?
 
What is meant by the term punctuated equillibrium?