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BIO I LECTURE STUDY GUIDE TO EXAMS 1-3
Dr. Peggy G. VanArman Spring 2016
1. During each exam, students will place all personal items, including cell phones (turned off) on the side of the classroom, well away from student desks.
2. Students need a #2 pencil and Scantron 882 E for each exam. Your name and test ID # should be
written on the upper right corner in indicated spaces on the exam and on the Scantron.
3. You may take to the desk: personal hygiene items or meds (tissues, cough drops, sweater or covering) and food or drink. Clean up when you are finished.
4. Turn in your exam and Scantron to the professor and sign in on a sign up sheet.
5. All exams will consist of a mix of: multiple choice, fill-in-the-blanks, true-false, short answers, essays, and on exams 2 and 3 there will be figures on which parts will be identified or functions of those parts will be questioned. A list of possible figures will be available one week before exams 2 and 3 in docshare.
6. You are responsible for all topics discussed in class, lecture notes, and indicated figures.
7. Each exam will cover only parts of chapters that were covered in class.
8. Study hints: use In-class study guides to reference specific figures or concepts. Read end of chapter summaries.
Answer end of chapter questions related to class lecture. Use lecture notes.
Exam 1. Study Guide
Chapters 1-4, only parts of 5 discussed in lecture
functional group (r)
di / polypeptide
10, 20, 30, 40
active/ passive transport
SCIENCE: Identify parts of scientific method
Identify control, dependent and independent variables. What is the purpose of the control?
What are some important aspects and limitations of science?
CHEMISTRY: Be able to use the Periodic Table of elements:nates
Know which elements on the right and left sides of the Periodic Table accept electrons and which elements donate electrons
Figure number of protons, electrons, neutrons per element
Know the mass and charge of each subatomic particle
Know most common elements (oxygen, carbon, hydrogen, nitrogen)
Understand information from a Bohr diagram of the atom
Which energy level fills with electrons first?
How many electrons at each level? (2, 8,...)
Know three typesand relative strenghts of bonds: ionic, covalent, hydrogen
Know water is polar (electrons are shared UNEQUALLY)
Properties: cohesion, capillary action, surface tension, etc.
Why does soap work: polar end and nonpolar end (emulsifier)
pH = concentration of H+ (Hydrogen ions)
Acid = H+ Donor Base = H+ Acceptor
pH scale (1--14) Low pH = acidic, 7=neutral, High = Basic
Know building blocks and function of organic molecules in categories:
carbohydrates, lipids, proteins, nucleic acids
Know examples of mono/di/polysaccharides
What makes a lipid saturated vs unsaturated?
Understand polar vs nonpolar
Proteins: Understand 10, 20, 30, 40 Structure
How is a protein denatured?
CELL: Know some history of the microscope
Compare anatomy and functions of plant, animal, and bacterial cells
Know all organelles and their functions
Compare prokaryotic and eukaryotic cells
Know: cell to cell interactions (types of cell junctions): adhesive junctions, septate or tight junctions, communicating junctions: adherens, cadherins, desmosomes, gap junctions, connexons ; plasmodesmata in plants
Exam 2. Study Guide
Chapters 5 through 10, only parts of 10 discussed in lecture
I. Chapter 5: Membranes: page 88
Know composition and morphology of bi-layer membrane (fluid mosaic model)
Know 4 types of component groups in component membranes and their functions (transmembrane proteins, integral member proteins, interior protein network, peripheral membrane proteins
Know page 94, Fig 5.6: summary of 6 functions of proteins
Know page 95, Fig 5.7 structural features of membrane proteins
1) passive transport: selective permeability, diffusion, osmosis, dialysis, facilitated diffusion. Vocab: concentration gradient, equilibrium, ion channels, membrane transport proteins, gated channels, membrane potential, channel proteins, carrier proteins, solvent, solute, solubility (polar, nonpolar), osmotic concentration, tonicity, isotonic, hypertonic, hypotonic, turgor pressure, aquaporins, page 97 Fig 5.10
Predict what a cell might do in different solutions: burst, shrivel, stay same
2) active transport: Vocab: uniporters, symporters, antiporters, coupled transport, countertransport, sodium-potassium pump, page 100 Fig 5.13, page 101 Fig 5.14
3) bulk transport: in vacuoles pg 102 fig 5.15; pg 103 fig 5.16, page 104 Table 5.2
a) endocytosis: phagocytosis, pinocytosis, receptor mediated endocytosis
Know which different types of transport across the cell membrane require energy or
a protein (active vs passive transport)
II. Chapter 9: Cell Communications: page 168
Know: How cells communicate: ligand, receptor, transduction, signal molecules
Know : four mechanisms of communication based on distance from source to receptor page 169 Figs 9.1, 9.2: direct contact, signaling: paracrine, endocrine, synaptic; hormone glucagons, hormone epinephrine (adrenalin)
Know : phosphorylation, dephosphorylation page 171 Fig 9.3
III. Chapter 6: Energy and Metabolism page 107
Be able to explain the energetic story of the lion and the giraffe page 107
Know: definitions of energy and work, types of energy, kinetic, potential
Know autotroph and heterotroph definitions and examples
Know redox: definitions of oxidation and reduction
Know: First and 2nd Laws of Thermodynamics: entropy page 108 Fig 6.2
Know : definitions for endergonic and exergonic, activation energy, catalyst page 111, Figs 6.4, 6.5
Know why ATP is the energy currency of cells
Know ATP: page 112 Fig 6.6, structure, functions, how it stores energy (2 high energy phosphate bonds), ADP+Pi, phosphorylation and dephosphorylation (again), ATP hydrolysis and endergonic reactions, ATP cycles
Know enzymes: functions as catalysts, substrate, reactant, product, active site, , enzyme-substrate –complex, page 114, Fig 6.8, page 115 Fig 6.10
Know how enzyme active sites attract substrates
Know optimal environmental conditions, and what results from suboptimal conditions (high or low pH, boiling temperatures, etc.)
Know about how competitive and non-competitive inhibitors work page 117, Fig 6.13
Be able to define cofactors and give examples and functions
Know the difference between catabolic and anabolic reactions
Know about feed back inhibition and what an allosteric site is
IV. Chapter 7: Respiration page 122
Be able to define and give examples of autotrophs and heterotrophs
Know the formula for respiration and for photosynthesis
Know the structure of a mitochondrium
Know about the breakdown of organics (glucose) in general, dehydrogenation, and how it fits into digestion
Review redox reactions, and know how respiration is the complete catabolic breakdown of organics page 125 fig 7.3,7.4 (substrate level phosphorylation)
Know that one of the important functions of electrons is that they carry energy, those closest to the atoms nucleus carry less energy than those further from the atoms nucleus
Know how the cofactor NAD+ functions, and know how and why NADH and NADPH form
page 123 Fig 7.1 super important
Know the final electron acceptor in aerobic respiration (oxygen, forms water as oxygen is oxidized), anaerobic respiration (inorganic molecule), and fermentation (organic molecule)
Know why burning carbs is similar to burning wood, which one is most efficient at conserving/using energy
Know why electron carriers are important
Know reactions that occur in each step of aerobic respiration page 126 Fig 7.5: glycolysis (page 127 Fig 7.6), pyruvate oxidation (page 130 Fig 7.9), Krebs Cycle (page 131 Fig 7.10), Electron Transport Chain (page 134 Fig 7.12, page 136 Fig 7.14)
Know how chemiosmosis works in the production of ATP, know how the electrons from a gradient, know about the ATP rotary engine (rotor and stalk) and how it works page 134 Fig 7.12, page 135 fig 7.13, page 136 Fig 7.15, be able to explain how protons move across the membrane with the concentration gradient and the locations of protons and ATP according to Figure 7.15
Know that mitochondrial ATP-synthetase catalyzes the formation of ATP
Know in which area of the cell each step of respiration occurs (glycolysis-cytoplasm) other steps in mitochondria
Know energy yield and net production of chemicals in each step: number of ATPs, NADHs, FADH
Know why there are differences in theoretical amount of ATP production between prokaryotes and eukaryotes, and why eukaryotes produce less ATP
Know what chemosynthesizers are, methanogens (reduce CO2 to CH4) , sulfur bacteria,
Know the differences between alcoholic and lactic acid fermentation and examples of each
Know catabolism of proteins (deamination) and fats (acetyl) and how these organics can be converted for metabolism or for production of other organics ( page 141 Figure 7.20)
V. Chapter 8: Photosynthesis page 147
Know the structure of a chloroplast page 148 Figure 8.1
Know the overview, in general what light-dependent reactions are and where they occur page 149 Figure 8.2
Know functions in general of the two stages of light dependent reactions and the function of light-independent reactions page 150, 151
Be able to define “pigment” and “accessory pigment” functions of each
Know why visible light is used for photosynthesis
Review electromagnetic spectrum, know colors of visible light, which end of visible light is high energy and which is low energy in nm and by colors page 151 Figure 8.4
Know definition of a photon, how wavelengths are measured
Know the definitions of absorption spectrum and action spectrum, and what that means in relation to chlorophylls a and b, and carotenoids page 152 Figure 8.5
Know structure of both chlorophylls a and b page 152 Figure 8.6
Know why leaves change colors in fall and winter
Know general organization of photosystems, antenna complex (accessory pigments-light harvesting) and reaction center (chlorophyll-excited electron) embedded in protein matrix page 155 Figure 8.10
Know 4 steps of light-dependent reactions page 156
Know cyclic photophosphorylation: how the single photosystem that bacteria (primitive and currently sulfur bacteria) use is similar to the PI photosystem page 156 Figure 8.12
Know the importance of why the two photosystems are connected in higher plants and some cyanobacteria
Be able to tell the difference in function between cyclic (ATP) and non-cyclic photophosphorylation (use of water as a weak electron donor) (formation of ATP and NADPH)
Know how P II and PI photosystems work
Know sequence of electron transfers and chemicals that transfer electrons, know path of electrons and protons Review page 158 Figure 8.14 Z diagram, and page 159 Figure 8.15
Review chemiosmosis in chloroplasts (similar to cyclic photophosphorylation in animal cells) using chloroplast ATP-ase to form ATP page 136, 159 Figure 8.15. As you review figures know on which side of the chloroplast reactions occur.
Know in the sequence when ATP is formed and when NADPH is formed
Review the Calvin cycle, know the three phases of the cycle, know how carbon fixation occurs, be able to trace each chemical and number of carbons around the cycle, how many molecules of each chemical are present for each chemical at each point in the cycle, know the sequence of chemical formation and the initials of each chemical ( RuBP, PGA, etc.) page 161 Figure 8.18
Know the summary formula for the Calvin cycle, how many molecules of each chemical are involved with the production of one glucose molecule on page 162
Compare chloroplasts and mitochondria in energy cycle page 162 Figure 8.19 important
Exam 3. Study Guide
Chapters 10 through 16, only parts of 16 discussed in lecture
VI. Chapter 10: How cells divide page 186
Know how bacterial cells divide by fission, septum formation and separation
Page 187 Figure 10.1
Know definition for oncogenes and how they work
Know why cells divide
Know the definition and function of mitosis
Know the definition and function of chromatin and chromosomes page 189 Figure 10.4;
Page 190 Fig 10.5
Know structure of chromosomes (histones, solenoids, scaffolds, nucleosomes, 30 nm fiber) Know composition of chromatin (euchromatin, heterochromatin)
Know karyotype, cohesions, sister chromatids, homologues page 191 Figs 10.6 and 10.7
Know the 5 phases of the cell cycle page 192 Figure 10.8
Learn chromosome anatomy (centromere, kinetochore) page 193 Figure 10.9
Know eukaryotic cell activities during all phases of division, interphase through cytokinesis
Know activities during chromosome segregation: spindle, centrioles, nuclear envelope breakdown pages 194 and 195 Figure 10.11, page 196 Figure 10.12,
a) prometaphase (chromosomes attach to spindle), microtubule attachment
Movement of chromosomes to cell center
b) metaphase: centromeres align
c) anaphase: chromatids separate
d) telophase: nucleus re-forms
Know about cytokinesis: division of cell contents page 197 Figure 10.14
Cytokinesis (in plants-cell plate, pectin; and animals-cleavage furrow)
Control of cell cycle page 200 Fig 10.18
1) Would binary fission work as well if bacteria had more than one chromosome (loop)?
Why or why not?
2) Is chromosome number related to organismal complexity?
3) At what point in the cell cycle is a cell irreversibly committed to cell division?
4) How would a mutation that deleted cohesion proteins affect cell division in mitosis and meiosis?
5) Be able to distinguish between a tumor-supressor gene and a proto-oncogene.
VII. Chapter 11: Sexual Reproduction/Meiosis page 207
1. Know terms related to genetic contribution to heredity: zygote (fertilization/syngamy),
haploid, diploid page 208 Fig 11.2
2. Know germ cell-lines (somatic versus sex cells)
3. Features of meiosis:
Homologous chromosomes pair: page 209 Fig 11.3
Meiosis I: reduction division
Meiosis II: acts like mitosis, no DNA replication
4. Know activities in each stage of Meiosis I and of Meiosis II: pages 212 and 213 Fig 11.6
Prophase I (synapsis, bivalent or tetrad, crossing over, recombination nodules, crossing over, genetic recombination, chiasmata) page 211 Fig. 11.4 and chromosome crossing over
Metaphase I (paired homologues align on equator or metaphase plate, terminal chaismata finish migrating to ends of chromosomes)
Anaphase I (loss of sister chromatid cohesion on arms, homologues separate, , Law of Independent Assortment)
Telophase I (sister chromatids still connected by centromeres)
Interphase II (short, no DNA replication)
Prophase II (brief)
5. Errors in meiosis: non-disjunction (failure of chromosomes to move to correct poles, gametes with incorrect number of chromosomes-one has no chromosome and the other has two copies), gametes are called aneuploid gametes, trisomy, monosomy
6. Know differences between mitosis and meiosis pages 216 and 217 Fig 11.7
1) How can the body maintain a constant supply of germ-line cells (sex cells that eventually undergo meiosis)?
2) If sister chromatids separated at metaphase I, would meiosis still work the way it does?
3) What would be the result of improper disjunction at the end of anaphase I? anaphase II?
4) If chromosomes of a mitotic cell behaved the same as choromsomes in meiosis I, would the resulting cells have proper chromosomal constitution?
5) Why are cohesin proteins at the centromeres of sister chromatids not destroyed at anaphase I of meiosis I?
6) What features of meiosis lead to genetic variation in the products?
VIII. Chapter 12: The Mystery of heredity page 221
1. Know what a true breeder is (homozygous parental lines)
2. Know what characters or traits are
3. Know history of Gregor Mendel (the Father of Genetics), know about his pea experiments, why he studied peas, why his expts. were different than previous expts. (he systematically studied results of crosses and quantitatively assessed results-counted the number of offspring with each cross or testcross)
4. Know what cross fertilization and self-fertilization mean, and why they are different genetically from each other (know Mendel’s expts.) page 223 Fig 12.3
5. Know what a monohybrid cross is (one trait or feature=2 classes), and be able to do parental, F1, and F2 crosses in Punnett Squares, know genotypes and phenotypes for each generation, know Mendel’s ratio (3:1 in F2) page 225 Fig 12.5, page 226 Fig 12.6,
6. Know these terms: homozygous, heterozygous, recessive, dominant, genes, alleles, loci
7. Know Mendel’s Experimental Design page 223; Principle of Segregation, and his five-element model page 225
8. Be able to define the term “pedigree”. Know how to read a pedigree chart (circles, squares, sectioned circles and squares-carriers) albinism, hemophilia, and other diseases pointed out in class page 227 Fig12.7
9. Know that some diseases exhibit dominant or recessive heritage page 227 Table 12.1
10. Be able to read a dihybrid cross page 229 Fig 12.9
11. Know the Principle of Independent Assortment (alleles sort independently)
12. Know how a testcross can reveal unknown genotypes (test for whether a dominant phenotype is homozygous or heterozygous for the dominant allele) page 231 Fig 12.10
13. Extensions to Mendel:
a) incomplete dominance page 234 Fig 12.12
b) Co-dominance page 235 Fig 12.13
Human ABO blood system (know how the three genes work together, what is the universal donor and the universal recipient and why)
14. How are genes affected by the environment? Know about Siamese cats and tyrosinase, think about global warming and how a cat’s black coat would affect quality of life in a warmer climate. page 235 Fig 12.14
1) Which contributed the most to Mendel’s success: his choice of peas or his experimental design?
2) What could have interfered with Mendel’s results if he had chosen a plant with fully exposed female and male reproductive structures?
3) What fraction of tall F2 plants are true-breeding in Mendel’s experiments? Page 228
4) Which phase may be more important in terms of explaining Mendel’s laws: meiosis I? or meiosis II? page 229
IX. Chapter 13: Chromosomes, Mapping, Meiosis page 239
Who is Walter Sutton (Chromosomal Theory of Inheritance)? Suttons experiment showed that Mendelian traits did reside on chromosomes, and that some traits are sex-linked
know Thomas Hunt Morgan’s fly eye experiment Know what sex-linkage is, and be able to explain why the white eyed male Drosophila melanogaster was so important, and why the test cross was so important (to check why all F2 males had white eyes and to determine if females could also have white eyes)
page 240 Fig 13.2
Review karyotypes, know differences between autosomes and sex-chromosomes, know that sex-chromosomes differ between species and be aware that not all sex chromosomes are XX or XY as they are in humans page 241 Table 13.1
Review genetic disorders, especially hemophilia, know the source in the Romanovs page 242 Fig 13.3
Know what dosage compensation is and how it affects males and female humans (Barr bodies) page 243 see figure
Know what a genetic mosaic is, females heterozygous for X chromosomes, how does this work in calico cats page 243 Fig 13.4
Know exceptions to the Chromosomal Theory of Inheritance, uniparental heredity from mother (organelles such as mitochondria and chloroplasts) page 244
Genetic mapping, historical pedigrees, human genome page 248 Fig 13.10
Know about selected human disorders (some recessive, some dominant), and some of the causes in general (change in a single nitrogenous base to gain or loss of chromosomal material or the entire chromosome): page 249 Table 13.2
c) sickle cell anemia (single amino acid in a protein)
d) malaria-heterozygous genome prevents the disease from expressing
Know about non-disjunction (Down syndrome-chromosome 21), know how age of the mother can result in this disease
Detection of genetic defects in pregnancy-at-risk parents, know different tests, what is tested for and how, which gives the most rapid results, etc.
1) What phenotype would offspring of a cross between a white eyed female fly and a red eyed male have? Use Punnett squares on page 240 to figure this one out.
2) Could an XXX individual live? Would it be male or female?
3) During spermatogenesis (sperm formation) or during oogenesis (egg formation) would there be a difference in allelic outcome between nondisjunction in meiosis I versus meiosis II? Page 253
X. Chapter 14: DNA: The Genetic Material page 256
1. Know the three anatomical components of DNA and RNA, be able to identify them on a diagram, or to draw them in general, know the differences between purines and pyrimadines and which bases are in each category), know base pairing, know about numbering carbons in the sugar ring, how the sugar-phosphate backbone of DNA and RNA forms, page 259 Fig 14.3
2. Know what a phosphodiester bond is page 260 Fig 14.4
3. Know Chargoff’s Rules page 260
4. Know about Rosalind Franklins contribution to the determination of DNA as a double helix, and Watson and Crick’s contributions page 261 Figs 14.5, 14.6
5. Know anatomy of a single strand of DNA, hydrogen bonding, covalent bonding (sugar-phosphate bonding) what is a complimentary copy of DNA (replication) page 261 Fig 14.7, base pairing page 262 Fig 14.9
6. Know basic features of DNA replication, what is semi-conservative, (check with lab manual also), page 263 Fig 14.10
7. Know about polarity in DNA strands: antiparallel ( one end of the helix DNA strand is 3” and the complimentary strand ends in 5”), parallel (both ends of DNA are 3” or 5”) page 265 Fig 14.12
8. Know details of three stages of DNA replication in prokaryotes and eukaryotes (initiation, elongation, termination), know what a template is, what part does DNA polymerase play? Page 265
9. In prokaryotes, know replication page 266 Fig 14.13, know function of helicases and DNA gyrases
10. Know about synthesis of DNA, know what a replication fork is, what is a leading and a lagging strand and how do they replicate page 267 Fig 14.15
11. Know about replication in eukaryotes (E. coli) and DNA ligases page 269 Figs 14.17 and 14.18
12. What is telomere? Telomerase? What happens in older cells? Page 272 Figs 14.21 and 14.22
13. Know about replication in eukaryotes and about senescence, caner cell formation, mutagens, photorepair and excision pages 273-274 Figs 14.23 and 14.24
XI. Chapter 15: Genes and How They Work: page 278
1. Who was Garrod and Beadle and Tatum? One gene-one polypeptide hypothesis? Pp 278 and 279
2. Know the central dogma of molecular biology (changing genotype to phenotype) page 280 figure 15.2
3. Know about the processes of transcription and translation, know where each type of RNA is found in the cell and functions of each:
4. Know what codons (mRNA) and anticodons (tRNA) are (each three bases = a triplet code= 1 codon codes for one amino acid
5. Know the structure and anatomy of a ribosome, where it is found in the cell, and its functions pp 69, 293 Fig 15.16 (also review ch 11 lab manual)
6. Know what a retrovirus, and reverse transcriptase is (makes DNA from RNA) page 280
7. Know how transcription (making of mRNA from DNA) occurs in prokaryotes and in eukaryotes page 280
8. Know about the genetic code, translation, and how the order of bases (template from DNA-complementary base pairing in formation of mRNA-tRNA-matching of mRNA codons with tRNA anticodon) codes for the sequence of amino acids in a polypeptide page 281- 284, page 283 Table 15.1; page 286 Fig 15.7, page 287 Fig 15.9, 292-296 Figs 15.15, page 294 Figs 15.18 and 15.19, pg 295 Fig 15.20, page 296 Fig 15.21
9. Know what a reading frame and frameshift mutations are
10. Peptide bond formation, ribosome protein unit causes peptide bonds to form between amino acids
11. Ways in which transcription/translation can go wrong (may or may not affect phenotype): be able to define in general each of the following types of mutations pages 299, 300 etc.
a) base substitution mutations:
b) nonsense mutations
c) frameshift mutations
VII. Chapter 16: Control of Gene Expression page 304
1. Know what transcription initiation is and why RNA polymerase is so important pages 304, 305
2. Know functions of regulatory proteins (either block or stimulate transcription) page 308
3. Know what the function of a promoter (sequence) is to provide DNA attachment sites for RNA polymerase during the initiation phase of transcription of mRNA (review on page 283) page 308
4. How do prokaryotes respond rapidly to changes in the environment?
5. Eucaryotic organisms can maintain homeostasis, do not need to produce proteins rapidly to respond to environmental changes.
6. Know what a repressor (negative control) is (prevent or decrease initiation of transcription) page 308
7. Know what an activator is (positive control) (help stimulate and initiate transcription) page 308
8. Know what induction is (form of activation of genes to produce proteins) page 308
9. Know what repression is (bacteria do not make enzymes, although they are capable of producing them) page 308
10. What is an operon (a cluster of adjacent genes part of a single transcription unit that accomplish a function). Genes may be repressors or inducers
11. Lac operon-know everything discussed in class (page 308 Fig 16.3)
a) 3 genes that code for proteins that break down lactose (disaccharide)
b) repressor gene regulates whether the three genes are expressed or not
c) know components of the lac operon ( promoter, operator, and the three genes Z, Y, A d) know how repression/induction work in relation to lac gene (page 309 Fig 16.4)
e) know function of cAMP-CAP
12. Know how protein degradation works in a proteosome (proteases, proteosomes, ubiquitin) pages 323-324 Figs
16.20, 16.21, 16.22