Chapter 1

1. List the levels of biological organization and define each term. Biosphere: all regions of Earth’s crust, water and atmosphere that sustain lifeEcosystem: group of communities interacting with their shared physical environmentCommunity: populations of all species that occupy the same areaPopulations: group of individuals of the same kind (same species) that occupy the same areaMulticellular organism: individuals consisting of interdependent cellsCell: smallest unit with capacity to live and reproduce; independently or as part of a multicellular organism

2. Describe the big picture of information flow in living organisms and describe the roll of each form of information.

3. Describe the flow of energy through living systems including loss of energy as heat.

4. List the hierarchy of relationships of living things.

DomainKingdomPhylumClass OrderFamily GenusSpecies**Used for identification**

5. List the domains and the kingdoms present on Earth. Domains: Bacteria, Eukarya, ArchaeaKingdom: Protists, Fungi, Plantae, Animalia

6. List the major parts of the scientific method and define each term.Scientific method: a method of inquiring that allows researchers to crystallize their thoughts about a topic and collect measurable data

1. Observations: make detailed observations about a phenomenon of interest2. Hypothesis: use inductive reasoning to create a testable hypothesis that provides

a working explanation of the observations via words or mathematical equations3. Predictions: Use deductive reasoning to make predictions about what would be

observed if the hypothesis were applied to a novel experiment4. Experiments: design and conduct a controlled experiment to test the prediction of

the hypothesis; must be clearly defined so that it can be repeated in future studies; must lead to the collection of measurable data that others can evaluate and reproduce it they choose to repeat the experiment

Chapter 2

1. What are the four most prevalent types of atoms found in living organisms? What are 4 other types of atoms found in living organisms?Hydrogen, Carbon, Nitrogen, OxygenSodium, Magnesium, Phosphorus, Sulfur

2. Given the atomic number and mass be able to draw the atomic structure (Bohr model) of any atom below:

3. List the types of interatomic bonds from highest to lowest energy and an example of each. Covalent double bonds (ex. O2)>covalent single bonds (ex. CH4)>ionic bonds (Na+Cl-)>hydrogen bonds (H2O to H2O)>Van der Waals interactions (Gecko to walls or other surfaces)

4. Draw a series of water molecules and their associated hydrogen bonds as water and as ice.

5. Write the equation for calculating pH

pH=-log10[H+] (in this case H+ is the concentration which is the number of moles divided by the volume)

6. Write the equation for a carbonate/bicarbonate buffer. Show direction of equation when acid or base is addedH2CO3↔HCO3

-+H+

If acid is added, equation ←If base is added, equation →**This system is used in our blood**

Chapter 3

1. Know the names and be able to draw the structures of the functional groups

2. Show dehydration synthesis and hydrolysis

3. Haworth Projection of glucose

4. General Structure of a phospholipid

5. The five parts of an amino acid

C- Alpha CarbonCOOH- Carboxyl GroupH2N- Amino groupR- R GroupH- Hydrogen (Glycine)

6. Classify amino acids into nonpolar, polar, acidic or basic. Polar- R group not very symmetric/not close in electronegativities

Nonpolar- R group symmetric/ close to symmetric/ atoms close in electronegativities

Acidic- Negative charge (ion) present

Basic- positive charged (cation) present

7. Peptide bond

8. Four levels of protein structure

9. Picture of ATP

10. Correct pairing of purines and pyrimidines in DNA and RNA with number of hydrogen bonds

DNA (deoxy ribose nucleic acid): C ≡G A=TRNA (ribose nucleic acid): C≡G A=U

Chapter 41. Write the equation for calculating the change in the Gibbs free energy of a system during

a chemical reaction. Define the terms. When is the reaction spontaneous (see Section 4.2)?ΔG=ΔH-TΔSΔG= Gfinal-Ginitial

S is entropy/disorderH is enthalpy/potential energyT is temperature in KExothermic: releases heat Endothermic: absorbs heat

2. Draw the reaction coordinates (plot of free energy vs. course of the reaction) for endergonic and exergonic reactions. How can the free energy change be quantitatively determined from the graph (Figure 4.4)?

Exergonic: energy is released, less free energy than reactants, spontaneously, comes firstEndergonic: energy is absorbed, more free energy that reactants, not spontaneous, can occur second to an exergonic reaction

3. Illustrate how coupled reactions can allow an exergonic reaction to drive the progress of an endergonic reaction using the synthesis of glutamine as an example (Figure 4.6 A and B only).

4. Draw a modified reaction coordinate including the concept of activation energy for both an exergonic reaction. How is the activation energy defined quantitatively from the graph? How would the presence of an enzyme change the graph? (Figure 4.9)

5. Draw the graphs of rate of a reaction as a function of enzyme concentration or substrate concentration. Note that the curves shown in the book are the “initial” rate of reaction (Figure 4.12).

6. Draw a diagram showing the difference between a competitive inhibitor of an enzyme and a non-competitive enzyme that binds at an allosteric site (Figure 4.13).

7. Draw a graph showing enzyme activity as a function of pH for stomach enzymes vs. a typical cellular enzyme (Figure 4.16).

Chapter 5 Topic Review (Part I)

1. Create a table showing the following characteristics of each of the following types of microscopy: transmission electron microscopy, scanning electron microscopy, brightfield microscopy, and fluorescence microscopy. Transmission electron microscopy (Dead) Fixation; staining with heavy electron

dense metals; imaging very thin sheets by shooting a beam of electrons through the tissue

Scanning electron microscopy (Dead) Fixation; coating of the outside of a sample with a thin sheet of metal; electrons bounce off the surface; detector creates image from reflected electrons

Brightfield microscopy (can be alive) Light passes through sample; dye used to differentiate features in the sampleOROptical methods are used to create contrast based on light paths (phase, differential interference, Nomarski, darkfield, polarization)

Fluorescence (can be alive) A stain is selectively introduced which is ableto absorb energy at one wavelength and emit at another

2. Draw the basic structure of a cellular membrane (Figure 5.6).

3. Draw a picture showing the major features of prokaryotic cells (Figure 5.7).

4. Draw and distinguish between the structure and function of the following organelles/organelle systems (Section 5.3):

a. Rough vs. smooth endoplasmic reticulum

b. Secretory vs. endocytic pathways

ex. Golgi complex/lysosomesc. Nucleus

5. Draw a mitochondrion and a chloroplast (include Section 5.4); label all membranes and compartments (see Figures 5.18 and 5.25).

Mitochondrion: Site of ATP synthesis; double lipid bilayer; contains DNA and ribosomes; proteins enter by pores; protein compliment has both mitochondrial and nuclear origin

Chloroplast: site of ATP synthesis but only to power glucose synthesis; triple lipid bilayer; DNA and ribosomes

6. Draw microtubules, intermediate filaments, and microfilaments; indicate whether each structure (i) has polarity, (ii) assembles in a reversible manner, (3) is involved in cell motility (and for those involved in motility, list 2 examples) (see Figure 5.20).Microtubule: Polar/reversible/responsible for junctionIntermediate: Nonpolar/not reversibleMicrofilaments: muscle contraction

7. Draw 3 types of cell junctions (Figure 5.27); describe the major function of each

Chapter 6 Topic Review

1. Draw a picture of a cross section of a membrane showing sufficient structure so that you can describe how unsaturated acyl chains in phospholipids, cholesterol, and integral membrane proteins contribute to the “Fluid Mosaic Model” of the membrane (e.g., Figure 6.5, but refer to Figures 6.2b and 6.3 for discussion).

2. Create a table comparing diffusion, facilitated diffusion, and active transport for the properties of substrate binding, energy requirements, and ability to saturate the transport process. (Table 6.1)Characteristics Sample Diffusion Facilitated Diffusion Active TransportBinding of transported substance

No Yes Yes

Energy Source Concentration Gradients

Concentration Gradients

ATP Hydrolysis

Saturation at high concentration of transported molecules

No Yes Yes

3. Draw a diagram showing how osmosis could cause a red blood cell to swell or shrink. Include a description of the salt concentration (qualitative, not quantitative) in the fluid surrounding the cells. (based on Figure 6.10)

4. Draw a plasma membrane symporter. Include a representation of the relative concentrations of the transported molecules/ions inside and outside of the cell. Which transported particle requires energy? (Figure 6.13a)

**requires energy5. Create a table comparing endocytosis and phagocytosis: for each process, list two

similarities and two differences between the processes. (Section 6.5)Endo Phago“cell drinking” “cell eating”Absorb extracellular fluid Endo inside phagoProcess inside cell→ outside cell Slated for destruction→ lysosome

Chapter 7 Topic Review Questions

1. Draw a diagram showing the basic series of events that occur after a ligand binds to a G-protein coupled receptor (Fig. 7.9).

2. Explain the difference between adenylyl cyclase and phospholipase C as effectors in the G protein pathway (Fig. 7.10 and 7.12).Adenlyl Cyclase Phospholipase CSecond Messenger= cAMP & 2Pi Second Messenger= IP3 & DAG (DAG

stays by the cell wall)ATP→cAMP+2Pi→Protein Kinase IP3 activates Ca2+ from Rough E.R.→

Protein kinaseCellular Response Cellular Response

3. Draw a diagram showing the basic series of events that occur after a ligand binds to a tyrosine kinase receptor (Fig. 7.7).

4. Draw a diagram showing the basic series of events that occur after a ligand binds to a ligand-gated ion channel (Slide #14 in Chapter 7 lecture).

** Happens with Potassium, Chlorine, Sodium, Calcium

5. Draw a diagram showing the basic series of events that occur after a ligand binds to a steroid hormone receptor (Fig. 7.14).

6. Describe three types of endocrine signaling and provide a brief description of the distinguishing feature of each type (Slide #8 in Chapter 7 lecture).Autocrine: secreted molecule acts on same cell/cell type; clonal amplification of lymphocytes via interleukin 2 secretionParacrine: molecule secreted has local effect; sonic hedgehog is a protein bound to cholesterol to limit diffusion; diffusion gradients provide information for pattern formation; also neuronal synapsesHormonal (classical endocrine): molecule secreted into blood stream and acts on a distant target; adrenaline secreted by adrenal gland acts on blood vessels, the heart, muscles, liver etc. **blood stream**

7. Draw a diagram that illustrates the concept of a signaling cascade (Fig. 7.5).

Chapter 8 Topic Review Questions

1. Draw the overview of energy flow from sunlight to ATP (Fig. 8.1).

2. Draw the summary of the three stages of cellular respiration (Fig. 8.4).

3. Explain the difference between “substrate-level phosphorylation” and “oxidative phosphorylation.”Substrate-level phosphorylation: uses enzymes; ADP+P substrate with P added to enzyme→ ATP + substrate; no P unphosphorylatedOxidative: phosphorylation→ synthesis of ATP by ATP synthase using H+ as an energy source

4. Draw the structure of a mitochondrion and show which aspects of cell respiration occur in each compartment (Figure 8.6).

5. Draw a diagram showing the process of chemiosmosis in mitochondria; include the inner and outer mitochondrial membranes, intermembrane space, protons, electrons, ATP synthase and electron transport chain (WITHOUT detail on the individual proteins in the chain) (Fig. 8.13).

Chapter 9 Topic Review Questions

1. Draw a “cutaway of a small section from the leaf” from Fig. 9.3 and show where gas exchange and photosynthesis occur.

2. Draw the “cutaway view of a chloroplast” from Fig. 9.3 and show where the major reactions of photosynthesis occur.

3. Draw a diagram showing the overview of light-dependent and light-independent reactions in photosynthesis in the context of chloroplast structure (Fig. 9.2).

4. Draw a diagram showing the process of chemiosmosis in chloroplasts; include the thylakoid membrane and lumen, the stroma, protons, electrons, light energy, ATP synthase and electron transport chain (WITHOUT detail on the individual proteins in the chain) (Fig. 9.10).

5. Write the reaction for cell respiration and the reaction for photosynthesis (Section 8.1, page 164; Section 9.1; page 184). 6CO2+12H2O→C6H12O6+6O2+6H2O

C6H12O6+6O2+32 ADP+32Pi→6H2O+6CO2+32 ATP

Chapter 10 Topic Review Questions

1. Describe the difference between a tumor suppressor gene and an oncogene (class notes…include BOTH the type of common function for each type of gene product - for tumor suppressor gene products, see Slide 14; for oncogene gene products, see Slide 15) as well as the number of mutations required to start cancer (see Slide 4).Tumor suppressor gene- codes for a protein that is like a break; you have to lose both copies of the gene to lost your ability to apply brakes; if you are born with one copy missing, you have a propensity to form a tumorOncogene- codes for protein that is like an accelerator; if the protein gets stuck in the on position, then you will form a tumor.

2. Draw the overall view of the cell cycle as shown on Figure 10.3.

3. Draw a diagram showing the plasma membrane, chromosomes, and microtubules indicating the major stages of mitosis as shown in Figure 10.4.

4. List three contributions to mitosis made by microtubules and one contribution of microfilaments to mitosis (based on the description of mitosis in the lecture and the textbook).Microtubules: help to line up the chromosomes in the middle of the cell (metaphase); help to separate the sister chromatids by pulling them from one pole to another (anaphase); help to maintain the shape of the cell during mitosis; bind to the kinetochores to preform metaphase and anaphaseMicrofilaments: help to pinch the two daughter cells apart in telophase and cytokinesis

5. List three checkpoints in the cell cycle and give a brief description of each checkpoint (Section 10.4).G1 checkpoint: either continue or go into G0G2 checkpoint: checks for accumulation of cyclin protein/check if it is ready for mitosisM phase checkpoint: checks for proper attachment of chromosome due to microtubules during anaphase/ check for bipolar tension

11 Topic Review Questions

1. Create a table showing the “reactants” and “products” of mitosis and meiosis starting in the G1 before mitosis or meiosis.

Mitosis MeiosisReactants 1 cell

1 genome23 pairs of chromosomes

1 cell1 genomes46 pairs of chromosomes

Products 2 cells1 genome2 sets of 46 chromosomes

4 cells2 genomes23 chromosomes

2. Using one pair of homologous chromosomes, draw the stages of meiosis as they are shown on Figure 11.2 (including one crossing over event).

3. Show how three pair of chromosomes create 8 possible combinations in gametes without taking crossing over into account (Figure 11.6).

4. Using the idea of homologous recombination in the synaptonemal complex, please show how a parental collection of alleles on one chromosome can be changed so that a new combination of alleles can be created (see Figure 11.5).

Chapter 12 Topic Review Questions

1. Draw a picture of two homologous chromosomes illustrating the difference between a locus and an allele; provide definitions of these two terms.

2. Starting with a cross between two true bred parents, use Punnett squares to show the possible offspring of the F1 and F2 generations. In the F2 generation, state the predicted genotypic and phenotypic ratios of the offspring.

3. Starting with a cross between two F1 plants that resulted from a cross of true bred parents, use a Punnett square to show how the 9:3:3:1 ratio of phenotypes results in the F2 generation.

4. State Mendel’s Law of Segregation and his Law of Independent Assortment. Whenever a Punnett square is drawn, the axes define the possible genotypes of the parents’ gametes while the boxes at the intersections of the columns and rows define the genotypes of the offspring. Show how the Law of Segregation is used to set up the parental gamete genotypes in a monohybrid cross and how both the Law of Segregation and the Law of Independent Assortment are needed to set up the parental gamete

genotypes in a dihybrid cross (such as the cross described in problem 3).Mendel’s Law of Segregation: the pairs of alleles that control a characteristic separate as gametes are formed; half the gametes carry one allele, and the other half carries the other allele. Each allele has an equal chance to be passed from parent to offspringMendel’s Law of Independent Assortment: the alleles of the genes that govern two characteristics are independent during the formation of gametes.

Chapter 13 Topic Review Questions

1. Draw a Punnett square that describes the genotypes of gametes and offspring for any cross involving an X‐linked trait. List two ways that this Punnett square differs from a Punnett Square that describes inheritance of autosomal traits.

2. Draw a pedigree showing three generations of a family that is carrying any X-linked trait. This pedigree does NOT have to be drawn from memory, but it MUST utilize the correct rules of inheritance for X‐linked traits. Assume that spouses in the second generation are unaffected. Please assume a minimum of 4 children from each marriage.

3. Using a Punnett square, show how would you expect linkage to affect the experimental outcome of a dihybrid cross. This answer may be qualitative rather than quantitative.

4. Define the terms “recombinant,” “parental,” and “centiMorgan” as they relate to the concept of linkage.Recombinant- phenotype with a different combination of traits from those of the original parentsParental- phenotypes identical to that of the parentCentiMorgan- map unit of linkage make equivalent recombinant frequency of 1%= 700kilobares

Chapter 14 Topic Review Questions

1. Draw a picture of double-stranded DNA showing nucleic acid base pairing, the backbones, the orientation of the backbones, and the dimensions of a single step in the

“ladder.”2. Draw the two levels of packing of DNA, nucleosomes and solenoids, as indicated on

Figure 14.21.

3. Draw a diagram distinguishing the three possible models of DNA replication (Figure 14.8a).

4. Draw a replication bubble showing the leading strands and lagging strands including

RNA primers and Okazaki fragments (summarize Fig. 14.15 re: DNA strands and RNA primers).

5. List the five enzymes required for DNA replication. Draw a diagram showing where they act (summarize Fig 14.15 re: enzyme activity).

Chapter 18 (Section1)

1. Draw an example of the PCR reaction including the template, primers, and products through 2 full cycles. Be sure to include designations for the 5’ and 3’ ends of each piece of DNA and clearly indicate complementary binding and sites of extension (Figure 18.6).

2. List the three main parts of the PCR cycle and describe what is happening during each part of the cycle.DenatureAnneal DNA PrimersExtension of DNA

3. Draw ‘before’ and ‘after’ pictures of an agarose gel that has been loaded with samples of DNA. At least one lane should include a ‘ladder’ (Figure 18.7). Describe the difference between ‘bands’ found at the ‘top’ of the gel and the ‘bottom’ of the gel.

4. Define the term ‘restriction enzyme.’ Draw a diagram showing how a restriction enzyme might result in a ‘sticky’ end (Figure 18.2).

Chapter 15 (part a) Topic Review Questions

1. Draw a picture of DNA and the RNA that is transcribed from the DNA. Apply labels including the orientation of the nucleic acid strands and the nomenclature (both coding/template and sense/antisense) (Figure 15.4 and lecture notes).

2. Draw a picture of RNA polymerase acting on a strand of DNA to produce an mRNA. Include nucleic acid backbone orientation (Figure 15.6).

3. Draw a schematic diagram showing an mRNA before and after processing. Include the orientation and all of the parts of the mRNA (Figure 15.7).

4. Draw a diagram showing an mRNA’s introns and exons (numbered for clarity) and at least 2 possible products that could result from alternative splicing (a simplification of Figure 15.9 will be acceptable).

Chapter 15 (part b) Topic Review Questions

1. Draw a picture of a ribosome with mRNA, tRNA w/nascent peptide, aminoacyl tRNA, ribosome subunits, and three functional sites within the assembled ribosome (Figure 15.10).

2. Draw a schematic showing an amino acyl tRNA including it’s secondary structure (exact nucleotides NOT required) and anti-codon interacting with a codon. Include the polarity of the mRNA and tRNA backbones and identify the wobble position

3. Draw a eukaryotic ribosome and its structural units as shown in Figure 15.13b

4. Draw a figure showing how nascent proteins with signal sequences ultimately insert across the endoplasmic reticulum membrane during protein synthesis (see Figure 15.19).

5. Define the terms “silent mutation,” “missense mutation,” “nonsense mutation,” and “frameshift mutation.” Draw a short segment of a coding region of an mRNA to show where these mutations are likely to occur (use Figure 15.20 for guidance)

Chapter 16 Topic Review Questions

1. Draw a diagram representing the overall structure of a gene (DNA sequence in the human genome) including locations of the enhancer, promoter, introns, exons, and 5’/3’ untranslated regions, transcription start and end sites (see Figure 16.6, but you will have to add translation start and end sites).

2. Draw a diagram showing the mechanism for enhancer activation of a promoter (see slide #9).

3. Be able to provide a diagram showing how either the Lac or Trp operons achieve regulation at the transcriptional level (Figure 16.3 or 16.5 – you are responsible for both).

4. Draw a diagram showing how microRNAs are processed prior to inhibiting gene expression from selected mRNAs (Figure 16.14).

Chapter 20/21 Topic Review Questions

1. State the Hardy-Weinberg Principle (your book does not have a concise statement of the Principle – please look for a concise statement on line).  States that allele and genotype frequencies in a population will remain constant from generations to generation in the absence of other evolutionary influences. These influences include non-random mating, mutation, selection, genetic drift, gene flow and meiotic drive.

2. For each of the Hardy-Weinberg assumptions, cite one piece of evidence that suggests that the assumption is NOT always correct. There are five questions and answers here.

3. Solve the problem on slide #11 of the Chapter 20/21 lecture (relating to hemochromatosis).

4. Write an equation expressing the population frequency of two alleles at a locus that has only two alleles.

5. Write an equation expressing the frequency of homozygotes and heterozygotes in a

population, where the equation relates to a single locus with only two alleles.