BIOSCI 107 Study Questions

Chapter 1-19

Source: Wikimedia commons; apoptosome

BIOSCI 107 Study Questions Chapter 1 What is Biology? 1) We know that biology is the study of living things, but what does it mean to be alive? Using the guidelines in your text and what you know about viruses, decide whether you think viruses should be considered living or nonliving.

2) Antibiotics are chemicals that inhibit the growth of microorganisms, reducing the number of bacteria or slowing their rate of growth. Unfortunately, some antibiotics are losing their effectiveness, as bacterial strains evolve resistance to them. Development of antibiotic resistance is an example of what biological principle? a. diversity b. speciation c. natural selection d. negative mutation

3) Describe the hierarchy of life, including the different levels of organization within an animal’s body starting at the level of the cell.

4) Which of the following statements about hypotheses is true? (There may be more than one correct answer.)

a. A hypothesis is a statement that must be testable. b. An experiment can be used to prove a hypothesis. c. An experiment can be used to falsify a hypothesis. d. A hypothesis is a scientific statement that can be made only after many years of research.

5) Observation:

Researchers observed that male rats are more aggressive than female rats, often attacking other males that enter their cages. Experiment: Experimental group: Males that have had their testes surgically removed. Control group: Males whose testes have not been removed. Rats recover from surgery in individual cages. Researchers then introduce a control-group male to each cage and count the number of times each male initiates an attack.

a. What question is the experiment answering?

b. Write a hypothesis and a prediction for this experiment.

c. What is the dependent variable?

d. What is the independent variable?

e. Based on your hypothesis and prediction, what does it mean if you find that rats in your experimental group attack other male rats more often than rats in your control group?

BIOSCI 107 Study Questions Chapter 2 Atomic Structure, Chemical Bonds, Water, pH 1) The element magnesium has an atomic number of 12 and a mass number of 24. Using the Bohr model for atomic structure, draw a magnesium atom. Then answer the following questions: a. How many electrons are in this atom? __________________

b. How many protons and neutrons are in the nucleus? ____________________________

c. Is the magnesium atom likely to bond with other atoms? Why or why not?

2) Evaluate each statement below and decide whether it is true or false. ______ a. An element contains only one kind of atom.

______ b. Isotopes are variants of an element with additional neutrons in the nucleus.

______ c. Atoms of different elements can have the same number of protons.

______d. All atoms of a particular element contain the same number of protons.

3) List the six main elements that make up living organisms.

4) An ionic compound made up of ion A and ion B is dissolved in water. Show how the molecules of water would interact with each of these ions in the solution. 5) Which of the following best describes what would happen to the concentration of H+ if the pH of a solution changed from pH 5 to pH 4? a. It would increase 1x b. It would increase 10x c. It would decrease 1x d. It would decrease 10x e. There is no way to tell 6) Write in the correct symbols (<. =. >) to indicate the relationship between hydrogen ions and hydroxyl ions in solutions that are acidic, basic, or neutral, then indicate the overall charge of each type of solution. Neutral H+ _________ OH-, overall charge of solution is __________________

Acids H+ _________ OH-, overall charge of solution is __________________

Bases H+ _________ OH -, overall charge of solution is __________________

- +

BIOSCI 107 Study Questions Chapter 3 Macromolecules: Carbohydrates, Lipids, & Proteins 1) Indicate the type of monomers which make up the following macromolecules found in living organisms.

Proteins

Carbohydrates

Nucleic Acids

Lipids

made up of structurally diverse components rather than repetitive monomers

2) Draw the ring structure of glucose ((indicate if or form), including all functional groups. Then answer the questions below: a. Which functional groups make glucose a water soluble (polar) molecule? ______________________

b. WHY do these functional groups make glucose water soluble/hydrophilic?

3) Below is the structure of an amino acid. Indicate names for the components labeled: #1, #2, and R

Component # 1 __________________________

Component #2 ___________________________

Component R ___________________________

4) Describe/Define the different levels of protein structure including the type of bonds which occur at each level.

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

5) Changing environmental conditions, such as increasing temperature, tends to disrupt proteins’ tertiary structure rather than their primary structure. Explain why this happens.

6) A gene mutation causes the histidine in a particular protein to be replaced with a glutamic acid. What level or levels of protein structure could this affect (if any) and why? HINT: you must think about the chemical properties of the “R Groups” associated with Histidine and Glutamic Acid and think about the types of bonds they can form to solve this problem

7) Compare and contrast the polysaccharides starch and glycogen.

Starch Glycogen

a. Where are these polysaccharides found? (organism)

b. What biological role does each polysaccharide play?

c. What do these molecules have in common?

d. How do they differ?

8) Compare saturated and unsaturated fatty acids with respect to the following characteristics:

Saturated Unsaturated

a. Presence of double bonds between carbon atoms in the hydrocarbon chain

b. Ability to pack tightly together

c. State of lipid at room temperature (liquid or solid)

d. Typical source (organism)

e. Effect on membrane permeability (increase or decrease)

BIOSCI 107 Study Questions Chapter 4 Nucleic Acids: RNA and DNA Structure/Function

1) Compare RNA and DNA with respect to the following characteristics of each molecule:

DNA RNA

a. type of sugar

b. types of nitrogenous bases

c. # of strands

d. 3 dimensional structure

2) Draw a typical DNA nucleotide and label its 3 parts.

3) A sample of DNA is made up of 28% adenine. How much of that sample is guanine?

a. 22%

b. 28%

c. 44%

d. 72%

e. There is not enough information to answer the question.

4) What is the function of coding DNA? (HINT: think Central Dogma) 5) Chapter 4 presents the theory that early Earth was “an RNA world.” Describe three pieces of evidence that support the idea that RNA was the first biological molecule to evolve on Earth?

BIOSCI 107 Study Questions Chapter 5 Cells and Organelles

1) Draw a representative bacterial (prokaryotic) cell and label the following structures and components: • Plasma membrane • Nucleoid • DNA/chromosome • Ribosomes • Cell wall • Flagella

2) Compare and contrast animal and plant cells

Animal Cells Plant Cells

Structure(s) surrounding cell/ cell boundary

Location of DNA/chromosomes

Organelle(s) used in energy conversion

Site of protein production (translation)

Components of endomembrane system ( for protein secretion)

Pores between cells for sharing nutrients/molecules

Presence of central water vacuole (yes or no)

Presence of lysosomes (yes or no)

3) Based on your understanding of the function of eukaryotic organelles, match the type of cell to the organelle or cell structure that might be particularly abundant in that cell

a. smooth endoplasmic reticulum b. cell wall c. mitochondria d. rough endoplasmic reticulum e. keratin (structural proteins)

_______ Pancreatic cell that secretes a digestive enzyme

_______Mammalian skin cell

_______Skeletal muscle cell

_______Liver cell that modifies toxins

_______Leaf cell

4) Compare and Contrast the three different filaments found in the cytoskeleton system.

Intermediate Filaments Actin (microfilaments) Microtubules

a. UNIQUE Function(s) of filament

b. Dynamic or Static

c. Interacts with which motor proteins?

5) Which piece of evidence best supports the endosymbiosis theory? a. Mitochondrial ribosomes are more similar to prokaryote ribosomes than to cytoplasmic ribosomes of eukaryotes. b. The Golgi apparatus releases many vesicles that fuse with the plasma membrane. c. Plants have chloroplasts, but both plants and animals have mitochondria. d. Many bacteria live within the human digestive tract and help us digest our food. e. Enclosed compartments are evolutionarily advantageous, because chemicals for related reactions can be concentrated.

BIOSCI 107 Study Questions Chapter 6 Cellular Membranes 1) Explain why phospholipids will spontaneously assemble themselves into a bilayer when placed in water. 2) What is the function of the following cell membrane components?

a. glycoproteins

b. transmembrane proteins

c. cholesterol

3) Fish, like carp, are able to survive in a wide range of water temperatures by adjusting the permeability of their cell membranes according to the temperature of their environment. What will happen to the phospholipid fatty acids of a carp’s membranes, when the fish are moved from a cold aquarium to a warm aquarium? They become________________________________. a. more saturated and with longer tails. b. more saturated and with shorter tails. c. less saturated and with longer tails. d. less saturated and with shorter tails. e. unchanged in their fatty acid composition.

4) Type 2 diabetes, often associated with obesity, results in an increase in blood-glucose levels. One early sign that a person or animal might be developing type 2 diabetes is excessive thirst. Discuss a possible reason for this, based on what you have learned about osmotic relationships between cells and environment.

5) A cell containing 1M K+ and 50mM Cl- is placed into a beaker containing 100mM K+ and 5000M Cl-. Determine the direction the ions will diffuse (into the cell or out of the cell) assuming they can freely cross the membrane according to their concentration gradients. (HINT: use metric conversions to compare concentration values) 6) Answer the following questions regarding the sodium potassium pump and paired glucose transporter in the image from the textbook shown below.

b) Why does the cell need to continually pump sodium (Na+) ions out of the cell? c) If hydrolysis of ATP is temporarily blocked, such that transport processes requiring energy are halted, what will most likely happen to the concentration of Na+ on either side of the membrane?

a) Why does the sodium potassium antiporter pictured at left use ATP when pumping sodium (Na+) out of the cell and potassium (K+) into the cell?

BIOSCI 107 Study Questions Chapter 7 Cell Signaling 1) What is the difference between endocrine and paracrine signaling? Provide an example of each. 2) What are the three parts of a cell signaling pathway? (See Figure below)

Step 1: _______________________

Step 2: _______________________

Step 3: _______________________

3) Based on your understanding of the cell signaling receptors, match the type of signaling molecule (ligand) with the appropriate receptor. a. Insulin (protein hormone) b. Acetylcholine neurotransmitter c. Odorant d. Vitamin D (steroid hormone) _____ G protein-linked receptor

_____ Ion channel receptor

_____ Protein kinase receptor

_____ Intracellular receptor

4) 2nd Messenger molecules like calcium and cAMP can move through gap junctions into adjacent cells to help coordinate/synchronize cellular responses within a tissue. a. True b. False

5) Based on your understanding of the mechanisms that shut off cell signaling pathways, match the inhibitor to the pathway it inhibits. a. Phosphodiesterase b. Phosphatase c. GTPase d. Calcium chelator _____ pathway using Ca2+ as a 2nd messenger

_____ MAP Kinase cascade

_____ pathway using cyclic AMP (cAMP) 2nd messenger

_____ pathway using G proteins/G protein linked receptor

5) The MAP Kinase Cascade is made up of kinase enzymes which phosphorylate their target substrates, meaning that they transfer a negatively charged phosphate group onto target proteins (this changes how they fold/3D shape). Explain how changing the shape of a protein affects how it functions inside the cell. 6) Explain why different cell receptors are required for different signaling molecules (ligands). 7) Upon binding a signal molecule/ligand, receptors undergo allosteric regulation to become “activated”…what does it mean for a protein to be regulated allosterically? See Figure below/right.

Before After

BIOSCI 107 Study Questions Chapter 8 Enzymes and Reaction Curves 1) The mass media almost always use metabolism to refer to the speed or efficiency with which bodies process food. What does metabolism really mean? 2) Compare and contrast catabolic and anabolic chemical reactions.

Anabolic Catabolic

Exergonic or Endergonic

Free Energy (G) (positive or negative)

The reactions build molecules or break molecules down

Reaction releases ATP or uses up ATP

3) Which of the following describes how your body uses the foods you eat? a. The food is broken down through catabolic reactions. b The food is broken down through anabolic reactions. c. The components of the food are used in anabolic reactions. d. The components of the food are used in catabolic reactions. e. Both a and c f. Both b and d 4) Which describes how ATP is used by the cell? a. ATP stores energy from anabolic reactions. b. ATP releases energy to endergonic reactions. c. ATP accepts energy from exergonic reactions. d. ATP is used once, then broken down by the cell.

5) Below is the plot for a chemical reaction with (B) and without (A) the presence of an enzyme a. For Reaction A, Label the reactants (substrates), products, activation energy (EA), and free energy

(G).

b. Is the Reaction A catabolic or anabolic? c. Reaction B, is the same reaction as Reaction A, except that an enzyme has been added. What changes between Reaction A and B?

a. energy level of substrates b. activation energy c. energy level of products

d. free energy (G) e. all of the above

d. Would Reaction A be more likely to represent starch being broken down into glucose, or starch being produced from glucose? 6) Without enzymes, our cells would not be able to complete the chemical reactions needed for life. Evaluate the statements below about enzymes. Indicate if the following statements are True or False

______ Each enzyme binds to only one specific substrate.

______Enzymes are used only once, then are recycled by the cell.

______Enzymes provide the activation energy needed to get a chemical reaction going.

______Some enzymes need coenzymes, some of which come from vitamins, to function.

B

A

7) Enzymes can speed up chemical reactions, but how do they do it? Describe three ways that enzymes can speed up chemical reactions through lowering the activation energy. 8) What type of macromolecule are enzymes (lipids, proteins, carbohydrates, or nucleic acids)? Explain why this makes enzymes so sensitive to changes in temperature. 9. Compare and contrast competitive and noncompetitive enzyme inhibitors.

Competitive Noncompetitive

Site where inhibitor binds to enzyme

Inhibitor and substrate have a similar shape (yes or no)

Inhibitor binding changes the shape of the active site (yes or no)

Used in feedback inhibition pathways

BIOSCI 107 Study Questions Chapter 9 Redox Reactions & Cellular Respiration 1) Use the diagram to answer the questions below.

a. Which compound is reduced and which compound is oxidized after the reaction takes place?

b. Which compound is the reducing agent and which is the oxidizing agent?

2) Where is energy “held” in an ATP molecule? Explain. 3) Summarize the inputs and outputs of glycolysis:

a. What goes in?

b. What comes out?

c. What is the net gain of ATP per glucose?

d. Where does glycolysis take place in eukaryotes?

4) Summarize the inputs and outputs of the citric acid cycle (Krebs cycle):

a. What goes in?

b. What comes out?

c. Has any ATP been produced? If so, what is the net gain of ATP per glucose?

d. Where does the citric acid cycle take place in eukaryotes?

5) At the end of the citric acid cycle (Krebs cycle), most of the energy from glucose has gone into which of the following molecules?

a. CO2 b. ATP c. NADH d. Pyruvate e. Acetyl CoA

6) What happens to the carbon dioxide that is produced in the citric acid cycle (Krebs cycle)? 7) Summarize the inputs and outputs of oxidative phosphorylation (Electron Transport Chain), with these questions in mind:

a. What goes in?

b. What comes out?

c. What is the net gain of ATP?

d. Where does the oxidative phosphorylation take place in eukaryotes? In prokaryotes?

8) Compare and contrast lactic acid fermentation and alcoholic fermentation by answering the following questions: a. What molecules result from lactic acid fermentation of pyruvate? b. What molecules ultimately result from alcoholic fermentation of pyruvate? c. Is oxygen required for lactic acid fermentation? ___________

d. Is it required for alcoholic fermentation? ___________

e. Can oxygen reduce the need for fermentation? ___________

f. Where in a cell does fermentation typically occur? g. Name a eukaryote that uses lactic acid fermentation and a eukaryote that uses alcoholic

fermentation. Lactic acid fermenter ________________________________________

Alcohol fermenter ________________________________________

h. In comparing cellular respiration and fermentation, which is more efficient at producing ATP from glucose?

BIOSCI 107 Study Questions Chapter 10 Photosynthesis 1) Summarize the light reactions of photosynthesis by answering the questions below a. What are the inputs? b. What are the outputs? c. Where is the location of the photosynthesis light reactions in plants? d. What is the source of excited electrons in the Thylakoid Electron Transport Chain?

2) What is the reduced form of the electron carrier NADP+? Does the reduced or oxidized form “hold” more energy?

3) The chlorophyll molecules of green plants chiefly absorb (select all that apply)

a. red light. b. blue light. c. green light. d. yellow light. e. All of the above

4) What is the purpose of the light reactions of photosynthesis?

a. To convert CO2 to sugars b. To make chemical energy from light energy c. To use the energy from light to form ATP and NADPH d. To produce oxygen for cellular respiration by splitting H2O

5) Define oxidative phosphorylation.

6) Trace how energy flows through the light reactions from light photons to energy products that enter the Calvin cycle.

5) Where does the oxygen generated during photosynthesis originate?

a. Atmospheric CO2 b. Chlorophyll molecules c. Water in the plant’s cells d. Both a and c e. a, b, and c

7) Answer the following questions about the Calvin cycle.

a. Where does the CO2 that enters the Calvin cycle originate? _____________________________

b. Is energy produced in the Calvin cycle or is it consumed? (ie is the Calvin Cycle an anabolic or catabolic process) _________________________________

c. Why must ribulose bisphosphate (RuBP) be regenerated for the Calvin cycle to continue?

d. What is the name of the enzyme that performs carbon fixation in the first step of the Calvin cycle?

8) Provide at least two reasons why photosynthesis is considered inefficient at converting light energy into

carbohydrates.

BIOSCI 107 Study Questions Chapter 11 Cell Division (Mitosis and Meiosis) 1) What are three functions of mitotic cell division in eukaryotic cells? 2) Which of the following describes a difference among binary fission, mitosis, and meiosis?

a. Binary fission and meiosis are used for sexual reproduction, while mitosis is used for growth. b. Prokaryotes use binary fission to reproduce, while eukaryotes use meiosis to reproduce. c. Prokaryotes use binary fission, animals use mitosis, and plants use meiosis for cell division. d. Binary fission and mitosis produce two genetically identical cells, while meiosis produces four

non-identical cells.

3) It is well established that cell division does not happen with the same frequency in all somatic cells in the human body. Provide examples of cells that are constantly undergoing cell division and cells that rarely (if ever) undergo division. Relate the cell division rate of these specific tissues, to their ability to be repaired after being damaged.

4) Discuss what occurs in each of the following stages of the cell cycle

G1 (Gap 1)

S (Synthesis)

G2 (Gap 2)

5) What is the mitotic spindle formed from and what is the purpose of the mitotic spindle?

6) Put the five substages of Mitosis in the correct order and then describe what happens in each stage. _____ Metaphase: ____________________________________________________________________

_____ Telophase: _____________________________________________________________________

_____ Prophase: ______________________________________________________________________

_____ Anaphase: _____________________________________________________________________

_____ Prometaphase: _________________________________________________________________

7) What are cell cycle checkpoints? How do they ensure that dangerous cells are removed from the

body?

8) Which is a true statement about Cdk’s and cyclins? a. Both are always present in the cell. b. Cyclins are always present; Cdk’s are made only at certain times. c. Cdk’s are always present; cyclins are made only at certain times. d. Cdk’s are active when not bound to a cyclin.

9) Compare and contrast Meiosis and Mitosis by filling out the table below

Mitosis Meiosis

Number of cells produced

Haploid or diploid cells produced

Genetically identical or unique cells produced

Homologous chromosomes pair and recombine (yes or no)

Occurs in reproductive cells or somatic cells

BIOSCI 107 Study Questions Chapter 12 Genetics and Heredity 1) What is the difference between an organism’s genotype and phenotype?

2) What gametes can be formed by a pea plant with a Rr; Yy genotype? (HINT: see Mendel’s Dihybrid

Cross Experiment)

3) Bob and Mary both have the genotype of Ff, though neither have the thin fingernail syndrome associated with the ff genotype. a. Is thin fingernail syndrome a dominant or recessive disease? b. If both Mary and Bob are “carriers” of the f allele, explain why they don’t they have thin fingernails? c. What is the probability they will have a child with thin fingernails? (show your work) d. What is the probability that their first AND second child will both have thin fingernails? (show your work)

4) A true-breeding petunia with red flowers is crossed with a true-breeding petunia with white flowers. In your pairs or groups, describe the genotypes and phenotypes of their offspring if the alleles for flower color are

a. completely dominant: red dominant, white recessive

b. incompletely dominant

c. codominant 5) A golden horse with a white mane and tail is known as a palomino. For many years the genetics of this color was a mystery. Suppose you’ve been hired by a horse breeder who hopes to produce a line of true-breeding palomino horses—palomino horses that, when crossed with one another, always produce palomino foals. However, when you mate one of his palomino stallions with several palomino mares, the resulting offspring are:

• 42 palomino foals (golden/dark cream colored) • 23 cremello foals (very pale cream color) • 18 chestnut foals (red colored)

a. What phenotypic ratio do these offspring represent?

b. Using this information, develop a hypothesis about the genetic relationship between chestnut, palomino, and cremello. How many alleles do you think are involved? Is this trait demonstrating complete dominance, incomplete dominance, or co-dominance. Explain. [Hint: Only one gene locus is involved.]

6) There are 5 modes of inheritance for human traits: autosomal recessive, autosomal dominant, sex-linked recessive, sex-linked dominant, and mitochondrial. Analyze the pedigree shown below to determine the mode of inheritance and genotypes of members of this family

Mode of Inheritance/Inheritance Pattern: a. Is the pedigree dominant or recessive? _________________________

How do you know? ______________________________________________________

______________________________________________________________________

b. Is the pedigree autosomal or sex-linked? ________________________

How do you know? ______________________________________________________

______________________________________________________________________

c. Genotypes:

I-1 ______ II-3 _______ III-4 _______

I-2 ______ III-1 _______ IV-2 _______

II-1 ______ III-2 _______ IV-6 _______

II-2 ______ III-3 _______ V-2 _______

BIOSCI 107 Study Questions Chapter 13 DNA Structure and Replication 1) Outline Griffith’s 1928 Transformation Experiment by answering the following questions: a. mice injected with live R strain ______________________________________ (died or survived)

b. mice injected with live S strain ______________________________________ (died or survived)

c. mice injected with heat killed S Strain_________________________________( died or survived)

d. mice injected with heat killed S Strain + live R strain _____________________ (died or survived)

e. Which results (a-d) was the first evidence of transformation: DNA transferring directly from one organism to another. Explain.

2) What experimental evidence did each of the following scientists contribute to discovering the structure of DNA?

a. Francis Crick & James Watson

b. Erwin Chargaff

c. Rosalind Franklin & Maurice Wilkens

3) In DNA, the number of purines is equal to the number of pyrimidines.

a. True b. False c. Sometimes, but not always

4) Write in the bases of the complementary strand for the DNA strand shown below. Be sure to label the 3′ and 5′ ends.

3′-A A T A C G A C G T A C T T T C G A A C A C T-5′

5) In the figure shown below, what best describes Strand B?

a. It is the lagging strand. b. It is the leading strand. c. It is the Okazaki strand.

6) On the figure above, label the 5’ and 3’ ends of the original DNA strands to demonstrate the antiparallel nature of DNA. 7) Draw a sketch illustrating why the lagging strand must be synthesized in small pieces, while the leading strand can be synthesized in one continuous piece. 8) Why are RNA primers needed to start each newly synthesized strand of DNA? 9) Review the functions of the following enzymes:

a. DNA ligase

b. Telomerase

c. DNA polymerase III

d. Primase

Strand A

Strand B

5’

3’

primer

primer

3’

5’

BIOSCI 107

Study Questions Chapter 14 Genes to Protein

1) Create a diagram depicting transcription and translation in a typical eukaryotic cell. Show where in the cell each takes place, and briefly describe what happens during each process. 2) Compare and contrast transcription and translation by filling out the table below:

Transcription Translation

Start Sequence

Stop Sequence

Macromolecule being created

Enzyme used to attach monomers together to from Macromolecule

3) Name the three types of RNA that are used in transcription and translation, and describe the role of each in the process in which it is active.

3) Which post-transcription modification results in the pre-mRNA being shortened? a. capping the 5’ end with a modified guanine b. adding a poly A tail on the 3’ end c. intron splicing d. exon splicing 4) What is a codon? a. A sequence of three nucleotides in a tRNA that codes for a specific amino acid b. A sequence of three nucleotides in an mRNA that codes for a specific amino acid c. A sequence of three nucleotides in a tRNA that binds to the code in DNA to make a protein d. A sequence of three nucleotides in a rRNA that binds onto the matching tRNA 5) One of the most important discoveries of the 20th century was the breaking of the genetic code. Understanding the genetic code provided the key to linking genetic sequences to their corresponding amino acid sequences (proteins). Use the Genetic Code Table from your textbook to answer the following questions: a. Determine the amino acid sequence that corresponds to the mRNA sequence shown below

Protein _______________________________________________________________________ b. Work backwards from your mRNA strand to construct the template strand of DNA from which it was

transcribed. Be sure to label the 3 and 5 ends.

DNA __________________________________________________________________________ 6) Refer to Genetic Code Table from textbook to help with the following questions. a. Given the DNA template sequence below, write the mRNA that would be transcribed

3-A A T A C G A C G T A C T T T C G A A C A C T-5 mRNA _________________________________________________________________________ b. Look at the sequence that you have just transcribed. Put a box around the START codon, and circle each of the subsequent codons until you reach a STOP codon. Underline the STOP codon.

7) What is the matching tRNA anticodon for the mRNA codon AUG? a. TAC b. UAC c. GUA d. AUG 8) Looking at the mRNA sequence below which is the correct reading frame (1, 2 OR 3)? Explain.

9) What are the E, P, and A sites of the large subunit of the ribosome? Why do some people refer to the large ribosomal subunit as a ribozyme? 10. What happens to “empty” tRNA molecules after they are ejected from the ribosome? 11. Which of the following describes post-translational processing?

a. It is changes in nuclear DNA after a protein has been translated from mRNA. b. It rarely occurs in eukaryotic protein synthesis. c. It is unnecessary for secretion of most proteins. d. It may involve modifications in the protein’s sequence or the addition of sugars or phosphate

groups. e. All of the above

BIOSCI 107

Study Questions Chapter 15 DNA Mutations & Genetic Testing 1) Mutations are always harmful to the organism.

a. True b. False

2) Find the mRNA and amino acid (protein) sequence for the given DNA template provided, using the Genetic Code Table from Chapter 14.

DNA : 3-A A T A C G A C G T A C T T T C G A A C A C T-5

mRNA: _______________________________________

protein _______________________________________

Draw an example of the change in DNA nucleotides and the resulting protein for the following: a. A SILENT MUTATION

original 3-A A T A C G A C G T A C T T T C G A A C A C T-5

mutant _____________________________________________

protein _____________________________________________

b. A MISSENSE MUTATION

original 3-A A T A C G A C G T A C T T T C G A A C A C T-5

mutant _____________________________________________

protein _____________________________________________

c. A NONSENSE MUTATION

original 3-A A T A C G A C G T A C T T T C G A A C A C T-5

mutant _____________________________________________

protein _____________________________________________

3) What best describes what it means when we say that a disease is multifactorial? a. The disease is the result of the interaction of multiple genes with one another. b. The disease is the result of the interaction of multiple proteins with one another. c. The disease is the result of the interaction of multiple mutations in one gene. d. The disease is the result of the interaction of multiple genes with the environment.

4) What is the difference between a somatic and a germline mutation? Which can be passed down to offspring?

5) The BRCA1 gene is a tumor suppressor gene. Mutations in the gene can increase a person’s risk of breast and ovarian cancers. Lane 1 contains a DNA fingerprint from an individual with the BRCA1 mutation. Which other individual or individuals have the BRCA1 mutation?

a. #2 b. #3 c. #4 d. #5

6) Pregnant women who are over the age of 35 are considered “high risk” pregnancies because they are more likely to have a child with chromosomal mutations than women who are younger. a. What two genetic tests can be done on a pregnant woman to determine if the developing fetus carries any chromosomal mutations? b. What is the name of the chromosomal mutation depicted in the figure below.

1 2 3 4 5

7) Tay Sachs is a genetic disease that destroys the developing nervous system and results in a painful death by age two. Newlyweds Lisa and Jeff both have family members that have had Tay Sachs and they want to determine if they are carriers of the Tay Sachs mutation. Their doctor takes blood samples from each and performs an allele specific oligonucleotide hybridization (ASOH) genetic test. a. Describe how the ASOH experiment works, then fill in the figure below for the + and – controls and to indicate that Lisa and Jeff are in fact both carriers.

b. Now knowing that they are both carriers, Lisa and Jeff are looking for a way to have a child that is guaranteed to NOT have Tay Sachs. Describe a genetic procedure that can be done to select from disease free embryos before they are implanted into Lisa’s womb.

BIOSCI 107

Study Questions Chapter 16 Eukaryotic Gene Regulation 1) Explore how a combination of transcription factors is typically needed to initiate transcription in eukaryotes. Be sure you can answer the following questions:

a. What is the difference in function between a general transcription factor and a specific transcription factor?

b. Prokaryotic cells use operons as a way to activate all the necessary genes for a specific process at the same time. How can the expression of several different genes be coordinated in eukaryotic cells which do NOT use operons?

2) Scientists were surprised to find that the human genome contains only about 21,000 genes that code for proteins. However, there are more than 100,000 different proteins made in human cells.

a. How is this possible?

b. Use the diagram below to explain how different proteins can be made from one gene. Show at

least three different mRNAs and proteins.

3) How does eukaryotic transcription differ from bacterial transcription? a. Functionally related genes are organized differently. b. Eukaryotes need three distinct RNA polymerases—one for rRNA, one for mRNA, and one

for tRNA and other small RNA molecules. c. Eukaryotic genes typically have several regulators. d. General transcription factors are needed before transcription can occur. e. All of the above

4) Eukaryotic cells differ from prokaryotic cells in that they form chromatin.

a. Explain how chromatin structure is formed between DNA and histones.

b. Explain how the histone acetyltransferase (HAT) activity of activator proteins is used to loosen chromatin during transcription.

5) What is gene silencing and what role does it play in cellular differentiation (See Chapter 19 for a definition of cellular differentiation)?

BIOSCI 107

Study Questions Chapter 17 Genomes and Genomics 1) Assembling sequenced DNA fragments into an entire genome sequence is possible because the fragments are

a. sequenced many times for accuracy. b. all the same size. c. double-stranded. d. overlapping. e. short.

2) Which of the following is not typical of bacterial and archaeal genomes?

a. They have a single, circular chromosome. b. Much of their DNA is noncoding. c. They have relatively small genomes. d. Most genes lack introns. e. There are often plasmids present.

3) Compare and contrast eukaryotic and prokaryotic genomes. List at least two unique characteristic for each.

4) Which of the following statements about the human genome is false?

a. Most human genes encode multiple proteins. b. Human genes typically have many introns. c. About 99.5% of the genome is the same in all people. d. Transposons and other repetitive sequences make up a very small percentage of the human

genome. e. Humans have about 21,000 protein-coding genes.

5) Comparing the unique proteins expressed by a cancerous breast cell to the proteins expressed by a normal breast cell in the same patient is an application of

a. gene therapy. b. metabolomics. c. proteomics. d. pharmacogenomics. e. all of the above

BIOSCI 107

Study Questions Chapter 18 Recombinant DNA & Biotechnology 1) You digest the lambda phage virus chromosome (total length 48Kb = 48,000 bp) with the restriction enzyme HIND III. It cuts at position 5000bp, 11,000bp, 14,000bp, and 23,000bp. a. How many fragments of DNA are created from the original chromosome? What are the sizes of each fragment? b. Next you separate the fragments created by the restriction enzyme digest using gel electrophoresis. Draw and label the size of the fragments on the gel below.

c. What chemical, derived from seaweed, is used to make DNA gels? d. What is the biological source of restriction enzymes?

2) Besides electroporation, name two additional ways that recombinant DNA can be inserted into a host cell. 3) Select the incorrect match of a term and its definition:

a. Vector: A eukaryotic host cell that receives recombinant DNA b. Reporter gene: Any gene whose expression is easily observed c. Selectable marker: A gene included in a vector that allows survival of only transgenic cells d. Transformation: Insertion of recombinant DNA into a bacterial host cell e. Transgenic organism: An organism with recombinant DNA

4) Describe what happens in the three stages of a polymerase chain reaction (PCR)

Denaturation: Annealing: Extension:

5) If you start with a single DNA molecule, how many molecules of DNA will you have after 20 rounds of PCR? 6) The polymerase chain reaction (PCR) is used to detect the presence of HIV in a standard HIV test. Fill in the results below for the two patients if patient 1 is HIV negative and patient 2 is HIV positive.

BIOSCI 107

Study Questions Chapter 19 Embryonic Development 1) Define morphogenesis. List two examples of morphogenesis that occurs during human embryonic development. 2) Drawing on your understanding of cytoplasmic segregation and polarity, answer the following questions:

a. How can polarity be determined by cytoplasmic segregation?

b. What is the role of the cytoskeleton in this process? 3) Compare and contrast the different types of stem cells by filling in the table below:

Definition Example

Totipotent Stem Cell

Pluripotent Stem Cell

Multipotent Stem Cell

4) Mesenchymal stem cells (MSCs) can be obtained from umbilical cord tissue and injected into damaged muscle to speed healing, as these cells differentiate into muscle cells. MSCs are best described as

a. totipotent. b. differentiated. c. unipotent. d. multipotent. e. pluripotent.

5) Describe the role that gene expression and silencing plays in cellular differentiation. How is gene silencing different from gene inactivation? 6) Compare and contrast the source and role maternal effect and zygotic genes play in embryonic development.