Genes and the DNA sequences between genes and how they determine development.

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. Genomics is the study of:
a. The structure and function of mutations and how they alter genetic traits.
b. Genes and the DNA sequences between genes and how they determine development.
c. The information provided by computer programs which analyzes mRNA.
d. The human genome as compared to other vertebrate genomes.
2. Microarrays are a very useful tool in genomics because they:
a. Help scientists examine intergenetic DNA by separating it from genes.
b. Provide a unique promoter region for polymerase chain reactions.
c. Allow scientists to examine thousands of genes all at once.
d. Decrease the time it takes for scientists to make copies of DNA.
3. Generally, every cell in our body contains the same 20,000 (or so) genes.  However, cells  in our body are different from each other because they:
a. Have different genes turned “on” or “off” to support different functions.
b. Contain different copies of genes for different functions.
c. Provide different nucleotide bases for each developmental function.
d. Function differently based on varying proteomics.

4. How can scientists determine the function of or differences between cell types?  They can examine the:
a. Number of nucleotide bases in genes versus intergenetic sequences.
b. Amount of mRNA expressed for each gene in a cell type, and then compare that information between cell types.
c. Amount of mutations between genes in the intergenetic spaces.
d. Number of tRNA copies for a particular cell type.

5. How is a microarray constructed?  In each spot, there are:
a. Copies of all the genes for an organism.
b. Multiple copies of one gene; each spot has copies for a different gene.
c. Multiple copies of intergenetic sequences, which bind to genes in the samples.
d. Copies of intergenetic sequences, which promote the replication of DNA in a sample.

6. The experiment that begins in Chapter 3 of the simulation seeks to answer the question:
a. What is the difference between intergenetic spaces in cancer cells versus healthy cells?
b. Why do different cell types express different amounts of mRNA?
c. How do different cancer cells produce different mutations?
d. What is the difference between healthy cells and cancer cells?

7. Why can’t doctors use cell appearance to diagnose cancer?
a. Not all cancer cells look different from healthy cells.
b. Cancer cells are too small to examine using cell appearance.
c. Not all cancer cells are able to be biopsied from the body.
d. Cancer cells change appearance when taken out of the body.

8. In the experiment, a solvent is added to each cell type (healthy cells and cancer cells).  After the sample tube containing each cell type is mixed on the vortex, the RNA is separated from the rest of the sample in a centrifuge.  Why does DNA settle to the bottom of the tube and RNA doesn’t?
a. RNA is much longer than DNA.
b. RNA is attached to proteins that help it stay in solution.
c. DNA is attached to biomolecules that weigh it down and help it settle to the bottom.
d. DNA is much longer than RNA.

9. What feature does mRNA have that tRNA and rRNA do not? mRNA always:
a. Contains a GABA box.
b. Contains a TATA sequence.
c. Ends with a G tail.
d. Ends with a poly-A tail.

10. How do the beads in the column separate mRNA from all other RNA?  The beads contain:
a. Sequences that magnetically separate the mRNA.
b. A glue-like substance derived from spider webs.
c. Poly-T’s.
d. A sequence of uracil’s that bind to the Poly-A tail.

11. After you isolate mRNA, you have to make a DNA copy.  Why can’t we just use mRNA?
a. DNA is much more stable than mRNA.
b. We have to add a fluorescent label that will allow us to see the sample.
c. mRNA will eventually transform into tRNA making it unusable.
d. A and B

12. Scientists call hybridization the key to microarrays.  Hybridization occurs when:
a. Two complimentary strands of DNA from different sources bind to each other.
b. Poly-A tails bind to Poly-Ts.
c. Different species interbreed and create new DNA base pairings.
d. Two strands of identical DNA bind without using the traditional nucleotide pairs.

13. When you scan the microarray in the scanner, the data show some dark spots.  What do these represent?
a. The DNA that has been replicated in healthy cells.
b. The mRNA that was washed away in the washing solution.
c. The DNA that was not transcribed and expressed in healthy cells.
d. The mRNA that was not bound by Oligo-d-tails in the beads.

14. When you scan the microarray in the scanner, some spots are yellow and represent places where the gene was expressed in both healthy and cancer cells.  These spots tell us:
a. Where to look for mutations.
b. Where DNA hybridized in cancer cells.
c. That DNA expression didn’t change in these genes when cancer occurred.
d. That the microarray didn’t work in these genes.

15. In our example, gene 6219 mRNA is made in both healthy and cancerous cells; however proteins are only translated from that mRNA in healthy cells.  Microarray analysis:
a. Shows us this defect by making yellow spots.
b. Cannot show us this defect, which is a limitation of this type of analysis.
c. Show us this defect by making red spots.
d. Cannot show us this defect, which is a benefit of this type of analysis.

 

Take a look around your house and identify household products that work by means of an enzyme. Name the products, and indicate how you know they work with an enzyme.

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INSTRUCTIONS:

 

 

 

·         On your own and without assistance, complete this Lab 4 Answer Sheet electronically and submit it via the Assignments Folder by the date listed in the Course Schedule (under Syllabus).

 

·         To conduct your laboratory exercises, use the Laboratory Manual located under Course Content. Read the introduction and the directions for each exercise/experiment carefully before completing the exercises/experiments and answering the questions.

 

·         Save your Lab 4 Answer Sheet in the following format:  LastName_Lab4 (e.g., Smith_Lab4).

 

·         You should submit your document as a Word (.doc or .docx) or Rich Text Format (.rtf) file for best compatibility.

 

 

 

 

 

Pre-Lab Questions

 

 

 

  1. How could you test to see if an enzyme was completely saturated during an experiment?

 

 

 

 

 

  1. List three conditions that would alter the activity of an enzyme. Be specific with your explanation.

 

 

 

 

 

  1. Take a look around your house and identify household products that work by means of an enzyme. Name the products, and indicate how you know they work with an enzyme.

 

 

 

 

 

 

 

Experiment 1: Enzymes in Food

 

 

 

 

 

Data Tables and Post-Lab Assessment

 

Table 1: Substance vs. Starch Presence

 

Table 1: Substance vs. Starch Presence
Substance Resulting Color Presence of Starch?
Positive Control: Ginger Root
Negative Control: Student Must Select
Food Product:
Food Product:
Saliva:

 

 

 

Post-Lab Questions

 

  1. What were your controls for this experiment? What did they demonstrate? Why was saliva included in this experiment?

 

 

 

  1. What is the function of amylase? What does amylase do to starch?

 

 

 

  1. Which of the foods that you tested contained amylase? Which did not? What experimental evidence supports your claim? 

     

     

  2. Saliva does not contain amylase until babies are two months old. How could this affect an infant’s digestive requirements? 

     

     

  3. There is another digestive enzyme (other than salivary amylase) that is secreted by the salivary glands. Research to determine what this enzyme is called. What substrate does it act on? Where in the body does it become activated, and why?

 

 

 

  1. Digestive enzymes in the gut include proteases, which digest proteins. Why don’t these enzymes digest the stomach and small intestine, which are partially composed of protein?

 

 

 

 

 

Experiment 2: Effect of Temperature on Enzyme Activity

 

 

 

Data Tables and Post-Lab Assessment

 

Table 2: Balloon Circumference vs. Temperature

 

 

 

Table 2: Balloon Circumference vs. Temperature
Tube Temperature (°C) Uninflated Balloon Circumference (cm) Final Balloon Circumference (cm) Difference in Balloon Circumference (cm)
1 – (Cold)
2 – (RT)
3 – (Hot)

 

 

 

 

 

Post-Lab Questions

 

  1. What reaction is being catalyzed in this experiment? 
  2. What is the enzyme in this experiment? What is the substrate? 
  3. What is the independent variable in this experiment? What is the dependent variable? 
  4. How does the temperature affect enzyme function? Use evidence from your data to support your answer. 
  5. Draw a graph of balloon diameter vs. temperature. What is the correlation? 
  6. Is there a negative control in this experiment? If yes, identify the control. If no, suggest how you could revise the experiment to include a negative control. 
  7. In general, how would an increase in substrate alter enzyme activity? Draw a graph to illustrate this relationship. 
  8. Design an experiment to determine the optimal temperature for enzyme function, complete with controls. Where would you find the enzymes for this experiment? What substrate would you use?

 

Which two pieces of information are absolutely critical in determining which additional tests must be done to identify the pathogen? a) Appearance on charcoal agar b) Endospore Stain c) Gram Stain d) Oxygen sensitivity  

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Question 1

 

You are reading culture plates today and identifying pathogens that grow from patient samples. 

Which two pieces of information are absolutely critical in determining which additional tests must be done to identify the pathogen?

 

a) Appearance on charcoal agar

b) Endospore Stain

c) Gram Stain

d) Oxygen sensitivity

 

Question 2

 

A 10 year old has a wound on the arm that the physician suspects is infected.

Upon culture, you see small white colonies growing on blood agar as well as chocolate agar.

You gram stain the colonies to find that they are gram positive cocci.

Which test will you perform first?

 

a) catalase

b) indole

c) lactose fermentation

d) coagulase

 

Question 3

 

You have isolated catalase positive gram positive cocci from a wound culture.

Which test will you perform next?

 

a) coagulase

b) P disc, containing optichin

c) A disc, containing bacitracin

 

Question 4

 

You are working on a sputum culture.

You see mucoid alpha hemolytic colonies that number many more than the normal flora present.

The gram stain of the colonies shows gram positive cocci that are in lancet shaped pairs.

Which test will you do?

 

a) P disc, containing optichin

b) A disc, containing bacitracin

c) motility

d) acid fast staining

 

Question 5

 

You are working up a throat culture.  

Standard procedure in plating throat cultures in your lab includes dropping an A disc near the initial inoculum in the first quandrant when streaking the specimen.

You examine the blood agar plate and see moderate normal flora and many beta hemolytic colonies that do not grow up to the A disc.  

The beta hemolytic colonies are catalase negative gram positive cocci.

Which pathogen is in this throat culture?

 

a)Streptococcus agalactiae

b) Staphylococcus aureus

c) Streptococcus pyogenes

d) Staphylococcus epidermidis

 

Question 6

 

You are working up a male genital culture.

You see no growth on the blood agar plate but small colonies growing on the chocolate agar plate. The gram stain shows gram negative cocci in pairs.

Which test will you do next?

 

a) oxidase

b) motility

c) catalase

d) indole

 

Question 7

 

You are working up a cerebrospinal fluid culture.

You find colonies growing on blood agar as well as chocolate agar.

The colonies are oxidase positive gram negative cocci.

The colonies ferment glucose and maltose but not sucrose or lactose.

You identify the pathogen as

 

a) Neisseria meningitidis

b) Haemophilus influenzae

c) Streptococcus pneumoniae

d) Neisseria gonorrhoeae

 

Question 8

 

You are working up a urine culture.

You see >100 colonies that are gray and flat on the blood agar plate and >100 colonies that are bright pink on the MacConkey agar.

The IMViC results are Indole positive, Methyl Red positive, Vogues-Proskauer negative, Citrate negative.

You have identified the pathogen as

 

a) Citrobacter freundii

b) Escherichia coli

c) Enterobacter aerogenes

d) Proteus vulgaris

 

Question 9

 

You are working up a stool culture.

On MacConkey agar you see many bright pink colonies and many clear colonies.

Which colonies are potential pathogens that require further testing?

 

a) Clear colonies, non lactose fermenters

b) Bright pink colonies, non lactose fermenters

c) Bright pink colonies, lactose fermenters

d) Clear colonies, lactose fermenters

 

Question 10

 

DNA technology is useful in the identification of :

 

a) pathogens that are unable to be grown readily on artificial lab media. 

b) pathogens that are no longer alive in the patient sample,

c) species that cannot be differentiated by conventional testing.

d) All of the above.

 

Question 11

 

You are preparing a sample of DNA from an unknown colony of bacteria.

After adding digestion buffer and incubating for the time suggested by the manufacturer, you centrifuge the sample.

The DNA is found:

 

a) stuck to the gel in the tube.

b) stuck to the sides of the tube.

c) in the pellet in the bottom of the tube.

d) in the supernatant in the tube.

 

Question 12

 

Which of the following is not true of the Polymerase Chain Reaction?

 

a) PCR is facilitated by a heat labile DNA polymerase.

b) PCR is a method of replicating DNA in a test tube.

c) PCR can facilitate the detection of DNA that is too low to detect by other methods.

 

Question 13

 

Why are dATP, dCTP, dTTP and dGTP added to a PCR reaction tube?

 

a) They catalyze the polymerase.

b) They buffer the mixture.

c) They allow the DNA in the sample to anneal.

d) They provide the building blocks of DNA.

 

Question 14

 

Why are universal 16S rDNA primers used in your experiment?

 

a) They will anneal to highly conserved areas of the gene that encodes bacterial 16S rRNA.

b) They will anneal to unique sequences of genes encoding 16S rRNA in specific bacteria.

 

 

 

 

 

Question 15

 

If universal primers are used to amplify DNA in a PCR reaction, then the PCR product must be sequenced to determine the bacteria that the DNA belongs to.

 

True

False

 

Question 16

 

How is the PCR product separated from the PCR mixture at the completion of the reaction?

 

a) Perform electrophoresis in an agarose gel, stain the gel and cut the band corresponding to the PCR product from the gel.

b) Pour the PCR mixture into a commercially prepared DNA microconcentrator column and follow the manufacturer’s directions to adhere and elute the PCR product from the column.

c) Both of the above procedures may be used.

d) Neither of the above procedures may be used.

 

Question 17

 

Your PCR product was sequenced by a method known as Cycle Sequencing.

Which of the following statements is false?

 

a) An automatic sequencer performs electrophoresis and reads the tagged DNA pieces, providing a read out of the nucleotide bases comprising the DNA sequence of the fragment being tested

b) Cycle sequencing is done in a PCR machine.

c)Tagged terminator nucleotides facilitate the creation of a series of nested DNA sequences of different length.

d) Cycle sequencing can be completed in just one test tube.

 

Question 18

 

The National Library of Medicine has a databank called GenBank that has deposited in it the DNA sequences of numerous genes isolated from known bacterial species.

 

True

False

 

 

Question 19

 

You obtained the following BLAST data from your sample:

99.9% Enterobacter sakazakii

95.2% Enterobacter aerogenes

93.7% Enterobacter cloacae

The pathogen in your sample is:

 

a)Enterobacter sakazakii

b)Enterobacter aerogenes

c)Enterobacter cloacae

d)Enterobacter species

Assemble a second pair of replicated sister chromatids; this time using 12 beads, instead of 20, per pair (six beads per each complete sister chromatid strand).

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INSTRUCTIONS:

 

·         On your own and without assistance, complete this Lab 5Answer Sheet electronically and submit it via the Assignments Folder by the date listed intheCourse Schedule (underSyllabus).

·         To conduct your laboratory exercises, use the Laboratory Manual located under Course Content. Read the introduction and the directions for each exercise/experiment carefully before completing the exercises/experiments and answering the questions.

·         Save your Lab 5Answer Sheet in the following format:  LastName_Lab5 (e.g., Smith_Lab5).

·         You should submit your document as a Word (.doc or .docx) or Rich Text Format (.rtf) file for best compatibility.

 

Pre-Lab Questions

 

  1. Compare and contrast mitosis and meiosis.

 

 

  1.  What major event occurs during interphase?

 

 

Experiment 1: Following Chromosomal DNA Movement through Meiosis

In this experiment, you will model the movement of the chromosomes through meiosis I and II to create gametes.

concept_tab_l

Materials

2 Sets of Different Colored Pop-it® Beads (32 of each – these may be any color)

8 5-Holed Pop-it® Beads (used as centromeres)

 

Procedure:

Part 1: Modeling Meiosis without Crossing Over

As prophase I begins, the replicated chromosomes coil and condense…

  1. Build a pair of replicated, homologous chromosomes. 10 beads should be used to create each individual sister chromatid (20 beads per chromosome pair). Two five-holed beads represent each centromere. To do this…
Figure 3: Bead set-up. The blue beads represent one pair of sister chromatids and the black beads represent a second pair of sister chromatids. The black and blue pair are homologous.
Figure 3: Bead set-up. The blue beads represent one pair of sister chromatids and the black beads represent a second pair of sister chromatids. The black and blue pair are homologous.
    1. Start with 20 beads of the same color to create your first sister chromatid pair. Five beads must be snapped together for each of the four different strands. Two strands create the first chromatid, and two strands create the second chromatid with a 5-holed bead at the center of each chromatid.  This creates an “I” shape.
    2. Connect the “I” shaped sister chromatids by the 5-holed beads to create  an “X” shape.
    3. Repeat this process using 20 new beads (of a different color) to create the second sister chromatid pair.
  2. Assemble a second pair of replicated sister chromatids; this time using 12 beads, instead of 20, per pair (six beads per each complete sister chromatid strand).
  3. Pair up the homologous chromosome pairs created in Step 1 and 2. DO NOT SIMULATE CROSSING OVER IN THIS TRIAL. You will simulate crossing over in Part 2.
  4. Configure the chromosomes as they would appear in each of the stages of meiotic division (prophase I and II, metaphase I and II, anaphase I and II, telophase I and II, and cytokinesis).
  5. Diagram the corresponding images for each stage in the sections titled “Trial 1 – Meiotic Division Beads Diagram”. Be sure to indicate the number of chromosomes present in each phase.
Figure 4: Second set of replicated chromosomes.
Figure 4: Second set of replicated chromosomes.
  1. Disassemble the beads used in Part 1. You will need to recycle these beads for a second meiosis trial in Steps 8 – 13.

Part 1 – Meiotic Division Beads Diagram

Prophase I

 

Metaphase I

 

Anaphase I

 

Telophase I

 

Prophase II

 

Metaphase II

Anaphase II

 

Telophase II

 

Cytokinesis

Part 2: Modeling Meiosis with Crossing Over

  1. Build a pair of replicated, homologous chromosomes. 10 beads should be used to create each individual sister chromatid (20 beads per chromosome pair). Two five-holed beads represent each centromere. To do this…
    1. a. Start with 20 beads of the same color to create your first sister chromatid pair. Five beads must be snapped together for each of the four different strands. Two strands create the first chromatid, and two strands create the second chromatid with a 5-holed bead at the center of each chromatid.  This creates an “I” shape.
    2. Connect the “I” shaped sister chromatids by the 5-holed beads to create  an “X” shape.
    3. Repeat this process using 20 new beads (of a different color) to create the second sister chromatid pair.
  2. Assemble a second pair of replicated sister chromatids; this time using 12 beads, instead of 20, per pair (six beads per each complete sister chromatid strand). Snap each of the four pieces into a new five-holed bead to complete the set up.
  3. Pair up the homologous chromosomes created in Step 8 and 9.
  4. SIMULATE CROSSING OVER. To do this, bring the two homologous pairs of sister chromatids together (creating the chiasma) and exchange an equal number of beads between the two. This will result in chromatids of the same original length, there will now be new combinations of chromatid colors.
  5. Configure the chromosomes as they would appear in each of the stages of meiotic division (prophase I and II, metaphase I and II, anaphase I and II, telophase I and II, and cytokinesis).
  6. Diagram the corresponding images for each stage in the section titled “Trial 2 – Meiotic Division Beads Diagram”. Be sure to indicate the number of chromosomes present in each cell for each phase. Also, indicate how the crossing over affected the genetic content in the gametes from Part1 versus Part 2.

Part 2 –  Meiotic Division Beads Diagram:

Prophase I

 

Metaphase I

 

Anaphase I

 

Telophase I

 

Prophase II

 

Metaphase II

 

Anaphase II

 

Telophase II

 

Cytokinesis

 

 

Post-Lab Questions

1.      What is the ploidy of the DNA at the end of meiosis I? What about at the end of meiosis II?

 

2.      How are meiosis I and meiosis II different?

 

3.      Why do you use non-sister chromatids to demonstrate crossing over?

 

4.      What combinations of alleles could result from a crossover between BD and bd chromosomes?

 

 

 

5.      How many chromosomes were present when meiosis I started?

 

6.      How many nuclei are present at the end of meiosis II? How many chromosomes are in each?

 

7.      Identify two ways that meiosis contributes to genetic recombination.

 

8.      Why is it necessary to reduce the number of chromosomes in gametes, but not in other cells?

 

9.      Blue whales have 44 chromosomes in every cell. Determine how many chromosomes you would expect to find in the following:

 

Sperm Cell:

Egg Cell:

Daughter Cell from Mitosis:

Daughter Cell from Meiosis II:

 

10.  Research and find a disease that is caused by chromosomal mutations. When does the mutation occur? What chromosomes are affected? What are the consequences?

 

11.  Diagram what would happen if sexual reproduction took place for four generations using diploid (2n) cells.

 

 

Experiment 2: The Importance of Cell Cycle Control

Some environmental factors can cause genetic mutations which result in a lack of proper cell cycle control (mitosis). When this happens, the possibility for uncontrolled cell growth occurs. In some instances, uncontrolled growth can lead to tumors, which are often associated with cancer, or other biological diseases.

In this experiment, you will review some of the karyotypic differences which can be observed when comparing normal, controlled cell growth and abnormal, uncontrolled cell growth. A karyotype is an image of the complete set of diploid chromosomes in a single cell.

 

 

 

 

concept_tab_lProcedure

Materials

*Computer Access

*Internet Access

  

*You Must Provide

 

 

 

  1. Begin by constructing a hypothesis to explain what differences you might observe when comparing the karyotypes of human cells which experience normal cell cycle control versus cancerous cells (which experience abnormal, or a lack of, cell cycle control). Record your hypothesis in Post-Lab Question 1.Note: Be sure to include what you expect to observe, and why you think you will observe these features. Think about what you know about cancerous cell growth to help construct this information
  2. Go online to find some images of abnormal karyotypes, and normal karyotypes. The best results will come from search terms such as “abnormal karyotype”, “HeLa cells”, “normal karyotype”, “abnormal chromosomes”, etc. Be sure to use dependable resources which have been peer-reviewed
  3. Identify at least five abnormalities in the abnormal images. Then, list and draw each image in the Data section at the end of this experiment. Do these abnormalities agree with your original hypothesis?

Hint: It may be helpful to count the number of chromosomes, count the number of pairs, compare the sizes of homologous chromosomes, look for any missing or additional genetic markers/flags, etc.

Data

 

 

 

 

 

Post-Lab Questions

1.      Record your hypothesis from Step 1 in the Procedure section here.

 

 

2.      What do your results indicate about cell cycle control?

 

 

3.      Suppose a person developed a mutation in a somatic cell which diminishes the performance of the body’s natural cell cycle control proteins. This mutation resulted in cancer, but was effectively treated with a cocktail of cancer-fighting techniques. Is it possible for this person’s future children to inherit this cancer-causing mutation? Be specific when you explain why or why not.

 

 

4.      Why do cells which lack cell cycle control exhibit karyotypes which look physically different than cells with normal cell cycle.

 

 

5.      What are HeLa cells? Why are HeLa cells appropriate for this experiment?