Two genes, A/a and B/b, control fruit color in squash. The inheritance pattern for this trait fits one of the multiple gene types that we discussed in class. A homozygous plant with white fruit was crossed with a homozygous plant with yellow fruit. All the progeny had red fruit. When two F1 plants were crossed, the F2 consisted of 38 white, 27 yellow, and 89 red.

(a) (2 pts) Which type of gene interaction do we see here? Explain your reasoning.

(b) (2 pts) What is the expected ratio of white to yellow to red fruit in the F2?

(c) (3 pts) What were the genotypes of the P generation plants?

(d) (5 pts) Test your hypothesized gene interaction model with Chi-square analysis. Please include all the components of Chi-square analysis in your answer.

(Continues on the back…)

(e) (5 pts) The diagram explains how the two genes interact at the molecular level. Compounds X, Y, and Z determine fruit color depending on which of the two chemical reactions occur. Each gene produces an enzyme that is either active or inactive depending on its genotype.

When an enzyme is active, the reaction it catalyzes occurs; when it is inactive, the reaction is blocked. Write in the boxes the genotypes that would explain the inheritance pattern.

(2 pts) Please fill in the box with the according genotypes.

(3 pts) Interpret the pathway with your own words (e.x. how to read this pathway? how you get white, yellow and red colors from different genotypes by following this pathway graph? Circle out the epistatic genotype in your pathway)

DNA Technologies   


Imagine that you are a graduate student working in a research laboratory. You are interested in the human enzyme chymotrypsin. There is a lot known about this protein, but you have some specific questions about its mechanism. In order to study this protein further, you will need to amplify the chymotrypsin gene (you have only a small sample of the cDNA containing the gene), clone the gene into an expression plasmid, use bacterial cells to propagate the plasmid and express protein, and purify the protein. Use the attached information to plan out the first part of your experiments (amplification and cloning). Answer the following questions IN THE SPACE PROVIDED.


1. What restriction endonucleases will you use for cloning? Highlight their recognition sites on the attached template DNA sequence.





2. Design two DNA primers for use in amplifying the gene. Give their sequences below (5' to 3') and label where they will bind on the attached template DNA sequence.







3. Outline the process of amplifying the gene (using PCR), then cloning, including all reaction components for each process.

PCR amplification  

Steps reaction components

Cloning

Steps reaction components

Type II Restriction Endonucleases
Enzyme Source Recognition Sequence EcoRI Escherichia coli 5'G│AATT C 3'C TTAA│G

BamHI Bacillus amyloliquefaciens 5'G│GATC C \

3'C CTAG│G

HindIII Haemophilus influenzae 5'A│AGCT T

3'T TCGA│A

NotI Nocardia otitidis 5'GC│GGCC GC

3'CG CCGG│CG

SmaI* Serratia marcescens 5'CCC│GGG

3'GGG│CCC

HaeIII* Haemophilus aegyptius 5'GG│CC

3'CC│GG

AluI* Arthrobacter luteus 5'AG│CT

3'TC│GA

EcoRV* Escherichia coli 5'GAT│ATC

3'CTA│TAG

KpnI Klebsiella pneumoniae 5'G GTAC│C

3'C│CATG G

PstI Providencia stuartii 5'C TGCA│G

3'G│ACGT C

SalI Streptomyces albus 5'G│TCGA C

3'C AGCT│G

SpeI Sphaerotilus natans 5'A│CTAG T

3'T GATC│A

SphI Streptomyces phaeochromogenes 5'G CATG│C

3'C│GTAC G

XbaI Xanthomonas badrii 5'T│CTAG A

3'A GATC│T
Key: * = blunt ends

DNA Sequence of Chymotrypsin in Context

GACCTATTAG GAATAAACAG GATACCATTG GCAAGCTTAC GTACACGACT TGATTGACAC TTACCCAGTA GGGGACGAAT GGATCCATCG AAGGCTGCAG GGATGAATTC TTTCACTATG TGTGGGGTGC CCAGCTTCCC GCCCAACCTA TCCGCCCGAG TGGTGGGAGG AGAGGATGCC CGGCCCCACA GCTGGCCCTG GCAGATCTCC CTCCAGTACC TCAAGGACGA CACGTGGAGG CATACGTGTG GCGGGACTTT GATTGCTAGC AACTTCGTCC TCACTGCCGC CCACTGCATC AGCAACACCT GGACCTACCG TGTGGCCGTG GGAAAGAACA ACCTGGAGGT GGAAGACGAA GAAGGATCCC TGTTTGTGGG TGTGGACACC ATCCACGTCC ACAAGAGATG GAATGCCCTC CTGTTGCGCA ATGATATTGC CCTCATCAAG CTTGCAGAGC ATGTGGAGCT GAGTGACACC ATCCAGGTGG CCTGCCTGCC AGAGAAGGAC TCCCTGCTCC CCAAGGACTA CCCCTGCTAT GTCACCGGCT GGGGGCGCCT CTGGACCAAC GGCCCCATTG CTGATAAGCT GCAGCAGGGC CTGCAGCCCG TGGTGGATCA CGCCACGTGC TCCAGGATTG ACTGGTGGGG CTTCAGGGTG AAGAAAACCA TGGTGTGCGC TGGGGGCGAT GGCGTTATCT CAGCCTGCAA TGGGGACTCC GGTGGCCCAC TGAACTGCCA GTTGGAGAAC GGTTCCTGGG AGGTGTTTGG CATCGTCAGC TTTGGCTCCC GGCGGGGCTG CAACACCCGC AAGAAGCCGG TAGTCTACAC CCGGGTGTCC GCCTACATCG ACTGGATCAA CGAGAAAATG CAGCTGTGAT TTGTTGCTGG GAGCGGCGGC AGCGAGTAAT AGTAGTACGG AAGTGCGGCC GCTAGACTGA GATATCGGCC TATCCGATAT CGATAGGGTC ATTAAGAACG GCTCGATAG

The table below contains data on the enzyme activity of mannose-6-phosphate isomerase (MPI) for three different genotypes (SS, FS, FF) in the amphipod crustacean Platorchestia platensis. Because the effects of sex are not known, specimens were classified by sex. Conduct a two-way ANOVA on this dataset. Test for the effect of genotype, the effect of sex, and whether there is an interaction effect between two factors. Show all calculations and state your conclusions.

1. Fill in the table below concerning chromatin modification.

2.Describe how X-chromosome inactivation occurs.

3.Outline the process of RNA interference (RNAi). Note the two types of small RNA molecules typically involved, as well as the three possible outcomes. Be able to define the following: Dicer, RISC, guide strand, passenger strand.

4.Review the three epigenetics case studies we discussed. Briefly discuss one of them here.

Ill rate you HIGH

Topic Genetics

Effects of Metal ion poisons on enzyme activity

1. Prepare 3 dry testube and place 1ml of alfa amylase into each tube

2. to testube 1 add 3ml distilled water, to testube 2 3ml of lead acetate soln and to testube 3 1% silver nitrate soln.

3. place all tubes in water bath and set at 37C for 15min then remove the tubes at the same time

4. prepare 3 vials and label A -1, B-1,C-1 and put 3ml of 1% starch soln into each vial then add 2 drops of iodine soln then mix

5. transfer 10 drops of soln into vials; tube1 to A-1, tube 2 to B-1 and tube 3 to C-1. incubate at room temp for 10 min while mixing the vial

6. record the color of soln and indicate if digestion took place (with complete digestion colorless, with partial digestion violet or red and with no digestion dark shade of blue).

Question: provide the color of soln or precipitate then rank from 1-3 (with 1 being colorless signifying the greatest digestion)

Testube (1,2,3)

Color of soln...

Rank...

As discussed during the lecture, the enzyme HIV-1 reverse transcriptae (HIV-RT) plays a significant role for the HIV virus and is an important drug target. Assume a concentration [E] of 2.00 µM (i.e. 2.00 x 10^-6 mol/l) for HIV-RT. Two potential drug molecules, D₁ and D₂, were identified, which form stable complexes with the HIV-RT.

The dissociation constant of the complex ED₁ formed by HIV-RT and the drug D₁ is 1.00 nM (i.e. 1.00 x 10^-9 mol/l). The dissociation constant of the complex ED₂ formed by HIV-RT and the drug D₂ is 100 nM (i.e. 1.00 x 10^-7 mol/l).

Compute the total concentration of [D₂]_tot that is needed to bind 99% of the HIV-RT at the given concentration [E]_tot. Provide your answer as a numerical expression with 3 significant figures in the unit mol/l.

You do NOT have to consider competition betwwen the drugs D₁ and D₂! They are administered separately.

Medical testing: enzyme linked immunosorbent assay (ELISA) test for presence of antigen or antibody

EXPERIMENTAL PROTOCOL

In this laboratory, you will test seven different patients using a direct ELISA. We have access to serum samples from the main characters of the TV show The Big Bang Theory. You will test each of them for the presence of ZIKA virus and HIV, as well as perform a pregnancy test, using known antigens/antibodies for those diseases/test. Students will work in pairs. Serum for each character of the Big Bang Theory has been incubated overnight at 4°C in the wells of an ELISA plate.

1) Interpretations: Summarize the interpretation of the findings about the results and the experiment

2) Future Scientific Directions: suggest future experiments using as base the results obtained in the lab

3) Create a question to the lab experiement approach.

5)  Approach: Create a summary of the overall lab experiment. Hypothesis.

Medical testing: enzyme linked immunosorbent assay (ELISA) test for presence of antigen or antibody

EXPERIMENTAL PROTOCOL

In this laboratory, you will test seven different patients using a direct ELISA. We have access to serum samples from the main characters of the TV show The Big Bang Theory. You will test each of them for the presence of ZIKA virus and HIV, as well as perform a pregnancy test, using known antigens/antibodies for those diseases/test. Students will work in pairs. Serum for each character of the Big Bang Theory has been incubated overnight at 4°C in the wells of an ELISA plate. You are taking it from here.

1.) What basic principles of antibody-mediated immunity are utilized in an ELISA assay?

2.) What might have caused some positive results to be lighter in color than others?

3.) Why can some viruses not be targeted by antibodies for destruction? Is this a limitation for developing an ELISA-based protocol for detecting the disease?

4.) Postulate a hypothesis on how the characters infected with Zika contracted the disease (in time and space); consider that two of them live in the same apartment and the others visit them frequently.

SYMBIOTS LAB different from above ^

1. If you give a high temperature and high light treatment to Symbiodinium linchaea and Symbiodinium minutum, what results do you expect after 3 weeks of treatment?

As discussed during the lecture, the enzyme HIV-1 reverse transcriptae (HIV-RT) plays a significant role for the HIV virus and is an important drug target. Assume a concentration [E] of 2.00 µM (i.e. 2.00 x 10^-6 mol/l) for HIV-RT. Two potential drug molecules, D₁ and D₂, were identified, which form stable complexes with the HIV-RT.

The dissociation constant of the complex ED₁ formed by HIV-RT and the drug D₁ is 1.00 nM (i.e. 1.00 x 10^-9 mol/l). The dissociation constant of the complex ED₂ formed by HIV-RT and the drug D₂ is 100 nM (i.e. 1.00 x 10^-7 mol/l).

1) Compute the difference in binding free energy (at a physiological temperature T=310 K) for the complexes. Provide the difference as a positive numerical expression with three significant figures in kJ/mol.

2) Divide the difference between the binding free energies of the ED₁ and ED₂ complexes by the thermal energy (at the physiological temperature). Provide a numerical expression with 3 significant figures.

3)

Compute the total concentration of [D₁]_tot that is needed to bind 90% of the HIV-RT at the given concentration [E]_tot. Provide your answer as a numerical expression with 3 significant figures in the unit mol/l.

You do NOT have to consider competition betwwen the drugs D₁ and D₂! They are administered separately.

4)

Compute the total concentration of [D₁]_tot that is needed to bind 99% of the HIV-RT at the given concentration [E]_tot. Provide your answer as a numerical expression with 3 significant figures in the unit mol/l.

You do NOT have to consider competition betwwen the drugs D₁ and D₂! They are administered separately.

5)

Compute the total concentration of [D₂]_tot that is needed to bind 90% of the HIV-RT at the given concentration [E]_tot. Provide your answer as a numerical expression with 3 significant figures in the unit mol/l.

You do NOT have to consider competition betwwen the drugs D₁ and D₂! They are administered separately.

6)

Compute the total concentration of [D₂]_tot that is needed to bind 99% of the HIV-RT at the given concentration [E]_tot. Provide your answer as a numerical expression with 3 significant figures in the unit mol/l.

You do NOT have to consider competition betwwen the drugs D₁ and D₂! They are administered separately.

Arrange the following in the decreasing order (most important first) of their importance, for the welfare of human society. Give reasons for your answer. Biogas, citric acid, penicillin and curd.