Q1.

(a) What should molecular properties of a small molecule drug be such that its ADME parameters
transports it efficiently across the blood brain barrier? Give examples of the drugs that have these
structural properties (e.g. active transporters)

(b) Use principles of molecular modeling and drug
design to explain the mechanisms of how enzymes evolve new functions.

(c) How is the Buckingham
potential a more realistic one compared to the Lennard Jones potential in modeling VDW interactions
in proteins and nucleic acids? Write out the potential energy expression using the Buckingham
potential. Define and explain its adjustable parameters.

(d) How would you combine a MC and a MD
algorithm to perform a molecular simulation on a biological system.

Q2.

(a) What are the differences between an energy based ligand design method such as GRID and a
knowledge based one like LUDI? What are the requirements of a knowledge based ligand design
method?

(b) Interpret the following QSAR equation: log (1/C)=k 1 ?-k 2 ? 2 + k 3 ?. How are factorial design
methods using in QSAR compound selection? Briefly outline how multiple linear regression analysis is
used in the derivation of a QSAR equation. How is cross-validation used for checking the quality of a
regression based QSAR model?

Q3.

(a) Use the example of molecular docking of the antibiotic netropsin to DNA to distinguish
quantitatively the differences between steepest descent and conjugate gradient methods for initial
refinement and stringent minimization. What qualitative conclusions can be drawn about the efficacy
of these two minimization techniques with respect to this docking experiment?

(b) Using two
examples, explain the thermodynamic differences between the Molecular Dynamics and Monte Carlo
methods. What are the advantages to choosing periodic boundary conditions in ANY molecular
simulation of a macromolecule? Use a diagram to plot 4 such periodic cell shapes. What important
class of applied molecular simulations have benefitted from the usage of periodic boundary
conditions?

Armadillo Questions

1. Taking the information on what you have learned in Microbiology, speculate why microbiologists have been unable to cultivate M. leprae in artificial bacteriological medium.

2. Besides acid-fast staining of skin smears, what other methods are used to diagnose leprosy? (Hint:https://www.cdc.gov/leprosy/health-care-workers/laboratory-diagnostics.html)

3. Because the mode of transmission for leprosy is not fully understood, researchers have not ruled out indirect modes of transmission such as contact with contaminated fomites or contaminated clothes and linens. Scientists collected soil samples in areas where leprosy patients were active (e.g. hospitals and resettlement villages for leprosy patients in India). An average of 35% of samples tested positive for the presence of M. leprae. Could contact with contaminated soil play an indirect role in the transmission of M. leprae, causing leprosy? Explain.

4. Google “armadillo recipes.” How is armadillo prepared and eaten? Could undercooked armadillo play a role in foodborne transmission of M. leprae? Explain.

5. Create a small basic world map. Shade/color all countries with endemic leprosy cases.

6. The development of antibiotic-resistant M. leprae is inevitable. Researchers are trying to develop antibiotics that would inhibit the biosynthesis of mycolic acids. Would this type of antibiotic be useful to treat M. leprae infections? Why or why not? Would this new antibiotic be bactericidal to E. coli or Staphylococcus aureus or to Mycobacterium tuberculosis? Why or why not? Do you anticipate this type of antibiotic to be highly toxic to humans? Why or why not?

7. Leprosy can be caused through zoonotic transmission. What is zoonosis? Besides leprosy, what are two other examples of zoonotic diseases? How are these diseases transmitted to humans?

8. The distribution of wild armadillos is expanding farther north. Could climte change play a role in this? Explain your answer. Provide an example of an infectious disease that has expanded into a region linked to climate change. What is the disease, and how is it transmitted?

Suppose samples of six different brands of diet or imitation margarine were analyzed to determine the level of physiologically active polyunsaturated fatty acids (PAPUFA, in percent), resulting in the data shown in the accompanying table. Imperial 14.1 13.6 14.4 14.3 Parkay 12.8 12.5 13.5 13.0 12.3 Blue Bonnet 13.5 13.4 14.1 14.3 Chiffon 13.2 12.7 12.6 14.1 Mazola 16.8 17.3 16.4 17.3 18.0 Fleischmann's 18.1 17.2 18.7 18.4 (a) Test for differences among the true average PAPUFA percentages for the different brands. Use α = 0.05. Calculate the test statistic. (Round your answer to two decimal places.) F = Correct: Your answer is correct. What can be said about the P-value for this test? P-value > 0.100 0.050 < P-value < 0.100 0.010 < P-value < 0.050 0.001 < P-value < 0.010 P-value < 0.001 Correct: Your answer is correct. What can you conclude? Reject H0. There is not convincing evidence that the mean PAPUFA percentages for the six brands are not all equal. Reject H0. There is convincing evidence that the mean PAPUFA percentages for the six brands are not all equal. Fail to reject H0. There is not convincing evidence that the mean PAPUFA percentages for the six brands are not all equal. Fail to reject H0. There is convincing evidence that the mean PAPUFA percentages for the six brands are not all equal. Correct: Your answer is correct. (b) Use the T-K procedure to compute 95% simultaneous confidence intervals for all differences between means. (Round your answers to three decimal places.) Imperial and Parkay Incorrect: Your answer is incorrect. , Incorrect: Your answer is incorrect. Imperial and Blue Bonnet , Imperial and Chiffon , Imperial and Mazola , Imperial and Fleischmann's , Parkay and Blue Bonnet , Parkay and Chiffon , Parkay and Mazola , Parkay and Fleischmann's , Blue Bonnet and Chiffon , Blue Bonnet and Mazola , Blue Bonnet and Fleischmann's , Chiffon and Mazola , Chiffon and Fleischmann's , Mazola and Fleischmann's ,

A1. Determine the concentration of the dissolved B₄O₅(OH)₄^2– in each sample titrated; show a complete calculation for beaker #1.

A2. Calculate K_sp for each borax solution.

A3. Prepare a graph of your results, plotting the two quantities x and y (as defined in the introduction). Label everything clearly! Draw a best fitted line.

A4. Using y=mx+b of your best fitted line, calculate DH° and DS° for this reaction. Make sure to keep track of units, especially for R, so that the units of DH° and DS° work out sensibly.

Q1) What would happen to experimental Ksp if the buret was contaminated with other acids?

My results :

amount of borax: 25.004g

concentration of HCl : 0.2150M

All gruop info.

QUESTION 5

1. The replication of DNA requires tRNA to bring nucleotides to the strand of DNA that is being synthesized.

   True

   False

QUESTION 6

1. Which of the following individuals is homozygous for both genes A and B?

   		AABb
   		AaBb
   		AAbb
   		AsBB QUESTION 7

2. A chromosome is a sequence of:

   		genes
   		alleles
   		both A and B are true
   		neither A or B are true

QUESTION 8

1. Different genes:

   		will have different nucleotide sequences
   		will cause the synthesis of proteins that have different amino acid sequences
   		both A and B are true
   		neither A or B are true

QUESTION 9

1. Mitosis produces

   		diploid homologous chromosome pairs
   		haploid homologous chromosome pairs
   		either diploid or haploid homologous chromosome pairs

QUESTION 10

1. A mutation in a gene is always harmful.

   True

   False

QUESTION 11

1. A mutation in the nucleotide sequence of a gene can result in a change in the codon in its mRNA that can result in change in the amino acid in the gene's protein

   		true
   		false

QUESTION 12

1. Which of the following is the best definition of the term “semi-conservative replication”?

   		the duplication of DNA results in a double strand of DNA having one original and one new strand
   		the duplication of DNA results in a double strand of DNA having two original strands
   		the duplication of DNA results in a double strand of DNA having two new strands
   		none of the above

QUESTION 13

1. During cell division in a eukaryote cell, mitochondria would be inherited by the daughter cells as part of

   		interphase
   		cytokinesis
   		meiosis
   		mitosis

QUESTION 14

1. By definition, the two chromosomes in a non-sex determining homologous chromosome pair have the same sequence of:

   		genes
   		alleles
   		both genes and alleles
   		neither genes or alleles

QUESTION 15

1. How many alleles determine an individual's specific phenotype?

   		one
   		two
   		three or more

QUESTION 16

1. Mutations can create variation in a species because mutations can create new alleles.

   True

   False

QUESTION 17

1. If a species has 20 pairs of homologous chromosomes, the number of chromosomes in a diploid cell of this species is:           

   		10
   		20
   		40
   		no way to tell based on the information given

QUESTION 18

1. Which cellular process(s) results in the formation of paired homologous chromosomes?

   		mitosis
   		meiosis
   		fertilization
   		mitosis and fertilization

QUESTION 19

1. Alleles for certain genes when they are heterozygous in an individual may produce a phenotype in which either allele does not fully mask the expression of the other allele resulting in a phenotype that is somewhere between the phenotype of the two alleles.

   True

   False

QUESTION 20

1. Autosomes are chromosomes that determine the sex of an individual.

   True

   False

QUESTION 21

1. An individual that has the dominant phenotype for a gene will have which of the following genotypes:

   		homozygous dominant
   		homozygous recessive
   		heterozygous
   		homozygous dominant or heterozygous

QUESTION 22

1. If the genotype of an individual is Ff for a trait, some of its gametes will have the F allele and some of its gametes will have the f allele.

   		True
   		False

QUESTION 23

1. Which of the following is part of cellular division (replication)?

   		meiosis
   		cytokinesis
   		meiosis and cytokinesis
   		none of the above

QUESTION 24

1. a Punnett Square can be described as a matrix that gives all of the possible genotypes (allele combinations) for a gene from a mating when given the genotypes (alleles0 of the parents for the gene.

   True

   False

QUESTION 25

1. Complementary base pairing in DNA means that adenine can only pair with guanine and thymine can only pair with cytosine.

   True

   False

QUESTION 26

1. Before a mutation a strand of DNA has the sequence: A-T-T-C-G. After a mutation it has the following the sequence. A-A-T-C-G. What type of mutation did the DNA strand undergo?

   		deletion
   		addition
   		substitution

QUESTION 27

1. If a cell is haploid, its number of chromosomes will be equal to its number of chromosome pairs.

   True

   False

QUESTION 28

1. An individual that is homozygous for the sex determining chromosome is:

   		male
   		female

QUESTION 29

1. When DNA undergoes a mutation:

   		a nucleotide base can be added, deleted or substituted
   		the resulting protein’s adaptiveness may increase, decrease, or not change
   		both A and B are true statements
   		neither A or B are true statements

QUESTION 30

1. Evoution can be described as:

   		a change is phenotype over time
   		a change in allele frequency or alleles over time
   		both A and B are true statements
   		neither A r B are true statements

True/False Directions: Read the following sentences. If the statement is true, place a “T” in the blank preceding the number. If it is false, place an “F” in the blank and then rewrite the sentence in the space provided beneath so that it is true. The first one is done for you as an example. ___F__ 1. The American Medical Association is responsible for creating the universal claim form known as the CMS-1500. The Health Care Financing Administration is responsible

1.The Centers for Medicare and Medicaid Services (CMS) initiated changes to promote uniformity in healthcare claim submission by adopting standards for electronic health information transactions

2. The intent of HIPAA’s Administrative Simplification legislation was to provide consumers with lower healthcare costs.

3. Roster billing of Medicare-covered vaccinations for multiple beneficiaries must be submitted electronically.

4. The HIPAA Administrative Simplification Compliance Act (ASCA) prohibits the Department of Health and Human Services (HHS) from paying all claims that are not submitted electronically, without exception.

5.HIPAA allows providers who conduct business electronically to use their own established healthcare transac tions, code sets, and identifiers.

The Mercantilist and Physiocratic economic schools of thought are the earliest recognizable school of thought in human history.

a) Identify a similarity and a difference between those schools of thought.
Your answer needs to provide at least two paragraphs.
The first paragraph discusses the similarity between these schools of thought.
The second paragraph discusses the difference between these schools of thought.

b) Discuss the economic idea or thought that you have found the most interesting from any of these schools of thought or their thinkers. Explain your reasoning.

c) Identify a local/global problem or a positive aspect in current societies that might be caused by an economic policy that is based on an economic concept that was originally identified by the Physiocrat School of Thought.

Your answer needs to provide at least two paragraphs.
The first paragraph discusses the local/global problem or a positive aspect in current societies.
The second paragraph explains how the concept that you identified is causing the problem or the positive aspect.

Answer all the questions in well developed paragraphs. The paragraphs should be at least five or six sentences long, and they should clearly include a topic sentence.

The Mercantilist and Physiocratic economic schools of thought are the earliest recognizable school of thought in human history.

a) Identify a similarity and a difference between those schools of thought.
Your answer needs to provide at least two paragraphs.
The first paragraph discusses the similarity between these schools of thought.
The second paragraph discusses the difference between these schools of thought.

b) Discuss the economic idea or thought that you have found the most interesting from any of these schools of thought or their thinkers. Explain your reasoning.

c) Identify a local/global problem or a positive aspect in current societies that might be caused by an economic policy that is based on an economic concept that was originally identified by the Physiocrat School of Thought.

Your answer needs to provide at least two paragraphs.
The first paragraph discusses the local/global problem or a positive aspect in current societies.
The second paragraph explains how the concept that you identified is causing the problem or the positive aspect.

Answer all the questions in well developed paragraphs. The paragraphs should be at least five or six sentences long, and they should clearly include a topic sentence.

Gene linkage. Study the fly experiment with b and vg. How would you figure out the expected frequencies of genotypes and phenotypes? Which are the recombinant phenotypes, and which are parental? How do you know if the loci are linked? What is the recombination frequency of unlinked loci? Which of Mendel’s laws is violated by gene linkage?

Linkage maps: What determines whether two loci are linked? How were the fruit fly linkage maps constructed? Could the whole human genome be shown on one linkage map? If not, how many maps would it take?

Sex-linked genes

Contrast X vs. Y chromosome. How are alleles on X & Y inherited differently from alleles on autosomes? Study the two examples of X-linked inheritance – from mother and from father.

Epigenetic inheritance: imprinting. Prader-Willi vs. Angelman: the same chromosomal deletion has different effects when inherited from father or mother.

Organelle genes. Why is a disorder such as Leber hereditary optic neuropathy not inherited in a Mendelian fashion?