1.The procedure used to align many sequences at the same time is called: *

• diversity sequence alignment
• multiple sequence alignment
• local alignment
• multiple statistical alignment
• substitution matrix alignment

2.The method of alignment that tries to align regions with high level matches without considering the alignment of the rest of the sequence is called: *

• global alignment
• multiple sequence alignment
• local alignment
• multiple statistical alignment
• high level matching alignment

3.The type of sequence alignments that is most suited for finding conserved patterns in DNA or protein sequences is called: *

• global alignment / multiple sequence alignment
• local multiple alignment
• local alignment / multiple polymorphism search
• multiple statistical alignment
• high level matching alignment

4. An outbreak of pneumonia has occurred. This outbreak appears to involve a family who had attended a family gathering and wedding ceremony. The samples from the patients were then tested by PCR using the primers for 16S rRNA and RT-PCR using primers for SARS and SARS-CoV-2 coronaviruses. Select statements that are TRUE pertaining to the case involving this family. The sequence of the amplified fragment from the PCR is provided here: AACACGGAGAGTTTGATCCTGGCTCAGAACTAACGCTGGCGGCGCGTCTTAAACATGCAAGTCAAGCGGAGTAGCAATACTCAGCGGCGAACGGGTGAGTAACACGTGGGTAATCTTCCTCTGAGTCTGGGATAACTTTCCGAAAGGGAAGCTAATACTGGATGGTCCCGAGAGATCACAAGATTTTTCGGGTAAAGATTTATTGCTCGGAGATGAGCCCGCGTCCGATTAGCTAGTTGGTGAGGTAAAGGCTCACCAAGGCGACGATCGGTAGCCGGCCTGAGAGGGTGTTCGGCCACAATGGAACTGAGACACGGTCC ATACTCCTACGGGAGGCAGCAGTTAAGAATCTTGCTCAATGGGGGGAACCTGAAGCAGCGACGCCGCGTGAACGATGAAGGTCTTCGGATTGTAAAGTTCAGTAAGCAGGGAAAAATAAGCAGCAATGTGATGATGGTACCTGCCTAAAGCCACCGGCTAACTACGTGCCAGCAGCCGCGGTAAAACGTATGGTGCAAGCGTTGTTCGGAATCATTGGGCGTAAAGGGTGCGTAGGCGGACATGTAAGTCAGGTGTGAAAACTGCGGGCTCAACTCGCAGCCTGCACTTGAAACTATGTGTCTGGAGTTTGGGAGAGGCAAGTGGAATTCCAGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCAGTGGCGAAGGCGACTTGCTGGCCTAAAACTGACCCTGAGGCACGAAAGCGTGGGTAGTGAACGGGATTAGATACCCCGGTAATCCACGCCCTAAACGTTGTCTACCAGTTGTTGGGGGTTTTAACCCTCAGTAACGAACCTAACGGATTAAGTAGACCGCCTGGGGACTATGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGTCCGCACAAGCGGTGGAGCATGGTGGTTTAATTCGATGATACGCGAAAAACCTCACCTAG GCTTGACATGGAGTGGAATCATGTAGAGATACATGAGCCTTCGGGCCGCTTCACAGTTGCTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCACCTTATGTTGCCATCATTCAGTTGGGCACTCGTAAGGAACTGCCGGTGACAAACCGGAGGAAGGCGGGGATGACGTCAAATCCTCATGGCCTTTATGTCTAGGGCAACACACG *

• The pathogen is a type of coronavirus.
• The physician can inform the family that they are suffering from a disease called leptospirosis.
• The patients should be quarantined because they have COVID-19
• The pneumonia is due to a bacterial infection.
• The pneumonia can be treated with antibiotics.

5.Your research group has just completed the genome sequencing for a new bacterial species named V. novela. This newly sequenced genome has not yet been annotated. Your colleague has been studying the VTOX protein in E. modeli for many years and is interested in finding out whether a homolog for the VTOX protein can be found in the bacterial species V. novela. Select the options that are TRUE that can be used to provide an answer to your colleague.

• Do a blastn against the PDB database.
• Use the blastp program with the VTOX protein as the query to search the UniProt database.
• Use the VTOX protein sequence as a query for the tblastn program to search the V. novela genome as the database.
• Search the E. modeli database using tblastn and the VTOX protein as the query.
• Carry out a gene prediction for the V. novela genome and use the resulting genes as blastx queries to search a protein sequence database.

HOMEWORK 8

- In your own words, describe the process of DNA replication

-In your own words, provide a detailed description of how DNA is packaged in the nucleus (10 pts).

-Identify the process and detail the steps of transcription from start to finish (In your own words) (10pts)

-RNA is derived from DNA by what process and which major enzyme? (5pts)

-What determines if a gene is functional (5 pts)

-How do mutations occur in cells? Further list 3 things that can increase the rate of mutations (10 pts)

For the following question, please answer in essay format( a page and half long minimum)( if hand written please print legibly and be clear about which part of the question are answering, in complete sentences, with as much detail as possible. Thanks!

Describe the Embden-Meyerhof pathway found in most eukaryotic cells. List all ten enzymes needed for this metabolic pathway, along with their substrates (include the number of carbon atoms in each substrate), products (include the number of carbon atoms in each product), and any high-energy molecules generated or consumed by each enzyme.

Which of the following is most accurate about DNA replication and transcription/translation (central dogma)?

Select one:

a. DNA replication and transcription/translation produce the same molecules.

b. DNA replication occurs in some cells, while transcription/translation occurs in virtually all cells.

c. The same enzyme is responsible for DNA replication and transcription/translation.

d. DNA replication occurs in virtually all cells, while transcription/translation occurs in some cells.

e. DNA replication occurs in somatic cells while transcription/translation occurs only in gametes.

Identify each statement in all questions of this section as T (for true statements) or F (for false statements). Each statement is worth one mark.

17. Eukaryotic mRNAs contain a poly(A) tail at the 3'-end, but the template DNA encoding the mRNA does not have poly(T)s. Identify the statements as true or false.

1. The poly A tail is formed by RNA polymerase
2. The poly A tail is formed by DNA polymerase II
3. The poly A tail is formed by poly A polymerase
4. The polyA tail is formed by reverse transcriptase
5. The enzyme that makes poly A tail is a template-independent polymerase

Medical Microbiology Lab Report 36

DNase Test

Name__________________________________ Date _________________

Draw your plate or take photos of your plate before and after the addition of HCl.

Before      After

S. aureus E. aerogenes S. aureus E. aerogenes

Interpretation and Questions:

Which organism secreted DNase?

Why would an organism’s ability to produce this enzyme be clinically significant?

S. aureus is a common component of the biota of the skin and nasal passages. What steps should be taken by the dialysis unit described in the case file to minimize nosocomial infection in its patients?

Unlike liver cells, muscle cells do not secrete glucose into the blood. What about glucose-6-P prevents its secretion and how do liver cells overcome this problem?

McArdle’s disease (also called glycogen storage disease V) is a genetic disorder in which muscle cannot make functional phosphorylase. Speculate as to why McArdle’s patients show muscle fatigue (tiredness) with even moderate exercise.

McArdle’s disease is inherited as a recessive trait. Consider the activity of the phosphorylase enzyme and suggest an explanation for the recessive nature of this disease.

In muscle, creatine phosphate is used to store high-energy phosphates. Creatine phosphate is made by the reaction

creatine + ATP « creatine phosphate + ADP.

The standard free energy change for this reaction, ?G?, = +11.7 kJ/mol. How is it possible for the muscle to produce creatine phosphate if the standard free energy change is so unfavorable?

      A. The reaction is catalyzed by an enzyme.

   B. The ATP concentration in the cell is high compared to the concentration of ADP.

C. The ADP concentration in the cell is high compared to the concentration of ATP.

      D. The reaction is kinetically favored even though it is thermodynamically unfavored.

      E.None of the above.

For the following question, please answer in essay format( a page and half long minimum)( if hand written please print legibly and be clear about which part of the question are answering, in complete sentences, with as much detail as possible. Thanks!

Describe the tricarboxylic acid cycle (Krebs cycle) found in most eukaryotic cells. List all nine enzymes needed for this metabolic pathway, along with their substrates (include the number of carbon atoms in each substrate), products (include the number of carbon atoms in each product), and any high-energy molecules generated or consumed by each enzyme.

In an attempt to create a biological battery for energy storage, you examine the possibility of incorporating a rare enzyme that facilitates the phosphorylation of 3-phosphoglycerate (3PG) in the presence of H+ to form 1,3 bisphosphoglycerate (1,3-BPG). The delta G for this enzymatically driven process is +59.6 kj/mol.

A.) Draw the reaction scheme for 3PG to (1,3-BPG).

B.) is this a spontaneous or nonspontaneous reaction?

C.) What is the Keq under standard biological conditions, based on the delta G value above?

D.) What effect should raising the pH habe on the free energy of the reaction?