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Biochem and microbiology work

biology multi-part question and need the explanation and answer to help me learn.

First complete this biochem assignment Purpose:
This assignment allows you to practice making up your own “test questions” as a study method for practicing your problem solving skills.
This discussion format allows you and your peers to help check each other’s calculations, gives you additional problems for problems, and to get feedback on the clarity of your work and calculations (e.g., are your peers able to follow your logic and your calculations?)
The ability to provide and respond to constructive feedback are skills that are critical for working with any team in laboratory, clinical, or administrative careers.
On a piece of paper (or on your tablet), do the following:
Choose ONE of the following amino acids (which have ionizable R-groups): Arg, Asp, Cys, Glu, His, Lys, Tyr
Look up the structure of your AA and the three pKas (α-COOH, α-NH3+, and the R-group) for your chosen amino acid.
Write the equilibria equation for the dissociation of your amino acid. Draw out the structure of each ionization form (skeletal structures or Fisher projections are ok.)
Label each ionization form with its net charge using the correct nomenclature (e.g., Gly+, Gly0, Gly-)
List/write down the pKas for the 3 ionizable groups (α-COOH, α-NH3+, and the R-group) for your chosen amino acid. Calculate the isoelectric point (pI).
Choose a pH between 2-13 that is NOT equal to any of the pKas of your amino acid AND which we did not do in class nor on the study questions.
Calculate the net charge on EACH ionizable group at this pH. Write out ALL your equations (e.g., Henderson-Hasselback) and calculations for the α-COOH, α-NH3+, and the R-group OR explain your justification briefly (e.g., when shortcut is used). Show all your work and/or calculations clearly in a step-wise manner so a reader can follow your logic and calculations.
Calculate the TOTAL net charge for your amino acid at your chosen pH. Show your work and highlight or draw a box around your final answer.
Calculate the ABSOLUTE net charge for your amino acid at your chosen pH. Show your work and highlight or draw a box around your final answer.
See Table 4.1 in your textbook (also on p. 8 of your lecture notes) for the amino acid pKas. There are several questions in lecture notes and in the study questions/problems for this unit. Please also watch the Panopto recording of Calculating Net Charge for any AA and given pH.
THen please complete the attached documents (this exact documents don’t give me a new one) for week 6 please use this article
Requirements: N/a
TBIO301 – Week 5 Reading Guide: Chapter 9 Genetics of Bacteria and Archaea Instructions: answer the questions below as you read Chapter 9 of the Brock textbook. This assignment replaces our weekly reading quiz and will be graded for completion. Key information is highlighted here and not everything will be covered in class. Topics/questions are listed in the order that they appear in the text. Do not simply google the answers! This assignment is meant to guide your reading and help you take notes. Answer in your own words. Intro (p 262): List four major categories of processes that contribute to genetic diversity in prokaryotes: Part I (Mutation): Definitions (describe in ~1 sentence that you can understand): Wild Type Strain: Mutant Strain: Genotype: Phenotype: Screening ( of mutants…p. 264): Selection: Auxotroph: Relationships between terms defined above (answer in 1-2 sentences…explain your answer!) Can a single prokaryotic species have more than wild type strain? How are mutants related to the wild type? Are they the same species? How do they differ? Do mutant strains always differ in phenotype from the wild type strain? Do mutant strains always differ in genotype from the wild type strain?
Is nutritional auxotrophy the only phenotype that mutants can be screened for (if not, give some other examples, if so, explain why)? Type of Mutations Choose the process(es ) where mutations occur: DNA replication, transcription, translation Choose the process(es) where mutations have can impact the final product: DNA replication, transcription, translation Define the terms below (in your own words, ~1 sentence): Silent Mutation: Nonsense Mutation: Missense Mutation: Frameshift Mutation: Reversion: Suppressor Mutation: List three possible initiators of damage to DNA that can lead to permanent changes (mutation) of the DNA sequence: How does the SOS repair system in bacteria sometimes cause mutations (answer in ~2 sentences): Part II Gene Transfer in Bacteria List the three major types of mechanisms that facilitate gene transfer in bacteria: What is genetic recombination in general terms (1 sentence in your own words)? What is homologous recombination and how does it contribute to genetic diversity in prokaryotes (~2 sentences)? What is exchanged/provided when a mutation is ‘complemented’?
Transformation Which of the molecules below is taken up by cells when genetic transformation occurs? mRNA a viral particle only plasmid DNA any free DNA A cell can do what when it is considered ‘competent’? DNA enters the cell during natural transformation through _________. Choose the correct option below: Simple diffusion through lipid bilayers Facilitated diffusion through specific DNA binding proteins *note that we also can manipulate bacteria that are not naturally competent to undergo transformation in the lab by temporarily altering the permeability of their cell envelopes! Transduction DNA is shuttled between bacteria by ____________ during transduction. The viral particles responsible for generalized transduction do/do not (select one) contain viral DNA. Previous host DNA/viral DNA (choose one) recombines with the new host genome during generalized transduction. During specialized transduction, viral particles can/cannot (select one) replicate. Define the terms below Prophage:
Lysogeny: Page Conversion: How are genes moved from one cell to another via specialized transduction (summarize in ~2 sentences)? Conjugation What is a plasmid (what type of macromolecule is it made of? Is it double of single stranded? Is it linear or circular? What types of genes does it encode?)? At the start of conjugation one/both (choose) cells contain a plasmid encoding the proteins required for replication and transfer of the plasmid. Describe the role of pili in conjugation (1-2 sentences): Describe rolling circle replication (p 280 in 1-2 sentences): Why is rolling circle replication needed during conjugation? Hfr strains are formed when _______________ occurs between the new host chromosome and the transferred plasmid. How do Hfr strains occasionally generate new F-plasmids (new chromosomal genes included on them)? Why is horizontal gene transfer in archaea poorly studied (answer in 1-2 sentences)? Transposable Elements Define transposable element (in 1-2 sentences):
What is the function of a transposase (1 sentence)? How do geneticists use transposable elements to study gene function (example: figure 9.35), summarize in 2-3 sentences? CRISPR (answer each in 1-2 sentences) What does CRISPR protect bacteria against? Where do the spacer sequences in the CRISPR/Cas9 pathway come from? What do the Cas proteins bind to? How does Cas protein binding to spacer sequences target incoming foreign DNAs? What happens to incoming foreign DNAs when Cas/spacer complexes bind?

TBIO301 – Week 6 Reading Guide This week we will discuss the article cited below during our Thursday class session. Please read the article and do your best to answer the questions below before our class discussion. Article: Nick JA, Dedrick RM, Gray AL, et al. Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection. Cell. 2022;185(11):1860-1874.e12. doi:10.1016/j.cell.2022.04.024 Introduction What is a bacteriophage? What does a lytic bacteriophage do to its host? What is Mycobacterium abscessus? Is it a common pathogen? Does it disproportionately impact a certain subset of patients? Which tissues does it most commonly reside in? Fig. 1 Description of Bacterial Infection(s) and Pathology – Clinical Summary A) What is shown in panel A? What does ‘NTM’ stand for? How many patients were involved in this study? What does n = 155 indicate? B) What is FEV1 (% pred.), the Y-axis, as highlighted in panel B? How does FEV1 change over time? C) What is shown in panel C? D) What is shown in panel D? E) Initial infection: how was this window determined? F) What was the observed relationship between Mycobacterium abscessus negative cultures and phage treatment? Do the results shown in panel F indicate that the phage treatment targeted other bacteria as well? G) Were there any differences between the sensitivities of different methods used to detect bacteria in lung tissues removed at the time of transplant? Summarize the clinical data shown here. What is the most important take-away?
Fig. 2 Choosing Therapeutic Phages A) How was efficacy of phages determined here? Which of the phages in panel A look to be most effective against the pre-treatment isolates? Why was Mycobacterium smegmatis also tested here? Did M. abscessus isolates from the post-treatment period show altered sensitivity to the phages? B) What is shown in panel B and what can we conclude from this experiment? C) Does panel C provide any new information not in B? Why was this included? D) How were the ‘survivor’ strains obtained? Are they sensitive to the therapeutic phages? Summarize what is shown here. What is the most important take-away? Fig. 3 Lung Changes Over Course of Phage Therapy A) What change was observed over time in panel A? B-D) What are bronchiectasis and mucoid impaction? How are they measured here and did they change in different regions of the lung over the course of treatment? Summarize what is shown here. What is the most important take-away? Fig. 4 Culture Independent Markers of Bacterial Killing by Phage A) How did the fraction of positive sputum cultures change after phage treatment and transplant? B) Why was the amount of ‘DNA’ in sputum measured? Was this total DNA in the sputum or DNA from a specific source? How did the DNA content in sputum reported here change over time? C) What is LAM? What is TBSA? What is D-ara? Why were TBSA and D-ara content in urine measured? How did these things change over time? D) What is IgA (immunoglobulin A)? What is IgG (immunoglobulin G)? Why are IgA and IgG levels over time measured here? How do IgG and IgA levels change after the onset of phage treatment? Summarize what is shown here. What is the most important take-away? Fig. 5 Genetic Diversity and Antibiotic Resistance of M. abscessus Isolates A) And B) Why are there certain gene names written on this phylogenetic tree? Were the sequences of the whole genomes of the isolates used to construct this phylogenetic tree? How did genetic diversity of the M.a isolates change over time? B) How was antibiotic resistance evaluated here and what do the data points on the plot in panel C represent? How does antibiotic resistance of isolates change over time?
Summarize what is shown here. What is the most important take-away? Fig. 6 Evaluating Antibody Binding to Phages *Antibodies are host (in this case human) proteins that bind to foreign substances (such as microbial proteins) and to facilitate their recognition and destruction by the immune system. -Why were the authors interested in whether or not the human host was mounting an immune response to the phages? Can a phage infect human cells? A) Did the production of IgG that binds to phage proteins change over time? How do you know? Connect your conclusion to the data shown in panel B. Discussion and Future Directions What was interesting about this study? Were there any clear short comings to this study? Explain. What would you do next if this were your research?