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Excerpts from the paper “Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria” are presented below. Consider an Ivy residue that forms a salt bridge with a complementary charge in the lysozyme active‑site rim. Which paired mutation is most likely to preserve inhibition?

The excerpts below were obtained from a 2022 Journal of Biological Chemistry publication called “Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants”. The paper reports that Omicron P132H mutations leave nirmatrelvir potency largely unchanged. What structural rationale is most consistent with this finding?

The excerpts below were obtained from a 2022 Journal of Biological Chemistry publication called “Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants”. In Figure 2, nitrogen atoms are colored blue, sulfur atoms are colored yellow, and oxygen atoms are colored red. Nirmatrelvir is known to form a reversible covalent bond to Cys 145. What is the side chain of Cys that is involved in the formation of the covalent bond?

No answers on this exam should be written as a decimal unless stated.  Express any fractions in lowest terms, not as mixed fractions. Keep any radicals.  Must show work using algebra – not calculator! Make sure to work in a single column.  Clearly mark the question number and part (a, b, c, etc.), if applicable.  Circle or box your final answer.  Keep track of time.  This is written for a normal 1 hour and 50 minute class and you have a time limit of 2 hours and 10 minutes.  That is PLENTY of time to scan and upload.  THERE IS A 5 POINT PER MINUTE DEDUCTION FOR LATE EXAMS.  If you run out of time, please make sure to email me the pdf of your exam as soon as possible. 

What type of growth is this an example of? 

Excerpts from the paper “Structure and evolution of the Ivy protein family, unexpected lysozyme inhibitors in Gram-negative bacteria” are presented below. If a key Ivy residue that donates a hydrogen bond to a catalytic residue in lysozyme is mutated from Ser to Val, which outcome is most likely?

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Contrast the three types of gated channels.

What stage in the Demographic Transition Model demonstrates a population growth rate close to 0?

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