SARS-CoV2 is a coronavirus that infects the cells of the mammalian respiratory epithelium. To replicate it needs to take over the host cells secretory pathway to generate essential viral proteins. You are working to try and find a treatment for this virus. Answer all the following questions related to the virus and the secretory system:

a) You discover that the virus needs to insert a protein called ‘Spike’ into the plasma membrane for newly formed viral particles to be infectious. The RNA for Spike is in the cytosol. Describe briefly SIX key steps for how the Spike protein gets into the plasma membrane.

b) You determine the sequence of the Spike protein and identify the following amino acid sequence motifs. What is the function of each sequence (i) Asn–X–Ser/Thr (ii) A long stretch of hydrophobic residues near the centre of the sequence. (iii) Asp-X-Glu (Di-acidic sequence)

c) The Spike protein also contains a sequence you recognise as a cleavage site for an enzyme called Furin. You know Furin cleavages can activate other pro-proteins. What does this tell you about Spike?

d) To infect epithelial cells the SARS-CoV Spike protein binds to a receptor on the plasma membrane and is endocytosed. Describe THREE key steps that are essential in this process.

e) Reading back over Questions a-d, name a protein you could target in a treatment for COVID-19 and explain why you chose it.

QUESTION 1

1. Every  eukaryotic cell

   	A.	contains a prokaryotic cell
   	B.	has a cell wall composed of cellulose that serves as the outer boundary of the cell
   	C.	possesses flagella and cilia, unlike prokaryotes
   	D.	has its genetic material concentrated in a membrane-enclosed nucleus
   	E.	contains  all of its genetic material in mitochondria

1.5 points   

QUESTION 2

1. A codon is

   	A.	a type of DNA repair enzyme
   	B.	a sequence of nucleotides that makes up a whole gene
   	C.	the part of the ribosome to which mRNA attaches
   	D.	a form of birth control for male or female
   	E.	a sequence of three nitrogenous bases on mRNA that corresponds to an amino acid

1.5 points   

QUESTION 3

1. A disorder of the nervous system in which the individual has an inflammation of the layers that surround the brain is called:

   	A.	meningitis
   	B.	lactose intolerance
   	C.	overnutrition
   	D.	Encephalitis
   	E.	shingles

1.5 points   

QUESTION 4

1. A molecule used by the body in a Specific Response is an immuniglobulin (I _gG), it is a class of  molecules known as

   	A.	NK cells
   	B.	CD 8 cells
   	C.	CD4 cells
   	D.	antibodies

1.5 points   

QUESTION 5

1. A neuron at rest has a charge difference across its cell membrane, with the interior of the cell negative relative to the exterior. This difference in charge across the plasma membrane is referred to as ________ membrane potential

   	A.	graded
   	B.	action
   	C.	depolarization
   	D.	refractory
   	E.	resting

Some photosynthetic Cyanobacteria can fix N2 to NH4 + (using the enzyme Nitrogenase) when they are otherwise starved for nitrogen. They sense nitrogen starvation by sensing an excess of the amino acid Glutamate (Glu) within the cell. If there is adequate nitrogen, much of the Glutamate is converted to Glutamine (Gln), so that the [Glutamate] remains low.

A. SKETCH the photosynthesis system in a typical aerobic Cyanobacterium. Be sure to show how O2 is involved, and how the three main forms of energy are generated.

B. When the [Glu] gets too high, the genes for Photosystem II are shut off, and the Nitrogenase genes are turned on. Assume that the Nitrogenase genes are under Negative control, and the PS-II genes are under Positive control. Make sketches showing how [Glu] affects both of these operons. Then explain each regulatory scheme in words. Be sure to label the regulatory proteins (‘A’ for activator and ‘R’ for repressor protein).

C. On your diagram from part (A), show and explain how turning off the genes for Photosystem II will affect the photosynthetic electron flow in this Cyanobacterium? Why is it important to turn off Photosystem II before the cells produce Nitrogenase?

D. Nitrogen fixation by Cyanobacteria (even with the normal regulation, as described above) is a lot more effective if the Cyanobacteria are grown in co-culture with nitrifying bacteria. Explain why the co-culture with nitrifiers helps with the process of nitrogen fixation.

Give the IUPAC name for each of the following carboxylic acids.

Discuss the functions of teichoic, dipicolinic acids chitin in microorganisms.

Fatty Acid Degradation

a) Cells with decreased glucose 6-phosphate dehydrogenase activity are more sensitive to oxidative stress because?  

b) What cellular conditions typically enhance fatty acid degradation?

c) What molecule transports fatty acids into the mitochondria?

d)  Hydroxybutyrate and acetoacetate are both ketone bodies derived during the degradation of fatty acids. How are ketone bodies used by the body?

what does endonuclease mean compared to enzyme?

Deficiency of this mitochondrial enzyme impairs heme synthesi

8. You discover an enzyme that catalyzes the reaction: AMP →

→→ → IMP + NH2. Based
on your experiments, you determine that the KM for substrate AMP is

3.0 µ

µµ µM and the kcat = 0.5 sec-1. At 8.0 mM AMP, you determine that the velocity of

the reaction is 0.6 µ

µµ µM/min. What was the concentration of total enzyme, [E]total,

used in this experiment?