During replication of the viral genome, distinct classes of nucleic acids are produced that are different than those normally present in an uninfected cell. Many of these are recognized as PAMPs. What are the unique features of foreign nucleic acids that are recognized by innate receptors? Identify and describe one of these receptors, its cognate nucleic acid ligand, and the general mechanism by which it alters gene expression.

1. All of the following are true of receptor kinases except:

2. During protein synthesis, a protein is made in which direction?

3. What type of molecule is ATCAGCTAG?

4. In the lytic cycle:

5. Which of the following organisms would be expected to have the largest genome size?

6. For a protein to be inserted into the endoplasmic reticulum membrane:

Answer the following questions using the sequence given below.

Non-template DNA 5’ – ATG CGT TCG TTA TGG CTG CTT – 3’

1. Provide sequence of template DNA

2. Provide sequence of mRNA

3. Provide sequence of tRNA anticodon for the 3rd triplet

4. Provide the sequence of the amino acid encoded by the mRNA

5. What is the effect on the amino acid sequence as a result of each of the following mutations?

substitution of T for G at position 8

addition of T between positions 8 and 9

deletion of C at position 15

substitution of T for C at position 18

deletion of GAC at positions 16-18

Which of the mutations above produces the greatest change in the amino acid sequence?

In clinical studies, Inulin and para-amino hippuric acid given intraveneously until steady state is reached in a 70 kg man. Once steady state was reached, the following measurements were collected: arterial plasma concentration of inulin 0.18 mg/ml, of paraamino hippuric acid 0.21 mg/ml; renal venous plasma concentration of para-amino hippuric acid 0.0014 mg/ml; urine flow 2.2 ml/min; urinary concentration of inulin 11.0 mg/ml, of para-amino hippuric acid 5.5 mg/ml. Calculate the renal venous concentration of inulin.

Total Body Water = 42L

Extracellular Fluid = 14L

Osmolarity = 300mOsmoles/L

Intracellular Fluid = 28L

Enzyme concentrations are often characterized by 'units' of activity per volume.

One enzyme we will be using, Sbfl, is supplied in a concentration of 10,000 units/mL

a. How many are there in 1 uL?

b. How much volume would you need for 20 units?

c. We have 500 units total, how much volume is that?

Enzyme catalysis catalyzes the breakdown of H2O2. Data are:

If the concentration of the enzyme is 4.0x10- 9 mol / L, plot the data from the data and calculate the Michaelis constant and turnover number to find the maximum starting speed?

What kind of enzyme is chymotrypsin? What are the specific substrates of chymotrypsin?

• What features of chymotrypsin make it specific to particular substrates ?

• Can you describe the main features of the reaction mechanism?

• What is a catalytic triad and what is its role in the active site of chymotrypsin?

• What is an acyl-enzyme intermediate?

• What is conformational selection vs. “induced fit”?

Pyruvate Dehydrogenase is a huge multi-enzyme complex in which substrates are channeled from one enzyme to the next. In fact, recent evidence suggests that many citric acid cycle enzymes may interact pass substrates along the pathway and that the components of the electron transport chain associate into an electron transfer super complex. What are the advantages of such an arrangement?

For hemoglobin and myoglobin, discuss the mechanism, similarities, differences, and effects of O₂ binding on the enzymes. What happens to the enzyme structure, and what do these structural changes then cause in terms of functional changes, if any? What role does BPG play for the enzyme and why would this be the case? What about H⁺? How does a baby breathe in the womb?  

**Biochemistry**

Clearly explain how the structure of hemoglobin is intricately connected to its function, using the principle listed below as the outline.

• NCFs rule everything from the structure of biomolecules, to protein ligand binding to enzyme catalysis. (consider protein folding, binding dissociation constants, enzyme mechanisms where binding energy reduces activation energy, etc.)