All of the following are true regarding a neurotransmitters Except:

a) they can generate a postsynaptic potential

b) they may be taken up through the membrane of the postsynaptic cell

c) they may diffuse away from the synapse

d) they may be degraded by an enzyme in the postsynaptic cell’s membrane

e) they may open a chloride ligand gated channel

2) Testosterone, estradiol (estrogen) and cortisol are all made from

a) eicosanoids

b) thromboxane

c) chains of amino acids

d) triglycerides

e) cholesterol

Part II – Resistance

Among the first antibiotics used on a large scale was penicillin, which was discovered in 1929 by Alexander Fleming.  It was finally isolated and synthesized in large quantities in 1943. Penicillin works by interfering with the bacterial cell wall synthesis. Without a cell wall, the bacterial cells cannot maintain their shape in changing osmotic conditions. This puts significant selective pressure on the microbes to evolve, as they cannot survive the osmotic stress. Any microbe that can resist these drugs

will survive and reproduce more, making the population of microbes antibiotic resistant.

The specific mechanism of penicillin is the prevention of cell wall

synthesis by the ß-lactam ring of the antibiotic (Figure 3), which binds and

inhibits an enzyme required by the bacterium in this process.

The enzyme is called penicillin-binding protein (PBP), even though it is an

Enzyme involved in cell wall synthesis. Normally enzymes have names that

indicate what they do and end in the suffix -ase, like lactase, the enzyme

that breaks down lactose. Figure 4 is a representation of PBP and its active

site.

Bacteria cell walls are layered structures, where each layer is made of peptidoglycan, a sugar and protein polymer. Each layer is cross-linked to the next, strengthening the wall and allowing the cell to resist osmotic pressure. The way the enzyme PBP works is to form those cross-bridges by joining strings of amino acids together in the active site, which is a groove in the protein (Figure 5).

The PBP takes amino acid residues attached to peptidoglycan layers and forms

Brides between the within the active site groove. This cross-linking, or cross-

bridging, stabilizes and strengthens the cell wall. ß-lactam antibiotics interfere

with the PBP enzyme by binding to the active site, blocking the site from the

amino acids (Figure 6).

There are over 80 natural and semi-synthetic forms of ß-lactam antibiotics, including cephalothin and methicillin. Vancomycin also interferes with cell wall synthesis, but its mechanism of action is to bind directly to the cell wall components (Figures 7 and 8).

The first MRSA case was discovered in 1961 in a British hospital, and was the result of a mutation in the enzyme normally inhibited by the ß-lactam ring of methicillin. The site where the antibiotic would bind no longer allowed access to the ring, so the enzyme continued to function normally. The microbe acquired a new gene that, when made into protein, was a different version of PBP, one that couldn’t be inhibited by penicillin.

Question

4. What is the difference in how ß-lactam antibiotics and vancomycin work?

Most amino acids are coded for by a set of similar codons. Provide an explanation for why amino acids are associated with such closely related codons?

What would be the expected orientation of an amphipathic alpha helix occurring in a globular protein in aqueous solution?

Select one:

a. Hydrophilic amino acids are complementary to hydrophobic amino acids, so the hydrophilic side of the alpha helix should be facing toward the hydrophobic core of the protein.

b. A soluble protein will have mostly hydrophilic amino acids in its core, so the helix will be arranged to have the hydrophilic side facing toward the core of the protein.

c. A soluble protein will have lots of hydrophilic amino acids on its surface, so the helix will be arranged to have the hydrophilic side facing toward the outside of the protein.

d. A soluble protein will have a hydrophobic core and a hydrophilic surface, so hydrophilic and hydrophobic amino acids will be equally distributed in the helix.

QUESTION 41

1. Where does synthesis of the product actually begin in Transcription?

QUESTION 42

1. What molecule or enzyme mediates the process of Translation?

QUESTION 43

1. Which of the following accurately lists the steps of Transcription?

QUESTION 44

1. Where does synthesis of the product actually begin in DNA Replication?

QUESTION 45

1. What attracts or directs the synthesis enzyme to the template in DNA Replication?

QUESTION 46

1. Which of the following enzymes is NOT involved in DNA replication?

QUESTION 47

1. What is the substrate for Translation?

QUESTION 48

1. How is synthesis terminated in Translation?

QUESTION 49

1. DNA replication is called semiconservative because ________________ of the original duplex appears in the duplex formed in replication.

QUESTION 50

1. What is the product of Translation?

1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

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1. (14 pts) Central Dogma – DNA to protein questions
   1. Think about the general flow of genetic information in living organisms. Summarize the three steps of the central dogm
   2. Imagine that a DNA section of the gene that codes for the enzyme phosphofructokinase read 3’ – TACTGGCGC-5’ What would be the resulting messenger RNA strand and why?

3. Use the codon chart above to answer this question. From left to right list, the exact amino acid chain that would be formed? (write the amino acids out in order).

4. Imagine that a mutation added an extra base was added at the start of the strand, so the strand now rea 3’-GTACTGGCGC-5’. How would this affect the outcome? Would a chain of amino acids still be created?

5. Imagine, a malfunction occurs in a cell.   The cell is no longer able to regulate the H₃O⁺ levels inside the cell, the amount of H₃O⁺ increases. Note you will have to call back on information from previous chapters (Ch 3, Ch 5) to answer this
   1. What would happen to the pH? Explain
   2. Which part of the central dogma steps would be most affected and why?
6. Why do genes code to make proteins, why don’t genes code to make carbohydrates, or fats, or nucleic acids? How do the proteins function in the body?
7. Imagine that a mutation occurred in the last codon in the DNA sequence from part B. Instead of 3’ – TACTGGCGC-5’ the DNA read 3’ – TACTGGTGC-5’.
   1. How would the amino acid sequence change? Explain how the mutation would or would not have an effect on the function of phosphofructokinase. You will need specific details relating to the chemistry of the molecules.
   2. How and why would a change in phosphofructokinase impact the health of the person with this mutation? Explain in details

Which of the four elements of secondary structures are NOT dependant on intra-chain hydrogen bonding?

1. Alpha Helices

2. Beta Loops

3. Beta Sheets

4. Beta Turns

2. What would be the expected orientation of this protein's alpha helix?

1. Hydrophilic amino acids are complementary to hydrophobic amino acids, so the hydrophilic side of the alpha helix should be facing toward the hydrophobic core of the protein

2. This protein will have mostly hydrophobic amino acids in its core, so the helix will be arranged to have the hydrophobic side facing toward the core of the protein

3. This protein will have a hydrophobic surface, so hydrophobic amino acids will be arranged facing the outside of the helix

4. This protein will have a hydrophobic core and a hydrophilic surface, so hydrophilic and hydrophobic amino acids will be equally distributed in the helix

3. If a protein is heated enough to disrupt weak interactions, will this have a greater impact on the primary or secondary structure? Explain your reasoning.

4.Where in a cell might a protein, with its amphipathic alpha helices oriented so that amino acids such as leucine and phenylalanine are pointing toward the OUTSIDE of the protein, be found? Explain your reasoning

What is false?

Describe how changing one amino acid in an enzyme could affect the function of that enzyme. Be sure to include in your answer how this change could affect the various levels of protein structure and function. Be specific with a concrete example of the change e.g. hydrophobic amino acid for a hydrophilic amino acid, or an ionic amino acid for a neutral amino acid. (Terms you want to include in your answer- active site, lock and key model or induced fit model- i.e. how does change in 3-d structure effect function of the enzyme).