Download AICE Biochemistry Applications Guided Reading

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AICE Biochemistry Applications Guided Reading
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Cambridge Text: Pages 407 – 440 (Chapter 28: The chemistry of life)
Brown Lemay: Pages 1080 – 1096 (Chapter 25.6 – 25.10: The Chemistry of Life)
1. Draw out the generic structure for an amino acid using “R” to represent the functional side chain.
2. Which type of macromolecule is composed of amino acids? What type of bonds holds the amino acids
together in these molecules? By which process are these bonds formed? Draw out the reaction
mechanism using 2 generic amino acid structures (R + R') as the reactants.
3. Draw out the structures of the 20 essential amino acids that occur in living organisms. Below each
structure also list the single letter and three letter abbreviations for these amino acids.
4. Amino acids are amphoteric, what does that mean?
5. How is the structure of proline different from that of the other amino acids? How does this effect the
structure of the larger molecules it is in?
6. What is the primary structure of a protein? Explain what it determines/affects and how it is described.
7. What are the two primary types of secondary structures in proteins? How are they different from one
another?
8. What type of intermolecular forces stabilizes the alpha-helix structure? Between what groups do they
form?
9. What type of intermolecular forces stabilizes the beta-pleated sheet structure? Between what groups
do they form?
10. What type of secondary structure exists in collagen? Which amino acid is the most common in this
structure?
11. What are the four stabilizing forces in tertiary structures? List them in order from strongest to
weakest.
12. Which amino acids do disulfide bonds form between? How are these bonds important to protein
structure?
13. How does the strength of the hydrogen bonds in tertiary structures compare to those in secondary
structures? What amino acids can participate in this type of interaction?
14. What types of amino acids form salt bridges? Name the amino acids that can participate in this type of
interaction (and indicate in which manner they behave).
15. Which type of amino acids commonly participate in van der Waals interactions in proteins? Name the
amino acids that are able to participate in this type of interaction.
16. What are quaternary structures? Give an example of an important biological molecule with a
quaternary protein structure.
17. What are two ways that enzymes are different than inorganic catalysts?
18. Outline the steps in an enzyme catalyzed reaction by the “lock and key” model.
19. How is the “induced fit” model different from the “lock and key” model?
20. How do competitive inhibitors work? What relation does the inhibitor generally have to the intended
substrate? What is the effect of greatly increasing the substrate concentration?
21. How are non-competitive inhibitors different from competitive inhibitors? What is the effect of
greatly increasing the substrate concentration?
22. Sketch diagrams that illustrate the effects of competitive and non-competitive inhibitors on the
structure and function of enzymes.
23. How are small molecules (or ions) that can bond irreversibly to enzymes dangerous?
24. What is the temperature range in which most enzymes possess activity? Why does activity drop off
suddenly above this temperature range for most enzymes?
25. Why do shifts in pH from their “optimum range” often result in loss of activity for enzymes?
26. Other than changing the pH of the solution, what are two other ways to chemically denature an
enzyme?
27. What are cofactors, prosthetic groups, and coenzymes? List three enzymes that require the presence of
a prosthetic group to function (include which ion).
28. Which type of macromolecule is composed of nucleotides? What are the three components of a
nucleotide? What type of bonds holds the nucleotides together in these macromolecules? Sketch a
diagram of the general block structure of DNA for a minimum of 3 base pairs (see Figure 28.31 for a
general idea).
29. Draw the complete structures for the 5 (not a typo) nitrogenous bases found in nucleic acids. Indicate
where the hydrogen bonds will form between adenine and thymine, adenine and uracil, and guanine
and cytosine. What other intermolecular force stabilizes the structure of DNA?
30. Proteins called histones wrap up DNA strands when they are not being replicated or transcribed. What
is special about the primary structure of the histone proteins? Why is this important when it comes to
winding the DNA into tight coils?
31. Outline the general process of DNA replication. In which direction is DNA replicated? What special
accommodation must be made in order for the complimentary strand to be replicated?
32. What is the difference between DNA and RNA? Draw the structures of the sugars. What are the three
major types of RNA and their abbreviations? What are the functions of these three types of RNA?
33. What is a gene? In what direction are genes read from a strand of DNA?
34. Outline the steps of transcription.
35. What is a codon? How many different codons are possible using the bases in the human genome?
What is the sequence of the start codon? What are the sequences of the stop codons?
36. Where does translation occur? Outline the steps of translation. In which direction are polypeptide
chains formed?
37. What is a mutation? Is it possible for a mutation to result in no change to the protein that it codes for?
Mutations to what codons are generally considered the most serious?
38. Explain how a genetic mutation results in the disease sickle cell anemia. (Include information about
how the mutation affects protein structure and function)
39. What type of mutation results in the disease cystic fibrosis?
40. Considering what you have read about the secondary and tertiary structures of proteins, how can the
change of a single amino acid in the primary structure result in a different overall structure?
41. Broadly speaking, what cellular processes require energy in the form of ATP? Where in the cell is
ATP synthesized?
42. Draw the structure for ATP. Indicate on your structure which bond is broken when ATP is hydrolyzed
to form ADP.
43. Normally we would expect that breaking bonds would be an endothermic process, explain why
breaking the phosphate bonds in ATP releases energy. Why is ATP hydrolyzed in the presence of
enzymes? How much ATP can be produced through the complete metabolism of 1 mole of glucose?
44. What four cations play important biological roles in the body? With what processes are they
associated?
45. What is the maximum number of molecules of oxygen that haemoglobin can bind to at once? Explain
why carbon monoxide is poisonous in terms of its relation to haemoglobin.
46. What important enzyme does the zinc ion act as a prosthetic group for? Outline the role of Zn+2 in the
reaction catalyzed by carbonic anhydrase. (We will learn about nucleophiles in the Spring).
47. On which side of the cell membrane are Na+ concentrations highest? On which side of the cell
membrane are K+ concentrations highest? Why is ATP needed for active transport? Outline the steps
in the transmission of nerve impulses. (Start with “The nerve is stimulated”)
48. How are heavy metals concentrated in living organisms? Why do organisms higher in the food chain
typically have higher heavy metal levels than organisms lower in the chain? What are common
sources of mercury in the food chain? What are common sources of lead in the food chain?