Download Exam 4 Review Sheet posted 10/18/12

Exam 4 Review Sheet
AP Biology
Exam 4 will cover:
Chapter 5 – Proteins to the end
Chapter 6 – Intro to 6.2
Make sure you look at ALL the questions in all chapters as well as bold words,
headings and figures, the PowerPoint, and this review sheet.
**I posted a macromolecule review chart online.
41. What is the monomer of the protein, how many are there, what makes each of these
different, how are they similar and how are they grouped (the three groups)? Can you
draw any two of them yet and connect them via dehydration synthesis (condensation
reaction)?...you need to be able to do this.
42. Where does the “amino acid” get its name from?
43. Why do I feel that proteins are the most important class of macromolecules (they are
all important of course)?
44. Compare an amino acid, dipeptide, polypeptide, and protein.
45. Describe how a dipeptide is formed (Figure 3.13). What do we call the bond that links
them? How is this analogous to what happens with carbohydrates?
46. Describe the three groups of amino acids. Which group has the acidic and basic ones?
47. What determines the structure of a particular protein? Explain why. Of course, the
structure then determines the…
48. Explain why a change in the DNA might lead to problems.
48.5 Know sickle-cell anemia example really well. You should be able to use this
example to convince to me that mutations can be both positive and negative. Really well!
49. Describe in general terms what happens to a polypeptide (or any polymer for that
matter) when you eat it. What happens to it, what do you do with it, etc…
50. Describe the four levels of protein structure. I could ask another 15 questions about
each level… Know all the details we went over in class like when the side chains come
into play or when only the backbone is involved, hydrophobic vs hydrophilic side chains,
where different types of side chains are located in proteins typically, etc…
50.5. All alpha helices are right or left handed? This is because they are made with…
51. Explain why these levels of structure have little to do with actual protein folding in
the cytoplasm.
52. Explain, starting with a gene, how a protein is formed. Make sure you include items
like mRNA, tRNA, ribosome, nuclear pore, RNA polymerase, amino acids, nucleus,
etc… Basically, describe the central dogma.
53. Be able to identify the various secondary structure elements in a protein and circle
them if presented with a ribbon diagram.
54. Explain how a ribbon diagram is generated. What are you looking at when you view a
ribbon diagram of a protein – (these are the colorful diagrams with sheets shown as
arrows and helices are cartoon-like spirals)?
55. Compare and contrast a polypeptide to a protein. When are they the same and when
would they be different?
56. What is meant by a subunit in a protein?
57. Explain what is meant by denature and renature. How and why do proteins denature?
You must be very specific. You cannot just say a lower pH than the protein evolved in
will cause it to denature…the question is WHY.
58. Know the functions of proteins. Know examples like hemoglobin, myosin, insulin,
insulin receptor, ATP synthase, photosystem II, antibodies, HIV protease, etc… and
under what category they would fall.
59. How small is a protein relative to the size of a cell? (use the analogy) How many
hemoglobin proteins are packed into a single red blood cell? How many red blood cells
do you have on average? How many oxygens can your blood carry if it were completely
saturated with oxygen?
60. Why are some people considered to be lactose intolerant? What does this mean and
why is it a problem?
61. Are glycogen, starch and cellulose the only three polysaccharides found in
organisms? Explain.
62. What is the fate of glucose? Basically, what do organisms use glucose monomers for?
Why do we store them? Where do humans store them?
63. If there is too much glucose in your blood, how does your body handle this? Where
does it end up? Where might this surge in glucose have come from?
64. For every polymer we eat (disaccharides, polysaccharides, polypeptides, etc…), we
need to have a ___________________ somewhere in our digestive tract to hydrolyze it.
This may seem obvious, but we eat cells (unless you are eating processed food, which
case the cells have already been destroyed and broken apart) of other organisms. There
we eat macromolecule or at least polymers for the most part. We need to hydrolyze them.
Why? Why not just keep them together?
65. Know who Linus Pauling was and what he did…
67. Identify kingdoms with organisms that have cell walls and the composition of these
walls in each.
68. Describe what 3.4 and n+4 mean in terms of alpha helices.
66. Describe the structure of a nucleotide.
67. How many different nucleotides are there that will build RNA and DNA? Be able to
draw them all the way we discussed in class. For example, I could ask you to draw dAMP
or AMP or dCMP etc… or I could ask you to draw an RNA nucleotide containing a
purine base, etc…
68. How do the purines differ structurally from the pyrimidines in general? Know the
names of the bases and to which group they belong, purine or pyrimidine.
69. Draw the ester, diester, phosphoester and phosphdiester functional group.
70. Explain how two nucleotides can be connected together to form a dinucleotide and so
on. You should be able to draw this. What type of linkage is formed? Why do we give it
this name?
71. Compare and contrast a DNA nucleotide to an RNA nucleotide (how are they the
same/different?).
72. What is the overall charge of DNA and why?
73. Describe the ink and the paper analogy for nucleic acid.
74. Describe the backbone of DNA. What do we call the backbone?
75. What is the optimum temperature, pH and salt concentration of proteins? (Explain
why this is a trick question).
76. How would the optimal pH of a protein in the stomach differ from that of a protein in
the blood?
77. Explain what happens to the polymers we are constantly eating. Where did most the
monomers that make up these polymers ultimately come from? (This will require some
logical thinking)
78. How would you define a lipid.
79. How are lipids chemically different from the other three classes of macromolecules?
80. Identify the four types of lipids discussed in class. Be able to draw each type as we
discussed in class.
81. How do unsaturated and saturated fatty acids differ structurally? How does this
change how they behave relative to each other?
82. Where does one find unsaturated fats in nature? What about saturated fats?
83. What does the term “hydrogenated vegetable oil” refer to? Give an example of
hydrogenated vegetable oil that you might find in the supermarket.
84. Describe why saturated fats tend to be solid at room temperature while unsaturated
fats tend to be liquid.
85. Identifty the functions of triglycerides in nature. Where are they found (what type of
cell and what location in humans)? What is the name given to the two general types of fat
in humans? Which is more prevalent in males? Females?
86. Compare and contrast a phospholipid to a triglyceride (What is similar and what is
different?).
87. Describe the function of phospholipids in nature.
88. Why do phospholipids tend to always have one kinked fatty acid (one kinked tail)?
89. Define the term amphiphilic.
90. How does the term amphiphilic relate to phospholipids and why is this an important
property of these molecules?
91. Be able to draw the two structures discussed in class that will result if you take moles
of phospholipids and add them to water. Know the names of the two resulting structures.
Which of these structures would be similar to a cell membrane?
92. Describe the general function of cell membranes in the cell.
93. Describe the structure and function of waxes in nature. Identify at least two places
where you would find them, one in plants and one in animals.
94. Describe the general structure of a steroid and give at least four examples in humans.
95. One example of a steroid is cholesterol. Describe the two functions of cholesterol in
our cells that we spoke about in class, and indicate how the structure of this molecule
determines its function.
96. What is a hormone? Which class of macromolecule and which subclass of a second
class can act as hormones in the body?
97. What is a hormone?
98. We learned that steroids can act as hormones (so now you know that protein amino
acid based molecules and steroids can act as hormones - signaling molecules that allow
cells to “talk” to each other that are not typically located near each other). Indicate the
three types of steroid hormones we discussed in class and describe their function in the
body.
99. Why does one not need to ingest cholesterol to survive?
100. How is cholesterol linked to the steroid hormones?
101. Describe Chargaff’s experiments and why the results were critical in determining
the three-dimensional structure of DNA.
102. Chargaff used a technique known in general terms as paper chromatography.
Describe how to do and the purpose of paper chromatography in general. For example, if
I gave you a solution containing a mixture of various food colorings, how might you
separate them? Explain how paper chromatography works.
103. Describe the three-dimensional structure of DNA.
104. Why is it important that the base pairs of DNA be held together by hydrogen bonds
as opposed to using covalent or ionic bonds?
105. One of the DNA strands is typically called the “complementary” strand. Why do you
think this strand was given this name?
106. What do I mean when I say that the strands of DNA are anti-parallel?
107. Be able to label the ends of the DNA strands (5’ and 3’) and be able to explain why
the ends are given these names.
108. Describe the function of DNA in organisms.
109. Explain the charge of DNA.
110. How does the structure of DNA compare to that of RNA? (Three major differences)
111. Identify the three types of RNA discussed in class and give their function.
112. Describe how the cell is able to make polypeptides using the information that is
encoded in the DNA. Be able to describe it both using the analogy and using the actual
terms. Be sure to include the following words: DNA, mRNA, tRNA, rRNA, protein,
RNA polymerase (why is this enzyme called RNA polymerase?), ribosome, polypeptide,
amino acids, library, paper, transcribe, translate, nuclear pores, nuclear membrane,
guards. You should be able to make a sketch of this process.
113. The process described above is known as “The Central Dogma” of molecular
biology. What does this mean? (google it)
114. Why is the nucleus NOT NOT NOT (just incase you didn’t see the first NOT) the
control center/brain of the cell?
115. We discussed the RNA world hypothesis in class. Describe why it is logical to
hypothesize that RNA was used by the most primitive of cells before the evolution of
DNA and protein. What specific evidence do we have that supports this? (I discussed two
major pieces of observational evidence) Why couldn’t protein have come first or DNA
have come first?
116. Why do you think protein and DNA exist today? Why aren’t organisms still solely
based on RNA? Use the term natural selection in your answer to these questions.
117. What is the name given to a stretch of DNA that codes (stores the information for)
for mRNA, tRNA or rRNA?
118. How are tRNA’s and rRNA’s made?
119. Describe the structure of the ribosome. What is it made of?
120. Where do the amino acids that our cells use to build polypeptides come from? Yes, I
know they are in the cytoplasm, but before that…
121. List each macromolecule class and identify where you would find each in a cell. The
next step is going to be to put these molecules together and build a cell. You should have
the basic location and function down before we start getting into details.
122. How many pieces of DNA (“books”) are found in a human nucleus? If you attached
all those pieces end to end, how long would the DNA be? Discuss the size of DNA in
terms of actual size and the MSG analogy. What do we call each piece (“book”)? How
many unique books are there? Explain.
123. Describe the Madison square garden analogy and be sure to include every
macromolecule class (the rope, the straight pin (a phospholipid), the baseball, the head of
a pin (a glucose molecule))
124. Explain why hydrophilic molecules like proteins, amino acids, carbohydrates,
nucleic acids, etc… are NOT able to move through a plasma membrane, while small
hydrophobic molecules can.
(Why do you think large hydrophobic molecules have trouble crossing?)
125. Why do think amino acid based hormones require a cell surface receptor protein to
tell the cell what to do (talk to the cell), while steroid hormones typically have protein
receptors inside the cell, in the cytoplasm?
126. Compare a phospholipid bilayer to a phospholipid monolayer. Which would make
up a cell membrane and why is this a logical choice (why would the other not work as a
cell membrane?).
1. Study the Prokaryote vs Eukaryote Chart under notes section
2. Study the Organelle Chart under notes section
3. What is the name of the artist who painted the painting shown in the PowerPoint?
What do art historians believe this is a painting of? Explain.
4. Describe the significance of the Dutch microscopist Anton van Leeuwenhoek (16321723) and the English Robert Hooke (1635 – 1703). Describe cell theory and identify the
three scientists accredited with this theory and their contributions.
5. Explain why hydrophilic molecules like proteins, amino acids, carbohydrates, nucleic
acids, Na+, other salts, etc… are NOT able to move through a plasma membrane, while
small hydrophobic molecules can. Why do you think large hydrophobic molecules have
trouble crossing?
6. What is a hormone? Give an example and include the origin of the hormone, the target
organ, and the affect on the body. Why does this hormone not target any other cells when
it is all over the body?
7. Explain why amino acid/polypeptide/protein hormones require a cell surface receptor
(embedded in the membrane) protein in order to send a signal to the cell (talk to the cell),
while steroid hormones typically have protein receptors inside the cell, soluble in the
cytoplasm?
8. Compare and contrast the three different types of microscopes we learned about. How
are they similar? How are they different? What are the advantages and disadvantages?
How are samples prepared for each? Magnifications? Resolutions? Know when to use
each if you were working in a lab.
9. Identify and describe the different types of light microscopes available. Explain how
the fluorescent microscope works – give a real like example.
10. What is the definition of resolution? What is a better resolution, 5um or 120nm?
Explain why.
10.5 Be able to calculate the magnification of a light microscope knowing the ocular and
objective magnifications.
11. You should be able to calculate either the FOV under high power, FOV under low
power, high power magnification, or low power magnification when you know three of
the four variables. Sample questions are in the PowerPoint.
12. Explain what happens to the size of the FOV under high power as compared to low
power. Why does this happen? Why can one not use a ruler under high power to measure
the FOV?
13. Explain the orientation of an object as viewed through a microscope as compared to
its orientation on the slide itself. Check out the virtual microscope under the misc section
on the lab page if you don’t recall what happens to the letter “e”.
14. Describe how to prepare a wet mount.
15. Describe how you would estimate the size of an object under low power if you know
the FOV diameter.
16. Explain how to focus a light microscope under high power beginning with placing the
slide on the microscope.
17. How many microns in a millimeter? How many nanometers in a micron? How many
nanometers in a millimeter? Be able to convert. Draw a ruler indicating a meter as we did
in class and show the definitions of mm, um and nm using the picture by breaking the
distances up into a 1000 equal lengths each time.
18. Give a structure-function example in terms of cells.
19. Explain why cells are limited in how big a cell can be. Be sure to discuss the surface
area to volume ratio. Use an example to show your reasoning.
20. What limits how small a cell can be?
21. Be able to label prokaryotic and eukaryotic cells.
22. Compare and contrast prokaryotic to eukaryotic cells. Be able to explain the function
and location of every structure.
29. Compare and contrast chromatin, chromosome and DNA?
30. How many chromosomes (books) are there in a human nucleus? Are all of these
books completely different/unique? Explain. Where did your chromosomes come from?
31. Explain why I call cytoskeletal elements an example of extreme quaternary structure.
32. Make a chart that details the organelles present only in animal cells vs. those that are
present only in plant cells.