Exam 2 Q2 Review Sheet
Honors Biology
This is to be used for REVIEW
Exam2 Q2 will cover:
Chapter 5: ALL
Your Resources
1.
2.
3.
4.
5.
6.
7.
Your notes from class
Your textbook with bold words and figures especially
The powerpoint
Dr. T’s notes
The misc section of the website with assorted tutorials (watch these)
This review sheet
The internet in general
ENERGY and the laws that govern its transfer
1. What is energy?
2. Describe the two major types of energy and give examples.
3. Identify and describe the two forms of potential energy (PE) discussed in class. You
should be able to explain the connection between the four forces of the universe and
energy.
4. What gives a substance like glucose energy?
5. Describe the first law of thermodynamics. Why can’t I create energy (why can’t I give
something the ability to accelerate without losing some of my own energy)?
6. Know the difference between renewable and nonrenewable resources and be able to
explain the function of these resources: Life is all about accelerating matter in a
controlled way. You accelerate yourself to school, yourself to class, yourself during
sports, in your cars, etc… Think about it, someone who is great at sports is simply
someone who is very good at accelerating himself or herself or some other object like a
bat or a ball into the proper position at the proper time. It is all about controlled
acceleration. If you can figure out a way to accelerate matter like electrons through wires,
your car, airplanes, etc… cheaply and efficiently without generating tons of pollution,
you will be the savior of this planet. We currently use mostly coal, oil, and natural gas
(burn them  electron rush to oxygen generating heat and light  use the heat to turn
things and push electrons; they are all chemical PE) and nuclear energy (nuclear power
plants). These are non-renewable resources because we are using them faster than they
are being made and burning them produces CO2, which is a greenhouse gas, among other
chemicals (recall acid rain section of book). Renewable forms of energy (a resource
being replaced faster than we are using it) include solar energy (we are not so good at this
yet), wind (wind turbines), rivers (dams), the tides, the heat of the Earth below our feet
(geothermal energy), timber (wood), and ethanol made from corn (look up E85 vehicles
(E85 means 85% ethanol). Basically, anything that has KE or chemical PE that we can
transfer in a controlled way to move electrons in wires (electricity) or to power engines,
etc....
7. Describe all the energy transfers that occur starting with you standing next to a tennis
ball on the floor, you pick up the ball, you drop it, it bounces a few times and eventually
stops. Make sure you describe where the energy started and where it went throughout
(follow the ability to accelerate).
8. What does the 1st law of thermodynamics tell us about the total energy in the universe?
9. Describe the second law of thermodynamics and the implications of this law in terms
of entropy.
10. Explain why if I throw a ball to you, 100% of the energy that I put into the ball is not
transferred to you. Where does some of it go?
11. Explain why your shoes, clothes, ipod, cell phone, computer, dishwasher, oven,
refridgerator, car, wii, xbox and everything else will eventually fall apart in terms of the
2nd law. Do not just say that things get more disordered with every energy transfer. Why
does this happen?
12. What is order? Disorder? Why does matter tend to “disorder” with energy transfers in
terms of probability?
13. What does the 2nd law tell us about our own life? What will happen to the DNA in our
cells over time regardless of how well our enzymes are at repairing it?
14. The 2nd law also dictates that energy goes from concentrated to dispersed. Likewise, it
goes from useful to less useful. Give an example of this in your life. Be very specific.
15. How are we able to generate the desired or ordered state if the universe is always
getting more disordered? What has to be generated whenever order is generated?
16. In order for your proteins to keep yourself ordered, you have to take in food. Some of
this food will be burned in cell respiration and the energy transferred into ATP as
discussed in class. Why do we need to keep eating in order to maintain order in our
bodies? For all the order your body maintains, you must be generating more disorder
around you. Explain how this is happening. Where is the disorder? How is your body
generating disorder around you as you sit here and read this?
17. Why can’t we win? Why can’t we continue to maintain the ordered state and live
forever?
18. If you wanted to preserve something that you love like a doll, how would you do this
and why?
19. What is the core energy source for 99.9% of life on this planet? Basically, if I track
back my body’s ability to accelerate, where did this ability come from? Explain in
general terms how you got this ability form that source.
20. We concluded in class that we are constantly fighting the 2nd law of thermodynamics
whether it is fixing items that break, buying new items to replace broken ones, or trying
to prevent items from breaking like putting those rubber cases around ipods and iphones,
or painting your house every so many years, etc... Our bodies are doing the same thing:
our proteins are constantly repairing their homes (cells), and certain cells that have too
much damage and are thrown out (apoptosis), you have enzymes that eliminate toxic
chemicals to prevent damage, and your cells will divide to replace those that have been
lost. All of this repair and maintenance requires matter to be accelerated in a specific
manner and therefore requires energy (ATP). The point of saying this is that it appears
that the 2nd law is terrible, but there is a silver lining. Without random changes in our
DNA evolution would not happen and we would never change, but more importantly, we
would never be here in the first place… Love it and hate it.
21. Why is reproduction so important in light of the 2nd law of thermodynamics?
22. Compare and contrast endergonic to exergonic reactions. Under which would you put
the overall reaction of photosynthesis? Cell respiration? Explain both.
23. Compare the PE of the reactants to the products for the two reactions (endergonic and
exergonic). For example, ATP  ADP + Pi ; This reaction is exergonic as the phosphate
on ATP has the ability to accelerate (you should know why). Therefore, energy is lost to
somewhere. Where does the energy (ability to accelerate) go? (It is not in the ADP and Pi
because: do these have the ability to accelerate?)
24. Describe what is meant by energy coupling.
25. The energy in question 23 must go to another substance(s) in an energy coupled
reaction. Maybe the phosphate jumps on a protein causing a conformational change. The
protein now has the ability to accelerate back to its original state when the phosphate is
hydrolyzed off.
26. What happens when you reverse an endergonic reaction like putting a phosphate onto
ADP? What type of reaction do you get?
27. Explain the following energy coupling examples (identify the exergonic process and
the endergonic process): 1. lifting a book off the ground, 2. Dropping the book, 3. Water
moving through a dam spinning turbines, 4. A gas powered engine, 5. Active transport
using a transporter protein like in figure 5.18, 6. Electrons moving from glucose to
oxygen allowing a phosphate to be placed on ADP to make ATP.
28. Explain fire (burning wood). Follow the energy flow.
29. Be able to draw the structure of ATP.
30. In class we said that one glucose can be used to make 36 ATP molecules. Compare
the amount of energy in the glucose to that in the 36 ATP.
31. Why use ATP? Why not just use glucose or amino acids or triglycerides or sucrose or
fatty acids directly?
32. How efficient is the production of ATP from glucose? What law of thermodynamics
does this observation support? Explain.
33. Which yields more ATP, glucose or triglycerides? Explain why.
34. After the third phosphate of ATP has been transferred to a protein, causing a
conformational change, what is the fate of the resulting ADP?
35. How many ATP are used per second per cell? 10,000,000 per cell per second on
average. That means this many are made and used per second!
36. Identify at least five endergonic reactions in the cell that must be powered using the
exergonic reaction of ATP hydrolysis.
37. Why do we breathe in air for molecular oxygen (O2)?
38. Describe the three major fates of the food that you eat. Which are exergonic and
which are endergonic?
39. Are glucose and triglycerides the only molecules you can use as an energy source?
Explain.
40. Exergonic reactions are spontaneous, while endergonic ones are not. You should
know what this means and why.
41. In class we determined two major problems with chemical reactions in terms of life.
First is that exergonic reactions typically happen way too __________________. The
second is that the desired reaction may not be the reaction that occurs. We said that
glucose + glucose + glucose… typically results in the formation of glycogen in animal
muscle and liver cells. However, this only happens if the glycosidic linkage is formed
between carbon 1 and carbon 4 of the two glucose molecules. Therefore, cells need…
HOW ENZYMES WORK
42. What is an enzyme?
43. Explain why enzymes CANNOT, by themselves, catalyze endergonic reactions like
putting a phosphate onto ADP. What would this enzyme need to allow this reaction to be
catalyzed?
44. What reaction does carbonic anhydrase catalyze? What is the rate per enzyme? What
cofactor does this enzyme require? How is this cofactor held in place?
45. What is activation energy? If you push a boulder off a cliff and it falls 300 feet
smashing a car below, what was the activation energy? Explain activation energy in terms
of lighting a match.
46. Explain how enzymes lower the activation energy of a reaction. Be specific.
47. Be able to describe the activation energy graph (Fig. 5.5B). You really should be able
to draw this.
48. Describe how an enzyme works starting with the binding of substrate(s) to the release
of product(s). Use the general overview of enzyme catalysis review slide.
49. Compare the lock and key to the induced fit model of enzyme catalysis. Which is the
current model? Why does this one make more sense? (You can use the hexokinase
example).
50. Construction workers use hammers in order to catalyze the specific reaction of
hammering nails into wood. This is analogous to what in proteins?
51. Describe the two types of cofactors and give examples of each.
52. Discuss the structure and function of hemoglobin. Where is it located? How many per
cell? Etc… What cofactor does hemoglobin require to function? Explain why if you do
not get enough iron in your diet, you will become anemic (have a reduced ability to carry
oxygen in your blood) on the molecular level.
53. When you eat, you are basically eating for monomers to build with (biosynthesis) and
to burn for energy. However, you also need the so-called vitamins and minerals. What are
these? How do they relate to protein cofactors?
54. Aside from heme and Zinc, we discussed two other cofactors, NAD+ and FAD. What
vitamins are required to synthesize these cofactors. Describe the structure of NAD+ and
FAD. You should know the full name of each. Describe how their names are related to
their structures. Describe the function of these two cofactors.
55. Read the recap slide 195. Make sure you have this down.
56. What is an enzymatic reaction rate? What factors affect reaction rates? You should
know all five factors discussed. I could ask you to graph for example the rate of a
reaction as I increase substrate concentration etc…
57. Sometimes we revert back to illogical reasoning and think that all enzymes function
best at body temperature and pH 7. Explain why this is far from the truth.
58. What would you hypothesize the optimal salt (NaCl) concentration to be for a human
protein? Why?
59. What are vitamins and what are minerals? Describe how they are used in your bodies.
60. Explain why, logically, enzymes or enzyme pathways need to be regulated (need to
be turned on and off). Give examples.
61. Compare competitive to non-competitive inhibitors.
61.5 Describe the other methods of enzyme inhibition/activation discussed in class.
62. We used phosphofructokinase, an enzyme in glycolysis, as an example of enzyme
inhibition. We saw that ATP and citrate both inhibit the enzyme. What I didn’t say is that
we observe AMP to activate the enzyme. Describe the logic behind this (glycolysis is part
of cell respiration - formation of ATP). These inhibitors are an example of what type of
feedback? Explain. – Use the figure in the powerpoint to help you.
63. Explain how enzyme inhibition is taken advantage of by humans to treat disease.
Give a few examples.
64. If you wanted to design an inhibitor of an enzyme of a bacterium that causes a certain
disease and you wanted it to be a competitive inhibitor, what might you try first (what
might you base it on)?
65. Explain how enzymes are typically activated during signal transduction and signal
amplification. What is signal amplification and how does it work?
66. Explain how phosphorylation can be used to both inhibit and activate different
enzymes.
67. What is the name given to the type of enzyme that catalyzes phosphorylation.
68. What is meant by an enzyme pathway? How are enzyme pathways typically
regulated?
69. Compare negative feedback to positive feedback and give examples of both. Which is
more stable (which would you use to maintain homeostasis of some substance?). Explain
why. Make a graph showing both types of feedback with product on the y-axis and time
on the x-axis.
70. How many different substrates can an enzyme typically work on?
71. Describe how pH, salt and temperature will affect enzyme catalyzed reaction rates.
Draw a graph to depict this.
72. Describe how enzyme concentration in the presence of overwhelming substrate
(saturated substrate) affects enzyme catalyzed reaction rates. Draw a graph to depict this.
73. Describe how substrate concentration affects enzyme catalyzed reaction rates. Draw a
graph to depict this.
The Cell Membrane (animation under misc section)
1. Describe the structure of a phospholipid in detail.
2. Indicate how phospholipids align relative to each other in an aqueous solution (we
discussed two ways), explain why they do this, and be able to draw both. Which of these
ways is representative of a cell membrane.
3. This question will be on the quiz: Describe the structure of a cell membrane. What are
they composed of and how are they organized? Be able to draw a two-dimensional
membrane that includes all three types of integral membrane proteins discusses in class,
peripheral membrane proteins, IMP glycoproteins, ECM, cytoskeleton, glycolipids, nonglycosylated phospholipids and cholesterol (This is a combination of figures 5.12 and
5.13).
4. Describe the general functions of integral membrane proteins (Be able to explain Fig.
5.13).
5. Explain the terms enzyme, substrate, and product.
6. Explain the terms ligand and receptor.
7. Explain signal transduction beginning with a hydrophilic (amino
acid/polypeptide/protein) hormone. There is a great tutorial here:
http://bcs.whfreeman.com/thelifewire/content/chp15/15020.html
This tutorial is under misc section of website.
This specific pathway, which is triggered by adrenaline (epinephrine) released from the
adrenal medulla or the adrenal gland in response to some fight or flight external stimulus
(ex. A bear chasing you). Adrenaline is a amino acid based hormone. This particular
animation does not show genes being turned on and off, but remember that they usually
are in response to a hormone signal.
8. What is the difference between a ligand and a substrate?
9. Describe the functions of cell membranes. You should be able to come up with many.
What kinds of molecules are able to diffuse across a plasma membrane that lacks
proteins? How would other types of molecules like amino acids and Na+ cross? Explain
in detail on the molecular level. Do not just say hydrophobic or nonpolar. Saying that the
molecule is nonpolar and the membrane is non polar does not explain anything. Include
the electromagnetic force (charges) in your answer.
10. Describe what is meant by selective (semi-) permeability.
11. Using the analogy of the cell, how thick is the cell membrane? What is the actual
thickness is nm?
12. Describe the fluid mosaic model of membranes. What does “fluid” and what does
“mosaic” refer to? The inner life of the cell video shows this nicely.
13. Just because it comes up in the cell membrane animation, an oligosaccharide is
essentially a carbohydrate polymer ranging from 3 to 10 units long. Oligos is greek for “a
few”. Its a short polysaccharide.
Simple Diffusion (simulator under misc section)
1. Describe the process of diffusion on the molecular level. Why do substances diffuse
from “high to low concentration”? include random motion and Newton’s first law of
motion in your explanation. Draw a picture that shows this.
2. What is meant when one says that diffusion is “passive”? Explain why it is passive.
3. Explain how concentration gradients relate to diffusion. What is a concentration
gradient?
Passive Transport – Diffusion (tutorial under misc section)
1. Explain passive transport (Be able to explain Figure 5.14). Remember that once we say
“transport” we are implying across a cellular membrane.
2. Make sure you understand the difference between the movement of molecules across a
membrane and the NET movement of molecules across a membrane.
3. Looking at figure 5.14A, explain what is happening in the middle image. In which
direction(s) do the molecules of dye move? What is the NET movement? Explain why
this is in detail in terms of likelihood or probability, random motion, the 1st law of
motion.
4. What is meant by “dynamic equilibrium”? What is happening during dynamic
equilibrium and why does this happen? (again…probability and likelihood) Why is it
called “dynamic” “equilibrium”.
5. Explain why when two different substances are placed on either side of a semipermeable membrane they diffuse independent of each other as shown in figure 15.4B.
6. What is osmosis?
7. Explain the process of osmosis in terms of a U-tube (Be able to explain figure 5.15).
8. Compare hypertonic, hypotonic and isotonic solutions. Why can’t a solution be one of
these types if it is the only solution you have?
9. Explain why water always diffuses from hypotonic to hypertonic solution.
10. What does osmoregulation mean and give two examples in nature. Why is it
important that our bodies are able to perform osmoregulation?
11. Be able to explain figure 5.16 in detail. Basically, Compare and contrast what would
happen to an animal cell vs. a plant cell when each is placed in a isotonic solution,
hypotonic solution, or hypertonic solution. You should be able to explain why this
happens on the MOLECULAR LEVEL in terms of concentration gradients, probability,
why the solutes don’t just cross the membrane instead of the water, etc… Put the big
picture together.
12. You should know the terms crenate and plasmolysis and the cell types they refer to.
In which of the three states in this figure are plants most happy? What about animal cells
(most happy)?
13. Explain why if you drink salt water your brain will inform you that you are thirsty.
What is happening to your blood and why would you need to drink water to help
yourself? Also tell me why if you ever get an IV at the hospital the fluid is 0.9% NaCl
(0.9g per 100ml of water). If you were going to make an eye drop solution for people
with contacts, what salt concentration do you think you would use?
For more info read here:
http://en.wikipedia.org/wiki/Saline_%28medicine%29
14. Explain what would happen to a fresh water fish if you put them into a saltwater
aquarium and why?
Passive Transport – Facilitated Diffusion (tutorial under misc section)
1. Explain how a cell moves small hydrophilic molecules across its membrane? What is
the name of this type of passive transport?
2. Give three examples of different types of transport proteins involved in facilitated
diffusion and explain how each works.
Active Transport (tutorial under misc section)
1. Compare and contrast passive to active transport.
2. After a muscle cell contracts, it must remove the calcium from the cytosol back into
the smooth ER. Initially, facilitated diffusion will work until the concentration on either
side of the membrane is similar. However, the rest of the calcium needs to be cleared
from the cytosol. Explain how the cell does this. What is the term used to describe this
type of transport?
3. Draw the structure of ATP? How is it related to active transport (what is the function
of ATP)? Explain why ATP has the ability to accelerate matter. Why do I usually refer to
ATP as a loaded gun? Does ATP have a high or low affinity for its third phosphate?
4. List the following in order from high to low affinity for phosphate: water, protein, ATP
5. After ATP has donated its phosphate to a protein or other substance, it becomes ADP.
If this happened without the reverse reaction, you would run out of ATP in seconds and
die. How does the cell, in very general terms, get that phosphate back on ADP to make
ATP again so that you can keep fueling your proteins?
6. What is the term we use to describe the addition of a phosphate onto a substance?
What about the removal of a phosphate from a substance?
7. New term I want you to know: KINASE. A kinase is obviously an enzyme (notice the
–ase ending) that adds phosphate to substances (catalyzes phosphorylation).
8. Be able to explain exactly what is happening in figure 5.18. Make sure you discuss
conformational changes and affinity for the phosphate. Explain why this allows
molecules to move from low to high concentration (against the concentration gradient).
9. Explain how large molecules enter and exit the cell. Is this active or passive transport.
Explain.
10. You should still be able to go from a gene on a chromosome in the nucleus to a
protein secreted from the cell via the endomembrane system (exocytosis).
11. You should be able to describe the three types of endocytosis discussed in class and
how they differ from each other. Which is the most specific? Explain. Which uses
pseudopods and why not just pinch in? Which use ATP?
12. Why would a cell want to perform endocytosis in general? Where does the vesicle
with the ingested material first go? Explain why. Your white blood cells will do
endocytosis of bacteria, bacterial parts and your own dead cells to clean up and recycle.
Explain.
13. Describe the structure and function of LDL’s. If your blood contains too high a
concentration of LDL’s, describe how your liver can reduce the concentration.
14. Explain the disease hypercholesterolemia and what it could lead to on the molecular
level.
STUDY WELL
“If you always put limit on everything you do, physical or anything else, it will
spread into your work and into your life. There are no limits. There are only
plateaus, and you must not stay there, you must go beyond them.”
-Bruce Lee
Life is just accelerating matter to your advantage.
-Dr. T.