Biology 107 at UConn: Study Guide Feedback

Study Guide Feedback
Last revised: Wednesday, March 6, 2002

Instructor's foreword: As a general rule, I do not provide an answer key for study guides. They are intended to help you in reading the text, and in most cases all the information needed to answer the question is clearly available from the text or from your own efforts. However, I will provide feedback for certain selected questions where there is some ambiguity or where the question causes anxiety.

Study Guide Q & A

1 - Q. 3 Q. What are "emergent properties?"
A. Emergent properties cannot be predicted from knowledge of the component parts alone. For example, knowing that the nervous system is made of neurons does not allow you to predict consciousness; consciousness is an emergent property.
Q. Identify 3 properties of a cell that are not present in cell molecules.
A. Motility, growth, division.
Q. Identify 3 properties of a human being that are not present in cells alone.
Speech, Thought, Dancing.

1 - Q. 9 Q. What are the characteristics of "science" that distinguish it from other ways of knowing?
A. Science is predicated on experimental investigation; to be scientific, a claim should be testable by some form of inquiry. Scientific claims need to be expressed in precise form, and should potentially be falsifiable. Dogmatic claims that cannot potentially be proved false under rigorous inquiry may or may not be true, but they are not scientific and do not belong in scientific literature.
Q. What is meant by the "hypothetico-deductive" method?
A. Scientific activity proceeds by formulating a specific hypothesis about what is being studied, then deducing from that hypothesis what can be predicted to follow if the hypothesis is true, then devising experiments to see whether such predictions are in fact valid.
Q. Is it theoretically possible to prove any hypothesis with absolute certainty?
A. A qualified "no". It is central to scientific inquiry that any hypothesis, no matter how widely accepted, can be potentially proven incorrect. In fact, however, established hypotheses (which may grow into theories as they continue to make successful predictions) are rarely discarded in the face of a few anomalies. Instead, people create new hypotheses to explain the anomalies.

1 - Q. 10 Q. What does the term "theory" mean in science?
A. A theory is a hypotheses with wide explanatory power that has been found to make many hypotheses that have been upheld by observation and inquiry. Examples include broad theories such as the cell theory, evolutionary theory, and more narrowly focused theories such as the chemiosmotic theory (which we will examine when we study how mitochondria work).
Q. How does this differ from everyday usage of this term?
A. In everyday language, a theory is something tentative. "I have a theory about why you lose your keys a lot". By contrast, a fact is something that is true. In science, however, there are no facts, just observed data with measurable error limitations. We link facts by making hypotheses and testing them, and certain hypotheses become so useful that they grow into theories. Theories, in science, represent the highest form of scientific knowledge -- explanatory concepts that have withstood testing in a variety of ways and provide good explanations for certain phenomena.

2 - Q. 6 Q. How does the abundance of elements in the earthąs crust compare with the abundance of elements in living tissue?
A. There is very little correlation. Aside from Oxygen, which is the most abundant element in both the crust and living tissues, the other most abudant elements of life (CHNPS) are present in amounts very different from the composition of the crust. We are not, for example, made of Silicon, which is the second most abundant element on Earth.

2 - Q. 16 Q. How many errors can you find in the following structural formula?
A.

2 - Q. 18 Q. Which of the following covalent bonds is not polar? More than one answer may apply. (a) -C-O- (b) -C-H (c) -C=O (d) -O-H (e) O=O
A. (b) and (e) are non-polar.

2 - Q. 21 Q. Is the shape of a molecule important in understanding its chemistry? Why or why not?
A. In biology, shape is of paramount importance. Almost everything that happens in biological systems is the result of molecular collisions and interactions between biological molecules, especially proteins. Such interactions are 3-dimensionally stereospecific -- precise geometric "fit" is crucial for successful interactions.

3 - Q. 5 Q. Relative to the previous question, imagine an organism whose interior liquid was 70% alcohol instead of water. What effect would this difference have on the organisms ability to dissipate heat generated during metabolism or activity?
A. Alcohol has a much lower specific heat than water. If cells had alcohol as their liquid environment, they would heat up quickly as energy was released, and biological molecules in the cell would denature and stop working effectively as temperatures rose.

3 - Q. 6 Q. Identify four properties of water that are of significance to life.
A. High heat capaciy, adhesion, cohesion, weak ionization

3 - Q. 10 Q. The atomic weights of several elements are: C = 12 daltons; O =16 daltons, H =1 dalton. How many grams of pure acid (CH₃COOH) are needed to make 1 liter of solution 0.2 molar in acetic acid?
A. Take the problem in stages.
Step 1: how to make a 1 M solution? The atomic formula is C₂O₂H₄, so the formula weight is: (2x12) + (2x16) + (4x1) = 24 + 32 + 4 = 60. To make 1 liter of 1 Molar solution, add 60 g/liter.
Step 2: How to make a 0.2 M solution? Just take 0.2 x 60 g = 12 g/liter.

3 - Q. 12 Q. How does a strong acid differ from a weak acid?
A. Strong acids ionize completely, weak acids only partially.
Q. How does a base differ from an acid?
A. Acids donate H⁺ ions, bases adsorb them.
Q. Give an example of each.
A. Strong acid: HCl. Weak acid: acetic acid (CH₃COOH). Base: ammonia (NH₃).

5 - Q. 7 Q. Identify the amino acids present, using Figure 5.15. Write the 3-letter and 1-letter sequence of this peptide.

A. Val-Phe-Leu (VFL)

8 - Q. 2 Q. What types of functions do membrane proteins carry out? What function(s) do membrane lipids serve?
A. Membranes create a permeability barrier that separates compartments and keeps polar and charged molecules from leaking across the membrane, a function due mainly to the lipid bilayer. Membranes also selectively transport certain substances across the membrane by the action of different protein carriers. They also carry specialized signals on the outer membrane surface that allow recognition of specific cell types by signaling molecules.

8 - Q. 6 Q. Explain what is meant by the terms "isotonic", "hypertonic", "hypotonic", "lysis", "plasmolysis", "shrinkage" and "osmosis". What is the equivalent salt concentration of a human cell?
A. "isotonic" = same ionic strength
"hypertonic" = higher osmotic concentration (e.g., brine or syrup)
"hypotonic" = lower osomotic concentration (e.g., pure water)
"lysis" = breakage
"plasmolysis" = shrinkage of a cell away from a surrounding wall
"osmosis" = movement of water across a membrane
equivalent salt concentration of a human cell = 0.9% saline

8 - Q. 10 Q. Ion gradients are vitally important to cells. With respect to human cells, which of the following ions are normally kept at very different concentrations across cell membranes: Ca++, Na+, K+, Cl-? Which ions are in higher concentration outside the cell? Inside the cell?
A. See table in lecture notes on membranes.

8 - Q. 12b Q. Explain the process by which iron gets from the bloodstream into human cells. Compare this with the uptake of glucose.
A. Iron is bound to protein carriers in the blood (transferrin), and is taken up by the carrier-mediated endocytosis pathway. Glucose, by contrast, uses single protein carrier proteins, either facilitated diffusion or active transport, depending on the tissue.

9 - Q. 1 Q. Why is ATP so useful in cell metabolism?
A. It can transfer phosphate groups easily, with release of energy and large negative delta G. This energy release can be used to make other reactions occur spontaneously, which ordinarily would have positive delta G and would not occur.

9 - Q. 4 Q. What is the difference between an electron carrier and a terminal electron acceptor? Give examples of each.
A. electron carriers are molecules like NAD+ that pick up electrons only temporarily. If they can't find an acceptor, they quickly become saturated with electrons. Terminal electron acceptors are the molecules that wind up with the electrons after they have been passed as far as they are going. These molecules must then leave the cell, carrying the electrons away as a kind of waste; for example, Oxygen is a terminal electron acceptor, and produces water as a waste product.

9 - Q. 5 Q. Relative to other biological molecules, how much NAD+ is there in a cell? Choose from: (a) a lot; (b) comparable to the concentration of amino acids; (c) extremely little.
A. (c)

10 - Q. 7 Q. Where does glycolysis occur? What are the end products? How many oxidation reactions are involved?
A. Glycolysis occurs in the cytoplasm. One molecule of glucose is converted to 2 molecules of pyruvic acid. After glucose splits into two 3-C molecules, there is one oxidation reaction for each 3C molecule.

10 - Q. 9 Q. How is a mitochondrion organized? Be able to identify the matrix, the cristae, and the intermembrane space in which H+ ions accumulate during proton gradient formation. What kinds of molecules make up the electron transport chain? Where do electrons entering this chain originate? Where do they end up?
A. Answers to these questions are in the lecture notes on metabolism. Note that electrons enter the ETS chain from redox carriers such as NADH. They travel through the chain to oxygen, ending up as water.

10 - Q. 10 Q. Ca⁺⁺ ion is widely used as a second messenger that controls different events than those controlled by cAMP. How does the intracellular and extracellular concentration of Ca⁺⁺ compare? On which side of the cell membrane is most Ca⁺⁺ ? What happens inside a cell when Ca⁺⁺ suddenly increases?
A. See table in the metabolism lecture for the distribution of Ca⁺⁺ across cell membranes. When Ca⁺⁺ rushes into a cell, this can trigger sudden and profound changes in cell activity; for example, a muscle cell will contract in response to a sudden rise in Ca⁺⁺ concentration.

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Study Guide	Q & A
1 - Q. 3	Q. What are "emergent properties?" A. Emergent properties cannot be predicted from knowledge of the component parts alone. For example, knowing that the nervous system is made of neurons does not allow you to predict consciousness; consciousness is an emergent property. Q. Identify 3 properties of a cell that are not present in cell molecules. A. Motility, growth, division. Q. Identify 3 properties of a human being that are not present in cells alone. Speech, Thought, Dancing.
1 - Q. 9	Q. What are the characteristics of "science" that distinguish it from other ways of knowing? A. Science is predicated on experimental investigation; to be scientific, a claim should be testable by some form of inquiry. Scientific claims need to be expressed in precise form, and should potentially be falsifiable. Dogmatic claims that cannot potentially be proved false under rigorous inquiry may or may not be true, but they are not scientific and do not belong in scientific literature. Q. What is meant by the "hypothetico-deductive" method? A. Scientific activity proceeds by formulating a specific hypothesis about what is being studied, then deducing from that hypothesis what can be predicted to follow if the hypothesis is true, then devising experiments to see whether such predictions are in fact valid. Q. Is it theoretically possible to prove any hypothesis with absolute certainty? A. A qualified "no". It is central to scientific inquiry that any hypothesis, no matter how widely accepted, can be potentially proven incorrect. In fact, however, established hypotheses (which may grow into theories as they continue to make successful predictions) are rarely discarded in the face of a few anomalies. Instead, people create new hypotheses to explain the anomalies.
1 - Q. 10	Q. What does the term "theory" mean in science? A. A theory is a hypotheses with wide explanatory power that has been found to make many hypotheses that have been upheld by observation and inquiry. Examples include broad theories such as the cell theory, evolutionary theory, and more narrowly focused theories such as the chemiosmotic theory (which we will examine when we study how mitochondria work). Q. How does this differ from everyday usage of this term? A. In everyday language, a theory is something tentative. "I have a theory about why you lose your keys a lot". By contrast, a fact is something that is true. In science, however, there are no facts, just observed data with measurable error limitations. We link facts by making hypotheses and testing them, and certain hypotheses become so useful that they grow into theories. Theories, in science, represent the highest form of scientific knowledge -- explanatory concepts that have withstood testing in a variety of ways and provide good explanations for certain phenomena.
2 - Q. 6	Q. How does the abundance of elements in the earthąs crust compare with the abundance of elements in living tissue? A. There is very little correlation. Aside from Oxygen, which is the most abundant element in both the crust and living tissues, the other most abudant elements of life (CHNPS) are present in amounts very different from the composition of the crust. We are not, for example, made of Silicon, which is the second most abundant element on Earth.
2 - Q. 16	Q. How many errors can you find in the following structural formula? A.
2 - Q. 18	Q. Which of the following covalent bonds is not polar? More than one answer may apply. (a) -C-O- (b) -C-H (c) -C=O (d) -O-H (e) O=O A. (b) and (e) are non-polar.
2 - Q. 21	Q. Is the shape of a molecule important in understanding its chemistry? Why or why not? A. In biology, shape is of paramount importance. Almost everything that happens in biological systems is the result of molecular collisions and interactions between biological molecules, especially proteins. Such interactions are 3-dimensionally stereospecific -- precise geometric "fit" is crucial for successful interactions.
3 - Q. 5	Q. Relative to the previous question, imagine an organism whose interior liquid was 70% alcohol instead of water. What effect would this difference have on the organisms ability to dissipate heat generated during metabolism or activity? A. Alcohol has a much lower specific heat than water. If cells had alcohol as their liquid environment, they would heat up quickly as energy was released, and biological molecules in the cell would denature and stop working effectively as temperatures rose.
3 - Q. 6	Q. Identify four properties of water that are of significance to life. A. High heat capaciy, adhesion, cohesion, weak ionization
3 - Q. 10	Q. The atomic weights of several elements are: C = 12 daltons; O =16 daltons, H =1 dalton. How many grams of pure acid (CH₃COOH) are needed to make 1 liter of solution 0.2 molar in acetic acid? A. Take the problem in stages. Step 1: how to make a 1 M solution? The atomic formula is C₂O₂H₄, so the formula weight is: (2x12) + (2x16) + (4x1) = 24 + 32 + 4 = 60. To make 1 liter of 1 Molar solution, add 60 g/liter. Step 2: How to make a 0.2 M solution? Just take 0.2 x 60 g = 12 g/liter.
3 - Q. 12	Q. How does a strong acid differ from a weak acid? A. Strong acids ionize completely, weak acids only partially. Q. How does a base differ from an acid? A. Acids donate H⁺ ions, bases adsorb them. Q. Give an example of each. A. Strong acid: HCl. Weak acid: acetic acid (CH₃COOH). Base: ammonia (NH₃).
5 - Q. 7	Q. Identify the amino acids present, using Figure 5.15. Write the 3-letter and 1-letter sequence of this peptide. A. Val-Phe-Leu (VFL)
8 - Q. 2	Q. What types of functions do membrane proteins carry out? What function(s) do membrane lipids serve? A. Membranes create a permeability barrier that separates compartments and keeps polar and charged molecules from leaking across the membrane, a function due mainly to the lipid bilayer. Membranes also selectively transport certain substances across the membrane by the action of different protein carriers. They also carry specialized signals on the outer membrane surface that allow recognition of specific cell types by signaling molecules.
8 - Q. 6	Q. Explain what is meant by the terms "isotonic", "hypertonic", "hypotonic", "lysis", "plasmolysis", "shrinkage" and "osmosis". What is the equivalent salt concentration of a human cell? A. "isotonic" = same ionic strength "hypertonic" = higher osmotic concentration (e.g., brine or syrup) "hypotonic" = lower osomotic concentration (e.g., pure water) "lysis" = breakage "plasmolysis" = shrinkage of a cell away from a surrounding wall "osmosis" = movement of water across a membrane equivalent salt concentration of a human cell = 0.9% saline
8 - Q. 10	Q. Ion gradients are vitally important to cells. With respect to human cells, which of the following ions are normally kept at very different concentrations across cell membranes: Ca++, Na+, K+, Cl-? Which ions are in higher concentration outside the cell? Inside the cell? A. See table in lecture notes on membranes.
8 - Q. 12b	Q. Explain the process by which iron gets from the bloodstream into human cells. Compare this with the uptake of glucose. A. Iron is bound to protein carriers in the blood (transferrin), and is taken up by the carrier-mediated endocytosis pathway. Glucose, by contrast, uses single protein carrier proteins, either facilitated diffusion or active transport, depending on the tissue.
9 - Q. 1	Q. Why is ATP so useful in cell metabolism? A. It can transfer phosphate groups easily, with release of energy and large negative delta G. This energy release can be used to make other reactions occur spontaneously, which ordinarily would have positive delta G and would not occur.
9 - Q. 4	Q. What is the difference between an electron carrier and a terminal electron acceptor? Give examples of each. A. electron carriers are molecules like NAD+ that pick up electrons only temporarily. If they can't find an acceptor, they quickly become saturated with electrons. Terminal electron acceptors are the molecules that wind up with the electrons after they have been passed as far as they are going. These molecules must then leave the cell, carrying the electrons away as a kind of waste; for example, Oxygen is a terminal electron acceptor, and produces water as a waste product.
9 - Q. 5	Q. Relative to other biological molecules, how much NAD+ is there in a cell? Choose from: (a) a lot; (b) comparable to the concentration of amino acids; (c) extremely little. A. (c)
10 - Q. 7	Q. Where does glycolysis occur? What are the end products? How many oxidation reactions are involved? A. Glycolysis occurs in the cytoplasm. One molecule of glucose is converted to 2 molecules of pyruvic acid. After glucose splits into two 3-C molecules, there is one oxidation reaction for each 3C molecule.
10 - Q. 9	Q. How is a mitochondrion organized? Be able to identify the matrix, the cristae, and the intermembrane space in which H+ ions accumulate during proton gradient formation. What kinds of molecules make up the electron transport chain? Where do electrons entering this chain originate? Where do they end up? A. Answers to these questions are in the lecture notes on metabolism. Note that electrons enter the ETS chain from redox carriers such as NADH. They travel through the chain to oxygen, ending up as water.
10 - Q. 10	Q. Ca⁺⁺ ion is widely used as a second messenger that controls different events than those controlled by cAMP. How does the intracellular and extracellular concentration of Ca⁺⁺ compare? On which side of the cell membrane is most Ca⁺⁺ ? What happens inside a cell when Ca⁺⁺ suddenly increases? A. See table in the metabolism lecture for the distribution of Ca⁺⁺ across cell membranes. When Ca⁺⁺ rushes into a cell, this can trigger sudden and profound changes in cell activity; for example, a muscle cell will contract in response to a sudden rise in Ca⁺⁺ concentration.