Part I: [66 pts]: For multiple choice, choose the one BEST answer. Circle its letter. Read each question and all 5 choices carefully because more than one answer might seem correct at first glance. 1 point each

1. Which of the following is NOT true
a. all biological membranes are asymmetric
b. membrane fluidity is controlled by fatty acid composition and cholesterol content
c. all biological membranes are fluid mosaics of lipids and proteins
d. some materials can pass through a biological membrane without an intrinsic protein carrier
e. none of the above are false

2. Glycogen is:
a. a large branched polymer of glucose
b. synthesized and degraded in order to regulate the blood glucose level
c. stored primarily in liver and skeletal muscle
d. a and b
e. all of the above

3. Which statement BEST describes oxidative phosphorylation?
a. it is the generation of a proton gradient across the inner mitochondrial membrane
b. it is an aerobic process that occurs along the cristae
c. it accounts for the synthesis of about 90% of the ATP generated by respiration
d. it is the coupling of oxidation and phosphorylation that generates ATP by transferring electrons from electron
carriers to O₂ via the ETS
e. none of the above

4. How does the twisting into a helix contribute to the stability of DNA’s structure?
a. it brings the stacked base pairs close to one another
b. water is excluded from the hydrophobic core
c. hydrophobic interactions with the core and the H bonds between the base pairs contribute to DNA stability
d. the major and minor grooves allow proteins to anchor there
e. all of the above

5. Nicks in DNA are repaired by
a. DNA pol I
b. DNA pol III
c. ligase
d. primase
e. replicase

6. Which of the following is NOT a function of phospholipid bilayer membranes?
a. it is a physical barrier with selective permeabilities
b. it separates different parts of the cell from each other
c. it separates the cell from its environment
d. the symmetry of the lipid bilayers enables it to be a barrier to the flow of polar and nonpolar molecules
e. none of the above - all are functions of bilayer membranes

7. Which of the following statements is NOT TRUE about RNA polymerases?
a. RNA polymerase II makes mRNA precursors
b. like DNA polymerases, RNA polymerases also need a primer to initiate RNA synthesis
c. RNA polymerases do not possess endonuclease and exonuclease capabilities
d. the promoter site of the lac operon is an RNA polymerase binding site
e. none of the above

8. In the breakdown of glycogen
a. phosphorylase adds a phosphate to the terminal glucose unit, which is then removed from the glycogen via
phosphorolytic cleavage
b. the 'released unit' of glycogen is glucose-1-P, which can be converted to glucose-6-P which in turn can enter
the glycolytic pathway for further reactions
c. the reactions involved are the reverse of those needed to make glycogen
d. a and b
e. all of the above

9. The "currency" of readily available reducing power for cellular anabolism is
a. NADH
b. FADH₂
c. NADPH
d. FADPH
e. all of the above

10. The 5’ cap
a. is added to mature mRNA transcripts
b. is a result of a polyadenylation process
c. serves as a timekeeping device
d. stabilizes mRNA by protecting their 5’ ends
e. none of the above

11. Most of the amino groups of surplus amino acids are converted into
a. acetyl CoA
b. alanine
c. pyruvate
d. one or another intermediate in the TCA cycle, depending on the amino acid
e. urea

12. Which statement is NOT true about membranes?
a. membrane lipids contain both a hydrophobic and a hydrophilic moiety
b. plasma membranes of both animal and plant cells are rich in cholesterol
c. membrane lipids serve as fuel molecules, energy stores, and signal molecules
d. glycolipids represent one of the major kinds of membrane lipids
e. none of the above

13. Splicing of immature RNA by splicesomes is part of processing
a. rRNA
b. tRNA
c. mRNA
d. a and b
e. all of the above

14. Protein synthesis
a. is synonymous with translation
b. not the same as transcription
c. occurs in the amino-to-carboxyl direction
d. involves initiation, elongation, and termination
e. all of the above

15. In eukaryotes
a. oxidative phosphorylation occurs in the inner mitochondrial membrane
b. the inner membrane is almost impermeable to most ions and polar molecules, and thus requires shuttles to
transport needed metabolites across the inner mitochondrial membrane
c. pumps drive protons into the cytosolic side of the inner mitochondrial membrane to establish a pH gradient
and membrane potential
d. all of the above are true.
e. all of the above are false: citric acid cycle and oxidative phosphorylation both occur in the cytosol

16. Which of the following is true with respect to production of glycogen?
a. it takes the equivalent of 1 ATP to add one glucose molecule to glycogen
b. any glucose molecule which can feed into glycogen synthesis will do so preferentially over feeding into the
glycolysis pathway
c. glycogen is synthesized by a pathway which uses UDP-glucose rather than glucose-1-P as the 'activated
glucose' donor
d. a and b
e. a and c

17. A promoter is
a. the transcription start site
b. the site RNA polymerase binds DNA
c. the site DNA polymerase binds DNA
d. only found in prokaryotes
e. all of the above

18. Membrane proteins
a. make up about 50% of typical plasma membranes
b. are called integral proteins if they span the lipid bilayer
c. can be analyzed by SDS-PAGE and freeze-fracture microscopy
d. are constantly in lateral motion
e. all of the above

19. The lac operon is stimulated by
a. lactose
b. cAMP
c. glucose
d. a and b
e. all of the above

20. The main purpose(s) of glycolysis is/are to
a. provide precursor molecules for biosynthetic processes such as the Krebs cycle
b. degrade glucose to generate pyruvate and a small amount of ATP
c. oxidize fuel molecules
d. a and c
e. a and b

21. The lac operon is inhibited by
a. glucose
b. cAMP
c. galactose
d. lactose
e. all of the above

22. When will most organisms liberate glucose from their glycogen stores?
a. only when absolutely necessary because the glycogen is not easily accessible
b. when there is an abundance of free glucose and glycogen
c. when there is no free glucose available
d. all the time
e. never

23. Each of the following is an important substrate for gluconeogenesis during fasting except
a. pyruvate
b. glycerol
c. lactate
d. amino acids
e. acetyl CoA

24. In the lac operon model, transcription of the polycistronic mRNA occurs only in the
a. presence of glucose and lactose
b. absence of glucose and lactose
c. presence of glucose and absence of lactose
d. absence of glucose and presence of lactose
e. none of the above

25. Which of the following is (are) involved in translation?
a. mRNAs
b. tRNAs
c. ribosomes
d. all of the above
e. none of the above

26. If lipids are hydrophobic, how are they transported in the body?
a. fatty acids are carried by very low density lipoproteins (VLDL's), which are produced by the liver and
released into the bloodstream
b. lipids do not need to be transported because fatty acids are produced locally wherever they are needed in the
body
c. they are shuttled in the bloodstream by enzymes knows as high density lipoproteins
d. adipose tissue breaks down triglyceride s, and attaches fatty acid chains to glucose molecules which are
released in the blood
e. all of the above are valid transport mechanisms for lipids

27. Pyruvate is the entry point into the citric acid cycle for
a. alanine
b. serine
c. cysteine
d. glycine
e. all of the above

28. The functions of the pentose phosphate pathway include
a. providing a source of NADPH (for reductive biosynthesis)
b. providing a source of ribose -5-P for nucleic acid synthesis
c. providing a route for the use of pentoses, and their conversion of F6P and G3P
d. a and b
e. all of the above

29. Which of the following are significant features of glycogen?
a. homopolymer of glucose
b. branched
c. mostly a-1,4, with some a-1,6 linkages
d. stored in cytoplasm
e. all of the above

30. Which of the following is NOT a characteristic of fatty acids?
a. configuration of double bonds in unsaturated FA is cis
b. contains an even number of C atoms
c. fluidity increases with shorter chain length
d. fluidity increases with decreased saturation
e. double bonds in saturated FAs are usually separated, seldom if ever adjacent

31. What is the main difference between NAD and NADP?
a. NAD is used in degradation pathways and NADP is used in biosynthetic pathways
b. NADP is used in degradation pathways and NAD is used in biosynthetic pathways
c. there is no difference
d. they both have similar enzymatic activity and very different redox functions
e. they are both so different that there is no comparison

32. In semiconservative replication, each replicated DNA molecule will consist of
a. old and new DNA dispersed on both strands
b. one old parental strand and one new strand
c. only the old parental DNA on both strands
d. new DNA on both strands
e. there is no such thing as semiconservative replication of DNA

33. Which of the following is NOT a physiological role of fatty acids?
a. fuel
b. phospholipid components
c. derivatized to form hormones
d. used to modify proteins, targeting them to membrane locations
e. none of the above -- all are functions

34. Coenzyme Q ...
a. is called ubiquinone
b. is ubiquitous in biological systems
c. is an important and mobile electron carrier involved in the ETS
d. is a stable evolutionary molecule
e. all of the above

35. The major functional difference between NADH and NADPH in most biochemical pathways is that
a. NADH is oxidized by the electron transport chain --> ATP; NADPH serves as an electron donor in anabolic
pathways
b. NADPH is oxidized by the electron transport chain --> ATP; NADH serves as an electron donor in anabolic
pathways
c. NADH is used in animals; NADPH is used in plants
d. NADH is used in animals; NADPH is used in plants
e. they are virtually interchangeable. The enzymes involved are specific for one or other, but there is no other
pattern

36. A complex of DNA associated with an octamer of histone proteins is called
a. nucleosome
b. spacer DNA
c. chromatin
d. solenoid
e. none of the above

37. In the pentose phosphate pathway, NADPH is generated when glucose-6-P -->
a. ribose-5-P
b. ribose -3-P
c. ribulose -5-P
d. xyulose -5-P
e. glyceraldehyde-3-P

38. Functions of, or uses for the acyl group of acetyl-CoA include
a. delivery from pyruvate to TCA cycle for degradation
b. energy resource
c. biosynthetic precursor
d. a and b
e. all of the above

39. Fatty acids are transported into mitochondria via
a. carnitine
b. VLDL
c. acetyl Co A
d. none of the above - fatty acids do not ordinarily enter mitochondria intact
e. none of the above - fatty acids diffuse through the membrane

40. The rate of oxidative phosphorylation in your body is determined mainly by
a. how much food you eat
b. how much ATP you need
c. how much ADP you need
d. whether or not you are breathing
e. how fast glycolysis is occurring

41. Gluconeogenesis
a. is a process that reconfigures pyruvate and other biomolecules back into glucose
b. occurs predominantly in the liver
c. is a reversal of glycolysis
d. a and b
e. a and c

42. For the most part, pyruvate --> lactate in , while lactate --> pyruvate in
a. liver, muscle
b. muscle, liver
c. fat, muscle
d. both reactions are prevalent in liver; lactate --> pyruvate in muscle
e. both reactions are prevalent in liver; pyruvate --> lactate in muscle

43. The first "phase" of oxidative phosphorylation is driven by NADH-Q reductase and
a. cytochrome reductase
b. cytochrome oxidase
c. hexokinase
d. a and b
e. all of the above

44. What is the major source of ATP in aerobic organisms?
a. glycolysis
b. TCA cycle
c. oxidative phosphorylation
d. a and b
e. all of the above

45. Zinc finger, helix-loop-helix, leucine zipper, and helix-turn-helix are examples of
a. cis-acting enhancers
b. upstream activating sequences
c. DNA binding domains
d. promoters
e. repressors

46. Fatty acid synthesis occurs in the ; fatty acid degradation occurs in the
a. mitochondrial matrix .... cytosol
b. mitochondrial matrix .... cytosol
c. cytosol ... mitochondrial matrix
d. cytosol ... cytosol
e. both occur in both places

47. Electron carrying groups include all of the following EXCEPT
a. flavin
b. heme
c. copper ion
d. iron-sulfur cluster
e. all vitamins

48. NADH has a reduction potential. Oxygen has a reduction potential.
a. positive .... negative
b. negative ... positive
c. fast ... slow
d. slow ... fast
e. none of the above

49. The presence of deoxyribose in DNA, compared with ribose in RNA, accounts for
a. the use of thymidine rather than uracil
b. base pairing specificity
c. increased stability of DNA in aqueous environments
d. the helical shape of DNA
e. specific protein binding properties

50. The enzyme catalyzing a committed step in a pathway is usually an important regulatory site, exemplified by PFK in glycolysis and in fatty acid synthesis by
a. PFK
b. acetyl CoA carboxylase
c. glycerol kinase
d. acyl CoA dehydrogenase
e. there are no committed steps in fatty acid synthesis

51. Which of the following linkages are found in glycogen?
a. a-1,4 and b-1,4
b. a-1,4 and a-1,6
c. b -1,4
d. a -1,6
e. b -1,4 and b - 1,6

52. Each round of fatty acid oxidation generates
a. acetyl CoA
b. NADH
c. FADH₂
d. a and b
e. all of the above

53. One enzymatic difference between glycolysis and gluconeogenesis is that where phosphofructokinase (PFK) is used for glycolysis, the related back reaction is catalyzed by
a. fructose 1,6-bisphosphatase
b. PFK-2
c. PK
d. a and b - it is a two step process
e. PFK: phosphofructokinase -- there is no difference

54. Oxidative phosphorylation involves transfer of electrons from .... to.....
a. NADH .... O₂
b. FADH₂ ... O₂
c. NADPH .... O₂
d. a and b
e. all of the above

55. Which of the following is false? Fatty acids are:
a. extremely hydrophobic
b. polar
c. hydrocarbon chains
d. stored as triglycerides
e. all of the above are true

56. The process of synthesizing glucose from non-carbohydrate sources
a. is known as gluconeogenesis
b. requires certain 'new' reactions to bypass the irreversible reactions in glycolysis
c. is the reversal of the steps of glycolysis
d. a and b
e. a and c

57. The respiratory chain consists of proton pumps linked by mobile electron carriers
a. 2, 3
b. 3, 2
c. 3, 3
d. 2,2
e. 1,1

58. Glucose-6-P, generated by phosphorylation of glucose, can be used in several pathways including
a. conversion to glycogen
b. conversion to pyruvate in glycolysis
c. conversion to ribose-5-phosphate via the pentose-phosphate shunt
d. all of the above
e. none of the above are pathways for glucose-6-phosphate metabolism

59. Which of the following is false? Fatty acids are:
a. extremely hydrophobic
b. polar
c. hydrocarbon chains
d. stored as triglycerides
e. all of the above are true

60. The rate of oxidative phosphorylation depends on the need for
a. oxygen
b. glucose
c. ATP
d. pyruvate
e. pH

61. In fatty acid metabolism
a. fatty acids are linked to CoA, and shuttled into the mitochondria via carnitine to be oxidized
b. triglycerides must be converted to glycogen in order to isolate fatty acid components
c. animals are above to convert fatty acids into glucose
d. fatty acids are both synthesized and oxidized in the mitochondria
e. none of the above are true

62. What is significant about the enzymes hexokinase, phosphofructokinase, and pyruvate kinase?
a. they are all involved in gluconeogenesis
b. they catalyze the 3 essentially irreversible steps of glycolysis
c. they are major regulatory enzymes in glycolysis
d. a and b
e. b and c

63. Glycogen is stored in the cell
a. in the endoplasmic reticulum
b. as glycogen granules which also contain the enzymes for glycogen metabolism
c. as granules associated with the plasma membrane ready for exocytosis
d. freely soluble in the cytosol
e. all of the above are used

64. Which of the following is the final component in the respiratory chain?
a. cytochrome reductase
b. NADH-Q reductase
c. cytochrome c
d. phosphofructokinase
e. ATPase

65. The strand of DNA is synthesized continuously

66. The strand of DNA is synthesized dis-continuously

Part II: [12 points] matching 1 point each
1. Match the metabolic pathway with its key regulatory enzyme (a pathway may have >1 regulated step)
1. pentose phosphate pathway a. acetyl CoA carboxylase

2. glycolysis b. glucokinase

3. gluconeogenesis c. NADH-Q reductase

4. TCA d. G-6-P dehydrogenase

5. fatty acid synthesis e. fructose 1,6-bisphosphatase

6. fatty acid b-oxidation f. UDP-glucose synthesis

7. glycogen biosynthesis = (UDP-glucose pyrophosphatase)

8. glycogen breakdown g. citrate synthase

h. phosphofructokinase

x. none (on this list)

2. Match the metabolite with the correct description:

1. preferred source of metabolic fuel for brain a. ketone bodies

2. primary source of metabolic fuel for skeletal muscle b. glucose

in starvation or late diabetes c. fatty acids

3. released by adipose tissue; converted by liver to pyruvate d. glycerol

4. preferred source of fuel for heart muscle & kidney e. lactate

EXTRA CREDIT: Write you own question and answer it. HINT: this is you opportunity to show what you know. Do not ask yourself a question if you aren't sure of the answer. Ask the question you were sure would be on the exam, so you studied the material, and then somehow it was left off! Your score will depend on the quality of the question as well as the answer - up to a possible maximum of 5 pts.

Part III. [60 pts] medium-length answer. Your option circle one:

Choose 5 (omit 1). 12 points each -- OR -- Choose 4 (omit 2). 15 points each

1. Sketch the molecular structure of DNA and RNA. Be sure that your sketches, or an explanation of them, shows the major structural differences between these two classes of nucleic acids. How do the functions of both of these classes of biomolecule require similar structure? How do the differences between their functions require the structural difference(s)?

2. Sketch the general structure of a neutral lipid and a phospholipid to point out their important similarities and differences. How do the functions of both of these classes of biomolecule require similar structure? How do the differences between their functions require the structural difference(s)?

3. Considering lipids, proteins, and carbohydrates: which class of molecule is the most efficient biological energy storage form? Which is the best for very fast mobilization of stored energy? Explain.

4. Why are ketone bodies formed during starvation or diabetes? The liver lacks CoA transferase, so it cannot use ketone bodies as a source of energy. What happens to them? Why is this more of a problem for the brain than for the heart?

5. Why is protein generally considered to be the final product of gene expression (rather than, e.g., carbohydrates or lipids)? Where do other biological molecules, like lipids and carbohydrates, come from? Does the genome control their production - and if so, how?

6. Explain how ATP is formed by oxidative phosphorylation and electron transport in mitochondria. Explain how the proton gradient is established in mitochondria and how it is used to generate ATP.

Part III. [15 pts] Shorter answer. Choose 3 (omit 2) 5 points each

1. The inner mitochondrial membrane is impermeable to NADH and NAD +. How does NADH formed by glycolysis become oxidized by the respiratory chain?

2. How many ATPs would you expect to be generated by complete metabolism of a 14C fatty acid? Show all work to explain your answer.

3. What are the two main functions of the pentose phosphate pathway (shunt)? Briefly explain why each of these is important.

4. Triacylglycerols are effective as highly concentrated energy storage forms because they are .... EXPLAIN

a. reduced
b. anhydrous
c. non-polar

5. Why do we get warm when we use our muscles?