Version I

There are two types of questions below.  The first is multiple choice.  Each multiple choice question or statement is numbered and has one, and only one, best response.  Mark the letter of the best response by the corresponding number on your answer sheet.  The second is True/False.  Each statement or question that is marked “TF” will be followed by a series of numbered responses that may be correct (T) or incorrect (F).  Mark each response True or False by the corresponding number on your answer sheet.

1.  An organelle that is directly associated with the part of the Carbon Cycle where carbon from carbon dioxide is incorporated into organic compounds is:
 A.  the nucleus.
 B.  the plasma membrane.
 C.  the chromosome.
 D.  the chloroplast.
 E.  the Golgi apparatus.

2.  Which of the following would not contain all of these elements:  carbon, hydrogen, nitrogen, oxygen, and phosphorus?
 A.  A typical enzyme.
 B.  A chromosome.
 C.  A cell.
 D.  ATP.
 E.  DNA.

3.  Which of the following can pass through a biological membrane only if a specific protein or proteins is present?
 A.  Water molecules.
 B.  Protons.
 C.  Carbon dioxide molecules.
 D.  Oxygen molecules.
 E.  All of these can pass through without the aid of proteins.

TF  Which of  the following may be true of an organism with prokaryotic cells?

4. T F  It may have one nucleus or many nuclei.
5. T F Its cells will contain no DNA.
6. T F Its cells will contain polymers of amino acids.
7.  T F Its cells will contain ribosomes.
8. T F Its cells will contain mitochondria.

TF Cell division gives rise to a relatively undifferentiated cell in a young leaf in the bud of a tobacco plant.  As the leaf expands and becomes mature, the cell differentiates into a mature photosynthetic cell.  During this process of differentiation:

9. T F new genes appear in the cell and others disappear.
10. T F new proteins appear in the cell and others disappear.
11. T F the cell loses all of its mitochondria.
 

12.  Autotrophic organisms with cells that carry out photosynthesis may be found in which of the following groups of organisms?
 A.  Plants.
 B.  Insects.
 C.  Fungi.
 D.  Organisms with prokaryotic cells.
 E.  A and D are correct.

TF Triglycerides and phospholipids share the following characteristics in common:

13 T F  molecules that have a very high content of carbon and hydrogen.
14. T F molecules that can be hydrolyzed to yield some fatty acids.
15. T F molecules that can be hydrolyzed to yield amino acids.
16. T F   molecules that are partly hydrophobic and partly hydrophilic.
 

17.  Which of the following organisms will have cells with nuclear envelopes, mitochondria, and cell walls?
 A.  Mice.
 B.  Paramecium.
 C.  Humans.
 D.  Wheat plants.
 E.  Cyanobacteria.

18.  Following mitosis and cell division, each of the offspring cells of a eukaryotic cell will have:
 A.  as many genes as the parent cell had.
 B.  as may chromosomes as the parent cell had.
 C.  a cytoskeleton.
 D.  A, B, and C are correct.
 E.  None of these are correct.

19.  ATPases are enzymes that hydrolyze ATP and release energy to do cellular work.  Which of  the following cellular processes does not require the activity of an ATPase?
 A.  The contraction of a muscle cell.
 B.  Allowing water to enter the cell.
 C.  Mitosis.
 D.  The beating of a flagellum.
 E.  Active transport.

TF Cell reproduction in Escherichia coli requires:

20. T F the replication of DNA.
21. T F male and female cells.
22. T F mitosis.
23. T F the hydrolysis of ATP.
 

24.  Which of the following would be present in the cells of  the last common ancestor of all animals but not in the common ancestor of both bacteria and animals?
 A.  Chloroplasts.
 B.  Ribosomes.
 C.  Plasma membrane.
 D.  Mitochondria.
 E.  ATP.

25.  U of A researchers participating in the new Center for Protein Structure and Function will be interested in the _______________ of certain proteins.
 A.  sequence of amino acids
 B.  shape
 C.  sequence of monosaccharides
 D.  pattern of folding
 E.  A, B, and D are correct.

TF  A cell membrane of any organism will:

26. T F be involved in the way the cell responds to its environment.
27. T F be a solid wall around the cell.
28.   T F allow any hydrophilic molecule into the cell.
29. T F be made, in part, of some molecules that contain sulfur.
30. T F be made, in part, of some molecules that are part of the Nitrogen
                Cycle.
31. T F regulate what chemicals can cross it.
32. T F contain only a bilayer of phospholipid molecules.
33. T F allow water molecules to pass freely through it.
34. T F consist entirely of triglycerides.
35. T F allow chemical building blocks into the cell.

36.  Mitosis does not occur in prokaryotic cells, but other processes associated with cell reproduction do.  Which of the following cell cycle events does not occur in prokaryotic cells?
 A.  Breakdown of the nuclear envelope.
 B.  DNA replication.
 C.  G1 phase of the cell cycle.
 D.  G2 phase of the cell cycle.
 E.  S phase of the cell cycle.

37.  During cell differentiation, some cell membrane proteins may:
 A. be replaced by other proteins.
 B.  remain part of the membrane.
 C.  fit together with proteins on other cells.
 D.  act as gateways for protons into and/or out of the cell.
 E.  All of these may be correct.

38.  We all are aware of the phenomenon that the roots of a plant will grow down in response to gravity.  If a plant in a pot is placed on its side, the tips of its roots will start to grow downward within an hour or so.  The root bends down in part because the walls on the upper sides of each cell are stretchier than the walls on the lower side.  Some of this stretchiness is due to a raised concentration of protons in the aqueous solution just outside the plasma membrane on the upper side of the cell.  These protons come from the inside of the cell and they are transported against a concentration gradient.  The movement of protons in this case is an example of:
 A.  facilitated diffusion.
 B.  active transport.
 C.  mitosis.
 D.  cell division.
 E.  DNA replication.

39.  In the previous question, the aqueous solution on the upper side of the cell ____________ than the aqueous solution on the lower side of the cell.
 A.  is less acid
 B.  is more acid
 C.  is more alkaline
 D.  A and B are correct.
 E.  has a higher pH

40.  DNA replicating enzymes are associated with the _______ stage of the cell cycle.
 A.  S
 B.  G1
 C.  M
 D.  G2
 E.  G3

TF An amoeba “eats” a Chlamydomonas cell by endocytosis and digests it in a food vacuole.  (Digestion involves the hydrolysis of macromolecules, and this hydrolysis is catalyzed by digestive enzymes.)  One of the organic macromolecules in the Chlamydomonas chloroplast is the polysaccharide, starch.  The ultimate product of the hydrolysis of starch is the monosaccharide, glucose.  One of the important enzymes in the digestion of starch is called alpha amylase.  After starch is digested in the food vacuole, glucose crosses the vacuole membrane and enters the cytoplasm of the amoeba.  The amoeba can then use the glucose in a number of different ways.  One of the ways the amoeba can use the glucose is to break it down by a process called glycolysis.  One end product of glycolysis is an organic compound called pyruvate.  Pyruvate can be used in a lot of ways by the amoeba.  It can be used as an energy source for aerobic respiration, or it can be used as a building block for certain amino acids, or it can be used to produce building blocks for fatty acids, etc.  From this information you know with certainty that:

41. T F the amoeba cell contains mitochondria.
42. T F there is a protein in the food vacuole membrane that recognizes the
            shape of a glucose molecule.
43. T F the amoeba is an autotrophic organism.
44. T F the hydrogen and oxygen in some water molecules in the food
            vacuole become incorporated into organic compounds.
45. T F the amoeba is prokaryotic.
46. T F Chlamydomonas has cells that are capable of mitosis.
47. T F Chlamydomonas has cells with mitochondria.
48. T F starch can be hydrolyzed to yield proteins.
49. T F Chlamydomonas is a producer.
50. T F starch molecules are the products of dehydration synthesis.
 

Version II

There are two types of questions below.  The first is multiple choice.  Each multiple choice question or statement is numbered and has one, and only one, best response.  Mark the letter of the best response by the corresponding number on your answer sheet.  The second is True/False.  Each statement or question that is marked “TF” will be followed by a series of numbered responses that may be correct (T) or incorrect (F).  Mark each response True or False by the corresponding number on your answer sheet.

1. Which of the following can pass through a biological membrane only if a specific protein or proteins is present?
 A.  Water molecules.
 B. Protons
 C.  Carbon dioxide molecules.
 D.  Oxygen molecules.
 E..All of these can pass through without the aid of proteins.

2.  Which of the following would not contain all of these elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus?
 A.  A typical enzyme.
 B.  A chromosome.
 C.  A cell.
 D.  ATP.
 E.  DNA.

3. An organelle that is directly associated with the part of the Carbon Cycle where carbon from carbon dioxide is incorporated into organic compounds is:
 A.  the nucleus.
 B.  the plasma membrane.
 C.  the chromosome.
 D.  the chloroplast.
 E.  the Golgi apparatus.

TF  Which of  the following may be true of an organism with prokaryotic cells?

4. T F  It may have one nucleus or many nuclei.
5. T F Its cells will contain mitochondria.
6. T F Its cells will contain polymers of amino acids.
7.  T F Its cells will contain ribosomes.
8. T F Its cells will contain no DNA.
 

TF Cell division gives rise to a relatively undifferentiated cell in a young leaf in the bud of a tobacco plant.  As the leaf expands and becomes mature, the cell differentiates into a mature photosynthetic cell.  During this process of differentiation:

9. T F new genes appear in the cell and others disappear.
10. T F the cell loses all of its mitochondria.
11. T F new proteins appear in the cell and others disappear.

12. Following mitosis and cell division, each of the offspring cells of a eukaryotic cell will have:
 A.  as many genes as the parent cell had.
 B.  as may chromosomes as the parent cell had.
 C.  a cytoskeleton.
 D.  A, B, and C are correct.
 E.  None of these are correct.

TF Triglycerides and phospholipids share the following characteristics in common:

13 T F  molecules that can be hydrolyzed to yield some fatty acids
14. T F molecules that have a very high content of carbon and hydrogen..
15. T F molecules that can be hydrolyzed to yield amino acids.
16. T F   molecules that are partly hydrophobic and partly hydrophilic.
 

17.  Which of the following organisms will have cells with nuclear envelopes, mitochondria, and cell walls?
 A.  Mice.
 B.  Paramecium.
 C.  Humans.
 D.  Wheat plants.
 E.  Cyanobacteria.

18. ATPases are enzymes that hydrolyze ATP and release energy to do cellular work.  Which of  the following cellular processes does not require the activity of an ATPase?
 A.  The contraction of a muscle cell.
 B.  Allowing water to enter the cell.
 C.  Mitosis.
 D.  The beating of a flagellum.
 E.  Active transport.

19. Autotrophic organisms with cells that carry out photosynthesis may be found in which of the following groups of organisms?
 A.  Plants.
 B.  Insects.
 C.  Fungi.
 D.  Organisms with prokaryotic cells.
 E.  A and D are correct.

TF Cell reproduction in Escherichia coli requires:

20. T F the hydrolysis of ATP.
21. T F male and female cells.
22. T F mitosis.
23. T F the replication of DNA.

24. U of A researchers participating in the new Center for Protein Structure and Function will be interested in the _______________ of certain proteins.
 A.  sequence of amino acids
 B.  shape
 C.  sequence of monosaccharides
 D.  pattern of folding
 E.  A, B, and D are correct.

25. Which of the following would be present in the cells of  the last common ancestor of all animals but not in the common ancestor of both bacteria and animals?
 A.  Chloroplasts.
 B.  Ribosomes.
 C.  Plasma membrane.
 D.  Mitochondria.
 E.  ATP.

TF  A cell membrane of any organism will:

26. T F consist entirely of triglycerides.
27. T F allow water molecules to pass freely through it.
28. T F allow any hydrophilic molecule into the cell.
29. T F be made, in part, of some molecules that contain sulfur.
30. T F be made, in part, of some molecules that are part of the Nitrogen
            Cycle.
31. T F regulate what chemicals can cross it.
32. T F contain only a bilayer of phospholipid molecules.
33. T F be a solid wall around the cell.
34. T F be involved in the way the cell responds to its environment.
35. T F allow chemical building blocks into the cell.
 

36. DNA replicating enzymes are associated with the _______ stage of the cell cycle.
 A.  S
 B.  G1
 C.  M
 D.  G2
 E.  G3

37.  During cell differentiation, some cell membrane proteins may:
 A. be replaced by other proteins.
 B.  remain part of the membrane.
 C.  fit together with proteins on other cells.
 D.  act as gateways for protons into and/or out of the cell.
 E.  All of these may be correct.

38.  We all are aware of the phenomenon that the roots of a plant will grow down in response to gravity.  If a plant in a pot is placed on its side, the tips of its roots will start to grow downward within an hour or so.  The root bends down in part because the walls on the upper sides of each cell are stretchier than the walls on the lower side.  Some of this stretchiness is due to a raised concentration of protons in the aqueous solution just outside the plasma membrane on the upper side of the cell.  These protons come from the inside of the cell and they are transported against a concentration gradient.  The movement of protons in this case is an example of:
 A.  facilitated diffusion.
 B.  active transport.
 C.  mitosis.
 D.  cell division.
 E.  DNA replication.

39.  In the previous question, the aqueous solution on the upper side of the cell ____________ than the aqueous solution on the lower side of the cell.
 A.  is less acid
 B.  is more acid
 C.  is more alkaline
 D.  A and B are correct.
 E.  has a higher pH

40. Mitosis does not occur in prokaryotic cells, but other processes associated with cell reproduction do.  Which of the following cell cycle events does not occur in prokaryotic cells?
 A.  Breakdown of the nuclear envelope.
 B.  DNA replication.
 C.  G1 phase of the cell cycle.
 D.  G2 phase of the cell cycle.
 E.  S phase of the cell cycle.

TF An amoeba “eats” a Chlamydomonas cell by endocytosis and digests it in a food vacuole.  (Digestion involves the hydrolysis of macromolecules, and this hydrolysis is catalyzed by digestive enzymes.)  One of the organic macromolecules in the Chlamydomonas chloroplast is the polysaccharide, starch.  The ultimate product of the hydrolysis of starch is the monosaccharide, glucose.  One of the important enzymes in the digestion of starch is called alpha amylase.  After starch is digested in the food vacuole, glucose crosses the vacuole membrane and enters the cytoplasm of the amoeba.  The amoeba can then use the glucose in a number of different ways.  One of the ways the amoeba can use the glucose is to break it down by a process called glycolysis.  One end product of glycolysis is an organic compound called pyruvate.  Pyruvate can be used in a lot of ways by the amoeba.  It can be used as an energy source for aerobic respiration, or it can be used as a building block for certain amino acids, or it can be used to produce building blocks for fatty acids, etc.  From this information you know with certainty that:

41. T F the amoeba cell contains mitochondria.
42. T F there is a protein in the food vacuole membrane that recognizes the
            shape of a glucose molecule.
43. T F the amoeba is an autotrophic organism.
44. T F the hydrogen and oxygen in some water molecules in the food
            vacuole become incorporated into organic compounds.
45. T F the amoeba is prokaryotic.
46. T F Chlamydomonas has cells that are capable of mitosis.
47. T F Chlamydomonas has cells with mitochondria.
48. T F starch can be hydrolyzed to yield proteins.
49. T F Chlamydomonas is a producer.
50. T F starch molecules are the products of dehydration synthesis.
 

Check out Dr. Ziegler's Web Site before Monday http://www.uark.edu/~susanz

Instructor: Dr. Frederick W. Spiegel

• Address: Department of Biological Sciences, FERR B2
• Phone: (501) 575-7393 (ignore the voice mail) or (501) 575-6343 (Please, no calls at home except in a major emergency)
• email: fspiegel@comp.uark.edu (This is the most effective way to contact me.)
• WebPage:http://comp.uark.edu/~fspiegel/
• Office hours: MWF - 10:30-11:15 and 3:30-4:15

• listen to some of Morning Edition and/or All Things Considered every day on National Public Radio (NPR). Our local NPR station, KUAF, is 91.3 FM.
• watch at least one newscast on TV every day.
• read at least one newspaper every day.
• read at least one news magazine each week.

Mantra #2: Biology is the hardest and most complex of the sciences.

Mantra #3: Science is not just a body of facts (no matter what the Kansas School Board may think).

Mantra #4: Sometimes you have to nag Dr. Spiegel.

Return to Principles of Biology Homepage

This course is called Principles of Biology. A principle in this sense is a major, overriding concept that ties all of biology together. We have been concentrating on the following principles throughout this semester:

• Science is a particular method by which we study the world.
• Biology is the scientific study of living organisms.
• All organisms are chemical and physical systems that obey the principles of chemistry and physics.
• All organisms interact with their environments.
• All organisms are cellular.
• All organisms reproduce.
• Offspring are very similar to their parents.
• Offspring are always a little different from their parents.
• All organisms share a common ancestry with each other.

Since these principles apply to all organisms, it is useful to remember that humans and other mammals are not the only critters out there. Therefore, I expect you to be familiar with the following when we go over the section on cell biology:
 

• Archaebacteria (Table 12.1, p. 282)
• Eubacteria (Table 12.1, p. 282; Fig. 12.3, p. 278) Examples:  Escherichia coli, Nostoc spp.
• Protists (Table 13.1, p. 309)  Examples: Amoeba spp., Paramecium spp., Euglena spp., Chlamydomonas spp.
• Fungi (Table 14.1, p. 326)  Examples:  Zygomycota (Fig. 14.8, p. 327), Ascomycota (Fig. 14.10, p.328), and Basidiomycota (Fig. 14.12, p. 329)
• Animals (Table 18.1, p. 402)  Examples: Nematodes (p. 415), Insects (p. 421)
• Plants (Table 15.1, p. 340)  Examples:  Mosses (Fig. 15.17, p. 342), Ferns (Fig. 15.11, p. 345), Angiosperms (Fig. 15.19, p. 352 [What's missing in this picture?])

If you wish to have a review session before the Exam, I will be available during the evening of Thursday, 26 October.  It is your job as a class (i.e., all 3 sections) to organize the time and place.

I will be putting a number of self grading quizzes on line for you to work on.  I will collect a maximum of three of them during this unit.  Each one you hand in will be worth one point to be added to your total on the next exam.

Here is how this works.  Copy each quiz from below to a word processing program, print it, and handwrite your answer on the sheet.  Write your name, ID#, and section # on the top right hand corner of the quiz and stick it in your class notebook. Then, go to the key (which will be found at the bottom of the page a few days after the quiz is posted) and see how you did.  Each quiz will be numbered.  If I call for the quiz, turn in your quiz only in one of the boxes provided.  The boxes will be monitored.  If you hand in more than one quiz, the monitor will take out all the quizzes you hand in and throw them away.  No quizzes may be turned in at a later time.  You will receive one percentage point for each quiz you turn in if:

• your name, ID, and section are written on it;
• you turn in the requested quiz (you can't substitute);
• your corrected answer is handwritten clearly on a printout of the quiz (no answers on notebook paper allowed); and
• you hand in only your own quiz.

It's always fun to find bonehead goofs in an authoritative work.  See if you can figure out this one that Dr. Johnson made by trying to make the Cell Theory read smoothly in your text (p. 75):

Most versions of the Cell Theory state principle 4 as:  "All cells come from preexisting cells."  Dr. Johnson states the principle as, "Cells arise only (emphasis mine) by division of a previously existing cell."  Where is his mistake? (Hint:  If he is right, then how come he has a mother and a father?)

Remember, we all make bonehead goofs, so be skeptical and be ready to call me on statements that might be goofs.

Key:  One other way that cells come from other cells is that two (or more) cells can fuse to make one.  For example, during the sexual life cycle, two gamete cells can fuse to make a zygote.  Cell fusion also occurs in the development of your skeletal muscle cells.

Key:  Green algae in the genus Caulerpa have giant cells that form runners under the sand and send up photosynthetic branches that look sort of like ferns.  Take my course Survey of the Plant Kingdom to find out more.

Quiz III.  Diagram a cell of the ciliate, Paramecium, and label the major parts.  How is this different from the cell of either a plant or an animal?

Key:  I am still lousy at pasting images so look at 13.15 in your book.  Unique features not in animals or plants include:  contractile vacuoles, pellicle, arrangement of cilia, nuclei as macro- and micronuclei, gullet, cytoproct

Key:  Nucleus or Endoplasmic Reticulum or Cytoskeleton with microtubules and filaments of actin...

Key:  Proteins are not DNA.  One important difference is that DNA molecules are polymers of nucleotides and proteins are polymers of amino acids.  Another is that DNA contains phosphorus but not sulfur while protein contains sulfur but not phosphorus.  Etc.

What the editorial writer should have said was something like:  The sequence of nucleotides in the DNA of the human (or other organism's) genome codes for all the proteins human (or other organism's) cells can make.  The center will study aspects of how some of those proteins work.

Key:  I'm still not so hot with graphics.  See Fig. 4.4 in your text.

Key:  They have different shapes.  They contain different amino acids.  They are coded for by different genes. Etc.

1. T F     the amoeba cell contains mitochondria.
2. T F     there is a protein in the food vacuole membrane that recognizes the
                    shape of a glucose molecule.
3. T F     the amoeba is an autotrophic organism.
4. T F     the hydrogen and oxygen in some water molecules in the food
                    vacuole become incorporated into organic compounds.
5. T F     the amoeba is prokaryotic.
6. T F     Chlamydomonas has cells that are capable of mitosis.
7. T F     Chlamydomonas has cells with mitochondria.
8. T F     starch can be hydrolyzed to yield proteins.
9. T F     Chlamydomonas is a producer.
10. T F   starch molecules are the products of dehydration synthesis

Important Points from 10/9

• Every aspect of biology requires that we remember events that occur at the level of the cells.
• All organisms are made up of cells.
• Cells were discovered because microscopes allow us to resolve smaller objects than those we can resolve with the unaided eye.  (If you care:  About the smallest separation between objects we can resolve with the unaided eye is about 0.2mm or 200um.  The light microscope increases our level of resolution about 1000 times, and the electron microscope increases it about 1,000,000 times.)
• This synthesis of Schleiden's observations of cells in plants and Schwann's observations of cells in animals is one of the first scientific unifying principles of biology ever stated.

• Cells are living things.
• Cells are the basic living units of living things.
• No part of a cell is a living thing (We'll get to this more in later lectures).
• All organisms on earth are descendants of a common ancestor.
• All cells demonstrate evidence (characters) of that common ancestry.

These are the parts of cells we began to cover on Friday.  They are shown just as they appeared on the transparencies:

CHARACTERS FOUND IN ALL CELLS
 

• PLASMA MEMBRANE (FLUID LAYER THAT FORMS THE BORDER BETWEEN THE INSIDE AND OUTSIDE OF THE CELL
• GENOME (LIBRARY OF INSTRUCTIONS FOR THE WORKINGS OF THE CELL.  COPIED PRIOR TO CELL REPRODUCTION.  DNA)
• CYTOPLASM (JUICY, JELLY-LIKE STUFF INSIDE THE PLASMA MEMBRANE) WITH
• RIBOSOMES (PROTEIN FACTORIES)
• ENZYMES (CATALYTIC PROTEINS THAT CATALYZE SPECIFIC REACTIONS)
• METABOLIC PRODUCTS (CHEMICALS PRODUCED BY THE CHEMICAL REACTIONS MEDIATED BY ENZYMES)
• ATP (ADENOSINE TRIPHOSPHATE, THE ENERGY CURRENCY OF CELLS)
• RAW MATERIALS (SOURCES OF C, H, N, O, P, S, etc.)
• LOTS OF WATER (THE MAJOR SOLVENT IN CELLS)

• USUALLY SURROUNDED BY A CELL WALL
• GENOME NOT SEQUESTERED FROM CYTOPLASM
• CYTOPLASM WITH
• SMALL RIBOSOMES
• RELATIVELY FEW OR NO SPECIAL MEMBRANE-BOUND SPACE

STRUCTURES FOUND IN ALL EUKARYOTIC CELLS

• NUCLEUS (SURROUNDED BY NUCLEAR ENVELOPE PENETRATED BY NUCLEAR PORES.  CONTAINS GENOME ON ONE OR MORE CHROMOSOMES WHERE DNA IS COMPLEXED WITH SPECIAL PROTEINS.  DIVIDES BY MITOSIS) SOME EUKARYOTIC CELLS HAVE MORE THAN ONE NUCLEUS.
• CYTOPLASM WITH
• LARGE RIBOSOMES (USUALLY)
• CYTOSKELETON (MICROTUBULES AND ACTIN FILAMENTS)
• ENDOMEMBRANE SYSTEM (ENDOPLASMIC RETICULUM, SPECIAL VESICLES AND VACUOLES)

• GOLGI APPARATUS (A SPECIALIZED PART OF THE ENDOMEMBRANE SYSTEM INVOLVED IN MODIFYING AND TRANSPORTING PROTEINS)
• FLAGELLA/CILIA (SENSORY AND MOTOR ORGANELLES MADE OF MICROTUBULES AND ASSOCIATED PROTEINS.  ARISE FROM BASAL BODIES [AKA CENTRIOLES].  MAY HAVE BEEN IN ORIGINAL EUKARYOTES AND LOST IN SOME GROUPS.  NOT OF SYMBIOTIC ORIGIN)
• MITOCHONDRIA (DESCENDANTS OF AEROBIC BACTERIA THAT TOOK UP LIVING INSIDE EUKARYOTES AND BECAME PERMANENT COMPONENTS OF THE CYTOPLASM.  FOUND IN ALL AEROBIC EUKARYOTES) WITH
• OUTER MEMBRANE
• INTERMEMBRANE SPACE
• INNER MEMBRANE
• MATRIX (MITOCHONDRIAL CYTOPLASM) WITH
• DEPLETED BACTERIAL GENOME
• ENZYMES OF RESPIRATION
• CHLOROPLASTS (AKA PLASTIDS.  DESCENDANTS OF CYANOBACTERIA THAT TOOK UP LIVING INSIDE SOME AEROBIC EUKARYOTES AND BECAME PERMANENT COMPONENTS OF THE CYTOPLASM.  FOUND IN ALL AUTOTROPHIC EUKARYOTES) WITH
• OUTER MEMBRANE
• INNER MEMBRANE
• STROMA (PLASTID CYTOPLASM) WITH
• DEPLETED CYANOBACTERIAL GENOME
• THYLAKOIDS (MEMBRANE BOUND PHOTOSYNTHETIC SACS)
• ENZYMES OF PHOTOSYNTHESIS

• Some structures of cells are universal
• These structures are mostly derived from the last common ancestor of all organisms.  (For instance, ribosomes were present in the last common ancestor of all organisms)
• The cells of some organisms contain structures not found in other organisms
• These structures are mostly derived from the ancestor of the evolutionary lineage these organisms belong to. (For instance the nucleus is found in the descendants of the last common ancestor of all eukaryotes)

Some important terms and ideas to know for the chemistry of biology:

• Element:  a pure substance that cannot be made lighter (less massive) by normal chemical means
• Basic unit:  an atom
• Components (subatomic particles):  electrons (e-), protons (H+), and maybe neutrons (n).  Each element has a fixed and equal number of protons and electrons per neutral atom, e.g. all neutral carbon atoms have 6 H+ and 6 e-
• Isotopes:  two forms of an element whose atoms differ with respect to the number of neutrons in their nuclei; all isotopes of an element are chemically identical.  E.g., the different isotopes of carbon may have 6, 7, or 8 neutrons to go with the 6 protons in their nuclei.
• Compound:  a pure substance that can be broken down into lighter (less massive) pure substances in fixed proportions by chemical means
• Basic unit:  a molecule (N.B. molecules are units that contain the components of 2 or more atoms.  Therefore, some molecules may contain atoms of only one element, e.g. molecular oxygen O2 or molecular nitrogen N2)
• Ion:  A charged particle of a pure substance where the total number of electrons does not equal the total number of protons (extra electrons results in a negative charge; too few electrons results in a positive charge)
• Chemical bond:  the forces that hold together atoms in a molecule as a result of the way electrons are "shared"
• Ionic bond:  electrons transferred completely between components, oppositely charged ions attract each other, like charged ions repel each other.  Therefore, + - packing results.
• Covalent bond:  electrons shared between components.
• Nonpolar covalent bond:  result of equal sharing of e- by components
• Polar covalent bond:  result of unequal sharing of e- by components; may result in ionization of molecule.  Polar molecules will form hydrogen bonds (Fig. 3.11) with other polar compounds but not with nonpolar compounds.
• Chemical Reaction (Rxn):  an event that takes place when chemical bonds are rearranged among chemicals.

• A major solvent in the chemistry of biology.
• As a rule polar compound will dissolve in water, are hydrophilic
• As a rule nonpolar compounds will not dissolve in water, are hydrophobic
• Water will ionize into H+ and OH- such that at any time pure water will have a pH of 7 (see Fig.3.15)
• Acids will add more H+ to an aqueous solution, lower its pH
• Bases will take up more H+ from an aqueous solution, raise its pH
• Buffers will cause the pH of an aqueous solution to stay about the same even if acids or bases are added to the solution (see Fig. 3.17)

Organic compound:  a compound whose molecules contain Carbon (C) and Hydrogen (H).  (Other elements commonly found in organic compounds: N, O, P, S and others)

• Macromolecules:  organic compounds made up of organic subunits (monomers) bonded together by dehydration synthesis reactions and broken down into monomers by hydrolysis (see Fig. 3.19)
• Some (but not all) important classes of macromolecules (see Table 3.3)
• Carbohydrates (CnH2nOn):  includes monosaccharides (e.g. glucose, fructose, etc.), disaccharides (e.g. sucrose, maltose, etc.), polysaccharides (e.g. cellulose, starch, etc.)
• Lipids (C, H, O, [P, N, S]):  largely nonpolar (phospholipids, steroids) to nonpolar molecules (triglycerides)
• Proteins (C, H, N, O, S):  polymers of amino acids connected by peptide bonds (see Fig 3.26)
• Nucleic Acids (C, H, N, O, P):  polymers of nucleotides (see Fig. 3.28, 3.29) connected by phosphodiester (who cares?) bonds (see Fig. 3.30, 3.31).  For Unit IV, remember, many modified nucleotides are important in transfers of chemical energy during metabolism (e.g., ATP, NAD, NADP)

• Cells (organisms) are chemical systems
• Remember the basic chemistry listed in the notes above
• Water is the important solvent in biological chemistry
• Important compounds in biological chemistry are organic compounds
• All organic compounds contain C and H
• Other important elements in organic compounds include O, N, P, S
• Some important organic compounds are:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

Shape counts!  Shape counts!  Shape counts!  (so do hydrophobicity and hydrophilicity and charge)

Remember, one "goal" of every living organism (cell) is to accumulate building block chemicals that can be used to put together the particular organic compounds it needs.

Therefore, every cell (organism) needs a source of C, H, N, O, P, S, etc.

All organisms are capable of using organic compounds as sources of building blocks.  E.g., all organisms can use glucose as the source of carbon to make the carbon skeleton of amino acids.

Some organisms can use inorganic carbon compounds, e.g., CO2, as their source of carbon.  That is, they can add H and other goodies to carbon fixed from the environment as CO2 and make brand new organic compounds.

• Organisms that can do this are autotrophs (aka producers).
• Autotrophic processes are the part of the Carbon Cycle where C goes from "geo" to "bio".
• Organisms that must get all their C from preexisting organic compounds are heterotrophs (aka consumers).

• Shape counts
• The different molecules of the cell membrane have different shapes and physical and chemical properties.  That helps explain how a membrane works.

• We discussed asexual reproduction of cells
• Offspring of asexual reproduction are genetically identical to their parent
• Cells have a life cycle, the cell cycle
• A new cell is formed from a preexisting cell
• It enters G1 where it accumulates resources and builds necessary molecules, organelles, etc., for the rest of the cell cycle
• If it is to reproduce, the cell enters S, during which the genome is copied, i.e, the DNA is replicated.
• After all the DNA is replicated, the cell produces more products necessary for reproduction.  This is G2.
• When all is ready, then the cell separates the two complete genomes from each other.  This is called M.
• Genome separation in eukaryotes is complex looking and is known as mitosis.
• Genome separation in prokaryotes is less complex looking and really is not given a name.
• After genome separation, the cell can divide.

• Cells (organisms) differentiate
• Why?
• Gotta stay healthy (fit) - At least that's one reason
• How do you stay healthy? - Maintain your organization
• How?
• Use energy sources from the environment
• You need to 'cause you're part of an open system
• Thermodynamics
• 1st Law:  Energy In = Energy Out, but energy can change from one form to another
• 2nd Law:  In a closed system, disorganization increases
• That's cause no energy transformation is completely efficient
• For instance, remember only a tiny percentage of light energy is converted to chemical energy by photosynthesis; all the rest of the energy in light becomes waste (unavailable) energy
• Therefore, living things can be closed systems for only a limited amount of time or they die; they have to be net open systems.
• You can be a closed system while you're living off energy stored in chemical reserves, but once they're gone - Bye Bye!
• Differentiation is often involved in making sure a cell (organism) can remain a net open system.  Remember Phytophthora infestans.

• Cells (organisms) respond to changes in their environment
• You gotta know what's going on out there
• Responses include
• Taking stuff up from outside
• Diffusion (including osmosis Fig. 4.26 and 4.27), Facilitated Diffusion(Fig. 4.31), Active Transport* (Figs 4.32-4.34), Endocytosis* (Fig. 4.29)
• Releasing stuff to the outside
• Diffusion (including osmosis Fig. 4.26 and 4.27), Facilitated Diffusion(Fig. 4.31), Active Transport* (Figs 4.32-4.34), Exocytosis* (Fig. 4.30)
• Moving* and/or reproducing*
• Turning genes on and off*
• This results in changes in the complement of proteins in the cell


*REQUIRES A SOURCE OF ENERGY

Some Review Points for Unit III.

The Origin of Species, by Charles Darwin is an abstract, written to the informed public, of a larger work he never finished. He ends this abstract with one of the most beautifully written (I think) sentences in English literature. This sentence is the hypothesis that all organisms alive today are descended from one or a few original organisms. Because organisms change over time, and because certain changes are favored by the environment and some are not, there will be differential survival leading to the origin of new species. This is a process that is still continuing. Note that Darwin offers no scientific hypothesis concerning how life originated.

There is grandeur in this view of life, with its several powers, having been originally breathed (by the Creator [this was added in later editions]) into a few forms or into one; and that, whilst this planet has gone cycling on according the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved. (Darwin, 1859)

Some Review Points for the Unit III Exam: Keep these in focus for the rest of the course.

Terms to know: Cell, Plasma membrane (=cell membrane), Cytoplasm, Genetic material (=genome, = all the cell's DNA, = the cell's store of instructions), Organic compounds (always contain C and H), Proteins (=polymers of amino acids, = polypeptides, function in cell as structural elements, enzymes, receptors, entry and exit ports, each protein has a unique shape and function), Carbohydrates (includes simple sugars [monosaccharides], and polysaccharides), Lipids (includes tryglycerides and phospholipids among others), Nucleic acids (=polymers of nucleotides, includes DNA and RNA), Hydrolysis, Condensation/Dehydration, Eukaryote, Prokaryote, ATP<->ADP + Pi

Some concepts to understand:

• All organisms are made of cells
• Cells are alive, the smallest living units of living things (i.e., they are living things)
• Cells reproduce
• Cells have an inside and an outside with the plasma membrane as the border
• Membranes have a phospholipid bilayer as a matrix and proteins that act as "border guards"
• Cells need an outside source of energy to stay alive
• A cell makes essentially all of its own proteins
• It takes energy to make proteins (as well as to carry out lots of other metabolic reactions)
• One internal source of energy is ATP
• ATP -> ADP + Pi is the major energy source for many chemical reactions in cells
• It takes an outside source of energy to make ATP (ADP + Pi ->ATP)
• ATP can be made several ways using several different energy sources
• A cell makes essentially all of its own ATP
• Cells contain areas that carry out specific functions
• In eukaryotes, these areas of specific function are often distinct organelles
• An organelle, in many eukaryotes, that makes a lot of ATP is the mitochondrion
• Most of the ATP for "housekeeping metabolism" is generated in the mitochondria of a respiring eukaryote.
• To keep making ATP by respiration, a cell needs a source of organic compounds, e.g., glucose
• Heterotrophic organisms (consumers) get their organic compounds from other organisms.
• Autotrophic organisms (producers) make their own organic compounds using carbon dioxide, a hydrogen source (such as water), and a source of energy
• Photosynthetic autotrophs use light as their energy source
• In photosynthetic eukaryotes, the photosystems are part of the thylakoids membranes of chloroplasts.

• All organisms interact with their environment.
• Living things, organisms, are physical systems, subject to the laws of physics.
• Living things need an outside source of energy, i.e., their source of energy must come from their environment; they are not self-contained.
• Living things need chemical building blocks (nutrients) from their environment.
• Living things release chemicals to the environment.
• Living things interact in various ways with other living things.
• We cannot understand how organisms interact with their environment on the basis of a single observation.
• All organisms are the products of evolution.

Multiple choice.  Indicate the one best answer for each of the following:

1.  The plasma membrane is a structure that is part of:
A.  all living cells.   B. the cells of prokaryotes but not eukaryotes.  C.  the nuclear envelope.  D.  mitochondria.

2.  Which of the following has (have) a body that has no cells?
A.  ferns.   B.  ciliates.  C.  Archaebacteria.  D.  Basidiomycota. E.  None of these.

3.  Which of the following has cells in which mitosis occurs?
A.  ferns.   B.  Basidiomycota.  C.  slime molds (yay!).   D.  Nostoc.  E.  All of these except D.

4.  Which of the following uses energy released from the breakdown of ATP to drive some of its cellular chemical reactions?
A.  The fruitfly, Drosophila melanogaster.  B. a slime mold.  C.  E. coli.  D.  Homo sapiens.  E.  All of these.

5.  Organelles that are involved in the part of the Carbon Cycle where carbon leaves organic compounds and becomes part of an inorganic compound are:
A.  Chloroplasts.  B. Centrioles.  C.  Endoplasmic reticulum.  D.  Mitochondria.  E.  Nuclei.

6.  A typical enzyme is:
A.  a lipid.  B.  an inorganic compound.  C. made of one or more polymers of amino acids.  D.  a polysaccharide.  E. DNA.

7.  The 2000 Nobel Prize in Physiology or Medicine went to biologists whose interest is in:
A.  how cells divide.  B.  how cells communicate.   C. nerve cells.  D. B and C.  E.  all of these.

True/False.  Below each of the following questions or statements are a number of responses that may be true or false.  Indicate which responses are true and which are false.

An organelle that is involved in the part of the Carbon Cycle where carbon from carbon dioxide is incorporated into organic compounds:

8.    T    F    would be found in an autotrophic eukaryote
9.    T   F    is a mitochondrion
10.  T    F    would typically be found in some of the cells of a fern
11.  T   F    is found in all cells of a mouse
12.  T    F    is a chloroplast

An organic compound is broken down into its constituent elements.  It is found to have one part carbon to one part oxygen to two parts hydrogen.

13.  T   F  This compound could be a fat.
14.  T    F  This compound could be glucose.
15.  T    F  This compound is a carbohydrate.
16.  T   F  This compound is an amino acid.

Organic compounds that are part of the Nitrogen Cycle include:

17.  T    F  DNA
18.  T    F  ATP
19.  T    F  Proteins
20.  T   F  Glucose

Mutations are changes in:

21.  T    F  DNA
22.  T   F  molecules that include carbon, hydrogen, oxygen, nitrogen, and sulfur
23.  T    F  molecules that include carbon, hydrogen, oxygen, nitrogen, and phosphorus
24.  T   F  polysaccharide molecules

New questions, a mixture of multiple choice and TF:

25.  A phospholipid bilayer makes up much of the plasma membrane of cells.  Which of the following organelles in a mouse cell would also have a phospholipid bilayer as one of its components?

A.  Chromosomes.  B.  Ribosomes.  C.  Mitochondria.  D.  Chloroplasts.  E.  Centrioles.

26.  Which of the following can cross a biological membrane without the aid of proteins?

A.  Glucose.   B.  Ions.   C.  Protons.  D.  Water.  E.  Proteins.

27.  Offspring nuclei that are the products of mitosis will contain ______ the same genes that were in the parent nucleus.

A.  half   B.  one third   C.  one quarter   D.  none of E. all

TF A chicken nerve cell is concentrating sodium ions inside the plasma membrane.  This will require that the cell:

28.    T    F    break down some ATP
29.    T    F    have special sodium transporting proteins in its plasma membrane
30.    T F    be able to carry out photosynthesis

TF    __________must precede mitosis in a eukaryotic cell.

31.    T    F    S phase of the cell cycle
32.    T    F    DNA replication
33.    T    F    G2 phase of the cell cycle
34.    T F    Cell division  (This is a mean one.  You may want to find out something about the Zygomycota.)

35.  Which of the following will not pass readily through a pure phospholipid bilayer?

A.  H2O molecules.   B.  O2.  C.  CO2.   D.  H+.   E.  A, B, and C.

TF  An autotrophic eukaryotic cell will contain:

36.    T    F    ER
37.    T    F    organelles with thylakoids.
38.    T    F    three kinds of organelles contain DNA (This is harder than will be on the exam, but try it.)
39.    T    F    mitochondria
40.    T F    DNA that is not sequestered from the cytoplasm by membranes.
41.    T    F    an enzyme(s) that adds CO2 to organic compounds.
42.    T F    two kinds of organelles that are descendants of archaebacteria (Another too hard one)
 

TF    __________must precede mitosis in a prokaryotic cell.

43.    T    F    S phase of the cell cycle
44.    T    F    DNA replication
45.    T    F    G2 phase of the cell cycle
46.    T F    Cell division

Boo! Dr. Spiegel screwed up here!

Oops! The 11:30 group caught me making a mistake on 43-46.  I did not read my question carefully, as I hurried to send out the key.  Prokaryotic cells do not undergo mitosis; therefore, none of these processes precedes mitosis in a prokaryotic cell.  All the responses are FALSE.  NICE JOB, 11:30 FOLKS!
I promise I am much more careful with the keys on the real thing.
 

47.  Which of the following compounds are not directly part of the Nitrogen Cycle?

A.  Proteins.   B.  ATP.   C.  DNA.  D.  Triglycerides.  E.  Amino acids.

TF    Hydrolysis is a class of reactions associated with:

48.    T    F    the breakdown of proteins into amino acids.
49.    T F    the synthesis of starch.
50.    T or  F    the synthesis of DNA from nucleotides. (This is a really mean one that I just caught myself on.  DNA is polymerized by dehydration synthesis so if that's all you thought of, you would be justified in answering F.  However, it is the case that the nucleotides that are the building blocks of DNA are "charged up" with some extra phosphate groups, and these are hydrolyzed from the building blocks prior to the dehydration synthesis.  If you go on in biology, you'll learn the details later on.)
 

Try these out, and look for more soon.  I know we have not covered some of this stuff yet, but we will.  It's a good way to get ahead in the course to try to answer these questions now.  I'll put up a key by early next week.