PART I CELL BIOLOGY

2
THE MOLECULES
OF

CELLS

CHAPTER REVIEW
All matter is composed of some 92 elements. Each element is made up of just one type of atom. An atom has a weight, which is dependent on the number of protons and neutrons in the nucleus, and its chemical properties are dependent on the number of electrons in the outer shell. Atoms react with one another by forming ionic bonds or covalent bonds. Ionic bonds are an attraction between charged ions. Atoms share electrons in covalent bonds, which can be single, double, or triple bonds. Oxidation is the loss of electrons (hydrogen atoms) and reduction is the gain of electrons (hydrogen atoms). Water, acids, and bases are important inorganic molecules. The polarity of water accounts for it being the universal solvent; hydrogen bonding accounts for it boiling at 100C and freezing at 0C. Because it is slow to heat up and slow to freeze, it is in liquid form at the temperature of living things. Pure water has a neutral pH; acids increase the hydrogen ion concentration [H +] but decrease the pH, and bases decrease the hydrogen ion concentration [OH ] but increase the pH of water. The chemistry of carbon accounts for the chemistry of organic compounds. Carbohydrates, lipids, proteins, and nucleic acids are macromolecules with specific functions in cells. Macromolecules are polymers that each contain (a) specific monomer(s). Glucose is the six-carbon sugar most utilized by cells for quick energy. Like the rest of the macromolecules to be studied, a condensation synthesis joins two or more sugars and a hydrolysis reaction splits the bond. Plants store glucose as starch, and animals store glucose as glycogen. Humans cannot digest cellulose, which forms plant cell walls. Lipids are varied in structure and function. Fats and oils, which function in long-term energy storage, contain glycerol and three fatty acids. Fatty acids can be saturated or unsaturated. Cell membranes contain phospholipids that have a polarized end. Certain hormones are derived from cholesterol, a complex ring compound. The primary structure of a protein is its own particular sequence of the possible twenty types of amino acids. The secondary structure is often an alpha helix. The tertiary structure occurs when the molecules bend and twist into a three-dimensional shape. Proteins can contain several polypeptides, and this accounts for a possible quaternary structure. Nucleic acids ( DNA and RNA ) are polymers of nucleotides, which have three parts: pentose sugar, nitrogen base, and phosphate. ATP, the high-energy molecule of cells, is a nucleotide with three phosphates.

S T U DY E X E R C I S E S
Study the text section by section as you answer the questions that follow.

2.1 ELEMENTS

AND

ATOMS(P . 20)

All matter is composed of elements, each having one type of atom. 1. Name the six elements commonly found in living things. ____________________________________________________ _____________________________________________________________________________________________________________

2. What subatomic particles are in the nucleus and the shells of an atom? nucleus
a.

______________

shells c. ______________

b. ______________ 3. The atomic number of fluorine is 9. How many protons does fluorine have? a. ______________ How many electrons does fluorine have when neutral? b. ______________. The atomic weight of fluorine is 19. How many neutrons does fluorine have? c. ______________ Diagram the structure of fluorine. Draw small circles to indicate the distribution of electrons in concentric levels around the nucleus. In the nucleus, indicate the number of protons and neutrons. d.

C and 13 C. 4. Two isotopes of carbon are 12 6 6 Do isotopes of carbon differ according to their atomic number? a. ______ number of electrons? b. ______ number of neutrons? c. ______

2.2 MOLECULES

AND

COMPOUNDS (P . 23)

Atoms react with one another, forming ions, molecules, and compounds. 5. Calcium (Ca) has an atomic number of 12; chlorine (Cl) has an atomic number of 17. The number of electrons in the outer shell of calcium is The number of electrons in the outer shell of chlorine is In a chemical reaction between these two atoms, ______________ chlorine atom(s). Which element will gain electrons in this reaction? What will its charge be after the reaction? What will its charge be after the reaction? Which element will lose electrons in this reaction? What type of bond forms between these two atoms?
d. ______________ a. ______________. b. ______________.

c. ______________

calcium atom(s) will react with

e. ______________ f. ______________

g. ______________ h. ______________ i. ______________

Write the formula for the compound produced through this chemical reaction.

6. Water is a polar molecule. a. Indicate on the following diagram which atoms are electronegative and which are electropositive in relation to the others. Put a + charge and charges where appropriate. b. Label a hydrogen bond.

7. Label each of the following statements as describing covalent bonding (C), ionic bonding (I), or hydrogen bonding (H): a. Electrons transfer between atoms. b. Atoms share electrons. c. This bond is present in sodium chloride. d. This bond is present in the oxygen molecule. e. A triple bond of this type is present in nitrogen gas. f. This bond forms between water molecules. g. The hydrogen atom in one molecule is attracted to the oxygen atom of another molecule. h. This bond forms within a water molecule. 8. Consider the following chemical reaction between a potassium (K) atom (atomic number 19) and a fluorine (F) atom (atomic number 9): K + F KF. Which atom is reduced in this reaction? Which atom is oxidized in this reaction? Write a short definition of oxidation. Write a short definition of reduction.
a. ______________ b. ______________

c. ______________ d. ______________

2.3 WATER

AND

LIVING THINGS (P . 26)

The existence of living things dependent on the characteristics of water. 9. In each of the pairs of statements that follow, check the one that correctly describes how hydrogen bonding affects the properties of water. Hydrogen bonding causes water Pair 1 a. to boil at a lower temperature than expected. b. to boil at a higher temperature than expected. Pair 2 c. to be more dense as ice than as liquid water. d. to be less dense as ice than as liquid water. Pair 3 e. to absorb heat with a minimal change in temperature. f. to absorb heat with a maximum change in temperature. Pair 4 g. to be cohesivethe water molecules cling to each other. h. molecules to shun one another. 10

10. Refer to the chemical properties of water when answering the following questions: What makes water a good solvent?
a.

________________________________________________________________
b.

_________________________________________________________________________________________________ How does water moderate temperatures? What allows ice to float on liquid water? ___________________________________________________________ ___________________________________________________________ _________________________________________________________________________________________________
c.

_________________________________________________________________________________________________ Acidic and Basic Solutions (p. 28) The hydrogen ion concentration in water changes when acids or bases are added to water. 11. Label each of the following statements as describing an acid (A) or a base (B): a. They take up hydrogen ions in solution. b. HCl is an example. c. NaOH is an example. d. They release hydrogen ions in solution. e. They lower the pH. f. They raise the pH. 12. Complete the table for the following hydrogen ion concentrations [H + ]:
[H + ] 1 10 7 1 10 3 1 10 8 pH Acid/Base/Neutral

13. Indicate whether the following statements are true (T) or false (F): a. If the pH of blood changes from 7.4 to 7.6, it becomes more acidic. b. When an acid is added to a solution, the pH decreases. c. A basic pH indicates that OH ions outnumber H + ions. d. An acidic pH indicates that H + ions outnumber OH ions. 14. The following questions relate to buffers: How do living things prevent drastic changes in pH?
a.

________________________________________________________________________________________________

_________________________________________________________________________________________________ Complete the following reaction, showing how the carbonic acid buffer system deals with increasing hydrogen ions in the blood: H + + HCO 3 hydrogen ions in the blood: H 2 CO 3
c. ______________ b.______________

Complete the following reaction, showing how the carbonic acid buffer system deals with decreasing

11

2.4 ORGANIC MOLECULES (P . 31)

Macromolecules are polymers that arise when their specific monomers (unit molecules) join together. The macromolecules found in cells are carbohydrates, lipids, proteins, and nucleic acids. 15. Indicate whether the following statements about a carbon atom are true (T) or false (F): a. There are two electrons in its outer shell. b. It can bond to other carbon atoms. c. It can share two pairs of electrons with another atom. d. Chains of fifty atoms are unusual in living systems. 16. For each term on the left, write in the corresponding term; the first one is completed for you. polymer polysaccharide fat protein nucleic acid monomer
a. ______________ b. d. e.

______________ ______________ ______________

and c. ______________

17. Label this diagram with the following terms: condensation hydrolysis monomers polymer synthesis
a.

b. H

OH H OH H OH H

OH

c.

H2O

H2O

H d.

OH

During hydrolysis, is water added to or taken away from the reactants?

e.

______________

During condensation synthesis, is water added to or taken away from the reactants? f. ______________

2.5 CARBOHYDRATES (P . 32)

Carbohydrates function as a ready source of energy in most organisms. Glucose is a simple sugar; starch, glycogen, and cellulose are polymers of glucose. Cellulose lends structural support to plant cell walls. 18. Write the molecular formula beneath glucose by indicating the number of carbons, hydrogens, and oxygens.
CH2OH
6 5

H
4

O
1

OH HO
3

H
2

OH

OH

12

19. Complete the following table:

Carbohydrate sucrose maltose starch glycogen cellulose a. c. e. g. i. Mono/di/polysaccharide? b. d. f. h. j. Biological Significance

2.6 LIPIDS (P . 34)

Lipids are varied molecules. Fats and oils, which function in long-term energy storage, are composed of glycerol and three fatty acids. Sex hormones are derived from cholesterol, a complex ring compound. 20. Complete the following table:
Lipid fats and oils phospholipids a. c. Monomers b. d. Biological Functions

21. Write the word saturated or unsaturated beneath the appropriate structure.

a.

b.

22. In this representation of a fat, draw a circle around the portion that is derived from glycerol. Draw lines under the portions that are derived from fatty acids.

23. When phospholipids are placed in water, the

a.

______________ face outward and the

c.

b.

______________ face

each other. This property makes phospholipids suitable molecules to form the

______________ of cells.

13

24. Examples of steroids are

a.

_______________________ and

b.

____________________.

25. Each steroid differs from other steroids by the ______________ attached to the ring.

2.7 PROTEINS (P . 37)

Proteins help form structures (e.g., muscles and membranes) and function as enzymes. Proteins are polymers of amino acids. 26. Label this diagram with the following terms acid (carboxyl) group, amino acid, amino group, and peptide bond (one term is used more than once).
a. _____________ b. _____________ d. _____________

H e. _______ H N

H C C

O OH

+
H

H N

R
C H C

OH O

Condensation

H H N

H C

O C N H

R
C H C

OH c. _______ O

Hydrolysis

27. Study this representation of a polypeptide.

This is the

a.

______________ structure of a protein.

b. ______________________________________________________________________________

What are R groups?

_________________________________________________________________________________________________ What shapes do the secondary structure of a protein normally assume? How does the tertiary shape of a globular protein come about? What would cause a protein to have a quaternary shape?
f. e. c.

______________
d.

What type of bond between amino acids is necessary to maintain secondary shape?

______________

________________________________________

_________________________________________________________________________________________________ _____________________________________________ _________________________________________________________________________________________________ _________________________________________________________________________________________________

2.8 NUCLEIC ACIDS (P . 40)

Nucleic acids are polymers of nucleotides. Genes are composed of DNA (deoxyribonucleic acid). DNA specifies the correct ordering of amino acids in proteins, with RNA as an intermediary.

14

28. On this diagram, label the following components of a nucleotide: base phosphate sugar a.

O b.

O HO P OH O c.

29. Study this representation of a nucleic acid.

Which molecules make up the backbone of a nucleic acid? Which molecules project to one side of the backbone?

a. ______________

b. ______________

30. a. Complete the following table to distinguish DNA from RNA:

DNA Sugar Bases Strands Helix a. c. e. g.
i.

RNA b. d. f. h.

What are the functions of DNA and RNA?

__________________________________________________________

_________________________________________________________________________________________________

15

ATP (Adenosine Triphosphate) (p. 41) 31. ATP is a(n) carbon

a. ______________;

its structure consists of three

b. ______________ groups

attached to the fivethey break down

c. ______________ of

the molecule.
a. ______________.

32. Complete this reaction: ATP ADP + P + the molecule

c. ______________.

When cells need

b. ______________,

Organic Chemistry Las Vegas Style

Assume that organic molecules have the following worth: amino acid 25 glucose 20 nucleotide 15 glycerol 10 fatty acid 5 1. How much should you bid in total for your first three cards? a.

H b. H N

H C C

OH R c. sugar-thymine phosphate How much should you raise in total for your next two cards? H d. H N H O C R H e. H H H C C C H 2. The next dealer opens a new deck of cards. How much should you bet in total for your first three cards? a. nucleic acid containing 100 units b. protein containing 150 units c. polysaccharide containing 50 units How much should you raise in total for your next two cards? d. tripeptide e. disaccharide 16 O O O O C O C O C (CH2)n (CH2)n (CH2)n CH3 CH3 CH3 C H N H C R C OH O

3. The next dealer has his own cards. How much should you bet, assuming that your first three cards are valued at their unit value? a. gene b. quick energy c. enzyme How much should you raise in total for your next two cards which are valued at their unit value? d. long-term stored energy e. plant structure 4. The next dealer opens her deck of cards. How much should you bet in total, assuming that each of your first three cards is the value of its matched molecule? a. peptide bond b. unsaturated c. straight chain of ring compounds How much should you raise for your next two cards? d. contains nitrogen e. contains a free carboxyl (acid) grouping 5. This dealer deals again. How much should you bet, assuming that each of your first three cards is the value of its matched molecule? a. DNA b. hydrocarbon chain c. ribose How much should you raise in total for your next two cards? d. glycogen e. amino group

CHAPTER TEST
OBJECTIVE QUESTIONS
Do not refer to the text when taking this test. ____ 1. The atomic weight of an atom is determined by the number of a. protons. b. neutrons. c. electrons. d. protons and neutrons. ____ 2. Isotopes differ due to the number of a. protons. b. neutrons. c. electrons. d. protons and neutrons. ____ 3. When an atom either gains or loses an electron, it becomes a. electrically neutral. b. an ion. c. stable. d. unreactive. ____ 4. Chlorine has 17 protons. When chlorine becomes the chloride ion (Cl ), it has a. gained an electron. b. lost an electron. c. gained a proton. d. lost a neutron.

17

____ 5. When sodium interacts with chlorine, sodium loses an electron while chlorine gains one. This interaction forms a. an ionic bond. b. a condensation synthesis. c. a condensation. d. a covalent bond. ____ 6. Bonds between carbon and hydrogen, or oxygen and hydrogen are generally a. hydrogen bonds. b. ionic bonds. c. covalent bonds. d. weak and highly transient. ____ 7. When a strong acid, such as hydrochloric acid, is added to water, a. hydrogen ions are taken up. b. hydroxide ions are released. c. hydrogen ions are released. d. the pH stays the same. ____ 8. A pH of 11.5 is considered to be a. slightly acidic. b. strongly acidic. c. strongly basic. d. about neutral. ____ 9. Which of these is true of organic molecules? a. usually ionic bonding b. always contain carbon and hydrogen c. mainly associated with nonliving matter d. are found only in organisms with organ systems ____10. Polymers are a. chains of building-block molecules. b. formed by dehydration. c. broken down by hydrolysis. d. All of these are correct. ____11. Which pair of molecules is mismatched? a. amino acid protein b. fatty acid lipid c. glucose starch d. glycerol nucleic acid For questions 1216, match the following answers for lipids to one of the statements that follows. a. triglyceride b. unsaturated fatty acid c. saturated fatty acid d. phospholipid e. soap ____12. Not truly a lipid, this substance helps to emulsify fats. ____13. Has one or more double bonds along the fatty acid chain. ____14. Made up of a glycerol and three fatty acid molecules. ____15. Has hydrogen at every position along the fatty acid chain. ____16. A major component of cell membranes.

____17. Which molecule is unsaturated?

____18. The primary structure of a protein refers to its a. three-dimensional shape. b. order of amino acids. c. order of nucleic acids. d. orientation of the amino acids. ____19. Proteins are polymers of ____________________ , which sometimes function to ________________. a. amino acids, catalyze chemical reactions b. glucose, build muscle strength c. nucleotides, synthesize proteins d. ribosomes, produce quick energy ____20. In any amino acid, NH2 is the ______________ group, and COOH is the _____________ group. a. carboxyl; amino b. amino; carboxyl c. peptide; fatty acid d. hydroxyl; carboxyl ____21. A bond forming between the NH 2 group of one amino acid and the COOH group of another amino acid is called a a. double bond. b. ionic bond. c. hydrogen bond. d. peptide bond. ____22. Twisting of a chain of amino acids into an helix is termed the _______________ structure of a protein. a. primary b. secondary c. tertiary d. quaternary For questions 2326, match the four terms to the statements that follow. a. RNA b. DNA c. nucleotide d. ATP ____23. Building block of the nucleic acids. ____24. Functions with DNA in the process of protein synthesis. ____25. The genetic material of the cell. ____26. The energy currency of the cell.

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THOUGHT QUESTIONS
Answer in complete sentences. 27. Soaps and water mix but oil and water do not mix. Explain Why, when soap is added to an oil, the oil will then mix with water.

28. How does the primary structure of a polypeptide determine its secondary structure?

Test Results: ______ Number right 28 = ______ 100 = ______ %

ANSWER KEY
STUDY EXERCISES
1. carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur 2. a. protons b. neutrons c. electrons 3. a. nine b. nine c. ten d. 7. a. I b. C c. I d. C e. C f. H g. H h. C 8. a. F b. K c. loss of electrons d. gain of electrons 9. b, d, e, g 10. a. The partial charges of the water molecule attract and disperse charged particles in solution. b. It takes up and releases large amounts of heat without much change in temperature. c. Water is most dense at 4 C. It expands as the temperature drops from this point; it is less dense at 0 C, the temperature of ice. 11. a. B b. A c. B d. A e. A f. B 12.
pH 7 3 Acid/Base/Neutral neutral acid base

9P 10 N

4. a. no b. no c. yes 5. a. two b. seven c. one, two d. Cl e. 1 f. Ca g. + 2 h. ionic i. CaCl 2 7. a. T b. F c. T d. F e. T 8. a. orbitals b. spherical c. spherical d. dumbbell 9. a. two b. seven 10. a. S b. Ne c. S has six electrons in its outer shell, and if it reacts to gain two more it will have a stable outer configuration of eight; Ne already has a stable outer shell. 6.

13. a. F b. T c. T d. T 14. a. The pH is stabilized through the action of buffers, which are chemical systems that absorb either H + or OH to keep the pH steady. b. H 2 CO 3 c. HCO 3 + H + 15. a. F b. T c. T d. F 16. a. glucose b. glycerol c. fatty acid d. amino acid e. nucleic acid 17. a. hydrolysis b. monomers c. condensation synthesis d. polymer e. added f. taken away 18. a. C 6 H 12 O 6 19.a. di b. table sugar derived from sugar cane and beets c. di d. breakdown product of starch e. poly f. short-term energy storage in plants g. poly h. short-term energy storage in animals i. poly j. plant cell walls 20. a. glycerol, three fatty acids b. longterm energy storage c. glycerol, two fatty acids, phosphate group d. plasma membrane structure 21. a. unsaturated b. saturated

19

22.

ORGANIC CHEMISTRY LAS VEGAS STYLE

1. a. .40 b. .25 c. .15 = $ .80 d. .50 e. .25 = $ .75 2. a. 100 .15 = $15.00 b. 150 .25 = 37.50 c. 50 .20 = 10.00 $62.50 d. 3 .25 = $ .75 e. 2 .20 = .40 $ 1.15 3. a. .15 b. .20 c. .25 = $ .60 d. .15 e. .20 = $ .35 4. a. .25 b. .05 c. .20 = $ .50 d. .25 + .15 = $ .40 e. .25 + .05 = .30 $ .70 5. a. .15 b. .05 c. .15 = $ .35 d. .20 e. .25 = $ .45

23. a. polar heads b. nonpolar tails c. plasma membrane 24. a. cholesterol b. aldosterone 25. functional groups 26. a. amino acid b. amino acid c. acid (carboxyl) group d. peptide bond e. amino group 27. a. primary b. they represent the variable parts of the amino acids (i.e., H, CH3, C chain, C ring) c. (alpha) helix and (beta) sheet d. hydrogen e. folding and twisting of polypeptide f. if it contained more than one polypeptide 28. a. base b. sugar c. phosphate 29. a. S P (sugar-phosphate) b. B (bases) 30. a. deoxyribose b. ribose c. ATCG d. AUCG e. double stranded f. single stranded g. yes h. no i. DNA stores information regarding the order of amino acids in a polypeptide (protein); RNA carries this information as an intermediary for the process of protein synthesis. 31. a. nucleotide b. phosphate c. sugar 32. a. energy b. energy c. ATP

CHAPTER TEST
1. d 2. b 3. b 4. a 5. a 6. c 7. c 8. c 9. b 10. d 11. d 12. e 13. b 14. a 15. c 16. d 17. b 18. b 19. a 20. b. 21. d 22. b 23. c 24. a 25. b 26. d 27. Soaps have a polar and nonpolar end. The nonpolar ends of the soap project into the nonpolar oil droplet while the polar ends of the soap project outward into the water, which is polar. 28. The secondary structure of a polypeptide depends on hydrogen bonding between the R groups of the amino acids making up the polypeptide. Each particular polypeptide has its own sequence of amino acids and therefore R groups.

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