2.3 from atoms to molecules 28 2.4 hydrogen bonds and ... · a shell model of an atom represents...

Molecules of Life

2.1 Fear of Frying 24

2.2 Start With Atoms 25

2.3 From Atoms to Molecules 28

2.4 Hydrogen Bonds and Water 30

2.5 Acids and Bases 32

2.6 Organic Molecules 33

2.7 Carbohydrates 34

2.8 Lipids 36

2.9 Proteins 38

2.10 Nucleic Acids 41

2.11 Fear of Frying (revisited) 41

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42 Unit One How Cells Work

SummarySection 2.1 All organisms consist of the same kinds of molecules. Seemingly small differences in the way those molecules are put together can have big effects inside a living organism.

Section 2.2 Atoms consist of electrons, which carry a negative charge, moving about a nucleus of positively charged protons and uncharged neutrons. The number of protons (the atomic number) determines the element; isotopes of an element differ in the num-ber of neutrons. The total number of protons and neutrons is the mass number. Tracers can be made with radioisotopes, which spontaneously emit particles and energy by radioactive decay. A shell model of an atom represents electron energy levels as concentric circles. Atoms tend to get rid of vacancies. Many do so by gaining or losing electrons, thereby becoming ions. Free radicals (atoms with unpaired electrons) tend to be very active chemically.

Section 2.3 Chemical bonds join atoms as molecules. A compound consists of two or more elements. An ionic bond is a strong mutual attraction of oppositely charged ions. Atoms share a pair of electrons in a covalent bond. Covalent bonds have polarity if the electrons are not shared equally.

Section 2.4 The two polar covalent bonds in water molecules give rise to an overall polarity of the mol-ecule. Hydrogen bonds that form among water molecules in tremendous numbers are the basis of water’s unique properties: a capacity to act as a sol-vent for salts and other polar solutes; resistance to temperature changes; and cohesion. Hydrophilic substances dissolve easily in water to form solutions; hydrophobic substances do not. evaporation is the transition of liquid to vapor.

Section 2.5 A solute’s concentration refers to the amount of solute in a given volume of fluid; pH reflects the number of hydrogen ions (H+). At neutral pH (7), the amounts of H+ and OH– ions are equal. Acids release hydrogen ions in water; bases accept them. A buffer can keep a solution within a consistent range of pH.

Most cell and body fluids are buffered because most molecules of life work only within a narrow range of pH.

Section 2.6 The molecules of life are organic, so they consist mainly of carbon and hydrogen atoms. Chains or rings of carbon atoms form the backbones of these molecules. Cells build complex carbohydrates, lipids, proteins, and nucleic acids from monomers of simple sugars, fatty acids, amino acids, and nucleotides, respectively. Reactions that assemble and break down these polymers require enzymes and are part of metabolism.

Section 2.7 Enzymes assemble complex carbohydrates such as cellulose, glycogen, and starch from simple car-bohydrate (sugar) subunits. Cells use carbohydrates for energy, and as structural materials.

Section 2.8 Cells use lipids for energy and as structural materials. Fats have fatty acid tails; triglycerides have three. Saturated fats are mainly triglycerides with three satu-rated fatty acid tails (only single bonds link their carbons). unsaturated fats are mainly triglycerides with one or more unsaturated fatty acids. A lipid bilayer (of mainly phospholipids) is the structural foundation of all cell membranes. Waxes are part of water-repellent and lubricating secretions. Steroids occur in cell membranes; some are remodeled into other molecules.

Section 2.9 The shape of a protein is the source of its function. Protein structure begins as a linear sequence of amino acids linked by peptide bonds into a polypeptide. Polypeptides twist into loops, sheets, and coils that can pack further into func-

tional domains. Many proteins, including most enzymes, consist of two or more polypeptides. Fibrous proteins aggregate into much larger structures. A protein’s shape may be disrupted by shifts in pH or temperature, or exposure to detergent or some salts. If that hap-pens, the protein unravels, or denatures, and it loses its function. Prion diseases are a consequence of misfolded proteins.

Section 2.10 Nucleotides consist of a sugar, a phos-phate group, and a nitrogen-containing base. Nucleotides are monomers of DNA and rNA, which are nucleic acids. Some nucleotides have additional functions. For example, ATP energizes many kinds of molecules by phosphate-group transfers. DNA encodes heritable infor-mation that guides the synthesis of RNA and proteins. RNA molecules carry out protein synthesis.

Self-Quiz AnswersinAppendixI

1. Which of the following statements is incorrect? a. Isotopes have the same atomic number and different mass numbers.b. Atoms have about the same number of electrons as protons. c. All ions are atoms.d. Free radicals are dangerous because they emit energy.e. A carbon atom can share electrons with up to 4 other atoms.

2. What is the name of an atom that has one proton and no elec-trons?

3. The mutual attraction of opposite charges holds atoms together as molecules in a(n) bond.

a. ionic c. polar covalentb. hydrogen d. nonpolar covalent

4. Rank the following types of bonds by polarity, with 1 being the least polar, and 3 being the most polar:

1 a. ionic 2 b. polar covalent 3 c. nonpolar covalent

5. A(n) substance repels water.a. acidic c. hydrophobicb. basic d. polar

6. When dissolved in water, a(n) donates H+ and a(n) accepts H+.

a. acid; base c. buffer; soluteb. base; acid d. base; buffer

glucoseglucose

vacancy



Chapter 2 Molecules of Life 43

15. Match each molecule with its component(s). protein a. glycerol, fatty acids, phosphate phospholipid b. glycerol, fatty acids fat c. nucleotide monomers nucleic acid d. glucose monomers cellulose e. sugar, phosphate, base nucleotide f. amino acid monomers wax g. glucose, fructose sucrose h. fatty acids, carbon rings

Critical Thinking1. Alchemists were the forerunners of modern-day chemists. Many of these medieval scholars and philosophers spent their lives trying to transform lead (atomic number 82) into gold (atomic number 79). Explain why they never did succeed in that endeavor.

2. Draw a shell model of a lithium atom (Li), which has 3 protons, then predict whether the majority of lithium atoms on Earth are uncharged, positively charged, or negatively charged.

3. Polonium is a rare element with 33 radioisotopes. The most common one, 210Po, has 82 protons and 128 neutrons. When 210Po decays, it emits an alpha particle, which is a helium nucleus (2 pro-tons and 2 neutrons). 210Po decay is tricky to detect because alpha particles do not carry very much energy compared to other forms of radiation. They can be stopped by, for example, a sheet of paper or a few inches of air. That is one reason that authorities failed to discover toxic amounts of 210Po in the body of former KGB agent Alexander Litvinenko until after he died suddenly and mysteriously in 2006. What element does an atom of 210Po change into after it emits an alpha particle?

4. In the following list, identify the carbohydrate, the fatty acid, the amino acid, and the polypeptide:

a. NH2—CHR—COOH c. (methionine)20b. C6H12O6 d. CH3(CH2)16COOH

7. is a simple sugar (a monosaccharide).a. Glucose c. Ribose e. a and cb. Sucrose d. Starch f. a, b, and c

8. Unlike saturated fats, the fatty acid tails of unsaturated fats incorporate one or more .

a. phosphate groups c. double bondsb. glycerols d. single bonds

9. Which of the following is a class of molecules that encompasses all of the other molecules listed?

a. triglycerides c. waxes e. lipids b. fatty acids d. steroids f. phospholipids

10. are to proteins as are to nucleic acids.a. Sugars; lipids c. Amino acids; hydrogen bondsb. Sugars; proteins d. Amino acids; nucleotides

11. A denatured protein has lost its .a. hydrogen bonds c. functionb. shape d. all of the above

12. Which of the following are not found in DNA?a. amino acids c. nucleotidesb. sugars d. phosphate groups

13. Match the terms with their most suitable description. hydrophilic a. protons > electrons atomic number b. number of protons in nucleus hydrogen bonds c. polar; dissolves easily in water positive charge d. collectively strong temperature e. protons < electrons negative charge f. measure of molecular motion

14. Match each molecule with its most suitable description. wax a. protein primary structure starch b. an energy carrier triglyceride c. water-repellent secretions DNA d. carries heritable information polypeptide e. sugar storage in plants ATP f. richest energy source in animals

Digging into DataEffects of Dietary Fats on Lipoprotein Levels

Cholesterol that is made by the liver or that enters the body from food does not dissolve in blood, so it is carried through the bloodstream by lipoproteins. Low-density lipoprotein (LDL) carries cholesterol to body tissues such as artery walls, where it can form deposits associated with cardiovascular disease. Thus, LDL is often called “bad” cholesterol. High-density lipoprotein (HDL) carries cholesterol away from tissues to the liver for disposal, so HDL is often called “good” cholesterol. In 1990, Ronald Mensink and Martijn Katan published a study that tested the effects of different dietary fats on blood lipoprotein levels. Their results are shown in Figure 2.23.

1. In which group was the level of LDL (“bad” cholesterol) highest?

2. In which group was the level of HDL (“good” cholesterol) lowest?

3. An elevated risk of heart disease has been correlated with increas-ing LDL-to-HDL ratios. Rank the three diets according to their predicted effect on cardiovascular health.

Figure 2.23 Effect of diet on lipoprotein levels. Researchers placed 59 men and women on a diet in which 10 percent of their daily energy intake consisted of cis fatty acids, trans fatty acids, or saturated fats. Blood LDL and HDL levels were measured after three weeks on the diet; averaged results are shown in mg/dL (milligrams per deciliter of blood). All subjects were tested on each of the diets. The ratio of LDL to HDL is also shown.This lipoprotein image was made by Amy Shih and John Stone using VMD and is owned by the Theoretical and Com-putational Biophysics Group, NIH Resource for Macromolecular Modeling and Bioinformatics, at the Beckman Institute, University of Illinois at Urbana-Champaign. Labels added to the original image by book author.

Main Dietary Fats

cis fattyacids

103

55

1.87

optimallevel

<100

>40

<2

trans fattyacids

117

48

2.44

saturatedfats

121

55

2.2

LDL

HDL

ratioan HDL particle

lipidprotein



2.3 from atoms to molecules 28 2.4 hydrogen bonds and ... · a shell model of an atom represents...

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