1. Chapter 3 Molecules of Life

2. 3.1 Fear of Frying
Trans fats in hydrogenated vegetable oil raise levels of cholesterol in our blood more than any other fat, and directly alter blood vessel function

3. Trans Fats
Trans fats
Partially hydrogenated vegetable oils formed by a chemical hydrogenation process
Double bond straightens the molecule
Pack tightly; solid at room temperature
Bonds are cis or trans, depending on the way the hydrogens are arranged around them

4. Cis and Trans Fatty Acids
A Oleic acid, a cis fatty acid.
Figure 3.1 Trans fats, an unhealthy food. A fat has three fatty acid tails, each a long carbon chain. Hydrogenation changes the arrangement of hydrogen atoms around double bonds in those chains from (A) a cis configuration to (B) a trans configuration. This small difference in structure makes a big difference in our bodies.
B Elaidic acid, a trans fatty acid.

5. 3.2 Organic Molecules
All molecules of life are built with carbon atoms
We can use different models to highlight different aspects of the same molecule

6. Carbon – The Stuff of Life
Organic molecules are complex molecules of life, built on a framework of carbon atoms
Carbohydrates
Lipids
Proteins
Nucleic acids

7. Carbon – The Stuff of Life
Carbon atoms can be assembled and remodeled into many organic compounds
Can bond with one, two, three, or four atoms
Can form polar or nonpolar bonds
Can form chains or rings

8. Carbon Rings A Carbon’s versatile bonding
Figure 3.2 Carbon rings.
Carbon rings form the framework of many sugars, starches, and fats, such as those found in doughnuts.
A Carbon’s versatile bonding
behavior allows it to form a variety of structures, including rings.
B Carbon rings form the
framework of many sugars,
starches, and fats, such as
those found in doughnuts.

9. Representing Structures of Organic Molecules
Structural model of an organic molecule
Each line is a covalent bond; two lines are double bonds; three lines are triple bonds
glucose

10. Representing Structures of Organic Molecules
Carbon ring structures are represented as polygons; carbon atoms are implied
glucose
glucose

11. Representing Structures of Organic Molecules
Ball-and-stick models show positions of atoms in three dimensions; elements are coded by color
glucose

12. Representing Structures of Organic Molecules
Space-filling models show how atoms sharing electrons overlap
glucose

13. Hemoglobin Molecule: Space-Filling Model
Figure 3.4 Visualizing the structure of hemoglobin, the oxygen-transporting molecule in red blood cells. Models that show individual atoms usually depict them color-coded by element. Other models may be shown in various colors, depending on which features are being studied.
A space-filling model of hemoglobin.
A A space-filling model of hemoglobin.

14. Hemoglobin Molecule: Surface Model
B A surface model of the same molecule reveals crevices and folds that are important for its function. Heme groups, in red, are cradled in pockets of the molecule.

15. Hemoglobin Molecule: Ribbon Model
C A ribbon model of hemoglobin shows all four heme groups, also in red, held in place by the molecule’s coils.

16. Take-Home Message: How are all molecules of life alike?
The molecules of life (carbohydrates, lipids, proteins, and nucleic acids) are organic, which means they consist mainly of carbon and hydrogen atoms
The structure of an organic molecule starts with its carbon backbone, a chain of carbon atoms that may form a ring
We use different models to represent different characteristics of a molecule’s structure; considering a molecule’s structural features gives us insight into how it functions

17. 3.3 From Structure to Function
The function of organic molecules in biological systems begins with their structure
The building blocks of carbohydrates, lipids, proteins, and nucleic acids bond together in different arrangements to form different kinds of complex molecules
Any process in which a molecule changes is called a reaction

18. Assembling Complex Molecules
Monomers
Molecules used as subunits to build larger molecules (polymers)
Polymers
Larger molecules that are chains of monomers
May be split and used for energy

19. What Cells Do to Organic Compounds
Metabolism
Activities by which cells acquire and use energy to construct, rearrange, and split organic molecules
Allows cells to live, grow, and reproduce
Requires enzymes (proteins that increase the speed of reactions)

20. Metabolism
Figure 3.5 Animated Metabolism. Two common reactions by which cells build and break down organic molecules are shown.
Metabolism refers to processes by which cells acquire and use energy as they make and break down molecules. Humans and other consumers break down the molecules in food. They use energy and raw materials from the breakdown to maintain themselves and to build new components.

21. ANIMATED FIGURE: Condensation and hydrolysis
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22. What Cells Do to Organic Compounds
Condensation
Covalent bonding of two molecules to form a larger molecule
Water forms as a product
Hydrolysis
The reverse of condensation
Cleavage reactions split larger molecules into smaller ones
Water is split

23. Condensation
B Condensation. Cells build a large molecule from smaller ones by this reaction.
An enzyme removes a hydroxyl group from one molecule and a hydrogen atom from another. A covalent bond forms between the two molecules, and water also forms.

24. Hydrolysis
C Hydrolysis. Cells split a large molecule into smaller ones by this water-requiring reaction.
An enzyme attaches a hydroxyl group and a hydrogen atom (both from water) at the cleavage site.

25. Functional Groups Hydrocarbon
An organic molecule that consists only of hydrogen and carbon atoms
Most biological molecules have at least one functional group
A cluster of atoms that imparts specific chemical properties to a molecule (polarity, acidity)

26. Table 3-1 p41

27. Table 3-1 p41

28. Table 3-1 p41

29. ANIMATION: Functional groups
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30. Glucose: Conversion of Straight Chain to Ring Form
Figure 3.6 Glucose. This simple sugar converts from a straight-chain into a ring form when the aldehyde group (on carbon 1) reacts with a hydroxyl group (on carbon 5). In water, the cyclic structure is the more common one.

31. Take-Home Message: How do organic molecules work in living systems?
All life is based on the same organic compounds: complex carbohydrates, lipids, proteins, and nucleic acids
By processes of metabolism, cells assemble these molecules of life form monomers. They also break apart polymers into component monomers.
Functional groups impart chemical characteristics to organic molecules; such groups contribute to the function of biological molecules
An organic molecule’s structure dictates its function in biological systems

32. 3.4 Carbohydrates
Carbohydrates are the most plentiful biological molecules in the biosphere
Cells use some carbohydrates as structural materials; they use others for fuel, or to store or transport energy

33. Carbohydrates Carbohydrates
Organic molecules that consist of carbon, hydrogen, and oxygen in a 1:2:1 ratio
Three types of carbohydrates in living systems
Monosaccharides (simple sugars)
Oligosaccharides (short-chain carbohydrates)
Polysaccharides (complex carbohydrates)

34. Simple Sugars
Monosaccharides (one sugar unit) are the simplest carbohydrates
Used as an energy source or structural material
Backbones of 5 or 6 carbons
Very soluble in water
Example: glucose

35. Short-Chain Carbohydrates
Oligosaccharides
Short chains of monosaccharides
Example: sucrose, a disaccharide
glucose fructose
sucrose
water
Stepped Art

36. Complex Carbohydrates
Polysaccharides
Straight or branched chains of many sugar monomers
The most common polysaccharides are cellulose, starch, and glycogen
All consist of glucose monomers
Each has a different pattern of covalent bonding, and different chemical properties

37. Cellulose Cellulose Polysaccharide Major structural material in plants
Consists of long, straight chains of glucose monomers
Does not dissolve in water; not easily broken down
Dietary fiber or “roughage” in our vegetable foods

38. Cellulose
Figure 3.8 Structure of (A) cellulose, (B) starch, and (C) glycogen, and their typical locations in a few organisms. All three carbohydrates consist only of glucose units, but the different bonding patterns that link the subunits result in substances with very different properties.
A Cellulose, a structural component of plants. Chains of glucose units stretch side by side and hydrogen-bond at many —OH groups. The hydrogen bonds stabilize the chains in tight bundles that form long fibers. Very few types of organisms can digest this tough, insoluble material.

39. Starch Starch Polysaccharide Energy reservoir in plants
Covalent bonding pattern between monomers makes a chain that coils up into a spiral
Does not dissolve easily in water, but less stable than cellulose
An important component of human food

40. Starch
Figure 3.8 Structure of (A) cellulose, (B) starch, and (C) glycogen, and their typical locations in a few organisms. All three carbohydrates consist only of glucose units, but the different bonding patterns that link the subunits result in substances with very different properties.
In amylose, one type of starch, a series of glucose units form a chain that coils. Starch is the main energy reserve in plants, which store it in their roots, stems, leaves, fruits, and seeds (such as coconuts).

41. Glycogen Glycogen Polysaccharide
Covalent bonding pattern forms highly branched chains of glucose monomers
Energy reservoir in animal cells; stored in muscle and liver cells

42. Glycogen
Figure 3.8 Structure of (A) cellulose, (B) starch, and (C) glycogen, and their typical locations in a few organisms. All three carbohydrates consist only of glucose units, but the different bonding patterns that link the subunits result in substances with very different properties.
Glycogen. In humans and other animals, this polysaccharide functions as an energy reservoir. It is stored in muscles and in the liver.

43. Chitin
Chitin
A nitrogen-containing polysaccharide that strengthens hard parts of animals such as crabs, and cell walls of fungi

44. Take-Home Message: What are carbohydrates?
Simple carbohydrates (sugars), bonded together in different ways, form various types of complex carbohydrates
Cells use carbohydrates for energy or as structural materials

45. ANIMATION: Structure of starch and cellulose

46. 3.5 Greasy, Oily – Must Be Lipids
Lipids function as the body’s major energy reservoir, and as the structural foundation of cell membranes
Lipids
Fatty, oily, or waxy organic compounds that are insoluble in water
Triglycerides, phospholipids, waxes, and steroids are lipids common in biological systems

47. Fatty Acids Many lipids incorporate fatty acids
Simple organic compounds with a carboxyl group joined to a backbone of 4 to 36 carbon atoms
Saturated fatty acids (animal fats)
Fatty acids with only single covalent bonds
Molecules are packed tightly; solid at room temperature
Unsaturated fatty acids (vegetable oils)
Fatty acids with one or more double bonds
Molecules are kinked; liquid at room temperature

48. Saturated and Unsaturated Fatty Acids
Figure 3.10 Fatty acids. (A) The tail of stearic acid is fully saturated with hydrogen atoms. (B) Linoleic acid, with two double bonds, is unsaturated. The first double bond occurs at the sixth carbon from the end of the tail, so linoleic acid is called an omega-6 fatty acid. Omega-6 and (C) omega-3 fatty acids are “essential fatty acids”: Your body does not make them, so they must come from food.

49. Fats
Fats
Lipids with one, two, or three fatty acids “tails” attached to glycerol
Triglycerides
Neutral fats with three fatty acids attached to glycerol
The most abundant energy source in vertebrates
Concentrated in adipose tissues (for insulation and cushioning)

50. Triglycerides
Figure 3.11 Animated Lipids with fatty acid tails. (A) Fatty acid tails of a triglyceride are attached to a glycerol head. (B) Fatty acid tails of a phospholipid are attached to a glycerol head with a phosphate group.

51. ANIMATED FIGURE: Triglyceride formation
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52. Phospholipids Phospholipids
Molecules with a polar head containing a phosphate and two nonpolar fatty acid tails
Heads are hydrophilic, tails are hydrophobic
The most abundant lipid in cell membranes
Form lipid bilayers with hydrophobic tails sandwiched between the hydrophilic heads

53. Phospholipids
Figure 3.11 Animated Lipids with fatty acid tails. (A) Fatty acid tails of a triglyceride are attached to a glycerol head. (B) Fatty acid tails of a phospholipid are attached to a glycerol head with a phosphate group.

54. Phospholipids in a Lipid Bilayer
hydrophilic head
two hydrophobic tails

55. Phospholipids in a Lipid Bilayer
one layer of lipids
one layer of lipids

56. Waxes
Waxes
Complex mixtures with long fatty-acid tails bonded to long-chain alcohols or carbon rings
Protective, water-repellant covering

57. Steroids
Steroids
Lipids with a rigid backbone of four carbon rings and no fatty-acid tails
Cholesterol
Component of eukaryotic cell membranes
Remodeled into bile salts, vitamin D, and steroid hormones such as the female sex hormone estrogen, and the male sex hormone testosterone

58. Estrogen and Testosterone
Figure 3.13 Estrogen and testosterone, steroid hormones that cause different traits to arise in males and females of many species such as wood ducks (Aix sponsa), pictured at right.
an estrogen
testosterone

59. Effects of Estrogen and Testosterone
female
wood duck
male
wood duck

60. Take-Home Message: What are lipids?
Lipids are fatty, waxy, or oily organic compounds. Common types include fats, phospholipids, waxes, and steroids
Triglycerides are lipids that serve as energy reservoirs in vertebrate animals
Phospholipids are the main lipid component of cell membranes
Waxes are lipid components of water-repelling and lubricating secretions
Steroids are lipids that occur in cell membranes; some are remodeled into other molecules

61. 3.6 Proteins – Diversity in Structure and Function
All cellular processes involve proteins, the most diverse biological molecule (structural, nutritious, enzyme, transport, communication, and defense proteins)
Cells build thousands of different proteins by stringing together amino acids in different orders

62. From Structure to Function
Protein
An organic compound composed of one or more chains of amino acids
Amino acid
A small organic compound with an amine group (—NH3+), a carboxyl group (—COO-, the acid), and one or more variable groups (R group)

63. Amino Acid Structure
Figure 3.14 Generalized structure of amino acids. The complete structures of the twenty most common amino acids found in eukaryotic proteins are shown in Appendix I.
Stepped Art

64. Polypeptides
Protein synthesis involves the formation of amino acid chains called polypeptides
Polypeptide
A chain of amino acids bonded together by peptide bonds in a condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid

65. Polypeptide Formation
methionine
serine
methionine
serine
glutamine
methionine
serine
arginine
Figure 3.15 Animated Polypeptide formation. Chapter 9 offers a closer look at protein synthesis.
Two amino acids (here, methionine and serine) are joined by condensation. A peptide bond forms between the carboxyl group of the methionine and the amine group of the serine.
Stepped Art

66. ANIMATED FIGURE: Peptide bond formation
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67. Levels of Protein Structure
Primary structure
The unique amino acid sequence of a protein
Secondary structure
The polypeptide chain folds and forms hydrogen bonds between amino acids
Tertiary structure
A secondary structure is compacted into structurally stable units called domains
Forms a functional protein

68. Levels of Protein Structure
Quaternary structure
Some proteins consist of two or more folded polypeptide chains in close association
Example: hemoglobin
Some proteins aggregate by thousands into larger structures, with polypeptide chains organized into strands or sheets
Example: hair

69. A protein’s primary structure consists of a linear sequence of amino acids (a polypeptide chain). Each type of protein has a unique primary structure. 1
glycine
lysine
arginine 2
Secondary structure arises as a polypeptide chain twists into a coil (helix) or sheet held in place by hydrogen bonds between different parts of the molecule. The same patterns of secondary structure occur in many different proteins. 3
Tertiary structure occurs when a chain’s coils and sheets fold up into a functional domain such as a barrel or pocket. In this example, the coils of a globin chain form a pocket. 4
Some proteins have quaternary structure, in which two or more polypeptide chains associate as one molecule. Hemoglobin, shown here, consists of four globin chains (green and blue). Each globin pocket now holds a heme group (red). 5
Many proteins aggregate by the thousands into much larger structures, such as the keratin filaments that make up hair.
Figure 3.16 Animated Protein structure.
Stepped Art
Figure 3-16 p47

70. ANIMATED FIGURE: Secondary and tertiary structure
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71. Some Functional Proteins
Some fibrous proteins contribute to the structure and organization of cells and tissues; others help cells, cell parts, and bodies move
Sugars bond to proteins to make glycoproteins that allow a tissue or a body to recognize its own cells
Lipids bond to proteins to make lipoproteins such as HDL and LDL, which transport cholesterol to and from the liver

72. HDL: A Lipoprotein
protein
lipid
an HDL particle

73. Take-Home Message: What are proteins?
Proteins are chains of amino acids. The order of amino acids in a polypeptide chain dictates the type of protein.
Polypeptide chains twist and fold into coils, sheets, and loops, which fold and pack further into functional domains
A protein’s shape is the source of its function

74. 3.7 Why Is Protein Structure So Important?
Proteins function only as long as they maintain their correct three-dimensional shape
Changes in a protein’s shape may have drastic health consequences

75. Denaturation
Heat, changes in pH, salts, and detergents can disrupt the hydrogen bonds that maintain a protein’s shape
When a protein loses its shape and no longer functions, it is denatured
Once a protein’s shape unravels, so does its function

76. Prions Prion diseases are caused by misfolded proteins
Mad cow disease (bovine spongiform encephalitis)
Creutzfeldt–Jakob disease in humans
Scrapie in sheep
All are infectious diseases characterized by deterioration of mental and physical abilities that eventually causes death

77. Variant Creutzfeldt–Jakob Disease (vCJD)
Figure 3.17 Variant Creutzfeldt–Jakob disease (vCJD). (A) Charlene Singh, here being cared for by her mother, was one of the three people who developed symptoms of vCJD disease while living in the United States. Like the others, Singh most likely contracted the disease elsewhere; she spent her childhood in Britain. She was diagnosed in 2001, and she died in (B) Slice of brain tissue from a person with vCJD. Characteristic holes and prion protein fibers radiating from several deposits are visible.

78. Take-Home Message: Why is protein structure important?
A protein’s function depends on its structure.
Conditions that alter a protein’s structure may also alter its function
Protein shape unravels if hydrogen bonds are disrupted

79. 3.8 Nucleic Acids
Nucleotides are subunits of nucleic acids such as DNA and RNA
Some nucleotides have roles in metabolism

80. Nucleotides Nucleotide
A small organic molecule consisting of a sugar with a five-carbon ring, a nitrogen-containing base, and one or more phosphate groups
ATP
A nucleotide with three phosphate groups
Important in phosphate-group (energy) transfer

81. base: adenine (A) 3 phosphate groups
Figure 3.18 Animated Nucleic acid structure.
A ATP, a nucleotide monomer of RNA, and also an essential participant in many metabolic reactions.
sugar: ribose
A ATP, a nucleotide monomer of RNA, and also an essential participant in many metabolic reactions.
Figure 3-18a p49

82. ANIMATED FIGURE: DNA close up
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83. A Chain of Nucleotides
B A chain of nucleotides is a nucleic acid. The sugar of one nucleotide is covalently bonded to the phosphate group of the next, forming a sugar–phosphate backbone.

84. Nucleic Acids Nucleic acids
Polymers of nucleotides in which the sugar of one nucleotide is attached to the phosphate group of the next
RNA and DNA are nucleic acids

85. RNA RNA (ribonucleic acid)
Contains four kinds of nucleotide monomers, including ATP
Important in protein synthesis

86. DNA DNA (deoxyribonucleic acid)
Two chains of nucleotides twisted together into a double helix and held by hydrogen bonds
Contains all inherited information necessary to build an organism, coded in the order of nucleotide bases

87. The DNA Molecule
The cell uses the order of nucleotide bases in DNA (the DNA sequence) guide production of RNA and proteins

88. Take-Home Message: What are nucleotides and nucleic acids?
Nucleotides are monomers of the nucleic acids DNA and RNA; some have additional roles
DNA’s nucleotide sequence encodes heritable information
RNA plays several important roles in the process by which a cell uses the instructions written in its DNA to build proteins