Chapter 3 The Chemistry of Life: Organic Compounds

Chapter 3 The Chemistry of Life: Organic Compounds

Organic Compounds In organic compounds, covalently bonded carbon atoms form the backbone of the molecule The carbon atom forms bonds with more different elements than any other type of atom More than 5 million organic compounds have been identified, including large macromolecules (e.g. proteins) constructed from modular subunits (e.g. amino acids)

3.1 CARBON ATOMS AND ORGANIC MOLECULES
LEARNING OBJECTIVES: Describe the properties of carbon that make it the central component of organic compounds Define the term isomer and distinguish among the three principal isomer types Identify the major functional groups present in organic compounds and describe their properties Explain the relationship between polymers and macromolecules

Properties of Carbon A carbon atom can complete its valence shell by forming a total of four covalent bonds Carbon-to-carbon bonds are strong and not easily broken Single bonds Double bonds Triple bonds Hydrocarbons (consisting only of carbon and hydrogen) can exist as unbranched or branched chains, or as rings

Molecular Shapes The shape of a molecule is important in determining its biological properties and function Carbon atoms link to one another and to other atoms to produce a wide variety of 3-D molecular shapes, because carbon’s four covalent bonds do not form in a single plane Freedom of rotation around each carbon-to-carbon single bond permits organic molecules to assume a variety of shapes, depending on degree of rotation

Organic Molecules Figure 3.1: Organic molecules.
Note that each carbon atom forms four covalent bonds, producing a wide variety of shapes. Fig. 3-1, p. 47

Carbon Bonding

Isomers The same components can link in more than one pattern, generating a wide variety of molecular shapes isomers Compounds with the same molecular formulas but different structures and properties Usually, one isomer is biologically active, another is not Three types: structural isomers, geometric isomers, and enantiomers

Three Types of Isomers structural isomers
Compounds that differ in covalent arrangements of atoms Large compounds have more possible structural isomers geometric isomers Compounds identical in arrangement of covalent bonds but different in spatial arrangement of atoms enantiomers Isomers that are mirror images of each other

Structural Isomers

Geometric Isomers

Enantiomers

Functional Groups Hydrocarbons lack distinct charged regions, are insoluble in water, and cluster together (hydrophobic interactions) Replacing one hydrogen with one or more functional groups (groups that determine types of chemical reactions and associations in which the compound participates) changes the characteristics of an organic molecule

Functional Groups (cont.)
Most functional groups readily form associations (such as ionic and hydrogen bonds) with other molecules Polar and ionic functional groups are hydrophilic because they associate strongly with polar water molecules

Important Functional Groups
methyl group Nonpolar hydrocarbon group (R—CH3) The hydroxyl group (R—OH) is polar because of a strongly electronegative oxygen atom The carbonyl group consists of a carbon atom that has a double covalent bond with an oxygen atom aldehyde has a carbonyl group at the end of the carbon skeleton (R—CHO) ketone has an internal carbonyl group (R—CO—R)

Important Functional Groups (cont.)
The carboxyl group (R—COOH) consists of a carbon joined by a double covalent bond to an oxygen, and by a single covalent bond to another oxygen bonded to a hydrogen Carboxyl groups are essential constituents of amino acids An amino group (R—NH2) includes a nitrogen atom covalently bonded to two hydrogen atoms Amino groups are components of amino acids and nucleic acids

Important Functional Groups (cont.)
The phosphate group (R—PO4H2) can release one or two hydrogen ions, producing ionized forms with 1 or 2 units of negative charge Constituents of nucleic acids and certain lipids The sulfhydryl group (R—SH), an atom of sulfur covalently bonded to hydrogen, is found in thiols Important in proteins

Table 3-1a, p. 50

Table 3-1b, p. 50

Polymers Many biological molecules (such as proteins and nucleic acids) consist of thousands of atoms (macromolecules) Most macromolecules are polymers, produced by linking small organic compounds (monomers) Example: 20 monomers (amino acids) in proteins

Polyethylene: A Simple Polymer

Making and Breaking Polymers
Polymers can be degraded to component monomers by hydrolysis reactions Hydrogen from a water molecule attaches to one monomer, and hydroxyl from water attaches to the adjacent monomer Monomers become covalently linked by condensation reactions (aka Dehydration synthesis) The equivalent of a molecule of water is removed during reactions that combine monomers

Condensation and Hydrolysis Reactions

ANIMATION: Condensation and hydrolysis
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KEY CONCEPTS 3.1 Carbon atoms join with one another or other atoms to form large molecules with a wide variety of shapes Hydrocarbons are nonpolar, hydrophobic molecules their properties can be altered by adding functional groups: hydroxyl and carbonyl groups (polar), carboxyl and phosphate groups (acidic), and amino groups (basic)

ANIMATION: Functional groups

3.2 CARBOHYDRATES LEARNING OBJECTIVE:
Distinguish among monosaccharides, disaccharides, and polysaccharides Compare storage polysaccharides with structural polysaccharides

Carbohydrates Carbohydrates contain carbon, hydrogen, and oxygen atoms in a ratio of approximately 1C:2H:1O (CH2O)n Sugars and starches (energy sources) Cellulose (structural component of plants) Carbohydrates contain one sugar unit (monosaccharides), two sugar units (disaccharides), or many sugar units (polysaccharides)

Monosaccharides are Simple Sugars
Contain three to seven carbon atoms A hydroxyl group is bonded to each carbon except one One carbon is double-bonded to an oxygen atom (carbonyl group), forming aldehydes and ketones

Monosaccharides

Dihydroxyacetone (C3H6O3)
Figure 3.6: Monosaccharides. Shown are 2-D chain structures of (a) three-carbon trioses, (b) five-carbon pentoses, and (c) six-carbon hexoses. Although it is convenient to show monosaccharides in this form, the pentoses and hexoses are more accurately depicted as ring structures, as in Figure 3-7. The carbonyl group (gray screen) is terminal in aldehyde sugars and located in an internal position in ketones. Deoxyribose differs from ribose because deoxyribose has one less oxygen; a hydrogen (white screen) instead of a hydroxyl group (blue screen) is attached to carbon 2. Glucose and galactose differ in the arrangement of the hydroxyl group and hydrogen attached to carbon 4 (red box). Glyceraldehyde (C3H6O3) (an aldehyde) Dihydroxyacetone (C3H6O3) (a ketone) Triose sugars (3-carbon sugars) Fig. 3-6a, p. 52

(the sugar component of RNA) (the sugar component of DNA)
Figure 3.6: Monosaccharides. Shown are 2-D chain structures of (a) three-carbon trioses, (b) five-carbon pentoses, and (c) six-carbon hexoses. Although it is convenient to show monosaccharides in this form, the pentoses and hexoses are more accurately depicted as ring structures, as in Figure 3-7. The carbonyl group (gray screen) is terminal in aldehyde sugars and located in an internal position in ketones. Deoxyribose differs from ribose because deoxyribose has one less oxygen; a hydrogen (white screen) instead of a hydroxyl group (blue screen) is attached to carbon 2. Glucose and galactose differ in the arrangement of the hydroxyl group and hydrogen attached to carbon 4 (red box). Ribose (C5H10O5) (the sugar component of RNA) Deoxyribose (C5H10O4) (the sugar component of DNA) (b) Pentose sugars (5-carbon sugars) Fig. 3-6b, p. 52

Glucose (C6H12O6) (an aldehyde) Fructose (C6H12O6) (a ketone)
Figure 3.6: Monosaccharides. Shown are 2-D chain structures of (a) three-carbon trioses, (b) five-carbon pentoses, and (c) six-carbon hexoses. Although it is convenient to show monosaccharides in this form, the pentoses and hexoses are more accurately depicted as ring structures, as in Figure 3-7. The carbonyl group (gray screen) is terminal in aldehyde sugars and located in an internal position in ketones. Deoxyribose differs from ribose because deoxyribose has one less oxygen; a hydrogen (white screen) instead of a hydroxyl group (blue screen) is attached to carbon 2. Glucose and galactose differ in the arrangement of the hydroxyl group and hydrogen attached to carbon 4 (red box). Glucose (C6H12O6) (an aldehyde) Fructose (C6H12O6) (a ketone) Galactose (C6H12O6) (an aldehyde) (c) Hexose sugars (6-carbon sugars) Fig. 3-6c, p. 52

Glucose Glucose (C6H12O6), the most abundant monosaccharide, is used as an energy source in most organisms During cellular respiration, cells oxidize glucose molecules, converting stored energy to a form used for cell work Homeostatic mechanisms maintain blood glucose levels

Glucose, Fructose, and Galactose
Glucose and fructose are structural isomers: glucose is an aldehyde and fructose is a ketone Glucose and galactose differ in the arrangement of the atoms attached to asymmetrical carbon atom 4 Molecules of glucose and other pentoses and hexoses in solution are rings rather than extended straight carbon chains

Isomers of Glucose Two isomeric forms, differing in orientation of the hydroxyl (OH) group attached to carbon 1, are important when glucose rings join to form polymers In beta glucose (β-glucose) the hydroxyl group is on the same side of the plane of the ring as the CH2OH side group In alpha glucose (α-glucose), it is on the side opposite the CH2OH side group

Isomers of Glucose

Disaccharides A disaccharide (two sugars) contains two monosaccharide rings joined by a glycosidic linkage, consisting of a central oxygen covalently bonded to two carbons, one in each ring Common disaccharides: Maltose (malt sugar): 2 covalently linked α-glucose units Sucrose (table sugar): 1 glucose + 1 fructose Lactose (milk sugar): 1 glucose + 1 galactose

Hydrolysis of Disaccharides

Polysaccharides A polysaccharide is a macromolecule (a single long chain or a branched chain) consisting of repeating units of simple sugars, usually glucose Common polysaccharides: Starches: Energy storage in plants Glycogen: Energy storage in animals Cellulose: Structural polysaccharide in plants

Starches starch Form of carbohydrate used for energy storage in plants
Polymer consisting of α-glucose subunits Starch occurs in two forms Amylose (unbranched chain) Amylopectin (branched chain) Plant cells store starch as granules in amyloplasts

Starch: A Storage Polysaccharide

Amyloplasts Figure 3.9: Starch, a storage polysaccharide. (a) Starch (stained purple) is stored in specialized organelles, called amyloplasts, in these cells of a buttercup root. Fig. 3-9a, p. 55

Glycogen glycogen Form in which glucose subunits are stored as an energy source in animal tissues Similar in structure to plant starch but more extensively branched and more water soluble In vertebrates, glycogen is stored mainly in liver and muscle cells

Cellulose cellulose Insoluble polysaccharide composed of many joined glucose molecules Structural component of plants (fibers) The most abundant carbohydrate Some microorganisms digest cellulose to glucose Humans lack enzymes to hydrolyze β 1—4 linkages

Cellulose: A Structural Polysaccharide

Figure 3.10: Cellulose, a structural polysaccharide.
(a) Cellulose fibers from a cell wall. The fibers shown in this electron micrograph consist of bundles of cellulose molecules that interact through hydrogen bonds. Fig. 3-10a, p. 56

Carbohydrates With Special Roles
amino sugars galactosamine and glucosamine Present in cartilage glycoproteins Functional proteins secreted by cells glycolipids Recognition compounds on surfaces of animal cells

KEY CONCEPTS 3.2 Carbohydrates are composed of sugar subunits (monosaccharides), which can be joined to form disaccharides, storage polysaccharides, and structural polysaccharides

3.3 LIPIDS LEARNING OBJECTIVE:
Distinguish among fats, phospholipids, and steroids, and describe the composition, characteristics, and biological functions of each

Lipids lipids Compounds soluble in nonpolar solvents, and relatively insoluble in water (hydrophobic) Consist mainly of carbon and hydrogen, with few oxygen-containing functional groups Biologically important groups of lipids include fatty acids, phospholipids, carotenoids, steroids, and waxes Some lipids are used for energy storage, structural components of cell membranes, or important hormones

Triacylglycerol Triacylglycerols (triglycerides or fats)
Most abundant lipids in living organisms Form of reserve fuel storage Consists of glycerol joined to three fatty acids 1. glycerol A three-carbon alcohol with three hydroxyl (–OH) groups 2. fatty acid A long, unbranched hydrocarbon chain with a carboxyl group (–COOH) at one end

Triacylglycerol: The Main Storage Lipid

ANIMATION: Triglyceride formation

Saturated and Unsaturated Fatty Acids
Contain the maximum number of hydrogen atoms Found in animal fat and solid vegetable shortening Solid at room temperature unsaturated fatty acids Include one or more pairs of carbon atoms joined by a double bond (not fully saturated with hydrogen) Tend to be liquid at room temperature

Unsaturated Fatty Acids
Each double bond produces a bend in the hydrocarbon chain that prevents close alignment with an adjacent chains monounsaturated fatty acids Fatty acids with one double bond Example: Oleic acid polyunsaturated fatty acids Fatty acids with more than one double bond Example: linoleic acid

Shapes of Fatty Acids Saturated Monounsaturated Polyunsaturated

Trans Fats Food manufacturers hydrogenate or partially hydrogenate cooking oils (convert unsaturated fatty acids to saturated fatty acids) to make fat more solid at room temperature In naturally-occurring unsaturated fatty acids the hydrogens on each side of the double bond are on the same side of the hydrocarbon chain (cis configuration) Artificial hydrogenation produces a trans configuration solid at room temperature and increases risk of cardiovascular disease

Trans and Cis Isomers

Phospholipids Phospholipids are amphipathic lipids, with one hydrophilic end and one hydrophobic end Hydrophilic head consists of a glycerol molecule, phosphate group, and organic group (such as choline) Hydrophobic tail consist of two fatty acids Phospholipids are basic components of cell membranes Amphipathic properties of phospholipids cause them to form lipid bilayers in aqueous (watery) solution

A Phospholipid

A Phospholipid Bilayer

Water Figure 3.13: A phospholipid and a phospholipid bilayer. (b) Phospholipid bilayer. Phospholipids form lipid bilayers in which the hydrophilic heads interact with water and the hydrophobic tails are in the bilayer interior. Fig. 3-13b, p. 58

Carotenoids carotenoids Orange and yellow plant pigments
Insoluble in water, with an oily consistency Function in photosynthesis Consist of 5-carbon hydrocarbon monomers (isoprene units) Most animals convert carotenoids to vitamin A, which can be converted to the visual pigment retinal

Isoprene-Derived Compounds

Steroids steroid Consists of carbon atoms arranged in four attached rings Side chains distinguish one steroid from another Synthesized from isoprene units Steroids of biological importance include cholesterol, bile salts, reproductive hormones, cortisol and other hormones secreted by the adrenal cortex Plant cell membranes contain molecules similar to cholesterol

Steroids

Chemical Mediators Some chemical mediators (used for communication or internal regulation) are produced by modification of fatty acids removed from membrane phospholipids Lipid chemical mediators include prostaglandins and certain hormones

KEY CONCEPTS 3.3 Lipids store energy (triacylglycerols) and are the main structural components of cell membranes (phospholipids)

3.4 PROTEINS LEARNING OBJECTIVES:
Give an overall description of the structure and functions of proteins Describe the features that are shared by all amino acids and explain how amino acids are grouped into classes based on the characteristics of their side chains Distinguish among the four levels of organization of protein molecules

Proteins proteins Macromolecules composed of amino acids
Characteristic forms, distributions, and amounts of protein determine what a cell looks like and how it functions Most enzymes are proteins enzymes Molecules that accelerate chemical reactions that take place in an organism

Protein Functions Table 3-2, p. 60

Amino Acids amino acids Subunits of proteins
Have an amino group (NH2) and a carboxyl group (COOH) bonded to the alpha carbon Amino acids in solution at neutral pH are mainly dipolar ions Each COOH donates a proton and becomes COO- Each NH2 accepts a proton and becomes NH3+

Amino Acid at pH 7 Figure 3.16: An amino acid at pH 7.
In living cells, amino acids exist mainly in their ionized form, as dipolar ions. Fig. 3-16, p. 61

Amino Acids in Proteins
Twenty amino acids are found in most proteins, identified by a variable side chain (R group) bonded to the α carbon Amino acids are grouped by properties of their side chains Nonpolar side chains are hydrophobic Polar side chains are hydrophilic A side chain with a carboxyl group is acidic A side chain that accepts a hydrogen ion is basic Some proteins have additional amino acids

20 Common Amino Acids

Essential Amino Acids Animal cells can manufacture some, but not all, biologically significant amino acids essential amino acids Amino acids an animal can’t synthesize in amounts sufficient to meet its needs and must obtain from the diet Differs in different species Nine essential amino acids for adult humans: Isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, histidine

Peptide Bonds Amino acids combine chemically by a condensation reaction between the carboxyl carbon of one amino acid and the amino nitrogen of another amino acid Two amino acids combine to form a dipeptide A longer chain of amino acids is a polypeptide peptide bond Covalent carbon-to-nitrogen bond linking two amino acids

Peptide Bonds

ANIMATION: Peptide bond formation

Polypeptides and Proteins
A protein consists of one or more polypeptide chains, with hundreds of amino acids joined in a specific linear order The 20 types of amino acids in proteins are like letters of a protein alphabet; each protein is a very long sentence made up of amino acid letters An almost infinite variety of protein molecules is possible, differing in number, types, and sequences of amino acids

Protein Shape Polypeptide chains are twisted or folded to form a protein with a specific conformation (3-D shape) Some form long fibers Globular proteins are folded into spherical shapes A protein’s function is determined by its conformation An enzyme’s shape allows it to catalyze a specific chemical reaction A protein hormone’s shape allows it to combine with receptors on its target cell

Four Levels of Protein Organization
There are four main levels of protein organization: primary, secondary, tertiary, and quaternary primary structure The sequence of amino acids in a polypeptide chain Specified by instructions in a gene Higher orders of structure (secondary, tertiary, quaternary) derive from interactions among the specific amino acids in the sequence (primary structure)

Primary Structure of a Polypeptide
Glucagon, a very small polypeptide made up of 29 amino acids, represented in a linear, “beads-on-a-string” form One end has a free positive ion (NH3+) ; the other has a free negative ion (COO-) Figure 3.19: Primary structure of a polypeptide. Glucagon is a very small polypeptide made up of 29 amino acids. The linear sequence of amino acids is indicated by ovals containing their abbreviated names (see Fig. 3-17). Fig. 3-19, p. 64

Levels of Protein Organization (cont.)
secondary structure Two common types: α-helix and β-pleated sheet Both types may occur in the same polypeptide chain 1. α–helix (helical coil) Hydrogen bonds form between oxygen and hydrogen Basic structural unit of fibrous, elastic proteins 2. β-pleated sheet H-bonds form between regions of polypeptides chains Proteins are strong and flexible, but not elastic

Secondary Structure of a Protein

ANIMATION: Secondary and tertiary structure

tertiary structure Overall 3-D shape of an individual polypeptide chain Determined by four main factors involving interactions among R groups of the same polypeptide chain Four factors in tertiary structure: 3 weak interactions (hydrogen bonds, ionic bonds, and hydrophobic interactions) Strong covalent bonds (disulfide bridges between sulfhydryl groups of two cysteines)

Tertiary Structure of a Protein

quaternary structure 3-D structure resulting from two or more polypeptide chains interacting in specific ways to form a biologically active molecule Examples: Hemoglobin, a globular protein consisting of 4 polypeptide chains (2 alpha chains and 2 beta chains) Collagen, a fibrous protein with 3 polypeptide chains

Quaternary Structure of a Protein

Amino Acid Sequence Determines Conformation
In vitro, a polypeptide spontaneously folds into its normal, functional conformation In vivo (within the living), proteins (molecular chaperones) mediate the folding of other protein molecules Molecular chaperones are thought to make the folding process more efficient, and to prevent partially folded proteins from becoming inappropriately aggregated

Protein Conformation Determines Function
Overall structure of a protein determines biological activity Biological activity can be disrupted by a change in amino acid sequence that results in change in protein conformation Example: sickle cell anemia

Protein Conformation Determines Function (cont.)
Denaturation of a protein: When a protein is heated, subjected to significant pH change, or treated with certain chemicals, its structure becomes disordered and peptide chains unfold Change in shape is typically accompanied by loss of normal function (biological activity) Denaturation generally cannot be reversed

Misfolded Proteins in Human Diseases
Studies of protein folding, and the relationship between protein activity and conformation, are of medical importance Serious diseases in which misfolded proteins play an important role include mad cow disease and related diseases in humans (caused by misfolded proteins called prions), Alzheimer’s disease, and Huntington’s disease

KEY CONCEPTS 3.4 Proteins have multiple levels of structure and are composed of amino acid subunits joined by peptide bonds

Describe the components of a nucleotide
3.5 NUCLEIC ACIDS LEARNING OBJECTIVES: Describe the components of a nucleotide Name some nucleic acids and nucleotides, and discuss the importance of these compounds in living organisms

Nucleic Acids Nucleic acids transmit hereditary information and determine what proteins a cell manufactures Deoxyribonucleic acid (DNA) Composes the hereditary material of the cell (genes) Contains instructions for making proteins and RNA Ribonucleic acid (RNA) Used in processes that link amino acids form polypeptides Ribozymes act as specific biological catalysts

Nucleotides Nucleic acids are polymers of nucleotides
Nucleotides are made up of three parts: A five-carbon sugar, either deoxyribose (in DNA) or ribose (in RNA) One or more phosphate groups (make the molecule acidic) A nitrogenous base (nitrogen-containing ring compound)

Nitrogenous Bases Nitrogenous base may be either a double-ring purine or a single-ring pyrimidine DNA contains four nitrogenous bases: Two purines: adenine (A) and guanine (G) Two pyrimidines: cytosine (C) and thymine (T) RNA contains the purines adenine and guanine, and the pyrimidines cytosine and uracil (U)

Purines and Pyrimidines

Nucleic Acid Structure
Nucleic acids are chains of nucleotides joined by phosphodiester linkages (a phosphate group and covalent bonds that attach it to sugars of adjacent nucleotides) RNA is usually composed of one nucleotide chain DNA consists of two nucleotide chains held together by hydrogen bonds in a double helix

RNA: A Nucleic Acid A nucleic acid molecule is uniquely defined by its specific sequence of nucleotides, which acts as a code

Phosphodiester linkage
Nucleotide Uracil Adenine Phosphodiester linkage Figure 3.24: RNA, a nucleic acid. Nucleotides, each with a specific base, are joined by phosphodiester linkages. Cytosine Guanine Fig. 3-24, p. 69

Nucleotides and Energy
adenosine triphosphate (ATP) Composed of adenine, ribose, and three phosphates Primary energy molecule of all cells Is converted to cyclic adenosine monophosphate (cyclic AMP, or cAMP) by the enzyme adenylyl cyclase guanosine triphosphate (GTP) Transfers energy by transferring a phosphate group Cyclic guanosine monophosphate (cGMP), has a role in certain cell signaling processes

Cyclic Adenosine Monophosphate (cAMP)
The single phosphate is part of a ring connecting two regions of the ribose Figure 3.25: Cyclic adenosine monophosphate (cAMP). The single phosphate is part of a ring connecting two regions of the ribose. Fig. 3-25, p. 69

Dinucleotides nicotinamide adenine dinucleotide
Primary role in oxidation and reduction reactions in cells Oxidized form (NAD+) is converted to a reduced form (NADH) when it accepts electrons NADH transfers electrons, along with their energy, to other molecules

KEY CONCEPTS 3.5 Nucleic acids (DNA and RNA) are informational molecules composed of long chains of nucleotide subunits ATP and some other nucleotides have a central role in energy metabolism

ANIMATION: Nucleotide subunits of DNA

3.6 IDENTIFYING BIOLOGICAL MOLECULES
LEARNING OBJECTIVE: Compare the functions and chemical compositions of the major groups of organic compounds: carbohydrates, lipids, proteins, and nucleic acids

Classes of Biologically Important Organic Compounds

Table 3-3c, p. 70

Chapter 3 The Chemistry of Life: Organic Compounds

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