The Science of Biology

Chapter 3: Biochemistry 1 3.1 Organic Molecules Organic molecules contain carbon and hydrogen atoms. Four classes of organic molecules (biomolecules) exist in living organisms: Carbohydrates Lipids Proteins Nucleic Acids 2 Inorganic versus Organic Molecules 3 The Carbon Skeleton and Functional Groups The carbon chain of an organic molecule is called its skeleton or backbone. Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structures and functions. Determine the chemical reactivity and polarity of organic molecules 4 Functional Groups Functional Groups 6 Functional Groups 7 Isomers Isomers are organic molecules that have identical molecular formulas but a different arrangement of atoms.

Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. glyceraldehyde H H H O C C C OH OH H dihydroxyacetone H H O H C C C OH H OH 8

Biomolecules Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules. Usually consist of many repeating units Each repeating unit is called a monomer. A molecule composed of monomers is called a polymer (many parts). Example: amino acids (monomer) are joined together to form a protein (polymer) 9 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Fig. 3.3 Biomolecules Category Polymer Subunit(s) Carbohydrates* Monosaccharide Polysaccharide Lipids Glycerol and fatty acids Fat Proteins* Amino acids Polypeptide Nucleic acids* Nucleotide

DNA,RNA *Polymers The McGraw Hill Companies, Inc./John Thoeming, photographer Synthesis and Degradation A dehydration reaction is a chemical reaction in which subunits are joined together by the formation of a covalent bond and water is produced during the reaction. Used to connect monomers together to make polymers Example: formation of starch (polymer) from glucose subunits (monomer) A hydrolysis reaction is a chemical reaction in which a water molecule is added to break a covalent bond. Used to breakdown polymers into monomers Example: digestion of starch into glucose monomers 11 Dehydration Synthesis building polymers 12 Dehydration Synthesis building polymers 13 Hydrolysis breaking polymers 14 15 Synthesis and Degradation Enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions. An enzyme is a molecule that speeds up a chemical reaction. Enzymes are not consumed in the reaction. Enzymes are not changed by the reaction.

16 3.2 Carbohydrates Functions: Energy source Provide building material (structural role) Contain carbon, hydrogen and oxygen in a 1:2:1 ratio Varieties: monosaccharides, disaccharides, and polysaccharides Monosaccharides A monosaccharide is a single sugar molecule. Also called simple sugars Have a backbone of 3 to 7 carbon atoms Examples: Glucose (blood), fructose (fruit) and galactose Hexoses - six carbon atoms Ribose and deoxyribose (in nucleotides) Pentoses five carbon atoms 18 Glucose 6 H C 4 HO a. 5 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Fig. 3.6 CH2OH

CH2OH C O H OH H C C 3 H H C O H H OH 1 OH H OH HO b. 2 OH H OH

C6H12O6 O O c. d. Steve Bloom/Taxi/Getty H Disaccharides A disaccharide contains two monosaccharides joined together by dehydration synthesis. Examples: Lactose (milk sugar) is composed of galactose and glucose. Sucrose (table sugar) is composed of glucose and fructose. Maltose is composed of two glucose molecules. 20 Synthesis and Degradation of Maltose Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH O H H O + OH glucose C6H12O6 HO glucose C6H12O6 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH

CH2OH O H H OH + glucose C6H12O6 O dehydration reaction HO glucose C6H12O6 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH O CH2OH H H O CH2OH dehydration reaction + OH CH2OH O O

O + H2O HO glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH O H H CH2OH O dehydration reaction + O O O + H2O HO

OH glucose C6H12O6 monosaccharide CH2OH + glucose C6H12O6 monosaccharide maltose C12H22O11 disaccharide water + water Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH O O maltose C12H22O11 O Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH O O O

maltose C12H22O11 + H2O water Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH O O hydrolysis reaction maltose C12H22O11 O + H2O water Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH O CH2OH H H + OH glucose C6H12O6

CH2OH O CH2OH O O HO hydrolysis reaction glucose C6H12O6 maltose C12H22O11 O + H2O water Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH O CH2OH H H + glucose C6H12O6 monosaccharide hydrolysisreaction HO OH

+ CH2OH O glucose C6H12O6 monosaccharide CH2OH O O maltose C12H22O11 disaccharide O + H2O water + water Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. dehydration reaction hydrolysis reaction glucose C6H12O6 monosaccharide + glucose C6H12O6 monosaccharide maltose C12H22O11 disaccharide water

+ water Polysaccharides A polysaccharide is a polymer of monosaccharides. Examples: Starch provides energy storage in plants. Glycogen provides energy storage in animals. Cellulose is found in the cell walls of plants. Chitin is found in the cell walls of fungi and exoskeleton of some animals. Peptidoglycan is found in the cell walls of bacteria. Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Amylose: nonbranched starch granule Amylopectin: branched a. Starch 250 m glycogen granule b . Glycogen 150 nm a: Jeremy Burgess/SPL/Photo Researchers, Inc.; b: Don W. Fawcett/Photo Researchers, Inc. 3.3 Lipids Lipids are varied in structure. Large nonpolar molecules that are insoluble in water Functions: Long-term energy storage Structural components Cell communication and regulation Protection

Varieties: fats, oils, phospholipids, steroids, waxes Triglycerides: Long-Term Energy Storage Also called fats and oils Functions: long-term energy storage and insulation Consist of one glycerol molecule linked to three fatty acids by dehydration synthesis Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H C OH H C OH H C OH H glycerol a. Formation of a fat Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H O C H C

HO OH + H C OH O HO O H C OH H glycerol a. Formation of a fat C HO C H H H H H C C C

C C H H H H H H H H H H H H C C C C C C C H H

H H H H H H H H C C C H H in 3 fatty acids H C H H H C H H Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H

O C H C HO OH + H C OH O HO O H C OH H glycerol a. Formation of a fat C HO C H H H H

H C C C C C H H H H H H H H H H H H C C C C C

C C H H H H H H H H H H C C C H H in 3 fatty acids H C H 3 H2O H H

H 3 H2 O C H 3 water molecules Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H C C O OH OH C HO + O C OH H glycerol a. Formation of a fat C HO O H

H HO C C H H H H 3 H2O C C C C H H H H H H H H H H

H H C C C C C C C H H H H H H H H H H C C C H

H in 3 fatty acids H C H H H C H H O H H H H H C O C C C C C C H

H H H H O H H H H H H H C C C C C C C C H H H

H H H H O H H H C C C C H H H C H 3 H2O H C H H H O in 3 water

molecules fat molecule H C H C H H H H Triglycerides: Long-Term Energy Storage Fatty acids are either unsaturated or saturated. Unsaturated - one or more double bonds between carbons Tend to be liquid at room temperature Example: plant oils Saturated - no double bonds between carbons Tend to be solid at room temperature Examples: butter, lard 40 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H O C H H OH C HO

OH C O + C HO H H H H H C C C C C H H H H H H H H

C C C C H H H H H H H C H OH C HO C H H C C C H H

H C C C H H H H H C H H in glycerol Fig. 3.10 3 H2O O C HO C O H H H H

H C C C C C C H H H H H O H H H H H H H C C C

C C C C C H H H H H H H O H H H C C C C O H H

C C H O H H 3 water molecules corn oil H H H H H H H H H H H H H H H

C C C C C C C C C C C C C C C C C H H H H H H

H H H H H H H H unsaturated fat H C HO butter H H H H H H H H H H

H H H H C C C C C C C C C C C C C C C H H H H

H H H H H H H H H H H saturated fatty acid with no double bonds b. Types of fatty acids H saturated fat c. Types of fats H H C H fat molecule unsaturated fatty acid with double bonds (yellow) O H C H

3 fatty acids mil H in a. Formation of a fat corn H H H O H 3 H2O H H H Phospholipids: Membrane Components Structure is similar to triglycerides Consist of one glycerol molecule linked to two fatty acids and a modified phosphate group The fatty acids are nonpolar and hydrophobic. The modified phosphate group is polar and hydrophilic. Function: form plasma membranes In water, phospholipids aggregate to form a lipid bilayer. Polar phosphate heads are oriented towards the water. Nonpolar fatty acid tails are oriented away from water. Nonpolar fatty acid tails form a hydrophobic core. 42

Phospholipids Form Membranes Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. glycerol O Polar Head 1 O CH2 2 CH2 3 R O P O CH2 O Fig. 3.11 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH CH2 CH2 2 CH2 CH3 CH 2 C fatty acids O C CH2 CH 2 CH2 CH CH2 CH2 CH2 CH CH 2 O

Nonpolar Tails phosphate CH 2 CH 2 CH 2 CH 2 a. Phospholipid structure CH 2 CH 2 CH 2 CH b.. Plasma membrane of a cell outside cell inside cell 3 Steroids: Four Fused Carbon Rings

Composed of four fused carbon rings Various functional groups attached to the carbon skeleton Functions: component of animal cell membrane, regulation Examples: cholesterol, testosterone, estrogen Cholesterol is the precursor molecule for several other steroids. 44 Steroid Diversity Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. OH CH3 CH3 O b. Testosterone CH3 HC CH3 (CH2)3 HC CH3 OH CH3 CH3 CH3 HO c. Estrogen HO a. Cholesterol Ernest A. Janes/Bruce Coleman/Photoshot

Waxes Long-chain fatty acid bonded to a long-chain alcohol Solid at room temperature Waterproof Resistant to degradation Function: protection Examples: earwax, plant cuticle, beeswax 46 Waxes Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. b. a: Das Fotoarchiv/Peter Arnold, Inc.; b: Martha Cooper/Peter Arnold, Inc. 47 3.4 Proteins Proteins are polymers of amino acids linked together by peptide bonds. A peptide bond is a covalent bond between amino acids. Two or more amino acids joined together are called peptides. Long chains of amino acids joined together are called polypeptides. A protein is a polypeptide that has folded into a particular shape and has function. 48 Functions of Proteins Metabolism Most enzymes are proteins that act as catalysts to accelerate chemical reactions within cells.

Support Keratin and collagen Transport Hemoglobin and membrane proteins Defense Antibodies Regulation Hormones are regulatory proteins that influence the metabolism of cells. Motion Muscle proteins and microtubules 49 Amino Acids: Protein Monomers There are 20 different common amino acids. Amino acids differ by their R groups. Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group H 2N H C R R = rest of molecule acidic group COOH Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Sample Amino Acids with Nonpolar (Hydrophobic) R Groups H H H3N +

H3N+ O C C C C (CH2)2 O CH H O H3N+ O H O C H3N+ C CH2 O O CH2 CH S CH3 H3C valine (Val) O

C C H C H2C CH2 CH3 CH3 CH3 methionine (Met) phenylalanine (Phe) leucine (Leu) O H2N + C O CH2 proline (Pro) Sample Amino Acids with Polar (Hydrophilic) R Groups H H3N+ H O C C CH2 H3N+ C

O CH SH cysteine (Cys) H H3N+ C O H3N+ C O CH2 H O C C H3N+ O C C O (CH2)2 NH2 O glutamine (Gln) OH tyrosine (Tyr) O

CH C NH2 O asparagine (Asn) O C C CH2 C H O OH serine (Ser) O H3N+ C H O OH CH3 threonine (Thr) Sample Amino Acids with Ionized R Groups H H H3N+ C O C CH2

H3N + C C CH2 O O H3N+ CH2 COO- N+H3 lysine (Lys) C CH2 O C O C O H3N + H CH2 CH2 glutamicacid (Glu) H

O O aspartic acid (Asp) C O C (CH2)3 H O NH C N+H2 NH2 arginine (Arg) H3N+ C O C CH2 O NH N+H histidine (His) Synthesis and Degradation of a Peptide Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group amino acid Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group

acidic group + amino acid amino acid Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group acidic group dehydration reaction amino acid amino acid Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group peptide bond acidic group dehydration reaction amino acid amino acid dipeptide water Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group peptide bond acidic group dehydration reaction hydrolysis reaction amino acid

amino acid dipeptide water Levels of Protein Structure Proteins cannot function properly unless they fold into their proper shape. When a protein loses it proper shape, it said to be denatured. Exposure of proteins to certain chemicals, a change in pH, or high temperature can disrupt protein structure. Proteins can have up to four levels of structure: Primary Secondary Tertiary Quaternary 57 Four Levels of Protein Structure Primary The sequence of amino acids Secondary Characterized by the presence of alpha helices and beta (pleated) sheets held in place with hydrogen bonds Tertiary Final overall three-dimensional shape of a polypeptide Stabilized by the presence of hydrophobic interactions, hydrogen bonding, ionic bonding, and covalent bonding Quaternary Consists of more than one polypeptide

58 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H3N+ Primary Structure This level of structure is determined by the sequence of amino acids coded by a gene that joins to form a polypeptide. amino acid C O C CH R O H O O C CH CH N C O R hydrogen bond C C

C N H O C H O CH R C H C N R N CH N R H C hydrogen bond O N R O R H N R H C Hydrogen bonding between amino acids

causes the polypeptide to form an alpha helix or a pleated sheet. N CH CH Secondary Structure CH C O COO peptide bond N O H C R C H N C R C N H R C O C R C C O H H N N R C

C O C R N H H O R C C alpha) helix O O Interactions of amino acid side chains with water, covalent bonding between R groups, and other chemical interactions determine the folded three-dimensional shape of a protein. disulfide bond Quaternary Structure This level of structure occurs when two or more folded polypeptides interact to perform a biological function. N H C O N C C N C H (beta) sheet = pleated sheet

Tertiary Structure C C N O R Protein-Folding Diseases Chaperone proteins help proteins fold into their normal shape. Defects in chaperone proteins may play a role in several human diseases such as Alzheimer disease and cystic fibrosis. Prions are misfolded proteins that have been implicated in a group of fatal brain diseases known as TSEs. Mad cow disease is one example of a TSE disease. 60 3.5 Nucleic Acids Nucleic acids are polymers of nucleotides. Two varieties of nucleic acids: DNA (deoxyribonucleic acid) Genetic material that stores information for its own replication and for the sequence of amino acids in proteins. RNA (ribonucleic acid) Perform a wide range of functions within cells which include protein synthesis and regulation of gene expression 61 Structure of a Nucleotide Each nucleotide is composed of three parts: A phosphate group A pentose sugar A nitrogen-containing (nitrogenous) base There are five types of nucleotides found in nucleic acids.

DNA contains adenine, guanine, cytosine, and thymine. RNA contains adenine, guanine, cytosine, and uracil. Nucleotides are joined together by a series of dehydration synthesis reactions to form a linear molecule called a strand. 62 Nucleotides Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. phosphate P C O 5' 4' S 1' 2' 3' pentose sugar nitrogencontaining base Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O P O C phosphate P

O O 5' 4' S 1' 2' 3' pentose sugar a. Nucleotide structure nitrogencontaining base Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O P O C phosphate P O O 5' 4' S 1'

2' 3' pentose sugar a. Nucleotide structure nitrogencontaining base CH2OH O OH C H H C H C C H H OH deoxyribose (in DNA) b. Deoxyribose versus ribose Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O P O C phosphate P O O 5' 4'

S 1' 2' 3' pentose sugar a. Nucleotide structure nitrogencontaining base CH2OH O CH2OH OH O OH C H H C C H H C H C C H H C C H OH H deoxyribose (in DNA) b. Deoxyribose versus ribose OH OH ribose (in RNA) Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Pyrimidines N NH2 O C C CH C CH O N H cytosine HN O T O CH3 C C HN CH N H thymine in DNA c. Pyrimidines versus purines Purines

C O U NH2 CH CH N H uracil in RNA N HC C C O N A N HN CH C N H adenine H2N C C N

G N CH C guanine N H Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O P O O nitrogencontaining base C phosphate P CH2OH 4' S OH O O 5' CH2OH 1'

C H H C C H H C H C C H H C C H H OH deoxyribose (in DNA) 2' 3' pentose sugar a. Nucleotide structure NH2 C CH C CH O N H cytosine Purines O HN O

OH OH ribose (in RNA) b. Deoxyribose versus ribose Pyrimidines N OH O C T O CH3 C HN CH N H thymine in DNA c. Pyrimidines versus purines C C O U NH2 CH CH N H uracil in RNA N

HC C O C N A N HN CH C adenine N H H2N C C N G N CH C guanine N H Structure of DNA and RNA The backbone of the nucleic acid strand is composed of alternating sugar-phosphate molecules. RNA is predominately a single-stranded molecule. DNA is a double-stranded molecule.

DNA is composed of two strands held together by hydrogen bonds between the nitrogen-containing bases. The two strands twist around each other to form a double helix. Adenine hydrogen bonds with thymine Cytosine hydrogen bonds with guanine The bonding between the nucleotides in DNA is referred to as complementary base pairing. 69 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. RNA Structure Fig. 3.19 N O N P G N N NH2 S H N O P N S Nitrogen-containing bases O U CH3 Backbone P

N A N N S S Ribose C Cytosine A G Guanine Adenine P Phosphate U Uracil NH2 N N O P N S C NH2 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. DNA Structure T A C G T A G C

C CCytosine S Sugar Guanine A AAdenine GG P Phosphate T TThymine b. Double helix a. Space-filling model H H N cytosine (C) sugar N O sugar N N H

N N N O H H guanine (G) H N N CH3 O H C H N N suga r N

N O adenine (A) Complementary Base Pairing in DNA N N sugar thymine (T) c. Complementary base pairing Photodisk Red/Getty RF A Special Nucleotide: ATP ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates. ATP is a high-energy molecule due to the presence of the last two unstable phosphate bonds. Hydrolysis of the terminal phosphate bond yields: The molecule ADP (adenosine diphosphate) An inorganic phosphate Energy to do cellular work ATP is called the energy currency of the cell. 73 ATP Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. adenosine triphosphate c.

NH2 NH2 N N N H2O P N adenosine b. P P triphosphate ATP N N N P N adenosine P diphosphate ADP c: Jennifer Loomis / Animals Animals / Earth Scenes + P

phosphate + ENERGY

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