Chapter 4~ Carbon & The Molecular Diversity of Life Chapter 5~ The Structure & Function of Macromolecules

Organic chemistry Carbon –tetravalence –Tetrahedron –shape determine function

Hydrocarbons Only carbon & hydrogen (petroleum; lipid ‘tails’) Covalent bonding; nonpolar High energy storage Isomers (same molecular formula, but different structure & properties) structural~differing covalent bonding arrangement geometric~differing spatial arrangement enantiomers~mirror images pharmacological industry (thalidomide)

Figure 4.6 Three types of isomers

Functional Groups, I Attachments that replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon Each has a unique property from one organic to another Hydroxyl Group H bonded to O; alcohols; polar (oxygen); solubility in water Carbonyl Group C double bond to O; At end of skeleton: aldehyde Otherwise: ketone

Functional Groups, II Carboxyl Group O double bonded to C to hydroxyl; carboxylic acids; covalent bond between O and H; polar; dissociation, H ion Amino Group N to 2 H atoms; amines; acts as a base (+1)

Functional Groups, III Sulfhydral Group sulfur bonded to H; thiols Phosphate Group phosphate ion; covalently attached by 1 of its O to the C skeleton;

Polymers Covalent monomers Condensation reaction (dehydration reaction): One monomer provides a hydroxyl group while the other provides a hydrogen to form a water molecule Hydrolysis: bonds between monomers are broken by adding water (digestion) D:\ImageLibrary1-17\05- Macromolecules\ Macromolecules.mov

Carbohydrates, I Monosaccharides √ CH 2 O formula; √ multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: aldehyde (aldoses) sugar ketone sugar √ cellular respiration; √ raw material for amino acids and fatty acids

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

Carbohydrates, II Disaccharides √ glycosidic linkage (covalent bond) between 2 monosaccharides; √ covalent bond by dehydration reaction Sucrose (table sugar) √ most common disaccharide

Figure 5.5 Examples of disaccharide synthesis

Carbohydrates, III Polysaccharides Storage: Starch~ glucose monomers Plants: plastids Animals: glycogen Polysaccharides Structural: Cellulose~ most abundant organic compound; Chitin~exoskeletons; cell walls of fungi; surgical thread

Lipids No polymers; glycerol and fatty acid Fats, phospholipids, steroids Hydrophobic; H bonds in water exclude fats Carboxyl group = fatty acid Non-polar C-H bonds in fatty acid ‘tails’ Ester linkage: 3 fatty acids to 1 glycerol (dehydration formation) Triacyglycerol (triglyceride) Saturated vs. unsaturated fats; single vs. double bonds

15 Fatty acids are either unsaturated or saturated.  Unsaturated - one or more double bonds between carbons GOOD type of fat Tend to be liquid at room temperature –Example: plant oils  Saturated - no double bonds between carbons Tend to be solid at room temperature BAD FAT –Examples: butter, lard Triglycerides: Long-Term Energy Storage

Phospholipids 2 fatty acids instead of 3 (phosphate group) ‘Tails’ hydrophobic; ‘heads’ hydrophilic Micelle (phospholipid droplet in water) Bilayer (double layer); cell membranes

Steroids Lipids with 4 fused carbon rings Ex: cholesterol: cell membranes; precursor for other steroids (sex hormones)

Proteins Importance: instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known Monomer: amino acids (there are 20) ~ carboxyl (-COOH) group, amino group (NH 2 ), H atom, variable group (R)…. Variable group characteristics: polar (hydrophilic), nonpolar (hydrophobic), acid or base Three-dimensional shape (conformation) Polypeptides (dehydration reaction): peptide bonds~ covalent bond; carboxyl group to amino group (polar)

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.

21 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

amino acid amino group Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Synthesis and Degradation of a Peptide

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

24 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

25 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

Primary Structure Conformation: Linear structure Molecular Biology: each type of protein has a unique primary structure of amino acids Ex: lysozyme Amino acid substitution: hemoglobin; sickle-cell anemia

Secondary Structure Conformation: coils & folds (hydrogen bonds) Alpha Helix: coiling; keratin Pleated Sheet: parallel; silk

Tertiary Structure Conformation: irregular contortions from R group bonding hydrophobic disulfide bridges hydrogen bonds ionic bonds

Quaternary Structure Conformation: 2 or more polypeptide chains aggregated into 1 macromolecule collagen (connective tissue) hemoglobin

Nucleic Acids, I Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA->RNA->protein Polymers of nucleotides (polynucleotide): nitrogenous base pentose sugar phosphate group Nitrogenous bases: pyrimidines~cytosine, thymine, uracil purines~adenine, guanine

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

32 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.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. S C O P nitrogen- containing base pentose sugar 5' 4' 1' 2' 3' phosphate Nucleotides

Figure 5.28 DNA  RNA  protein: a diagrammatic overview of information flow in a cell Figure 5.28 DNA  RNA  protein: a diagrammatic overview of information flow in a cell

Nucleic Acids, II Pentoses: –ribose (RNA) –deoxyribose (DNA) –nucleoside (base + sugar) Polynucleotide: –phosphodiester linkages (covalent); phosphate + sugar

Nucleic Acids, III Inheritance based on DNA replication Double helix (Watson & Crick ) H bonds~ between paired bases van der Waals~ between stacked bases A to T; C to G pairing Complementary

37 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.

38 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.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ATP N N N N + + P PP P P P N N N N ENERGY phosphatediphosphate ADP triphosphate ATPb. NH 2 H2OH2O adenosinetriphosphatec.a. adenosine c: © Jennifer Loomis / Animals Animals / Earth Scenes