Learning Objectives. Learning Objectives (cont.) Chapter 3: Organic Chemistry 1. Lectures by Tariq Alalwan, Ph.D.

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1 Biology, 10e Sylvia Mader Lectures by Tariq Alalwan, Ph.D. Learning Objectives List the features of carbon that result in the diversity of organic molecules. Describe how macromolecules are assembled and disassembled. Distinguish among monosaccharides, disaccharides, and polysaccharides. Compare storage polysaccharides with structural polysaccharides. Distinguish among fats, phospholipids, and steroids, and describe the composition, characteristics, and biological functions of each. Learning Objectives (cont.) Describe 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. Compare the structure and function of DNA and RNA in cells Relate the structure of ATP to its function in cells. Chapter 3: Organic Chemistry 1

2 Organic Molecules Inorganic Chemistry of elements other than carbon Organic Carbon based chemistry Carbon Atom Carbon atoms: Contain a total of 6 electrons Only four electrons in the outer (valence) shell Very diverse as one atom can bond with ih up to four other atoms Often bonds with other carbon atoms to make hydrocarbons chains of carbon atoms bonded exclusively to hydrogen atoms Can exist as unbranched (e.g. octane) or branched chains, or as rings (e.g. cyclohexane) Functional Groups Functional groups: Specific combinations of bonded atoms Attached as a group to other molecules Always react in the same manner, regardless of where attached Determine activity and polarity of large organic molecules Many functional groups, but only a few are of major biological importance Chapter 3: Organic Chemistry 2

3 Functional Groups (cont.) Six functional groups are of biological importance Hydroxyl group ( OH) Carbonyl group (C=O) Carboxyl group (HO C=O) Amino group ( NH 2 ) Sulfhydryl group ( SH) Phosphate group Functional Groups Hydroxyl Composed of a hydrogen atom bonded to an oxygen atom: OH Organic molecules containing a hydroxyl group are known as alcohols l Polar, why? Forms hydrogen bonds; present in sugars and some amino acids Example: Methanol Functional Groups Carbonyl Composed of a carbon atom double bonded to an oxygen atom: C=O Polar If carbonyl group at the end of the skeleton: kl aldehyde d If carbonyl group within (internal) the skeleton: ketone Present in sugars Formaldehyde Acetone Chapter 3: Organic Chemistry 3

4 Functional Groups Carboxyl Composed of an oxygen double bonded to a carbon atom that is also bonded to a hydroxyl group (hydroxyl group + carbonyl group = carboxyl group) Organic molecules containing a carboxyl group are known as carboxylic acids Polar and acidic, why? Carboxyl groups are essential constituents of amino acids Example: acetic acid Functional Groups Amino Composed of a nitrogen atom covalently bonded to two hydrogen atoms: NH 2 Organic molecules containing an amino group are known as amines Polar Forms hydrogen bonds Present in amino acids and nucleic acids Example: Glycine Functional Groups Sulfhydryl Composed of a sulfur atom covalently bonded to a hydrogen atom: SH Organic molecules containing a sulfhydryl group are known as thiols Forms disulfide bonds Present in some amino acids (i.e. proteins) Example: Ethanethiol Chapter 3: Organic Chemistry 4

5 Functional Groups Phosphate An ion composed of a phosphate ion covalently attached by one of its oxygen atoms to the carbon skeleton Can release one or two hydrogen ions, producing ionized forms with 1 or 2 units of negative charge Polar, acidic Present in nucleotides (i.e. nucleic acids) and phospholipids Un-ionized form Isomers Isomers organic molecules that have: Identical molecular formulas, but Differing internal arrangement of atoms (i.e. structures) and properties Macromolecules Some molecules are called macromolecules because of their large size Usually consist of many repeating units Resulting molecule is a polymer (many parts) Repeating units are called monomers Chapter 3: Organic Chemistry 5

6 Making and Breaking Macromolecules Dehydration (synthesis) Macromolecule is assembled by removing an OH group from one subunit and an H from other subunit Thus removing a water molecule (H 2 O) for every subunit that is added to a macromolecule Also called water losing or condensation reaction Energy is required to break the chemical bonds when water is extracted Cells must supply energy to assemble macromolecules Making and Breaking Macromolecules (cont.) Hydrolysis (digestion) Macromolecules are disassembled into their constituent parts by adding an OH group to form one subunit and an H to form the other subunit Thus adding a water molecule for every macromolecule that is disassembled Energy is released when the energy storing bonds are broken Synthesis and Degradation of Polymers Polymers large molecules consisting of long chains of repeating subunits (monomers) Chapter 3: Organic Chemistry 6

7 1. Carbohydrates Loosely defined group of molecules that contain C, H, and O in molecular ratio of 1C:2H:1O, with an empirical formula of (CH 2 O) n Are named based on the number of sugar units they contain Monosaccharides one sugar unit (mono ) Disaccharides two sugar units (di ) Polysaccharides many sugar units (poly ) Monosaccharides Single sugar molecules Quite soluble and sweet to taste Play central role in energy storage Examples Glucose, fructose and galactose Hexoses Six carbon atoms Isomers of C 6 H 12 O 6 Ribose and deoxyribose Pentoses Five carbon atoms C 5 H 10 O 5 & C 5 H 10 O 4 Disaccharides Contain two monosaccharides joined by a covalent bond Soluble and sweet to taste Play a role in the transport of sugars Common disaccharides: Sucrose (table sugar) 1 glucose + 1 fructose joined by dehydration Maltose (malt sugar) Two glucose units joined by dehydration Lactose (milk sugar) 1 glucose + 1 galactose joined by dehydration Chapter 3: Organic Chemistry 7

8 Synthesis and Degradation of Maltose, a Disaccharide Polysaccharides Polymers of monosaccharides (a single long chain or a branched chain) consisting of repeating units of simple sugars, usually glucose Low solubility; not sweet to taste Common polysaccharides: Starches: Energy storage in plants Glycogen: Energy storage in animals Cellulose: Structural polysaccharide in plants Starch Form of carbohydrate used for short term energy storage in plants Polymer consisting of glucose subunits Starch occurs in two forms Amylose (unbranched chain) Amylopectin (branched chain) Plant cells store starch as granules in amyloplasts Chapter 3: Organic Chemistry 8

9 Structure of Starch 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 Stored mainly in liver and muscle cells Structure of Glycogen Chapter 3: Organic Chemistry 9

10 Cellulose Cellulose Long, coiled insoluble polymer of glucose Glucoses connected differently than in starch Structural component of plants (fibers) The most abundant carbohydrate Indigestible by most animals Structure of Cellulose Other Carbohydrates Chitin Polymer of glucose Each glucose with an amino group Very resistant to wear and digestion Forms the exoskeletons of arthropods and cell walls of fungi Chapter 3: Organic Chemistry 10

11 2. Lipids Compounds soluble in nonpolar solvents, and relatively insoluble in water (hydrophobic) Consist mainly of carbon and hydrogen, with few oxygen containing g functional groups Types of Lipids: Triglycerides Triglycerides (Fats) Structure = glycerol + 3 fatty acids Glycerol: a 3 carbon alcohol with each carbon bearing a hydroxyl group Fatty acids: long hydrocarbon chains (ranging from 4 to 36 carbons) ending in a carboxyl group The 3 fatty acids of a triglyceride are not necessarily the same Dehydration Synthesis of Triglyceride Three fatty acids attached to each glycerol molecule Carboxylic acid at one end Carboxylic acid connects to OH on glycerol in dehydration reaction Chapter 3: Organic Chemistry 11

12 Triglycerides (cont.) Functions Long term energy storage Efficient energy storage molecules because of their high concentrations of C H bonds Insulation The fat (blubber) beneath the skin in marine animals Cushioning Excellent shock absorber and provides natural cushioning to vital organs Saturated and Unsaturated Fatty Acids Saturated fats All internal C atoms are bound to at least two H atoms, no double bonds between C atoms Results in maximum number of hydrogen atoms therefore, said to be saturated Tend to be straight and fit close together Found in animal fat and solid vegetable shortening Solid at room temperature Example: butter Saturated and Unsaturated Fatty Acids Unsaturated fats Double bonds between at least one pair of C atoms Results in less than maximum number of hydrogen atoms therefore, said to be unsaturated Have low melting points because the fatty acids chains cannot closely align Double bonds cause kinks or bends in the chains Most are liquid at room temperature Example: vegetable oil Chapter 3: Organic Chemistry 12

13 Types of Fatty Acids Phospholipids Derived from triglycerides Modified fats with two fatty acid chains rather than three Two fatty acids attached instead of three Third fatty acid is replaced by a phosphate group The fatty acids are nonpolar and hydrophobic The phosphate group is polar and hydrophilic Phospholipids are amphipathic lipids, with one hydrophilic end and one hydrophobic end Phospholipids (cont.) Molecules self arrange when placed in water Polar phosphate heads next to water Nonpolar fatty acid tails overlap and exclude water Spontaneously form double layer and a sphere Phospholipids are basic components of cell membranes Phospholipid bilayer Chapter 3: Organic Chemistry 13

14 Phospholipid Bilayer in Cell Membranes Steroids Steroids lipids composed of four attached C rings Side chains distinguish one steroid from another Steroids of biological importance include: Cholesterol Hormones (e.g. reproductive, cortisol, etc.) Bile salts (emulsify fats) Found in eukaryotic cell membrane Plant cell membranes contain molecules similar to cholesterol High levels of cholesterol in the blood may contribute to cardiovascular disease Steroid Diversity Chapter 3: Organic Chemistry 14

15 Waxes Long chain fatty acid bonded to a long chain alcohol High melting point Waterproof coating on leaves, bird feathers, mammalian skin and arthropod exoskeleton Resistant to degradation 3. Proteins Classification of proteins according to biological function Support collagen in ligaments and tendons & keratin in nails and hair Enzymes biological catalysts that accelerate chemical reactions within cells Transport hemoglobin that carry oxygen in RBCs; channel & carrier membrane proteins Defense antibodies that prevent infections Hormones regulatory hormones that influence metabolism in cells (e.g. insulin) Motion contractile proteins; actin and myosin in muscles, microtubules Amino Acids Proteins are made up of various combinations of 20 types of repeating subunits called amino acids are joined together by peptide bonds are organic molecules consist of two characteristic end groups a side group (or side chain) Chapter 3: Organic Chemistry 15

16 Structure of Amino Acids Each amino acid has a central alpha carbon atom Two end groups an amino group (NH2) a carboxyl group (COOH) A side (R group) bonded to the α carbon between the two end groups varies from one amino acid to another determines the unique chemical properties of the amino acid Amino Acids in Proteins 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 The Polypeptide Backbone Amino acids joined together end to end COOH of one amino acid covalently bonds to the NH 2 of the next amino acid Special name for this bond Peptide Bond 2 amino acids bonded together Dipeptide 3 amino acids bonded together Tripeptide Many amino acids bonded together Polypeptide Characteristics of a protein are determined by composition and sequence of amino acids Virtually unlimited number of proteins Chapter 3: Organic Chemistry 16

17 Synthesis and Degradation of a Peptide Four Levels of Protein Organization There are four main levels of protein organization: Primary refers to the linear sequence of amino acids that make up the polypeptide chain Secondary refers to the formation of a regular pattern of twists or folds of the polypeptide chain Tertiary refers to the 3 D shape formed by bending and twisting of the polypeptide chain Quaternary refers to the 3 D structure of resulting from two or more polypeptide chains interactions Levels of Protein Structure Primary level The specific amino acid sequence producing a long chain with a COOH group on one end and NH 2 group on the other Specified by instructions in a gene Slight change in primary structure can be detrimental Example: Sickle cell anemia Chapter 3: Organic Chemistry 17

18 Primary Structure of a Protein Levels of Protein Structure (cont.) Secondary level Results from H bonding between individual amino acids of the polypeptide chain Two common patterns: α helix (helical coil) was the first pattern discovered β pleated sheet was the second pattern discovered Both types may occur in the same polypeptide chain Fibrous proteins are either mostly alpha helices or beta pleated sheets Secondary Structure α Helix Hydrogen bonds form between every 4 th amino acid Basic structural unit of fibrous, elastic proteins (e.g. hair and horn) β Pleated Sheet Chain folded back with regions of chain parallel to itself Hydrogen bonds hold it in this conformation Spider silk and silkworm silk are mostly β pleated sheets Chapter 3: Organic Chemistry 18

19 Secondary Protein Structure Levels of Protein Structure (cont.) Tertiary level 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 bonds between SH groups of two cysteines) Denaturation process by which a protein changes its shape (tertiary and secondary) or even unfolds when its tolerance range for some factor is exceeded Levels of Protein Structure (cont.) Quaternary level 3 D structure resulting from two or more polypeptide chains interacting in specific ways to form a biologically active molecule l Examples: Hemoglobin, a globular protein consisting of 4 polypeptide chains (2 alpha chains and 2 beta chains) with a central heme (iron) unit Collagen, a fibrous protein with 3 helical polypeptide chains Chapter 3: Organic Chemistry 19

20 Quaternary Structure of Proteins 2009 Cengage - Wadsworth 4. Nucleic acids Nucleic acids long polymers of repeating subunits called nucleotides transmit hereditary information and determine what proteins a cell manufactures Two types DNA Deoxyribonucleic acid RNA Ribonucleic acid Chapter 3: Organic Chemistry 20

21 Nucleic acids Deoxyribonucleic acid (DNA) Double stranded helical spiral (twisted ladder) Serves as genetic information center (blueprint) in genes or chromosomes Specifies the amino acid sequence of proteins through the sequences of nucleotides Ribonucleic acid (RNA) Part single stranded, part double stranded Serves primarily in assembly of proteins In nucleus and cytoplasm of cell The Nucleotides of Nucleic Acids Nucleotides are made up of three parts: A phosphate group (makes the molecule acidic) A five carbon sugar, either deoxyribose (in DNA) or ribose (in RNA) A nitrogenous base (4 kinds in DNA, 3 kinds in RNA, 3 common to both Nucleotide subunits connected end to end to make nucleic acid Sugar of one connected to the phosphate of the next Sugar phosphate backbone 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) Chapter 3: Organic Chemistry 21

22 Structure of DNA and RNA DNA is double stranded with complementary base pairing; RNA is single stranded Complementary base pairing occurs where two strands of DNA are held together by hydrogen bonds between purine and pyrimidine bases The number of purine bases always equals the number of pyrimidine bases In DNA, thymine is always paired with adenine; cytosine is always paired with guanine; A + G = C + T Two strands of DNA twist to form a double helix; RNA does not form helices Nucleotide Structure DNA Chapter 3: Organic Chemistry 22

23 RNA Comparison of DNA and RNA Other Nucleic Acids Adenosine triphosphate (ATP) Composed of adenine, ribose, and three phosphates Primary energy molecule of all cells In cells, one phosphate h bond is hydrolyzed d yields: ild The molecule adenosine diphosphate (ADP) An inorganic phosphate molecule p i Energy Other high energy molecules nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD + ) Chapter 3: Organic Chemistry 23

24 ATP Chapter 3: Organic Chemistry 24