Chapter 4 – Carbon and the Molecular Diversity of Life Chapter 5 – The Structure and Function of Macromolecules

Carbon All living things are made up of carbon based compounds All living things are made up of carbon based compounds Organic Chemistry is the study of carbon and carbon based compounds Organic Chemistry is the study of carbon and carbon based compounds Carbon compounds can range in size from the simple to the extremely complex Carbon compounds can range in size from the simple to the extremely complex

Bonding Carbon has 4 valence electrons Carbon has 4 valence electrons This allows carbon to form 4 different covalent bonds in a variety of orientations This allows carbon to form 4 different covalent bonds in a variety of orientations

Carbon Skeletons Can create an infinite variety of carbon skeletons Can create an infinite variety of carbon skeletons Variations include length, branching, double bonds, and rings Variations include length, branching, double bonds, and rings

Isomers Compounds that have the same number of atoms of the same elements but different structures and hence different properties Compounds that have the same number of atoms of the same elements but different structures and hence different properties 3 different types 3 different types Structural Structural Geometric Geometric Enantiomers Enantiomers

Types of Isomers

Functional Groups The components of organic molecules that are most commonly involved in chemical reactions The components of organic molecules that are most commonly involved in chemical reactions Usually replace one of the hydrogen atoms attached to a carbon atom in a hydrocarbon Usually replace one of the hydrogen atoms attached to a carbon atom in a hydrocarbon Gives rise to a variety of different chemical and physical properties Gives rise to a variety of different chemical and physical properties

Types of Functional Groups

Functional Groups Hydroxyl Hydroxyl Structure = –OH Structure = –OH Name = alcohols Name = alcohols Properties Properties polar as a result of the electronegative oxygen atom polar as a result of the electronegative oxygen atom Attracts water molecules, helps dissolve organic compounds Attracts water molecules, helps dissolve organic compounds Carbonyl Structure = see board Name = Ketone – if carbonyl is within a carbon skeleton Aldehyde – if carbonyl is at the end of a carbon skeleton Properties = Polar, water soluble Aldehyde and ketone may be isomers with different properties

Functional Groups Carboxyl Carboxyl Structure = -COOH Structure = -COOH Name = carboxylic acids Name = carboxylic acids Properties Properties Acidic properties (releases H+) Acidic properties (releases H+) Very polar, H+ tends to dissociate forming an ion molecule Very polar, H+ tends to dissociate forming an ion molecule Usually found in ionic form in cells Usually found in ionic form in cells Amino Structure = -NH 2 Name = Amines Properties Alkaline properties (picks up H+) Ionized with a + charge under cellular conditions

Functional Groups Sulfydryl Sulfydryl Structure = -SH Structure = -SH Name = thiols Name = thiols Properties = interact to form disulfide bridges in tertiary protein structure Properties = interact to form disulfide bridges in tertiary protein structure Phosphate Structure = -OPO 3 2- Name = organic phosphates Properties = Makes molecule attached to an anion Can transfer energy between organic molecules (ATP)

Functional Groups Ester Ester Structure = C-O-C Structure = C-O-C Name = none Name = none Properties = usually a connection between two molecules (ester linkages between carbohydrates Properties = usually a connection between two molecules (ester linkages between carbohydrates Methyl Structure = -CH 3 Name = none Properties = nonpolar

Molecules of Life 4 major classes of biological molecules 4 major classes of biological molecules Carbohydrates Carbohydrates Lipids Lipids Proteins Proteins Nucleic acids Nucleic acids Also called macromolecules – large molecules (polymers) usually containing many smaller subunits (monomers) Also called macromolecules – large molecules (polymers) usually containing many smaller subunits (monomers)

Synthesis and Breakdown of Polymers Polymer synthesis = condensation or dehydration reaction Polymer synthesis = condensation or dehydration reaction Polymer breakdown = hydrolysis reaction Polymer breakdown = hydrolysis reaction

Carbohydrates Serve as fuel and building materials Serve as fuel and building materials Include the basic sugars and their polymers Include the basic sugars and their polymers Simplest are the monosaccharides Simplest are the monosaccharides Can be linear, but usually in the form of rings Can be linear, but usually in the form of rings

Monosaccharides GlucoseGalactose

Disaccharides Consists of 2 monosaccharide Consists of 2 monosaccharide Held together with a glycosidic linkage Held together with a glycosidic linkage

Types of Disaccharides Sucrose – glucose and fructose Sucrose – glucose and fructose Lactose – glucose and galactose Lactose – glucose and galactose Maltose – glucose and glucose Maltose – glucose and glucose..\ppt lectures cd\animations\05_05Disaccharides_A.swf..\ppt lectures cd\animations\05_05Disaccharides_A.swf..\ppt lectures cd\animations\05_05Disaccharides_A.swf..\ppt lectures cd\animations\05_05Disaccharides_A.swf

Polysaccharides Polymers of sugar Polymers of sugar Examples include: Examples include: Starch Starch Consists entirely of glucose Consists entirely of glucose Storage form of glucose in plants Storage form of glucose in plants Glycogen – similar to starch, but is storage form of glucose in animals Glycogen – similar to starch, but is storage form of glucose in animals Cellulose – similar to starch but held together with a different glycosidic linkage; 1-4 β linkages as compared to 1-4 α linkages Cellulose – similar to starch but held together with a different glycosidic linkage; 1-4 β linkages as compared to 1-4 α linkages Chitin – found in animal exoskeletons and surgical thread Chitin – found in animal exoskeletons and surgical thread..\ppt lectures cd\animations\05_07Polysaccharides_A.swf..\ppt lectures cd\animations\05_07Polysaccharides_A.swf..\ppt lectures cd\animations\05_07Polysaccharides_A.swf..\ppt lectures cd\animations\05_07Polysaccharides_A.swf

Starch and Glycogen

Cellulose

Lipids Only class of organic macromolecules without a true monomer Only class of organic macromolecules without a true monomer Examples include fats, phospholipids, and hormones/steriods Examples include fats, phospholipids, and hormones/steriods Common characteristic = hydrophobic Common characteristic = hydrophobic

Fats Glycerol and 3 fatty acids = triacylglycerol or triglyceride (..\ppt lectures cd\animations\05_10Fats_A.swf)..\ppt lectures cd\animations\05_10Fats_A.swf FAs differ in length (# of C) and number of double bonds FAs attached to glycerol with ester linkages Saturated vs unsaturated

Phospholipids Replace a fatty acid with a phosphate group Replace a fatty acid with a phosphate group Gives “head” region (glycerol region) polar and hydrophillic properties while “tail” region or fatty acid tails retain non polar and hydrophobic properties Gives “head” region (glycerol region) polar and hydrophillic properties while “tail” region or fatty acid tails retain non polar and hydrophobic properties

Steroids Contain 4 carbon rings Contain 4 carbon rings Example is cholesterol Example is cholesterol Basic precursor molecule for many other hormones (particularly the sex hormones) Basic precursor molecule for many other hormones (particularly the sex hormones)

Protein Importance – instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules Importance – instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules

Protein Structure Monomer = amino acid, 20 different (see figure 5.17) Monomer = amino acid, 20 different (see figure 5.17) Have both a carboxyl and an amino group Have both a carboxyl and an amino group Difference between AAs is R group Difference between AAs is R group AA properties include – polar/hydrophilic, nonpolar/hydrophobic, acid, or base AA properties include – polar/hydrophilic, nonpolar/hydrophobic, acid, or base Polymer = polypeptide Polymer = polypeptide

Protein Structure 4 levels of proteins structure 4 levels of proteins structure Primary Primary Secondary Secondary Tertiary Tertiary Quaternary Quaternary

Primary Structure Linear arrangement of amino acids Linear arrangement of amino acids Each protein has its own unique primary structure Each protein has its own unique primary structure Determined by organisms genes Determined by organisms genes Slightest change can affect protein function (sickle cell, val for glu) Slightest change can affect protein function (sickle cell, val for glu)..\ppt lectures cd\animations\05_20aIntr oProteinStruct_A.swf..\ppt lectures cd\animations\05_20aIntr oProteinStruct_A.swf..\ppt lectures cd\animations\05_20aIntr oProteinStruct_A.swf..\ppt lectures cd\animations\05_20aIntr oProteinStruct_A.swf

Secondary Structure Regular, repeated coiling and folding of the polypeptide backbone, held together with hydrogen bonds Regular, repeated coiling and folding of the polypeptide backbone, held together with hydrogen bonds Alpha helix – helical coils, fibrous proteins Alpha helix – helical coils, fibrous proteins Beta pleated sheet – anti-parallel chains folded into pleats, globular proteins Beta pleated sheet – anti-parallel chains folded into pleats, globular proteins..\ppt lectures cd\animations\05_20cSecondaryStructure_A.swf..\ppt lectures cd\animations\05_20cSecondaryStructure_A.swf..\ppt lectures cd\animations\05_20cSecondaryStructure_A.swf..\ppt lectures cd\animations\05_20cSecondaryStructure_A.swf

Tertiary Structure 3D shape of protein 3D shape of protein Irregular contortions due to side chain interactions Irregular contortions due to side chain interactions Weak interactions Weak interactions H-bonds H-bonds Ionic bonds Ionic bonds Hydrophobic interactions Hydrophobic interactions Strong interactions Strong interactions Covalent disulfide bridges Covalent disulfide bridges..\ppt lectures cd\animations\05_20dTertiaryS tructure_A.swf..\ppt lectures cd\animations\05_20dTertiaryS tructure_A.swf..\ppt lectures cd\animations\05_20dTertiaryS tructure_A.swf..\ppt lectures cd\animations\05_20dTertiaryS tructure_A.swf

Quarternary Structure Interactions between and among several polypeptide chains Interactions between and among several polypeptide chains Example hemoglobin (contains 4 subunits) Example hemoglobin (contains 4 subunits)..\ppt lectures cd\animations\05_20eQuatern aryStructure_A.swf..\ppt lectures cd\animations\05_20eQuatern aryStructure_A.swf..\ppt lectures cd\animations\05_20eQuatern aryStructure_A.swf..\ppt lectures cd\animations\05_20eQuatern aryStructure_A.swf

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