Organic Chemistry Carbon The Backbone of Life Organic
Organic Chemistry
Carbon: The Backbone of Life • Organic chemistry is the study of carbon compounds • Life is carbon-based due to the ability to form large, complex molecules • Carbon usually bonds in conjunction with hydrogen, oxygen, nitrogen, phosphorus, and sulfur in living things (CHONPS). • These compounds can be simple or massive. 2
Carbon has 4 valence electrons, thus makes 4 bonds • With four valence electrons, carbon can form four covalent bonds with a variety of atoms • This ability makes large, complex molecules possible 3
Those four bonds can vary… 4
Carbon Skeletons Vary • Carbon chains form the skeletons of most organic molecules and can vary in length and shape
Functional Groups A few chemical groups are key to the function of biomolecules • The carbon skeleton often has accessory chains (functional groups) that determine what the compound can do 6
Functional Groups • FGs are the pieces that are most commonly involved in chemical reactions • The number and arrangement of functional groups give each molecule its unique properties • Let’s meet the FGs 7
Hydroxyl STRUCTURE (may be written HO—) EXAMPLE Ethanol Alcohols (Their specific names usually end in -ol. ) NAME OF COMPOUND • Is polar as a result FUNCTIONAL of the electrons PROPERTIES spending more time near the electronegative oxygen atom. • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.
Carbonyl STRUCTURE Ketones if the carbonyl group is within a carbon skeleton NAME OF COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Acetone Propanal • A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. • Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups). FUNCTIONAL PROPERTIES
Carboxyl STRUCTURE Carboxylic acids, or organic acids EXAMPLE • NAME OF COMPOUND Acts as an acid; can FUNCTIONAL PROPERTIES donate an H+ because the covalent bond between oxygen and hydrogen is so polar: Acetic acid Nonionized • Ionized Found in cells in the ionized form with a charge of 1– and called a carboxylate ion.
Amino STRUCTURE Amines EXAMPLE • NAME OF COMPOUND Acts as a base; can. FUNCTIONAL pick up an H+ from PROPERTIES the surrounding solution (water, in living organisms): Glycine Nonionized • Ionized Found in cells in the ionized form with a charge of 1.
Sulfhydryl Thiols STRUCTURE NAME OF COMPOUND (may be written HS—) EXAMPLE Cysteine • Two sulfhydryl groups FUNCTIONAL can PROPERTIES react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. • Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds.
Phosphate STRUCTURE Organic phosphates EXAMPLE • FUNCTIONAL Contributes negative PROPERTIES charge to the molecule of which it is a part (2– when at the end of a molecule, as at left; 1– when located internally in a chain of phosphates). • Molecules containing phosphate groups have the potential to react with water, releasing energy. Glycerol phosphate NAME OF COMPOUND
Methyl STRUCTURE Methylated compounds EXAMPLE • Addition of a methyl FUNCTIONAL group PROPERTIES to DNA, or to molecules bound to DNA, affects the expression of genes. • Arrangement of methyl groups in male and female sex hormones affects their shape and function. 5 -Methyl cytidine NAME OF COMPOUND
Example of FG in action. ATP: Chemical Energy for Cells • Adenosine triphosphate (ATP), is made of adenosine bonded to three phosphate groups. Adding or removing phosphate groups stores and releases energy. • Draw 15
Organic Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids
The FOUR Classes of Large Biomolecules • All living things are made of four classes of biomolecules: • • Carbohydrates Lipids Protein Nucleic Acids • Macromolecules are large molecules composed of thousands of covalently bonded atoms • Their structure determines their function!!! 17
The FOUR Classes of Large Biomolecules • Most Macromolecules are polymers, built from monomers • A polymer is a long molecule made of repeating smaller pieces called monomers • Three of the four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids 18
Building polymers • A dehydration reaction links monomers together by removing a water molecule 19
Building polymers • Hydrolysis is the reverse, and disassembles polymers by adding water • Why is water important for food digestion? 20
Biomolecule 1: Carbohydrates • Include sugars (monomer) and starches (polymer). Both provide chemical energy (sugar = fast, starch = long) and building material (starch only, common in plants) • The simplest carbohydrates (sugars) are monosaccharides, or single sugars with formula ratios of 1 C: 2 H: 1 O used for quick energy (draw one) • Carbohydrate macromolecules (starches) are polysaccharides, or chains of sugars; used to build cell parts or store energy (draw one) 21
Sugars: Monosaccharides • Glucose (C 6 H 12 O 6) is the most common monosaccharide • Monosaccharides are classified by – The location of the carbonyl group – The number of carbons in the carbon skeleton 22
Sugars: Disaccharides • A disaccharide is formed when dehydration reaction joins two monosaccharides; still a sugar 23
Synthesizing Maltose & Sucrose 24
Types of Polysaccharides • Starch is a storage polysaccharide of plants that consists entirely of glucose monomers • Plants store surplus starch as granules within chloroplasts and other plastids • The simplest form of starch is amylose 25
Types of Polysaccharides • Glycogen is a storage polysaccharide in animals (“animal starch”) • Humans and other vertebrates store glycogen mainly in liver and muscle cells 26
Types of Polysaccharides • Cellulose is a polysaccharide used to build plant cell walls • Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ 27
Such Elegance! 28
Polysaccharide Random Acts of Biology • Cellulose in human food passes through the digestive tract as insoluble fiber • Some microbes use enzymes to digest cellulose • Many herbivores, from cows to termites, have symbiotic relationships with these microbes • Chitin is the structural polysaccharide in animal exoskeletons (crunch!) and fungi cell walls (surprise!) 29
Biomolecule 2: Lipids are a diverse group of hydrophobic molecules • Lipids are the one class of large biological molecules that do not form polymers • The unifying feature of lipids is having little or no affinity for water (water fearing) • Lipids are hydrophobic because they are nonpolar • The most biologically important lipids are fats, phospholipids, and steroids 30
Fats: Start with a Simple Little Glycerol Molecule • Fats are constructed from two types of smaller molecules: glycerol and fatty acids • Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon • A fatty acid consists of a carboxyl group attached to a long carbon skeleton 31
Dehydration Rxn 1: Add a Fatty Acid • Next, add a “fatty acid” through a dehydration synthesis reaction • What makes it an acid? The C double bond O, single bond OH! 32
Dehydration Rxn 2!! • Next, add a SECOND “fatty acid” through a dehydration synthesis reaction
Dehydration Reaction THREE!!! • How many water molecules will it take to disassemble this molecule? 34
Saturated or Unsaturated? • Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature • Most animal fats are saturated (lard) • Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds, so they are straight 35
Saturated or Unsaturated? • Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature • Plant fats and fish fats are usually unsaturated • Unsaturated fatty acids have one or more double bonds, so they bend 36
Fats: Major function is storage! • The major function of fats is long-term energy storage! • Humans and other mammals store their fat in adipose cells • Adipose tissue also cushions and insulates the body 37
Phospholipids • Phospholipids are the major component of all cell membranes; b/c the phosphate head is hydrophilic and the lipid tail is hydrophobic, they self assemble into a bi-layer in water (draw) 38
Hydrophobic tails Hydrophilic head A Single Phospholipid Molecule Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol
Steroids • Steroids are lipids with a carbon skeleton consisting of four fused rings • Ex: The steroid Cholesterol is a component in animal cell membranes • Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease • Ex: Many hormones are also steroids 40
Biomolecule 3: Proteins • Proteins are very diverse. • Cells are mostly made of and run by Proteins, as they account for more than 50% of the dry mass of most cells • Protein functions include structural support, storage, transport, cellular communication, movement, and defense (basically everything that keeps you alive…) • Let’s take a look at a few we’ll learn this year! 41
Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Enzyme 42
Storage proteins Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Ovalbumin Amino acids for embryo 43
Hormonal proteins Function: Coordination of an organism’s activities Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration High blood sugar Insulin secreted Normal blood sugar 44
Defensive proteins Function: Protection against disease Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Virus Bacterium 45
Transport proteins Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Transport protein Cell membrane 46
Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Signaling molecules Receptor protein 47
Structural proteins Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Collagen Connective tissue 60 m
Enzymes • SPECIAL PROTEIN: Enzymes are protein catalysts that speed up reactions; they are reusable and specific to one function (based on their shape); ex: digestive enzymes, buffers, etc 49
Protein Monomer • Amino acids are the monomers of all proteins. • Amino acids differ in their properties due to differing side chains, called R groups Side chain (R group) carbon Amino group Carboxyl group 50
Polypeptides • Polypeptide chains (protein polymers) are made of chained arrangements of the 20 available amino acids and then folded into proteins. • A protein consists of one or more polypeptides 51
Hydrophobic Amino Acids Nonpolar side chains; hydrophobic Side chain Glycine (Gly or G) Methionine (Met or M) Alanine (Ala or A) Valine (Val or V) Phenylalanine (Phe or F) Leucine (Leu or L) Tryptophan (Trp or W) Isoleucine (Ile or I) Proline (Pro or P)
Hydrophilic Amino Acids 53
Electrically charged Amino Acids 54
Peptide Bonds • Amino acids are linked by peptide bonds (through dehydration synthesis) • A polypeptide is a polymer of amino acids • Polypeptides range in length from a few to more than a thousand monomers (Yikes!) • Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) 55
Peptide Bonds 56
Peptide Bonds 57
Protein Structure & Function • At first, all we have is a string of AA’s bound with peptide bonds. • Once the string of AA’s interacts with itself and its environment (often aqueous), then we have a functional protein that consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape • The sequence of amino acids determines a protein’s three-dimensional structure • A protein’s structure determines its function 58
Protein Structure: 4 Levels • Primary structure is the amino acid chain pipe cleaner • Secondary structure consists of alpha helices (coils) or beta pleats (folds) coiled/folded pipe cleaner • Tertiary structure is determined by interactions among side chains (IMFs and bonds) within the helix/pleat pipe cleaner connected to itself with paper clip • Quaternary structure consists of multiple polypeptide chains multiple pipe cleaners 59
Primary Structure • Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word • Primary structure is determined by inherited genetic information
Secondary Structure • The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone • Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet 61
Tertiary Structure • Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents • These interactions between R groups include actual ionic bonds and strong covalent bonds called disulfide bridges which may reinforce the protein’s structure. • IMFs such as London dispersion forces (LDFs a. k. a. and van der Waals interactions), hydrogen bonds (IMFs), and hydrophobic interactions (IMFs) may affect the protein’s structure 62
Tertiary Structure 63
Quaternary Structure • Quaternary structure results when two or more polypeptide chains form one macromolecule • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope 64
Four Levels of Protein Structure Revisited 65
Sickle-Cell Disease: A change in Primary Structure • A slight change in primary structure can affect a protein’s structure and ability to function • Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin 66
Sickle-Cell Disease: A change in Primary Structure 67
Changing Protein Structure • Proteins are fragile. The environment can affect protein structure and therefore function. • Alterations in p. H, salt, temperature, etc can cause a protein to unravel; this is denaturing and the protein doesn’t function anymore • A denatured protein is biologically inactive 68
Biomolecule 4: Nucleic Acids • Nucleic acids store, transmit, and help express hereditary information • The amino acid sequence of a protein is programmed by a unit of inheritance in the nucleic acid called a gene • Genes are made of DNA, a nucleic acid made of monomers called nucleotides 69
Two Types of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) • DNA provides directions for its own replication • DNA directs synthesis of messenger RNA (m. RNA) and, through m. RNA, controls protein synthesis • Protein synthesis occurs on ribosomes 70
Figure 5. 25 -1 DNA 1 Synthesis of m. RNA NUCLEUS CYTOPLASM
Figure 5. 25 -2 DNA 1 Synthesis of m. RNA NUCLEUS CYTOPLASM m. RNA 2 Movement of m. RNA into cytoplasm
Figure 5. 25 -3 DNA 1 Synthesis of m. RNA NUCLEUS CYTOPLASM m. RNA 2 Movement of m. RNA into cytoplasm Ribosome 3 Synthesis of protein Polypeptide Amino acids
The Components of Nucleic Acids • Nucleic Acids are made of monomers called nucleotides, which consist of a nitrogenous base, a pentose sugar, and a phosphate group (draw) 74
The Devil is in the Details • Types of nitrogenous bases – Pyrimidines (cytosine, thymine, and uracil) have a single ring, that has six-members – Purines (adenine and guanine) have two rings; a six-membered ring fused to a five-membered ring • DNA vs. RNA nucleotides: • In DNA, “T” is used and the sugar is deoxyribose; in RNA, “U” is used and the sugar is ribose 75
The Devil is in the Details • The backbone of both NAs are made of phosphate-sugar covalent bonds. VERY STRONG! 76
The Devil is in the Details • When NAs link sides it is with hydrogen bonds between complementary base pairs (A w/ T, C w/ G). WEAK BOND! • Complementary pairing can also occur between two RNA molecules or DNA to RNA • Note: In RNA, thymine is replaced by uracil (U) so A and U pair 77
5 3 Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 5 (a) DNA Base pair joined by hydrogen bonding (b) Transfer RNA
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