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 carbon’s 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 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
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 14
Organic Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids
The FOUR Classes of Large Biomolecules • All life is 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!!! 16
The FOUR Classes of Large Biomolecules • Most Macromolecules are polymers, built from monomers • A polymer = molecule made of repeating smaller monomers • Three of the four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids 17
Building polymers • A dehydration synthesis links monomers by removing a water molecule 18
Digesting polymers • Hydrolysis is the reverse, and disassembles polymers by adding a water • Why is water important for food digestion? 19
Carbohydrates • Monosaccharide sugars (monomer) and polysaccharide starches (polymer). • Both used for chemical energy (sugar = fast, starch = long) and sometimes structure (e. g. wood, 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) 20
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 21
Sugars: Disaccharides • A disaccharide is formed when dehydration synthesis joins two monosaccharides; still a sugar 22
Synthesizing Maltose & Sucrose 23
Special 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 24
Special Polysaccharides • Glycogen is a storage polysaccharide in animals (“animal starch”); branched structure as compared to amylose starch • Humans and other vertebrates store glycogen mainly in liver and muscle cells as a tier 2 energy option 25
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; very difficult to digest! 26
Cellulose Structure - Such Elegance! 27
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 fungal cell walls (surprise!) 28
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 non-polare and hydrophobic • The most biologically important lipids are fats/oils/wax, phospholipids, and steroids 29
Fats: Start with a Simple Little Glycerol Molecule • Triglyceride 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 30
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! 31
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? 33
Saturated or Unsaturated? • Some fats called saturated fats 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 (dense/solid at room temp) 34
Saturated or Unsaturated? • Fats that are liquid are unsaturated. • Plant fats and fish fats are usually unsaturated • Unsaturated fatty acids have one or more double bonds cause them to bend 35
Fats: Major function is storage! • Fats mostly function for long term energy storage, but also waterproof/insulate, protect and/or communicate • Humans and other mammals store their fat in adipose cells 36
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 37
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 used for communication • 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 steroids 39
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 structure, storage, transport, communication, movement, defense… (basically everything that keeps you alive…) • Let’s take a look at a few we’ll learn this year! 40
Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Enzyme 41
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 42
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 43
Defensive proteins Function: Protection against disease Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Virus Bacterium 44
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 45
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 46
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 control chemical reactions; they are reusable and specific to one function (based on their shape); ex: digestive enzymes, buffers, etc 48
Protein Monomer • Amino acids are the monomers of all proteins. • Only 20 amino acids exist. They differ in their properties due to differing side chains, called R groups Side chain (R group) carbon Amino group Carboxyl group 49
Polypeptides • Polypeptide chains (protein polymers) are made of chained arrangements of the 20 available amino acids, then folded into proteins. • A protein consists of one or more polypeptides 50
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 52
Electrically charged Amino Acids 53
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) 54
Peptide Bonds 55
Peptide Bonds 56
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 57
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 connects multiple polypeptide chains multiple pipe cleaners 58
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 60
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 61
Tertiary Structure 62
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 63
Four Levels of Protein Structure Revisited 64
Sickle-Cell Disease: A change in Primary Structure • A change in protein primary structure can affect a protein’s structure and function • Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin 65
Sickle-Cell Disease: A change in Primary Structure 66
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 (denaturing) and the protein doesn’t function anymore • A denatured protein is biologically inactive 67
Nucleic Acids • Nucleic acids store, transmit, and help express hereditary information • More specifically, the nucleic acids hold the instructions for how to arrange the amino acids to make proteins 68
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 and protein synthesis • DNA directs messenger RNA (m. RNA) to carry out protein synthesis • Protein synthesis occurs on ribosomes 69
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 (polymer) are made of monomers called nucleotides, which consist of a nitrogenous base, a pentose sugar, and a phosphate group 73
The Devil is in the Details • 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: • DNA is double sided, has “T”, and the sugar is deoxyribose; RNA is single sided, has “U” and the sugar is ribose 74
The Devil is in the Details • The backbone of both NAs are made of phosphate-sugar covalent bonds. VERY STRONG! 75
The Devil is in the Details • The sides are linked by hydrogen bonding complementary base pairs (A w/ T, C w/ G). WEAK BOND! • Complementary pairing can also occur between two RNA molecules or DNA to RNA • Remember: In RNA, thymine is replaced by uracil (U) so A and U pair 76
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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