Lecture 1 - Organic Molecules PDF

The Chemistry of Organic Molecules Dr. Joanne Sadier  Learning objectives Explain how the properties of carbon enable it to produce diverse organic molecules Explain the relationship between a functional group and the chemical reactivity...

The Chemistry of Organic Molecules Dr. Joanne Sadier  Learning objectives Explain how the properties of carbon enable it to produce diverse organic molecules Explain the relationship between a functional group and the chemical reactivity of an organic molecule. Compare the role of dehydration synthesis and hydrolytic reactions in organic chemistry. Explain the structure and the function of carbs Distinguish between saturated and unsaturated fatty acids. Contrast the structures of fats, phospholipids, and steroids and compare their functions Describe the functions of proteins in cells. Explain how a polypeptide is constructed from amino acids. Compare the four levels of protein structure. Distinguish between a nucleotide and nucleic acid. Compare the structure and function of DNA and RNA nucleic acids. Explain how ATP is able to store energy.  Chemistry of life Chemists of the nineteenth century thought that the molecules of cells must contain a vital force, so they divided chemistry into: organic chemistry the chemistry of living organisms inorganic chemistry the chemistry of nonliving matter  Organic Molecules Organic molecules contain both carbon and hydrogen atoms. Four classes of organic molecules (biomolecules) exist in living organisms: Functions of the four biomolecules in the cell are Carbohydrates Lipids diverse. Despite their functional differences, the variety of organic molecules is based on the unique chemical properties of Proteins Nucleic acids the carbon atom.  What is there about carbon that makes organic molecules the same but also different? Generally, carbon forms those bonds with other atoms of carbon, plus hydrogen, nitrogen, oxygen, phosphorus, and sulfur—  The Carbon Atom Carbon can form four covalent bonds. Bonds with carbon, nitrogen, hydrogen, oxygen, phosphorus and sulfur. The C-C bond is very stable. Long carbon chains, hydrocarbons, can be formed. Besides single bonds, double bonds, triple bonds, and ring structures are also possible. Branches may also form at any carbon atom, making complex carbon chains.  The Carbon Skeleton and Functional Groups The carbon chain of an organic molecule is called its skeleton or backbone. Likewise, the diversity of organic molecules comes from the attachment of different functional groups to the carbon skeleton Functional groups is a specific combination of bonded atoms that always has the same chemical properties and therefore always reacts in the same way, regardless of the carbon skeleton to which it is attached. Functional groups determine the chemical reactivity and polarity of organic molecules. Typically, the carbon skeleton acts as a framework for the positioning of the functional groups Example: Replacement of an H by -OH in the 2-carbon hydrocarbon ethane turns it into ethanol, and from hydrophobic to hydrophilic. lists some of the more common functional groups The R indicates the “remainder” of the molecule. This is the place on the functional group that attaches to the carbon skeleton. R = remainder of molecule  Isomers Isomers are organic molecules that have identical molecular formulas but different arrangements of atoms.  The Biomolecules of Cells Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules. Usually consist of many repeating units Each repeating unit is called a monomer. A molecule composed of monomers is called a polymer (many parts). Example: amino acids (monomer) are joined together to form a protein (polymer) Lipids are not polymers because they contain two different types of subunits ((glycerol and fatty acids).  The Biomolecules of Cells Category Subunits (monomers) Polymer Carbohydrates* Monosaccharide Polysaccharide Lipids Glycerol and fatty acids N/A Proteins* Amino acids Polypeptide Nucleic acids* Nucleotide DNA, RNA  Synthesis and Degradation A dehydration reaction is a chemical reaction in which subunits are joined together by the formation of a covalent bond and water is produced during the reaction. Because the equivalent of a water molecule(H2O)—that is, an −OH(hydroxyl group) and an −H (hydrogen atom)—is removed as subunits are joined. Used to connect monomers together to make polymers Example: formation of starch (polymer) from glucose subunits (monomer)  Synthesis and Degradation A hydrolysis reaction is a chemical reaction in which a water molecule is added to break a covalent bond. Used to break down polymers into monomers Example: digestion of starch into glucose monomers  Synthesis and Degradation Special molecules called enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions. An enzyme is a molecule that speeds up a chemical reaction. Enzymes are not consumed in the reaction. Enzymes are not changed by the reaction. Enzymes are catalysts. Carbohydrates Functions: are almost universally used as an immediate energy source in living  Contain carbon, organisms, but in some organisms they hydrogen, and also have a structural function oxygen atoms in a 1:2:1 ratio (CH2O).  Chain length varies from a few sugars to hundreds of sugars. The monomer subunits, called monosaccharides, are assembled into long polymer chains called polysaccharides.  Monosaccharides A monosaccharide is a single sugar molecule. It is also called a simple sugar. It has a backbone of 3 to 7 carbon atoms. Examples: Glucose (blood sugar), fructose (fruit sugar), and galactose (dairy products, avocados, sugar beets) Hexoses – six carbon atoms Ribose and deoxyribose (sugars contained in nucleotides, the monomer of DNA) Pentoses – five carbon atoms  Disaccharides A disaccharide contains two monosaccharides joined together by dehydration synthesis. Examples: Lactose (milk sugar) is composed of galactose and glucose. Sucrose (table sugar) is composed of glucose and fructose. Maltose is composed of two glucose molecules. Lactose intolerant individuals lack the enzyme lactase which breaks down lactose into galactose and glucose.  Polysaccharides: Energy-Storage and Structural Molecules A polysaccharide is a polymer of monosaccharides. Examples: Starch provides energy storage in plants. Glycogen provides energy storage in animals. Cellulose is found in the cell walls of plants. Most abundant organic molecule on earth Animals are unable to digest cellulose. Chitin is found in the cell walls of fungi and in the exoskeleton of some animals. Peptidoglycan is found in the cell walls of bacteria. Monomers contain an amino acid chain. Polysaccharides: Energy-Storage and Structural Molecules (2) (photos): (a): ©Jeremy Burgess/SPL/Science Source; (b): ©Don Fawcett/Science Source  Polysaccharides: Structural Molecules Structural polysaccharides include cellulose in plants, chitin in animals and fungi, and peptidoglycan in bacteria. The cellulose monomer is simply glucose. Wood, a cellulose plant product, is used for construction, and cotton is used for cloth. over 100 billion tons of Figure 3.8 Cellulose fibrils. Cellulose fibers criss-cross in plant cellulose are produced by cell walls for added strength. A cellulose fiber contains several plants each year microfibrils, each a polymer of glucose molecules—notice that the linkage bonds differ from those of starch. Every other glucose is flipped, permitting hydrogen bonding and greater strength between the microfibrils.  Lipids Varied in structure Type Functions Human Uses Fats Long-term energy Butter, lard Large, nonpolar molecules storage and insulation in that are insoluble in water animals Oils Long-term energy Cooking oils Functions: storage in plants and their seeds Long-term energy storage Phospholipids Component of plasma Food additive membrane Structural components Steroids Component of plasma Medicines Heat retention membrane (cholesterol), Sex hormones Cell communication and Waxes Protection, prevention Candles, polishes regulation of water loss (cuticle of Protection plant surfaces), beeswax earwax  Triglycerides: Long-Term Energy Storage Also called fats and oils Functions: long-term energy storage and insulation Consist of one glycerol molecule linked to three fatty acids by dehydration synthesis  Saturated fatty acids Each fatty acid consists of a long hydrocarbon Fatty acids may be either chain with an even number of carbons and a −COOH (carboxyl) unsaturated or saturated. opposite (trans) side of the double bond Saturated – no double bonds between carbons Tend to be solid at room temperature Examples: butter, lard  Unsaturated fatty acids Unsaturated – one or more double bonds between carbons Tend to be liquid at room temperature Example: plant oils Can have chemical groups on the same (cis) or Trans– a triglyceride with at least one bond in a trans configuration  Do you know? Triglycerides containing fatty acids with unsaturated bonds melt at a lower temperature than those containing only saturated fatty acids. The reason is that a double bond creates a kink in the fatty acid chain that prevents close packing between the hydrocarbon chains This difference has applications useful to living organisms. For example, the feet of reindeer and penguins contain unsaturated triglycerides, and this helps protect those exposed parts from freezing.  Phospholipids: Membrane Components The structure is similar to triglycerides. It consists of one glycerol molecule linked to two fatty acids and a modified phosphate group. The fatty acids (tails) are nonpolar and hydrophobic. The modified phosphate group (head) is polar and hydrophilic. Phospholipids Form Membranes Function: forms plasma membranes of cells. In water, phospholipids aggregate to form a lipid bilayer (double layer). Polar phosphate heads are oriented towards the water. Nonpolar fatty acid tails are oriented away from water.  Steroids: Four Fused Carbon Rings They are composed of four fused carbon rings. Various functional groups attached to the carbon skeleton Functions: component of animal cell membrane, regulation Cholesterol is an essential component of an animal cell’s plasma membrane, where it provides physical stability. Cholesterol is the precursor of several other steroids, such as the sex hormones testosterone and estrogen Cholesterol can also contribute to circulatory disorders.  Proteins Proteins are polymers of amino acids linked together by peptide bonds. A peptide bond is a covalent bond between amino acids. As much as 50% of the dry weight of most cells consists of proteins. Several hundred thousand have been identified. There are 20 different common amino acids. Amino acids differ by their R, or variable groups, which range in complexity.  Amino Acids: The building blocks of proteins In the physiological pH range, both carboxylic and amino groups are completely ionized  Zwitterionic form of amino acids Under normal cellular conditions amino acids are zwitterions (dipolar ions) have both a positive and a negative charge : Amino group = -NH3+ Carboxyl group = -COO- They can act as either an acid or a base Prentice Hall c2002 Chapter 3 33  Amino acids are the building blocks of proteins Three major parts: carboxyl group, amino group, and side chain. Central C atom called alpha carbon. Amino acids can differ in their side chains (R). L-form found almost exclusively in proteins The D form of amino acids is only found in a few isolated instances which mainly consist of short peptide chains of bacterial cell walls and certain peptide antibiotics.  Peptide bonds Proteins are sometimes called polypeptides since they contain many peptide bonds R1 O H R2 O + H3N C C OH + H N C C O- H H R1 O R2 O + C N C C O- + H2O H3N C H H H  Amino acids can form peptide bonds Amino acid residue Proteins are peptide units molecules that dipeptides consist of one or more polypeptide tripeptides chains oligopeptides polypeptides Peptides are linear polymers that range from ~8 to 4000 amino acid residues How many different naturally occurring amino acids are there in most species encoded by the genome? Linear arrays of amino acids can make a huge number of molecules Consider a peptide with two amino acids AA1 AA2 20 x 20 = 400 different molecules AA1 AA2 AA3 20 x 20 x 20 = 8000 different molecules For 100 amino acid protein the # of possibilities are: 20100 = 1.27 x10130 Characteristics of R side Chain The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine  Proteins 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, which is essential for its proper functioning.  Functions of Proteins Metabolism Most enzymes are proteins that act as catalysts to accelerate chemical reactions within cells. Support Some proteins have a structural function, for example, keratin and collagen. Transport Membrane channel and carrier proteins regulate what substances enter and exit cells. Hemoglobin protein transports oxygen to tissues and cells. Defense Antibodies are proteins of our immune system that bind to antigens and prevent them from destroying cells. Regulation Hormones are regulatory proteins that influence the metabolism of cells. Motion Microtubules move cell components to different locations. Actin and myosin contractile proteins allow muscles to contract. Functions of proteins… Enzymes: the most highly specialized proteins are those with catalytic activity – the enzymes. All the chemical reactions of organic biomolecules in cells are catalyzed by enzymes. Transport proteins: These proteins in blood bind and carry specific molecules or ions from one organ to another, e.g. Hemoglobin, lipoprotein Nutrient and storage proteins: The seeds of many plants store nutrient proteins required for the growth of germinating seedling,. The ferritin found in some bacteria and in plant and animal tissues stores iron.  Functions of proteins… Contractile or motile proteins: Some proteins endow cells and organisms with the ability to contract, change shape, or move about. Actin and myosin function in the contractile system of skeletal muscle and in many other cells. Structural proteins: Many proteins serve as supporting filaments. The major component of tendons and cartilage is the fibrous protein of collagen, which has very high tensile strength. Leather is almost pure collagen. Hairs, fingernails and feathers consist of the tough, insoluble protein keratin. The major component of silk fibers and spider webs is fibroin.  Functions of proteins… Defense proteins: Many proteins defend organism against invasion by other species or protect them from injury. The immunoglobulins or antibodies, the specialized proteins made by the lymphocytes of vertebrates can recognize and precipitate or neutralize invading bacteria, viruses or foreign proteins of another species. Fibrinogen and thrombin are blood-clotting factors that prevent loss of blood when the vascular system is injured.  Functions of proteins Regulatory proteins: Some proteins help regulate cellular or physiological activities, e.g. Insulin, a hormone regulates the metabolism of sugars. Other regulatory proteins bind to DNA and regulates the biosynthesis of enzymes and RNA molecules, involved in cell division in both prokaryotes and eucaryotes.  Shapes of Proteins and 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  Four Levels of Protein Structure Primary level Primary level is the linear sequence of amino acids. Hundreds of thousands of different polypeptides can be built from just 20 amino acids. Changing the sequence of amino acids can produce different proteins. Secondary level Secondary level is characterized by the presence of alpha helices and beta (pleated) sheets held in place with hydrogen bonds.  Four Levels of Protein Structure Tertiary level Tertiary level is the overall three-dimensional shape of a polypeptide. It is stabilized by the presence of hydrophobic interactions, hydrogen, ionic, and covalent bonding. Quaternary level Quaternary level consists of more than one polypeptide.  The Importance of Protein Folding and Protein-Folding Diseases Chaperone proteins help proteins fold into their normal shapes and may also correct misfolding of new proteins. Defects in chaperone proteins may play a role in several human diseases, such as Alzheimer’s disease and cystic fibrosis.  The Importance of Protein Folding and Protein-Folding Diseases Prions are misfolded proteins that have been implicated in a group of fatal brain diseases known as TSEs. Transmissible spongiform encephalopathies , also known as prion diseases, are a group of rare degenerative brain disorders characterized by tiny holes that give the brain a "spongy" appearance Mad cow disease is one example of a TSE. Prions are believed to cause other proteins to fold the wrong way.  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) Performs a wide range of functions within cells which include protein synthesis and regulation of gene expression  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 a. Nucleotide structure b. Deoxyribose versus ribose Nucleotides are joined together by a series of dehydration synthesis reactions to form a linear molecule called a strand, which is a sequence of nucleotides. Structure of DNA and RNA The backbone of the nucleic acid strand is composed of alternating sugar-phosphate molecules. DNA is composed of two strands held together by hydrogen bonds between the nitrogen-containing bases. The two strands twist around each other, forming a double helix.  Structure of DNA and RNA The nucleotides may be in any order within a strand but between strands: Adenine (purine) makes hydrogen bonds with thymine (pyrimidine). Cytosine (pyrimidine) makes hydrogen bonds with guanine (purine). The bonding between the nitrogen- containing bases in DNA is referred to as complementary base pairing. The number of A + G (purines) always equals the number of T + C (pyrimidines). DNA packaging  Structure of DNA and RNA Table 3.4 DNA Structure Compared to RNA Structure DNA RNA Sugar Deoxyribose Ribose Adenine, guanine, Adenine, guanine, uracil, Bases thymine, cytosine cytosine Strands Double stranded with Single stranded base pairing Helix Yes No  Figure 1-5 Central Dogma © 2017 Pearson Education, Ltd.  ATP (Adenosine Triphosphate) ATP (adenosine triphosphate) is a nucleotide composed of adenine and ribose (adenosine) and three phosphates. ATP is a high-energy molecule due to the presence of the last two unstable phosphate bonds, which are easily broken. Hydrolysis of the terminal phosphate bond yields: The molecule ADP (adenosine diphosphate) An inorganic phosphate, P Energy to do cellular work The hydrolysis of the ATP molecule can be coupled with chemically unfavorable reactions in the cell to allow the reactions to proceed. Example: key steps in the synthesis of carbohydrates and proteins, and muscle contraction and nerve impulse conduction  ATP ATP is therefore called the energy currency of the cell. Slide Title