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Organic Chemistry What is it? define Why do we care? Major groups of organic molecules... Refer to chapter 3 in text. Carbon: the defining atom of organic chemistry. Mader defines as C and H, but that is debated. ← Four electrons available for covalent bonding (valence electrons). -Forms chains, branches, rings. → - Can carry a wide variety of “add-ons”. Carbon molecules in living things that are NOT organic… carbonates: CO3-2… hydrocarbonates: HCO3- … oxides of carbon: CO, CO2… so, pretty simple things, but methane (CH4) IS organic, produced by the anaerobic decomposition of living things. Vitalism: early idea that “organics” only come from living things, but urea is a non-example. (There are many others). Mostly we will focus on the carbon-based macromolecules of which you are made http://web.mnstate.edu/provost/Provost/ Do you recognize what the “functional” groups are? Macromolecules … BIG molecules Polymer: Macromolecule formed by stringing together smaller monomers. Dehydration synthesis: → aka condensation (←IB) a water molecule is removed to form a bond between monomers. Hydrolysis: → a water molecule is inserted, breaking (lysing) a bond. (What are the 4 kinds of organic molecules?) Types of organic molecules; 1 of 4 Carbohydrates One to many sugars: mono-, di-, polysaccharides. Uses: energy, structure, components of other molecules. Examples of monosaccharides: Note especially: -general formula (CnH2nOn) -the ending “-ose” denotes a sugar -used for energy, or as subunits of other molecules, glucose: the currency of cellular energy exchange. ribose: part of nucleic acids. galactose: subunit of lactose, “brain sugar”. fructose: found in fruit, part of (and twice as sweet as) sucrose. http://getyournotes.blogspot.com/2011/01/glucose.html http://gt.inkblue.net/biokeemia/Biokeemia%20I/Kontroll/ribose.jpg Can you see the differences between these? You should be able to draw these. Note: - dehydration reaction - called a glycosidic bond - used for short-term energy storage -maltose made by amylase from starch (glu + glu) - sucrose is table sugar, can’t further polymerize (glu + fruc) -lactose is in milk In mammals, adult lactose intolerance is normal. (glu + gal) Carbohydrates (cont.) Disaccharides Carbohydrates (cont.) Polysaccharides Note: - these ones are for longer-term energy storage; starch amylose: unbranched amylopectin: branched Degrading enzymes act from loose ends, therefore…. in plants glycogen (more branched) in animals Link to visualization software: http://jmol.sourceforge.net/ . Carbohydrates (cont.) Polysaccharides (cont.) Note: -cellulose is a structural carbohydrate (in plants) - The difference between digestible (to us) starch and indigestible cellulose is… (can you see it?) [Only certain bacteria make the enzymes to digest cellulose. Generally, any animal living off grass or wood has these specific bacteria in their guts to break the cellulose into digestible disaccharides.] triglycerides Glycerol backbone with 3 fatty acid add-ons, so aka Note: - another dehydration! - called an ester linkage - C, H,… very little O. - non-polar, hydrophobic - This is NOT a polymer. ←methyl group Uses: long-term energy storage (twice the energy/g as carbs.), thermal insulation, structural, hormonal, waterproofing … ←hydocarbon chain Lipids ←acid group Types of organic molecules; 2 of 4 Lipids (cont.) Saturated fatty acids (draw) are solid at lower temperatures, and may contribute more to blocked blood vessels than Unsaturated fats, which have double bonds. Oleic acid is a cis unsaturated fatty acid that comprises 55-80% of olive oil. Eleidic acid is a trans unsaturated fatty acid found in partially hydrogenated vegetable oils. (Trans is rare in nature, and seems to contribute to heart disease.) Stearic acid is a saturated fatty acid found in animal fats and is the intended product of hydrogenation. http://en.wikipedia.org/wiki/Trans_fat Lipids (cont.) Phospholipids - Instead of the third fatty acid, these have a phosphate group, which is hydrophilic ← Things can be added to the phosphate group. The choline here makes this ‘lecithin’. As the “heads” stay in contact with water, and the “tails” stay away, small droplets and bilayers spontaneously form. Cells and organelles are surrounded by these phospholipid bilayers. Lipids (cont.) Cholesterol is a lipid that doesn’t fit the structural model. -It is hydrophobic. -It is required for membrane flexibility (though too much in the diet precipitates out). -It can be converted into any of many steroid hormones.→ (There are hydrophobic, so can enter cells and act directly on gene expression.) student.britannica.com/eb/art-62250 LDL… HDL…? Lipoproteins transport lipids in blood (recall that lipids are… non-soluble in water). Low density lipoproteins also regulate cholesterol synthesis and transport into the blood, so lots of them may indicate a cholesterol problem, so these complexes are called “bad cholesterol”. High-density lipoproteins tend to transport cholesterol back into the liver for storage, so tend to be called “good cholesterol”. It’s all the same cholesterol…. wax such as for a plant leaf cuticle, or the cells in a bee hive, lanolin in wool, paraffin from petroleum, or in your ear. Hey! What kind of a reaction does that involve? http://en.wikipedia.org/wiki/File:Cetyl_palmitate.png Types of organic molecules; 3 of 4 Nucleic Acids Polymers of 4 Uses: Information transformation from cell generation to generation (DNA) and from genome to protein (RNA) (Some RNA also works as a catalyst/enzyme) We will have more detail later, when we study DNA replication (making sure that all cells get the same information), Transcription (DNA sequence directing RNA sequence), and Translation (RNA directing amino acid sequence in proteins). (What do you recall about nucleic acid structure?) Nucleic Acids (cont.) Note: - nucleotides have three parts - letters correspond to the nitrogenous base - differences between DNA and RNA ribose→ Nucleic Acids (cont.) Note: -complementary base pairing -held together by hydrogen bonds, -to form the double helix -chains run in opposite directions… -Phosphodiester linkage is another dehydration reaction!↓ original.britannica.com/eb/art-106485/The-hum... We will get into a lot more detail when we do genetics. www.web-books.com/MoBio/Free/Ch3A5.htm Types of organic molecules; 4 of 4 Proteins Polymer of amino acids (20) Uses: many … structural amino acid storage transport hormones (some) receptors sensors movement defense enzymes chaperonins web silk, collagen in cartilage, keratin in nails…. ovalbumin in eggs, casein in milk… hemoglobin in blood, membrane proteins… insulin to control blood glucose… on cell membranes, so they can sense chemicals.. e.g. rhodopsin in retina senses light… actin and myosin in muscles… antibodies of the immune system… facilitate chem. reactions, like peptidase, rubisco… protein chambers to sequester other proteins during folding…. IB wants you to know four functions, with named examples, and strangely exclude membrane proteins from this directive… (We will encounter many of these throughout the year…) the Amino Acids Note -common core structure: carbon atom “amine” (nitrogen) group “acid” (here a carboxyl group) variable “R” group (R=“radical”) generalized amino acid (draw) Peptide bond This is another dehydration reaction. (Can you identify the amino acids illustrated?) Proteins: Their complex structure contributes to their functioning. primary structure: sequence of amino acids. secondary structure: H bonds, mostly between repeating cores, form α helices and β pleated sheets. tertiary structure: R group interactions. Note the bond types involved. Amino acids with non-polar R groups will hide inside, and hydrophilic ones outside… if the protein is soluble. Integral membrane proteins will tend to be the other way around... and maybe a channel lined with polar amino acids. Why? Polarity also affects active site specificity. quaternary structure: multiple molecules; maybe a (non-protein) prosthetic group to make a conjugated protein, like glycoprotein, lipoprotein, cytochrome… Globular proteins have less 2o structure, but lots of 3o structure, and often 4o structure. This provides the active site specificity to enzymes, and makes them more susceptible to denaturation. ←sperm whale myoglobin catalase → www.phschool.com/.../labbench/lab2/active.html a fibrous protein has 2o structure, little or no 3o structure, and often 4o structure. Only made in animals This makes a strong, usually insoluble strand. ↓tropocollagen in tendons (α) spider silk (β) → Chaperonin proteins form something like a dressing room for newly polymerized proteins to acquire 2o, 3o and 4o structure in the absence of environmental interference. (May be more about re-folding/ editing/correcting....) http://en.wikipedia.org/wiki/Chaperonin Identify the following: What are the major categories of organic molecules? What are the uses of each type? Give named examples. What are the monomers for each group? How many different ones are there? How many can you name? Names ways in which the various groups are interconnected… How is each type manufactured? What kind of bond? What 3 dimensional structure does each assume? Branching increases H bonds in starches, so which makes a better adhesive? organic chemistry carbohydrate lipid nucleic acid protein valence electron monosaccharide glycerol nucleotide amino acid vitalism glucose triglyceride phosphate group peptide bond macromolecule ribose ester linkage ribose primary structure polymer galactose saturated fatty acid nitrogenous base secondary structure monomer fructose unsaturated fatty acid complementary base pairing α helix dehydration synthesis glycosidic bond phospholipid double helix β pleated sheet condensation disaccharide phosphate group phosphodiester linkage tertiary structure hydrolysis maltose phospholipid bilayer quaternary structure sucrose cholesterol prosthetic group lactose steroid hormone conjugated protein polysaccharide lipoprotein fibrous protein starch wax globular protein amylose denaturation amylopectin chaperonin glycogen cellulose