<p>Chapter 3 – The Molecules of Cells How small molecular units are assembled into larger ones</p><p>I. Life’s molecular diversity is based on the properties of carbon (Aim: What makes carbon so special?)</p><p>A. Organic compounds – have at least one carbon and almost always has hydrogen (so CO2 is NOT organic)</p><p>B. 4 electons in outer shell, but wants 8</p><p>C. To get 8 it can share with other carbons or other atoms like H, N, O, S, etc...</p><p>D. Because it wants 4 electrons, it can make up to 4 covalent bonds with other atoms leading to long, complicated chains as well as rings, spheres, etc…) – simply put, it is a great building block!!</p><p>E. Hydrocarbons – C and H only</p><p>F. Carbon skeleton</p><p>G. structural Isomers – same molecular formula, different structures and thus different properties (a screwdriver and wrench are both made of metal). II. Functional Groups help determine the properties of organic compounds. (AIM: What’s so great about functional groups?)</p><p>A. Functional groups – groups of atoms, acting as a unit, that give organic molecules their physical properties, chemical reactivity, & solubility in aqueous solutions. </p><p>1. Methane, methanol, acetic acid, methanethiol, methylamine</p><p>B. Hydrophilic as a result</p><p>C. Compounds can have far more than one functional group attached!</p><p>D. Go over different functional groups III. Cells make a huge number of large molecules from a small set of molecules (AIM: How does the cell make big from small?)</p><p>A. Macromolecules – gigantic molecules (proteins, nucleic acids (DNA/RNA), carbohydrates, lipids)</p><p>B. Cells make macromolecules by linking together small units</p><p>1. Monomers (individual paper clips) – building blocks (small organic molecules) of polymers</p><p>2. Polymers (all the paper clips connected to each other) – chains of many similar small organic molecules</p><p>3. Reactions to build or breakdown polymers (water involved in both)</p><p> a) Dehydration synthesis – combining two monomers by the removal of a water molecule (dehydrate)</p><p> b) Hydrolysis – “breaking apart with water” – used to break apart two attached monomers through addition of a water molecule</p><p>IV. Carbohydrates – (“carbon and water” class of molecules ranging from small sugar molecules to large polysaccharides (polymers of sugar monomers)</p><p>A. Monosaccharides – sugar monomers (“single sugar”) Ex. Glucose, Fructose – show these 1. Have the general formula (CH2O)n</p><p>2. Many monosacchrides form ring-shaped molecules in solution</p><p>3. Used mainly for fuel, raw material to form carbon backbones of other molecules (ie amino acids), as monomers from which di- and polysaccharides are synthesized.</p><p>4. –ose suffix</p><p>5. Sugar = monosaccharide or disaccharide</p><p>B. Cells link together monosaccharides to form disaccharides</p><p>1. Accomplished by dehydration synthesis</p><p>2. Glycosidic linkage links the two monosaccharides</p><p>3. Disaccharide Monosaccharide Maltose Glucose + Glucose Sucrose Glucose + Fructose Lactose Glucose + Galactose V. How sweet is sweet (optional)</p><p>A. Sweet receptors on our tongue</p><p>B. Sugar binds to these receptors, but not the only compound that can do this</p><p>1. Aspartame (Equal or Nutrasweet) made of amino acids</p><p>C. All sweetness is relative to sucrose (table sugar)</p><p>1. Bitter aftertaste; compounds are also binding to bitter receptors on tongue VI. Polysaccharides are long chains of sugar units (“many sugar units”)</p><p>A. Polymers of a few 100 to 1000 monosaccharides</p><p>B. Using only glucose, different organisms can build several different polymers: plant starch, animal starch (glycogen), and cellulose</p><p>C. Dehydration synthesis</p><p>D. Plant Starch – </p><p>1. Long, relatively unbranched, coiled polymer of glucose in plants. (one kind of bond)</p><p>2. Long term energy storage – plants hydrolyze when energy is needed. </p><p>3. Can be consumed by animals like humans and hydrolyzed to obtain energy (potatoes, grains, etc…)</p><p>E. Glycogen – </p><p>1. Storage polysaccharide of animals</p><p>2. Very similar to starch (made using glucose, same bond type) , but with far more branches</p><p>F. Cellulose – a polysaccharide used for building 1. Different kind of bond resulting in linear polymers, which crosslink to other chitin polymers</p><p>2. Main structural molecule in the cell walls of plants and algae</p><p>3. Animals cannot hydrolyze cellulose (that’s why you can’t eat wood) only certain bacteria, protozoans, and fungi. How come cows can eat grass? VII. Lipids</p><p>A. Include fat (triglyceride), which are mostly energy- storage molecules</p><p>1. Many carbon and hydrogen, little Oxygen</p><p>2. Many different types of lipids with different functions, all essentially hydrophobic</p><p>3. Fat – Three fatty acids and glycerol – formed by dehydration synthesis</p><p> a) Triglyceride = “fat” = 3 fatty acids + 1 glycerol</p><p>4. Saturated fats – no double bonds b/w carbons of fatty acids –carbons are saturated with H. – chains can pack into tight globules to form things like butter (solid at room temp)</p><p>5. Most plant fats are unsaturated, while animal fats tend to be richer in saturated</p><p>6. Unsaturated fats – double bonds b/w carbons of fatty acids – chains are bent and can’t pack as well – liquid at room temp – veg. oil, corn oil, olive oil, etc… (What happens if we hydrogenate unsaturated fats?) </p><p>7. functions: energy storage, cushion vital organs, insulation VIII. Phospholipids, waxes, and steroids are lipids with a variety of functions A. Phospholipids are the major component of cell membranes</p><p>1. Similar to fat (triglycerides) except only two tails and has a phosphate containing head</p><p>2. Unique in that PO4 has a negative charge and gives it a hydrophilic head while having hydrophobic tails = amphipathic (a molecule that is both hydrophobic and hydrophilic)</p><p>3. forms the membranes of cells</p><p>B. Waxes – essentially a hydrophobic coating formed by numerous organisms to ward off water.</p><p>1. More hydrophobic than fats</p><p>2. One fatty acid linked to alcohol</p><p>C. Steroids – lipids whose carbon skeleton forms 4 fused rings</p><p>1. Cholesterol – important steroid formed by animals (carbon hydrogen emission in structural drawing. Show 3D view and emphasize that we are seeing 2D – not real).</p><p> a) Functions in digestion of fats, starting material for synthesis of female and male sex hormones, and fluidity of cell membranes D. Anabolic steroids – big bodies, big problems</p><p>1. Synthetic variants of the male hormone testosterone</p><p> a) Causes build up of muscle and bone during puberty in men among other things</p><p> b) Downside = liver damage, testicular atrophy, cholesterol issues, high blood pressure, breast development in males, masculinization in females, and antisocial behavior. IX. Proteins (“first place” in greek)</p><p>A. Proteins are essential to the structures and activities of life – They are the workers</p><p>1. Roles played by proteins:</p><p> a) Structural (hair, cell cytoskeleton)</p><p> b) Contractile (muscles and motile cells)</p><p> c) Storage (ovalbumin (egg white) – source of amino acids for developing embryo)</p><p> d) Defense (antibodies, membrane proteins)</p><p> e) Transport (hemoglobin, membrane proteins)</p><p> f) Signaling (hormones, membrane proteins, intracellular signaling proteins)</p><p> g) Catalysts (enzymes both free and membrane bound)</p><p>2. Enzymes – protein that serves as a chemical catalyst – increases the rate of specific reactions without being used up (hammer and nails analogy) ****does not make a reaction happen that normally wouldn’t</p><p>B. Proteins are made from just 20 kinds of amino acids 1. Amino acids – (monomer) – all have a central alpha carbon covalently bonded to a -H, amino group -NH2, carboxyl group –COOH, and one other chemical group –R (variable group). </p><p>2. There are 20 different –R or variable groups, which give the amino acid its distinct properties.</p><p>C. Amino acids can be linked by peptide bonds</p><p>1. Amino acids are monomers that are linked together by peptide bonds via dehydration synthesis to form polymers.</p><p>2. Dipeptide – 2 linked amino acids</p><p>3. Polypeptide – many linked amino acids (NOT necessarily a protein).</p><p>X. Overview : A protein’s specific shape determines its function (hammer, screwdriver, wrench, etc…)</p><p>1. Proteins consist of one or more polypeptide chains folded into a unique shape</p><p>2. This 3D shape determines the proteins function</p><p>3. The shape the protein takes depends solely on its amino acid sequence (show this).</p><p>4. Proteins can unravel (denature) with changes in heat, pH, saltiness, etc…</p><p>5. The 4 levels of protein structure using transthyretin – found in blood - important in transport of a thyroid hormone and Vit. A</p><p> a) Primary – aa sequence – aa represented by a three letter abbreviation or a single letter code. </p><p>(1) The amino acids are in a precise order</p><p>(2) There are 4 identical polypeptide chains, each with 127 aa (3) Changes in the primary structure affect the 3D structure (show this) b) Secondary Structure – polypeptide coiling or folding produced by hydrogen bonding</p><p>(1) H-bonds occur b/w –NH (amino) groups and – C=O group (carbonyl) groups</p><p>(2) Depending on amino acid sequence, the secondary structure takes the form of an alpha helix, pleated sheet, or omega loop</p><p>(3) The R-groups do not play a direct role, but are important for the type of sec. structure formed</p><p>(4) Go over diagramming convention c) Tertiary structure – is the overall shape of the polypeptide</p><p>(1) Results from the clustering of hydrophobic and hydrophilic R groups and the bonding (hydrogen, ionic and covalent) b/w certain R-groups along the helices, sheets, and loops.</p><p>(2) hydrophobic (nonpolar) R groups tend to cluster within the interior of the protein, away from water – drives folding</p><p>(3) Tertiary shape of transthyretin is globular d) Quarternary structure - relationship among multiple polypeptides of a protein</p><p>(1) Many, but not all, proteins consist of a relationship b/w more than one polypeptide chain (show examples)</p><p>(2) Transthyretin – 4 chains, all identical. Some proteins can consist of different chains or be additionally complexed with other atoms or molecules (show examples). XI. Nucleic Acids – information rich polymers of nucleotides</p><p>A. Nucleotides (monomer) – has 3 functional parts</p><p>1. Phosphate group</p><p>2. Five-carbon sugar (deoxyribose in DNA, ribose in RNA)</p><p>3. Nitrogenous base – (contain nitrogen) five types: A, T, G, C in DNA. RNA also has A, G, and C, but instead of T it has U. </p><p> a) purines vs. pyrimidines</p><p>4. ATP (adenosine triphosphate) is a nucleotide used as fuel for proteins </p><p>B. Nucleic acid polymer form from dehydration synthesis of nucleotide monomers (just like polysacs and polypeps).</p><p>1. Phosphate of one bonds to sugar of next</p><p>2. RNA is usually a single polynucleotide strand, but DNA is a double helix – two polynucleotide strands wrap around each other</p><p>C. DNA double helix</p><p>1. Nitrogenous bases point toward the center of the helix</p><p>2. A single base hydrogen bonds to the base across from it on the other strand forming a base pair (A-T, C-G) (zipper analogy)</p><p>3. Most DNA molecules have 1000’s to millions of base pairs. </p><p>4. DNA molecules store the information for building the primary sequence of proteins in sections called genes.</p><p>5. DNA is just a large parts list for the cell (instructions on how to build every protein)!!!! D. Two types of nucleic acids</p><p>1. DNA – deoxyribonucleic acid</p><p>2. RNA – ribonucleic acid</p>