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Biochemistry pH Paul Anderson / Bozeman Science https://www.youtube.com/watch?v=Xeuyc 55LqiY Physical Vs Chemical Change Organic Chemistry Organic = it contains carbon, or was once alive. Organic Chemistry Carbon can covalently bond with up to four other atoms. Organic Compounds 1. 2. 3. 4. Carbohydrates Lipids Proteins Nucleic Acids Carbohydrates Contain: Carbon / Hydrogen & Oxygen Provide energy for the organism Ratio: 1:2:1 Monosaccharides = 1 sugar Disaccharides = 2 sugars Polysaccharides = 3 sugars Monosaccharides = C6H12O6 = “one sugar” Glucose Fructose Galactose These are ISOMERS = same chemical formula different structural formula Monosaccharides Disaccharides Polysaccharides How do monosaccharides make a disaccharide or polysaccharide? It’s “dehydrated” – a WATER molecule is removed – often called condensation or dehydration synthesis. Glycogen Consists of glucose monomers Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m Glycogen Figure 5.6 17 (b) Glycogen: an animal polysaccharide Structural Polysaccharides Cellulose Is a polymer of glucose 18 Has different glycosidic linkages than starch H O C CH2OH H 4 O H OH H OH HO H C H H OH glucose CH2OH OH HO C H H C OH H C OH H C OH H O H OH 4 HO OH 1 H H H OH glucose (a) and glucose ring structures CH2OH CH2OH O HO O 4 1 OH O O O 1 OH 4 O 1 OH OH OH CH2OH CH2OH O 4 1 OH O OH OH (b) Starch: 1– 4 linkage of glucose monomers CH2OH O HO O OH 1 4 OH OH CH2OH O O O OH OH O O OH Figure 5.7 A–C OH CH2OH OH (c) Cellulose: 1– 4 linkage of glucose monomers 19 CH2OH OH Is a major component of the tough walls that enclose plant cells Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. Figure 5.8 OH CH2OH OH CH2OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H Glucose monomer 20 Cellulose molecules A cellulose molecule is an unbranched glucose polymer. Cellulose is difficult to digest Cows have microbes in their stomachs to facilitate this process Figure 5.9 21 Chitin, another important structural polysaccharide Is found in the exoskeleton of arthropods Can be used as surgical thread CH2O H O OH H H OH H OH H H NH C O CH3 (a) The structure of the (b) Chitin forms the exoskeleton of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging Figure 5.10 A–C in adult form. 22 (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Polysaccharides Hydrolysis In a reaction opposite to dehydration, a water molecule can be added to split a polymer in two: Hydrolysis Think of chewing a Saltine cracker Basic Chemistry https://www.youtube.com/watch?v=MYuh5 yErdfA (Part 1) https://www.youtube.com/watch?v=Juw7H Bg0zZs (Part 2) Animations: Campbell LIPIDS Lipids Lipids are molecules that have a Glycerol molecule… Connected to three fatty acid chains hydrocarbon chains. Lipids are NON polar. Glycerol LIPIDS Three Fatty Acids Saturated vs. Unsaturated Fat Phospholipids Have only two fatty acids Have a phosphate group instead of a third fatty acid 39 Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails” CH2 + N(CH ) 3 3 Choline CH2 O O P O– Phosphate O CH2 CH O O C O C CH2 Glycerol O Fatty acids Hydrophilic head Hydrophobic tails Figure 5.13 (b) Space-filling model (a) Structural formula 40 (c) Phospholipid symbol LAB: Organic Compounds Carbs, Proteins, Lipids Constructed in similar way Organic Compounds Lab Tests BENEDICT’S TEST test for monosaccharide (simple sugar) IODINE TEST – DO NOT HEAT!! TEST for STARCH/Polysaccharide Proteins Amino Acids are building blocks of Proteins A peptide bond forms between amino acids by dehydration synthesis. They contain: C, H, O & N (Nitrogen) BIURET’S TEST: Test for PROTEIN https://www.youtube.com/watch?v=lijQ3a8 yUYQ What Determines Protein Shape? Protein shape (conformation) depends on the physical and chemical conditions of the protein’s environment Temperature, pH, etc. affect protein structure 58 •Denaturation is when a protein unravels and loses its native conformation (shape) Denaturation Normal protein Figure 5.22 Denatured protein Renaturation 59 The Protein-Folding Problem Most proteins Probably go through several intermediate states on their way to a stable shape Denaturated proteins no longer work in their unfolded condition 60 Nucleic Acids: DNA & RNA (the fourth type of Organic Compound) Most cells contain DNA /RNA Nucleic Acids are made up of long chain of nucleotides Nucleotides are made up of three parts: Sugar Base Phosphate group RNA molecule Each polynucleotide Consists of monomers called nucleotides Sugar + phosphate + nitrogen base 64 DNA Vs RNA DNA: Remains in the nucleus Has four bases (A,C,T,G) Double Stranded RNA: Can go from nucleus to cytoplasm Has four bases (A,C,U,G) Single Stranded Enzymes ENZYMES: End in - ase EXAMPLES: (do not copy this!) Catalase Reductase Ligase Nuclease Maltase Primase Helicase ENZYMES Enzymes are “CATALYSTS” = They speed up a reaction All enzymes are PROTEINS BUT: not all proteins are ENZYMES Chaperonins Are protein molecules that assist in the proper folding of other proteins 75 X-ray crystallography Is used to determine a protein’s threedimensional structure Figure 5.24 76 Proteosome Once a protein has completed its job It is disposed of It recycles it’s amino acids (in a type of mini trash compactor / recycler) HHMI Proteosome http://www.hhmi.org/biointeractive/proteas ome http://www.youtube.com/watch?v=iaHHgE oa2c8 ATP = Adenosine triphosphate A high energy molecule “ENERGY CURRENCY” of cells When food is broken down – it is converted to ENERGY = ATP pH – measures the concentration of H+ ions in solution Acid Vs Base Acid – pH value of: 0 - 6.9 (red litmus) Base – pH value of: 7.1 – 14 (blue litmus) Neutral = 7 Buffer: a substance that resists changes in pH when an acid or base is added Protein Structure Level Primary Secondary Description The amino acid sequence Helices and Sheets Disulfide bridges Tertiary Quaternary Multiple polypeptides connect Animations Carbs: http://www.youtube.com/watch?v=QckfYvIl Vu4 Lipids: http://www.youtube.com/watch?v=3xF_LK 9pnL0&feature=channel Proteins: http://www.youtube.com/watch?v=wctkPUUpUc&feature=relmfu