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Biochemistry

Biochemistry. Using Organic chemistry for Life. Clicker. Why are organic molecules important to biology? Living objects are constructed mostly of organic molecules. Organic molecules are so varied that they are capable of many different functions.

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Biochemistry

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  1. Biochemistry Using Organic chemistry for Life

  2. Clicker Why are organic molecules important to biology? • Living objects are constructed mostly of organic molecules. • Organic molecules are so varied that they are capable of many different functions. • Only God knows for sure and she’s not saying. • Look, I’m here, isn’t that good enough?

  3. Organic molecules are Life If you think of all the different things an organism needs to do: • Create energy • Repair itself. • Grow • Transport materials • Hold its structure • Fend off invaders • Protect from hostile nature (heat, light, storms, electricity…) • Reproduce • Store blueprints • Store memories • Acquire sensory data • Process sensory data Lots of functions require lots of molecules

  4. Lipids Lipids are water-insoluble components of cells including fats, fatty acids, oils, phospholipids, glycolipids, and steroids. Your body is mostly water (aids transport, temperature control), so if every molecule in your body were water soluble, you’d melt into a salty puddle!!! Lipids, among other uses, make up cell membranes – to keep you from collapsing into a puddle!

  5. O CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 C OH Fatty Acids Guess what kind of acid? Carboxylic acid!!! A fatty acid is a long alkane/alkene chain with a carboxylic acid on the end! Myristic acid (common name) Tetradecoic acid (IUPAC name) Butterfat or coconut oil

  6. O O CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH CH2 CH2 CH2 CH2 CH2 C C OH OH CH3 CH3 C CH C CH2 CH2 CH2 CH2 CH2 CH2 H H Oleic acid (common name) cis-octadec-9-enoic acid) In olive oil, peanut oil What does the “cis” mean? It means the two H are on the same side!

  7. Fatty Acids Stearic Acid – C18H36O2 a saturated fatty acid Oleic Acid – C18H36O2 a monounsaturated fatty acid Tro, Chemistry: A Molecular Approach

  8. Fatty Acids Tro, Chemistry: A Molecular Approach

  9. Structure and Melting Point • Larger fatty acid = Higher melting point • Double bonds decrease the melting point • More DB = lower MP • Saturated = no DB • Monounsaturated = 1 DB • Polyunsaturated = many DB Tro, Chemistry: A Molecular Approach

  10. It’s all about the solubility The alkane/alkene portion of the molecule is water insoluble. Why? It’s non-polar. Water is polar. Remember, “like dissolves like”. The carboxylic acid portion is water soluble. Why? The carboxylic acid (C=0 and –OH) is polar, and so is water.

  11. If I throw oleic acid in water… What happens? It forms little micelles (beads) with the hydrophobic tails all mixed together and the hydrophilic acid portion facing the water. This is why “oil and water don’t mix”…

  12. Lipid Bilayer Tro, Chemistry: A Molecular Approach

  13. O CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 C OH OH O OH O CH2 CH2 CH CH CH2 CH2 OH O O CH3 (CH2 )11 C CH3 (CH2 )11 C O Fats and oils “Triglycerides” You’ve heard the term, what does it mean? A triglyceride is actually a combination of glycerol (a triol) and 3 fatty acids. It’s actually a tri-ester! glycerol Myristic acid 3 + O C(CH2)11CH3 Trimystirin

  14. O O CH2 CH CH2 O O O CH3 (CH2 )11 C C(CH2)11CH3 CH3 (CH2 )11 C Trimystirin O Fats and oils This a “saturated” fat – the hydrocarbon chain is an alkane, no double bonds.

  15. O O C C OH OH O OH O CH2 CH2 CH CH CH2 CH2 CH3 CH3 CH3 (CH2)4 (CH2)4 (CH2)4 CH CH CH CH (CH2)7 (CH2)7 OH O CH CH CH CH (CH2)7 Fats and oils An “unsaturated” fat would have double bonds. If we did the same reaction with oleic acid. Oleic acid glycerol 3 + O (CH2)4 CH3 C (CH2)7 C Triolein O

  16. Tristearin a simple triglyceride found in lard Tro, Chemistry: A Molecular Approach

  17. Triglycerides Saturated triglycerides tend to be at room temperature. • Solid • Liquid • Gas • All of the above, it depends on the type.

  18. Triglycerides Saturated triglycerides tend to be solids at room temperature because of: • Van der Waal’s forces • Hydrogen bonding • Dipole-dipole interactions • A and B • B and C

  19. Triglycerides Unsaturated triglycerides tend to be at room temperature. • Solid • Liquid • Gas • All of the above, it depends on the type.

  20. Triglycerides Unsaturated triglycerides (oils) tend to be liquids at room temperature because of: • Van der Waal’s forces • Hydrogen bonding • Dipole-dipole interactions • A and B • B and C

  21. Triglycerides They are big molecules. They tend to form solids due to a combination of Van der Waal’s forces and dipole forces. BUT, unsaturated molecules can be sterically hindered so that the polar parts can’t get near the other polar parts. That leaves us with just Van der Waal’s forces and it reduces the melting point relative to saturated molecules.

  22. Trioleina simple triglyceride found in olive oil Tro, Chemistry: A Molecular Approach

  23. Other Lipids Phospholipids – take a triglyceride and replace one of the fatty acids with a phosphate group. Glycolipids – Use glucose instead of glycerol. These are ideal for cell walls: they are strong and have a polar end and non-polar end. The polar end faces the inside (aqueous) part of the cell and the non-polar ends are internal.

  24. Phospholipids • Esters of glycerol • Glycerol attached to 2 fatty acids and 1 phosphate group • Phospholipids have a hydrophilic head due to phosphate group, and a hydrophobic tail from the fatty acid hydrocarbon chain • part of lipid bilayer found in animal cell membranes Tro, Chemistry: A Molecular Approach

  25. Phosphatidyl Choline Tro, Chemistry: A Molecular Approach

  26. Glycolipids • similar structure and properties to the phospholipids • the nonpolar part composed of a fatty acid chain and a hydrocarbon chain • the polar part is a sugar molecule • e.g., glucose Tro, Chemistry: A Molecular Approach

  27. Glucosylcerebroside(found in plasma membranes of nonneural cells) Tro, Chemistry: A Molecular Approach

  28. Steroids Steroids are lipids with a four-ring central structure. OH CH3 CH3 O Testosterone

  29. Steroids testosterone cholesterol estrogen b-estradiol Tro, Chemistry: A Molecular Approach

  30. H H H H OH O H H C C C C C C OH OH OH OH H Carbohydrates Structurally much simpler than lipids. Carbohydrates are polyhydroxy aldehydes or ketones. Glucose (C6H12O6) – a monosaccharide

  31. H H H H OH O H H C C C C C C OH OH OH OH H Carbohydrates You can actually string together monosaccharides to make more complicated carbohydrates. But even monosaccharides have variety! Carbons 2, 3, 4, and 5 are all “chiral” – 4 different atoms are attached

  32. H H H H H OH H H OH OH O O H H H H C C C C C C C C C C C C OH H OH OH OH OH OH OH H H Carbohydrates But even monosaccharides have variety! Mannose is an optical isomer of glucose – differing only in the relative 3D orientation of the -OH Mannose Glucose

  33. H H H H OH O OH H H H C C C C C C OH C H C C OH OH OH H OH H OH H H C C OH CH2 OH O Intramolecular rearrangement Glucose can actually react with itself by addition to the carbonyl to form a 6 membered ring (5 or 6 membered rings are more stable and, therefore more likely)

  34. H H H H OH O OH H H H C C C C C C OH C H C C OH OH OH H OH H OH H H C C OH CH2 OH Intramolecular rearrangement Equivalent representations of glucose. Similar pairs of structures exist for all sugar. Glucose is an example of one type of sugar, called an “aldose” because of the aldehyde group in the linear structure. O

  35. H H H OH O H H2 OH OH OH OH H C C C C C C Fructose (C6H12O6) Fructose is a ketose. It’s structure is similar to aldoses (like glucose) but it is a ketone in the linear representation rather than an aldehyde. Notice: Fructose is a structural isomer of glucose!

  36. Dehydration returns! Monosaccharides can be linked together via dehydration reactions to form “glycosidic linkages”. A glycosidic linkage is really just an ether linkage created by dehydration of 2 alcohols!

  37. OH H OH C H C C H OH H H C C OH CH2 OH O Dehydration returns! While it might seem that we can create the linkage using multiple different alcohol (-OH) sites to form the bond, there is one –OH that is more reactive than all the others! Because of the presence of the O next to it, this C-OH bond is more reactive!

  38. OH OH H H OH OH OH C C H H C C C C H H OH OH H H H H C C C C OH CH2 CH2 OH OH O O Dehydration returns! The dehydration reaction that creates the “glycosidic linkage” occurs preferentially at this site!

  39. OH OH H H OH OH OH C C H H C C C C H H OH OH H H H H C C C C OH CH2 CH2 OH OH O O Dehydration returns! OH OH H H C OH OH C H H C C C C OH H H OH + H2O H H H H C C C C CH2 CH2 O OH OH O O

  40. Size matters.. If 2 sugar molecules can form a glycosidic linkage, then the most reactive site is used. BUT, there’s no reason why you can’t use the less preferred sites. Carbohydrates are “polysaccharides” formed by multiple glycosidic linkages between sugar molecules.

  41. Clicker Question • I’m here • I’m not here

  42. O C OH H2N CH2 Amino Acids Amino Acids are building blocks of proteins. Amino Acids are exactly what the name suggests: amines AND carboxylic acids Glycine

  43. O C OH H2N CH2 α - Amino Acids Glycine is the simplest of the α - amino acids. The α refers to the carbon immediately next to the carbonyl group. To be an α - amino acid, the amine must be bonded to this carbon. Glycine α

  44. O O O C C C OH OH OH H2N H2N H2N CH CH2 CH Different substituents, different α - amino acid If the α – carbon has different substituents (besides the 2 H’s of glycine) it is a different amino acid. CH2 CH2 C = 0 OH OH Serine Aspartic acid Glycine

  45. Let’s think together… bases Amines are… Carboxylic acids are… What happens when you mix an acid and a base together? They neutralize each other! acids

  46. O O O O C C C C O OH O OH H3 N H2N H3N H2N CH2 CH2 CH2 CH2 How would that neutralization occur? The –COOH is an acid, the –NH2 is a base. Any –COOH can donate a proton to any –NH2. Some amino acids are stronger acids/bases than others based on the side group, but they are all acids/bases. - Base form of Glycine Amphoteric form of Glycine + + - Zwitterion form of Glycine Acid form of Glycine

  47. O O O O C C C C O- OH OH OH H2N H2N H3N H2N CH2 CH2 CH2 CH2 Which one is it? If you had a beaker full of glycine in distilled water at 25 C and 1 atm of pressure, which one would be the dominant form? Base form of Glycine Amphoteric form of Glycine + Zwitterion form of Glycine Acid form of Glycine

  48. O O O O C C C C O- OH OH OH H2N H2N H3N H2N CH2 CH2 CH2 CH2 Which one is it? Could you ever have any of the other forms? Sure! Change the pH! Base form of Glycine Amphoteric form of Glycine + Zwitterion form of Glycine Acid form of Glycine

  49. O O C C OH OH CH2 OH H2N H2 N CH2 CH What happens if I mix serine and glycine? Let’s make H2O! Glycine Serine

  50. O O O O O O C C C C C C OH OH OH OH OH OH CH2 CH2 CH2 OH OH OH HNH H2N H2N HNH H2 N H2 N CH2 CH CH CH2 CH CH2 Dehydration…not always a bad thing! [Called “condensation”] + Glycine Serine OR

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