Today is Wednesday, October 15 th , 2014

1. In This Lesson: Biochemistry (Lesson 2 of 5) Today is Wednesday,October 15th, 2014 Pre-Class: You remember the four types of organic molecules, don’t you? DON’T YOU? Please turn in your Root Words for Unit 3.

2. Today’s Agenda • Basic chemistry and biochemistry. • Basic organic chemistry. • Basically, a review of a lot of stuff you’ve learned already. • Plus some stuff you didn’t. • Where is this in my book? • Chapter 5 and a little bit of 4.

3. By the end of this lesson… • You should be able to describe the four basic molecules that make up just about everything organic. • You should be able to explain why carbon is the primary element of life. • You should be able to categorize molecules in terms of chemical properties based on functional groups.

4. Where to begin…? • I could begin with a review of atomic structure (protons, neutrons, electrons), but you already know that. • And you already know that the number of protons is equal to the atomic number. • And you know that the mass numberof an atom is the number of protons plus the number of neutrons, so I can skip that. • You’re good with the whole, “valence electrons are the outermost electrons” thing too. • What else can I skip?

5. Where to begin…? • I guess I don’t need to tell you that ionic bonds involve a transfer of electrons, while covalent or molecular bonds involve a sharing or fighting-over of electrons. • You’re also completely solid on the idea that the electrons, being located at a distance from the nucleus, are the only things involved in bonding directly. • So that’s good. I guess we can skip straight to the new material. • I guess we should probably review first, though.

6. Video Review • CrashCourse – That’s Why Carbon is a Tramp

7. Carbon • Carbon is uniquely positioned on the periodic table as it has only four valence electrons, allowing it to form one, two, three, or four bonds. • Other elements also have four valence electrons, but they’re not as small nor as plentiful as carbon. • Thanks to the fact that carbon can form so many different bonds, and thus form many larger building blocks, any compound containing carbon and hydrogen is called an organic compound. • In fact, organic chemistry is an entire (challenging) branch of chemistry devoted to the study of carbon compounds.

8. Sample Carbon Compounds

9. Organic Chemistry Vocabulary • Before we get into the big molecules formed by carbon, let’s look at the little “attachments” that you’ll find on the main molecule. • Keep in mind, most hydrocarbons are non-polar and therefore hydrophobic. • These molecular attachments, called functional groups, change the characteristics of the molecule. • Like branches from a tree. • Like pimples on a teenage hydrocarbon’s face.

10. Let’s start slow…Hydroxyl Group • Hydroxyl = -OH • Note: Hydroxide = OH- - that’s different. • Important Properties • It’s polar/hydrophilic, so molecules containing it can usually dissolve. • A molecule containing this group is known as an alcohol (“____ol”).

11. Carboxyl Group • Carboxyl = -COOH • Important Properties • Polar/hydrophilic. • Acts as an acid by donating its hydrogen atom (H+). • Common in carbon-based acids. • A molecule containing this group is known as a carboxylic acid or organic acid.

12. Amino Group • Amino = -NH2 • Important Properties • Polar/hydrophilic. • Acts as a base by receiving H+ ions. • This is the Brønsted-Lowry base definition. • A molecule containing this group is known as an amine. • Note: Amino acids commonly have both amines and carboxylic acids on their molecules. • Whether the entire molecule acts as a base or an acid depends on the pH of the surrounding solution. http://chemistry2.csudh.edu/rpendarvis/aminoacids.html

13. Sulfhydryl Group • Sulfhydryl = -SH • Important Properties • Very weakly polar. • Found in proteins to help tertiary and quaternary structure. • Think of them as “shapers.” • Book example: This is what makes hair stay curly or straight and sulfhydryl-containing compounds are used in perms to change the natural structure. • A molecule containing this group is known as a thiol. • Fun fact: Thiols are used as the smell in natural gas.

14. Phosphate Group • Phosphate = -OPO32- • Important Properties • Provides a 1- or 2- charge. • Can react with water to release energy. • Look for this group in ATP and other nucleotides (like DNA). • A molecule containing this group is known as an organic phosphate.

15. Methyl Group • Methyl = -CH3 • Important Properties • Non-polar and unreactive…that’s the point of a methyl group. • Often methyl groups are used to deactivate portions of DNA and larger molecules. • A molecule containing this group is known as a methylated compound.

16. Back to Carbon • Because carbon can form MASSIVE structures, it’s best to break them down into their basic building blocks. • Hence: • Monomers are the basic building blocks. • Mono – get it? • Polymers are the large complex chains of monomers. • Poly – want a cracker? • Macromolecules are the big four categories of polymers out there.

17. The Four Macromolecules • The four organic molecules are: • Carbohydrates • Lipids • Proteins • Nucleic Acids • They each have some defining features: • Composition • Functional Groups

18. But, before we get to them… • It’s at this point that I hope a certain thought has crossed your mind. • We’re talking about atoms and now are talking about the molecules they form in combination with one another. • Exactly where does “life” come into play? • Living things are composed of non-living atoms. • Read that again. We’re going to take a couple minutes to just…think about that.

19. (Also) About Functional Groups -OH >C=O The Lost Ark Paper Clips Biebs • Imagine a strange train. • The contents of the train can be almost anything as long as the links between them are the same. • The links might as well be called functional groups. • As we’ve seen, they impart certain properties to molecules and also help to link them.

20. Functional Groups • Again, functional groups are small clusters of atoms present in larger monomers. • They’re not part of the hydrocarbon – the long chain of…hydrogens and carbons. • They give the molecule its properties, especially in linking it to other molecules.

21. How small are we talking? • Scale of the Universe! • Scale of the Universe

22. Heads-Up ! • On the next slides, we’re going to examine each of the organic molecules one-by-one. • First Slide: Summary • Then: Monomer Detail • Then: Polymer Detail(s) and Examples • Then: Summary again • However, we’re going to explore some additional details in the carbohydrate section regarding bonding and “unbonding,” so leave about a quarter of the page blank right now. • We’ll fill it in later.

23. #1 – CarbohydratesSummary • Composition: C, H, O • Functional Group(s): -OH [hydroxyl group] • Function(s): Energy source, plant building material, cell markers. • Monomer: Monosaccharide • Polymer: Disaccharide, polysaccharide

24. #1 – CarbohydratesMonomers • Carbohydrate monomers can be spotted by the 1:2:1 pattern of their C, H, O atoms. • Example: Glucose (cell fuel) is C6H12O6 • Example: Fructose (very sweet) is C6H12O6 • Example: Galactose (milk sugar) is C6H12O6 • The difference? Their shapes. • Because they’re all the same formula, they’re called isomers of one another. • Iso- (same)

25. Aside: Sugar is Sweet (!) • There are lots of sugars out there and they can be ranked by “sweetness.” Here are a few, all compared to sucrose (table sugar). • Lactose: Not as sweet. • Maltose: Equal sweetness. • Glucose: Slightly sweeter. • Fructose: 4x sweeter. • Aspartame*: 150x sweeter. • Saccharine*: 450x sweeter. • Sucralose*: 600x sweeter. • Neotame*: 8000x sweeter. *Artificial sweeteners

26. #1 – CarbohydratesFunctional Groups • Remember, -OH (hydroxyl) is the functional group for carbohydrates.

27. #1 – CarbohydratesDisaccharides • A disaccharide, like the name suggests, is simply two linked monosaccharides. • The monosaccharides were linked by a dehydration synthesis reaction – details next slide. • Examples: • Glucose + Glucose = Maltose (malt sugar) • Glucose + Fructose = Sucrose (table sugar) • Glucose + Galactose = Lactose (milk sugar)

28. Dehydration Synthesis • Do I really need to tell you what happens in a dehydration synthesis reaction? • Follow the word stems! • Water… • …is removed… • …to put things together. • Sure enough…

29. Hydrolysis • The opposite of dehydration synthesis is hydrolysis. • Follow the word stems! • Water… • …breaks apart. • Think of it like “hydro-slices.” • Sure enough…

30. Isomers Did you happen to notice something about the formulas of glucose and fructose on the previous slide? Take another look: Molecules with the same formula but different shapes are called isomers.

31. #1 – CarbohydratesBonds • Once the bond has formed, it’s known as a glycosidic bond, less commonly as a C-O-C bridge.

32. #1 – CarbohydratesPolysaccharides • A polysaccharide is a complex molecule made of three or more monosaccharides. • Example: Starch (plant sugar storage) • Example: Glycogen (animal sugar storage – muscles) • Example: Cellulose (cell walls – fiber) • Example: Chitin (insect exoskeletons – crunch)

33. #1 – CarbohydratesExamples

34. #1 – CarbohydratesSummary • Composition: C, H, O • Functional Group(s): -OH [hydroxyl group] • Function(s): Energy source, plant building material, cell markers. • Monomer: Monosaccharide • Glucose, fructose, galactose. • Polymer: Disaccharide, polysaccharide • Disaccharide: Sucrose, maltose, lactose • Polysaccharide: Starch, glycogen, cellulose

35. #2 – LipidsSummary • Composition: C, H, O (except they’re mostly non-polar). • Functional Group(s): Carboxyl [-COOH]...sorta. • Function(s): Fats, oils, waxes, steroids, cholesterol, hormones, pigments…and energy storage. • Monomer: Um… • Polymer: Sigh… • Lipids are weird. The best thing you can do is remember that.

36. #2 – LipidsMonomers • There is no true monomer for lipids. • That said, many lipids contain something called a triglyceride, which is made of a glycerol molecules along with three (tri) fatty acids. Glycerol Molecule Fatty Acid Chains

37. Fatty Acids • What do you see here on this fatty acid? • First, there’s a long hydrocarbon chain. • Highlighted in red(ish) is the functional group – carboxyl – given by –COOH. • The carboxyl is the only polar part.

38. Fatty Acids • Fatty acids also govern the nature of the lipid: • Are all hydrocarbon bonds single? • The fat is saturated (with H) and is a solid at room temperature. • Fatty acid tails can pack tightly together to form a solid. • Each carbon in the chain is bound to four atoms.

39. Fatty Acids • Are some bonds double? • The fat is unsaturated (with H) and is liquid at room temperature – an oil. • Kinked fatty acid tails can’t pack closely together, keeping the substance a liquid. • Some carbons have doublebonds and therefore are bonded to only three other atoms.

40. Aside: Hydrogenation • You may have seen the term “partially hydrogenated” or “fully hydrogenated” in a food product (peanut butter’s a big one). • Maybe you’ve heard of trans fats? • Hydrogenation in food products is the forced addition of hydrogen to unsaturated fats in order to make them saturated. • Trans fats can be formed when the hydrogenation process doesn’t fully saturate the oil. • They’s bad for you. Avoid ‘em. http://media.fooducate.com/blog/posts/regularjif.jpg

41. Lipid Types

42. Lipid Stuff • With no true monomer, lipids have no real polymers either, and they don’t have characteristic bonds. • Keep in mind one extra thing, though: • Carbohydrates and lipids both provide the cell with energy, but lipids tend to be a longer-term source of energy.

43. #2 – LipidsSummary • Composition: C, H, O (except they’re mostly non-polar). • Functional Group(s): Carboxyl [-COOH]...sorta. • Function(s): Fats, oils, waxes, steroids, cholesterol, hormones, pigments…and energy storage. • Monomer: Um… • Polymer: Sigh… • Lipids are weird. The best thing you can do is remember that.

44. #3 – ProteinsSummary • Composition: C, H, O, N • Functional Group(s): Amino group [-NH2], carboxyl group [-COOH] • Function(s): Enzymes, receptors, structural components, skin, hemoglobin, antibodies…the list goes on. • Monomer: Amino acid • Polymer: Polypeptide

45. #3 – ProteinsMonomer and Functional Groups Each amino acid has a central carbon… …an amino group (NH2) and carboxyl group (COOH)… …a hydrogen… …and the R (radical) group which is different for each amino acid)…

46. #3 – ProteinsStructure Key: Amino acids take an N-C-C central structure. Key: The central C has an H on one side and the R-group comes off the other.

47. #3 – ProteinsMonomers • There are 20 very different amino acids. • Key: The R-group gives the amino acid its traits. • Consider them the “alphabet of life.” • Look at the headings for the various groups: http://nobelprize.org/educational/medicine/dna/a/translation/aminoacids.html

48. #3 – ProteinsPolymers and Bonds • Dehydration synthesis reactions allow for the joining of amino acids into dipeptides and polypeptides. • The bonds between them are called peptide bonds. • Peptide bonds link a nitrogen and carbon (N-C). • Let’s take a look…

49. #3 – ProteinsBonds

50. Protein Structure • Okay, this gets a little complicated. • Completed polypeptides have four levels of structure. • We’re going to look at the steps on new slides. • Before that, one more bond type: • A disulfide bond occurs in proteins and joins two sulfhydryl (-HS) groups.