Chapter 3 – Biochemistry The chemistry of Life

AP Biology ‘Big Ideas’ that require Biochem. The process of evolution drives the diversity and unity of life A. Unity : all living things made of same 4 basic types of molecules B. the basic molecules are the individual subunits of larger molecules C. basic molecules are referred to as monomers or building blocks

D. monomers gain their chemical properties from functional groups: small groups of atoms that confer specific chemical traits 1. Hydroxyl group (-OH) makes things polar & water soluble 2. Carboxyl groups (-COOH) makes things acids & water soluble 3. Phosphate groups (-OPO3-) energizes & makes water soluble

4. Amino groups (-NH2) makes things bases 5. Methyl groups (-CH3) makes things nonpolar and insoluble 6. Sulfhydral group (-SH) stabilize proteins E. The combination and arrangement of functional groups on the exterior of the monomer gives that monomer its unique properties What do water soluble functional groups have in common?

Example : importance of functional groups male hormone converted to female hormone by changing functional groups What functional groups do each of these molecules have? The ring structures are all nonpolar carbon-hydrogen bonds, would these molecules be predominantly polar or non-polar? Water soluble or not?

F. Types of Chem Rxns 1. functional group transfer 2. electron transfer (redox rxn) 3. Rearrangement of atoms

4. Condensation dehydration rxn (synthesis) fig 3.6 Remove water (in form of H from one molecules and OH from the other) In order to stick to molecules together

5. Hydrolysis rxn fig 3.6 Using water to break 2 molecules apart Put water (in form of H and OH) back in Video of hydrolysis and condensation rxns https://www.youtube.com/watch?v=ZMTeqZLXBSo

Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, reproduce and to maintain dynamic homeostasis. A. Molecular building blocks = monomers B. Monomers covalently bonded together form giant Macromolecules 1. Any large biological molecule made by fusing together monomers can be called a macromolecule 2. If all of the monomers are of the same type then the giant molecule can be called a polymer.

Example 1: glycerol is one type of monomer, fatty acid is a different type so this is a macromolecule but not a polymer Example 2:peptides are both macromolecules and polymers since they are very large and all the monomers are the same type…amino acids.

Identify these macromolecules as polymer or not polymer:

I. Organic Chemistry A. All Organic molecules must have both carbon and hydrogen 1. Hydrocarbons have only C & H 2. Carbohydrates have only C, H & O 3. Adding other functional groups makes other monomers Which of the molecules is water soluble? Why?

Which of the compounds listed above is a carbohydrate? Which of the inorganic compounds listed would you expect to find in you? What is the inorganic carbon source used by plants to make sugars?

II. Why Carbon Based Life Forms? A. Carbon can bond to 4 other atoms B. Bonds = strong covalent C. Small size of atom: Short bonds D. Can from double bonds, rings and chains What type of molecules are shown above?

Side Note on Relative Bond Strength in Living Systems Living systems are Aqueous systems Chemical reactions take place in solution Therefore the strongest bonds are….COVALET What happens to ionic molecules in an aqueous solution? Bond strength order in living systems: Covalent bond > ionic bond > hydrogen bond

Review: Organic Compounds made up of smaller molecules/groups of atoms Functional Groups – clumps of atoms that give chemical properties to anything they bond to Monomers – small organic molecules that can be joined together to form larger molecules Polymers/macromolecules – large molecules that are formed by joining many smaller molecules (in polymers, smaller molecules are the same type)

III. All living things made of: A. Saccharides (sugars) 1. Composed of Monosaccharides 2. All are carbohydrates Only C, O & H 3. All have –OH (hydroxyl) 4. Most dissolve easily in H2O

5. Monosaccharides a. Single monomers of sugar b. smallest unit of saccharide c. Examples to know: Glucose Fructose Galactose What is different among these 3? What could you write in at each point of the circle on the fructose molecule above?

6. Disaccharides a. two monosaccharide bonded together b. Examples to Know: Sucrose (table sugar) Lactose What could be drawn at the ends of the vertical lines shown on the sucrose diagram?

7. Oligosaccharides a. Oligosaccharides: a few monosaccharides b. Often part of glycoproteins or glycolipids (glyco- sugar) c. serve as membrane receptors or identification markers.

8. Polysaccharides (many) a. Different properties based on bonding patterns and chain shape b. Examples to know (all made of glucose) plant glucose storage plant cell walls/fiber animal glucose storage

c. Folding patterns of chains also change properties i. Hydroxyl groups facing out = soluble ii. Hydroxyl groups facing in = insoluble

Chitin = modified polysaccharide N-acetyl functional group added Is Chitin a carbohydrate?

High fructose corn syrup? https://www.youtube.com/watch?v=i09of7ufRlU Dr hyman https://www.youtube.com/watch?v=8RDCnDK2K6Y brian dunning ‘in fact’ https://www.youtube.com/watch?v=qYNcLy0wYVg agave

B. Lipids 1. Macromolecules(bcs large) but not polymers (not repeating units) 2. Grouped together due to hydrophobic nature. What is hydrophobic? Are they polar or non-polar? * The few polar groups vastly outnumbered by nonpolar hydrocarbon structure What functional groups are on the lipids shown above? Are they polar or non-polar?

3. Triglycerides: Fats & oils a. Use: compact, longer term E storage i. takes less room than glycogen/starch (9 calories/gram vs. 4 calories/gram) ii. takes more steps to convert into glucose (the energy form usable to mitochondria) so less readily available b. Fats usually solids mostly in animals c. oils usually liquids in plants

d. Triglyceride structure i. one glycerol molecule bound to three fatty acid molecules ii. Glycerol = an alcohol that binds up to 3 monomers (one on each 0H group) iii. Fatty acids are hydrocarbon chains with a carboxyl group on one end

What property does a carboxyl functional group give to a molecule What property does a carboxyl functional group give to a molecule? Draw a carboxyl group. What property does a methyl group give to a molecule. Draw a methyl group.

Triglycerides are hydrophobic because the long non-polar hydrocarbon portion greatly outweighs the few polar bonds of the oxygens

E. Fat or Oil? i. Fat made of Saturated fatty acids -no double bonds (full of H) -pack tightly so dense & solid ii. Oil:1 or more Unsaturated fatty acid - not enough H to take up all bonds -double bonds make chain bend -do NOT pack well, less dense, liquid

- Is this triglyceride a fat or an oil? - What does polyunsaturated mean?

The type of fatty acids in a Triglyceride determine how healthy a food source it is. Do not memorize individual Fatty Acid names

F. Trans fatty acids i. made by adding hydrogen to unsaturated fatty acids ii. Called partially hydrogenated oils iii. Makes oils more solid (margarine) iv. Creates trans shape double bonds

v. implicated in atherosclerosis (plaque deposits in blood vessels) - increased risk of heart attack & stroke iv. Upsets cholesterol levels Read the articles at http://www.nejm.org/doi/full/10.1056/NEJMp1314072#t=article and https://www.usatoday.com/story/money/2015/06/16/trans-fat-elimination-consequences/28813439/ Answer the following questions in AP free response style which includes supporting evidence for your reasoning. * How is regulating trans fats fundamentally different from regulating sugar or salt? * what is the difference between GRAS substances and additives and how does the FDA treat them differently? * In your opinion, should the FDA have the power to ban the sale of substances like trans fats? Support your reasoning.

Extra info on fats…do not memorize Foods free of trans fats aren't automatically good for you. Food manufacturers may have substituted other ingredients for trans fat that may not be healthy either. Some of these ingredients, such as tropical oils — coconut, palm kernel and palm oils — contain a lot of saturated fat. Saturated fat raises your total cholesterol. In a healthy diet, 20 to 35 percent of your total daily calories can come from fat — but saturated fat should account for less than 10 percent of your total daily calories. Monounsaturated fat — found in olive, peanut and canola oils — is a healthier option than is saturated fat. Nuts, fish and other foods containing unsaturated omega-3 fatty acids are other good choices of foods with healthy fats. Mayo clinic

Hank explains fatty acids https://www.youtube.com/watch?v=mvvx2yQRbzQ

G. Essential fatty acids i. Fatty acids our bodies can’t manufacture ii. Required so we must eat them iii. Omega 3 and Omega 6 - we get more than enough Omega 6 - Do not get enough Omega 3 iv. Sources ***Don’t need to memorize sources*** - Some fish: Halibut, Herring, Mackerel, Oyster, Salmon, Sardines, Trout, fresh Tuna very little in talapia, cod, shrimp, lobster, crab, canned tuna - Some vegetables: (only ALA form of omega-3)Brussels sprouts, Kale, Spinach, Broccoli, Cauliflower -Some oils: Canola, cod liver, Flaxseed, Mustard, Soybean, - also: kidney beans, walnuts, winter squash & supliments

4. Steroids a. Made of 4 fused Carbon rings with different functional groups attached b. Cholesterol : animal cell membranes & precursor for steroid hormones, vit. D & bile salts List the functional groups shown In these steroids

5.Phospholipids a. Glycerol bonds with 2 FA & 1 Phosphate b. Fatty acid tails are hydrophobic c. Phosphate/glycerol head hydrophilic d. phospholipids are amphipathic (both like and fear water, one end likes the other fears)

a.Long chain FA tightly packed to long chain alcohols or carbon rings b.Repel water .. beeswax, plant cuticle What functional group would you expect to be most common in waxes? 6. Waxes

C. Proteins (polypeptides) 1.Polymers made of amino acid monomers 2.Bonds btwn amino acids called peptide bonds 3. make enzymes, hormones, muscle

4. Each amino acid is a carbon bonded to.. *1 amino group *1 carboyxl group *1 hydrogen *and one of 20 different R groups R group gives the amino acid characteristics (polar or non-polar) (acidic neg. charge or basic + charge) What functional group would make an R group into a base? What R group would make it hydrophilic?

5. Levels of protein structure 1˚= chain of aa 2˚= chain of aa folds over on itself and sticks due to H-bonds 3˚=3-D shape due to disulfide bonds 4˚>one chain of aa bonded together

6. Denaturation of Proteins a. 3-D shape of protein altered b. Protein no longer functions properly c. H-bonds and disulfide bonds broken

D. Nucleotides 1. Nucleotides are largest monomer made of 3 different groups/monomers.. * a sugar (ribose or deoxyribose) * a phosphate group * a nitrogen base (A, T, G, C, or U)

2. Nucleotides can a. Function alone as… i. coenzymes that transfer e- or H+ (NAD+ or FAD) ii. ATP (adenosine triphosphate) (transfers phosphate group to energize molecules) b. form polymers called nucleic acids (DNA/RNA)

3. Nucleic Acids are polymers of many nucleotides a. Nucleotides are covalently bonded into chains b. DNA = made of nucleotides with the sugar deoxyribose c. RNA = made of nucleotides with the sugar ribose What would you do to a ribose molecule to make it into a deoxy ribose?

E. Types of Chem Rxns 1. functional group transfer 2. electron transfer (redox rxn) 3. Rearrangement of atoms

4. Condensation dehydration rxn (synthesis) fig 3.6 Remove water (in form of H from one molecules and OH from the other) In order to stick to molecules together

5. Hydrolysis rxn fig 3.6 Using water to break 2 molecules apart Put water (in form of H and OH) back in Video of hydrolysis and condensation rxns https://www.youtube.com/watch?v=ZMTeqZLXBSo