1. AP Biology BIOCHEMISTRY

2. Carbon  Tetravalence influences number of bonds, and tendency toward covalent interactions  BTW: we should understand the term “covalent” from the term’s components.  Valent refers to actions / interactions in the valence electron shell.  Co- refers to the mutual sharing / possession of those electrons.  The definition should not need to be “memorized”.

3. Recall  25 elements are essential to life!  Carbon, Nitrogen, Hydrogen, & Oxygen collectively make up 96% of living matter https://en.wi kipedia.org/ wiki/Compo sition_of_the _human_bo dy

4. Carbon “Skeletons” Variations in carbon skeletons contribute to the complexity & diversity of organic molecules. (Images from Pearson & NIH.gov, respectively)

5. Hydrocarbons (C & H only) Ciesin.org & Wisegeek.com

6. Condensation v. Hydrolysis In a condensation reaction, an H and an OH are removed from the components to form a water molecule. The components become covalently bonded to one another. In a hydrolysis reaction, water is an input, a covalent linkage is broken, and water supplies the H and the OH to the now-separate components. Image: bbc.co.uk

7. Biological Unity & Diversity  An immense variety of polymers can be built from a small set of monomers  Structural variation of macromolecules is the basis for the enormous diversity of life.  There is unity in life as there are only about 40 to 50 common monomers used to construct macromolecules.  There is diversity in life as new properties emerge when these universal monomers are arranged in different ways.

8.  Carbohydrates = Organic molecules made of sugars and their polymers  Monomers or building block molecules are simple sugars called monosaccharides.  Polymers are formed by condensation reactions.  Carbohydrates are classified by the number of simple sugars. Carbohydrates

9. Polysaccharides  Polysaccharides = Macromolecules that are polymers of a few hundred or thousand monosaccharides. Image: Wikipedia

10. Storage Polysaccharides: Starch Storage polysaccharide in plants “Foods such as potatoes, rice, corn and wheat contain starch granules which are important energy sources for humans. The human digestive process breaks down the starches into glucose units with the aid of enzymes, and those glucose molecules can circulate in the blood stream as an energy source.” - http://hyperphysics.phy- astr.gsu.edu/hbase/organic/carb.htmlhttp://hyperphysics.phy- astr.gsu.edu/hbase/organic/carb.html Image: "Amylose2" by NEUROtiker - Own work. Licensed under Public Domain via Commons - https://commons.wikimedia.org/wiki/File:Amylose2.svg#/media/File:Amylose2.svg https://commons.wikimedia.org/wiki/File:Amylose2.svg#/media/File:Amylose2.svg

11. Carbohydrates in Catholicism

12. Medical gallery of Mikael Häggström 2014 Storage Polysaccharides: Glycogen Storage polysaccharide in animals “Glycogen is a readily mobilized storage form of glucose. It is a very large, branched polymer of glucose residues that can be broken down to yield glucose molecules when energy is needed. Most of the glucose residues in glycogen are linked by α-1,4- glycosidic bonds. Branches at about every tenth residue are created by α-1,6-glycosidic bonds. Recall that α-glycosidic linkages form open helical polymers, whereas β linkages produce nearly straight strands that form structural fibrils, as in cellulose… The two major sites of glycogen storage are the liver and skeletal muscle. The concentration of glycogen is higher in the liver than in muscle (10% versus 2% by weight), but more glycogen is stored in skeletal muscle overall because of its much greater mass.” http://www.ncbi.nlm.nih.gov/books/NBK21190/

13. Glycogen: alpha 1-6 and alpha 1-4 linkages Biochemistry. 5th edition. Berg JM, Tymoczko JL, Stryer L. New York: W H Freeman; 2002.

14. Structural Polysaccharides: Cellulose  Cellulose = Linear unbranched polymer of D-glucose in (α 1-4, β 4-6) linkages.  A major structural component of plant cell walls  Cellulose reinforces plant cell walls. Hydrogen bonds hold together parallel cellulose molecules in bundles of microfibrils. Image: Alevelnotes.com Above: Electron microscope image of wood cellulose http://www.scienceclarified.com/Ca- Ch/Cellulose.htmlhttp://www.scienceclarified.com/Ca- Ch/Cellulose.html

15. Chitin  Monomer is an amino sugar, which is similar to beta-glucose with a nitrogen-containing group replacing the hydroxyl on carbon 2. "Exoskeleton fly 1" by Karthik Easvur - Own work. Licensed under CC BY-SA 3.0 via Commons - https://commons.wikimedia.org/wiki/File:Exoskeleton_fly_1.jpg#/media/File:Exoskeleton_fly_1.jpg Blc.Arizona.edu

16. Starch = Helical glucose polymer with α 1-4 linkages. Glucose monomers are in α configuration (–OH group on carbon one is below the ring's plane). Monomers are connected with α 1-4 linkage. Cellulose differs from starch (also a glucose polymer) in its glycosidic linkages. Glucose monomers in cellulose are in β configuration (–OH group on carbon one is above the ring's plane). Monomers are connected with β 1-4 linkage. “Cellulose: Beta glucose is the monomer unit in cellulose. As a result of the bond angles in the beta acetal linkage, cellulose is mostly a linear chain. Starch: Alpha glucose is the monomer unit in starch. As a result of the bond angles in the alpha acetal linkage, starch-amylose actually forms a spiral much like a coiled spring.” http://chemwiki.ucda vis.edu/Biological_Ch emistry/Carbohydrate s/Polysaccharides/Cel lulose

17. Lipids Lipids = Diverse group of organic compounds that are insoluble in water, but will dissolve in nonpolar solvents (e.g., ether, chloroform, benzene). Important groups are fats, phospholipids, and steroids. Fats store large amounts of energy

18. Lipids: Saturated v. Unsaturated fats Image: authoritynutrition.com Saturated fats are solids at room temperature. Unsaturated fats, due to molecular geometry, are not as tighly packed, and so exist as liquids at room temperature.

19. Energy storage. One gram of fat stores roughly twice as much energy as a gram of polysaccharide. (Fat has a higher proportion of energy rich C–H bonds.) More compact fuel reservoir than carbohydrate. Animals store more energy with less weight than plants which use starch, a bulky form of energy storage. Cushions vital organs in mammals (e.g., kidney). Insulates against heat loss (e.g., in mammals such as whales and seals). Lipids: Fats

20. Cholesterol is the precursor to many other steroids including vertebrate sex hormones and bile acids. Cholesterol is a common component of animal cell membranes. “Steroids occur in plants, animals, yeasts, and molds but not in bacteria. They may exist in free form or combined with fatty acids or carbohydrates. All steroids have a characteristic structural component consisting of four fused rings. Chemists identify the rings by capital letters and number the carbon atoms as shown in part (a). Slight variations in this structure or in the atoms or groups attached to it produce profound differences in biological activity.” The Basics of General, Organic, and Biological Chemistry, v. 1.0 by David W. Ball, John W. Hill, and Rhonda J. Scott Lipids: Steroids

21. Proteins  Protein = A macromolecule that consists of one or more polypeptide chains folded and coiled into specific conformations.  Vary extensively in structure; each type has a unique three-dimensional shape (conformation)  Composed from amino acid monomers (there exist 20 amino acids of which long polypeptides are composed).  Amino acid = Building block molecule of a protein; most consist of an asymmetric carbon, termed the alpha carbon, which is covalently bonded to a(n):  1. Hydrogen atom.  2. Carboxyl group.  3. Amino group.  4. Variable R group

22. Proteins: Amino Acid Structure www.studyblue.com

23. Protein functions 1.Structural support 2. Storage (of amino acids) 3. Transport (e.g., hemoglobin) 4. Signaling (chemical messengers) 5. Cellular response to chemical stimuli (receptor proteins) 6. Movement (contractile proteins) 7. Defense against foreign substances and disease-causing organisms (antibodies) 8. Catalysis of biochemical reactions (enzymes)

24. Images: hairkeratins.com, news.com.au Proteins: Keratin example

25. Amino acids contain both carboxyl and amino functional groups. Since one group acts as a weak acid (carboxyl) and the other group acts as a weak base (amino), an amino acid can exist in three ionic states. The pH of the solution determines which ionic state predominates. Image: chemistry.tutorvista.com Proteins: Zwitterions

26. http://www.ncbi.nlm.nih. gov/books/NBK26830/fig ure/A391/?report=object only

27. http://www.ncbi.nlm.nih.gov/books/NBK26 830/figure/A395/?report=objectonly Figure 3-5 Three types of noncovalent bonds that help proteins fold Although a single one of these bonds is quite weak, many of them often form together to create a strong bonding arrangement, as in the example shown.

28. Amino Acid Categories: R groups Uic.edu

29. Protein Conformation  Enables a protein to recognize and bind specifically to another molecule (e.g., hormone/receptor, enzyme/substrate, and antibody/antigen)  Is a consequence of the specific linear sequence of amino acids in the polypeptide  Is produced when a newly formed polypeptide chain coils and folds spontaneously, mostly in response to hydrophobic interactions  Is stabilized by chemical bonds and weak interactions between neighboring regions of the folded protein www.ausetute.com.au s10.lite.msu.edu

30. Protein Conformation

31. Images: faculty.ccbcmd.edu, alevelnotes.com

32. Hemoglobin: Quaternary structure wikipedia

33. www.austincc.edu Hemoglobin: Quaternary structure

34. Proteins: Denaturation Denaturation = A process that alters a protein’s native conformation and biological activity. Proteins can be denatured by: Transfer to an organic solvent. Hydrophobic side chains, normally inside the protein’s core, move towards the outside. Hydrophilic side chains turn away from the solvent towards the molecule’s interior. Chemical agents that disrupt hydrogen bonds, ionic bonds and disulfide bridges. Excessive heat. Increased thermal agitation disrupts weak interactions.

35. Collagen 1.Quaternary structure = Structure that results from the interactions between and among several polypeptides chains (subunits) Example: Collagen, a fibrous protein with three helical polypeptides supercoiled into a triple helix; found in animal connective tissue, collagen’s supercoiled quaternary structure gives it strength. Some globular proteins have subunits that fit tightly together. Example: Hemoglobin, a globular protein that has four subunits (two α chains and two β chains)