1. Recognize the 20 amino acids that commonly occur in proteins and classify them according to polarity and charge.

Nonpolar – glycine, alanine, proline, valine, leucine, isoleucine, phenylalanine.

Slightly polar – tyrosine, tryptophan

Polar – asparagine, glutamine, serine, threonine, methionine, cysteine

charged – (negative) aspartate, glutamate, (positive) arginine, lysine, histidine

2. Define and recognize the bonds and forces (peptide, disulfide, hydrogen bonds; hydrophobic, dipole-dipole, van der Waals, electrostatic interactions) that contribute to protein structure and function.

Peptide bonds are covalent bonds linking the amine group of an amino acid to the carboxyl group on a different amino acid. This is how the primary structure of proteins is formed.

Disulfide bonds are covalent bonds between the sulfur atoms on two cysteine residues. They help contribute to the tertiary and quaternary structure of proteins.

Hydrogen bonds are interactions between a covalently bonded hydrogen atom to a donor group (-OH or -NH) and another paid of non-bonded electrons on a recipient group (C=O). These are not covalent bonds, but rather weak bonds and help contribute to the secondary structure of proteins

Hydrophobic interactions are when hydrophobic residues cluster together on the inside of a protein.

Dipole-dipole interactions are interactions between polar molecules. They are not bonds, merely interactions.

Van der Waals interactions are attractions between dipoles, whether induced or permanent. They are among the weakest of the molecular interactions; the Van der Waals forces between neighboring fatty acid tails are readily broken to allow the lipids to move throughout the membrane.

Electrostatic interactions are the attraction between opposite charges or repulsion between like charges, usually on side chains. They are not bonds, merely interactions.

3. Understand the basis of primary, secondary, tertiary, and quaternary protein structure.

Primary structure is the chain of bonded amino acids. Secondary structure largely relates to alpha-helices and beta-sheets. Tertiary structure includes additional interactions between various residues on the amino acid chain, and quaternary structure comes into play when there are more than one subunits involved in the making of the protein.

4. Define the following features of protein structure: 'α'-helix, 'β'-sheet, 'β'-strand, parallel, anti-parallel, 'β'-turn, loop, motif, helix-turn-helix,''' leucine zipper, zinc finger''', triple helix, fibrils.

Alpha-helix: side chains extend outward, there are 3.6 amino acids per turn of the helix, and residue 1 is hydrogen bonded to residue 4 in the chain and so forth.

Beta-sheet: made up of beta-strands (peptide chains) that are fully extended; has a pleated appearance, can run in the parallel (where the peptides run N-terminus to C-terminus each time) or anti-parallel (where the peptides alternate directions—one strand runs in the N-->C direction and the next runs in the C-->N direction). Hydrogen bonding holds the sheets together.

Beta-turn: these reverse the direction of the polypeptide chain, helping it form a compact, globular shape. These often contain proline, as it creates a 'kink' in the conformation of the chain due to the imino group. Glycine is also commonly found in beta-turns (or beta-bends).

Loops and coils are non-repetitive secondary structures that aren't necessarily 'random', but don't have as regular of a structure as alpha helices and beta sheets.

Motifs form super-secondary structures and are part of the conformation of globular proteins. In motifs, the secondary structures form the core region of the protein, and are often linked together on the surface by beta-turns.

Helix-turn-helix is a motif in which an alpha-helix links together two beta-strands/sheets. (chapter 2) //two alpha helices are connected by short strand of amino acids// //

A triple helix describes the structure of collagen, in which three polypeptides in alpha-helix structure are wound together in a rope-like structure. These structures are called fibrils. (Chapter 4)

A zinc finger motif is one related to DNA transcription and requires two Cys-Cys residues to be followed shortly by two His-His residues, with several zinc molecules trailing between them. See photo.

A leucine zipper is when a leucine is periodically found in an alpha-helix structure such that the leucines lie on top of each other and can 'zip' up into a compact form.

5. List common protein post-translational modifications.

Phosphorylation – when a phosphate group (PO32-) is added to a side group. This is the most common post-translational modification.

Glycosylation – when a carbohydrate is linked to the protein via an O-link or an N-link

Hydroxylation – when a hydroxy group (OH) is added to a side chain

Carboxylation – when a carboxyl group (COOH) is added to a side chain

methylation – when a methyl group (CH3) is added to a side chain

Acetylation – when an acetyl group (C=OCH3) is added to a side chain

Lipid addition.

6. Provide examples of how abnormal protein structure promotes human disease.

In emphysema, the substitution of a Lys residue with another residue will result in the loss of the ionic bond with Glutamate in alpha-1-antitrypsin, which causes large aggregates of the protein to form. Without this enzyme, the enzymatic activity of elastase is not blocked, and the lungs will have the loss of proper expansion and contraction.

7. Define the terms “peripheral” and “integral” with respect to membrane proteins.

Integral proteins have one or more transmembrane segments, and thus can only be dissciated from the lipid bilayer by detergents (which dissolve the bilayer alltogether). Peripheral proteins are only associated with the lipid bilayer by an anchor, and can often be dissociated by a high pH buffer.

8. Recognize common protein membrane anchors.

Phosphatidylinositol (PI) can have a carbohydrate bridge used to bond proteins, such as alkaline phosphatase and acetyl-choline esterase to the membrane. Glycosyl PI is a common membrane anchor in protozoans. This type of anchor contains several mannose residues and glucosamine. The Ras protein is modified by prenylation on its carboxyl terminus. Similar proteins with the CAAX motif can be inserted into the membrane in much the same way.

9. Define and differentiate between proteoglycans, glycoproteins and glycolipids.

Proteoglycans are molecules consisting of one or more glycosaminoglycan chains (long chains of sugars that have at least one amino sugar in them) attached to a core protein. Glycoproteins, on the other hand, are ogliosaccharide chains covalently attached to amino acid side chains and usually associated with the plasma membrane. Glycolipids are membrane lipids where a sugar molecule or ogliosaccharide is attached to the polar headgroup.

10. Recognize the major carbohydrates in the human body.

Sucrose (glucose + fructose alpha-1,2 linkage), Lactose (glucose + galactose beta-1,4 linkage), maltose (glucose + glucose alpha-1,4 linkage). Starch is composed of many maltose/glucose molecules linked together. Cellulose (fiber) is many glucose molecules linked in a beta-1,4 linkage pattern.

11. Review the structures and nomenclature of mono-, di-, tri- and polysaccharides (including glucose, maltose, fructose, sucrose, galactose, lactose).

Monosaccharides generally have 3-7 carbon atoms, and are classified based on the number of carbon atoms. Glucose is a 6-membered-ringed sugar; maltose is a glucose-glucose disaccharide with an a-1,4-linkage; fructose is a 5-membered-ringed sugar (6 carbon sugar); galactose is a 6-membered-ring sugar; and lactose is a glucose-galactose disaccharide with a b-1,6-linkage.

12. Define the following terms with respect to carbohydrate structure: D and L designation, aldose vs. ketose, aldehyde vs. keto group, chiral center, enantiomer, isomer, epimer, hemiacetal vs. hemiketal, anomeric carbon, a and b designation, mutarotation. Lippincotts Chapter 7

Aldoses are sugars that have the carbonyl group as an aldehyde (carbonyl group at the end of the carbon chain) and ketoses are sugars that have the carbonyl group as a ketone (carbonyl group in the middle of a carbon chain).

Both aldoses and ketoses have chiral centers, where there are 4 different groups attached to a given carbon.

Sugars are given D and L designation based on the configuration of the highest numbered asymmetrical carbon. If the OH group is on the right (when drawing an open chain, not the ring structure), the sugar is given a D designation. If the OH group is on the left, the sugar is given the L designation. The vast majority of the sugars in humans are D-sugars. D and L sugars are enantiomers of each other, meaning they are mirror images of each other.

Isomers have the same chemical formulas, thus glucose, mannose, galactose, and fructose are all isomers (formula C6H12O6). Epimers are sugars that differ in configuration around one specific carbon. Galactose and glucose are C4 epimers, while mannose and glucose are C2 epimers. Galactose and mannose differ around 2 carbons, so they are not epimers.

A hemiacetal is formed through a nucleophilic addition of an alcohol to a carbonyl (aldehyde) group. Hence, when aldoses form rings, they are hemiacetals. A hemiketal is formed through the nucleophilic addition of an alcohol to a carbonyl (ketone) group. Thus, when ketoses form rings, they are hemiketals. Fructose is a hemiketal and is a five-member ring, whereas glucose is a hemiacetal and is a six-member ring. The carbon atom that carried the carbonyl function becomes an asymmetric carbon and is called an anomeric carbon. Sugars that differ in configuration around the anomeric carbon are anomers. If the hydroxyl group of an anomeric carbon is on the same side (Fischer projection) of the oxygen bound to the highest numbered asymmetric carbon, it is designated an alpha configuration. If the hydroxyl group of an anomeric carbon is on the opposite side (Fischer projection) of the oxygen bound to the highest numbered asymmetric carbon, it is designated a beta configuration. Enzymes are specific to one or another of these forms. The sugars can also convert from an alpha configuration, to an open chain, to a beta configuration and visa versa. This is referred to as mutarotation.

13. List some common modifications to sugar structure.

Oxidation of the C6 carbon. Adding an amino group to the C2 carbon, then adding an acetyl group to the amine. Removing a hydroxyl group (to form a deoxy sugar, as used for DNA), and adding a phosphate group to form a phosphate ester.

14. Appreciate the significance of the orientation of the glycosidic bonds for digestion and metabolism.

Lactose is a beta-1,4 linkage, maltose is an alpha-1,4 linkage, and sucrose is an alpha-1,2 linkage. Each linkage requires a specific enzyme for hydrolysis and digestion. Amylase is highly active towards alpha-1,4 linkages, but not the beta-1,4 linkages found in cellulose.

15. Understand the standard nomenclature for fatty acids (define omega and alpha carbons and recognize their location on a diagram).

Omega carbons are counted from the end of a fatty acid chain. For instance, in an 18-carbon chain, the omega-3 carbon will be the 15th carbon in the chain, or the third counted from the end. The omega designation refers to the position of double bonds in the chain. The alpha carbon is the carbon attached to the carboxyl group, or carbon 2 in the chain. Saturated fatty acids have no double bonds, unsaturated fatty acids have one or more double bonds.

16. List the essential fatty acids in the human diet.

Linoleic and linolenic acids. Arachidonic acid becomes essential If linoleic acid is limiting in the diet.

17. Recognize the structure of cis vs. trans unsaturated fatty acids and the effects on the fatty acid’s physical properties.

cis-unsaturated fatty acids have both acyl chains on the same side of the double bond. This creates a kink in the acyl chain and reduces packing in a membrane. trans-unsaturated fatty acids have acyl chains on the opposite side of the double bond. This configuration does not exist in nature and is induced by hydrogenation in the manufacturing process. Trans Fas raise plasma LDL cholesterol levels and raise triglyceride levels.

18. Draw the basic structure of a triglyceride. Recognize the structural components of a phospholipid and sphingolipid.

19. Understand the effects of chain length and double bonds on the melting point of fatty acids.

In general, the longer the chain, the higher the melting point, and the fewer double bonds, the higher the melting point. For instance, an 18-carbon chain with three double bonds will melt at a lower temperature than an 18-carbon chain with no double bonds, and an 18-carbon chain will melt at a lower temperature than a 24-carbon chain with the same number of double bonds.

20. Describe the structure and common components of a lipid bilayer.

Sphingolipids help to make up lipid 'rafts' where many proteins are concentrated in such a way to enhance their function. Unlike other parts of the lipid bilayer, sphingolipids in the rafts interact with each other across the bilayer, allowing communication across the rafts. Other components include phospholipids,