Macromolecules

I.         Carbon skeletons

            A.        Isomers

                        1.         Structural isomers - differ in the arrangement of their atoms

                        2.         Geometric isomers - differ in the arrangement of atoms around a double bond

                        3.         Enantiomers

                                    a          molecules that are mirror images of each other

                                    b          cells can tell the two apart

                                    c          usually one is biologically active while the other is not

            B.        Polymers

                        1.         large molecules made by linking many individual building blocks together in long chains.

                        2.         The building block subunits are called monomers.

                        3.         Subunits are linked by a reaction called dehydration synthesis and can be cleaved by a reaction called hydrolysis.

II.        Carbohydrates (p. 65) - the most important energy source for cells and include sugars and their polymers

            A.        Nomenclature

                        1.         Monosaccharides (Fig. 5.3) - single sugar units - note the -ose suffix in the names.

                        2.         Disaccharides (Fig. 5.5) - formed by linking two monosaccharides by dehydration synthesis.

                        3.         Polysaccharides (Fig. 5.6)

                                    a          formed by linking many sugar units together

                                    b          starch, glycogen, and cellulose are the three common polysaccharides

            B.        Storage Polysaccharides (Fig. 5.6)

                        1.         Starch - the storage carbohydrate in plants - formed by linking many glucose units using dehydration synthesis; α-glucose has the hydroxyl group of C₁ below the plane of the ring while β-glucose has the hydroxyl group of C₁ above the plane of the ring. The isomer of glucose (and, therefore, the position of the oxygen molecule) determines whether α- or β-glucose is formed. Starch is made using α 1-4 linkages between monomers of α-glucose.

                                    a          amylose - straight chain carbohydrate - up to 1000 glucose

                                    b          amylopectin - branches of 24-36 glucose off main chain (β 1-6 linkage); 1000-6000 glucose

                        2.         Glycogen - the storage carbohydrate in animals; glycogen is more extensively branched than amylopectin to increase the efficiency of storage. Why?; glycogen is stored in liver and muscle; humans store enough glycogen for about 1 day; the levels of blood glucose and glycogen are controlled by insulin and glucagon. Insulin promotes the storage of glucose while glucagon promotes its release.

            C.        Structural Polysaccharides (p. 68)

                        1.         Cellulose - the structural component of the plant cell wall; about 50% all organic carbon in biosphere is tied up in cellulose. Globally plants produce 10¹¹ t cellulose per year. It is formed from glucose monomers connected by dehydration synthesis in β 1-4 linkages. The β link has the oxygen on C₁ above the plane of the ring so cellulose has a totally different shape from starch; tends not to coil (Fig. 2.14N); enzymes which digest starch by hydrolyzing α bonds cannot recognize β links and so cannot digest cellulose. Cellulose is called fiber or roughage in our diet. Why is cellulose an important part of a healthy diet?

                        2.         Chitin - the structural component in the exoskeleton of arthropods. It is found in the fungal cell wall rather than cellulose as in plants.

III.       Lipids (p. 70) - nonpolar (hydrophobic) compounds that are insoluble in water.

            A.        Fats

                        1.          Many fats are triglycerides made by dehydration synthesis of glycerol and 3 fatty acids (Fig. 5.10).

                        2.         The C-H bonds in the tails are the reason fats are hydrophobic.

                        3.         The main purpose is energy storage; lipids store >2x energy per gram as carbohydrate; Why did fat evolve?

                                    a          Saturated lipids (called fats) - contain the maximum possible hydrogen atoms; no double bonds; “straight” chains; most animal fats are saturated; solid at room temperature; e.g., bacon grease, lard, butter (Fig 5.11)

                                    b          Unsaturated lipids (called oils) - missing one or more hydrogen atoms, resulting in double bonds which cause the chains to “kink” or “bend”; plant fats and those of fish are unsaturated; liquid at room temperature because kinks prevent close packing of molecules; e.g., canola oil, peanut oil. Why are most plant oils found in the seeds of the plant? If peanut butter is made from peanuts (a plant) why is it solid rather than liquid?

            B.        Phospholipids - in a triglyceride, one fatty acid is replaced with a phosphate. The negative charge(s) of the phosphate makes the “head” of the phospholipid hydrophilic. The long, hydrocarbon tail is non-polar and, therefore, hydrophobic (Fig 5.12)

            C.        Waxes - long chain lipids joined to an alcohol or carbon ring; function in waterproofing; e.g., plant cuticle, feathers.

            D.        Steroids - display characteristic 4 interconnected rings; cholesterol is the precursor for most steroids and is an important component in the cell membrane (Fig 5.14)

IV.      Proteins - (p. 73) the primary structural and functional components of cells; 50% of dry weight of cell; What are some important dietary sources of protein? If you eat plenty of chicken, why don’t you turn into a chicken?

            A.        Uses (Table 5.1)

                        1.         Support - collagen, elastin, keratin

                        2.         Storage of amino acids - ovalbumin, casein

                        3.         Transport - hemoblobin

                        4.         Communication

                                    a          hormones - insulin

                                    b          neurotransmitters - dopamine

                        5.         Receptors - cell membrane proteins

                        6.         Movement - actin, myosin

                        7.         Defense - antibodies

                        8.         Reactions - enzymes

            B.        Formation

                        1.         Proteins are made from linking together long chains (sound familiar?) of amino acid building blocks (Fig 5.15); dehydration synthesis forms a peptide bond between two adjacent amino acids; many amino acids linked together is called a polypeptide. Is a polypeptide the same as a protein?

                        2.         Amino acids differ from each other only by a variable part of the molecule called the R group. Based on the R group, amino acids are categorized into three types. Each type has characteristics which cause the amino acid to behave differently in different environments. This is important for the formation of the three dimensional shape of proteins. The shape of the protein is important for its specific function.

                                    a          polar - the R group contains poalr O-H or N-H bonds

                                    b          non-polar - the R group contains nonpolar C-H bonds

                                    c          charged - the R group contains either a charged carboxyl or amino group

            C.        Structure - (p. 77) a polypeptide folds spontaneously into a specific shape; the shape is determined by the amino acid sequence and is reinforced by interactions between R groups

                        1.         Primary structure (Fig. 5.18) - the specific sequence of amino acids; Does every protein have a unique amino acid sequence?

                        2.         Secondary structure - H-bonds cause segments of the protein to be coiled or folded (Fig 5.20)

                                    a          α-helix

                                    b          pleated sheet

                        3.         Tertiary structure - results from interactions between amino acid side chains (Fig. 5.22)

                                    a          hydrophobic/hydrophilic - a polar amino acid will “prefer” to be in a polar environment. For example, imagine a protein in an aqueous environment (i.e., polar) which has a series of non-polar amino acids as part of its primary structure. This section of the polypeptide will be found inside the protein away from the polar environment. This contributes to its overall shape.

                                    b          electrostatic - segments of the polypeptide can be held together by ionic bonds using amino acids of opposite charge.

                                    c          disulfide bridges - very strong chemical bonds formed between the -SH groups of two cysteine monomers.

                                    d          H-bonds - weak interactions which can be used to reinforce sections of three dimensional shape.

                        4.         Quaternary structure (Fig. 5.23) - 2 or more polypeptide chains associate to form the complete protein

            D.        Denaturation - disrupting native (or natural) conformation; if denaturation not too great the protein may return to its native conformation; proteins can be denatured in several ways. How could each of them disrupt the protein conformation?

                        1.         pH

                        2.         salt

                        3.         heat

                        4.         different solvent

                        5.         chemical treatment

            E.        Protein folding

                        1.         In order to fold proteins into such complex shapes, several steps are required.

                        2.         Chaperone proteins function as temporary braces to hold parts of the polypeptide in place as interactions between R groups are formed.

V.        Nucleic Acids - (p. 83) DNA and RNA are polymers formed by linking together long chains (here we go again) of nucleotide monomers. A nucleotide is formed from a 5 carbon sugar, a phosphate and a nitrogen base.

            A.        Nucleic acids and evolution (Table 5.2) - just as your DNA is more similar to your siblings than to your neighbour, so the DNA of two closely related species is more similar than two distantly related species. We can use DNA similarities to establish evolutionary relationships.