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Review for Exam Four
Introduction to Organic and Biochemistry
Spring 2016
Chapter 19. Lipids
1. Know what lipids are and how to classify them as saponifiable and nonsaponifiable
2. Know what fatty acids are and how they are classified as saturated, monounsaturated,
or polyunsaturated and how that affects their melting temperatures.
3. Know what waxes are
4. Know what a triacylglycerol is and why some are solid and some are liquid at room
temperature.
5. Know what the products are of oxidation, catalytic hydrogenation or acid or base
hydrolysis of triacylglycerols. What are the conditions for each?
6. Be able to pick out a glycerophospholipid, a sphingolipid, or a sphingoglycolipid from
a “lipid line up”. All three are used to make membranes. Why do they form bilayers
instead of micelles? What do form micelles? Why?
7. All steroids are made from cholesterol and have a steroid nucleus.
8. Fat -soluble vitamins are hydrophobic molecules used in our bodies; vitamin A for
vision, vitamin E as an antioxidant vitamin K for clotting, vitamin D for Ca2+
metabolism.
9. Know the function of and what is in a membrane. Be able to draw and label a
membrane including what is in the cell and out of the cell.
10. Know how molecules enter and exit the cell. There are three ways, understand them.
Chapter 20. Proteins
1. Know why proteins are important
2. Amino acids are the monomer units of proteins. Know their structure. If presented
with an amino acid, be able to tell what classification it should follow: hydrophobic,
polar-uncharged, acidic, or basic. All but glycine are chiral and L.
3. Amino acids are affected by pH. Be able to draw amino acids (if given a structure) at
a pH of 7. What is pI? What is a zwitterion?
4. Be able to make a peptide if given amino acids to work with.
7. Know that the primary structure of proteins is the amino acid sequence and the peptide
bond that joins them, which determines all other levels of structure.
8. Secondary structure is the recognizable patterns seen in protein structure; α-helix, βsheet and β-turns. Random loops are seen, but are not true secondary structure. Hbonding holds these structures together.
9. Tertiary structure is the unique 3-D structure of a protein. How is this structure
attained? The protein only works (has activity) in this structure. This structure is held
together by IAF and by disulfide bridges (cystine bridges) which are covalent. This
structure can be destroyed (denatured) by use of denaturants which break the IAF, but not
the covalent bonds (other than disulfides). This structure may have prosthetic groups
held in it. A protein missing its prosthetic group is devoid of activity and is called an
apoprotein.
10. Quaternary structure is when more than one polypeptide is interacting together either
non-covalently or covalently.
11. Fibrous proteins like collagen and keratin are structural proteins which are
hydrophobic. They do not show tertiary structure, just primary, secondary (and I argue
quaternary). They have great strength due to quaternary structure.
12. Keratin, of hair, horn, hooves, skin, wool and shells, has coiled-coils of α-helix which
are attached via disulfide bonds. Giving hair a perm involves these bonds.
13. Collagen, the most abundant protein in vertebrate animals, has a unique collagen
helix due to a preponderance of proline and hydroxyproline in the structure. 3 collagen
helixes coil around one another and held together by H-bonding.
14. Globular proteins like myoglobin and hemoglobin are water soluble and show tertiary
structure. (hemoglobin shows quaternary structure, too.) Hydrophobic amino acids are
sequestered into the center of the protein. Why?
15. Myoglobin carries oxygen in the muscles. It is made mainly of α-helix (8). It has a
heme prosthetic group with Fe2+ in it which actually holds the oxygen.
16. Hemoglobin carries oxygen in the blood within your red blood cells. (Oxygen is not
very soluble in the blood and so hemoglobin is necessary.) The structure of each subunit
resembles myoglobin, but there are four subunits associated non-covalently in its
quaternary structure of 2 α and 2β subunits.
Chapter 21. Nucleic Acids
1. Nucleic acids are biopolymers of nucleotides.
2. Nucleotides are phosphate, base and sugar. (How does that differ from nucleosides?)
Know the difference between purines and pyrimidine bases.
3. DNA is deoxyribonucleic acid. It is made of deoxyribose sugar, phosphate and the
bases adenine, guanine, cytosine and thymine. The 3-D structure of DNA is doublestranded. It adopts a double-helical structure with extensive H-bonding between the
bases. Each strand is opposite the other such that one strand is 53 and the other is
35. The bases bond with their complementary base. (What are the pairings?)
4. RNA is ribonucleic acid. It is made of ribose sugar, phosphate and the bases adenine,
guanine, cytosine and uracil. It has unique 3-D structure, even though it is single
stranded. How?
5. How are DNA and RNA alike and different?
6. Know the central dogma of how DNA is replicated, transcribed into RNA and how
RNA is translated into protein.
7. Know specifics about replication. Where does this happen? How does DNA
polymerase do this? In what direction does it work? What does it need?
8. Know the specifics about transcription. Where does this happen? How does RNA
polymerase do this? In what direction does it work? What does it need? How is
mRNA matured at this point?
9. Know the specifics about translation. Where does this happen? Be able to use the
codon table to decipher an RNA code into the protein code. Understand how this
actually happens via ribosome, tRNA, amino acids, start and stop codons.
10. Know the affect of substitution mutations (sickle-cell disease) and frameshift
mutations. Why are they sometimes really bad and sometimes silent?
Chapter 22. Metabolism and Enzymes: An Overview.
1. Metabolism is the sum of all the reactions in the body. Catabolism is the breakdown
of large biomolecules to smaller ones, anabolism is the build-up of large biomoelcules to
smaller ones.
2. What are the three steps of catabolism? What is the point?
3. ATP is the energy currency of the cell. What does it look like? How is this energy?
4. Enzymes are biological catalysts. How do they increase the rate of a reaction? Why
use them instead of raising temperature or concentration of reactants?
5. How do enzymes do what they do? What is the catalytic site? How do enzymes bind
to their substrates?
6. What are cofactors? Coenzymes? How do we get these into our bodies?
7. Michaelis-Menten kinetics. Know Km, Vmax. Know our three types of reversible
inhibition (competitive, non-competitive, uncompetitive).
8.Know about irreversible inhibition. Why would a transition state analog/ covalent
bonder work this way?