Study Guide Aid:
* Means that there is an accompanying picture for the question at the end of the section Chapters 1 and 2:
1.) Learn AA structure, 1 and 3-letter names: he has flash cards on his site.
2.) * Know functional groups, bonds, and names of organic compounds common in biochemistry.
3.) * sp2 = results in a trigonal planar structure. sp3 = results in a tetrahedral structure. If carbon has a lone pair or double bond it will be sp2, if all the four bonds on it are single bonds then it is sp3. NH3 = sp3 (N has a lone pair).
4.) Know the Gibbs equation: delta(G) = delta(H) – T(delta)S. Free energy rules the world. -delta(G) = spontaneous/ favorable, releases energy, H<0, S>0. +delta(G) = non-spontaneous/ not favorable, absorbs energy, H>0, S<0. This equation says nothing about the rate of the reaction.
5.) Given a chemical equilibrium, calculate Keq. (Kforward/Kreverse) = [C][D] / [A][B]. [X] = the concentration of X in mol/L. Whenever Keq < 1, the reaction is possible, and the equilibrium favors making the reactant. Keq > 1, means the products are favored. We also discuss several other topics like What are the three levels of the state court system?
6.) Le Chatelier’s Principle states that a system will strive toward equilibrium.
7.) * The electrophiles usually have a positive charge, meaning they want/need electrons to be donated to them: “electron loving”. The nucleophiles usually have a negative charge, meaning they have extra electrons to give/donate: the electrons are “nucleus loving”.
8.) The 4 non-covalent interactions are ionic bonds (or salt bridges), hydrogen bonds, van der waals, and hydrophobic effects. All of these except for the hydrophobic effect are electrostatic interactions. From strongest to weakest: ionic bonds -> hydrogen bonds (within this energy range is the hydrophobic effect) -> van der waals. Ionic bonds involve formal charge. Hydrogen bonds involve dipole-dipole. Van der waals involve induced dipoles.
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9.) Water can accept 4 hydrogen bonds; the oxygen accepts two because there is two lone pairs and each hydrogen accepts one. Any electronegative atom such as O or N can hydrogen bond to H. Any H that is bonded to an electronegative atom can also hydrogen bond to another electronegative atom. Alcohols can take on one more hydrogen bonds since they are already bound to one H. If you want to learn more check out In physics, are scalar and vectors the same?
10.) * The chemical formula is CO(NH2)2.
11.) The distance between the molecules in ice is shorter, this means that the bonds are stronger and therefore have more energy/ are stronger. In liquid water, each water has 3.4 hydrogen bonds. In ice, each water had 4 hydrogen bonds = this means that ice is held together stronger. Don't forget about the age old question of What is the socialist economy?
12.) * 8 hydrogen bonds: 2 on oxygen, 1 on nitrogen, I on each hydrogen.
13.) The hydrophobic effect is when nonpolar substances form cages and aggregate around polar substances and the two eventually separate. This maximizes the hydrogen bonds between water and minimizes the amount of hydrogen bonds between the other substances. “hydrophobic interaction” is a bad term because the hydrophobic and hydrophilic don’t actually interact.
14.) An amphipathic molecule has both nonpolar and polar regions in it like a lipid. A micelle is a ball of lipids with a hydrophobic interior and hydrophilic exterior, they are also self-forming. Detergent molecules form on the surface of water.
15.) Know how the [H3O+] changes with pH unit = it changes by a factor of 10 for every pH unit. pH 0 = 1, pH 2 = 10^-2, pH 14 = 10^-14. The pH of water is 7. The pH of .1 M HCl: HCl = .1 M = .1 H3O+ because it is a strong acid and will break up completely. HCl -> H+ + Cl-: .1 M HCl * (1 mol H+/ 1 mol HCl) = .1 M H. pH = -log[H+] = -log[.1] = 1.0 pH If you want to learn more check out What is ancient greek art?
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16.) pKa is a measure of acid strength. A smaller number means it is more acidic/ stronger. Be able to sketch the Henderson-Hasselbach (titration) curve for a given pKA. If the values are in the acidic range it will be protonated, if it is in the basic area it won’t be. The acid dissociated at the pKa = it is 50% acid and 50% base. If you are adding an acid the curve will move from basic to acidic and vice versa.
17.) pKa tells who wants the proton, tells who the better leaving group is, and tells the buffering range of weak acids/ bases. The leaving group has the lowest pKa in its conjugate acids form. When pH is less than pKa the acidic form will dominate in the solution (the protonated form) and vice versa.
18.) Given pKa, be able to plot the titration curve fothe them and identify on the curve the dominant form of the acid.
19.) * If CO2 leaves, pH goes up. Hyperventilation increases blood pH by removing CO2.
20.) During diabetic ketoacidosis the pH of the blood decreases. At low pHs HCO3- will stabilize it and shift the equilibrium to the left. If the pH is high, there will be reactions with carbonic acids that will shift the equilibrium right. The body tries to maintain the pH, because protein operate at a specific pH.
21.) The paper bag breathing technique increases the amount of CO2 and then that decreases pH. A bicarbonate drip stabilizes the blood’s pH by acting as a buffer.
1.) Know the names of all the 20 natural occurring amino acids. Know the pKa rule of thumb for the alpha amino (~9) and carboxylate group (~3) of the amino acid backbone.
3.) * The L form is found in proteins.
5.) Micelles and proteins both have a hydrophobic interior and hydrophobic exterior.
6.) Hydropathy scales measure the degree of hydrophobic character a residue has. Disadvantage: doesn’t take neighboring residue into account.
7.) Tyrosine at 280 nm is useful for calculating molar concentrations of proteins.
8.) Cysteine can help in redox reactions. BME is 2-mercaptoethanol and it cleaves disulfide bonds. The redox buffer is glutathione: a coenzyme in oxidation reaction in cells and a tripeptide made from glutamic acid, cysteine and glycine
9.) pI = where net charge is 0.
10.) Asp has low pKa (4.1) and likes to donate H. Lys has high pKa (10.8) and likes to keep H. There are far less protonated Asp at high pH. Asp rarely has a proton at 7.5 and it can’t donate, so lysine is more likely to donate.
11.) 3.9 = 1:1, 4.9 = 1:10, and 5.9 = 1:100
12.) Glycine is achiral.
13.) Threonine and isoleucine are both achiral
14.) Amino and carboxyl contribute to the pI of a protein. The difficulty in calculating the pI of a protein is that there are multiple pI’s.
1.) The native conformation is the folded shape is where it is biologically active and with the lowest energy (3-dimensional). Alzheimer’s and mad cow disease are neuro degenerative disorder due to protein misfolding. Prions are infectious agents composed of a protein material that can fold in multiple ways.
2.) Globular proteins are soluble, compact proteins with a hydrophobic core and a polar/charged surface. Fibrous proteins are structural.
3.) Enzymes speed up reaction rate by stabilizing the transition state. They do not participate in the reaction and do not modify the equilibrium.
4.) Through recrystallization (many times), Sumner purified an enzyme and saw that the chemical activity was that of a protein which was named Urease. He also saw that
crystals react with dyes specific for proteins and proteases breakdown proteins and kills urease. He also saw that heat denatures proteins.
5.) Sanger found that there is a precise amino acid sequence and every protein has a unique one. You add amino acids together by taking oxygen off one end and hydrogen off the other. Then, the number of nitrogen’s matches the number of amino acids and only the ends should have a charge.
6.) The process cleaves large protons and not proteases. It removes one residue at a time from the amino end. Phenyl isothiocyanate reacts with the amine and breaks it off. This results in an intact peptide that is shortened by one amino acid and it is a cyclic compound. This process yields the amino acid sequence by knowing the sequence of multiple segments then finding the overlap between them.
7.) Iodoacetate inhibits glycolysis by inhibiting the glycolytic enzyme. It has high reactivity to sulfhydryl cysteine residues and modifies the thiol group.
8.) Homologous proteins share a common ancestor and have similar structures.
9.) The six atoms of the peptide are plane because there are two resonance contributors – the bond between the carbonyl carbon and nitrogen has partial double bond character and rotation about the bond is restricted.
10.) * The four basic assumptions are: there are bulky hydrophobic groups, they obey stereochemical restraints, they expose charged groups or neutralize with salt bridges, and they expose polar groups or satisfy H-bonding.
11.) And I can’t find this question at all.
12.) Secondary structure involves interactions of H-bond doors and acceptors, eesidues of the repeating peptide unit, helices and beta sheets.
13.) Know that the alpha helix is right handed.
14.) An amphipathic helix is the segregation of hydrophobic/polar residues between the opposite faces of the alpha helix at the surface of a water soluble globular protein. Hydrophobic on one side, hydrophilic on the other in the wheel. You can expect the single amphipathic helix to fold, because they would retain shape.
15.) Antiparallel = H-bond between the amino acid across from it. Parallel = H-bonds with two different amino acids across. You can’t have a single sheet because it won’t coil as tightly.
17.) * Ramachandran plot are where the possible angles in amino acids are.
18.) Proline can’t be part of an alpha helix, because it doesn’t have the N-H group for bonding. It can “kink” it – cause very tight turns. It can be that last residue of a chain
19.) Omega 0 degree are cis and 180 degrees is trans. The trans conformation is favored because there are steric clashes in R groups in cis conformation. Proline is sometimes found as cis, because smaller energy difference of Proline between cis and trans states compared to others.
20.) Gly and Pro are often the most conserved residues in homologous protein, because they are small and only found on turns.
21.) Loops connect alpha- and beta- structure by changing direction to fold back on itself to be more compact. A beta turn is a tight loop when carbonyl oxygen forms H bond with amide proton of an amino acid three residues down the chain. Type II seems to violate the plot because it lies in a place only occupied by Glycine which occupies uncommon regions.
22.) Domains are the section of polypeptide that folds independently off the rest. Folds are order and topology of secondary structure elements in a domain- can contain one or more motifs. Motif (secondary structure) – recognizable combination of secondary structure (helices strands and turns) that appear in different proteins and usually associated with a certain function.
24.) Alpha-beta dimer – dimer of two different polypeptides. Alpha2beta2 – two dimers combined. (Alpha-Beta)2 heterotetramer – tetramer of two different homodimers (hemoglobin)
1.) Isoelectric focusing is separation based on pI. A protein is applied to the middle of the gel and an electric current is applied. The proteins migrate to their pI (where there is 0 charge on the protein)
2.) Anion exchange uses a resin containing a positively charged groups for anions to attach to. The exchange is between the anions in the resin being displaced by the anions in the solution. 3.) During gel filtration large proteins elute first. This is the opposite of SDS-PAGE.
4.) Affinity chromatography works by specific interactions between proteins and ligands having high affinity for specific chemical groups on each other. The ligand is immobilized and a protein is passed over it, only the protein with affinity for the ligand will attach and can be separated.
5.) SDS is negatively charged and denatures proteins. It binds to the denatured protein at a constant ratio of one SDS for every two amino acids. This results in the same charge to mass ratio of the proteins; the proteins only differ in mass. The small proteins move faster.
6.) 2-D PAGE is a means of getting high resolution separation of proteins. They are first separated by one dimension by isoelectric focusing then the tray is placed horizontally on top of an SDS gel and electrophoresis is performed in two dimensions. The horizontal separation is based on pI and the vertical is based on mass.
7.) Selenomethionine can be used in x ray crystallography and it is easy to observe it function and structure. It is readily oxidized and used as a substitute for methionine.
8.) Proteins are loaded to the middle of the gel so that they are able to move to the positive and negative end of the gel easier.
9.) Hexahistidine tags are important for immobilized metal affinity chromatography. This is separation based on the protein having the tab.
10.) Gel filtration give the pI of proteins and ultracentrifugation gives the different densities of proteins – the densest are the furthest from the center of the centrifuge.
1.) Know the hemoglobin is an (alpha beta)2 tetramer. Know that Hb and Mh are homologous.
2.) The proximal histidine is the histidine attached on the fifth coordination site. Distal is on the sixth. Hb keep O2 from oxidizing the iron by having it form a hydrogen bond with the distal histidine, is contains a reducing system by transforming methemoglobin into hemoglobin, and the hydrophobic cleft that contain the iron is too small for oxygen to get through and interact with the iron.
3.) * Mb has a hyperbolic curve and hemoglobin has a sigmoidal curve. The significance of Hb’s curve is that is can shift is affinity for oxygen.
4.) Hemoglobin is in the R state when oxygen is bound to it. If it were stuck in this state the body would not get enough oxygen because it would stay attached to Hb. If it were stuck in the T state there would be too much oxygen because oxygen doesn’t bind to the T state. The purpose of the T state in tissues is to release oxygen.
5.) The cooperative mechanism of hemoglobin is that when one oxygen molecule binds to it, the affinity for oxygen goes up and more oxygen bind.
6.) The Bohr Effect is that adding CO2 or H+ decreases the oxygen intake of hemoglobin by stabilizing the T form of the protein by stabilizing salt bridges in the T state. Lower pH means the more O2 is released. H146 has a pKa of 6.5. It would increase the oxygen delivery because the T state would no longer be favored.
7.) Muscles require large amounts of oxygen and generate CO2 and thus decrease pH which then increases the release of oxygen.
8.) An allosteric enzyme is one that changes conformation when bound to an effector. An effector is a small molecule that selectively binds to a protein and regulates biological activity 2,3 BPG helps oxygen to bind to hemoglobin by changing the binding affinity. Whenever pH is lowered BPG unbinds and oxygen is released. This works with the bohr effect.
9.) Training at higher altitudes will make it more strenuous by decreasing the amount of oxygen intake.
10.) Carbonic Anhydrase is a protein that takes bicarbonate and CO2 and forms either one. This aids in buffering blood. Hb helps this by taking in CO2.
11.) Hb acts as the second major buffer system in the blood by taking in and releasing small amount of H+ protons and thus affecting pH. Hb can help to get rid of CO2 in the body by transporting it to the lungs for it to be exhaled and by using it to stabilize its T state.