Download Biochemistry ACS Review: Comprehensive Guide to Amino Acids, Protein Structure, and Enzyme and more Exams Biochemistry in PDF only on Docsity!
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What amino acids have nonpolar, aliphatic R groups? - ✔✔Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine What amino acids have polar, uncharged R groups? - ✔✔Serine, Threonine, Cysteine, Asparagine, and Glutamine What amino acids have aromatic R groups? - ✔✔Phenylalanine, Tyrosine, and Tryptophan What amino acids have negatively charged R groups? - ✔✔Aspartate and Glutamate What amino acids have positively charged R groups? - ✔✔Lysine, Arginine, and Histidine What is isoelectric focusing? - ✔✔Proteins are electrophoresed in a pH gradient gel. Each protein will move in the gel as long as the protein contains a charge What does SDS do? - ✔✔It binds to proteins and denatures it. All proteins have same mass/ charge ratio How do you determine the Amino Terminus? - ✔✔1. Make a derivative of the N-terminus with a marker molecule
- Hydrolyze the peptide
- N-terminal AA is identified by chromatography- modified amino acid will elute differently than unmodified AA What molecule does Edman Degradation use? - ✔✔Phenyl Isothiocyanate (PTH) What does Edman Degradation do? - ✔✔It removes one amino acid at a time. The limit is 50 amino acids. After 50 amino acids, the polypeptide must be hydrolyzed into smaller fractions
Where does Cyanogen Bromide cleave? - ✔✔Cleaves only on the caryboxyl side of Methionine residues Where does Trypsin cleave? - ✔✔Trypsin cleaves on the carboxyl side of positive residues such as Arginine and Lysine What happens in Disulfide Position? - ✔✔It is a diagonal electrophoresis. The peptides are cleaved without destroying the disulfide bonds and then exposed to performic acid vapors. The performic acid vapors convert any S-X bond to a SO3-. These fragments will be off the diagonal In Peptide Synthesis, what is the protecting group? - ✔✔Fmoc What is the group that activates amino acid 2? - ✔✔DCC- Dicyclohexylcarbodiimide What acts as the nucleophile in Peptide Synthesis? - ✔✔Amino acid 1 that is connected to the polystyrene bead. What causes the polystyrene bead to disconnect from amino acid 1? - ✔✔HF In what order does peptide synthesis, synthesize amino acids? - ✔✔Carboxy end to the amine end In what order does the body synthesize amino acids? - ✔✔Amino terminus to carboxy terminus What are the hydrogen bonds in Alpha Helix? - ✔✔The carboxyl group is hydrogen bonded with the Hydrogen on the Nitrogen 4 residues away. Alpha helix is clockwise, or right handed Which Beta Pleated sheet is more stable, parallel or antiparallel? - ✔✔Antiparallel, because there is a direct overlap of electrons which creates more stability
What in myoglobin prevents the oxidation of Fe2+ to Fe3+? - ✔✔The polypeptide What causes the heme group to have a lower affinity for CO in myoglobin? - ✔✔The bent conformation The interior of myoglobin is mostly what? - ✔✔Nonpolar residues Myoglobin has mostly what secondary structure? - ✔✔Alpha helices Hemoglobin contains how many subunits? - ✔✔4 and each subunit contains a heme group What does Hemoglobin transport? - ✔✔H+, CO2, and O What does Myoglobin transport? - ✔✔O2 only What happens when O2 binds to one heme in hemoglobin? - ✔✔The affinity will increase in other heme groups Does myoglobin have cooperative binding? - ✔✔NO, there is only one chain What lowers Hemoglobin's affinity for O2? - ✔✔1. Hemoglobin is pH dependent. The affinity for O2 is lowered by a high concentration of H+
- Hemoglobin's affinity for O2 is lowered by CO2 binding
- Hemoglobin's affinity for O2 is lowered by BPG (2,3-bisphosphoglycerate). BPG binds tightly to deoxy Hb What is the Bohr Effect? - ✔✔CO2 and H+ binding to Hb stimulates the release of O2, which occurs rapidly in metabolizing tissues What happens to Hb in the absence of BPG? - ✔✔It binds O2 like myoglobin does
How does BPG bind to Hb? - ✔✔There is a binding pocket in deoxy Hb that consists of positive residues. Negatively charged BPG binds tightly to the pocket. When Hb is oxygenated, the pocket is too small for BPG Why do allosteric interactions occur in Hb? - ✔✔The alpha and beta Hb subunits What happens if the alpha chain of Hb is alone? - ✔✔Hb behaves like Mb and is insensitive to pH, CO2, and BPG What happens to the COO- terminus in oxy and deoxy Hb? - ✔✔Oxy Hb- the COO- terminus have freedom of movement Deoxy Hb- the COO- termini participate in salt linkages, and structure is very rigid In Hb, when are salt linkages formed? - ✔✔In the Tense form. There is a lower affinity for O2. What happens to Fe in deoxy Hb? - ✔✔The Fe atom is out of the plane of the porphyrin ring and will move into the plane upon oxygenation What causes a shift in equilibrium between the Relaxed form and Tense form? - ✔✔When the Fe atom moves into the plane of the polyphyrin ring What happens when the first O2 binds to deoxy Hb? - ✔✔Salt bridges must be broken, most salt bridges will be broken and it becomes easier for more oxygen to bind What does a Hill Plot indicate? - ✔✔Cooperative binding What is indicated in a Hill Plot if n=1? - ✔✔There is no cooperativity When n increases in a Hill Plot, what does that indicate? - ✔✔The increase of cooperativity
What is IgA? - ✔✔The major class in external secretions. First line of defense against bacterial and viral antigens What is IgE? - ✔✔Protects against parasites and is responsible for causing allergic reactions What is IgD? - ✔✔The role is not known What is Complement Fixation? - ✔✔Started by the binding of the Fc region of an antibody to C1 protein. C1 initiates a "membrane attack complex" The MAC inserts into the cell membrane What are Major Histocompatability Complexes (MHC)? - ✔✔Integral proteins that present peptides derived from within the cell on the cell surface What binds to I MHC proteins? - ✔✔Killer T Cells What binds to II MHC proteins? - ✔✔Helper T Cells When is a reaction spontaneous? - ✔✔delta G < 0 Which active site binding causes a conformational change of the enzyme, induced fit or lock and key? - ✔✔Induced fit What is maximum velocity? - ✔✔All of the active sites are filled with substrates What does V=? - ✔✔V= Vmax * [S]/ [S] + Km What is Km? - ✔✔Concentration of substrate needed to fill half of the active sites
In a Lineweaver-Burk plot, what does the y-intercept =? - ✔✔1/ Vmax In a Lineweaver-burk plot, what does the x-intercept=? - ✔✔-1/ Km In a Lineweaver-burk plot, what does the slope=? - ✔✔Km/ Vmax What is the Turnover Number of an Enzyme? - ✔✔Number of substrate molecules converted into products by an enzyme per unit of time, when the enzyme is fully saturated with substrate. K In competitive inhibition, what happens? - ✔✔the molecule binds to the active site. Vmax is not altered and the x-intercept changes In noncompetitive inhibition, what happens? - ✔✔the inhibitor binds somewhere else on the enzyme at the same time the substrate binds. Vmax is alteredd, y-intercept changes
