ACS BIOCHEMISTRY EXAM

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252 Terms

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Henderson-Hasselbach Equation
pH = pKa + log ([A-] / [HA])
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FMOC Chemical Synthesis
Used in synthesis of a growing amino acid chain to a polystyrene bead. FMOC is used as a protecting group on the N-terminus.
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Salting Out (Purification)
Changes soluble protein to solid precipitate. Protein precipitates when the charges on the protein match the charges in the solution.
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Size-Exclusion Chromatography
Separates sample based on size with smaller molecules eluting later.
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Ion-Exchange Chromatography
Separates sample based on charge. CM attracts +, DEAE attracts -. May have repulsion effect on like charges. Salt or acid used to remove stuck proteins.
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Hydrophobic/Reverse Phase Chromatography
Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).
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Affinity Chromatography
Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar ligand.
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SDS-PAGE
Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based off of mass with smaller molecules moving faster. Visualized with Coomassie blue.
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SDS
Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative charge.
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Isoelectric Focusing
Variation of gel electrophoresis where protein charge matters. Involves electrodes and pH gradient. Protein stops at their pI when neutral.
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FDNB (1-fluoro-2,3-dinitrobenzene)
FDNB reacts with the N-terminus of the protein to produce a 2,4-dinitrophenol derivative that labels the first residue. Can repeat hydrolysis to determine sequential amino acids.
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DTT (dithiothreitol)
Reduces disulfide bonds.
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Iodoacetate
Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.
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Homologs
Shares 25% identity with another gene
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Orthologs
Similar genes in different organisms
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Paralogs
Similar "paired" genes in the same organism
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Ramachandran Plot
Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
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Glycine Ramachandran Plot
Glycine can adopt more angles. (H's for R-group).
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Proline Ramachandran Plot
Proline adopts fewer angles. Amino group is incorporated into a ring.
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α-helices
Ala is common, Gly & Pro are not very common. Side-chain interactions every 3 or 4 residues. Turns once every 3.6 residues. Distance between backbones is 5.4Å.
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Helix Dipole
Formed from added dipole moments of all hydrogen bonds in an α-helix. N-terminus is δ+ and C-terminus is δ-.
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ß-sheet
Either parallel or anti-parallel. Often twisted to increase strength.
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Anti-parallel ß-sheet
Alternating sheet directions (C & N-termini don't line-up). Has straight H-bonds.
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Parallel ß-sheet
Same sheet directions (C & N-termini line up). Has angled H-bonds.
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ß-turns
Tight u-turns with specific phi-psi angles. Must have gly at position 3. Proline may also be at ß-turn because it can have a cis-omega angle.
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Loops
Not highly structured. Not necessary highly flexible, but can occasionally move. Very variable in sequence.
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Circular Dichroism
Uses UV light to measure 2° structure. Can be used to measure destabilization.
Uses UV light to measure 2° structure. Can be used to measure destabilization.
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Disulfide-bonds
Bonds between two -SH groups that form between 2° and 3° structure.
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ß-mercaptoethanol
Breaks disulfide bonds.
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α-keratin
formed from 2 α-helices twisted around each other. "Coiled coil". Cross-linked by disulfide bonds.
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Collagen
Repeating sequence of Gly-X-Pro. 3 stranded "coiled coil". Contains gly core.
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Myoglobin 4° Structure
Symmetric homodimer,
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Hemoglobin 4° Structure
Tetramer. Dimer of dimers. α2ß2 tetramer.
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α/ß Protein Folding
Less distinct areas of α and ß folding.
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α+ß Protein Folding
Two distinct areas of α and ß folding.
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Mechanism of Denaturants
Highly soluble, H-binding molecules. Stabilize protein backbone in water. Allows denatured state to be stabilized.
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Temperature Denaturation of Protein
Midpoint of reaction is Tm.
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Cooperative Protein Folding
Folding transition is sharp. More reversible.
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Folding Funnel
Shows 3D version of 2D energy states. Lowest energy is stable protein. Rough funnel is less cooperative.
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Protein-Protein Interfaces
"Core" and "fringe" of the interfaces. Core is more hydrophobic and is on the inside when interfaced. Fringe is more hydrophilic.
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π-π Ring Stacking
Weird interaction where aromatic rings stack on each other in positive interaction.
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σ-hole
Methyl group has area of diminished electron density in center; attracts electronegative groups
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Fe Binding of O2
Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.
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Ka for Binding
Ka = [PL] / [P][L]
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ϴ-value in Binding
ϴ = (bound / total)x100%
ϴ = [L] / ([L] + 1/Ka)
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Kd for binding
Kd = [L] when 50% bound to protein.
Kd = 1/Ka
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High-Spin Fe
Electrons are "spread out" and result in larger atom.
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Low-Spin Fe
Electrons are less "spread out" and are compacted by electron rich porphyrin ring.
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T-State
Heme is in high-spin state. H2O is bound to heme.
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R-State
Heme is in low-spin state. O2 is bound to heme.
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O2 Binding Event
O2 binds to T-state and changes the heme to R-state. Causes a 0.4Å movement of the iron.
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Hemoglobin Binding Curve
4 subunits present in hemoglobin that can be either T or R -state. Cooperative binding leads to a sigmoidal curve.
4 subunits present in hemoglobin that can be either T or R -state. Cooperative binding leads to a sigmoidal curve.
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Binding Cooperativity
When one subunit of hemoglobin changes from T to R-state the other sites are more likely to change to R-state as well. Leads to sigmoidal graph.
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Homotropic Regulation of Binding
Where a regulatory molecule is also the enzyme's substrate.
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Heterotropic Regulation of Binding
Where an allosteric regulator is present that is not the enzyme's substrate.
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Hill Plot
Turns sigmoid into straight lines. Slope = n (# of binding sites). Allows measurement of binding sites that are cooperative.
Turns sigmoid into straight lines. Slope = n (# of binding sites). Allows measurement of binding sites that are cooperative.
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pH and Binding Affinity (Bohr Affect)
As [H+] increases, Histidine group in hemoglobin becomes more protonated and protein shifts to T-state. O2 binding affinity decreases.
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CO2 binding in Hemoglobin
Forms carbonic acid that shifts hemoglobin to T-state. O2 binding affinity decreases. Used in the peripheral tissues.
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BPG (2,3-bisphosphoglycerate)
Greatly reduces hemoglobin's affinity for O2 by binding allosterically. Stabilizes T-state. Transfer of O2 can improve because increased delivery in tissues can outweigh decreased binding in the lungs.
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Michaelis-Menton Equation
V0 = (Vmax[S]) / (Km + [S])
V0 = (Vmax[S]) / (Km + [S])
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Km in Michaelis-Menton
Km = [S] when V0 = 0.5(Vmax)
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Michaelis-Menton Graph
knowt flashcard image
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Lineweaver-Burke Graph
Slope = Km/Vmax
Y-intercept = 1/Vmax
X-intercept = - 1/Km
Slope = Km/Vmax
Y-intercept = 1/Vmax
X-intercept = - 1/Km
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Lineweaver-Burke Equation
Found by taking the reciprocal of the Michaelis-Menton Equation.
Found by taking the reciprocal of the Michaelis-Menton Equation.
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Kcat
Rate-limiting step in any enzyme-catalyzed reaction at saturation. Known as the "turn-over number". Kcat = Vmax/Et
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Chymotripsin
Cleaves proteins on C-terminal endof Phe, Trp, and Tyr
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Competitive Inhibition Graph
Slope changes by factor of α. Slope becomes αKm/Vmax.
X-intercept becomes 1/αKm
Y-intercept does not change.
Vmax does not change.
Slope changes by factor of α. Slope becomes αKm/Vmax.
X-intercept becomes 1/αKm
Y-intercept does not change. 
Vmax does not change.
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Uncompetitive Inhibition Graph
Does not change slope.
Changes Km and Vmax.
Results in vertical shift up and down.
Y-intercept becomes α'/Vmax
X-intercept becomes -α'/Km
Does not change slope.
Changes Km and Vmax. 
Results in vertical shift up and down.
Y-intercept becomes α'/Vmax
X-intercept becomes -α'/Km
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Mixed Inhibition Graph
Allosteric inhibitor that binds either E or ES.
Pivot point is between X-intercept and Y-intercept.
Allosteric inhibitor that binds either E or ES. 
Pivot point is between X-intercept and Y-intercept.
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Non-Competitive Inhibition Graph
Form of mixed inhibition where the pivot point is on the x-axis. Only happens when K1 is equal to K1'.
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Ionophore
Hydrophobic molecule that binds to ions and carries them through cell membranes. Disrupts concentration gradients.
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ΔGtransport Equation
ΔGtransport = RTln([S]out / [S]in) + ZFΔΨ
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Pyranose vs. Furanose
Pyranose is a 6-membered ring.
Furanose is a 5-membered ring.
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Mutarotation
Conversion from α to ß forms of the sugar at the anomeric carbon.
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Anomeric Carbon
Carbon that is cyclized. Always the same as the aldo or keto carbon in the linear form.
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α vs. ß sugars
α form has -OR/OH group opposite from the -CH2OH group.
ß form has -OR/OH group on the same side as the -CH2OH group.
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Starch
Found in plants. D-glucose polysaccharide. "Amylose chain". Unbranched. Has reducing and non-reducing end.
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Amylose Chain
Has α-1,4-linkages that produce a coiled helix similar to an α-helix. Has a reducing and non-reducing end.
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Amylopectin
Has α-1,4-linkages. Has periodic α-1,6-linkages that cause branching. Branched every 24-30 residues. Has reducing and non-reducing end.
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Reducing Sugar
Free aldehydes can reduce FeIII or CuIII. Aldehyde end is the "reducing" end.
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Glycogen
Found in animals. Branched every 8-12 residues and compact. Used as storage of saccharides in animals.
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Cellulose
Comes from plants. Poly D-glucose. Formed from ß-1,4-linkage. Form sheets due to equatorial -OH groups that H-bond with other chains.
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Chitin
Homopolymer of N-acetyl-ß-D-glucosamine. Have ß-1,4-linkages. Found in lobsters, squid beaks, beetle shells, etc.
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Glycoproteins
Carbohydrates attached to a protein. Common outside of the cell. Attached at Ser, Thr, or Asn residues.
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Membrane Translayer Flip-Flop
Typically slow, but can be sped up with Flippase, Floppase, or Scramblase.
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Membrance Fluidity
Membrane must be fluid. Cis fats increase fluidity, trans fats decrease fluidity.
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Type I Integral Membrane Protein
Membrane protein with C-terminus inside and N-terminus outside
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Type II Integral Membrane Protein
Membrane protein with N-terminus inside and C-terminus outside
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Type III Integral Membrane Protein
Membrane protein that contains connected protein helices
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Type IV Integral Membrane Protein
Membrane protein that contains unconnected protein helices
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Bacteriorhodopsin
Type III integral membrane protein with 7 connected helices.
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ß-Barrel Membrane Protein
Can act as a large door. Whole proteins can fit inside.
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α-hemolysin
Secreted as a monomer. Assembles to punch holes in membranes.
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Cardiolipin
"Lipid staple" that ties two proteins (or complexes) together in a membrane. Formed from two phosphoglycerols.
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Hydrolysis of Nucleotides
Base hydrolyzes RNA, but not DNA. DNA is stable in base because of 2' deoxy position.
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Chargaff's Rule
Ratio of A:T and G:C are always equal or close to 1
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DNA Double-Helix
Opposite strand direction. 3.4Å distance between complementary bases. 36Å for one complete turn.
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A-form DNA
Condensed form of DNA. Deeper major groove and shallower minor groove.
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B-form DNA
Watson-Crick model DNA. Deep, wide major groove.
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Z-form DNA
Left-handed helical form of DNA