ACS Biochemistry Exam Flashcards
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Questions and Answers

What is the Henderson-Hasselbach equation?

pH = pKa + log ([A-] / [HA])

What is FMOC used for in chemical synthesis?

  • Separation based on size
  • Attaching ligands to membranes
  • Protecting group on the N-terminus (correct)
  • Changing soluble proteins to precipitate

    • What does salting out achieve in purification?

    It changes soluble protein to solid precipitate.

    What does size-exclusion chromatography separate samples based on?

    <p>Size</p> Signup and view all the answers

    How does ion-exchange chromatography work?

    <p>Separates sample based on charge.</p> Signup and view all the answers

    How do hydrophobic/reverse phase chromatography beads interact with proteins?

    <p>Hydrophobic proteins stick better.</p> Signup and view all the answers

    What is the main function of affinity chromatography?

    <p>To attach a ligand that binds a protein to a bead.</p> Signup and view all the answers

    What does SDS-PAGE separate based on?

    <p>Mass</p> Signup and view all the answers

    What is the function of sodium dodecyl sulfate (SDS)?

    <p>Unfolds proteins and gives them a uniform negative charge.</p> Signup and view all the answers

    What does isoelectric focusing utilize for protein separation?

    <p>Electrodes and pH gradient.</p> Signup and view all the answers

    What does FDNB label in proteins?

    <p>The N-terminus of the protein.</p> Signup and view all the answers

    What is the effect of DTT (dithiothreitol) on proteins?

    <p>Reduces disulfide bonds.</p> Signup and view all the answers

    What does iodoacetate do to -SH groups?

    <p>Adds carboxymethyl groups.</p> Signup and view all the answers

    What percentage identity do homologs share?

    <p>25%</p> Signup and view all the answers

    What are orthologs?

    <p>Similar genes in different organisms.</p> Signup and view all the answers

    What are paralogs?

    <p>Similar 'paired' genes in the same organism.</p> Signup and view all the answers

    What does a Ramachandran plot show?

    <p>Favorable phi-psi angle combinations.</p> Signup and view all the answers

    Why does glycine have a unique Ramachandran plot?

    <p>Glycine can adopt more angles.</p> Signup and view all the answers

    What is the effect of proline on angles in a Ramachandran plot?

    <p>Proline adopts fewer angles.</p> Signup and view all the answers

    What are the common amino acids in α-helices?

    <p>Alanine (Ala) is common, Glycine (Gly) and Proline (Pro) are not.</p> Signup and view all the answers

    What creates the helix dipole in an α-helix?

    <p>The added dipole moments of all hydrogen bonds.</p> Signup and view all the answers

    What are the two types of ß-sheets?

    <p>Parallel and anti-parallel.</p> Signup and view all the answers

    What characterizes an anti-parallel ß-sheet?

    <p>Alternating sheet directions.</p> Signup and view all the answers

    What defines a parallel ß-sheet?

    <p>Same sheet directions.</p> Signup and view all the answers

    What are ß-turns and what is their requirement?

    <p>Tight u-turns with specific phi-psi angles.</p> Signup and view all the answers

    What distinguishes loops in proteins?

    <p>Not highly structured.</p> Signup and view all the answers

    How is circular dichroism used in biochemistry?

    <p>Uses UV light to measure secondary structure.</p> Signup and view all the answers

    What are disulfide bonds?

    <p>Bonds between two -SH groups.</p> Signup and view all the answers

    What role does ß-mercaptoethanol serve in protein chemistry?

    <p>Breaks disulfide bonds.</p> Signup and view all the answers

    What is α-keratin composed of?

    <p>Two α-helices twisted around each other.</p> Signup and view all the answers

    What characterizes collagen's structure?

    <p>Repeating sequence of Gly-X-Pro.</p> Signup and view all the answers

    How is myoglobin's 4° structure classified?

    <p>Symmetric homodimer.</p> Signup and view all the answers

    What is unique about hemoglobin's 4° structure?

    <p>Tetramer, dimer of dimers.</p> Signup and view all the answers

    How distinct are α/ß protein folding regions?

    <p>Less distinct areas.</p> Signup and view all the answers

    What distinguishes α+ß protein folding?

    <p>Two distinct areas of α and ß folding.</p> Signup and view all the answers

    What do denaturants do to protein structure?

    <p>Stabilize protein backbone in water.</p> Signup and view all the answers

    What is the midpoint of the temperature denaturation of protein referred to as?

    <p>Tm</p> Signup and view all the answers

    What describes cooperative protein folding?

    <p>Folding transition is sharp.</p> Signup and view all the answers

    What does a folding funnel illustrate?

    <p>3D version of 2D energy states.</p> Signup and view all the answers

    What are protein-protein interfaces composed of?

    <p>Core is hydrophobic, fringe is hydrophilic.</p> Signup and view all the answers

    What do π-π ring stacking interactions involve?

    <p>Aromatic rings stacking on each other.</p> Signup and view all the answers

    What does a σ-hole refer to?

    <p>Area of diminished electron density around the methyl group.</p> Signup and view all the answers

    What is the significance of Fe binding to O2?

    <p>Fe2+ binds reversibly, Fe3+ binds irreversibly.</p> Signup and view all the answers

    What does the Ka for binding equation represent?

    <p>Ka = [PL] / [P][L]</p> Signup and view all the answers

    What does the ϴ-value in binding indicate?

    <p>ϴ = (bound / total)x100%</p> Signup and view all the answers

    What is Kd for binding?

    <p>Kd = [L] when 50% bound to protein.</p> Signup and view all the answers

    What defines high-spin iron?

    <p>Electrons are spread out.</p> Signup and view all the answers

    What characterizes low-spin iron?

    <p>Electrons are less spread out.</p> Signup and view all the answers

    What is the state of heme in the T-state?

    <p>Heme is in high-spin state.</p> Signup and view all the answers

    What describes the R-state of heme?

    <p>Heme is in low-spin state.</p> Signup and view all the answers

    What occurs during the O2 binding event in hemoglobin?

    <p>O2 binds to T-state and changes the heme to R-state.</p> Signup and view all the answers

    What structure does the hemoglobin binding curve exhibit?

    <p>Sigmoidal curve.</p> Signup and view all the answers

    What is binding cooperativity?

    <p>One subunit change leads other sites to change.</p> Signup and view all the answers

    What characterizes homotropic regulation of binding?

    <p>Regulatory molecule is also the enzyme's substrate.</p> Signup and view all the answers

    What is heterotropic regulation of binding?

    <p>An allosteric regulator is present.</p> Signup and view all the answers

    What does a Hill plot illustrate?

    <p>Turns sigmoid into straight lines.</p> Signup and view all the answers

    What is the Bohr effect in relation to pH and binding affinity?

    <p>As [H+] increases, O2 binding affinity decreases.</p> Signup and view all the answers

    How does CO2 affect hemoglobin binding?

    <p>Forms carbonic acid that shifts hemoglobin to T-state.</p> Signup and view all the answers

    What is the effect of BPG on hemoglobin?

    <p>Reduces hemoglobin's affinity for O2.</p> Signup and view all the answers

    What is the Michaelis-Menton equation?

    <p>V0 = (Vmax[S]) / (Km + [S])</p> Signup and view all the answers

    What does Km in the Michaelis-Menton equation indicate?

    <p>Km = [S] when V0 = 0.5(Vmax)</p> Signup and view all the answers

    What is the Lineweaver-Burke equation?

    <p>It's the reciprocal of the Michaelis-Menton equation.</p> Signup and view all the answers

    What do the slope and intercepts of the Lineweaver-Burke graph represent?

    <p>Slope = Km/Vmax, Y-intercept = 1/Vmax, X-intercept = -1/Km.</p> Signup and view all the answers

    What does Kcat represent?

    <p>Rate-limiting step in enzyme-catalyzed reaction at saturation.</p> Signup and view all the answers

    What does chymotrypsin cleave?

    <p>Proteins on the C-terminal end of Phe, Trp, and Tyr.</p> Signup and view all the answers

    What type of inhibitor has an effect on the slope of the competitive inhibition graph?

    <p>Changes slope by a factor of α.</p> Signup and view all the answers

    What does the uncompetitive inhibition graph illustrate?

    <p>Does not change slope, but changes Km and Vmax.</p> Signup and view all the answers

    What best describes mixed inhibition?

    <p>Allosteric inhibitor binds either E or ES.</p> Signup and view all the answers

    What is the structure of an ionophore?

    <p>Hydrophobic molecule that binds ions.</p> Signup and view all the answers

    What does the ΔGtransport equation define?

    <p>ΔGtransport = RTln([S]out / [S]in) + ZFΔΨ</p> Signup and view all the answers

    What is the difference between pyranose and furanose?

    <p>Pyranose is a 6-membered ring, furanose is a 5-membered ring.</p> Signup and view all the answers

    What does mutarotation refer to in sugars?

    <p>Conversion from α to ß forms at the anomeric carbon.</p> Signup and view all the answers

    What is an anomeric carbon?

    <p>Carbon that is cyclized.</p> Signup and view all the answers

    What distinguishes α from ß sugars?

    <p>α has -OR/OH group opposite of -CH2OH; ß has it on the same side.</p> Signup and view all the answers

    What is starch, and where is it found?

    <p>Found in plants; D-glucose polysaccharide.</p> Signup and view all the answers

    What defines the amylose chain structure?

    <p>Has α-1,4-linkages forming a coiled helix.</p> Signup and view all the answers

    What describes amylopectin?

    <p>Has α-1,4-linkages and periodic α-1,6-linkages.</p> Signup and view all the answers

    What is true about reducing sugars?

    <p>Free aldehydes can reduce FeIII or CuIII.</p> Signup and view all the answers

    What is glycogen and its primary function?

    <p>Found in animals; storage of saccharides.</p> Signup and view all the answers

    What type of linkage characterizes cellulose?

    <p>ß-1,4-linkage.</p> Signup and view all the answers

    What is chitin and where is it found?

    <p>Homopolymer of N-acetyl-ß-D-glucosamine; found in lobsters and beetle shells.</p> Signup and view all the answers

    What are glycoproteins?

    <p>Carbohydrates attached to a protein.</p> Signup and view all the answers

    What is the function of membrane translocators like flippase?

    <p>Speed up membrane flip-flop.</p> Signup and view all the answers

    What affects membrane fluidity?

    <p>Cis fats increase fluidity, trans fats decrease fluidity.</p> Signup and view all the answers

    What defines a Type I integral membrane protein?

    <p>C-terminus inside, N-terminus outside.</p> Signup and view all the answers

    What is a characteristic of Type II integral membrane proteins?

    <p>N-terminus inside, C-terminus outside.</p> Signup and view all the answers

    What does a Type III integral membrane protein contain?

    <p>Connected protein helices.</p> Signup and view all the answers

    What is a defining feature of Type IV integral membrane proteins?

    <p>Contains unconnected protein helices.</p> Signup and view all the answers

    What characterizes bacteriorhodopsin?

    <p>Type III integral membrane protein with 7 connected helices.</p> Signup and view all the answers

    What is unique about ß-barrel membrane proteins?

    <p>Can act as a large door.</p> Signup and view all the answers

    What does α-hemolysin do?

    <p>Assembled to punch holes in membranes.</p> Signup and view all the answers

    What is cardiolipin's function?

    <p>Ties two proteins together in a membrane.</p> Signup and view all the answers

    What happens to RNA in base hydrolysis?

    <p>Base hydrolyzes RNA, but not DNA.</p> Signup and view all the answers

    What does Chargaff's rule state?

    <p>Ratio of A:T and G:C are always equal or close to 1.</p> Signup and view all the answers

    What describes the DNA double-helix structure?

    <p>Opposite strand direction; 3.4Å distance between complementary bases.</p> Signup and view all the answers

    What defines A-form DNA?

    <p>Condensed form with a deeper major groove.</p> Signup and view all the answers

    What is the significance of B-form DNA?

    <p>Watson-Crick model DNA with deep, wide major groove.</p> Signup and view all the answers

    What characterizes Z-form DNA?

    <p>Left-handed helical form.</p> Signup and view all the answers

    Study Notes

    Henderson-Hasselbach Equation

    • pH = pKa + log ([A-] / [HA]) helps relate pH to the concentrations of acids and their conjugate bases in solution.

    FMOC Chemical Synthesis

    • FMOC is a protecting group used in the synthesis of amino acids on a polystyrene bead to facilitate chain elongation.

    Salting Out (Purification)

    • A purification technique that precipitates proteins from a solution by matching their charges to those in the solution.

    Size-Exclusion Chromatography

    • Technique that separates molecules by size, allowing larger molecules to elute first while smaller ones take longer.

    Ion-Exchange Chromatography

    • Method for separating proteins based on charge, where negatively charged DEAE and positively charged CM attract oppositely charged proteins.

    Hydrophobic/Reverse Phase Chromatography

    • Utilizes beads coated with carbon chains, favoring the binding of hydrophobic proteins and eluting them with non-hydrogen bonding solvents.

    Affinity Chromatography

    • Involves attaching a ligand to beads that binds specifically to a target protein, with the potential to elute by using harsh chemicals.

    SDS-PAGE

    • Utilizes SDS to denature proteins for separation based on mass in a polyacrylamide gel, visualized using Coomassie blue dye.

    Sodium Dodecyl Sulfate (SDS)

    • A detergent that unfolds proteins and imparts a uniform negative charge, aiding their separation during electrophoresis.

    Isoelectric Focusing

    • A gel electrophoresis variant where proteins migrate to their isoelectric point (pI), where they are neutral and stop moving.

    FDNB (1-fluoro-2,3-dinitrobenzene)

    • Reacts with N-terminus of proteins to label the first amino acid residue, enabling sequential analysis of amino acid composition.

    DTT (dithiothreitol)

    • A reducing agent that breaks disulfide bonds, often used in protein studies.

    Iodoacetate

    • Reagents that add a carboxymethyl group to free thiol (-SH) groups, effectively blocking disulfide bond formation.

    Homologs, Orthologs, Paralogs

    • Homologs share 25% identity between genes; orthologs are similar genes found in different organisms; paralogs are related genes within the same organism.

    Ramachandran Plot

    • Illustrates favorable phi-psi angle pairs in protein structures, featuring distinct regions for α-helices and β-sheets.

    Glycine and Proline Ramachandran Plots

    • Glycine allows for more flexibility in angle variety; proline has restricted angles due to its cyclic nature.

    α-helices

    • Common α-helix features include Ala prevalence, interaction every 3-4 residues, and a helical turn every 3.6 residues.

    Helix Dipole

    • The helix's dipolar nature arises from hydrogen bonds, with the N-terminus having a partial positive charge and the C-terminus a partial negative charge.

    β-sheets

    • Can be either parallel or anti-parallel; anti-parallel sheets are characterized by straight H-bonds, while parallel sheets have angled H-bonds.

    β-turns

    • Characterized by tight u-turns and specific phi-psi angles, often involving glycine or proline.

    Circular Dichroism

    • A spectroscopy method that utilizes UV light to analyze the secondary structure of proteins, indicating structural stability.

    Disulfide Bonds

    • Form between two thiol groups, playing a critical role in stabilizing protein secondary and tertiary structures.

    α-keratin and Collagen

    • α-keratin forms from coiled α-helices, while collagen consists of a repeating Gly-X-Pro sequence, forming a triple helical structure.

    Hemoglobin Structure

    • Hemoglobin is a tetramer (α2β2) with a cooperative binding mechanism leading to a sigmoidal oxygen binding curve.

    Cooperative Protein Folding

    • Characterized by sharp folding transitions, allowing proteins to revert to native states more readily.

    Protein-Protein Interfaces

    • Comprise a hydrophobic core and a hydrophilic fringe, aiding in protein interactions.

    Binding and Regulation

    • Includes concepts of homotropic and heterotropic regulation where the substrate also acts as a regulator or other factors are involved.

    Michaelis-Menton Equation

    • Describes enzyme kinetics with V0 = (Vmax[S])/(Km + [S]), providing insights into substrate concentration effects.

    Types of Inhibition

    • Competitive inhibition decreases Km while maintaining Vmax; uncompetitive decreases both; mixed inhibition alters both independently.

    Ion Transport

    • Ionophores facilitate the movement of ions across membranes, disrupting concentration gradients.

    Carbohydrates

    • Starch and glycogen serve as polysaccharide energy stores, differing in branching frequency; cellulose forms strong sheets due to β-1,4 linkages.

    Nucleic Acids and Chargaff's Rule

    • DNA contains a double helix structure with complementary base pairing, where the ratio of A:T and G:C is approximately equal.

    DNA Forms

    • A-form DNA is condensed; B-form is the standard Watson-Crick model; Z-form is a left-handed helix with distinct structural properties.

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    Prepare for your ACS Biochemistry exam with these flashcards covering essential concepts. Each card includes key terms like the Henderson-Hasselbalch equation and FMOC chemical synthesis, along with their definitions for quick revision. Perfect for mastering biochemistry topics swiftly.

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