Podcast
Questions and Answers
What is the Henderson-Hasselbach equation?
What is the Henderson-Hasselbach equation?
pH = pKa + log ([A-] / [HA])
What is FMOC used for in chemical synthesis?
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?
What does salting out achieve in purification?
It changes soluble protein to solid precipitate.
What does size-exclusion chromatography separate samples based on?
What does size-exclusion chromatography separate samples based on?
How does ion-exchange chromatography work?
How does ion-exchange chromatography work?
How do hydrophobic/reverse phase chromatography beads interact with proteins?
How do hydrophobic/reverse phase chromatography beads interact with proteins?
What is the main function of affinity chromatography?
What is the main function of affinity chromatography?
What does SDS-PAGE separate based on?
What does SDS-PAGE separate based on?
What is the function of sodium dodecyl sulfate (SDS)?
What is the function of sodium dodecyl sulfate (SDS)?
What does isoelectric focusing utilize for protein separation?
What does isoelectric focusing utilize for protein separation?
What does FDNB label in proteins?
What does FDNB label in proteins?
What is the effect of DTT (dithiothreitol) on proteins?
What is the effect of DTT (dithiothreitol) on proteins?
What does iodoacetate do to -SH groups?
What does iodoacetate do to -SH groups?
What percentage identity do homologs share?
What percentage identity do homologs share?
What are orthologs?
What are orthologs?
What are paralogs?
What are paralogs?
What does a Ramachandran plot show?
What does a Ramachandran plot show?
Why does glycine have a unique Ramachandran plot?
Why does glycine have a unique Ramachandran plot?
What is the effect of proline on angles in a Ramachandran plot?
What is the effect of proline on angles in a Ramachandran plot?
What are the common amino acids in α-helices?
What are the common amino acids in α-helices?
What creates the helix dipole in an α-helix?
What creates the helix dipole in an α-helix?
What are the two types of ß-sheets?
What are the two types of ß-sheets?
What characterizes an anti-parallel ß-sheet?
What characterizes an anti-parallel ß-sheet?
What defines a parallel ß-sheet?
What defines a parallel ß-sheet?
What are ß-turns and what is their requirement?
What are ß-turns and what is their requirement?
What distinguishes loops in proteins?
What distinguishes loops in proteins?
How is circular dichroism used in biochemistry?
How is circular dichroism used in biochemistry?
What are disulfide bonds?
What are disulfide bonds?
What role does ß-mercaptoethanol serve in protein chemistry?
What role does ß-mercaptoethanol serve in protein chemistry?
What is α-keratin composed of?
What is α-keratin composed of?
What characterizes collagen's structure?
What characterizes collagen's structure?
How is myoglobin's 4° structure classified?
How is myoglobin's 4° structure classified?
What is unique about hemoglobin's 4° structure?
What is unique about hemoglobin's 4° structure?
How distinct are α/ß protein folding regions?
How distinct are α/ß protein folding regions?
What distinguishes α+ß protein folding?
What distinguishes α+ß protein folding?
What do denaturants do to protein structure?
What do denaturants do to protein structure?
What is the midpoint of the temperature denaturation of protein referred to as?
What is the midpoint of the temperature denaturation of protein referred to as?
What describes cooperative protein folding?
What describes cooperative protein folding?
What does a folding funnel illustrate?
What does a folding funnel illustrate?
What are protein-protein interfaces composed of?
What are protein-protein interfaces composed of?
What do π-π ring stacking interactions involve?
What do π-π ring stacking interactions involve?
What does a σ-hole refer to?
What does a σ-hole refer to?
What is the significance of Fe binding to O2?
What is the significance of Fe binding to O2?
What does the Ka for binding equation represent?
What does the Ka for binding equation represent?
What does the ϴ-value in binding indicate?
What does the ϴ-value in binding indicate?
What is Kd for binding?
What is Kd for binding?
What defines high-spin iron?
What defines high-spin iron?
What characterizes low-spin iron?
What characterizes low-spin iron?
What is the state of heme in the T-state?
What is the state of heme in the T-state?
What describes the R-state of heme?
What describes the R-state of heme?
What occurs during the O2 binding event in hemoglobin?
What occurs during the O2 binding event in hemoglobin?
What structure does the hemoglobin binding curve exhibit?
What structure does the hemoglobin binding curve exhibit?
What is binding cooperativity?
What is binding cooperativity?
What characterizes homotropic regulation of binding?
What characterizes homotropic regulation of binding?
What is heterotropic regulation of binding?
What is heterotropic regulation of binding?
What does a Hill plot illustrate?
What does a Hill plot illustrate?
What is the Bohr effect in relation to pH and binding affinity?
What is the Bohr effect in relation to pH and binding affinity?
How does CO2 affect hemoglobin binding?
How does CO2 affect hemoglobin binding?
What is the effect of BPG on hemoglobin?
What is the effect of BPG on hemoglobin?
What is the Michaelis-Menton equation?
What is the Michaelis-Menton equation?
What does Km in the Michaelis-Menton equation indicate?
What does Km in the Michaelis-Menton equation indicate?
What is the Lineweaver-Burke equation?
What is the Lineweaver-Burke equation?
What do the slope and intercepts of the Lineweaver-Burke graph represent?
What do the slope and intercepts of the Lineweaver-Burke graph represent?
What does Kcat represent?
What does Kcat represent?
What does chymotrypsin cleave?
What does chymotrypsin cleave?
What type of inhibitor has an effect on the slope of the competitive inhibition graph?
What type of inhibitor has an effect on the slope of the competitive inhibition graph?
What does the uncompetitive inhibition graph illustrate?
What does the uncompetitive inhibition graph illustrate?
What best describes mixed inhibition?
What best describes mixed inhibition?
What is the structure of an ionophore?
What is the structure of an ionophore?
What does the ΔGtransport equation define?
What does the ΔGtransport equation define?
What is the difference between pyranose and furanose?
What is the difference between pyranose and furanose?
What does mutarotation refer to in sugars?
What does mutarotation refer to in sugars?
What is an anomeric carbon?
What is an anomeric carbon?
What distinguishes α from ß sugars?
What distinguishes α from ß sugars?
What is starch, and where is it found?
What is starch, and where is it found?
What defines the amylose chain structure?
What defines the amylose chain structure?
What describes amylopectin?
What describes amylopectin?
What is true about reducing sugars?
What is true about reducing sugars?
What is glycogen and its primary function?
What is glycogen and its primary function?
What type of linkage characterizes cellulose?
What type of linkage characterizes cellulose?
What is chitin and where is it found?
What is chitin and where is it found?
What are glycoproteins?
What are glycoproteins?
What is the function of membrane translocators like flippase?
What is the function of membrane translocators like flippase?
What affects membrane fluidity?
What affects membrane fluidity?
What defines a Type I integral membrane protein?
What defines a Type I integral membrane protein?
What is a characteristic of Type II integral membrane proteins?
What is a characteristic of Type II integral membrane proteins?
What does a Type III integral membrane protein contain?
What does a Type III integral membrane protein contain?
What is a defining feature of Type IV integral membrane proteins?
What is a defining feature of Type IV integral membrane proteins?
What characterizes bacteriorhodopsin?
What characterizes bacteriorhodopsin?
What is unique about ß-barrel membrane proteins?
What is unique about ß-barrel membrane proteins?
What does α-hemolysin do?
What does α-hemolysin do?
What is cardiolipin's function?
What is cardiolipin's function?
What happens to RNA in base hydrolysis?
What happens to RNA in base hydrolysis?
What does Chargaff's rule state?
What does Chargaff's rule state?
What describes the DNA double-helix structure?
What describes the DNA double-helix structure?
What defines A-form DNA?
What defines A-form DNA?
What is the significance of B-form DNA?
What is the significance of B-form DNA?
What characterizes Z-form DNA?
What characterizes Z-form DNA?
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.
