ACS Biochemistry Exam Flashcards

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?

Size Signup and view all the answers

How does ion-exchange chromatography work?

Separates sample based on charge. Signup and view all the answers

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

Hydrophobic proteins stick better. Signup and view all the answers

What is the main function of affinity chromatography?

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

What does SDS-PAGE separate based on?

Mass Signup and view all the answers

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

Unfolds proteins and gives them a uniform negative charge. Signup and view all the answers

What does isoelectric focusing utilize for protein separation?

Electrodes and pH gradient. Signup and view all the answers

What does FDNB label in proteins?

The N-terminus of the protein. Signup and view all the answers

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

Reduces disulfide bonds. Signup and view all the answers

What does iodoacetate do to -SH groups?

Adds carboxymethyl groups. Signup and view all the answers

What percentage identity do homologs share?

25% Signup and view all the answers

What are orthologs?

Similar genes in different organisms. Signup and view all the answers

What are paralogs?

Similar 'paired' genes in the same organism. Signup and view all the answers

What does a Ramachandran plot show?

Favorable phi-psi angle combinations. Signup and view all the answers

Why does glycine have a unique Ramachandran plot?

Glycine can adopt more angles. Signup and view all the answers

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

Proline adopts fewer angles. Signup and view all the answers

What are the common amino acids in α-helices?

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

What creates the helix dipole in an α-helix?

The added dipole moments of all hydrogen bonds. Signup and view all the answers

What are the two types of ß-sheets?

Parallel and anti-parallel. Signup and view all the answers

What characterizes an anti-parallel ß-sheet?

Alternating sheet directions. Signup and view all the answers

What defines a parallel ß-sheet?

Same sheet directions. Signup and view all the answers

What are ß-turns and what is their requirement?

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

What distinguishes loops in proteins?

Not highly structured. Signup and view all the answers

How is circular dichroism used in biochemistry?

Uses UV light to measure secondary structure. Signup and view all the answers

What are disulfide bonds?

Bonds between two -SH groups. Signup and view all the answers

What role does ß-mercaptoethanol serve in protein chemistry?

Breaks disulfide bonds. Signup and view all the answers

What is α-keratin composed of?

Two α-helices twisted around each other. Signup and view all the answers

What characterizes collagen's structure?

Repeating sequence of Gly-X-Pro. Signup and view all the answers

How is myoglobin's 4° structure classified?

Symmetric homodimer. Signup and view all the answers

What is unique about hemoglobin's 4° structure?

Tetramer, dimer of dimers. Signup and view all the answers

How distinct are α/ß protein folding regions?

Less distinct areas. Signup and view all the answers

What distinguishes α+ß protein folding?

Two distinct areas of α and ß folding. Signup and view all the answers

What do denaturants do to protein structure?

Stabilize protein backbone in water. Signup and view all the answers

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

Tm Signup and view all the answers

What describes cooperative protein folding?

Folding transition is sharp. Signup and view all the answers

What does a folding funnel illustrate?

3D version of 2D energy states. Signup and view all the answers

What are protein-protein interfaces composed of?

Core is hydrophobic, fringe is hydrophilic. Signup and view all the answers

What do π-π ring stacking interactions involve?

Aromatic rings stacking on each other. Signup and view all the answers

What does a σ-hole refer to?

Area of diminished electron density around the methyl group. Signup and view all the answers

What is the significance of Fe binding to O2?

Fe2+ binds reversibly, Fe3+ binds irreversibly. Signup and view all the answers

What does the Ka for binding equation represent?

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

What does the ϴ-value in binding indicate?

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

What is Kd for binding?

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

What defines high-spin iron?

Electrons are spread out. Signup and view all the answers

What characterizes low-spin iron?

Electrons are less spread out. Signup and view all the answers

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

Heme is in high-spin state. Signup and view all the answers

What describes the R-state of heme?

Heme is in low-spin state. Signup and view all the answers

What occurs during the O2 binding event in hemoglobin?

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

What structure does the hemoglobin binding curve exhibit?

Sigmoidal curve. Signup and view all the answers

What is binding cooperativity?

One subunit change leads other sites to change. Signup and view all the answers

What characterizes homotropic regulation of binding?

Regulatory molecule is also the enzyme's substrate. Signup and view all the answers

What is heterotropic regulation of binding?

An allosteric regulator is present. Signup and view all the answers

What does a Hill plot illustrate?

Turns sigmoid into straight lines. Signup and view all the answers

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

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

How does CO2 affect hemoglobin binding?

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

What is the effect of BPG on hemoglobin?

Reduces hemoglobin's affinity for O2. Signup and view all the answers

What is the Michaelis-Menton equation?

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

What does Km in the Michaelis-Menton equation indicate?

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

What is the Lineweaver-Burke equation?

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

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

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

What does Kcat represent?

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

What does chymotrypsin cleave?

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

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

Changes slope by a factor of α. Signup and view all the answers

What does the uncompetitive inhibition graph illustrate?

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

What best describes mixed inhibition?

Allosteric inhibitor binds either E or ES. Signup and view all the answers

What is the structure of an ionophore?

Hydrophobic molecule that binds ions. Signup and view all the answers

What does the ΔGtransport equation define?

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

What is the difference between pyranose and furanose?

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

What does mutarotation refer to in sugars?

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

What is an anomeric carbon?

Carbon that is cyclized. Signup and view all the answers

What distinguishes α from ß sugars?

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

What is starch, and where is it found?

Found in plants; D-glucose polysaccharide. Signup and view all the answers

What defines the amylose chain structure?

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

What describes amylopectin?

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

What is true about reducing sugars?

Free aldehydes can reduce FeIII or CuIII. Signup and view all the answers

What is glycogen and its primary function?

Found in animals; storage of saccharides. Signup and view all the answers

What type of linkage characterizes cellulose?

ß-1,4-linkage. Signup and view all the answers

What is chitin and where is it found?

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

What are glycoproteins?

Carbohydrates attached to a protein. Signup and view all the answers

What is the function of membrane translocators like flippase?

Speed up membrane flip-flop. Signup and view all the answers

What affects membrane fluidity?

Cis fats increase fluidity, trans fats decrease fluidity. Signup and view all the answers

What defines a Type I integral membrane protein?

C-terminus inside, N-terminus outside. Signup and view all the answers

What is a characteristic of Type II integral membrane proteins?

N-terminus inside, C-terminus outside. Signup and view all the answers

What does a Type III integral membrane protein contain?

Connected protein helices. Signup and view all the answers

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

Contains unconnected protein helices. Signup and view all the answers

What characterizes bacteriorhodopsin?

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

What is unique about ß-barrel membrane proteins?

Can act as a large door. Signup and view all the answers

What does α-hemolysin do?

Assembled to punch holes in membranes. Signup and view all the answers

What is cardiolipin's function?

Ties two proteins together in a membrane. Signup and view all the answers

What happens to RNA in base hydrolysis?

Base hydrolyzes RNA, but not DNA. Signup and view all the answers

What does Chargaff's rule state?

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

What describes the DNA double-helix structure?

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

What defines A-form DNA?

Condensed form with a deeper major groove. Signup and view all the answers

What is the significance of B-form DNA?

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

What characterizes Z-form DNA?

Left-handed helical form. 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.