What are the axes, intercepts, and slope on a Lineweaver-Burk double-reciprocal plot?

• x-axis: 1/[S] • y-axis: 1/v0 • x-intercept: -1/Km • y-intercept: 1/Vmax • Slope: Km / Vmax.

What is the structural difference between alpha-D-glucose and beta-D-glucose?

They are anomers differing in configuration at C-1 (the anomeric carbon). In Haworth projection: alpha-D-glucose has the C-1 -OH group pointing DOWN (trans to C-6 -CH2OH); beta-D-glucose has the C-1 -OH pointing UP (cis to C-6, equatorial in chair conformation, more stable).

What are the three primary Ketone Bodies and under what metabolic conditions are they synthesized?

Acetoacetate, beta-Hydroxybutyrate, and Acetone (non-metabolized byproduct exhaled). Synthesized in hepatic mitochondrial matrix during prolonged fasting, starvation, or uncontrolled type 1 diabetes when oxaloacetate is depleted by gluconeogenesis.

What is the Michaelis-Menten equation and what does Km represent?

v0 = (Vmax * [S]) / (Km + [S]). Km is the substrate concentration at which the initial reaction velocity is half-maximal (v0 = Vmax / 2). A lower Km indicates higher enzyme-substrate affinity.

What shuttle transports activated fatty acyl-CoA into the mitochondrial matrix for beta-oxidation?

The Carnitine Shuttle. Carnitine Palmitoyltransferase-1 (CPT-1) on the outer mitochondrial membrane is the rate-limiting enzyme, allosterically inhibited by Malonyl-CoA (preventing simultaneous synthesis and breakdown).

How does 2,4-Dinitrophenol (DNP) act as an uncoupler of oxidative phosphorylation?

DNP is a lipid-soluble proton ionophore that transports H+ across the inner mitochondrial membrane, dissipating the proton gradient. Electron transport runs at maximum rate, oxygen consumption increases, ATP synthesis stops, and energy is released entirely as heat (hyperthermia).

Which seven standard amino acids have nonpolar, aliphatic side chains?

Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), and Proline (Pro, P). Glycine is achiral; Proline has a cyclic pyrrolidine side chain that disrupts alpha-helices.

Which two amino acids are negatively charged (acidic) at physiological pH (7.4)?

Aspartate / Aspartic acid (Asp, D, pKa ~3.9) and Glutamate / Glutamic acid (Glu, E, pKa ~4.2). Both carry deprotonated carboxylate side chains (-COO-) with a net charge of -1 at pH 7.4.

What gives the peptide bond its planar geometry and rigidity?

Resonance delocalization of the lone pair on the amide nitrogen into the carbonyl group gives the C-N peptide bond ~40% double-bond character, preventing free rotation around the C-N bond.

What forces stabilize primary, secondary, tertiary, and quaternary protein structures?

• Primary: Covalent peptide bonds. • Secondary: Hydrogen bonds between backbone carbonyl oxygens and amide hydrogens (alpha-helices, beta-sheets). • Tertiary: Hydrophobic collapse, hydrogen bonds, salt bridges, disulfide bonds between R-groups. • Quaternary: Same non-covalent interactions and disulfide bonds between multiple polypeptide subunits.

What is the rate-limiting enzyme of Fatty Acid Synthesis and where does it take place?

Acetyl-CoA Carboxylase (ACC): Converts Acetyl-CoA to Malonyl-CoA using ATP and Biotin (CO2 carrier). Occurs in the cytoplasm; stimulated by Insulin and Citrate; inhibited by Glucagon and Palmitoyl-CoA.

Which three amino acids have aromatic side chains and which absorbs UV light most strongly at 280 nm?

Phenylalanine (Phe, F), Tyrosine (Tyr, Y), and Tryptophan (Trp, W). Tryptophan absorbs UV light most strongly at 280 nm due to its bicyclic indole ring, followed by tyrosine.

How does a Noncompetitive Inhibitor alter Km, Vmax, and the Lineweaver-Burk plot?

• Binds to an allosteric site on either E or ES complex with equal affinity. • Vmax DECREASES; Km remains UNCHANGED. • Lineweaver-Burk: y-intercept shifts upward (1/Vmax increases); x-intercept is unchanged; slope increases.

How does an Uncompetitive Inhibitor alter Km, Vmax, and the Lineweaver-Burk plot?

• Binds ONLY to the enzyme-substrate (ES) complex at an allosteric site. • Both Km and Vmax DECREASE by the exact same factor (Km / Vmax ratio remains constant). • Lineweaver-Burk: Parallel line shifted upward and to the left (same slope).

How do you calculate the isoelectric point (pI) for neutral, acidic, and basic amino acids?

• Neutral: pI = (pKa1 + pKa2) / 2 • Acidic (Asp, Glu): pI = (pKa_carboxyl + pKa_R-group) / 2 (average of the two lowest pKas) • Basic (Lys, Arg, His): pI = (pKa_amino + pKa_R-group) / 2 (average of the two highest pKas).

What reaction does the Pyruvate Dehydrogenase Complex (PDC) catalyze and where does it occur?

Pyruvate + CoA + NAD+ -> Acetyl-CoA + CO2 + NADH, occurring in the mitochondrial matrix. Irreversible link between glycolysis and the citric acid cycle; allosterically inhibited by Acetyl-CoA, ATP, and NADH.

How does a Competitive Inhibitor alter Km, Vmax, and the Lineweaver-Burk plot?

• Binds to the free enzyme active site. • Km INCREASES (apparent affinity decreases); Vmax remains UNCHANGED (can be overcome by high [S]). • Lineweaver-Burk: x-intercept shifts right (closer to 0); y-intercept is unchanged; slope increases.

What are the rate-limiting enzymes of Glycogenesis and Glycogenolysis?

• Glycogenesis: Glycogen Synthase (forms alpha-1,4 glycosidic bonds; activated by Insulin and Glucose-6-phosphate). • Glycogenolysis: Glycogen Phosphorylase (breaks alpha-1,4 bonds via phosphorolysis; activated by Glucagon, Epinephrine, and AMP; inhibited by ATP).

What is the rate-limiting enzyme of the Citric Acid (Krebs) Cycle and its regulators?

Isocitrate Dehydrogenase: Isocitrate + NAD+ -> alpha-Ketoglutarate + CO2 + NADH. • Inhibited by: ATP and NADH. • Activated by: ADP and NAD+.

What is the role of Cyanide and Carbon Monoxide in the electron transport chain?

Both bind irreversibly to the Fe3+/Fe2+ heme in Cytochrome c Oxidase (Complex IV), halting electron transfer to oxygen, stopping proton pumping, collapsing the proton-motive force, and causing cellular asphyxiation and severe lactic acidosis.

What does a Hill coefficient (nH) greater than 1 indicate about enzyme kinetics?

Positive Cooperativity (sigmoidal/S-shaped saturation curve, like hemoglobin). Substrate binding at one subunit increases the affinity of remaining subunits for subsequent substrate molecules.

What is the function of the Malate-Aspartate Shuttle vs the Glycerol-3-Phosphate Shuttle?

Transfers cytosolic NADH electrons from glycolysis into the mitochondrial matrix: • Malate-Aspartate (heart, liver): Yields ~2.5 ATP per cytosolic NADH. • Glycerol-3-Phosphate (skeletal muscle, brain): Transducts electrons to FAD in Complex II, yielding ~1.5 ATP per NADH.

What are the three irreversible bypass steps of Gluconeogenesis and their corresponding enzymes?

1. Pyruvate -> PEP: Pyruvate Carboxylase (Pyruvate -> Oxaloacetate) + PEP Carboxykinase (PEPCK). 2. Fructose-1,6-bisphosphate -> Fructose-6-P: Fructose-1,6-bisphosphatase (rate-limiting). 3. Glucose-6-P -> Glucose: Glucose-6-Phosphatase (in ER of liver and kidney).

How many ATP molecules are generated per NADH and per FADH2 via oxidative phosphorylation?

~2.5 ATP per mitochondrial NADH and ~1.5 ATP per FADH2 (which donates electrons to Complex II / CoQ, bypassing the 4 protons pumped by Complex I).

Which complexes in the mitochondrial Electron Transport Chain pump protons and where are they pumped?

Complex I (4 H+), Complex III (4 H+), and Complex IV (2 H+) pump a total of 10 H+ per NADH from the mitochondrial matrix into the intermembrane space, generating the proton-motive force. Complex II pumps 0 protons.

Which amino acids are positively charged (basic) at physiological pH (7.4) and what is the pKa of Histidine?

Lysine (Lys, K, side chain pKa ~10.5) and Arginine (Arg, R, pKa ~12.5) are fully protonated (+1). Histidine (His, H) has an imidazole side chain pKa ~6.0, meaning it is ~10% protonated at pH 7.4, allowing it to act as both a proton donor and acceptor in enzyme active sites.

What are the primary metabolic functions and rate-limiting enzyme of the Pentose Phosphate Pathway (PPP)?

Occurs in cytosol; rate-limiting enzyme is Glucose-6-Phosphate Dehydrogenase (G6PDH). • Produces NADPH: For reductive biosyntheses (fatty acids, steroids) and regenerating reduced glutathione against oxidative damage. • Produces Ribose-5-Phosphate: For nucleotide and nucleic acid synthesis.

What is the formula for enzyme catalytic efficiency and what is kcat?

Catalytic Efficiency = kcat / Km. kcat (turnover number) = Vmax / [E]_total, representing the number of substrate molecules converted to product per enzyme active site per unit time (units: s^-1).

What is the committed, rate-limiting step of Glycolysis, its enzyme, and its allosteric regulators?

Fructose-6-phosphate + ATP -> Fructose-1,6-bisphosphate + ADP, catalyzed by Phosphofructokinase-1 (PFK-1). • Activated by: AMP, ADP, and Fructose-2,6-bisphosphate (produced by PFK-2). • Inhibited by: ATP and Citrate.

Which five amino acids have polar, uncharged side chains and which can form covalent disulfide bonds?

Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), and Glutamine (Gln, Q). Cysteine forms covalent disulfide bonds (cystine) via oxidation of its thiol (-SH) group.

What is the net yield of ATP, NADH, and Pyruvate per glucose molecule in aerobic glycolysis?

Net yield per 1 glucose: • 2 ATP net (4 ATP produced via substrate-level phosphorylation minus 2 ATP consumed in investment phase) • 2 NADH • 2 Pyruvate.

What is the net energetic yield per Acetyl-CoA molecule in one turn of the Citric Acid Cycle?

Per 1 Acetyl-CoA: • 3 NADH • 1 FADH2 • 1 GTP (equivalent to 1 ATP via substrate-level phosphorylation) • 2 CO2 released.

Biochemistry Amino Acids, Enzymes & Metabolism

20 standard amino acid structures, pKa values, enzyme kinetics (Michaelis-Menten, Lineweaver-Burk, inhibition types), glycolysis, Krebs cycle, and oxidative phosphorylation.

Level: basic
Languages: en → en
Cards: 32
Markdown: Biochemistry Amino Acids, Enzymes & Metabolism (.md)

Flashcards (32)

#	Front (Term / Question)	Back (Definition / Answer)
1	What are the axes, intercepts, and slope on a Lineweaver-Burk double-reciprocal plot?	• x-axis: 1/[S] • y-axis: 1/v0 • x-intercept: -1/Km • y-intercept: 1/Vmax • Slope: Km / Vmax.
2	What is the structural difference between alpha-D-glucose and beta-D-glucose?	They are anomers differing in configuration at C-1 (the anomeric carbon). In Haworth projection: alpha-D-glucose has the C-1 -OH group pointing DOWN (trans to C-6 -CH2OH); beta-D-glucose has the C-1 -OH pointing UP (cis to C-6, equatorial in chair conformation, more stable).
3	What are the three primary Ketone Bodies and under what metabolic conditions are they synthesized?	Acetoacetate, beta-Hydroxybutyrate, and Acetone (non-metabolized byproduct exhaled). Synthesized in hepatic mitochondrial matrix during prolonged fasting, starvation, or uncontrolled type 1 diabetes when oxaloacetate is depleted by gluconeogenesis.
4	What is the Michaelis-Menten equation and what does Km represent?	v0 = (Vmax * [S]) / (Km + [S]). Km is the substrate concentration at which the initial reaction velocity is half-maximal (v0 = Vmax / 2). A lower Km indicates higher enzyme-substrate affinity.
5	What shuttle transports activated fatty acyl-CoA into the mitochondrial matrix for beta-oxidation?	The Carnitine Shuttle. Carnitine Palmitoyltransferase-1 (CPT-1) on the outer mitochondrial membrane is the rate-limiting enzyme, allosterically inhibited by Malonyl-CoA (preventing simultaneous synthesis and breakdown).
6	How does 2,4-Dinitrophenol (DNP) act as an uncoupler of oxidative phosphorylation?	DNP is a lipid-soluble proton ionophore that transports H+ across the inner mitochondrial membrane, dissipating the proton gradient. Electron transport runs at maximum rate, oxygen consumption increases, ATP synthesis stops, and energy is released entirely as heat (hyperthermia).
7	Which seven standard amino acids have nonpolar, aliphatic side chains?	Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), and Proline (Pro, P). Glycine is achiral; Proline has a cyclic pyrrolidine side chain that disrupts alpha-helices.
8	Which two amino acids are negatively charged (acidic) at physiological pH (7.4)?	Aspartate / Aspartic acid (Asp, D, pKa ~3.9) and Glutamate / Glutamic acid (Glu, E, pKa ~4.2). Both carry deprotonated carboxylate side chains (-COO-) with a net charge of -1 at pH 7.4.
9	What gives the peptide bond its planar geometry and rigidity?	Resonance delocalization of the lone pair on the amide nitrogen into the carbonyl group gives the C-N peptide bond ~40% double-bond character, preventing free rotation around the C-N bond.
10	What forces stabilize primary, secondary, tertiary, and quaternary protein structures?	• Primary: Covalent peptide bonds. • Secondary: Hydrogen bonds between backbone carbonyl oxygens and amide hydrogens (alpha-helices, beta-sheets). • Tertiary: Hydrophobic collapse, hydrogen bonds, salt bridges, disulfide bonds between R-groups. • Quaternary: Same non-covalent interactions and disulfide bonds between multiple polypeptide subunits.
11	What is the rate-limiting enzyme of Fatty Acid Synthesis and where does it take place?	Acetyl-CoA Carboxylase (ACC): Converts Acetyl-CoA to Malonyl-CoA using ATP and Biotin (CO2 carrier). Occurs in the cytoplasm; stimulated by Insulin and Citrate; inhibited by Glucagon and Palmitoyl-CoA.
12	Which three amino acids have aromatic side chains and which absorbs UV light most strongly at 280 nm?	Phenylalanine (Phe, F), Tyrosine (Tyr, Y), and Tryptophan (Trp, W). Tryptophan absorbs UV light most strongly at 280 nm due to its bicyclic indole ring, followed by tyrosine.
13	How does a Noncompetitive Inhibitor alter Km, Vmax, and the Lineweaver-Burk plot?	• Binds to an allosteric site on either E or ES complex with equal affinity. • Vmax DECREASES; Km remains UNCHANGED. • Lineweaver-Burk: y-intercept shifts upward (1/Vmax increases); x-intercept is unchanged; slope increases.
14	How does an Uncompetitive Inhibitor alter Km, Vmax, and the Lineweaver-Burk plot?	• Binds ONLY to the enzyme-substrate (ES) complex at an allosteric site. • Both Km and Vmax DECREASE by the exact same factor (Km / Vmax ratio remains constant). • Lineweaver-Burk: Parallel line shifted upward and to the left (same slope).
15	How do you calculate the isoelectric point (pI) for neutral, acidic, and basic amino acids?	• Neutral: pI = (pKa1 + pKa2) / 2 • Acidic (Asp, Glu): pI = (pKa_carboxyl + pKa_R-group) / 2 (average of the two lowest pKas) • Basic (Lys, Arg, His): pI = (pKa_amino + pKa_R-group) / 2 (average of the two highest pKas).
16	What reaction does the Pyruvate Dehydrogenase Complex (PDC) catalyze and where does it occur?	Pyruvate + CoA + NAD+ -> Acetyl-CoA + CO2 + NADH, occurring in the mitochondrial matrix. Irreversible link between glycolysis and the citric acid cycle; allosterically inhibited by Acetyl-CoA, ATP, and NADH.
17	How does a Competitive Inhibitor alter Km, Vmax, and the Lineweaver-Burk plot?	• Binds to the free enzyme active site. • Km INCREASES (apparent affinity decreases); Vmax remains UNCHANGED (can be overcome by high [S]). • Lineweaver-Burk: x-intercept shifts right (closer to 0); y-intercept is unchanged; slope increases.
18	What are the rate-limiting enzymes of Glycogenesis and Glycogenolysis?	• Glycogenesis: Glycogen Synthase (forms alpha-1,4 glycosidic bonds; activated by Insulin and Glucose-6-phosphate). • Glycogenolysis: Glycogen Phosphorylase (breaks alpha-1,4 bonds via phosphorolysis; activated by Glucagon, Epinephrine, and AMP; inhibited by ATP).
19	What is the rate-limiting enzyme of the Citric Acid (Krebs) Cycle and its regulators?	Isocitrate Dehydrogenase: Isocitrate + NAD+ -> alpha-Ketoglutarate + CO2 + NADH. • Inhibited by: ATP and NADH. • Activated by: ADP and NAD+.
20	What is the role of Cyanide and Carbon Monoxide in the electron transport chain?	Both bind irreversibly to the Fe3+/Fe2+ heme in Cytochrome c Oxidase (Complex IV), halting electron transfer to oxygen, stopping proton pumping, collapsing the proton-motive force, and causing cellular asphyxiation and severe lactic acidosis.
21	What does a Hill coefficient (nH) greater than 1 indicate about enzyme kinetics?	Positive Cooperativity (sigmoidal/S-shaped saturation curve, like hemoglobin). Substrate binding at one subunit increases the affinity of remaining subunits for subsequent substrate molecules.
22	What is the function of the Malate-Aspartate Shuttle vs the Glycerol-3-Phosphate Shuttle?	Transfers cytosolic NADH electrons from glycolysis into the mitochondrial matrix: • Malate-Aspartate (heart, liver): Yields ~2.5 ATP per cytosolic NADH. • Glycerol-3-Phosphate (skeletal muscle, brain): Transducts electrons to FAD in Complex II, yielding ~1.5 ATP per NADH.
23	What are the three irreversible bypass steps of Gluconeogenesis and their corresponding enzymes?	1. Pyruvate -> PEP: Pyruvate Carboxylase (Pyruvate -> Oxaloacetate) + PEP Carboxykinase (PEPCK). 2. Fructose-1,6-bisphosphate -> Fructose-6-P: Fructose-1,6-bisphosphatase (rate-limiting). 3. Glucose-6-P -> Glucose: Glucose-6-Phosphatase (in ER of liver and kidney).
24	How many ATP molecules are generated per NADH and per FADH2 via oxidative phosphorylation?	~2.5 ATP per mitochondrial NADH and ~1.5 ATP per FADH2 (which donates electrons to Complex II / CoQ, bypassing the 4 protons pumped by Complex I).
25	Which complexes in the mitochondrial Electron Transport Chain pump protons and where are they pumped?	Complex I (4 H+), Complex III (4 H+), and Complex IV (2 H+) pump a total of 10 H+ per NADH from the mitochondrial matrix into the intermembrane space, generating the proton-motive force. Complex II pumps 0 protons.
26	Which amino acids are positively charged (basic) at physiological pH (7.4) and what is the pKa of Histidine?	Lysine (Lys, K, side chain pKa ~10.5) and Arginine (Arg, R, pKa ~12.5) are fully protonated (+1). Histidine (His, H) has an imidazole side chain pKa ~6.0, meaning it is ~10% protonated at pH 7.4, allowing it to act as both a proton donor and acceptor in enzyme active sites.
27	What are the primary metabolic functions and rate-limiting enzyme of the Pentose Phosphate Pathway (PPP)?	Occurs in cytosol; rate-limiting enzyme is Glucose-6-Phosphate Dehydrogenase (G6PDH). • Produces NADPH: For reductive biosyntheses (fatty acids, steroids) and regenerating reduced glutathione against oxidative damage. • Produces Ribose-5-Phosphate: For nucleotide and nucleic acid synthesis.
28	What is the formula for enzyme catalytic efficiency and what is kcat?	Catalytic Efficiency = kcat / Km. kcat (turnover number) = Vmax / [E]_total, representing the number of substrate molecules converted to product per enzyme active site per unit time (units: s^-1).
29	What is the committed, rate-limiting step of Glycolysis, its enzyme, and its allosteric regulators?	Fructose-6-phosphate + ATP -> Fructose-1,6-bisphosphate + ADP, catalyzed by Phosphofructokinase-1 (PFK-1). • Activated by: AMP, ADP, and Fructose-2,6-bisphosphate (produced by PFK-2). • Inhibited by: ATP and Citrate.
30	Which five amino acids have polar, uncharged side chains and which can form covalent disulfide bonds?	Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), and Glutamine (Gln, Q). Cysteine forms covalent disulfide bonds (cystine) via oxidation of its thiol (-SH) group.
31	What is the net yield of ATP, NADH, and Pyruvate per glucose molecule in aerobic glycolysis?	Net yield per 1 glucose: • 2 ATP net (4 ATP produced via substrate-level phosphorylation minus 2 ATP consumed in investment phase) • 2 NADH • 2 Pyruvate.
32	What is the net energetic yield per Acetyl-CoA molecule in one turn of the Citric Acid Cycle?	Per 1 Acetyl-CoA: • 3 NADH • 1 FADH2 • 1 GTP (equivalent to 1 ATP via substrate-level phosphorylation) • 2 CO2 released.