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 structural difference between alpha-D-glucose and beta-D-glucose?

They are anomers differing at C-1 in cyclic glucose. In the usual Haworth view of D-glucopyranose, alpha has the C-1 OH trans to the C-5 CH2OH substituent (drawn down), whereas beta has it cis (drawn up). In the usual 4C1 chair, beta’s anomeric OH is equatorial, helping make beta the more abundant anomer in aqueous equilibrium.

How is mitochondrial NAD+-dependent isocitrate dehydrogenase regulated in the citric acid cycle?

It converts isocitrate + NAD+ → alpha-ketoglutarate + CO2 + NADH + H+. ADP promotes activity; ATP and NADH inhibit it. It is an important regulatory site alongside other cycle enzymes, not the uniquely rate-limiting enzyme under all conditions. NAD+ is a required substrate.

What gives the peptide bond its planar geometry and rigidity?

Resonance delocalizes the amide nitrogen lone pair into the carbonyl group, giving the peptide C–N bond partial double-bond character. This restricts rotation and makes the peptide group approximately planar.

How do cyanide and carbon monoxide impair mitochondrial respiration?

Both can inhibit cytochrome c oxidase (Complex IV), impairing electron transfer to oxygen and oxidative ATP production. Binding to the enzyme can be reversible. Carbon monoxide also binds hemoglobin, reducing oxygen delivery; severe poisoning can cause tissue hypoxia and lactic acidosis.

Which enzymes bypass the three essentially irreversible glycolytic reactions during gluconeogenesis?

Pyruvate → oxaloacetate → PEP uses pyruvate carboxylase and PEP carboxykinase. Fructose-1,6-bisphosphate → fructose-6-phosphate uses fructose-1,6-bisphosphatase. Glucose-6-phosphate → glucose uses glucose-6-phosphatase in the ER, notably in liver and kidney. These are three bypasses involving four enzymes.

Which five amino acids are commonly grouped as polar and uncharged, apart from aromatic tyrosine, and which forms 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 formula for enzyme catalytic efficiency and what is kcat?

Catalytic efficiency is kcat/Km, with units M^−1 s^−1 when concentration is molar. kcat = Vmax/[E]total, where [E]total counts catalytic sites consistently, is the turnover rate per site at saturating substrate (s^−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.

In simple reversible uncompetitive inhibition, how do apparent Km, Vmax and the Lineweaver–Burk plot change?

The inhibitor binds ES rather than free E. Apparent Km and Vmax decrease by the same factor, keeping Km/Vmax unchanged. The double-reciprocal line therefore shifts upward and leftward, parallel to the uninhibited line.

How do long-chain fatty-acid acyl groups enter the mitochondrial matrix for beta-oxidation?

The carnitine shuttle transfers long-chain acyl groups: CPT-1 forms acylcarnitine outside the inner membrane, a translocase exchanges it across that membrane, and CPT-2 regenerates acyl-CoA in the matrix. Malonyl-CoA inhibits CPT-1, limiting entry during fatty-acid synthesis. The shuttle transfers the acyl group, not intact acyl-CoA across the inner membrane.

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.

In the simple reversible competitive-inhibition model, how do apparent Km, Vmax and the Lineweaver–Burk plot change?

The inhibitor binds free enzyme and excludes substrate binding. Apparent Km increases, while Vmax is unchanged because sufficiently high substrate can overcome inhibition. The y-intercept stays at 1/Vmax; the x-intercept moves toward zero and the slope increases.

Which seven standard amino acids are commonly grouped as nonpolar and aliphatic?

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’s ring constrains the backbone and often disrupts or kinks an alpha-helix.

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.

Which key enzymes control glycogen synthesis and breakdown, and how does their regulation differ by tissue?

Glycogen synthase forms alpha-1,4 bonds and is favored by insulin signaling and glucose-6-phosphate. Glycogen phosphorylase releases glucose-1-phosphate by phosphorolysis of alpha-1,4 bonds. Glucagon promotes liver glycogen breakdown; epinephrine acts in liver and muscle. AMP activates muscle phosphorylase, while ATP opposes that activation.

How do you select the pKa values used to calculate an amino acid’s isoelectric point (pI)?

Average the two pKa values that bracket the net-zero-charge form. For an amino acid without an ionizable side chain, these are its alpha-carboxyl and alpha-ammonium pKas. For Asp/Glu use the two carboxyl pKas; for Lys/Arg/His use the two higher pKas. For other ionizable side chains, determine the charge sequence rather than relying only on a “neutral” label.

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.

What does a Hill coefficient greater than 1 indicate in a cooperative binding or substrate-response model?

It indicates positive cooperativity: binding at one site favors further ligand binding, producing a steeper, often sigmoidal response. Hemoglobin oxygen binding is a classic example, although hemoglobin is not an enzyme. The Hill coefficient is not generally the number of binding sites.

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.

What committed glycolytic reaction does PFK-1 catalyze, and how is it regulated?

Fructose-6-phosphate + ATP → fructose-1,6-bisphosphate + ADP. PFK-1 is a major regulatory enzyme: AMP, ADP and fructose-2,6-bisphosphate favor activity, whereas high ATP and citrate inhibit it. Fructose-2,6-bisphosphate is produced by PFK-2; regulatory details vary with tissue and isoform.

How do the malate–aspartate and glycerol-3-phosphate shuttles transfer cytosolic NADH reducing equivalents?

The malate–aspartate shuttle regenerates NADH in the matrix, supporting a conventional yield of about 2.5 ATP per cytosolic NADH. The glycerol-3-phosphate shuttle uses mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenase to reduce CoQ, bypassing Complex I and yielding about 1.5 ATP. That enzyme is not Complex II; neither shuttle moves NADH itself across the inner membrane.

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.

In pure reversible noncompetitive inhibition, how do Km, Vmax and the Lineweaver–Burk plot change?

The inhibitor binds E and ES with equal affinity. Vmax decreases while Km is unchanged. The y-intercept and slope increase; the x-intercept remains −1/Km. Unequal affinity for E and ES gives mixed inhibition, which can also change Km.

What approximate ATP yields are commonly used for mitochondrial NADH and electrons entering at CoQ?

About 2.5 ATP per matrix NADH entering at Complex I and about 1.5 ATP per electron pair entering at CoQ, such as from succinate oxidation through Complex II. Bypassing Complex I yields less proton pumping. These are useful approximate coupling yields, not fixed ATP counts for every condition.

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

In human mitochondria, PDC converts pyruvate + CoA + NAD+ → acetyl-CoA + CO2 + NADH + H+ in the matrix. This essentially irreversible reaction links glycolysis to the citric acid cycle. Acetyl-CoA and NADH inhibit activity; high-energy conditions also favor inhibitory phosphorylation by PDH kinase.

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

Acetoacetate, beta-hydroxybutyrate and acetone. Hepatic mitochondria increase ketone production when fatty-acid oxidation is high and carbohydrate/insulin availability is low, as in prolonged fasting or severe insulin deficiency. Oxaloacetate diversion toward gluconeogenesis can limit acetyl-CoA entry into the citric acid cycle. Acetone is volatile and exhaled, but is not wholly metabolically inert.

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 three amino acids form the usual aromatic group in introductory biochemistry, and which absorbs most strongly at 280 nm?

Phenylalanine (Phe, F), tyrosine (Tyr, Y) and tryptophan (Trp, W). Tryptophan absorbs most strongly at 280 nm, followed by tyrosine; phenylalanine contributes little at that wavelength. Histidine also has an aromatic ring but is usually grouped with basic amino acids.

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

For simple Michaelis–Menten kinetics, v0 = Vmax[S]/(Km + [S]); Km is the substrate concentration giving v0 = Vmax/2. Km is a kinetic parameter, not generally the enzyme–substrate dissociation constant. Interpreting a lower Km as stronger binding requires additional mechanistic assumptions.

How do lysine, arginine and histidine side-chain charges differ at pH 7.4?

Lysine (side-chain pKa about 10.5) and arginine (about 12.5) are overwhelmingly protonated and positively charged. With a histidine side-chain pKa of 6.0, the protonated fraction is 1/(1 + 10^(7.4−6.0)) ≈ 3.8%. Histidine can donate or accept protons; local protein environments can shift these pKa values.

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

DNP carries protons across the inner mitochondrial membrane, dissipating the proton-motive force. This reduces ATP production coupled to electron transport and increases heat release. With adequate substrate and oxygen, respiration and oxygen consumption can rise. The magnitude depends on dose and conditions; neither a universal maximum respiratory rate nor loss of every source of ATP follows.

Biochemistry Amino Acids, Enzymes & Metabolism

Selected biochemistry review: amino-acid properties and acid–base calculations, protein structure, enzyme kinetics, central metabolic pathways 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 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.
2	What is the structural difference between alpha-D-glucose and beta-D-glucose?	They are anomers differing at C-1 in cyclic glucose. In the usual Haworth view of D-glucopyranose, alpha has the C-1 OH trans to the C-5 CH2OH substituent (drawn down), whereas beta has it cis (drawn up). In the usual 4C1 chair, beta’s anomeric OH is equatorial, helping make beta the more abundant anomer in aqueous equilibrium.
3	How is mitochondrial NAD+-dependent isocitrate dehydrogenase regulated in the citric acid cycle?	It converts isocitrate + NAD+ → alpha-ketoglutarate + CO2 + NADH + H+. ADP promotes activity; ATP and NADH inhibit it. It is an important regulatory site alongside other cycle enzymes, not the uniquely rate-limiting enzyme under all conditions. NAD+ is a required substrate.
4	What gives the peptide bond its planar geometry and rigidity?	Resonance delocalizes the amide nitrogen lone pair into the carbonyl group, giving the peptide C–N bond partial double-bond character. This restricts rotation and makes the peptide group approximately planar.
5	How do cyanide and carbon monoxide impair mitochondrial respiration?	Both can inhibit cytochrome c oxidase (Complex IV), impairing electron transfer to oxygen and oxidative ATP production. Binding to the enzyme can be reversible. Carbon monoxide also binds hemoglobin, reducing oxygen delivery; severe poisoning can cause tissue hypoxia and lactic acidosis.
6	Which enzymes bypass the three essentially irreversible glycolytic reactions during gluconeogenesis?	Pyruvate → oxaloacetate → PEP uses pyruvate carboxylase and PEP carboxykinase. Fructose-1,6-bisphosphate → fructose-6-phosphate uses fructose-1,6-bisphosphatase. Glucose-6-phosphate → glucose uses glucose-6-phosphatase in the ER, notably in liver and kidney. These are three bypasses involving four enzymes.
7	Which five amino acids are commonly grouped as polar and uncharged, apart from aromatic tyrosine, and which forms 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.
8	What is the formula for enzyme catalytic efficiency and what is kcat?	Catalytic efficiency is kcat/Km, with units M^−1 s^−1 when concentration is molar. kcat = Vmax/[E]total, where [E]total counts catalytic sites consistently, is the turnover rate per site at saturating substrate (s^−1).
9	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.
10	In simple reversible uncompetitive inhibition, how do apparent Km, Vmax and the Lineweaver–Burk plot change?	The inhibitor binds ES rather than free E. Apparent Km and Vmax decrease by the same factor, keeping Km/Vmax unchanged. The double-reciprocal line therefore shifts upward and leftward, parallel to the uninhibited line.
11	How do long-chain fatty-acid acyl groups enter the mitochondrial matrix for beta-oxidation?	The carnitine shuttle transfers long-chain acyl groups: CPT-1 forms acylcarnitine outside the inner membrane, a translocase exchanges it across that membrane, and CPT-2 regenerates acyl-CoA in the matrix. Malonyl-CoA inhibits CPT-1, limiting entry during fatty-acid synthesis. The shuttle transfers the acyl group, not intact acyl-CoA across the inner membrane.
12	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.
13	In the simple reversible competitive-inhibition model, how do apparent Km, Vmax and the Lineweaver–Burk plot change?	The inhibitor binds free enzyme and excludes substrate binding. Apparent Km increases, while Vmax is unchanged because sufficiently high substrate can overcome inhibition. The y-intercept stays at 1/Vmax; the x-intercept moves toward zero and the slope increases.
14	Which seven standard amino acids are commonly grouped as nonpolar and aliphatic?	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’s ring constrains the backbone and often disrupts or kinks an alpha-helix.
15	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.
16	Which key enzymes control glycogen synthesis and breakdown, and how does their regulation differ by tissue?	Glycogen synthase forms alpha-1,4 bonds and is favored by insulin signaling and glucose-6-phosphate. Glycogen phosphorylase releases glucose-1-phosphate by phosphorolysis of alpha-1,4 bonds. Glucagon promotes liver glycogen breakdown; epinephrine acts in liver and muscle. AMP activates muscle phosphorylase, while ATP opposes that activation.
17	How do you select the pKa values used to calculate an amino acid’s isoelectric point (pI)?	Average the two pKa values that bracket the net-zero-charge form. For an amino acid without an ionizable side chain, these are its alpha-carboxyl and alpha-ammonium pKas. For Asp/Glu use the two carboxyl pKas; for Lys/Arg/His use the two higher pKas. For other ionizable side chains, determine the charge sequence rather than relying only on a “neutral” label.
18	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.
19	What does a Hill coefficient greater than 1 indicate in a cooperative binding or substrate-response model?	It indicates positive cooperativity: binding at one site favors further ligand binding, producing a steeper, often sigmoidal response. Hemoglobin oxygen binding is a classic example, although hemoglobin is not an enzyme. The Hill coefficient is not generally the number of binding sites.
20	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.
21	What committed glycolytic reaction does PFK-1 catalyze, and how is it regulated?	Fructose-6-phosphate + ATP → fructose-1,6-bisphosphate + ADP. PFK-1 is a major regulatory enzyme: AMP, ADP and fructose-2,6-bisphosphate favor activity, whereas high ATP and citrate inhibit it. Fructose-2,6-bisphosphate is produced by PFK-2; regulatory details vary with tissue and isoform.
22	How do the malate–aspartate and glycerol-3-phosphate shuttles transfer cytosolic NADH reducing equivalents?	The malate–aspartate shuttle regenerates NADH in the matrix, supporting a conventional yield of about 2.5 ATP per cytosolic NADH. The glycerol-3-phosphate shuttle uses mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenase to reduce CoQ, bypassing Complex I and yielding about 1.5 ATP. That enzyme is not Complex II; neither shuttle moves NADH itself across the inner membrane.
23	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.
24	In pure reversible noncompetitive inhibition, how do Km, Vmax and the Lineweaver–Burk plot change?	The inhibitor binds E and ES with equal affinity. Vmax decreases while Km is unchanged. The y-intercept and slope increase; the x-intercept remains −1/Km. Unequal affinity for E and ES gives mixed inhibition, which can also change Km.
25	What approximate ATP yields are commonly used for mitochondrial NADH and electrons entering at CoQ?	About 2.5 ATP per matrix NADH entering at Complex I and about 1.5 ATP per electron pair entering at CoQ, such as from succinate oxidation through Complex II. Bypassing Complex I yields less proton pumping. These are useful approximate coupling yields, not fixed ATP counts for every condition.
26	What reaction does the Pyruvate Dehydrogenase Complex (PDC) catalyze and where does it occur?	In human mitochondria, PDC converts pyruvate + CoA + NAD+ → acetyl-CoA + CO2 + NADH + H+ in the matrix. This essentially irreversible reaction links glycolysis to the citric acid cycle. Acetyl-CoA and NADH inhibit activity; high-energy conditions also favor inhibitory phosphorylation by PDH kinase.
27	What are the three primary Ketone Bodies and under what metabolic conditions are they synthesized?	Acetoacetate, beta-hydroxybutyrate and acetone. Hepatic mitochondria increase ketone production when fatty-acid oxidation is high and carbohydrate/insulin availability is low, as in prolonged fasting or severe insulin deficiency. Oxaloacetate diversion toward gluconeogenesis can limit acetyl-CoA entry into the citric acid cycle. Acetone is volatile and exhaled, but is not wholly metabolically inert.
28	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.
29	Which three amino acids form the usual aromatic group in introductory biochemistry, and which absorbs most strongly at 280 nm?	Phenylalanine (Phe, F), tyrosine (Tyr, Y) and tryptophan (Trp, W). Tryptophan absorbs most strongly at 280 nm, followed by tyrosine; phenylalanine contributes little at that wavelength. Histidine also has an aromatic ring but is usually grouped with basic amino acids.
30	What is the Michaelis-Menten equation and what does Km represent?	For simple Michaelis–Menten kinetics, v0 = Vmax[S]/(Km + [S]); Km is the substrate concentration giving v0 = Vmax/2. Km is a kinetic parameter, not generally the enzyme–substrate dissociation constant. Interpreting a lower Km as stronger binding requires additional mechanistic assumptions.
31	How do lysine, arginine and histidine side-chain charges differ at pH 7.4?	Lysine (side-chain pKa about 10.5) and arginine (about 12.5) are overwhelmingly protonated and positively charged. With a histidine side-chain pKa of 6.0, the protonated fraction is 1/(1 + 10^(7.4−6.0)) ≈ 3.8%. Histidine can donate or accept protons; local protein environments can shift these pKa values.
32	How does 2,4-Dinitrophenol (DNP) act as an uncoupler of oxidative phosphorylation?	DNP carries protons across the inner mitochondrial membrane, dissipating the proton-motive force. This reduces ATP production coupled to electron transport and increases heat release. With adequate substrate and oxygen, respiration and oxygen consumption can rise. The magnitude depends on dose and conditions; neither a universal maximum respiratory rate nor loss of every source of ATP follows.