Question 1

Membrane-spanning segments: which amino acids dominate? Which amino acids are most likely to reside within a hydrophobic membrane-anchoring domain of an integral membrane protein?

Accepted Answer

Introduction / Context: Transmembrane helices of proteins traverse lipid bilayers. Their side chains must be compatible with the hydrophobic core of membranes rich in fatty acyl chains. Given Data / Assumptions: Bilayer interior is nonpolar. Membrane-anchoring segments are typically alpha-helical and hydrophobic. We compare amino acid side chain properties. Concept / Approach: Hydrophobic residues (Leu, Ile, Val, Phe, Met, Ala) favor membrane cores. Polar/charged residues (Asp, Glu, Lys, Arg, His) are energetically unfavorable in the hydrocarbon interior unless specifically stabilized (for example, by pores or ion pairs). Step-by-Step Solution: Identify hydrophobic side chains: isoleucine, valine, phenylalanine are strongly hydrophobic.Contrast with options that include polar/charged residues (aspartate, lysine, histidine).Choose the set comprised entirely of hydrophobics. Verification / Alternative check: Kyte–Doolittle hydropathy plots reveal transmembrane segments enriched in these residues. Why Other Options Are Wrong: Inclusion of acidic/basic residues indicates water-exposed or functional sites, not core-spanning regions; serine/threonine/asparagine are polar. Common Pitfalls: Assuming aromatic residues are always surface-exposed; phenylalanine often stabilizes helices in membranes. Final Answer: Isoleucine, valine and phenylalanine.

Question 2

Definition check: what makes an amino acid “essential” in human nutrition? Select the most accurate definition used in biochemistry and dietetics.

Accepted Answer

Introduction / Context: Dietary planning and clinical nutrition rely on the distinction between essential and nonessential amino acids. Essential amino acids must be provided in adequate amounts through food. Given Data / Assumptions: Applies to humans (species dependence exists). Focus is on biosynthetic capability under normal physiology. Concept / Approach: Essential amino acids are those humans cannot synthesize de novo in adequate amounts. They must be ingested. Examples include leucine, isoleucine, valine, lysine, threonine, tryptophan, phenylalanine, methionine, and in some contexts histidine (and arginine conditionally for growth). Step-by-Step Solution: Define “essential” as dietary requirement due to absent or insufficient biosynthesis.Eliminate options that refer to ease of synthesis or unrelated cellular functions.Select the definition stating the body cannot synthesize. Verification / Alternative check: Clinical formulas and RDAs reflect this requirement, ensuring these amino acids are included. Why Other Options Are Wrong: Flagellar motion is unrelated to nutritional classification; “under essential conditions” is vague and incorrect. Common Pitfalls: Confusing “conditionally essential” (for example, during growth or illness) with universally essential amino acids. Final Answer: The body cannot synthesize.

Question 3

Amino acid catabolism: primary product of alanine breakdown During catabolic metabolism, alanine is most directly converted to which central metabolic intermediate?

Accepted Answer

Introduction / Context: Linking amino acid catabolism to central carbon metabolism is crucial for understanding gluconeogenesis and energy production. Alanine plays a central role in the glucose–alanine cycle between muscle and liver. Given Data / Assumptions: We consider standard transamination pathways. Co-substrate for alanine transamination is often alpha-ketoglutarate. Concept / Approach: Alanine aminotransferase (ALT) transfers alanine’s amino group to alpha-ketoglutarate to form glutamate, leaving carbon skeleton pyruvate. In liver, pyruvate can serve as a gluconeogenic substrate, while glutamate releases ammonia for urea synthesis. Step-by-Step Solution: Write reaction: alanine + alpha-ketoglutarate → pyruvate + glutamate.Identify the carbon product entering central metabolism: pyruvate.Relate to pathways: pyruvate ↔ oxaloacetate (via pyruvate carboxylase) or → acetyl-CoA (via PDH). Verification / Alternative check: Elevated ALT in serum reflects hepatic handling of alanine and is a clinical marker. Why Other Options Are Wrong: Fumarate and oxaloacetate arise from other amino acids (for example, aspartate → oxaloacetate, phenylalanine/tyrosine → fumarate); malate is downstream of oxaloacetate; acetyl-CoA is obtained after pyruvate decarboxylation. Common Pitfalls: Confusing direct catabolic product (pyruvate) with downstream conversions. Final Answer: Pyruvate.

Question 4

Amino acid catabolism: principal carbon product of arginine breakdown Catabolic processing of arginine in humans yields which key TCA-linked intermediate as its carbon skeleton end-product?

Accepted Answer

Introduction / Context: Arginine is a urea cycle amino acid. Its catabolism intersects nitrogen disposal and carbon metabolism. Correctly identifying its carbon fate helps in understanding glucogenic versus ketogenic classifications. Given Data / Assumptions: Human hepatic metabolism with functional urea cycle. We track carbon skeleton fate, not transient cycle by-products. Concept / Approach: Arginase hydrolyzes arginine to urea and ornithine. Ornithine converts to glutamate semialdehyde, then to glutamate, which undergoes oxidative deamination/transamination to yield alpha-ketoglutarate. Thus, arginine is glucogenic via alpha-ketoglutarate. Although fumarate appears within the urea cycle (from argininosuccinate cleavage), the principal carbon skeleton end-product after complete catabolism is alpha-ketoglutarate. Step-by-Step Solution: Arginine → ornithine + urea (arginase).Ornithine → glutamate semialdehyde → glutamate.Glutamate → alpha-ketoglutarate (via GDH or transamination).Therefore, the net carbon fate is alpha-ketoglutarate entering the TCA cycle. Verification / Alternative check: Biochemical charts classify arginine as glucogenic through conversion to alpha-ketoglutarate; clinical metabolism texts corroborate this route. Why Other Options Are Wrong: Fumarate is an intermediate generated in the urea cycle from argininosuccinate but not the final carbon skeleton product of arginine’s breakdown; oxaloacetate or succinate are not direct outcomes; acetoacetate would indicate a ketogenic route, which does not apply to arginine. Common Pitfalls: Equating transient urea cycle fumarate formation with the ultimate carbon skeleton product. Final Answer: Alpha-ketoglutarate.

Question 5

Aromatic residues and protein spectroscopy: strongest UV absorption at 280 nm Which pair of amino acids together accounts for the strongest absorbance signal near 280 nm used to estimate protein concentration?

Accepted Answer

Introduction / Context: UV absorbance at 280 nm is a standard method for estimating protein concentration. The signal arises primarily from aromatic side chains with strong electronic transitions in this region. Given Data / Assumptions: We consider typical amino acid chromophores. Assume neutral pH and standard pathlengths for spectrophotometry. Concept / Approach: Tryptophan (Trp) contributes the largest molar absorptivity at 280 nm, followed by tyrosine (Tyr). Phenylalanine absorbs mainly closer to 257 nm and much more weakly at 280 nm. Disulfide-linked cystines also absorb but contribute less than Trp or Tyr. Step-by-Step Solution: Identify primary chromophores: Trp > Tyr > Phe.Select the pair that maximizes 280 nm signal: Trp and Tyr.Exclude pairs lacking strong aromatic transitions at 280 nm. Verification / Alternative check: Common protein assays (A280) and extinction coefficient calculations weight Trp and Tyr residues most heavily. Why Other Options Are Wrong: Threonine, histidine, cysteine, asparagine, proline, glycine, serine lack strong 280 nm absorbance; phenylalanine’s contribution is modest. Common Pitfalls: Overestimating phenylalanine’s role at 280 nm; forgetting that buffer components can also absorb UV. Final Answer: Trp & Tyrosine.

Question 6

Side-chain chemistry: which amino acid contains an imidazole/imidazolium ring? Identify the amino acid whose side chain features the imidazole ring capable of protonation to form an imidazolium.

Accepted Answer

Introduction / Context: Side-chain functional groups determine enzyme catalysis and buffering near physiological pH. Histidine’s imidazole ring has a pKa near 6, enabling it to donate or accept protons in active sites. Given Data / Assumptions: We focus on canonical amino acids. Physiological pH is approximately 7.2–7.4. Concept / Approach: The imidazole ring (neutral) can be protonated to the imidazolium cation. Histidine uniquely bears this ring, making it prevalent in catalytic triads and metal-binding motifs. Step-by-Step Solution: Scan residues: alanine/valine/leucine are aliphatic; cysteine contains a thiol but no imidazole.Identify histidine as the only residue with an imidazole side chain.Conclude histidine is correct. Verification / Alternative check: Active sites of many proteases (for example, serine proteases) require histidine’s proton-transfer capacity. Why Other Options Are Wrong: They lack an imidazole ring and do not exhibit the same acid–base behavior near neutral pH. Common Pitfalls: Confusing histidine with histamine (a decarboxylation product) or with aromatic residues tyrosine/tryptophan. Final Answer: Histidine.

Question 7

Rule of thumb for protein mass calculations: average residue mass When estimating the mass of a polypeptide from its amino acid count, what average mass per residue is typically used?

Accepted Answer

Introduction / Context: Rapid back-of-the-envelope mass estimates are common in proteomics and molecular biology. A practical constant is the average mass of an amino acid residue in a polypeptide. Given Data / Assumptions: Residue mass excludes water lost during peptide bond formation. Typical cellular amino acid composition assumed. Concept / Approach: While free amino acids average about 128–138 Da, formation of a peptide bond removes one molecule of water (approximately 18 Da). Empirically, the average residue mass in proteins is approximated as 110 Da, allowing quick estimates: mass ≈ number_of_residues * 110 Da. Step-by-Step Solution: Recognize “residue” = amino acid minus H2O after polymerization.Use the 110 Da convention for a representative proteome composition.Apply in practice: a 300-residue protein ≈ 33,000 Da (33 kDa). Verification / Alternative check: Detailed calculations using exact sequence and modification states refine this number but rarely deviate massively for rough estimates. Why Other Options Are Wrong: 118 or 150 Da overestimate typical residue mass; 80 or 95 Da underestimate and would produce large errors. Common Pitfalls: Forgetting to include tags, post-translational modifications, or disulfide-linked partners in mass estimates. Final Answer: 110 daltons.

Question 8

Amino acid classification by polarity and charge: Which of the following trios is NOT a sensible grouping based on side-chain polarity/charge properties used in biochemistry courses and protein science?

Accepted Answer

Introduction / Context: Amino acids are commonly grouped by their side-chain properties because polarity and charge strongly influence protein folding, enzyme catalysis, and membrane interactions. Typical sets include nonpolar aliphatic (e.g., Ala, Val, Leu), polar/uncharged (e.g., Ser, Thr, Asn, Gln), aromatic (e.g., Phe, Tyr, Trp), acidic (Asp, Glu), and basic (Lys, Arg, His). Given Data / Assumptions: We are judging whether each trio represents a coherent polarity/charge class. Standard undergraduate/graduate biochemistry conventions apply. Minor nuances (e.g., Tyr being more polar than Phe) are acknowledged but still fit the aromatic set. Concept / Approach: Cohesive groupings share similar polarity/charge: nonpolar aliphatics cluster together; basic residues cluster together; aromatics cluster together; mixing acidic with nonpolar residues is not sensible for polarity grouping. Step-by-Step Solution: Evaluate Ala, Leu, Val → all nonpolar, aliphatic: sensible.Evaluate Arg, His, Lys → basic/positively charged at physiological pH range: sensible (His is weakly basic but grouped here).Evaluate Phe, Trp, Tyr → aromatic set: sensible despite Tyr’s phenolic OH increasing polarity.Evaluate Asp, Ile, Pro → Asp is acidic/polar negative; Ile is strongly hydrophobic; Pro is nonpolar cyclic imino acid: mixed properties → not a sensible polarity group. Verification / Alternative check: Most textbooks and protein parameter tables organize residue properties similarly; hydropathy scales support that Ile/Pro are hydrophobic while Asp is hydrophilic and negatively charged. Why Other Options Are Wrong: Ala, Leu, Val: classic hydrophobic cluster. Arg, His, Lys: basic side chains, engage in salt bridges. Phe, Trp, Tyr: aromatic ring systems often grouped together. Common Pitfalls: Overthinking Tyr’s polarity and assuming it disqualifies the aromatic grouping; forgetting His’s context-dependent charge yet its placement among basics for pedagogy. Final Answer: Asp, Ile, and Pro

Question 9

Proteinogenic diversity: In standard genetic code–based biology, how many different canonical amino acids are incorporated into proteins?

Accepted Answer

Introduction / Context: The central dogma uses a standard set of building blocks to construct proteins. Knowing how many canonical amino acids the ribosome incorporates clarifies genetic coding, post-translational modification, and evolutionary conservation. Given Data / Assumptions: Question refers to the canonical, proteinogenic amino acids encoded by the standard genetic code. Rarely, organisms incorporate selenocysteine (Sec, U) and pyrrolysine (Pyl, O), but these require specialized recoding. Concept / Approach: ‘‘Canonical’’ means the common 20 residues encoded by 61 sense codons in the standard code. Variants (Sec/Pyl) are exceptional and not typically counted in the baseline number. Step-by-Step Solution: Identify the definition: proteinogenic = incorporated by ribosomes under the standard code.Recall the well-established list of 20 amino acids (e.g., Ala, Arg, Asn, …, Val).Select the count ‘‘20’’ as the correct answer. Verification / Alternative check: Genetic code charts universally list 20 common amino acids; Sec and Pyl are exceptional additions through recoding of UGA and UAG respectively. Why Other Options Are Wrong: 3 or 100: biologically incorrect and not reflective of the standard code. An infinite number: proteins use a finite alphabet; diversity arises from sequence and length, not infinite building blocks. Common Pitfalls: Confusing post-translationally modified residues (e.g., hydroxyproline) with distinct encoded amino acids; conflating non-standard amino acid incorporation in synthetic biology with the canonical number. Final Answer: 20

Question 10

Cysteine chemistry: The sulfur-containing side chain of cysteine exhibits which property profile and reactivity toward another cysteine residue?

Accepted Answer

Introduction / Context: Cysteine (Cys) plays an outsized role in protein structure and catalysis due to its thiol (–SH) side chain. Understanding its polarity and reactivity explains disulfide bond formation, metal binding, redox regulation, and active-site chemistry. Given Data / Assumptions: Cysteine side chain = sulfhydryl (thiol). Disulfide formation occurs via oxidation of two cysteine residues to cystine (–S–S–). Physiological aqueous environment makes thiols relatively polar/ionizable. Concept / Approach: The –SH group is polarizable and can be deprotonated to a thiolate (–S^−), increasing nucleophilicity. Two cysteines can oxidize to a disulfide, stabilizing extracellular proteins and secreted peptides; intracellularly, reducing environments often keep cysteines in thiol state. Step-by-Step Solution: Classify polarity: the thiol participates in hydrogen bonding and ionization → broadly hydrophilic relative to aliphatic residues.Identify reactivity: thiol/thiolate is nucleophilic and redox-active.Recognize structural consequence: two cysteines form disulfide bridges that stabilize tertiary/ quaternary structure.Select the description that matches these properties. Verification / Alternative check: Many enzymes (e.g., cysteine proteases) rely on the thiolate’s nucleophilicity; secreted proteins (e.g., antibodies, insulin) contain stabilizing disulfide bonds. Why Other Options Are Wrong: Amphiphilic/hydrophobic: mischaracterizes the thiol’s polar/ionizable nature. None of the above: invalid because cysteine does form disulfides and is reactive. Common Pitfalls: Assuming all sulfur-containing residues are hydrophobic; confusing methionine (thioether, less reactive) with cysteine (thiol, reactive). Final Answer: Hydrophilic, highly reactive, and forms a disulfide with another cysteine

Question 11

Chirality in proteins: What is the stereochemical configuration of the alpha-amino acids found in naturally occurring proteins (ignoring achiral glycine)?

Accepted Answer

Introduction / Context: Biological homochirality is a defining feature of life. Proteins overwhelmingly use the L-enantiomers of amino acids, while sugars in nucleic acids are D-configured. Recognizing this pattern helps in understanding enzyme specificity and peptide synthesis. Given Data / Assumptions: We consider alpha-amino acids encoded by the genetic code. Glycine is achiral and is excluded from the chirality rule. Concept / Approach: Ribosomal protein synthesis selects L-amino acids via aminoacyl-tRNA synthetases and the ribosome. D-amino acids may occur in bacterial cell walls (e.g., D-Ala) but not in ribosomally synthesized proteins. Step-by-Step Solution: Identify convention: proteinogenic amino acids are L-form.Note exception: glycine lacks chirality (R = H).Select ‘‘L’’ as the correct configuration for chiral residues in proteins. Verification / Alternative check: Crystal structures and biochemical analyses confirm L-stereochemistry at alpha carbon for natural proteins; synthetic peptides using D-residues alter folding and protease susceptibility. Why Other Options Are Wrong: D: not used in ribosomal protein synthesis. L and D: mixed chirality does not reflect natural ribosomal products. None: contradicted by extensive structural biology data. Common Pitfalls: Confusing D-amino acids in peptidoglycan or non-ribosomal peptides with ribosomal proteins; mixing up L/D with R/S notation. Final Answer: L

Question 12

Why are serine and threonine classified as polar amino acids? Identify the functional group in their side chains that confers polarity and enables common modifications.

Accepted Answer

Introduction / Context: Serine (Ser) and threonine (Thr) are central to enzyme catalysis, hydrogen bonding, and post-translational modification. Their classification as polar stems from a shared functional group that engages in aqueous interactions and chemistry. Given Data / Assumptions: Ser and Thr both contain side-chain alcohols. Polarity is assessed by capacity for hydrogen bonding and interaction with water. Common PTMs include O-linked glycosylation and phosphorylation. Concept / Approach: The hydroxyl (–OH) group is polar, donates/accepts hydrogen bonds, and serves as a nucleophilic site for kinase-mediated phosphorylation (Ser/Thr kinases) and glycosyltransferase reactions (O-glycans). Step-by-Step Solution: Identify functional group: side-chain alcohol for Ser and Thr.Link to polarity: –OH increases hydrophilicity via hydrogen bonding with solvent and residues.Connect to biology: –OH enables phosphorylation, a core regulatory switch in signaling pathways.Choose the option specifying the hydroxyl group. Verification / Alternative check: Proteomic datasets show abundant Ser/Thr phosphorylation; structural models depict –OH groups forming intra-protein hydrogen bonds that guide folding and active-site geometry. Why Other Options Are Wrong: Sulfhydryl: characteristic of cysteine, not Ser or Thr. Keto/aldehyde: not present in standard amino acid side chains here. Common Pitfalls: Confusing threonine with tyrosine (which is aromatic phenolic OH) or with cysteine (thiol); assuming all polar residues are charged (Ser/Thr are polar uncharged). Final Answer: A reactive hydroxyl (–OH) group in the side chain

Question 13

How do proteins attain higher-order structure? Choose the most complete statement about mechanisms leading to native folding and maturation.

Accepted Answer

Introduction / Context: Protein structure emerges from an interplay of intrinsic sequence information and cellular quality-control systems. Understanding these routes explains why some proteins fold spontaneously while others require cofactors, chaperones, or proteolytic processing. Given Data / Assumptions: Proteins have a thermodynamically favored native state. Cells contain chaperone networks (e.g., Hsp70, GroEL/ES) to assist folding. Many proteins are synthesized with signal peptides or pro-domains that are removed post-translationally. Concept / Approach: Folding can be spontaneous (Anfinsen’s principle), but crowded cytosolic conditions and kinetic traps necessitate chaperone aid. Precursor sequences target proteins to membranes/organelles or keep them inactive until cleavage. Step-by-Step Solution: Recognize self-assembly: many small, soluble proteins fold without helpers.Acknowledge chaperone action: they bind exposed hydrophobics, prevent aggregation, and facilitate productive folding cycles.Account for precursor processing: removal of signal peptides/pro-segments finalizes structure/function.Conclude that all mechanisms are valid and complementary → choose ‘‘All of the above.’’ Verification / Alternative check: Structural biology shows both chaperone-free and chaperone-assisted folding pathways; secretory proteins universally undergo signal peptide cleavage. Why Other Options Are Wrong: Each single mechanism alone is incomplete; real biology uses multiple, context-dependent routes. Common Pitfalls: Thinking chaperones encode folding information (they do not); overlooking proteolytic maturation as part of structural finalization. Final Answer: All of the above

Question 14

Residue mass comparison: Among the twenty standard amino acids, which has the greatest molecular mass and is therefore the heaviest?

Accepted Answer

Introduction / Context: Residue mass affects mass spectrometry interpretation, peptide mobility, and protein engineering. Recognizing the heaviest common residue helps in rapid checks of theoretical peptide masses. Given Data / Assumptions: Compare standard average or monoisotopic masses of side chains. Aromatic residues (Trp, Tyr, Phe) are heavier than aliphatic residues. Concept / Approach: Tryptophan has an indole ring system, giving it the largest side chain and greatest mass among canonical residues. Tyrosine and phenylalanine follow, with histidine lighter due to the imidazole ring. Step-by-Step Solution: Recall relative masses: Trp > Tyr > Phe > His, approximately.Identify the top candidate: tryptophan.Select ‘‘Tryptophan’’. Verification / Alternative check: Mass tables: Trp ~204 Da; Tyr ~181 Da; Phe ~165 Da; His ~155 Da (average masses; monoisotopic similar ordering). Why Other Options Are Wrong: Phenylalanine and tyrosine are heavy but not heavier than tryptophan. Histidine is lighter than the three listed aromatics. Common Pitfalls: Confusing hydrophobicity with mass; assuming tyrosine’s oxygen increases mass above tryptophan (the indole ring still dominates). Final Answer: Tryptophan

Question 15

Ionization constants of alpha-amino acids: Typical pK values are approximately what for the alpha-carboxyl group and the alpha-amino group, respectively?

Accepted Answer

Introduction / Context: The acid–base behavior of amino acids underlies protein charge, buffering, and electrophoresis. Knowing approximate pK values for the alpha-carboxyl and alpha-amino groups helps predict net charge across pH and interpret titration curves. Given Data / Assumptions: We consider typical, average pK values for free amino acids in water. Side-chain pK values vary (e.g., Lys ~10.5, Asp ~3.9), but the backbone groups have characteristic ranges. Concept / Approach: Alpha-carboxyl groups are relatively acidic with pK near ~2.0–2.5; alpha-amino groups are weak bases with pK near ~9.0–10.0. These values explain zwitterion formation near neutral pH. Step-by-Step Solution: Estimate carboxyl pK: ~2.2 (deprotonated above this pH).Estimate amino pK: ~9.4 (protonated below this pH).Match to the provided options → 2.2 and 9.4. Verification / Alternative check: Textbook titration curves for glycine show inflection points consistent with pK1 ~2.3 and pK2 ~9.6, aligning with the selected values. Why Other Options Are Wrong: 1.1/12.1: unrealistically extreme for alpha groups. 6.5/8.0 and 3.3/10.5: do not reflect typical paired values for free alpha groups. Common Pitfalls: Confusing side-chain pK values with backbone pK values; forgetting environmental effects (ionic strength, temperature) shift precise numbers slightly. Final Answer: 2.2 and 9.4

Question 16

Nutrition terminology: Amino acids required in the human diet because they are not synthesized endogenously are termed what?

Accepted Answer

Introduction / Context: Dietary protein quality depends on essential amino acids—those the body cannot synthesize in sufficient amounts. Understanding this term informs meal planning, clinical nutrition, and sports supplementation. Given Data / Assumptions: Humans require a set of amino acids from food (e.g., lysine, tryptophan, leucine). Conditionally essential amino acids can become essential during growth or illness. Concept / Approach: ‘‘Essential’’ refers to dietary indispensability. Complete proteins (e.g., eggs, dairy) supply all essentials; complementary proteins (e.g., grains + legumes) together provide the full set. Step-by-Step Solution: Identify the nutritional term for indispensable amino acids → essential.Rule out distractors that lack specific nutritional meaning in this context.Select ‘‘Essential.’’ Verification / Alternative check: WHO/FAO guidelines list essential amino acids and recommended intakes by age group. Why Other Options Are Wrong: Specialized/Trace/Accessory: not standard categories for amino acids in human nutrition. Common Pitfalls: Confusing ‘‘essential’’ with ‘‘important’’; in nutrition, it has a specific biochemical meaning—dietary requirement. Final Answer: Essential

Question 17

Metabolic fate of leucine: Considering that leucine is a strictly ketogenic amino acid, what is a principal end product of its catabolism?

Accepted Answer

Introduction / Context: Amino acids are categorized as glucogenic, ketogenic, or both based on the metabolic products they yield. Leucine is the prototypical strictly ketogenic amino acid, important in muscle metabolism and signaling via mTOR. Given Data / Assumptions: Leucine catabolism generates acetyl-CoA and acetoacetate but not net glucose precursors. Question asks for a principal end product among provided options. Concept / Approach: Ketogenic amino acids degrade to acetyl-CoA or acetoacetate, feeding ketone body synthesis or the TCA cycle for energy without net gluconeogenesis (since acetyl-CoA carbons are lost as CO2 in TCA). Step-by-Step Solution: Recall leucine pathway: transamination → oxidative decarboxylation → ultimately acetyl-CoA + acetoacetate.Compare options: only acetyl-CoA matches a canonical leucine end product listed.Select ‘‘Acetyl-CoA.’’ Verification / Alternative check: Biochemical charts show leucine as purely ketogenic alongside lysine; both feed acetyl-CoA/acetoacetate pools. Why Other Options Are Wrong: Pyruvate and oxaloacetate are glucogenic entry points; leucine does not yield these. Acetyl carnitine is a transport/storage form derived from acetyl-CoA and carnitine, not the primary metabolic end product itself. Common Pitfalls: Assuming all amino acids can be converted to glucose; overlooking that acetyl-CoA carbons cannot contribute net to gluconeogenesis. Final Answer: Acetyl-CoA

Question 18

Amino acids in biochemistry — Which of the following is best classified as a non-protein (non-proteinogenic) amino acid or amino-acid–related compound that is not incorporated directly into proteins?

Accepted Answer

Introduction / Context: Amino acids can be grouped into standard proteinogenic amino acids (directly encoded by the genetic code), post-translationally modified amino acids found in proteins, and non-protein amino acids that occur in metabolism but are not incorporated into polypeptide chains. Distinguishing these categories is essential for understanding protein structure, metabolism, and analytical methods. Given Data / Assumptions: Dopamine is a catecholamine neurotransmitter derived from tyrosine. Hydroxylysine is a post-translational modification of lysine found in collagen. Cystine is the disulfide-linked dimer of cysteine commonly present in folded proteins. The task is to select the option that is a non-protein amino acid or related compound not incorporated into proteins. Concept / Approach: Proteinogenic amino acids are the 20 standard residues (plus selenocysteine and pyrrolysine in special cases). Post-translational modifications (e.g., hydroxylysine, hydroxyproline) are present within proteins after enzymatic modification. Non-protein amino acids or amino-acid–related compounds may be biosynthesized and physiologically important, yet they are not used by ribosomes to build proteins. Step-by-Step Solution: Classify dopamine: it lacks the carboxylate group typical of amino acids and functions as a neurotransmitter, not as a building block of proteins.Classify hydroxylysine: formed by enzymatic hydroxylation of lysine residues in collagen; it is a bona fide amino acid derivative present in proteins.Classify cystine: occurs when two cysteine residues form a disulfide bond; frequently found stabilizing protein tertiary/tertiary structures.Therefore, the non-protein option is dopamine. Verification / Alternative check: Analytical biochemistry texts list dopamine among biogenic amines rather than amino acids. In contrast, hydroxylysine and cystine are routinely detected during protein hydrolysis and structural studies. Why Other Options Are Wrong: Hydroxylysine: post-translationally modified amino acid within collagen; not “non-protein.” Cystine: a common protein component formed from two cysteines; present in many extracellular proteins. None of these: incorrect because dopamine fits the description. Common Pitfalls: Equating “not one of the 20” with “non-protein.” Some nonstandard residues (e.g., hydroxylysine) are indeed in proteins after modification, whereas small amines like dopamine are not incorporated into polypeptides. Final Answer: Dopamine

Question 19

Human nutrition and metabolism — Which of the following is not an essential amino acid for humans (i.e., it can be synthesized endogenously)?

Accepted Answer

Introduction / Context: Essential amino acids must be obtained from the diet because humans cannot synthesize their carbon skeletons. Nonessential amino acids can be synthesized de novo. Recognizing which amino acids are essential helps in clinical nutrition, formulation of culture media, and dietary planning. Given Data / Assumptions: Aspartic acid, glutamic acid, and glycine are listed. We use the standard human classification (not specific to other organisms or life stages). “Essential” refers to dietary indispensability for adults. Concept / Approach: The canonical essential amino acids for adult humans are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine (plus conditionally essential residues depending on state). Aspartate, glutamate, and glycine are nonessential because metabolic pathways (e.g., transamination, one-carbon metabolism) can supply them. Step-by-Step Solution: Check each candidate against the essential list.Aspartic acid: produced via transamination of oxaloacetate → nonessential.Glutamic acid: synthesized from alpha-ketoglutarate via transamination or glutamate dehydrogenase → nonessential.Glycine: formed from serine via serine hydroxymethyltransferase and other routes → nonessential.Therefore, all listed are nonessential → choose “All of these.” Verification / Alternative check: Dietary references and biochemistry texts consistently classify these three as nonessential under normal conditions. Why Other Options Are Wrong: Aspartic acid: not essential; humans synthesize it. Glutamic acid: not essential; central in nitrogen metabolism. Glycine: not essential; abundant, easily synthesized. Common Pitfalls: Confusing “conditionally essential” amino acids (e.g., arginine in rapid growth) with strictly essential; mixing up neurotransmitters (glutamate) with dietary essentiality. Final Answer: All of these

Question 20

Acid–base chemistry of amino acids — Molecules bearing both a positive and a negative charge on different functional groups at the same time are called what?

Accepted Answer

Introduction / Context: At physiological pH, amino acids commonly exist as internal salts in which the amino group is protonated (positive) and the carboxyl group is deprotonated (negative). This dipolar state is essential for solubility, isoelectric behavior, and electrophoretic mobility. Given Data / Assumptions: We are naming molecules with simultaneous positive and negative charges. Standard biochemical terminology is expected. Examples include free amino acids in aqueous solution near neutral pH. Concept / Approach: The term “zwitterion” (from German “Zwitter,” meaning hybrid) precisely describes molecules with both charges. Amino acids, betaines, and certain phospholipids often exist in zwitterionic forms, especially around their isoelectric point where the net charge is zero but internal charges are present. Step-by-Step Solution: Identify the functional groups: –NH3+ and –COO− on amino acids.Recognize simultaneous opposite charges → zwitterionic form.Select the established term “zwitterions.” Verification / Alternative check: Electrophoresis and titration curves demonstrate amino acids behaving as dipolar ions near their pI, reinforcing the zwitterion concept. Why Other Options Are Wrong: Ambions / amphions: nonstandard or obsolete terms; not accepted modern nomenclature. Ion conversion: not a molecular class; refers to a process, not a species. Common Pitfalls: Assuming “no net charge” means “uncharged.” Zwitterions have charges that cancel overall but strongly affect solvation and reactivity. Final Answer: zwitterions

Structure and Properties of Amino Acids Questions