Biomolecules Set-8

Q1. The amino acid glycine has $pK_{1}=2.34$ (carboxyl) and $pK_{2}=9.60$ (amino). Using $pI=\dfrac{pK_{1}+pK_{2}}{2}$, the isoelectric point $pI$ of glycine is approximately:

Q2. A freshly prepared solution of pure $\alpha$-D-glucose has observed specific rotation $[\alpha]_{\alpha}=+112.2^\circ$, pure $\beta$-D-glucose has $[\alpha]_{\beta}=+18.7^\circ$, and the equilibrium rotation is $[\alpha]_{eq}=+52.7^\circ$. At equilibrium, the percentage of $\beta$-anomer present is closest to:

Q3. An enzyme catalyses reactions of two substrates S$_1$ and S$_2$ with the following parameters: $k_{cat1}=100\ \text{s}^{-1},\ K_{m1}=10\ \mu\text{M}$ for S$_1$ and $k_{cat2}=50\ \text{s}^{-1},\ K_{m2}=1\ \mu\text{M}$ for S$_2$. Which statement correctly describes which substrate is preferred at very low substrate concentration ($[S]\ll K_m$) and which gives higher rate at saturating substrate concentration?

Q4. Assertion (A): In a Lineweaver–Burk plot (plot of $1/v$ vs $1/[S]$) a pure noncompetitive inhibitor produces the same x-intercept as the uninhibited reaction.
Reason (R): A noncompetitive inhibitor increases the apparent $K_m$ while decreasing $V_{max}$.

Q5. Assertion (A): $\beta$-D-glucopyranose is thermodynamically more stable than $\alpha$-D-glucopyranose in the chair conformation.
Reason (R): In the $\beta$-anomer the hydroxyl at the anomeric carbon $C_1$ is equatorial, minimizing 1,3-diaxial steric interactions; in the $\alpha$-anomer that hydroxyl is axial.

Q6. Consider alanine with $pK_a(\mathrm{COOH})=2.35$ and $pK_a(\mathrm{NH_3^+})=9.87$. What is the net electric charge on alanine at $pH=7.0$?

Q7. The dipeptide $\mathrm{Ala\!-\!Lys}$ has ionizable groups with $pK_a(\mathrm{COOH})=2.20$, $pK_a(\mathrm{NH_3^+})=9.60$ and $pK_a(\mathrm{Lys\ side\ chain})=10.50$. Calculate its isoelectric point (pI).

Q8. The peptide sequence is $\mathrm{Arg\!-\!Ala\!-\!Phe\!-\!Lys\!-\!Tyr\!-\!Ser}$. Trypsin cleaves peptide bonds after Arg and Lys (unless followed by Pro). Which set of fragments will result on complete digestion by trypsin?

Q9. Assertion (A): A globular protein treated with 8 M urea becomes partially unfolded but may still retain covalent disulfide bonds; subsequent addition of $\beta$-mercaptoethanol ($\beta$-ME) leads to complete unfolding into separate polypeptide chains.
Reason (R): 8 M urea disrupts noncovalent interactions (hydrogen bonds and hydrophobic packing) but does not cleave disulfide bonds, whereas $\beta$-ME chemically reduces S–S bridges to thiol groups, breaking covalent cross-links.

Q10. An enzyme follows Michaelis–Menten kinetics with $K_m=5.0\ \mathrm{mM}$ and $V_{max}=100\ \mu\mathrm{mol\,min^{-1}}$ in absence of inhibitor. In presence of $[I]=10.0\ \mathrm{mM}$ of a reversible inhibitor the apparent $K_m$ becomes $25.0\ \mathrm{mM}$ while $V_{max}$ is unchanged. Assuming competitive inhibition, the inhibition constant $K_i$ (in mM) is:

Q11. Glycine has $pK_a(\mathrm{COOH})=2.34$ and $pK_a(\mathrm{NH_3^+})=9.60$. Using $pI=\dfrac{pK_a(\mathrm{COOH})+pK_a(\mathrm{NH_3^+})}{2}$, the isoelectric point of glycine is closest to:

Q12. Consider the tripeptide $\mathrm{H_2N\text{-}Glu\text{-}His\text{-}Lys\text{-}COOH}$ with $pK_a$ values $pK_a(\mathrm{COOH})=2.0$, $pK_a(\mathrm{Glu\ side\ chain})=4.25$, $pK_a(\mathrm{His\ side\ chain})=6.00$, $pK_a(\mathrm{NH_3^+})=9.0$, $pK_a(\mathrm{Lys\ side\ chain})=10.5$. Using Henderson–Hasselbalch where fraction protonated $=\dfrac{1}{1+10^{pH-pK_a}}$, the approximate net charge of this peptide at $pH=6.0$ is:

Q13. For the dipeptide $\mathrm{H_2N\text{-}Gly\text{-}Lys\text{-}COOH}$ the ionizable groups have $pK_a$ values $pK_a(\mathrm{COOH})=2.0$, $pK_a(\mathrm{NH_3^+})=9.0$, $pK_a(\mathrm{Lys\ side\ chain})=10.5$. The isoelectric point $pI$ of this dipeptide is best approximated by:

Q14. Assertion (A): Acetylation of lysine residues in histone proteins reduces their net positive charge and weakens histone–DNA interaction. Reason (R): Acetylation converts the $\varepsilon$-amino group of lysine from positively charged $-\mathrm{NH_3^+}$ to a neutral amide $-\mathrm{NHCOCH_3}$, thereby reducing electrostatic attraction to the negatively charged DNA backbone.

Q15. During DNA replication a rare imino tautomer of cytosine pairs with adenine instead of guanine. After two rounds of replication the original $C\!:\!G$ pair is ultimately converted into which fixed base pair?