Biomolecules — Proteins & Nucleic Acids

Question 1 (10 marks)

(a) General amino acid structure: central (alpha) carbon bonded to four groups.

        H   H
        |   |
   H — N — C — C — OH
        |   ||
        R   O

Labels required: central C (1), amino group –NH₂ (1), carboxyl group –COOH (1), R-group (variable side chain) + H on central C (1). Why: the four different attachments make the alpha-carbon a chiral centre; the variable R determines amino acid identity.

(b) Condensation (dehydration synthesis) reaction. (1 for naming) –COOH of AA1 reacts with –NH₂ of AA2. The –OH from carboxyl + H from amino leave as H₂O. (2) The new C–N bond formed is the peptide bond. (1)

(c) Reaction is endergonic — energy needed to form the covalent peptide bond and remove water. (1) The –OH is removed from the carboxyl group and an –H from the amino group, combining to form water. (1)

Question 2 (10 marks)

(a) (1 each)

• Primary: the linear sequence/order of amino acids in the polypeptide.
• Secondary: local regular folding into α-helices and β-pleated sheets.
• Tertiary: overall 3-D folding of the whole polypeptide into a specific shape.
• Quaternary: association of two or more polypeptide subunits into a functional protein.

(b) (1 each)

• Primary — peptide (covalent) bonds.
• Secondary — hydrogen bonds between backbone C=O and N–H groups.
• Tertiary — combination of hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions between R-groups.
• Quaternary — same R-group interactions/hydrogen & hydrophobic bonds between subunits.

(c) A single amino acid change alters R-group interactions, changing folding of tertiary structure → active site/binding shape altered → protein cannot function (e.g. sickle-cell haemoglobin). (2)

Question 3 (8 marks)

(a) Denaturation = loss of a protein's specific 3-D (tertiary/quaternary) shape due to breaking of bonds stabilising the structure, without breaking peptide bonds. (2)

(b) Any three, 2 marks each (cause + mechanism):

• Heat: increased kinetic energy → vibration breaks weak H-bonds and ionic interactions.
• Extreme pH: excess H⁺/OH⁻ alters charges on R-groups → disrupts ionic bonds/H-bonds.
• Heavy metals / salts: ions bind to charged groups, breaking ionic bonds and disrupting folding.
• (Also acceptable: organic solvents/detergents disrupting hydrophobic interactions.)

Question 4 (12 marks)

(a) Nucleotide = phosphate group – pentose sugar – nitrogenous base joined. (3) Phosphate attached to C5 of sugar; base attached to C1 of sugar.

(b) Table (1 mark per correct row):

(c) By Chargaff: %A = %T, %G = %C, and total = 100%. %A = 22% → %T = 22%. A + T = 44%. Remaining = 100 − 44 = 56% for G + C. %G = %C = 56 / 2 = 28%. (3)

(d) A–T form 2 hydrogen bonds; G–C form 3 hydrogen bonds. A purine (2-ring) always pairs with a pyrimidine (1-ring) so the helix stays a constant width; complementary shapes and H-bond donor/acceptor geometry allow specific pairing. (2)

Question 5 (5 marks)

(a) ATP = adenine base + ribose sugar + three phosphate groups in a chain (adenosine + triphosphate). (3)

(b) Hydrolysis of the terminal (third) phosphate bond releases energy (ATP → ADP + Pᵢ). This releasable, usable energy powers cellular reactions, and ATP is readily reformed — hence "energy currency". (2)

Question 6 (5 marks)

(a) (2 marks each)

• Protein — Biuret test: add Biuret reagent (NaOH + copper sulfate); positive = colour changes blue → purple/violet.
• Reducing sugar — Benedict's test: add Benedict's reagent and heat; positive = blue → green/yellow/orange/brick-red.

(b) Run a negative control using distilled water (no colour change expected) to confirm any colour change is due to the sample, not the reagent. (1)

[
  {"claim":"DNA with 22% adenine has 28% guanine (Chargaff)","code":"A=22\nT=A\nGC=100-(A+T)\nG=GC/2\nresult=(G==28)"},
  {"claim":"A+T+G+C sums to 100% for the sample","code":"A=22\nT=22\nG=28\nC=28\nresult=(A+T+G+C==100)"},
  {"claim":"A-T pairs have 2 H-bonds, G-C have 3, total in one A-T + one G-C = 5","code":"at=2\ngc=3\nresult=(at+gc==5)"},
  {"claim":"Condensation removes one water per peptide bond; a tripeptide from 3 amino acids loses 2 water","code":"n=3\nwaters=n-1\nresult=(waters==2)"}
]