Molecular Biology

1. In aerobic respiration, oxygen serves as the final electron acceptor at the end of the electron transport chain, forming water.

Answer: True

Oxygen accepts electrons and protons at the end of the chain to form water, which lets the carriers keep passing electrons.

2. Build the term for ATP made by transferring a phosphate directly to ADP during glycolysis and the Krebs cycle, without the electron transport chain.

Answer: substrate level phosphorylation

Substrate-level phosphorylation forms ATP by direct enzymatic phosphate transfer from a substrate, unlike the chemiosmotic ATP of oxidative phosphorylation.

3. Which of the following happen during the light-dependent reactions of photosynthesis? Select all that apply.

• Water is split by photolysiscorrect
• NADPH is producedcorrect
• ATP is generated by photophosphorylationcorrect
• CO2 is fixed into sugar
• RuBisCO carboxylates RuBP

The light reactions in the thylakoids split water and make ATP and NADPH; carbon fixation by RuBisCO occurs later in the Calvin cycle.

4. During oxidative phosphorylation, the electron transport chain pumps protons from the matrix into the ____ space, building the gradient that drives ATP synthase.

• intermembranecorrect
• thylakoid
• cytosolic
• nuclear

Protons are pumped into the intermembrane space between the inner and outer mitochondrial membranes, creating the electrochemical gradient used to make ATP.

5. What is the NET number of ATP molecules produced directly by glycolysis per glucose?

Answer: 2 ATP

Glycolysis uses 2 ATP and generates 4 ATP by substrate-level phosphorylation, for a net gain of 2 ATP per glucose.

6. Match each coenzyme to the vitamin it is derived from.

Answer: NAD+ = Niacin (B3); FAD = Riboflavin (B2); Thiamine pyrophosphate (TPP) = Thiamine (B1); Tetrahydrofolate = Folate (B9)

Many coenzymes are built from B-vitamins: NAD+ from niacin, FAD from riboflavin, TPP from thiamine, and tetrahydrofolate from folate.

7. The enzyme DNA ____ joins Okazaki fragments by sealing the sugar-phosphate backbone on the lagging strand.

• ligasecorrect
• helicase
• primase
• polymerase

DNA ligase catalyses the phosphodiester bond that seals the nick between adjacent Okazaki fragments.

8. Build the sentence describing how biological polymers are assembled.

Answer: monomers are joined by condensation releasing water

In a condensation reaction, monomers are joined together and a molecule of water is released for each new bond.

9. DNA replication is semiconservative, so each new double helix contains one original strand and one newly synthesized strand.

Answer: True

Meselson and Stahl showed replication is semiconservative: the parental strands separate and each serves as a template, so every daughter helix is half old and half new.

10. Match each DNA repair mechanism to the kind of damage it fixes.

Answer: Nucleotide excision repair = Removes bulky lesions such as UV thymine dimers; Mismatch repair = Corrects base-pairing errors left after replication; Base excision repair = Removes a single damaged or altered base; Photoreactivation = Uses light-driven photolyase to reverse dimers

Different repair pathways target different lesions, from single altered bases to bulky helix-distorting damage.

11. How does DNA polymerase improve replication accuracy through proofreading?

• Its 3' to 5' exonuclease activity removes a wrongly paired nucleotide before continuingcorrect
• It methylates mismatched bases so they are ignored
• It replaces the entire strand whenever an error occurs
• It adds extra RNA primers around every mistake

The polymerase's 3' to 5' exonuclease clips out a mispaired base so the correct nucleotide can be inserted, greatly lowering the error rate.

12. Three of these are found in a DNA nucleotide. Which one does NOT belong in DNA?

• Ribose sugarcorrect
• Deoxyribose sugar
• A phosphate group
• The base thymine

DNA nucleotides contain deoxyribose, not ribose; ribose is the sugar used in RNA.

13. A regulatory molecule that binds an enzyme at a site away from the active site, changing the enzyme's shape and activity, is acting as an ____ regulator.

• allostericcorrect
• active
• catalytic
• substrate

Allosteric regulators bind a separate regulatory site and shift the enzyme between more- and less-active shapes.

14. Match each enzyme term to its correct description.

Answer: Active site = Pocket where the substrate binds; Substrate = Molecule the enzyme acts on; Denaturation = Loss of shape from heat or pH; Cofactor = Non-protein helper for catalysis

Enzymes bind a substrate at the active site, can be denatured by heat or extreme pH, and often need cofactors to function.

15. Allosteric effectors are always inhibitors, so no molecule can bind an allosteric site and increase an enzyme's activity.

Answer: False

Allosteric activators also exist: binding at a regulatory site can stabilise the active shape and raise, not just lower, enzyme activity.

16. How do enzymes increase the rate of a biochemical reaction?

• By lowering the activation energy of the reactioncorrect
• By raising the activation energy so reactants collide harder
• By supplying extra heat to the reactants
• By shifting the reaction's equilibrium toward products

Enzymes provide an alternative pathway with a lower activation energy; they speed reactions without changing the equilibrium position.

17. Three of these interactions stabilise a protein's folded shape. Which one instead joins amino acids in the primary backbone?

• Peptide bondcorrect
• Hydrogen bond
• Ionic bond
• Disulfide bridge

Peptide bonds link amino acids in the primary sequence, while hydrogen, ionic, and disulfide interactions stabilise the folded structure.

18. Sort each interaction that stabilises proteins as a covalent or a non-covalent interaction.

Answer: Disulfide bridge = Covalent; Peptide bond = Covalent; Hydrogen bond = Non-covalent; Hydrophobic interaction = Non-covalent; Ionic bond = Non-covalent

Peptide and disulfide bonds are covalent, whereas hydrogen bonds, ionic attractions, and hydrophobic interactions are weaker non-covalent forces.

19. Which enzyme binds the promoter and synthesizes an mRNA strand from a DNA template during transcription?

• RNA polymerasecorrect
• DNA polymerase
• Helicase
• DNA ligase

RNA polymerase recognizes the promoter, unwinds the DNA, and builds messenger RNA complementary to the template strand.

20. Sort each component into the process it belongs to: transcription or translation.

Answer: RNA polymerase = Transcription; Promoter = Transcription; Ribosome = Translation; tRNA anticodon = Translation

RNA polymerase and the promoter act in transcription, while the ribosome and tRNA anticodons work during translation.

21. Build the sentence describing how a mature eukaryotic mRNA is made.

Answer: Introns are removed and exons are joined

Splicing removes the non-coding introns and joins the exons to produce the mature, translatable mRNA.

22. A 5' cap and a 3' poly-A tail are added to eukaryotic mRNA. Which statements about them are correct? Select all that apply.

• The 5' cap helps ribosomes recognise and bind the mRNAcorrect
• The poly-A tail helps protect the mRNA from degradationcorrect
• Both modifications increase mRNA stabilitycorrect
• The cap and tail are removed before the mRNA leaves the nucleus
• The poly-A tail is translated into a stretch of lysine residues

The cap aids ribosome binding while both the cap and poly-A tail stabilise the mRNA and assist export and translation; neither is a template for amino acids.

23. A eukaryotic mRNA's 5' cap is a modified guanine nucleotide known as 7-____guanosine.

• methylcorrect
• hydroxy
• phospho
• amino

The cap is 7-methylguanosine, joined to the transcript by an unusual 5'-to-5' triphosphate bridge that protects the mRNA and aids ribosome binding.

24. Match each chromatin-modifying enzyme to what it does.

Answer: Histone acetyltransferase (HAT) = Adds acetyl groups to loosen chromatin; Histone deacetylase (HDAC) = Removes acetyl groups to condense chromatin; DNA methyltransferase = Adds methyl groups to cytosine bases; Histone demethylase = Removes methyl marks from histone tails

Acetyltransferases and deacetylases add or remove acetyl marks on histones, while DNA methyltransferases and histone demethylases add or remove methyl marks.

25. During translation, ____ molecules carry amino acids to the ribosome and pair their anticodons with the mRNA codons.

• tRNAcorrect
• mRNA
• rRNA
• DNA

Transfer RNA (tRNA) has an anticodon that base-pairs with a codon while carrying the matching amino acid to the ribosome.

26. Roughly how many different amino acids are commonly used by cells to build proteins?

Answer: 20 amino acids

There are 20 standard amino acids specified by the genetic code that combine in different sequences to make all proteins.

27. Build the sentence that describes how a polypeptide chain is assembled.

Answer: Amino acids are joined by peptide bonds

Amino acids are linked by covalent peptide bonds formed during translation, creating the backbone of a polypeptide chain.

28. Match each ribosome feature to its role during translation.

Answer: A site = Accepts the incoming aminoacyl-tRNA; P site = Holds the tRNA bearing the growing polypeptide; E site = Releases the spent, empty tRNA; Peptidyl transferase = Catalyses formation of the peptide bond

tRNAs move A to P to E: the A site accepts the new charged tRNA, the P site holds the chain, the E site releases the used tRNA, and peptidyl transferase links the amino acids.

29. According to the wobble hypothesis, which modified base often sits in the wobble position of a tRNA anticodon and can pair with U, C, or A?

• Inosinecorrect
• Uracil
• Thymine
• Xanthine

Inosine in the 5' (wobble) position of the anticodon can pair with U, C, or A, allowing one tRNA to read several synonymous codons.

30. Three of these mRNA codons are stop (termination) codons. Which one is NOT?

• AUGcorrect
• UAA
• UAG
• UGA

UAA, UAG, and UGA signal termination, whereas AUG is the start codon and also encodes methionine.