BIOL 304: Advanced Cell & Molecular Biology
Study Guide: 2026/2027 Syllabus
New Version: Integrated Cellular & Molecular Principles
This guide is divided into thematic units corresponding to the new syllabus.
Unit 1: The Central Dogma & Beyond (Gene Expression &
Regulation)
1. What are the three key differences between DNA replication and transcription
in eukaryotes?
ANSWER ✓ 1. Replication uses DNA polymerase (requires primer); transcription uses
RNA polymerase (no primer). 2. Replication copies entire genome; transcription
selectively copies genes. 3. Replication produces identical dsDNA; transcription
produces ssRNA.
2. Describe the function of the 5' cap and poly-A tail in eukaryotic mRNA.
ANSWER ✓ The 5' 7-methylguanosine cap protects mRNA from degradation, facilitates
nuclear export, and is required for translation initiation by binding eIF4E. The poly-A tail
(50-250 adenines) also protects from degradation, aids in nuclear export, and enhances
translation by binding poly-A-binding proteins (PABPs).
3. How does alternative splicing contribute to proteomic diversity? Provide an
example.
ANSWER ✓ Alternative splicing allows a single gene to produce multiple mRNA
isoforms by differentially including or excluding exons. For example,
the Drosophila Dscam gene can generate over 38,000 isoforms, crucial for neuronal
wiring and immune recognition.
4. What is the role of a spliceosome?
ANSWER ✓ The spliceosome is a large ribonucleoprotein complex (snRNPs and
proteins) that catalyzes the removal of introns from pre-mRNA and ligates exons
together through two transesterification reactions.
,5. Compare and contrast the three eukaryotic RNA polymerases.
ANSWER ✓ RNA Pol I transcribes most rRNA genes (except 5S). RNA Pol II transcribes
all protein-coding genes (mRNAs) and most snRNAs. RNA Pol III transcribes small RNAs
like tRNA, 5S rRNA, and U6 snRNA. Pol II is unique in requiring a large set of
transcription factors (TFIIA-TFIIH) for initiation.
6. What is RNA interference (RNAi) and what are its two primary cellular
functions?
ANSWER ✓ RNAi is a biological process where small non-coding RNAs (miRNA, siRNA)
guide Argonaute proteins to complementary mRNA targets. Its functions are: 1) Post-
transcriptional gene silencing via mRNA degradation or translational repression; 2)
Defense against viruses and transposable elements.
7. Explain the concept of a "transcription factor" and its DNA-binding domains.
ANSWER ✓ A transcription factor is a protein that binds to specific DNA sequences
(enhancers, promoters) to regulate transcription. Common DNA-binding domains
include the helix-turn-helix, zinc finger, and leucine zipper domains.
8. How does chromatin structure regulate transcription?
ANSWER ✓ Transcription is regulated by chromatin compaction. Euchromatin (loosely
packed, acetylated histones) is transcriptionally active. Heterochromatin (tightly packed,
deacetylated, methylated histones) is transcriptionally silent. ATP-dependent chromatin
remodelers and histone-modifying enzymes (e.g., HATs, HDACs) dynamically alter this
structure.
9. What is a long non-coding RNA (lncRNA) and give one example of its function.
ANSWER ✓ lncRNAs are RNAs longer than 200 nucleotides that are not translated. They
act as scaffolds, guides, or decoys. For example, Xist is an lncRNA that coats one X
chromosome in female mammals, recruiting repressive chromatin modifications to
mediate X-chromosome inactivation.
10. Describe the process of nonsense-mediated decay (NMD).
ANSWER ✓ NMD is a quality control mechanism that degrades mRNAs containing a
premature termination codon (PTC). It relies on the deposition of exon-junction
complexes (EJCs) during splicing; if translation terminates >50-55 nucleotides upstream
of an EJC, the mRNA is targeted for degradation.
Unit 2: Cellular Compartments & Protein Trafficking
, 11. What is the signal hypothesis?
ANSWER ✓ The signal hypothesis posits that proteins destined for the endoplasmic
reticulum (ER) contain an N-terminal signal sequence (a stretch of hydrophobic amino
acids) that directs the ribosome to the ER membrane via the Signal Recognition Particle
(SRP) and its receptor, enabling co-translational translocation.
12. How are proteins targeted to the nucleus?
ANSWER ✓ Nuclear proteins contain a nuclear localization signal (NLS), a short stretch
of basic amino acids. This signal is recognized by importins, which mediate transport
through the nuclear pore complex (NPC) in a Ran-GTP-dependent manner. Ran-GTP in
the nucleus releases the cargo.
13. What is the difference between constitutive and regulated secretion?
ANSWER ✓ Constitutive secretion is a continuous, unregulated pathway delivering
proteins (e.g., ECM components) to the plasma membrane. Regulated
secretion involves storage of proteins in secretory vesicles that only fuse with the
plasma membrane upon an external signal (e.g., hormone or neurotransmitter release).
14. Describe the role of clathrin and dynamin in endocytosis.
ANSWER ✓ Clathrin forms a triskelion structure that assembles into a coated pit on the
plasma membrane, providing the mechanical scaffold for vesicle formation. Dynamin is
a GTPase that assembles around the neck of the invaginated vesicle and constricts it,
pinching off the vesicle from the membrane.
15. How do lysosomal hydrolases acquire their mannose-6-phosphate (M6P) tag?
ANSWER ✓ In the cis-Golgi network, a two-step enzymatic process occurs: 1) N-
acetylglucosamine phosphotransferase adds GlcNAc-phosphate to mannose residues; 2)
Phosphodiesterase removes the GlcNAc, exposing M6P. M6P receptors in the trans-
Golgi network then sort these enzymes to lysosomes.
16. What is the function of the ER chaperone BiP (GRP78)?
ANSWER ✓ BiP is an Hsp70 family chaperone that binds to unfolded or misfolded
proteins in the ER lumen, preventing aggregation, facilitating proper folding, and
regulating the unfolded protein response (UPR) by remaining bound to ER stress
sensors (PERK, IRE1, ATF6) under non-stressed conditions.
17. Explain the unfolded protein response (UPR).
ANSWER ✓ The UPR is a cellular stress response triggered by misfolded protein
accumulation in the ER. It involves three sensors (IRE1, PERK, ATF6) that: 1) transiently
halt general translation (via PERK/eIF2α), 2) upregulate ER chaperone expression (via
ATF6 and IRE1/XBP1s), and 3) enhance ERAD (ER-associated degradation). If unresolved,
it triggers apoptosis.
Study Guide: 2026/2027 Syllabus
New Version: Integrated Cellular & Molecular Principles
This guide is divided into thematic units corresponding to the new syllabus.
Unit 1: The Central Dogma & Beyond (Gene Expression &
Regulation)
1. What are the three key differences between DNA replication and transcription
in eukaryotes?
ANSWER ✓ 1. Replication uses DNA polymerase (requires primer); transcription uses
RNA polymerase (no primer). 2. Replication copies entire genome; transcription
selectively copies genes. 3. Replication produces identical dsDNA; transcription
produces ssRNA.
2. Describe the function of the 5' cap and poly-A tail in eukaryotic mRNA.
ANSWER ✓ The 5' 7-methylguanosine cap protects mRNA from degradation, facilitates
nuclear export, and is required for translation initiation by binding eIF4E. The poly-A tail
(50-250 adenines) also protects from degradation, aids in nuclear export, and enhances
translation by binding poly-A-binding proteins (PABPs).
3. How does alternative splicing contribute to proteomic diversity? Provide an
example.
ANSWER ✓ Alternative splicing allows a single gene to produce multiple mRNA
isoforms by differentially including or excluding exons. For example,
the Drosophila Dscam gene can generate over 38,000 isoforms, crucial for neuronal
wiring and immune recognition.
4. What is the role of a spliceosome?
ANSWER ✓ The spliceosome is a large ribonucleoprotein complex (snRNPs and
proteins) that catalyzes the removal of introns from pre-mRNA and ligates exons
together through two transesterification reactions.
,5. Compare and contrast the three eukaryotic RNA polymerases.
ANSWER ✓ RNA Pol I transcribes most rRNA genes (except 5S). RNA Pol II transcribes
all protein-coding genes (mRNAs) and most snRNAs. RNA Pol III transcribes small RNAs
like tRNA, 5S rRNA, and U6 snRNA. Pol II is unique in requiring a large set of
transcription factors (TFIIA-TFIIH) for initiation.
6. What is RNA interference (RNAi) and what are its two primary cellular
functions?
ANSWER ✓ RNAi is a biological process where small non-coding RNAs (miRNA, siRNA)
guide Argonaute proteins to complementary mRNA targets. Its functions are: 1) Post-
transcriptional gene silencing via mRNA degradation or translational repression; 2)
Defense against viruses and transposable elements.
7. Explain the concept of a "transcription factor" and its DNA-binding domains.
ANSWER ✓ A transcription factor is a protein that binds to specific DNA sequences
(enhancers, promoters) to regulate transcription. Common DNA-binding domains
include the helix-turn-helix, zinc finger, and leucine zipper domains.
8. How does chromatin structure regulate transcription?
ANSWER ✓ Transcription is regulated by chromatin compaction. Euchromatin (loosely
packed, acetylated histones) is transcriptionally active. Heterochromatin (tightly packed,
deacetylated, methylated histones) is transcriptionally silent. ATP-dependent chromatin
remodelers and histone-modifying enzymes (e.g., HATs, HDACs) dynamically alter this
structure.
9. What is a long non-coding RNA (lncRNA) and give one example of its function.
ANSWER ✓ lncRNAs are RNAs longer than 200 nucleotides that are not translated. They
act as scaffolds, guides, or decoys. For example, Xist is an lncRNA that coats one X
chromosome in female mammals, recruiting repressive chromatin modifications to
mediate X-chromosome inactivation.
10. Describe the process of nonsense-mediated decay (NMD).
ANSWER ✓ NMD is a quality control mechanism that degrades mRNAs containing a
premature termination codon (PTC). It relies on the deposition of exon-junction
complexes (EJCs) during splicing; if translation terminates >50-55 nucleotides upstream
of an EJC, the mRNA is targeted for degradation.
Unit 2: Cellular Compartments & Protein Trafficking
, 11. What is the signal hypothesis?
ANSWER ✓ The signal hypothesis posits that proteins destined for the endoplasmic
reticulum (ER) contain an N-terminal signal sequence (a stretch of hydrophobic amino
acids) that directs the ribosome to the ER membrane via the Signal Recognition Particle
(SRP) and its receptor, enabling co-translational translocation.
12. How are proteins targeted to the nucleus?
ANSWER ✓ Nuclear proteins contain a nuclear localization signal (NLS), a short stretch
of basic amino acids. This signal is recognized by importins, which mediate transport
through the nuclear pore complex (NPC) in a Ran-GTP-dependent manner. Ran-GTP in
the nucleus releases the cargo.
13. What is the difference between constitutive and regulated secretion?
ANSWER ✓ Constitutive secretion is a continuous, unregulated pathway delivering
proteins (e.g., ECM components) to the plasma membrane. Regulated
secretion involves storage of proteins in secretory vesicles that only fuse with the
plasma membrane upon an external signal (e.g., hormone or neurotransmitter release).
14. Describe the role of clathrin and dynamin in endocytosis.
ANSWER ✓ Clathrin forms a triskelion structure that assembles into a coated pit on the
plasma membrane, providing the mechanical scaffold for vesicle formation. Dynamin is
a GTPase that assembles around the neck of the invaginated vesicle and constricts it,
pinching off the vesicle from the membrane.
15. How do lysosomal hydrolases acquire their mannose-6-phosphate (M6P) tag?
ANSWER ✓ In the cis-Golgi network, a two-step enzymatic process occurs: 1) N-
acetylglucosamine phosphotransferase adds GlcNAc-phosphate to mannose residues; 2)
Phosphodiesterase removes the GlcNAc, exposing M6P. M6P receptors in the trans-
Golgi network then sort these enzymes to lysosomes.
16. What is the function of the ER chaperone BiP (GRP78)?
ANSWER ✓ BiP is an Hsp70 family chaperone that binds to unfolded or misfolded
proteins in the ER lumen, preventing aggregation, facilitating proper folding, and
regulating the unfolded protein response (UPR) by remaining bound to ER stress
sensors (PERK, IRE1, ATF6) under non-stressed conditions.
17. Explain the unfolded protein response (UPR).
ANSWER ✓ The UPR is a cellular stress response triggered by misfolded protein
accumulation in the ER. It involves three sensors (IRE1, PERK, ATF6) that: 1) transiently
halt general translation (via PERK/eIF2α), 2) upregulate ER chaperone expression (via
ATF6 and IRE1/XBP1s), and 3) enhance ERAD (ER-associated degradation). If unresolved,
it triggers apoptosis.
