Section 1: Structure and Function of the Nucleus
- Describe the structure of the nuclear envelope and its significance.
Answer:
The nuclear envelope is a double membrane structure that encloses the nucleus in eukaryotic cells. It consists of an inner and an outer membrane, separated by a perinuclear space. The outer membrane is continuous with the endoplasmic reticulum. The envelope contains nuclear pores, which regulate the transport of molecules like RNA, proteins, and ions between the nucleus and cytoplasm. This structure is critical for protecting genetic material and maintaining the environment required for DNA replication and transcription. - Explain the role of nuclear pores in cellular function.
Answer:
Nuclear pores are large protein complexes embedded in the nuclear envelope that allow selective transport of molecules. They enable the import of nuclear proteins, such as transcription factors, and the export of mRNA and ribosomal subunits. The selective transport ensures that only appropriate molecules enter or leave the nucleus, maintaining cellular homeostasis. - What is the nucleolus, and what functions does it serve?
Answer:
The nucleolus is a dense, spherical structure located within the nucleus. It is not membrane-bound and is primarily involved in ribosomal RNA (rRNA) synthesis and ribosome assembly. Ribosomal proteins imported from the cytoplasm combine with rRNA in the nucleolus to form ribosomal subunits, which are then exported to the cytoplasm for protein synthesis. - How does the nuclear matrix contribute to the organization of the nucleus?
Answer:
The nuclear matrix is a network of fibers within the nucleus that provides structural support and organizes chromatin. It helps maintain the shape of the nucleus, anchors chromosomal domains, and regulates gene expression by influencing the spatial arrangement of genes and regulatory elements. - Discuss the relationship between the nucleus and the endoplasmic reticulum.
Answer:
The outer membrane of the nuclear envelope is continuous with the rough endoplasmic reticulum (ER). This relationship facilitates the direct transfer of synthesized proteins and lipids between the nucleus and ER. The nucleus provides instructions for protein synthesis via mRNA, which is processed and exported to the cytoplasm for translation, often by ribosomes attached to the rough ER.
Section 2: DNA Organization and Chromatin
- What are histones, and how do they facilitate DNA packaging?
Answer:
Histones are positively charged proteins around which negatively charged DNA wraps to form nucleosomes, the basic units of chromatin. Each nucleosome consists of DNA wrapped around an octamer of histones (H2A, H2B, H3, and H4). This organization compacts DNA and regulates gene accessibility for transcription, replication, and repair. - Differentiate between euchromatin and heterochromatin.
Answer:
Euchromatin is lightly packed chromatin that is transcriptionally active, allowing access to genes for transcription. It appears less dense under a microscope. Heterochromatin, on the other hand, is tightly packed, transcriptionally inactive, and often associated with structural and regulatory roles, such as centromeres and telomeres. - Describe the structure and function of nucleosomes.
Answer:
A nucleosome consists of 146 base pairs of DNA wrapped around a histone octamer. The linker DNA connects adjacent nucleosomes. This structure compacts DNA into chromatin and serves as a regulatory mechanism for gene expression, as the accessibility of DNA to transcription factors is influenced by its packaging. - What are telomeres, and why are they important?
Answer:
Telomeres are repetitive nucleotide sequences at the ends of chromosomes that protect them from degradation and prevent the fusion of chromosomes. They play a crucial role in maintaining genomic stability. During cell division, telomeres shorten, which is linked to cellular aging and senescence. - Explain the levels of chromatin organization in the nucleus.
Answer:
Chromatin is organized into several levels:- Nucleosomes: DNA wraps around histones.
- 30-nm fiber: Nucleosomes fold into a solenoid structure.
- Looped domains: Fibers form loops anchored to the nuclear matrix.
- Higher-order folding: Loops compact further during mitosis to form visible chromosomes.
Section 3: DNA Replication and Repair
- Outline the steps involved in DNA replication.
Answer:- Initiation: Helicase unwinds the DNA helix, creating replication forks. Primase synthesizes RNA primers.
- Elongation: DNA polymerase adds complementary nucleotides to the template strand. Leading and lagging strands are synthesized.
- Termination: DNA ligase seals Okazaki fragments on the lagging strand, and replication ends when the entire molecule is duplicated.
- What is the role of helicase in DNA replication?
Answer:
Helicase unwinds the DNA double helix by breaking hydrogen bonds between complementary bases, creating replication forks. This unwinding is essential for DNA polymerase to access single-stranded DNA templates. - Describe the mechanisms of base excision repair.
Answer:
Base excision repair corrects damaged bases:- A glycosylase enzyme removes the damaged base, leaving an abasic site.
- An endonuclease cleaves the DNA backbone at the site.
- DNA polymerase fills the gap, and DNA ligase seals the strand.
- How do mismatch repair mechanisms function?
Answer:
Mismatch repair corrects errors missed by DNA polymerase during replication. Proteins recognize mismatched bases, excise the incorrect nucleotide, and fill the gap with the correct base using DNA polymerase and ligase. - What is the significance of homologous recombination in DNA repair?
Answer:
Homologous recombination repairs double-strand breaks using a homologous sequence as a template. This ensures high fidelity in repair, maintaining genomic integrity.
Section 4: Gene Regulation
- Explain the role of promoters in transcription.
Answer:
Promoters are DNA sequences upstream of genes that act as binding sites for RNA polymerase and transcription factors. They initiate transcription and regulate gene expression levels by interacting with enhancer or silencer elements. - What are enhancers, and how do they influence gene expression?
Answer:
Enhancers are DNA elements located far from the gene they regulate. They bind activator proteins to increase the transcription efficiency of associated genes by looping the DNA to interact with the promoter region. - How do transcription factors regulate gene expression?
Answer:
Transcription factors bind to specific DNA sequences in promoters or enhancers. They recruit or block RNA polymerase and co-activators, controlling the initiation and rate of transcription. - What is epigenetics, and how does it affect gene regulation?
Answer:
Epigenetics involves heritable changes in gene expression without altering the DNA sequence. Mechanisms include DNA methylation, histone modification, and chromatin remodeling, which regulate gene accessibility. - Describe the process of alternative splicing and its significance.
Answer:
Alternative splicing removes introns and joins exons in pre-mRNA, generating multiple mRNA variants from a single gene. This process increases proteomic diversity and allows tissue-specific gene expression.
Section 5: RNA Processing and Translation
- What modifications occur in eukaryotic mRNA before translation?
Answer:- 5′ capping: Adds a modified guanine nucleotide.
- Polyadenylation: Adds a poly-A tail to the 3′ end.
- Splicing: Removes introns and joins exons.
These modifications stabilize mRNA and facilitate translation.
- Discuss the significance of the 5′ cap in mRNA.
Answer:
The 5′ cap protects mRNA from degradation, facilitates ribosome binding for translation, and assists in nuclear export. - What is the role of tRNA in translation?
Answer:
tRNA transports specific amino acids to the ribosome during translation. Each tRNA has an anticodon that pairs with a codon on mRNA, ensuring accurate protein synthesis. - How is translation initiated in eukaryotes?
Answer:
The small ribosomal subunit binds to the mRNA’s 5′ cap, locating the start codon (AUG). The initiator tRNA (carrying methionine) binds to the start codon, followed by the attachment of the large ribosomal subunit. - Explain the elongation process during translation.
Answer:
Aminoacyl-tRNA enters the ribosome’s A site, where its anticodon pairs with the mRNA codon. A peptide bond forms between the growing chain in the P site and the new amino acid. The ribosome translocates, moving the tRNA to the P site.
Section 6: Advanced Topics
- What is the role of DNA methylation in gene regulation?
Answer:
DNA methylation involves adding a methyl group to cytosine residues, silencing gene expression by preventing transcription factor binding and recruiting repressive proteins. - How do operons function in prokaryotic gene regulation?
Answer:
Operons are clusters of genes transcribed together, regulated by operators and repressors. For example, the lac operon is activated in the presence of lactose and repressed when lactose is absent. - What is chromatin remodeling, and why is it important?
Answer:
Chromatin remodeling involves altering nucleosome positioning to regulate DNA accessibility for transcription, replication, and repair. This is achieved through ATP-dependent chromatin-remodeling complexes. - Describe the function of proteasomes in cellular regulation.
Answer:
Proteasomes degrade misfolded or damaged proteins tagged with ubiquitin, maintaining protein quality control and regulating cellular processes like the cell cycle and apoptosis. - How do microRNAs (miRNAs) regulate gene expression?
Answer:
miRNAs bind to complementary sequences in mRNA, leading to mRNA degradation or translation inhibition. This post-transcriptional regulation fine-tunes gene expression.
