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What is euchromatin?
less condensed, loosely packed form of chromatin that is transcriptionally active, allowing gene expression.
What is heterochromatin?
highly condensed, tightly packed form of chromatin that is transcriptionally inactive, leading to repressed gene expression.
Where is euchromatin typically found?
found in gene-rich regions of the genome.
Where is heterochromatin typically located?
found near centromeres and telomeres of chromosomes.
What histone modifications are associated with euchromatin?
characterized by acetylated histones, which contribute to its less compact structure.
What histone modifications are found in heterochromatin?
associated with methylated histones, which create a tighter chromatin structure.
What is the function of euchromatin?
participates in gene transcription and replication.
What role does heterochromatin play in the genome?
structural and regulatory role in maintaining genome stability.
How does euchromatin facilitate transcription?
allows transcription factors and RNA polymerase to access DNA for transcription.
What is the role of heterochromatin in gene regulation?
prevents access to DNA, silencing genes that should not be expressed in specific cells or conditions.
What is a nucleosome?
A structural unit of chromatin formed by DNA wrapped around a core of histone proteins (H2A, H2B, H3, H4), resembling a 'beads-on-a-string' structure.
What is the 30 nm fiber in chromatin organization?
A more compact structure formed when nucleosomes coil together into a solenoid configuration.
What are loop domains in chromatin?
Higher-order structures formed by chromatin loops that are stabilized by scaffold proteins, facilitating gene regulation.
What occurs during chromosome condensation?
During mitosis and meiosis, chromatin loops coil further to form tightly packed metaphase chromosomes.
How does nucleosome structure contribute to DNA packaging?
Nucleosomes allow for efficient DNA packaging by reducing the length of the DNA and regulating access to genetic information.
What role do scaffold proteins play in chromatin structure?
Scaffold proteins organize loop domains and help maintain the overall structure and regulation of chromatin.
How does chromatin structure change during the cell cycle?
Chromatin becomes more condensed during mitosis and meiosis and is less condensed during interphase to allow for gene expression.
What is supercoiling in prokaryotic DNA?
a necessary process that twists DNA beyond its normal double-helix shape to fit into the small bacterial cell.
What is negative supercoiling?
involves twisting the DNA in the opposite direction, aiding in unwinding for replication and transcription.
What is positive supercoiling?
tightens the DNA structure, making it less accessible and preventing strand separation.
What is the role of DNA gyrase (Topoisomerase II)?
introduces negative supercoils into DNA, which helps in genome stability and accessibility during replication and transcription.
What does Topoisomerase I do?
relieves excess negative supercoiling by making single-strand breaks in the DNA, allowing it to unwind.
What is Mismatch Repair (MMR)?
A DNA repair mechanism that corrects errors that occur after DNA replication.
What is Base Excision Repair (BER)?
A repair process that fixes small base modifications, such as deamination or oxidation.
What is Nucleotide Excision Repair (NER)?
A repair system that addresses bulky DNA lesions, such as UV-induced thymine dimers.
What is Non-Homologous End Joining (NHEJ)?
A repair mechanism that fixes double-strand breaks in DNA without a template.
What is Homologous Recombination Repair (HRR)?
A repair process that uses a sister chromatid as a template for accurate DNA repair.
What is the role of telomerase?
A reverse transcriptase enzyme that extends telomeres using an RNA template to counteract DNA shortening.
How does telomerase counteract chromosome shortening?
By adding repetitive DNA sequences to the ends of chromosomes, thus maintaining their length during replication.
Why are telomeres important for cellular aging?
Telomeres shorten with each cell division, and their length is associated with the replicative lifespan of a cell.
What is homologous recombination?
The exchange of DNA between similar sequences, using a homologous DNA strand as a guide.
What is non-homologous recombination?
A process where DNA is inserted at a random location without requiring a homologous sequence.
What are some examples of homologous recombination?
Meiosis and double-strand break repair.
What are some examples of non-homologous recombination?
Viral DNA integration and antibody gene rearrangement.
Why is homologous recombination important?
It contributes to genetic diversity and enables error-free DNA repair.
How does non-homologous recombination benefit the immune system?
It allows for adaptations such as antibody gene rearrangement, despite being more error-prone.
What is the location of transcription in prokaryotic cells?
Transcription occurs in the cytoplasm.
Where does transcription take place in eukaryotic cells?
Transcription occurs in the nucleus.
How many types of RNA polymerase are present in prokaryotes?
a single RNA polymerase.
How many types of RNA polymerase are present in eukaryotes?
three types of RNA polymerases: RNA Pol I, II, and III.
What type of promoters do prokaryotes have?
simple promoters with -10 (Pribnow box) and -35 sequences.
What characterizes eukaryotic promoters?
promoters are complex and include a TATA box, enhancers, and silencers.
What regulatory proteins are involved in prokaryotic transcription?
Activators and repressors bind near the promoter.
What regulatory mechanisms are present in eukaryotic transcription?
involves transcription factors, enhancers, silencers, and chromatin remodeling proteins.
What is an operon in prokaryotic transcription regulation?
An operon system allows coordinated regulation of multiple genes.
How is gene transcription organized in eukaryotes?
Each gene has its own promoter, resulting in monocistronic mRNA.
How does chromatin structure differ between prokaryotes and eukaryotes?
Prokaryotes have naked DNA, while eukaryotic DNA is wrapped around histones.
What happens to mRNA in prokaryotic cells after transcription?
mRNA is immediately translated.
What post-transcriptional modifications occur in eukaryotic mRNA?
mRNA undergoes capping, splicing, and polyadenylation.
Why is transcription regulation more complicated in eukaryotes?
chromatin structure, the presence of multiple regulatory elements, cell-specific regulation, and post-transcriptional modifications.
What is the role of chromatin remodeling in transcription regulation?
necessary to expose DNA wrapped around histones, allowing transcription machinery access to genes.
What are enhancers and silencers in eukaryotic transcription?
Enhancers increase transcription levels, while silencers decrease them, contributing to precise gene expression control.
How do different cell types influence gene expression in eukaryotes?
Different cell types express unique sets of genes governed by specific transcription factors and epigenetic modifications.
What post-transcriptional modifications occur in eukaryotic mRNA?
capping, splicing, and polyadenylation before being translated.
What is 5' capping in eukaryotic mRNA processing?
The addition of a 7-methylguanosine cap to the 5' end of the RNA molecule, which protects it from degradation and aids in translation initiation.
What is splicing in mRNA processing?
The process of removing introns from the primary RNA transcript and joining the remaining exons together to form a mature mRNA molecule.
What is polyadenylation in eukaryotic mRNA modification?
The addition of a poly-A tail to the 3' end of the mRNA transcript, enhancing its stability and translation efficiency.
Why is 5' capping important for mRNA?
It protects mRNA from degradation and is crucial for the recognition and binding of the ribosome during translation.
Why is splicing critical for mRNA maturation?
It ensures that only the coding sequences (exons) are retained, allowing for the correct translation into a protein.
How does polyadenylation affect mRNA stability?
The poly-A tail helps protect the mRNA from enzymatic degradation and promotes efficient translation by facilitating ribosome recognition.
What are cell-specific transcription factors?
Unique activators and repressors in different cell types that bind to enhancers or silencers to regulate gene expression.
How does chromatin accessibility affect gene expression?
Histone modifications, such as acetylation, can open or close chromatin, influencing the ability of transcription machinery to access genes.
What is epigenetic regulation?
The influence of DNA methylation and histone modifications on gene expression without altering the DNA sequence.
How do cells regulate mRNA stability?
Cells can control how long an mRNA molecule lasts, which affects the levels of the corresponding protein.
What is the role of translation control in protein expression?
Cells regulate the efficiency of mRNA translation, impacting the amount of protein produced from the mRNA.
What is splicing in mRNA processing?
The process where introns are removed, and exons are joined together by the spliceosome.
What is alternative splicing?
A mechanism that allows different exons to be included or excluded, enabling a single gene to produce multiple protein variants.
What is self-splicing?
A process where some RNA molecules remove their own introns without the need for proteins, seen in Group I and II introns.
What is DNA methylation and its effect on transcription?
DNA methylation at CpG sites silences genes by preventing transcription factor binding.
In which processes is DNA methylation commonly involved?
gene imprinting and X-chromosome inactivation.
What is acetylation in histone modifications?
facilitated by HAT enzymes, loosens chromatin and activates transcription.
What is the role of deacetylation of histones?
Deacetylation by HDAC enzymes tightens chromatin, repressing transcription.
How does methylation of histones affect gene expression?
Histone methylation can either activate or repress genes, depending on the location and type of modification.
What is the role of mRNA in translation?
carries the genetic code from DNA to the ribosome, containing codons that specify amino acids.
What is the function of tRNA during translation?
matches amino acids to corresponding codons on mRNA using its anticodon region, linking specific amino acids via aminoacyl-tRNA synthetase.
What is rRNA and its function in translation?
structural and catalytic component of ribosomes, playing a key role in assembling proteins.
What is the ribosome's structure?
molecular machine made of rRNA and proteins, consisting of two subunits: a small subunit for binding mRNA and tRNA, and a large subunit with the peptidyl transferase site for peptide bond formation.
What occurs during the initiation step of translation?
The small ribosomal subunit binds to mRNA at the start codon (AUG), the initiator tRNA binds, and the large ribosomal subunit joins to form the complete ribosome.
What happens during the elongation phase of translation?
The ribosome moves along mRNA, with each new tRNA bringing an amino acid linked to the growing polypeptide chain at the A site, while the peptide chain is held at the P site.
What are the three sites of the ribosome during translation?
The A (Aminoacyl) site for new tRNA, the P (Peptidyl) site for the growing peptide chain, and the E (Exit) site for empty tRNA.
What signals the termination of translation?
A stop codon (UAA, UAG, or UGA) is reached, leading to the binding of release factors and disassembly of the ribosome, releasing the completed protein.
What is alternative splicing?
A process by which a single gene can produce multiple mRNA transcripts by including or excluding certain exons.
What are post-translational modifications (PTMs)?
Chemical modifications that occur after translation, diversifying protein function.
What is phosphorylation in the context of PTMs?
The addition of phosphate groups to proteins, which can regulate their activity.
What is glycosylation?
The addition of sugar molecules to proteins, influencing their stability.
What role does ubiquitination play in protein regulation?
It marks proteins for degradation by the proteasome.
What is RNA editing?
The process where some mRNA sequences are altered before translation, leading to different protein variants.
How do protein complexes and folding contribute to protein function?
Proteins can interact to form functional units, and chaperone proteins assist in ensuring correct folding.
What is gene regulation in terms of tissue-specific expression?
The phenomenon where different tissues express different sets of genes, producing unique proteins based on cellular needs.
What determines protein folding?
determined by its amino acid sequence (primary structure), which influences its interactions and final shape.
What is the role of hydrophobic interactions in protein folding?
Nonpolar (hydrophobic) amino acids cluster inside the protein to avoid water, driving the folding process.
Where do polar amino acids typically reside in a folded protein?
usually found on the protein's surface, interacting with the aqueous environment.
How do hydrogen bonds contribute to protein structure?
Hydrogen bonds stabilize α-helices and β-sheets, which are key elements of the secondary structure.
What are ionic interactions in proteins?
Charged amino acids (acidic and basic) form salt bridges that contribute to the stability of the protein structure.
What are van der Waals forces?
Weak interactions between atoms that help stabilize the tertiary structure of proteins.
What is the significance of disulfide bonds in proteins?
Covalent bonds between cysteine residues help lock a protein's shape, especially in extracellular proteins.
What is the function of chaperone proteins?
assist in proper folding of proteins in vivo and prevent misfolding or aggregation.
What happens to proteins in prokaryotes after translation?
proteins fold spontaneously or with help from chaperones, and some proteins may be secreted via signal sequences.
Where does translation occur in prokaryotic cells?
Translation occurs in the cytoplasm.
What guides proteins to the membrane in prokaryotes?
Signal sequences guide proteins to the membrane for secretion.
