Exam 2

What is genetic alteration?

A permanent change in the DNA nucleotide sequence that alters genetic information.

What is epigenetic modification?

A heritable and reversible change in gene expression that occurs without altering the DNA sequence.

What is DNA methylation?

Addition of a methyl group to cytosine residues in DNA, typically forming 5-methylcytosine and regulating gene expression.

What are DNA methyltransferases (DNMTs)?

Enzymes that catalyze the transfer of methyl groups to cytosine residues in DNA.

What is S-adenosylmethionine (SAM)?

Universal methyl donor used during DNA methylation reactions.

What is 5-methylcytosine?

Methylated form of cytosine produced after DNMT-mediated methyl transfer.

What is the mechanism of DNA methylation?

DNMT cysteine attacks cytosine, covalent intermediate forms, methyl group transferred from SAM, enzyme released, methylated cytosine restored in DNA.

What is de novo methylation?

Establishment of new methylation patterns on previously unmethylated DNA, mainly by DNMT3A/3B.

What is maintenance methylation?

Copying of existing methylation patterns onto newly synthesized DNA strands after replication, performed by DNMT1.

What is DNA demethylation?

Removal of methylation marks through passive dilution or enzymatic oxidation pathways.

How do histone H3 modifications influence methylation?

Histone states influence DNMT recruitment; compact chromatin promotes methylation while active chromatin inhibits it.

What is a CpG island?

A cytosine-guanine–rich promoter region where methylation usually represses transcription.

How does DNA methylation cause transcriptional repression?

Methylation blocks transcription factor binding and recruits chromatin-compacting protein complexes.

What are methyl-CpG binding proteins (MBD proteins)?

Proteins that recognize methylated DNA and recruit repressors such as histone deacetylases.

What is the effect of methylation on chromatin?

Promotes heterochromatin formation and reduces promoter accessibility.

What happens during DNA demethylation and activation?

Loss of methylation opens chromatin and allows transcription machinery access.

What is transcription?

Synthesis of RNA complementary to a DNA template.

What is mRNA (messenger RNA)?

RNA that carries coding information for protein synthesis.

What is tRNA (transfer RNA)?

RNA that delivers amino acids to the ribosome during translation.

What is rRNA (ribosomal RNA)?

Structural and catalytic RNA component of ribosomes.

What does RNA polymerase I synthesize?

Large ribosomal RNAs.

What does RNA polymerase II synthesize?

mRNA and many regulatory RNAs.

What does RNA polymerase III synthesize?

tRNA, 5S rRNA, and small RNAs.

What is the pre-initiation complex (PIC)?

Assembly of RNA polymerase II and general transcription factors at a promoter before transcription begins.

What is the TATA box?

Core promoter DNA sequence recognized by transcription machinery.

What is the role of TBP (TATA-binding protein)?

It binds the TATA box and initiates PIC assembly.

What is TFIID?

General transcription factor containing TBP that recognizes promoter DNA.

What do TFIIA and TFIIB do?

They stabilize promoter binding and position RNA polymerase II.

What is the function of TFIIF?

It escorts RNA polymerase II to the promoter.

What does TFIIE do?

It recruits TFIIH to the initiation complex.

What is TFIIH?

Helicase and kinase that unwinds DNA and phosphorylates RNA Pol II CTD to initiate transcription.

What is the mediator complex?

Protein complex linking transcription activators to RNA polymerase II.

What is transcription initiation?

RNA polymerase binds to the promoter and begins RNA synthesis.

What is transcription elongation?

Continuous addition of nucleotides to the growing RNA strand.

What is transcription termination?

Release of RNA transcript and dissociation of polymerase.

What is a primary transcript (pre-mRNA)?

Initial RNA product that must be processed before translation.

What is the 5′ cap?

7-methylguanosine added to the 5′ end of pre-mRNA that protects RNA and promotes translation.

What does RNA triphosphatase do?

Removes the γ-phosphate from the 5′ end during cap formation.

What is Guanylyltransferase?

Adds GMP to the 5′ end via a 5′–5′ triphosphate linkage.

What is RNA methyltransferase?

Adds methyl groups to the cap using SAM.

What is the poly(A) tail?

Stretch of adenine nucleotides added to the 3′ end of mRNA for stability and export.

What is the polyadenylation signal (AAUAAA)?

RNA sequence directing cleavage and addition of the poly(A) tail.

What is CPSF (cleavage and polyadenylation specificity factor)?

Protein complex that recognizes AAUAAA signal.

What is CstF?

Protein that binds downstream GU-rich region during polyadenylation.

What is Poly(A) polymerase (PAP)?

Enzyme that adds adenine residues to the 3′ end of mRNA.

What is RNA splicing?

Removal of introns and joining of exons to produce mature mRNA.

What is a spliceosome?

Large ribonucleoprotein complex that catalyzes pre-mRNA splicing.

What are snRNPs (small nuclear ribonucleoproteins)?

Core spliceosome components composed of snRNA and proteins.

What are the major snRNPs involved in splicing?

U1, U2, U4, U5, and U6 particles.

What is a branch point in RNA splicing?

Adenine residue within an intron required for lariat formation.

What occurs during the first transesterification reaction?

Branch-point A attacks the 5′ splice site forming a lariat intermediate.

What occurs during the second transesterification reaction?

3′-OH of exon attacks the 3′ splice site joining exons.

What is RNA interference (RNAi)?

Gene silencing mechanism using small RNAs to inhibit gene expression.

What is miRNA (microRNA)?

Endogenous small RNA that represses translation through imperfect base pairing with target mRNA.

What is siRNA (small interfering RNA)?

Small RNA derived from double-stranded RNA that typically causes mRNA cleavage.

What is RISC (RNA-induced silencing complex)?

Protein complex that uses small RNAs to recognize and silence target mRNAs.

What is the role of the Argonaute protein?

Catalytic component of RISC that binds guide RNA and targets mRNA.

What is pri-miRNA?

Primary microRNA transcript produced by RNA polymerase II.

What is the Drosha–DGCR8 complex?

Nuclear enzyme complex that cleaves pri-miRNA into pre-miRNA.

What is pre-miRNA?

Hairpin RNA exported from the nucleus for further processing.

What is Exportin-5?

Transport protein that exports pre-miRNA from the nucleus to the cytoplasm.

What is Dicer?

RNase enzyme that cleaves pre-miRNA into mature miRNA duplex.

What is the guide strand in RNA interference?

miRNA strand retained in RISC to direct target recognition.

What is the seed region of miRNA?

Critical nucleotides at the miRNA 5′ end required for target binding.

What is a mirtron?

miRNA precursor generated from spliced introns without Drosha processing.

What are the steps in mirtron biogenesis?

Splicing → debranching → hairpin formation → export → Dicer processing → RISC loading.