Exam 2

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

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

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

DNA methyltransferases (DNMTs)
Enzymes that catalyze transfer of methyl groups to cytosine residues in DNA.

S-adenosylmethionine (SAM)
Universal methyl donor used during DNA methylation reactions.

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

Mechanism of DNA methylation
DNMT cysteine attacks cytosine → covalent intermediate forms → methyl group transferred from SAM → enzyme released → methylated cytosine restored in DNA.

De novo methylation
Establishment of new methylation patterns on previously unmethylated DNA (mainly DNMT3A/3B).

Maintenance methylation
Copying of existing methylation patterns onto newly synthesized DNA strands after replication (DNMT1).

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

Role of histone H3 modifications in methylation
Histone states influence DNMT recruitment; compact chromatin promotes methylation while active chromatin inhibits it.

CpG island
Cytosine-guanine–rich promoter region where methylation usually represses transcription.

Transcriptional repression by DNA methylation
Methylation blocks transcription factor binding and recruits chromatin-compacting protein complexes.

Methyl-CpG binding proteins (MBD proteins)
Proteins that recognize methylated DNA and recruit repressors such as histone deacetylases.

Effect of methylation on chromatin
Promotes heterochromatin formation and reduces promoter accessibility.

DNA demethylation and activation
Loss of methylation opens chromatin and allows transcription machinery access.

Transcription
Synthesis of RNA complementary to a DNA template.

mRNA (messenger RNA)
RNA that carries coding information for protein synthesis.

tRNA (transfer RNA)
RNA that delivers amino acids to the ribosome during translation.

rRNA (ribosomal RNA)
Structural and catalytic RNA component of ribosomes.

RNA polymerase I
Synthesizes large ribosomal RNAs.

RNA polymerase II
Synthesizes mRNA and many regulatory RNAs.

RNA polymerase III
Synthesizes tRNA, 5S rRNA, and small RNAs.

Pre-initiation complex (PIC)
Assembly of RNA polymerase II and general transcription factors at a promoter before transcription begins.

TATA box
Core promoter DNA sequence recognized by transcription machinery.

TBP (TATA-binding protein)
Protein that binds the TATA box and initiates PIC assembly.

TFIID
General transcription factor containing TBP that recognizes promoter DNA.

TFIIA & TFIIB
Factors that stabilize promoter binding and position RNA polymerase II.

TFIIF
Factor that escorts RNA polymerase II to the promoter.

TFIIE
Recruits TFIIH to the initiation complex.

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

Mediator complex
Protein complex linking transcription activators to RNA polymerase II.

Transcription initiation
RNA polymerase binds promoter and begins RNA synthesis.

Transcription elongation
Continuous addition of nucleotides to growing RNA strand.

Transcription termination
Release of RNA transcript and dissociation of polymerase.

Primary transcript (pre-mRNA)
Initial RNA product that must be processed before translation.

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

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

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

RNA methyltransferase
Adds methyl groups to the cap using SAM.

Poly(A) tail
Stretch of adenine nucleotides added to the 3′ end of mRNA for stability and export.

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

CPSF (cleavage and polyadenylation specificity factor)
Protein complex that recognizes AAUAAA signal.

CstF
Protein that binds downstream GU-rich region during polyadenylation.

Poly(A) polymerase (PAP)
Enzyme that adds adenine residues to the 3′ end of mRNA.

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

Spliceosome
Large ribonucleoprotein complex that catalyzes pre-mRNA splicing.

snRNPs (small nuclear ribonucleoproteins)
Core spliceosome components composed of snRNA and proteins.

Major snRNPs
U1, U2, U4, U5, and U6 particles involved in splicing.

Branch point
Adenine residue within intron required for lariat formation.

First transesterification reaction
Branch-point A attacks 5′ splice site forming lariat intermediate.

Second transesterification reaction
3′-OH of exon attacks 3′ splice site joining exons.

RNA interference (RNAi)
Gene silencing mechanism using small RNAs to inhibit gene expression.

miRNA (microRNA)
Endogenous small RNA that represses translation through imperfect base pairing with target mRNA.

siRNA (small interfering RNA)
Small RNA derived from double-stranded RNA that typically causes mRNA cleavage.

RISC (RNA-induced silencing complex)
Protein complex that uses small RNAs to recognize and silence target mRNAs.

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

pri-miRNA
Primary microRNA transcript produced by RNA polymerase II.

Drosha–DGCR8 complex
Nuclear enzyme complex that cleaves pri-miRNA into pre-miRNA.

pre-miRNA
Hairpin RNA exported from nucleus for further processing.

Exportin-5
Transport protein that exports pre-miRNA from nucleus to cytoplasm.

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

Guide strand
miRNA strand retained in RISC to direct target recognition.

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

Mirtron
miRNA precursor generated from spliced introns without Drosha processing.

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