Molecular Biology Review Flashcards

Flashcards for lectures 9-20 focusing on molecular biology concepts.

RecBCD

Processes double-strand breaks (DSBs), unwinds DNA, degrades strands, and loads RecA.

RecA

Binds ssDNA, performs homology search, and catalyzes strand invasion.

RuvA and RuvB

Promote branch migration of the Holliday junction.

RuvC

Resolves the Holliday junction by cleavage.

SSB (single-stranded binding protein)

Stabilizes ssDNA.

Chi sequence

Acts as a regulatory signal; enhances homologous recombination efficiency. Sequence: 5'-GCTGGTGG-3'

SDSA pathway

A conservative form of homologous recombination (no crossover); used in mitotic cells to avoid chromosomal crossover.

Site-specific recombination

Occurs at defined DNA sequences via recombinases; allows programmed rearrangements in somatic cells (e.g., immune system).

LINEs (Long Interspersed Nuclear Elements)

Autonomous retrotransposons (e.g., L1); encode reverse transcriptase and endonuclease.

SINEs (Short Interspersed Nuclear Elements)

Non-autonomous (e.g., Alu elements); use LINE machinery to transpose.

Cut-and-paste transposition

Transposase excises element and inserts it elsewhere; no copy remains at original site.

Replicative transposition

Transposon is replicated, and new copy is inserted; original copy stays in place.

Transcription bubble

Region (~17 base pairs) of unwound DNA where RNA polymerase is actively synthesizing RNA.

Template strand (antisense)

Used by RNA polymerase to synthesize RNA; read 3′ → 5′.

Coding strand (sense)

Has the same sequence as RNA (except T → U); not used for synthesis.

Sigma factor

Binds to -10 and -35 promoter regions; directs RNA polymerase to specific gene promoters; different sigma factors allow the cell to respond to environmental changes.

Abortive termination

RNA polymerase synthesizes and releases short RNA fragments (~2–9 nucleotides) during initiation; a natural part of promoter clearance.

Intrinsic termination (rho-independent)

RNA forms a GC-rich hairpin loop followed by a U-rich sequence; hairpin causes RNA polymerase to stall; weak A-U base pairing causes RNA to dissociate.

Rho-dependent termination

Requires Rho protein (ATP-dependent helicase); Rho binds to rut site on the RNA, travels along RNA to catch up with RNA polymerase, and disrupts RNA-DNA hybrid.

α-Amanitin

Used to distinguish eukaryotic RNA polymerases by sensitivity; Pol I: Insensitive, Pol II: Highly sensitive, Pol III: Moderately sensitive.

CTD of RNA Pol II

Consists of heptad repeats undergoing phosphorylation; recruits capping enzymes, splicing factors, and 3′ end processing machinery; coordinates transcription with RNA processing.

TBP (TATA-binding protein)

Binds to the TATA box in the promoter; bends DNA, facilitates transcription complex assembly, and brings in TFIID.

Mediator complex

Large multiprotein complex; acts as a bridge between transcription factors and RNA Pol II; transmits signals from enhancers to the transcription machinery.

Poly(A) polymerase (PAP)

Adds the poly-A tail (~200 A residues) to the 3′ end of pre-mRNA after cleavage.

5′ Capping

Addition of a 7-methylguanosine (m⁷G) cap to the 5′ end of mRNA; protects from degradation, facilitates ribosome binding, and assists in nuclear export.

3′ Polyadenylation

Addition of a poly(A) tail (~200 adenines) to the 3′ end of mRNA; increases mRNA stability, promotes nuclear export, and enhances translation.

Splicing

Removal of introns (noncoding regions); exons (coding regions) joined together to form mature mRNA.

Group I introns

Found in rRNA genes; self-splicing using a free guanosine nucleotide (G) as a cofactor.

Group II introns

Found in mitochondria and chloroplasts; self-splicing, but mechanism resembles spliceosome-mediated splicing.

Spliceosome

A large RNA-protein complex made of snRNPs (small nuclear ribonucleoproteins); recognizes 5′ and 3′ splice sites and the branch point.

Lariat

A looped RNA structure formed during splicing when the 2′ OH of an internal adenosine attacks the 5′ splice site.

Alternative splicing

Different combinations of exons are joined to produce multiple mRNA isoforms from a single gene; increases protein diversity.

Exonic Splicing Enhancer (ESE)

Sequence elements in exons that promote splicing; bind SR proteins to recruit spliceosome components.

Exonic Splicing Silencer (ESS)

Elements that repress splicing at nearby sites; bind hnRNPs, blocking spliceosome assembly.

Wobble hypothesis

Flexibility in base pairing at the third codon position, allowing one tRNA to pair with multiple codons.

Aminoacyl-tRNA synthetases (AARS)

Attach the correct amino acid to tRNA (charging); ATP-dependent reaction.

Shine-Dalgarno sequence

A ribosomal binding site in prokaryotic mRNA, generally located around 8 bases upstream of the start codon AUG. It helps recruit the ribosome to the mRNA to initiate protein synthesis by base-pairing with the anti-Shine-Dalgarno sequence on the 3' end of the 16S rRNA.