mcb 121 exam 4

Flashcards covering vocabulary from MCB 121 S2025 Lecture 14, including mRNA vaccines, VDJ recombination, transposons, and ATAC-seq.

mRNA vaccines

Vaccines that use in vitro transcribed mRNA to instruct cells to produce an antigen, such as the SARS-CoV-2 spike protein, to elicit an immune response.

Lipid nanoparticles (LNPs)

Delivery systems that encapsulate mRNA, protecting it from degradation and facilitating uptake by immune cells.

N1-methyl-pseudouridine

A modified nucleotide used instead of uridine in mRNA vaccines to reduce innate immune activation and improve stability and translation.

Memory B cells

Long-lived B cells that are produced after vaccination or infection and can rapidly respond to future encounters with the same antigen.

VDJ recombination

The process by which immunoglobulin genes are rearranged to generate antibody diversity.

Immunoglobulin (Ig)

Antibodies composed of two light and two heavy chains that recognize and bind to antigens.

V, D, J, C regions

Gene segments that are recombined to form the variable and constant regions of antibodies.

RAG1 and RAG2

Enzymes that mediate V(D)J recombination by binding recombination signal sequences and forming hairpin intermediates.

Recombination signal sequences (RSS)

Conserved DNA sequences adjacent to V, D, and J segments that guide RAG-mediated recombination.

12/23 rule

Ensures proper recombination of gene segments by allowing only RSS pairs with 12- and 23-bp spacers to be joined.

Allelic exclusion

A process ensuring that each B or T cell expresses a single antigen receptor specificity, influenced by replication timing and chromatin state.

Transposons

Mobile genetic elements that can change position within the genome; discovered by Barbara McClintock.

Transposase

The enzyme that mediates movement of DNA transposons.

DNA transposons

Move by a 'cut and paste' mechanism, excising from one location and inserting into another.

Retrotransposons

Move through an RNA intermediate that is reverse transcribed into DNA and inserted into the genome.

Endogenous retroviruses (ERVs)

Ancient retroviral sequences in the genome that resemble retrotransposons.

LINEs (Long Interspersed Nuclear Elements)

Autonomous retrotransposons that encode proteins necessary for their own transposition.

SINEs (Short Interspersed Nuclear Elements)

Nonautonomous elements that rely on LINE-encoded proteins to transpose; Alu elements are a common example in primates.

CTCF

A transcription factor involved in genome organization; CTCF sites often occur near SINEs and may help define TAD boundaries.

Target-primed reverse transcription (TPRT)

Mechanism used by LINE-1 elements for insertion, using a polyA tail to prime reverse transcription at T-rich sites.

ATAC-Seq

A method to assess chromatin accessibility using a hyperactive Tn5 transposase loaded with sequencing adapters.

Tn5 transposase

An enzyme used in ATAC-Seq to insert sequencing adapters into open chromatin regions for high-throughput analysis.

Homologous recombination (HR)

A precise DNA repair mechanism that uses a homologous sequence as a template to repair double-strand breaks.

Nonhomologous end joining (NHEJ)

An error-prone DNA repair pathway that directly joins the ends of DNA double-strand breaks without requiring a homologous template.

Frameshift mutation

A genetic mutation caused by insertions or deletions of a number of nucleotides not divisible by three, disrupting the reading frame.

CRISPR-Cas9

A genome-editing tool that introduces double-strand breaks at specific DNA locations using a guide RNA and the Cas9 nuclease.

Homology-directed repair (HDR)

A DNA repair pathway that uses a homologous sequence as a template to accurately repair double-strand breaks.

Ku70/Ku80

A heterodimer protein complex that binds to DNA ends and initiates NHEJ repair.

DNA-PKcs

DNA-dependent protein kinase catalytic subunit that participates in NHEJ by processing DNA ends and recruiting other repair factors.

XRCC4

A DNA repair protein essential for ligating DNA ends during NHEJ.

DNA ligase IV

An enzyme that seals DNA nicks in the final step of NHEJ.

RAG1/RAG2

Recombinase enzymes that introduce DSBs at specific sites in V(D)J recombination.

Artemis

A nuclease that opens hairpin structures at coding ends during V(D)J recombination.

Philadelphia chromosome

A chromosome abnormality caused by a reciprocal translocation between chromosomes 9 and 22, producing the BCR-ABL fusion gene.

BCR-ABL

A fusion gene resulting from the Philadelphia chromosome translocation that encodes an oncogenic tyrosine kinase.

Unequal crossover

A recombination event between misaligned homologous chromosomes that can lead to duplications, deletions, or other rearrangements.

LINEs/SINEs

Long and short interspersed nuclear elements; repetitive sequences that can promote recombination and exon shuffling.

Exon shuffling

An evolutionary mechanism where exons are mixed between genes through recombination, leading to new gene variants.

Meiosis

A type of cell division that produces haploid gametes from diploid cells, involving two rounds of chromosome segregation.

Synaptonemal complex

A proteinaceous structure that forms between homologous chromosomes during meiosis to mediate alignment and recombination.

Leptotene

The first stage of meiotic prophase I where chromosomes begin to condense and DSBs are introduced.

Zygotene

The meiotic stage where homologous chromosomes begin to pair and the synaptonemal complex starts forming.

Pachytene

The stage of meiosis where homologs are fully synapsed and the transition from the Double-Holiday Junction to crossovers occurs.

Spo11

A transesterase enzyme that initiates meiotic recombination by forming DSBs through a reaction involving a tyrosine nucleophile.

Exo1

A 5′ to 3′ exonuclease that processes DNA ends to produce 3′ ssDNA tails during homologous recombination.

Rad51/Dmc1

Recombinases that mediate strand invasion during homologous recombination to find and pair with a homologous sequence.

Double-Holliday junction

A recombination intermediate formed during homologous recombination, whose resolution can lead to crossovers or non-crossovers.

Synthesis Dependent Strand Annealing (SDSA)

A recombination mechanism that avoids crossover by synthesizing new DNA and annealing it to the other DSB end.

ZMM proteins

A group of meiosis-specific proteins that promote crossover formation and regulate recombination outcomes.

Aneuploidy

A condition in which cells have an abnormal number of chromosomes, often leading to genetic disorders or pregnancy loss.

Trisomy

The presence of an extra chromosome in a diploid organism, such as in Down syndrome (trisomy 21).

Maternal age effect

The increased risk of chromosomal abnormalities, particularly aneuploidy, with advancing maternal age.

Chiasmata

Physical connections between homologous chromosomes formed by crossovers, essential for proper chromosome segregation.

Cohesin

A protein complex that holds sister chromatids together and is crucial for chromosome alignment and segregation.

Cisplatin

A chemotherapy drug that forms DNA crosslinks, blocking DNA replication and leading to cell death.

Etoposide

A topoisomerase II inhibitor that prevents the resealing of DNA breaks, inducing lethal DNA damage in rapidly dividing cells.

Topoisomerase II

An enzyme that introduces and reseals double-strand breaks in DNA to relieve supercoiling during replication and transcription.

Ciprofloxacin (Cipro)

A broad-spectrum antibiotic that inhibits bacterial topoisomerases, preventing DNA replication in bacteria.