BIOB11: Molecular Aspects of Cellular and Genetic Processes (Lectures 1–6)

Comprehensive practice flashcards defining foundational concepts, macromolecular machines, and key regulatory mechanisms from Lectures 1 through 6 of Molecular Aspects of Cellular and Genetic Processes.

Law of Segregation

Mendel's principle stating that an organism's two alleles for a trait segregate from one another during gamete formation, such that each gamete carries only one allele for each trait.

Law of Independent Assortment

Mendel's principle stating that the segregation of a pair of alleles for one trait has no effect on the segregation of alleles for another trait during gamete formation.

Chiasma

The point of connection at which paired homologous chromosomes cross over and exchange genetic material during meiotic recombination.

Transforming Principle

The heritable molecule demonstrated by Oswald Avery, Colin MacLeod, and Maclyn McCarty in 1944 to be DNA, which transformed harmless R-strain Streptococcus pneumoniae into virulent S-strain cells.

Nucleotide

A molecular subunit composed of a five-carbon sugar (ribose or deoxyribose), a nitrogenous base attached to the 1' carbon, and one or more phosphate groups attached to the 5' carbon.

Phosphodiester Linkage

The covalent chemical bond joining adjacent nucleotides in DNA or RNA, linking the 3' hydroxyl group of one sugar to the 5' phosphate group of the next.

Chargaff's Rules

The empirical rules of DNA base composition stating that the amount of adenine equals thymine ($[A] = [T]$) and the amount of guanine equals cytosine ($[G] = [C]$).

Nucleosome

The fundamental structural unit of chromatin, composed of a disc-shaped histone octamer (two molecules each of H2A, H2B, H3, and H4) wrapped by approximately $147\,nucleotide\,pairs$ of double-stranded DNA.

Histone H1

A linker histone protein that binds to both the nucleosome octamer and the entry/exit path of DNA, facilitating higher-order compaction into the $30\,nm$ chromatin fiber.

Constitutive Heterochromatin

Permanently condensed, transcriptionally inactive chromatin that is enriched at centromeres, telomeres, and repeat sequences, characteristically marked by H3K9me3.

Facultative Heterochromatin

Chromatin that is reversibly condensed to regulate gene expression across cell types or developmental stages, such as developmentally repressed genes or the inactive X chromosome.

Barr Body

The condensed, transcriptionally inactive X chromosome formed during dosage compensation in female mammalian somatic cells, mediated by the long noncoding RNA Xist.

Position Effect

The alteration or silencing of gene expression that occurs when a gene is repositioned into or adjacent to heterochromatin by a chromosomal rearrangement, such as the White gene inversion in fruit flies.

Histone Acetyltransferases (HATs)

Chromatin-modifying enzymes ('writers') that add acetyl groups to specific lysine residues on histone amino-terminal tails, neutralizing positive charges and promoting an open, active chromatin state.

CpG Island

A DNA region of approximately $1000\,nucleotide\,pairs$ with a high frequency of CG dinucleotides, typically unmethylated and surrounding the promoters of mammalian housekeeping genes.

Synteny

The conservation of gene order and linkage along chromosomes between different species, such as between human and mouse genomes.

DNA Transposon

A mobile genetic element flanked by terminal inverted repeats that moves within a genome via a cut-and-paste mechanism catalyzed by the enzyme transposase.

Retrotransposon

A class of mobile genetic elements (including LINEs and SINEs) that transpose via a copy-and-paste mechanism utilizing an RNA intermediate and reverse transcriptase.

Unequal Crossing Over

An aberrant meiotic recombination event caused by misalignment of homologous sequences, resulting in a deletion on one chromosome and a tandem gene duplication on the other.

Paralogs

Genes related by descent that arose from a gene duplication event within a single genome, often evolving divergent or specialized biological functions.

Single Nucleotide Polymorphism (SNP)

A single base-pair variation in a DNA sequence present among individuals of a population, representing the most common type of human genetic variation.

Melting Temperature ($T_m$)

The temperature at which thermal denaturation of double-stranded DNA reaches $50\%$ completion, monitored by an increase in UV absorbance at $260\,nm$.

$C_0t$ Plot

A kinetic curve measuring DNA renaturation as a product of initial concentration ($C_0$) and incubation time ($t$), used to analyze sequence complexity and genome size.

Okazaki Fragments

Short, discontinuous stretches of newly synthesized DNA formed on the lagging-strand template during replication, initiated by RNA primers and stitched together by ligase.

DNA Primase

An RNA polymerase that synthesizes short RNA primers ($\sim 10\,nucleotides$) using ribonucleoside triphosphates to supply a free $3'\text{-OH}$ group for DNA polymerase elongation.

DNA Topoisomerase I

An enzyme that relieves torsional stress ahead of the replication fork by making a reversible, transient single-strand break in the phosphodiester backbone without requiring ATP.

DNA Topoisomerase II

An ATP-dependent enzyme that resolves DNA tangling and catenation by generating a transient double-strand break in one double helix and passing a second double helix through the break.

Telomerase

A specialized ribonucleoprotein reverse transcriptase that synthesizes telomeric repeat sequences ($\text{GGGTTA}$) at the $3'$ ends of eukaryotic chromosomes using its own RNA template.

t-loop

A protective structure at eukaryotic chromosome ends formed when the single-stranded $3'$ overhang loops back and invades homologous double-stranded telomeric repeats.

Nucleotide Excision Repair (NER)

A DNA repair pathway that identifies and removes bulky lesions (such as pyrimidine dimers) by excising an oligonucleotide fragment of $12\text{--}30\,nucleotides$ from the damaged strand.

Base Excision Repair (BER)

A DNA repair pathway initiated by DNA glycosylases that excise damaged or unnatural bases (such as uracil or 8-oxoguanine), generating an AP site repaired by endonucleases, polymerase, and ligase.

Nonhomologous End Joining (NHEJ)

A rapid double-strand break repair pathway active in somatic cells that aligns and rejoins broken ends without a template, often resulting in nucleotide deletions at the junction site.

Homologous Recombination (HDR)

An accurate, high-fidelity repair pathway for double-strand breaks active during S and G2 phases, involving $5'$ end resection, strand invasion mediated by RecA/Rad51, and repair synthesis from a sister chromatid.

Sigma Factor ($\sigma$)

A bacterial protein subunit that binds core RNA polymerase to assemble the holoenzyme, enabling specific recognition and binding of $-10$ and $-35$ promoter elements.

Polycistronic mRNA

A bacterial mRNA molecule containing open reading frames for multiple distinct proteins transcribed under the regulation of a single operon promoter.

TATA Box

A eukaryotic core promoter consensus sequence ($5'\text{-TATAAA-}3'$) located approximately $30\,nucleotides$ upstream of the transcription start site, recognized by the TBP subunit of TFIID.

TFIIH

A multi-subunit general transcription factor possessing ATP-dependent helicase activity to unwind promoter DNA and kinase activity to phosphorylate serine residues on the RNA Polymerase II CTD tail.

5' Cap

A modified 7-methylguanosine residue added to the $5'$ end of newly transcribed eukaryotic pre-mRNA via an unusual $5'\text{–}5'$ triphosphate bridge, protecting transcripts from degradation and aiding export.

Spliceosome

A dynamic catalytic complex composed of five snRNAs (U1, U2, U4, U5, and U6) and more than 100 proteins that removes introns from pre-mRNA through two consecutive transesterification reactions.

Exon Junction Complex (EJC)

A set of proteins deposited on spliced mRNA transcripts near exon-exon boundaries following splicing, serving as a molecular marker for successful processing and nuclear export.

Nuclear RNA Exosome

A nine-member ring-shaped macromolecular complex containing $3' \rightarrow 5'$ exonucleases that functions in the nucleus to degrade excised intron lariats and aberrant RNAs.

Small Nucleolar RNAs (snoRNAs)

A class of noncoding guide RNAs encoded in introns that base-pair with precursor rRNAs in the nucleolus to direct site-specific modifications, such as 2'-O-methylation and pseudouridylation.

Transfer RNA (tRNA)

An adaptor RNA molecule of approximately $80\,nucleotides$ that features an L-shaped tertiary structure, an anticodon loop for codon matching, and an amino acid acceptor stem ending in a $3'\text{-OH}$ group.

Wobble Hypothesis

The mechanism permitting a single tRNA to recognize multiple codons by requiring strict Watson-Crick base-pairing at codon positions 1 and 2, while accommodating nonstandard base pairing at position 3.

Aminoacyl-tRNA Synthetase

An enzyme that activates a specific amino acid via ATP hydrolysis to form an adenylated amino acid intermediate, transfers it to the $3'\text{-OH}$ of cognate tRNA, and utilizes an editing pocket for hydrolytic proofreading.