Molecular Biology: DNA Structure, Genome Organization, and Transcription

Comprehensive vocabulary flashcards covering DNA physical structure, topology, repetitive elements, mobile transposons, genome variations, and prokaryotic transcription mechanisms based on lecture notes.

Genome

The complete set of DNA instructions contained within a single cell, including all 23 pairs of chromosomes and mitochondrial DNA in humans.

Chromosome Theory of Inheritance

The principle stating that inherited biological traits are controlled by genes residing on chromosomes, ensuring genetic continuity across generations.

Homologous Chromosomes

Pairs of matching chromosomes found in diploid organisms, where one chromosome is inherited from each parent.

Complement Gene

A gene located on the opposing, antiparallel DNA strand that runs in the reverse orientation relative to a reference gene, transcribed in its own $5' \rightarrow 3'$ direction.

Relaxed DNA

The standard, non-supercoiled structural conformation of double-stranded DNA characterized by approximately 10 nucleotide base pairs per complete helical turn.

Positive Supercoiling

The overwound state of DNA that results when there are more than 10 base pairs per helical turn.

Negative Supercoiling

The underwound state of DNA resulting from fewer than 10 base pairs per helical turn, which allows long genomic DNA to compact efficiently inside cells.

Type 1 Topoisomerase

An enzyme that alters the supercoiling of DNA by producing a transient break in only one strand of the double helix.

Type 2 Topoisomerase

An enzyme that alters DNA topology by cleaving both strands of the duplex, allowing another DNA segment to pass through before resealing the break.

Catenation

The interlinking of two separate, closed-circular DNA duplexes into a chain-like structure, mediated by type 2 topoisomerases.

Thermal Denaturation (DNA Melting)

The separation of double-stranded DNA into single strands via heat, caused by the disruption of hydrogen bonds between complementary nitrogenous bases.

Melting Temperature ($T_m$)

The midpoint temperature at which DNA thermal denaturation occurs, which increases proportionally with the percentage of guanine-cytosine ($\text{GC}$) base pairs.

Renaturation (Re-annealing)

The spontaneous reassociation of complementary single-stranded DNA into a double-stranded helix when temperature is lowered slowly.

Satellite DNA

A class of highly repetitive DNA consisting of short tandem repeats, localized predominantly at centromeres and telomeres, accounting for $1\%$ to $10\%$ of the genome.

Minisatellite DNA (VNTRs)

Unstable, highly polymorphic tandem DNA repeat sequences in the genome that historically served as the foundation for DNA fingerprinting.

Microsatellite DNA (STRs)

Very short, variable repeated DNA sequences (such as $\text{CA}$ dinucleotide repeats) used in modern forensic DNA fingerprinting.

Fluorescence In Situ Hybridization (FISH)

A molecular cytogenetic technique utilizing fluorescently labeled single-stranded probes to locate and visualize specific DNA sequences on chromosomes.

Moderately Repeated DNA Sequences

DNA sequences repeated from a few to tens of thousands of times that comprise approximately two-thirds of the genome, including ribosomal RNA genes, histone genes, SINEs, and LINEs.

Non-repeated DNA Sequences

Unique, single-copy genomic sequences that encode most cellular proteins, comprising less than $1.5\%$ of the human genome.

Polyploidization

A whole-genome duplication event resulting from hybridization between related species or failed embryonic cytokinesis, creating redundant gene copies available for evolutionary divergence.

Unequal Crossing Over

An aberrant meiotic recombination event occurring between misaligned homologous chromosomes, resulting in one gamete gaining a duplicated gene and another losing that gene.

Pseudogenes

Non-functional, duplicated gene copies that have accumulated disabling mutations over evolutionary time, numbering approximately 11,000 in the human genome.

Transposition

The biochemical process by which a discrete segment of DNA moves from one location in a chromosome or genome to another.

Transposons

Discrete DNA segments capable of moving directly from one genomic location to another via a cut-and-paste mechanism requiring transposase.

Transposase

The enzyme that recognizes terminal nucleotide footprints on a transposable element, cuts the element out of its original site, and inserts it into a new target site.

Retrotransposons

Eukaryotic mobile genetic elements that mobilize through a copy-and-paste mechanism involving transcription into RNA, reverse transcription into cDNA, and insertion into a new target site.

Short Interspersed Elements (SINEs)

Non-autonomous mobile DNA elements roughly 300 base pairs long, exemplified by Alu repeats, which number over 1 million copies in the human genome.

Long Interspersed Elements (LINEs)

Autonomous mobile DNA elements roughly 6,000 base pairs long, exemplified by L1 elements, which number approximately 500,000 copies in the human genome.

Alternative Splicing

A eukaryotic post-transcriptional process where exons of a single pre-mRNA are assembled in varying combinations, allowing one gene to produce multiple distinct protein isoforms.

Post-Translational Modifications

Covalent biochemical alterations added to translated proteins—such as phosphorylation, ubiquitination, or acetylation—that generate structural and functional complexity.

Sequence Conservation

The preservation of specific nucleotide or amino acid sequences across divergent species over millions of years of evolution, indicating essential biological function.

FOXP2

A gene encoding a transcription factor essential for speech and language that exhibits specific sequence differences between humans and chimpanzees.

Mutation

A permanent, uncorrected alteration in an organism's genotype, occurring in the nucleotide sequence, chromosome structure, or chromosome number.

Germline Mutation

A heritable genetic alteration originating in sperm or egg cells, which is transmitted to progeny and found in every cell of the offspring's body.

Somatic Mutation

A non-heritable genetic mutation arising in non-reproductive body cells that accumulates with age and can lead to malignancies such as cancer.

Single Nucleotide Polymorphism (SNP)

A specific single-base nucleotide variation within a species genome that occurs at a frequency of at least $1\%$ in the general population.

Genome-Wide Association Study (GWAS)

An observational study comparing SNP frequencies between large cohorts of affected and control individuals to identify genetic loci linked to polygenic diseases.

Copy Number Variation (CNV)

A form of structural genomic variation where the number of copies of a specific gene or large DNA segment varies among individuals, exemplified by the amylase 1 ($\text{AMY1}$) gene.

One Gene, One Polypeptide Hypothesis

The refined version of Beadle and Tatum's original hypothesis, establishing that individual genes encode specific single polypeptide chains rather than entire multimeric enzymes.

Transcription

The enzymatic synthesis of a complementary RNA molecule from a specific DNA template strand.

Translation

The cellular process of decoding the nucleotide triplet codons of messenger RNA into a sequence of amino acids to synthesize a polypeptide chain.

RNA Polymerase

A DNA-dependent enzyme that synthesizes RNA strands in a $5' \rightarrow 3'$ direction complementary to an antiparallel DNA template.

Promoter

A specific regulatory region of DNA located upstream of a gene that provides binding sites for transcription factors and RNA polymerase to initiate transcription.

Template Strand

The non-coding DNA strand ($3' \rightarrow 5'$) that physically pairs with ribonucleotides during transcription to guide the synthesis of an antiparallel RNA transcript.

Coding Strand

The non-template DNA strand ($5' \rightarrow 3'$) whose base sequence matches the resulting RNA transcript, with thymine present in place of uracil.

Sigma ($\sigma$) Factor

A bacterial accessory protein that complexes with the core RNA polymerase enzyme, enabling recognition of and binding to specific promoter consensus sequences.

Transcription Start Site ($+1$)

The specific DNA nucleotide at which transcription begins, with upstream bases assigned negative values and downstream transcribed bases assigned positive values.

Pribnow Box

A bacterial promoter consensus sequence ($\text{TATAAT}$) centered approximately 10 base pairs upstream ($-10$ region) from the transcription start site.

$-35$ Consensus Sequence

A conserved bacterial promoter sequence ($\text{TTGACA}$) located approximately 35 base pairs upstream of the transcription start site that is recognized by the bacterial sigma factor.

Intrinsic (Rho-Independent) Termination

Bacterial transcription termination mediated by the formation of an RNA hairpin structure followed by an adenine-uracil-rich ($\text{poly-U}$) region, causing RNA polymerase to stall and detach.

Rho-Dependent Termination

Bacterial transcription termination where the Rho protein binds the nascent transcript, tracks behind RNA polymerase, and unwinds the RNA-DNA hybrid once the polymerase pauses at a hairpin.