Molecular Biology: Gene Expression, Genomes, and Mutations

Comprehensive practice flashcards covering prokaryotic and eukaryotic gene regulation, genome sequencing and architecture, types and causes of mutations, and molecular medicine techniques.

Structural Motif

A specific 3D structural element within a larger protein region that contacts and binds target DNA by inserting into grooves and hydrogen-bonding with base pairs.

Helix-Turn-Helix Motif

A conserved DNA-binding structural motif composed of two $\alpha$-helices separated by a short "turn" sequence, allowing insertion into the DNA double helix.

Zinc Finger Motif

A conserved structural motif where an $\alpha$-helix and $\beta$-sheet coordinate a central zinc ion to mediate specific contact with target DNA.

Constitutive Proteins

Proteins that are constantly produced and expressed at continuous basal levels by a cell (always "on").

Inducible Proteins

Proteins synthesized only when required in response to specific molecular inducers that stimulate transcription.

Operon

A prokaryotic unit of transcriptional regulation consisting of a single promoter, an operator, and two or more structural genes transcribed together into a single mRNA transcript.

Operator

A regulatory DNA sequence positioned between the promoter and structural genes of an operon that functions as the binding site for repressor or activator proteins.

Repressor Protein

A regulatory protein that blocks or reduces transcription by binding to target DNA at an operator or repressor binding site.

Inducer

A small regulatory molecule (often a metabolic substrate) that binds to a repressor protein, inactivating it and stimulating gene transcription.

Co-repressor

A small molecule (often a metabolic end product) that binds to an inactive repressor protein, activating it to bind the operator and repress transcription.

trp Operon

A repressible operon that encodes enzymes required for tryptophan biosynthesis; actively transcribed when tryptophan is low and repressed when tryptophan acts as a co-repressor.

lac Operon

An inducible prokaryotic operon encoding enzymes for lactose metabolism; transcribed efficiently only when lactose is present and glucose is absent.

$\beta$-Galactosidase

An enzyme encoded by the $lacZ$ gene of the lac operon that hydrolyzes the disaccharide lactose into glucose and galactose.

$\beta$-Galactoside Permease

A bacterial membrane carrier protein encoded by $lacY$ that transports extracellular lactose into the cytoplasm.

Catabolite Activator Protein (CRP)

A prokaryotic transcriptional activator protein that binds cyclic AMP (cAMP) when glucose levels drop, binding to the lac promoter to enhance RNA polymerase recruitment.

Sigma Factor

A prokaryotic regulatory protein that binds RNA polymerase and directs it to specific recognition sequences in promoters to shift global gene expression.

Transcription Factors

Eukaryotic regulatory proteins that bind specific DNA sequences to recruit RNA polymerase and regulate transcriptional initiation and rates.

TATA Box

A conserved 8-base-pair A-T rich sequence in eukaryotic promoters located approximately $-25$ base pairs upstream from the transcription initiation site.

Enhancer

A regulatory DNA element located near or distant from a promoter that binds activator transcription factors to stimulate transcription.

Silencer

A regulatory DNA element located outside the promoter region that binds repressor transcription factors to decrease or prevent transcription.

Epigenetics

The study of changes in gene expression and chromatin state that occur without alterations to the underlying primary DNA sequence.

DNA Methylation

The enzymatic addition of a methyl group ($-\text{CH}_3$) to cytosines, predominantly at CpG islands in promoters, leading to transcriptional repression.

Histone Acetylation

The covalent addition of acetyl groups to positively charged histone tails, weakening histone-DNA interactions and opening chromatin to permit transcription.

Alternative RNA Splicing

A post-transcriptional process in eukaryotes where introns are excised and exons are joined in varying combinations, allowing a single gene to encode multiple protein isoforms.

MicroRNA (miRNA)

A short, endogenous noncoding RNA transcript that binds to complementary messenger RNAs to inhibit their translation.

Small Interfering RNA (siRNA)

A short, double-stranded regulatory RNA molecule that targets complementary messenger RNAs for endonucleolytic cleavage and degradation.

Ubiquitin-Proteasome Pathway

A cellular mechanism where proteins slated for destruction are tagged with ubiquitin chains and subsequently degraded into peptide fragments within the proteasome.

Lytic Cycle

A viral reproductive cycle where a virus commandeers host cell machinery to replicate viral nucleic acid, produce proteins, assemble virions, and lyse the host cell.

Lysogenic Cycle

A viral life cycle in which phage DNA stably integrates into the bacterial chromosome as a dormant prophage, replicating passively until excising into a lytic phase.

Human Genome Project

An international 13-year, $\$3\text{ billion}$ initiative that sequenced the $3.1\text{ billion}$ base pairs of human DNA, revealing approximately $20{,}000$ protein-coding genes.

Shotgun Sequencing

A high-throughput sequencing method where genomic DNA is fragmented at random, sequenced in short reads, and reassembled using overlapping sequence alignments.

Sanger Sequencing

A classic DNA sequencing method based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro synthesis.

Dideoxynucleotide (ddNTP)

A chain-terminating nucleotide analog lacking a $3^\prime\text{-OH}$ group on its ribose ring, preventing the formation of the next phosphodiester bond.

Next-Generation Sequencing (NGS)

Automated, highly parallel DNA sequencing platforms capable of generating millions to billions of short sequence reads simultaneously at low cost.

Genome Assembly

The bioinformatic reconstruction of a continuous genome sequence from numerous shorter fragmented sequence reads using computer algorithms.

Functional Genomics

The subfield of genomics aimed at identifying the biological roles, expressions, and phenotypic consequences of genetic sequences.

Genome Annotation

The process of identifying gene boundaries, regulatory sequences, open reading frames, and noncoding features across a sequenced genome.

Transcriptomics

The comprehensive quantitative analysis of all RNA transcripts expressed in a cell, tissue, or organism at a specific time or condition using tools such as RNA-seq.

Comparative Genomics

The comparative study of complete genome sequences from different species to trace evolutionary relationships and determine gene functions.

Metagenomics

The genomic sequencing of mixed microbial genetic material recovered directly from environmental or biological samples without prior laboratory cultivation.

C-Value Paradox

The finding that eukaryotic genome size does not correlate with organismal complexity or the total number of functional coding genes.

Gene Family

A group of evolutionarily related genes within a genome that arose via historical gene duplication events from an ancestral gene (such as globin genes).

Pseudogene

A duplicated gene copy that has accumulated deleterious mutations (e.g., loss of promoters, premature stop codons, or frame shifts) and lost its protein-coding ability.

Somatic Mutation

A genetic mutation occurring in a non-reproductive cell that is passed to daughter cells via mitosis but is not transmitted to offspring.

Germ-Line Mutation

A mutation occurring within gametes or reproductive germ cells that can be inherited by offspring through fertilization.

Loss-of-Function Mutation

A mutation resulting in reduced gene expression or the formation of an inactive protein; typically inherited in a recessive manner in diploids.

Gain-of-Function Mutation

A mutation that confers an altered or completely new biochemical activity upon a gene product; typically dominant.

Point Mutation

A localized DNA mutation caused by the substitution, addition, or deletion of a single base pair within a genetic sequence.

Transition

A point mutation substitution where a purine is replaced by another purine ($\text{A} \leftrightarrow \text{G}$) or a pyrimidine is replaced by another pyrimidine ($\text{C} \leftrightarrow \text{T}$).

Transversion

A point mutation substitution where a purine base is replaced by a pyrimidine base, or vice versa ($\text{A}/\text{G} \leftrightarrow \text{C}/\text{T}$).

Frame-Shift Mutation

A point mutation caused by an insertion or deletion of nucleotides not divisible by three, shifting the triplet reading frame of all downstream codons.

Chromosomal Inversion

A chromosomal rearrangement resulting when an excised double-stranded DNA segment flips $180^\circ$ and reinserts into the chromosome in reverse orientation.

Chromosomal Translocation

A large-scale chromosomal mutation where a segment broken from one chromosome becomes attached to a non-homologous chromosome.

Aneuploidy

A condition in which a cell or organism possesses an abnormal number of chromosomes due to meiotic nondisjunction (e.g., trisomy 21).

Polyploidy

The condition wherein an organism possesses more than two complete sets of chromosomes ($>2$) per somatic cell.

Tautomer

A spontaneous structural isomer of a purine or pyrimidine base that exhibits altered hydrogen-bonding properties, causing incorrect base pairing during replication.

Transposable Element (Transposon)

A discrete DNA sequence able to excise or replicate and insert into alternative locations within the genome via cut-and-paste or copy-and-paste transposition.

Ethyl Methanesulfonate (EMS)

A chemical alkylating mutagen that adds an ethyl group to guanine, forming $6\text{-ethylguanine}$ which incorrectly pairs with thymine during DNA replication.

Thymine Dimer

A covalent intrastrand cross-link formed between adjacent thymine bases on a DNA strand following absorption of ultraviolet (UV) radiation.

Restriction Enzyme

A bacterial endodeoxyribonuclease that cuts double-stranded DNA at palindromic recognition sequences, serving as an innate defense against bacteriophage infection.

Restriction Fragment Length Polymorphism (RFLP)

Variation in the length profiles of restriction fragments produced across individuals because mutations create or eliminate specific restriction cleavage sites.

Short Tandem Repeats (STRs)

Highly polymorphic, variable-length tandem repeats of short nucleotide sequences situated in noncoding genomic regions, widely utilized for DNA fingerprinting.

Single Nucleotide Polymorphism (SNP)

A common point polymorphism consisting of a single base-pair variation present across individuals that can serve as a linked genetic marker for traits or disease.

Ex Vivo Gene Therapy

A medical intervention where target cells (such as stem cells) are harvested from a patient, genetically modified in the laboratory, and reintroduced into the patient.

CRISPR-Cas9 Complex

An RNA-guided bacterial endonuclease complex consisting of Cas9 protein and a guide RNA that introduces targeted double-strand breaks in DNA for precise genome editing.