EXAM 2

BIO 111 Foundations of Biology

Point mutation

A mutation in which a single nucleotide base in a DNA or RNA sequence is altered.

Substitution mutation

A point mutation where one nucleotide is exchanged for another, which does not cause a frameshift.

Frameshift mutation

A mutation caused by the insertion or deletion of a nucleotide in an mRNA codon that alters every subsequent codon and produces a completely different protein.

DNA polymerase proofreading

A replication repair mechanism where DNA polymerase edits and corrects mismatched complementary base pairs as they form, leaving only about one error per $10^9$ bases after additional repair proteins act.

Photo 51

An X-ray diffraction photograph of crystallized DNA taken by Raymond Gosling under Rosalind Franklin's supervision that provided critical evidence for the double-helix structure.

Transformation

The transfer of genetic material from one cell or strain to another, demonstrated by Frederick Griffith when heat-killed virulent S strain S. pneumoniae permanently transformed non-virulent R strain bacteria into live S cells.

Transforming principle

The chemical substance responsible for transformation, demonstrated by Avery, MacLeod, and McCarty to be DNA because treatment with DNase destroyed transforming capability, while proteases, RNase, and ultracentrifugation did not.

Semiconservative replication

A DNA replication model confirmed by Meselson and Stahl where each original DNA strand serves as a template, producing two daughter double helices that each consist of one conserved parental strand and one newly synthesized strand.

Histone octamer

An eight-protein complex in chromatin around which approximately $146\text{--}147$ base pairs of DNA wrap, featuring long amino-terminal tails that undergo chemical modifications.

Histone acetylation

An epigenetic modification that loosens nucleosome packing, rendering DNA accessible for transcription factors to bind and activate gene expression.

DNA methylation

The addition of methyl groups to DNA bases (such as cytosine) or histones, causing tight nucleosome condensation and transcriptional silencing of the targeted gene.

Lcyc gene

The gene responsible for floral asymmetry in Linnaeus's "Monster Flower" (Antirrhinum) that is silenced by extensive DNA methylation; this epigenetic modification is heritable but can revert upon demethylation.

Hemoglobin

A tetrameric protein containing four subunits, each covalently bound to an iron-containing heme molecule, with each mature red blood cell carrying approximately $2.5 \times 10^8$ molecules to transport up to $10^9$ oxygen molecules.

Sickle cell anemia

An autosomal recessive disease caused by a point mutation in the $\beta$-hemoglobin gene that changes the codon GAG to GTG, substituting valine for glutamic acid and causing hemoglobin to clump into sickle-shaped polymers.

Casgevy (exagamglogene autotemcel)

The first FDA-approved CRISPR gene-editing therapy designed to edit a patient's mobilized hematopoietic stem cells ex vivo to produce functional hemoglobin before reinfusion.

Genomic imprinting

An epigenetic phenomenon during gametogenesis where specific genes are silenced by methylation in either the sperm or the egg, producing monoallelic expression determined by the parent of origin.

Prader-Willi syndrome (PWS)

A genetic disorder characterized by weak muscle tone and severe hyperphagia, resulting from the deletion or silencing of the paternal region on chromosome $15$.

Angelman syndrome (AS)

A neurodevelopmental disorder marked by seizures, intellectual delay, and a jerky gait, caused by the deletion or silencing of the maternal region on chromosome $15$.

Parthenogenesis

A form of asexual reproduction observed in some reptiles where an unfertilized egg develops into a viable embryo without paternal genetic contribution.

Spermatogenesis

The continuous production of male gametes beginning at puberty in a mitotically dividing stem cell population, completing meiosis in days or weeks to produce four haploid sperm per meiotic cycle.

Oogenesis

The production of female gametes initiated during embryogenesis ($2\text{--}7$ months of gestation), arresting at diplotene until puberty, and producing only one functional haploid ovum per meiotic division.

Gene

The basic physical and functional unit of heredity, consisting of a specific stretch of DNA on a chromosome that encodes a single protein or RNA molecule.

Allele

An alternate version of a specific gene that shares the same locus but possesses slight differences in nucleotide sequence.

Law of segregation

Mendel's first law stating that the two alleles of each gene separate during meiosis, ensuring each gamete receives only one allele.

Law of independent assortment

Mendel's second law stating that the alleles of two or more different genes sort into gametes independently of one another, provided they reside on different chromosomes.

Incomplete dominance

A non-Mendelian inheritance pattern where neither allele is fully dominant, producing a heterozygous phenotype that is an intermediate blend of the two homozygotes.

Codominance

An inheritance pattern where the distinct effects of both alleles are fully and simultaneously expressed in the phenotype of a heterozygote, such as spotted dog gum color.

Sex chromosomes

The pair of chromosomes ($\text{X}$ and $\text{Y}$ in humans) that determines an individual's biological sex, where the $\text{X}$ contains $1{,}180$ loci and the $\text{Y}$ contains $60$ loci.

Autosomes

All chromosomes that do not function directly as sex chromosomes, comprising $22$ homologous pairs in humans.

Genetic carrier

A heterozygous individual ($\text{X}^A\text{X}^a$ or $\text{Aa}$) who carries a single copy of a recessive disorder-causing allele without displaying symptoms.

Pedigree

A standardized genealogical diagram showing the transmission of a genetic trait or disease across two or more generations of a family.

Trisomy 21 (Down syndrome)

An aneuploidy condition in which an individual possesses three copies of chromosome $21$ ($2N + 1$) instead of the normal homologous pair.

Optogenetics

A biological technique pioneering the control of targeted neuronal activity with light using light-gated ion channels, developed by Karl Deisseroth, Peter Hegemann, and Georg Nagel.

Channelrhodopsin-2

A light-gated ion channel protein derived from the green alga Chlamydomonas reinhardtii that allows ions to cross the membrane upon optical stimulation to generate action potentials.

Ploidy

The number of complete sets of chromosomes present in a cell, such as haploid ($1N$) in gametes or diploid ($2N$) in somatic cells.

Crossing-over

The exchange of genetic material between nonsister chromatids of homologous chromosomes during prophase I of meiosis, creating novel recombinant chromosome arrangements.

Central Dogma of Molecular Biology

The principle formulated by Francis Crick stating that genetic information flows sequentially from DNA to RNA via transcription, and from RNA to protein via translation.

Differential gene expression

The mechanism whereby cells possessing identical genomes express different subsets of genes to synthesize specialized proteins according to cell type and developmental stage.

Transfer RNA (tRNA)

A short folded RNA molecule that functions as an adaptor, carrying a specific amino acid at one end and displaying an anticodon complementary to an mRNA codon at the other.

Ribosomal RNA (rRNA)

The catalytic and structural RNA components that assemble together with proteins to construct functional ribosomes in the cytoplasm.

Promoter

A specific sequence of DNA upstream of a gene where RNA polymerase binds to initiate transcription.

Terminator

A regulatory DNA sequence at the end of a gene that signals RNA polymerase to stop transcription and release the newly synthesized transcript.

RNA splicing

A post-transcriptional processing event in eukaryotes where non-coding introns are excised from pre-mRNA and coding exons are covalently linked together.

Codon

A three-nucleotide sequence in mRNA that specifies a single amino acid, a start signal (AUG), or a termination signal (UAA, UAG, UGA) during protein synthesis.

Phosphodiester bond

The covalent chemical linkage connecting the $3'$ hydroxyl group of one sugar molecule to the $5'$ phosphate group of the adjacent sugar in a nucleic acid strand.

Antiparallel

The structural arrangement of double-stranded DNA where the two sugar-phosphate backbones run in opposite directions, with one oriented $5' \rightarrow 3'$ and the complement oriented $3' \rightarrow 5'$.

Deoxyribonucleoside triphosphate (dNTP)

The monomer precursor for DNA synthesis (consisting of a deoxyribose sugar, a nitrogenous base, and three phosphate groups) that supplies energy when two phosphates are cleaved off during polymerization.

Origin of replication

A designated nucleotide sequence within a chromosome where initiator proteins bind to unwind the double helix and initiate DNA replication.

DNA helicase

An enzyme that breaks the hydrogen bonds between complementary base pairs to unwind and separate parental DNA strands at the replication fork.

Topoisomerase

An enzyme (also known as DNA gyrase) that cleaves and rejoins the phosphodiester backbone ahead of the replication fork to relieve torsional strain and prevent supercoiling.

Single-strand binding protein (SSB)

A protein that coats separated single strands of parental DNA near the replication fork to stabilize them and prevent premature re-annealing.

Primase

An RNA polymerase that synthesizes a short complementary RNA primer to provide a free $3'$ hydroxyl group required for DNA polymerase III to initiate chain elongation.

DNA polymerase III

The primary catalytic enzyme of DNA replication that elongates new DNA strands in the $5' \rightarrow 3'$ direction by catalyzing phosphodiester linkages between incoming dNTPs and the $3'$\text{-OH} end of a growing chain.

Leading strand

The newly synthesized DNA strand that is extended continuously in the $5' \rightarrow 3'$ direction toward the advancing replication fork.

Lagging strand

The newly synthesized DNA strand that is replicated discontinuously away from the replication fork in short, individual segments.

Okazaki fragments

Short stretches of newly synthesized DNA separated by RNA primers formed on the lagging strand during discontinuous replication.

DNA ligase

An enzyme that seals single-strand nicks in the phosphodiester backbone by covalently joining adjacent Okazaki fragments on the lagging strand.

Acyclovir (Zovirax)

An antiviral guanosine analogue medication that lacks a $3'$ hydroxyl group on its sugar moiety, acting as an obligate chain terminator to halt viral DNA replication.