BIOS 1700: Chapters 11, 12, and 13 - DNA Replication, Genetic Manipulation, and Mutation

Comprehensive practice flashcards defining essential vocabulary terms from BIOS 1700 covering DNA replication, genetic manipulation, PCR, electrophoresis, Sanger sequencing, cell division, the eukaryotic cell cycle, and mutations leading to cancer.

Mutation

Any heritable change in the genetic material of an organism that occurs spontaneously and randomly, which can have positive, negative, or neutral effects on an organism's fitness.

Allele

Different versions or sequence variants of a specific gene present at the same locus on homologous chromosomes.

Polymorphism

Genetic differences at a particular site or locus in the genome that are found in multiple individuals within a population.

Selective Pressure

Environmental conditions that promote the survival and persistence of one allele or genotype over another within a population (e.g., malaria providing an advantage to the $S$ allele of $\beta$-globin in heterozygotes).

Genotype

The specific genetic makeup or combination of alleles carried by an organism (e.g., $hgbA/hgbA$, $hgbS/hgbA$, or $hgbS/hgbS$).

Phenotype

The observable physical, behavioral, or biochemical characteristics of an individual, produced by the interaction between its genotype and the environment.

Somatic Cells

Non-reproductive cells of the body; mutations arising in somatic cells affect only that individual and are not inherited by future generations.

Germ Cells

Reproductive cells (sperm and eggs) and their precursors that transmit genetic material to offspring; mutations occurring in these cells can be inherited.

Point Mutation

A mutation that involves a change in a single base pair (base substitution) within a DNA sequence.

Synonymous Mutation (Silent Mutation)

A point mutation within a protein-coding region that changes a nucleotide without altering the amino acid specified by the codon.

Nonsynonymous Mutation (Missense Mutation)

A nucleotide substitution in a coding sequence that alters a codon so that it specifies a different amino acid, which may alter protein structure and function.

Nonsense Mutation

A base substitution that converts an amino acid-specifying codon into a premature stop codon, resulting in a truncated and typically nonfunctional protein.

Single Nucleotide Polymorphism (SNP)

A single nucleotide variation found commonly at a specific site in the genome across individuals in a population, located primarily in noncoding regions.

Frameshift Mutation

A mutation caused by an insertion or deletion of nucleotides not in multiples of $3$, which shifts the translational reading frame and alters every subsequent amino acid.

Transposon (Transposable Element)

A mobile genetic element ('jumping gene') capable of excising or copying itself and inserting into new sites within a genome, often inactivating genes if integrated into them.

Recombinant DNA

A synthetic or engineered DNA molecule created in the laboratory by joining together genetic sequences from two or more distinct biological sources.

Restriction Enzyme

A bacterial endonuclease that recognizes a specific palindromic DNA sequence ($4\text{--}8$ nucleotides in length) and cleaves the phosphodiester backbones of both strands.

Sticky Ends

Single-stranded overhangs created when a restriction enzyme cuts double-stranded DNA at asymmetric, staggered sites, allowing complementary fragments to anneal.

Plasmid

A small, circular, double-stranded extrachromosomal DNA molecule found in bacteria and fungi that replicates autonomously and can be engineered as a cloning vector.

Polymerase Chain Reaction (PCR)

An in vitro technique that exponentially amplifies a targeted sequence of DNA across repeated cycles of denaturation, primer annealing, and extension.

Taq Polymerase

A heat-tolerant DNA polymerase isolated from a thermophilic bacterium that does not denature during the $95^\circ\text{C}$ strand separation phase of PCR.

Agarose Gel Electrophoresis

A technique that uses an electric current to separate negatively charged DNA fragments through an agarose mesh based on molecular size, where smaller fragments travel faster toward the positive electrode.

Dideoxyribonucleotide (ddNTP)

A modified nucleotide lacking a $3'\text{-OH}$ group on its deoxyribose ring, causing obligatory chain termination when added to a growing DNA strand during Sanger sequencing.

Sanger Sequencing

A chain-termination sequencing method that utilizes DNA polymerase, standard dNTPs, and fluorescently labeled ddNTPs to deduce nucleotide sequence via capillary electrophoresis.

Binary Fission

The asexual reproductive process in prokaryotes where the circular chromosome replicates, attaches to the cell membrane, and splits into two identical daughter cells.

FtsZ Protein

A prokaryotic protein related to tubulin that forms a contractile ring at the mid-cell division plane to separate daughter cells during binary fission.

Semiconservative Replication

The mechanism of DNA replication in which each newly formed double helix consists of one conserved parental template strand and one newly synthesized daughter strand.

Leading Strand

The daughter DNA strand synthesized continuously in the $5' \rightarrow 3'$ direction toward the unwinding replication fork.

Lagging Strand

The daughter DNA strand synthesized discontinuously in the $5' \rightarrow 3'$ direction away from the replication fork, producing Okazaki fragments.

Okazaki Fragments

Short stretches of newly synthesized DNA formed discontinuously on the lagging strand template during DNA replication.

Replication Fork

The Y-shaped region where the double-stranded parental DNA is unwound by helicase into two single template strands for replication.

DNA Helicase

An enzyme that breaks hydrogen bonds between paired nitrogenous bases to unwind and separate the parental DNA strands ahead of the polymerase.

Topoisomerase II (DNA Gyrase)

An enzyme that relieves torsional stress and downstream topological strain caused by the unwinding action of DNA helicase.

Single-Strand Binding Protein (SSB)

A protein that binds to exposed single-stranded template DNA to prevent the two strands from prematurely reannealing or being degraded.

RNA Primase

An RNA polymerase that synthesizes short complementary RNA primers that provide the necessary free $3'\text{-OH}$ group for DNA polymerase to begin synthesis.

DNA Polymerase III

The primary prokaryotic enzyme responsible for elongating leading and lagging DNA strands in the $5' \rightarrow 3'$ direction with intrinsic $3' \rightarrow 5'$ exonuclease proofreading activity.

DNA Polymerase I

A prokaryotic enzyme that removes RNA primers via its $5' \rightarrow 3'$ exonuclease activity and fills in the resulting gaps with DNA nucleotides.

DNA Ligase

An enzyme that catalyzes phosphodiester bond formation between adjacent Okazaki fragments and seals breaks in the sugar-phosphate backbone of DNA.

Proofreading

The $3' \rightarrow 5'$ exonuclease mechanism of DNA polymerases that detects mispaired nucleotides, excises them from the growing strand, and replaces them with correct bases.

Telomere

A noncoding repetitive DNA sequence (e.g., $5'\text{-TTAGGG-}3'$) located at the terminal ends of linear eukaryotic chromosomes to prevent the loss of critical coding sequences during replication.

Telomerase

A ribonucleoprotein reverse transcriptase enzyme that uses its internal RNA molecule as a template to lengthen the ends of linear chromosomes, active in germ and cancer cells.

Nucleosome

The basic repeating packaging unit of chromatin, consisting of roughly $200$ base pairs of eukaryotic DNA wound around an octamer core of histone proteins.

Histone

Positively charged, basic nuclear proteins that package and condense eukaryotic DNA into nucleosomes via electrostatic interactions with the negatively charged sugar-phosphate backbone.

Chromatin

The complex of genomic DNA and packaging proteins (histones and non-histones) within the eukaryotic nucleus that condenses to form discrete chromosomes during mitosis.

Centromere

The constricted chromosomal region that physically tethers duplicated sister chromatids together and serves as the assembly site for kinetochores.

Kinetochore

A proteinaceous multi-subunit complex assembled on the centromeric DNA of each chromatid that binds to spindle microtubules during cell division.

Centrosome

The primary microtubule-organizing center (MTOC) in animal cells consisting of a pair of centrioles that duplicates and migrates to opposite poles to establish the mitotic spindle.

Sister Chromatids

Two identical copies of a single replicated chromosome joined together at a shared centromere, produced during the S phase of interphase.

Homologous Chromosomes

A matched pair of chromosomes (one maternal, one paternal) of equal length that carry the same genes in the same sequence, but potentially with different alleles.

Autosomes

Any chromosomes that are not sex chromosomes; diploid human somatic cells contain $22$ homologous pairs of autosomes.

Interphase

The non-dividing phase of the eukaryotic cell cycle comprising $G_1$, S, and $G_2$ phases, during which cell growth, organelle replication, and DNA synthesis take place.

Prophase

The first stage of mitosis, characterized by chromosome condensation, migration of duplicated centrosomes to opposite poles, and initiation of mitotic spindle formation.

Prometaphase

The mitotic phase in which the nuclear envelope breaks down and spindle microtubules physically attach to the kinetochores of condensed sister chromatids.

Metaphase

The stage of mitosis where spindle microtubules align all replicated chromosomes along the center of the cell at the metaphase plate.

Anaphase

The mitotic stage where centromeres split and sister chromatids are pulled apart toward opposite spindle poles by shortening kinetochore microtubules.

Telophase

The final stage of mitosis wherein chromosomes reach opposite poles, decondense back into chromatin, and nuclear envelopes reform around each daughter set.

Cytokinesis

The physical division of the cytoplasm and cell body following karyokinesis, splitting the parental cell into two daughter cells.

Contractile Ring

A ring of actin microfilaments and myosin motor proteins located beneath the plasma membrane in animal cells that constricts to complete cytokinesis.

Cyclins

Regulatory proteins whose intracellular concentrations rise and fall in a cyclical pattern throughout the cell cycle, serving to activate cyclin-dependent kinases.

Cyclin-Dependent Kinases (CDKs)

Enzymes that remain at constant levels throughout the cell cycle and require cyclin binding to become catalytically active, subsequently phosphorylating target proteins that trigger cell cycle progression.

p53 Protein

A tumor suppressor protein ('guardian of the genome') that accumulates and acts as a transcription factor in the nucleus upon DNA damage, arresting the cell cycle or initiating apoptosis.

Apoptosis

Genetically programmed cell death triggered to safely destroy unrepairable, damaged, or redundant cells without provoking an inflammatory response.

Tumor Suppressor Genes

Genes that normally function as negative regulators ('brakes') of the cell cycle to prevent abnormal proliferation; loss-of-function mutations remove these blocks and promote cancer.

Proto-oncogenes

Normal cellular genes that act as positive regulators ('accelerators') to promote cell division; when mutated to overactive forms, they drive uncontrolled growth.

Oncogenes

Mutated, hyperactive, or overexpressed versions of proto-oncogenes that stimulate relentless cellular division and malignancy.