Bio 97: DNA Structure, Replication, and Genetics Review

Comprehensive vocabulary flashcards covering DNA structure, replication, transcription, translation, Mendelian genetics, population genetics, and biotechnology based on the Bio 97 lecture transcript.

DNA Nucleotide

The basic building block of DNA consisting of a phosphate group, a deoxyribose sugar, and a nitrogenous base.

Phosphodiester Bond

The linkage that joins nucleotides in chains to form DNA molecules.

Complementary Base Pairing

The specific matching of nitrogenous bases in DNA, where Adenine ($A$) pairs with Thymine ($T$) and Guanine ($G$) pairs with Cytosine ($C$) through hydrogen bonds.

Deoxyribose

The five-carbon sugar found in DNA which lacks an oxygen atom on the carbon-$2$ ($2'$) position compared to ribose.

Semi-conservative Replication

The process of DNA replication where each parental strand serves as a template, resulting in two new daughter strands each containing one parental and one new strand.

DNA Polymerase III

The enzyme responsible for copying parental DNA strands at a replication fork, synthesizing new daughter strands in a $\text{5'}$ to $\text{3'}$ direction.

Leading Strand

The daughter strand that is synthesized continuously toward the replication fork.

Lagging Strand

The daughter strand synthesized in segments away from the replication fork, requiring multiple primers.

Polymerase Chain Reaction (PCR)

A technique described as "DNA replication in a test tube" consisting of denaturation, annealing, and replication cycles to amplify DNA sequences.

Gene Expression

The process by which information from a gene is used to synthesize functional gene products, regulated in space and time.

Promoter

A DNA sequence, such as the $-10$ and $-35$ elements in prokaryotes, where RNA polymerase binds to initiate transcription.

Transcription Factor

A protein that regulates the transcription of genes by binding to specific DNA sequences like promoters, enhancers, or silencers.

Alternative Splicing

A process that increases protein diversity by producing different mRNA molecules from the same primary transcript.

Anticodon

A three-nucleotide sequence on a tRNA molecule that is complementary to an mRNA codon.

Histones

Positively charged proteins that interact with negatively charged DNA to form nucleosomes and facilitate DNA compaction.

Euchromatin

A less condensed form of chromatin that is typically transcriptionally active.

Heterochromatin

A highly condensed form of chromatin that is generally transcriptionally inactive.

Allele

Alternative forms of a single gene that can result in different phenotypes.

Law of Segregation

Mendel's law stating that alleles segregate during gamete formation so that each gamete carries only one allele for each gene.

Law of Independent Assortment

Mendel's law stating that the alleles of two or more different genes get sorted into gametes independently of one another.

Sister Chromatids

Two identical DNA molecules produced by DNA replication that are tightly attached at the centromere.

Centromere

The region where identical DNA molecules (sister chromatids) are most tightly attached to each other.

Hemizygosity

The state of having only one copy of a gene or chromosome, often explaining why $\text{X}$-linked traits are more frequent in males.

Aneuploidy

A chromosomal aberration characterized by an abnormal number of chromosomes, often caused by non-disjunction during meiosis.

Hardy-Weinberg Model

A mathematical model used to calculate allele and genotype frequencies in a population, assuming no migration, drift, mutation, selection, or non-random mating.

Heterozygote Superiority

A phenomenon, also known as balanced polymorphism, where the heterozygous genotype has a higher fitness than either homozygous genotype, keeping "bad" alleles in the gene pool.

Conjugation

A process of lateral gene transfer in bacteria requiring direct cell-to-cell contact, often mediated by F-factor plasmids.

Restriction Enzymes

Enzymes that recognize specific DNA sequences and cut the DNA, used in creating recombinant DNA molecules.

CRISPR-Cas9

A modern gene-editing technology used for precise modifications of DNA sequences.

Broad Sense Heritability

A measure used in twin studies to distinguish the proportion of trait variation due to genetic versus environmental factors.

Eugenics

A movement focused on improving the genetic quality of a human population, historically significant in the U.S.

Somatic cell nuclear transfer (SCNT)

The technique used to clone an entire organism (e.g., Dolly the sheep) by transferring the nucleus of a somatic cell into an enucleated egg cell

Cloning a gene (recombinant DNA)

The process of isolating and copying a single gene using molecular tools (restriction enzymes, vectors, host cells), rather than cloning a whole organism

Enucleated egg

An egg cell that has had its own nucleus (and thus its genetic material) removed, used as the recipient in SCNT

Cloning a sheep - basic steps

Remove nucleus from a donor somatic cell; insert it into an enucleated egg; stimulate the egg to divide; implant the resulting embryo into a surrogate mother

Reproductive cloning

Cloning aimed at producing a new living organism genetically identical to the donor

Therapeutic cloning

Cloning aimed at producing embryonic stem cells for research or treating disease, not at creating a new organism

Key difference: reproductive vs therapeutic cloning

Reproductive cloning results in a live-born organism; therapeutic cloning stops at the embryonic stem cell stage for medical use

Ethical issues in human reproductive cloning

Concerns include identity/individuality of the clone, high failure/abnormality rates seen in animal cloning, consent, and potential for exploitation

Stem cell therapy & therapeutic cloning link

Therapeutic cloning can produce patient-matched embryonic stem cells, avoiding immune rejection, for use in regenerative stem cell therapies

Restriction enzyme

A bacterial enzyme that cuts DNA at specific recognition sequences, often producing "sticky ends"; used as a tool in recombinant DNA technology

Sticky ends

Short single-stranded overhangs left after a restriction enzyme cut, which can base-pair with complementary sticky ends on other DNA fragments

Basic steps to create recombinant DNA

Cut both a plasmid vector and the gene of interest with the same restriction enzyme; mix fragments so sticky ends anneal; use DNA ligase to seal the fragments; transform the recombinant plasmid into a host cell (e.g., bacteria)

DNA ligase

An enzyme that seals the sugar-phosphate backbone, joining DNA fragments together (used after restriction enzyme cutting)

Plasmid

A small circular piece of DNA, separate from chromosomal DNA, commonly used as a vector to carry foreign genes into a host cell

Plasmid mapping / banding pattern problems

Problems that use the sizes of DNA fragments produced by restriction enzyme digestion (seen on a gel) to determine the location of cut sites on a plasmid

Gel electrophoresis

A technique that separates DNA fragments by size using an electric current through a gel matrix; smaller fragments migrate farther

DNA molecular probe

A short, single-stranded, labeled piece of DNA used to locate a complementary sequence in a mixture of DNA (e.g., on a Southern blot or in a library)

Southern blotting

A technique that transfers DNA fragments from a gel onto a membrane, then uses a probe to detect a specific DNA sequence

Cloning by hybridization

A method of finding a gene of interest in a DNA library by using a labeled probe that base-pairs with the complementary target sequence

DNA library

A collection of DNA fragments (cloned into vectors) representing all or part of an organism's genome or expressed genes

Genomic library

A DNA library containing all of an organism's DNA, including introns, exons, and non-coding regions

cDNA library

A DNA library made from mRNA (via reverse transcription), so it contains only expressed, intron-free coding sequences

Genomic vs cDNA library

Genomic libraries include the entire genome (introns + exons); cDNA libraries reflect only genes expressed in a given cell type at a given time (no introns)

Hybridization (gene-finding method)

Locating a gene of interest in a library using a labeled probe that binds a complementary sequence

Complementation (gene-finding method)

Locating a gene of interest by introducing DNA fragments into mutant cells and identifying which fragment restores normal function

Positional cloning

Locating a gene of interest based on its known chromosomal location (linkage to markers), without knowing its function first

Transgene

A gene from one organism that has been inserted into the genome of another organism

Transgenic organism

An organism that carries a foreign gene (transgene) inserted into its genome

Expression vector

A vector engineered with the necessary sequences (promoter, etc.) to allow a foreign gene to be transcribed and translated in a host cell

Forward genetics

An approach that starts with a phenotype/mutant and works to identify the responsible gene

Reverse genetics

An approach that starts with a known gene and manipulates it to determine its resulting phenotype/function

Recombinant protein production

An application of transgenic technology where a gene for a useful protein (e.g., insulin) is inserted into host cells to mass-produce that protein

Knockout mice

Transgenic mice in which a specific gene has been deliberately disabled ("knocked out") to study that gene's function

Reporter gene

A gene (e.g., GFP) attached to a gene of interest whose easily observable product indicates when/where the gene of interest is expressed

CRISPR-Cas9

A gene-editing technology that uses a guide RNA to direct the Cas9 enzyme to cut DNA at a specific target sequence, allowing genes to be disabled, edited, or replaced

Guide RNA (in CRISPR)

A short RNA sequence that directs the Cas9 enzyme to the specific complementary DNA sequence to be cut

First genetically modified crop

The Flavr Savr tomato, approved in the early 1990s, engineered for delayed ripening/extended shelf life

GM foods in the U.S.

GM crops (notably corn, soy, and cotton) are widely grown and are present in a large majority of processed foods sold in the U.S.

GM food benefits (debate)

Cited benefits include higher crop yields, pest/herbicide resistance, reduced pesticide use, and enhanced nutritional content

GM food controversies (debate)

Cited concerns include unknown long-term health effects, environmental impact (gene flow to wild plants), corporate control of seed supply, and labeling transparency

Quantitative trait

A trait that varies continuously and is influenced by multiple genes plus environment (e.g., human height)

Multifactorial trait

A trait influenced by both multiple genes and environmental factors (e.g., diabetes risk)

Additive effects and normal distribution

When multiple genes each contribute a small additive effect to a trait, the result is a continuous, bell-shaped (normal) distribution in the population

Threshold trait

A trait that is discontinuous (present/absent) but has an underlying continuous liability; the trait appears only once a genetic + environmental threshold is exceeded (e.g., pyloric stenosis)

Twin studies (genetic vs environmental variation)

Comparing trait concordance between monozygotic (identical) and dizygotic (fraternal) twins to estimate how much variation is due to genetics vs environment

Broad sense heritability (H²)

The proportion of total phenotypic variation in a population that is due to genetic variation (not environmental)

Quantitative trait loci (QTL)

Regions of the genome associated with variation in a quantitative trait; often difficult to identify because many loci contribute small effects

Allelic similarity vs DNA sequence similarity

Allelic similarity ("relatedness") measures shared ancestry/inherited alleles between individuals, while DNA sequence similarity measures overall genetic similarity, which can be high even between unrelated/distant species

Eugenics

The belief and practice aimed at improving the genetic quality of a human population, historically through selective breeding or restricting reproduction

History of eugenics in the U.S.

Included forced sterilization laws (early-to-mid 1900s), immigration restriction based on perceived genetic "fitness," and influence on Nazi eugenics programs

Designer babies (ethical debate)

The controversial concept of using genetic selection or editing to choose or enhance a child's traits, raising concerns about consent, inequality, and "playing God"

Allele frequency (AF)

The proportion of a specific allele among all alleles for a gene in a population

Genotype frequency (GF)

The proportion of individuals in a population with a specific genotype

Gene pool

The total collection of all alleles for all genes present in a population

Calculating allele frequency from genotype frequency

AF of an allele = (frequency of homozygotes for that allele) + (1/2 × frequency of heterozygotes)

Hardy-Weinberg (HW) model

A mathematical model (p² + 2pq + q² = 1) that predicts genotype frequencies from allele frequencies in a non-evolving population

Hardy-Weinberg assumptions

No mutation, no migration, no selection, random mating, infinitely large population size

HW equation for two alleles

p² (homozygous dominant) + 2pq (heterozygous) + q² (homozygous recessive) = 1, where p + q = 1

Using HW to find genotype frequencies from allele frequencies

Substitute known allele frequencies (p and q) into p² + 2pq + q² = 1 to calculate expected genotype frequencies

Carrier frequency (HW context)

The frequency of heterozygotes (2pq) in a population, representing individuals who carry one copy of a recessive allele without expressing the trait

HW with more than two alleles

Extends the equation to include all allele combinations (e.g., three alleles: p² + q² + r² + 2pq + 2pr + 2qr = 1)

HW with X-linked loci

Allele frequencies are calculated differently for males (hemizygous, genotype frequency = allele frequency) vs females (diploid, follows standard p² + 2pq + q²)

Migration (gene flow)

The movement of alleles into or out of a population due to individuals moving between populations, which can alter allele frequencies

Genetic drift

Random fluctuations in allele frequencies due to chance, especially pronounced in small populations

Mutation (as an evolutionary force)

The introduction of new alleles into a population through changes in DNA sequence; usually a slow but constant force

Natural selection (as an evolutionary force)

Differential survival and reproduction of individuals based on genotype/phenotype, causing systematic changes in allele frequencies

Non-random mating

Mating patterns (e.g., assortative mating, inbreeding) that are not random with respect to genotype, altering genotype frequencies without necessarily changing allele frequencies

Natural selection's effect on the gene pool

Increases the frequency of alleles that improve reproductive fitness and decreases the frequency of alleles that reduce it, over generations

Delayed age of onset

A mechanism keeping harmful alleles in the gene pool because the disease phenotype (and reduced fitness) doesn't appear until after reproductive age