Biology 110 Unit 2 + PCR

Biology 110 at PSU

Heredity

Transmission of genetic information from parent to offspring; the process by which traits are passed down through genes.

Gregor Mendel

19th-century monk known as the father of genetics; used pea plant crosses to discover patterns of inheritance and formulate foundational genetic laws.

True-breeding

A line of organisms that, when self-fertilized or crossed with the same line, produces offspring identical to the parent for particular traits (homozygous).

Unit factors (Mendel's First Postulate)

Concept that traits are controlled by discrete 'unit factors' (now called genes) that exist in pairs in individuals.

Dominance (Mendel's Second Postulate)

One allele can mask the expression of another allele at the same locus; the visible trait in a heterozygote is the dominant phenotype.

Segregation (Mendel's Third Postulate)

Paired unit factors (alleles) separate during gamete formation so each gamete carries only one allele for each trait (explained by meiosis).

Independent Assortment (Mendel's Fourth Postulate)

Alleles of different genes segregate independently of one another during gamete formation, producing characteristic dihybrid ratios when genes are on different chromosomes.

Locus

The specific physical location or position of a gene on a chromosome.

Allele

Different versions or forms of a gene that occupy the same locus on homologous chromosomes and can produce different phenotypes.

Homozygous

Having two identical alleles for a particular gene (e.g., AA or aa).

Heterozygous

Having two different alleles for a particular gene (e.g., Aa).

Phenotype

The observable physical traits or characteristics of an organism resulting from the interaction of genotype and environment.

Genotype

The genetic makeup of an organism — the combination of alleles it carries for a particular trait or set of traits.

P generation (Parental)

The original parent generation in a breeding experiment; often true-breeding lines used by Mendel.

F1 generation

The first filial generation — offspring resulting from a cross between the parental (P) generation.

F2 generation

The second filial generation — offspring produced by crossing or selfing F1 individuals, showing segregation ratios (e.g., 3:1 for a monohybrid cross).

Monohybrid cross

A cross between two individuals that are both heterozygous (or between homozygous parents differing at one gene) for a single trait; reveals 3:1 phenotypic ratio in F2 when one allele is dominant.

Dihybrid cross

A cross examining inheritance of two different traits (two loci) at once; when unlinked, produces a 9:3:3:1 phenotypic ratio in F2 offspring.

Linked genes

Genes located close together on the same chromosome that tend to be inherited together and do not show independent assortment (unless recombination separates them).

Punnett square

A grid tool used to predict the genotypic and phenotypic outcomes of a genetic cross by listing possible gametes of each parent and combining them.

Chi-square analysis (χ²)

A statistical test used to compare observed experimental results to expected ratios to evaluate whether deviations are due to chance; uses degrees of freedom and p-values to accept or reject the null hypothesis.

Null hypothesis (genetics)

The assumption in χ² tests that observed data fit the expected Mendelian ratios — any deviations are due to random chance.

Degrees of freedom (df)

In genetics χ² tests, df = number of phenotypic categories − 1; used to determine critical χ² values for significance testing.

Sex chromosomes (human)

The pair of chromosomes (XX in females, XY in males) that determine biological sex; males are hemizygous for X-linked genes since they carry only one X chromosome.

SRY gene

Sex-determining Region Y: a gene on the Y chromosome that encodes a transcription factor initiating testes development and male sexual differentiation.

Dosage compensation

Mechanism balancing expression of X-linked genes between males and females; in mammals, this occurs by X-chromosome inactivation (forming a Barr body) in females.

Barr body

A densely staining, transcriptionally inactive X chromosome visible in the nuclei of female mammals due to X-chromosome inactivation.

Polygenic inheritance

A trait controlled by many genes (polygenes), each contributing a small effect to the phenotype; often produces continuous variation (e.g., skin color, height).

Transformation (Griffith experiment)

Process by which genetic material from one cell is taken up by another cell, changing its phenotype; Griffith's 1928 experiment suggested transforming principle when nonvirulent R bacteria became virulent after exposure to heat-killed S strain lysate.

Avery-MacLeod-McCarty experiment

A 1944 study that identified DNA as the 'transforming principle' by showing that treating bacterial extracts with DNase prevented transformation, while protease or RNase did not.

Hershey-Chase experiment

1952 bacteriophage experiment using radioactive labeling that confirmed DNA (not protein) is the genetic material transmitted by viruses into host bacteria.

DNA structure (Watson & Crick)

Double helical structure of DNA: two antiparallel strands of nucleotides held by complementary base pairing (A-T, G-C) with a sugar-phosphate backbone and specific helical dimensions.

Nucleotide

Monomer of nucleic acids composed of a pentose sugar (deoxyribose in DNA), a phosphate group, and a nitrogenous base (A, T, G, or C in DNA).

Phosphodiester bond

Covalent linkage between the 3' carbon of one sugar and the 5' phosphate of the next nucleotide that forms the sugar-phosphate backbone of DNA or RNA.

Antiparallel strands

Orientation of the two DNA strands running in opposite directions: one 5'→3' and the complementary strand 3'→5'.

Chargaff's rules

Observation that in double-stranded DNA the amount of adenine equals thymine (A=T) and guanine equals cytosine (G=C), hinting at base pairing.

Semiconservative replication

Model of DNA replication in which each new double helix consists of one parental (old) strand and one newly synthesized strand; supported by the Meselson-Stahl experiment.

Meselson-Stahl experiment

1958 experiment showing semiconservative replication: E. coli grown in heavy 15N then shifted to 14N produced hybrid and eventually light DNA bands consistent with semiconservative replication.

Origin of replication (ORI)

Specific DNA sequence where replication begins; prokaryotes often have a single ORI, while eukaryotes have multiple origins per chromosome.

Helicase

Enzyme that unwinds the double helix at replication forks by breaking hydrogen bonds between base pairs, enabling replication to proceed.

Single-strand binding proteins (SSBPs)

Proteins that bind to and stabilize single-stranded DNA during replication to prevent reannealing or secondary structures.

Topoisomerase

Enzyme that relieves torsional strain (supercoiling) ahead of replication forks by making transient cuts in DNA and re-ligating it.

Primase (RNA primase)

RNA polymerase that synthesizes short RNA primers providing a free 3'-OH for DNA polymerases to extend during DNA replication.

DNA polymerase III (prokaryotes)

Primary enzyme that synthesizes new DNA strands in the 5'→3' direction with high processivity and proofreading activity (in bacteria).

Leading strand synthesis

Continuous DNA synthesis occurring on the template strand oriented 3'→5' relative to the fork, allowing DNA polymerase to add nucleotides continuously toward the replication fork.

Lagging strand synthesis

Discontinuous DNA synthesis away from the replication fork, producing Okazaki fragments that are later joined, due to polymerase only synthesizing 5'→3'.

Okazaki fragments

Short DNA fragments synthesized on the lagging strand during DNA replication that are later replaced (RNA primers removed) and ligated to form a continuous strand.

DNA ligase

Enzyme that seals nicks in the sugar-phosphate backbone (joins Okazaki fragments) by forming phosphodiester bonds.

Exonuclease proofreading

3'→5' exonuclease activity of some DNA polymerases that removes incorrectly paired nucleotides, increasing replication fidelity.

Telomerase

Ribonucleoprotein enzyme that extends telomeres by adding repetitive DNA sequences at chromosome ends to prevent progressive shortening; active in germ cells and many cancer cells.

Mutation

Heritable change in DNA sequence ranging from single base substitutions to large rearrangements; source of genetic variation and evolution, but often harmful.

Point mutation (base substitution)

Alteration of a single nucleotide pair; can be silent (no amino acid change), missense (different amino acid), or nonsense (creates a stop codon).

Frameshift mutation

Insertion or deletion of nucleotides not in multiples of three that shifts the reading frame, often producing drastically altered, nonfunctional proteins.

Transposon (jumping gene)

Mobile DNA element that can move within the genome, potentially disrupting genes or regulatory regions and causing mutations; significant component of many genomes.

Central dogma

Flow of genetic information: DNA → RNA → Protein; DNA is transcribed into RNA, which is translated into polypeptides.

mRNA (messenger RNA)

RNA copy of a gene's coding sequence that is translated by ribosomes into a protein.

tRNA (transfer RNA)

Adapter RNA that carries specific amino acids and contains anticodons that base-pair with mRNA codons during translation.

rRNA (ribosomal RNA)

Structural and functional RNA component of ribosomes; essential for translation and peptide bond formation.

Genetic code

Triplet codon system in mRNA where each three-nucleotide codon specifies an amino acid or a stop signal; nearly universal across organisms.

Codon

Three-nucleotide sequence in mRNA that codes for a specific amino acid or a stop signal during translation.

Start and stop codons

Start codon (AUG) signals initiation and codes for methionine; stop codons (UAA, UAG, UGA) signal termination and do not encode amino acids.

Wobble hypothesis

Flexibility in base pairing at the third codon position allowing fewer tRNA molecules to recognize multiple codons for the same amino acid, providing redundancy.

Ribosome sites (A, P, E)

Three functional sites: A (aminoacyl) site binds incoming charged tRNA, P (peptidyl) site holds the tRNA with growing peptide, E (exit) site releases empty tRNA.

Translation initiation

Assembly of mRNA, initiator tRNA, and ribosomal subunits at the start codon with help of initiation factors to begin polypeptide synthesis.

Translation elongation

Cyclic process where charged tRNAs enter the A site, peptide bonds form transferring the polypeptide to the A-site tRNA, and the ribosome translocates, shifting tRNAs through P and E sites.

Translation termination

Occurs when a stop codon enters the A site; release factors bind, freeing the completed polypeptide and causing ribosome subunit dissociation.

Chaperonins (molecular chaperones)

Protein complexes that assist newly synthesized polypeptides to fold into their correct three-dimensional structures, preventing misfolding and aggregation.

Operon

A cluster of functionally related genes under the control of a single promoter and operator (common in prokaryotes), allowing coordinated regulation of gene expression.

Lactose operon

Classic inducible operon in E. coli that encodes enzymes (lacZ, lacY, lacA) for lactose utilization; repressed by a regulatory protein unless lactose (inducer) is present.

Inducible gene

Gene normally turned off that can be activated in response to an inducer molecule (e.g., lactose for the lac operon).

Constitutive gene

Gene expressed continuously at a relatively constant level, often encoding essential 'housekeeping' functions.

Polycistronic mRNA

Single mRNA molecule that encodes multiple proteins (common in prokaryotes, as in the lac operon), allowing simultaneous translation of functionally related genes.

Operator (in operons)

DNA regulatory sequence where a repressor protein binds to block RNA polymerase and prevent transcription of downstream structural genes.

Repressor protein

Regulatory protein that binds to an operator to prevent transcription; its binding can be modulated by inducers or corepressors.

Allosteric regulation (operon context)

Binding of small molecules (like lactose) to the repressor at a separate site induces conformational changes that alter DNA binding, enabling transcription.

Cis-acting elements

DNA sequences (like promoters or operators) located on the same molecule of DNA they regulate; they influence gene expression locally.

Trans-acting factors

Regulatory molecules (usually proteins, e.g., transcription factors) that can diffuse and act on multiple target genes not necessarily on the same DNA molecule.

Eukaryotic vs prokaryotic transcription

Eukaryotes have more complex regulation with multiple RNA pol enzymes, chromatin structure, and monocistronic mRNAs; prokaryotes often use polycistronic messages and simpler regulation.

Heterochromatin

Densely packed chromatin that is transcriptionally inactive and often associated with gene silencing.

Euchromatin

Loosely packed chromatin that is accessible to transcription machinery and associated with active gene expression.

DNA methylation

Epigenetic modification where methyl groups are added to DNA (commonly at CpG sites), often leading to reduced gene expression.

Genomic imprinting

Epigenetic phenomenon where only one allele (maternal OR paternal) is expressed due to parent-specific DNA methylation patterns.

Epigenetics

Study of heritable changes in gene function that do not involve changes in DNA sequence, including methylation and histone modification.

Gene amplification

Selective replication of specific gene regions to increase copy number and rapidly raise expression of needed gene products.

PCR (Polymerase Chain Reaction)

Technique that amplifies specific DNA sequences exponentially via repeated cycles of denaturation, primer annealing, and extension using a thermostable polymerase.

Taq polymerase

Heat-stable DNA polymerase from Thermus aquaticus used in PCR that withstands high denaturation temperatures and efficiently extends primers at ~72°C.

PCR primers

Short single-stranded DNA oligonucleotides that flank the target region and provide starting points for DNA synthesis during PCR.

dNTPs

Deoxyribonucleotide triphosphates (dATP, dTTP, dGTP, dCTP) — substrates used by DNA polymerase to synthesize new DNA strands.

Denaturation (PCR)

High-temperature step (~95–98°C) in PCR that separates double-stranded DNA into single strands so primers can anneal.

Annealing (PCR)

Temperature-controlled step where primers bind (anneal) to complementary sequences on single-stranded target DNA.

Extension (PCR)

Step where DNA polymerase synthesizes new DNA from the primers by adding dNTPs at ~72°C.

Target DNA (PCR)

The DNA segment intended for amplification; can be genomic DNA, plasmid DNA, or DNA isolated from samples.

Applications of PCR

Used in cloning, sequencing library preparation, forensic analysis, pathogen detection, diagnostics, and ecological barcoding.