(extra notes 8 and 6) Genetics History, Chromosome Structure, and DNA Sequencing

What methodological decision by Gregor Mendel distinguished his genetics research from previous breeders?

He categorized and counted offspring systematically to analyze numerical ratios.

Why did Mendel's breeding principles fail to replicate when tested in hawkweed?

Hawkweed reproduces primarily through apomixis, forming seeds without fertilization.

Which three botanists independently rediscovered Mendel's principles in 1900?

Hugo de Vries, Carl Correns, and Erich von Tschermak

What did Harriet Creighton and Barbara McClintock demonstrate in maize in 1931?

Genetic recombination is directly accompanied by physical exchange of chromosome material.

How did Avery, MacLeod, and McCarty identify DNA as the transforming principle in 1944?

Transforming activity survived destruction of proteins and RNA, but disappeared when DNA was destroyed.

What structural feature of DNA was revealed by Rosalind Franklin's X-ray diffraction data?

A helical geometry with the sugar-phosphate backbone on the outside and bases pointing inward.

What is paramutation?

An epigenetic interaction where one allele heritably alters the expression of its partner without changing the DNA sequence.

How was the classical "one gene, one enzyme" hypothesis experimentally refined?

It expanded to "one gene, one polypeptide," and later accounted for alternative splicing and non-coding functional RNAs.

How do transposable elements produce spotted patterns in maize kernels?

An element inserts into a pigment gene to disrupt it, and subsequent excision during development restores gene function in descendant cells.

What historical distinction does Barbara McClintock hold regarding the Nobel Prize in Physiology or Medicine?

She is the only woman to receive an unshared Nobel Prize in Physiology or Medicine.

What repeating six-letter sequence forms human telomeres?

TTAGGG

What are the two primary functions of telomeres?

Preventing DNA repair machinery from treating chromosome ends as breaks, and acting as sacrificial buffer sequence during replication.

Why is a centromere essential for proper chromosome inheritance during cell division?

It is the assembly site for the kinetochore, which spindle fibers attach to in order to pull chromosomes to opposite poles.

What do the letters $p$ and $q$ designate in chromosome nomenclature?

$p$ designates the shorter arm (from petit), and $q$ designates the longer arm.

Why must meiosis halve the chromosome number in germ cells?

To ensure that fertilization restores the normal diploid chromosome count rather than doubling it every generation.

What is the key difference between sister chromatids and homologous chromosomes?

Sister chromatids are identical replicated copies joined at a centromere; homologous chromosomes are maternal and paternal versions carrying the same genes.

During which specific division and substage of meiosis does crossing over occur?

Prophase of meiosis I, specifically during the pachytene substage.

What is a chiasma?

The visible physical connection between homologous chromosomes at the site where crossing over has taken place.

What is the biological significance of crossover assurance (the obligate crossover)?

It ensures every homologous pair forms at least one chiasma, holding homologues together until proper meiotic separation.

What is crossover interference?

The phenomenon where the formation of one crossover suppresses the occurrence of another crossover nearby on the same chromosome.

What is heterochiasmy?

A difference in crossover frequency or distribution between male and female meiosis within the same species.

How is one map unit (or centimorgan) defined in genetic mapping?

The distance between two genes that results in a one percent recombination frequency among offspring.

Which regions of the electromagnetic spectrum carry sufficient photon energy to induce chromosome breakage?

Ultraviolet radiation and ionizing radiation (such as X-rays and gamma rays).

What did Hermann Muller demonstrate by exposing fruit flies to X-rays in 1927?

He proved that an external physical agent can artificially induce heritable genetic mutations.

What is the ultimate cell division fate of an acentric fragment formed during a chromosome break?

It is lost and degraded because it lacks a centromere for spindle fiber attachment.

What is pseudodominance?

The phenotypic expression of a recessive allele when its dominant counterpart on the homologous chromosome has been deleted.

What structural chromosomal deletion causes Cri du chat syndrome?

A deletion on the short arm of chromosome 5, designated as $5p$.

What reciprocal translocation produces the Philadelphia chromosome associated with chronic myeloid leukaemia?

An exchange between chromosome 9 and chromosome 22 that fuses the $BCR$ and $ABL1$ genes.

Through what meiotic event are chromosomal duplications and deletions frequently produced together?

Unequal crossing over between misaligned homologous chromosomes.

How did Palmer amaranth populations evolve resistance to the herbicide glyphosate via gene duplication?

They amplified the $EPSPS$ gene up to over 160 copies, producing enzyme levels too high for normal herbicide doses to block.

Why does gene duplication provide crucial raw material for evolutionary innovation?

One copy maintains original essential function while the redundant copy accumulates mutations that can yield new functions.

What distinguishes a pericentric inversion from a paracentric inversion?

A pericentric inversion includes the centromere within the inverted segment; a paracentric inversion lies entirely within a single arm.

What chromosomal products result from a crossover inside a paracentric inversion loop?

One dicentric chromosome (which forms a bridge and breaks) and one acentric fragment (which is lost).

Why do inversions act as crossover suppressors in genetic mapping studies?

Recombinant gametes resulting from crossovers inside the inversion loop are structurally unbalanced and unviable.

What is a supergene?

A block of functional genes held together by suppressed recombination (often inside an inversion) and inherited as a single unit.

What four-chromosome structure forms during meiotic prophase I in a reciprocal translocation heterozygote?

A cross-shaped structure called a quadrivalent.

Which segregation pattern in a reciprocal translocation carrier yields balanced, viable gametes?

Alternate segregation.

Why does adjacent segregation in a reciprocal translocation carrier lead to unviable gametes?

It sends one normal and one translocated chromosome together, leaving each gamete duplicated for some regions and deleted for others.

Why does a plant carrying a reciprocal translocation often show semisterility?

Unbalanced gametes from adjacent segregation fail to develop, resulting in roughly half the pollen grains collapsing.

What structural modification occurs in a Robertsonian translocation?

Two acrocentric chromosomes fuse near their centromeres with the loss of their short arms.

Why is a dominant allele of both $R1$ and $C1$ required to produce pigment in maize kernels?

$R1$ and $C1$ encode distinct transcription factors that must partner to activate structural genes in the anthocyanin pathway.

What ratio of coloured to colourless kernels results from a testcross of a double heterozygote ($R1r1 C1c1 \times r1r1 c1c1$) under independent assortment?

1:3 (one-fourth coloured to three-fourths colourless).

What total sequence components are included in the formal definition of a genome?

All nuclear sequence, including coding genes, regulatory regions, repetitive DNA, transposons, centromeres, and telomeres.

Approximately what percentage of the human genome consists of protein-coding exons?

1 to 2

What evolutionary origin accounts for the presence of circular genomes inside mitochondria and chloroplasts?

The endosymbiotic theory: both organelles descend from free-living bacteria engulfed by an ancestral cell.

How are organellar genomes typically inherited in most flowering plants?

Uniparentally through the maternal line.

Which DNA base pair is held together by three hydrogen bonds rather than two?

Guanine and cytosine (G-C).

How do purines and pyrimidines differ structurally in DNA?

Purines (adenine and guanine) have a double-ring structure; pyrimidines (thymine and cytosine) have a single-ring structure.

What core logic distinguishes Sanger sequencing from the Maxam-Gilbert method?

Maxam-Gilbert degrades DNA chemically; Sanger synthesizes a new complementary strand using chain-terminating nucleotides.

What modified molecules cause chain termination in Sanger sequencing?

Dideoxynucleotides (ddNTPs), which lack the 3'-OH group needed to form a phosphodiester bond.

Why do next-generation sequencing platforms struggle to assemble highly repetitive plant genomes?

Their short reads (50â€"300 bp) cannot span long repetitive stretches to anchor in unique surrounding sequence.

What causes the signal from a flow cell cluster to degrade as next-generation sequencing cycles progress?

Loss of synchrony among molecules within the cluster, as some fail to add a base while others run ahead.

What primary advantage do third-generation long-read technologies offer over next-generation sequencing?

They produce reads tens of thousands of bases long that can span complex repetitive regions entirely.

What is the C-value paradox?

The observation that genome size varies by orders of magnitude among organisms of similar complexity without reflecting gene count.

What is a single nucleotide polymorphism (SNP)?

A DNA sequence variation occurring at a single base position among individuals of the same species.

What is linkage disequilibrium?

The non-random association of alleles at different loci in a population, occurring more frequently than expected by chance.

How does the underlying genetic architecture of a qualitative trait differ from that of a quantitative trait?

Qualitative traits are controlled by one or few genes of large effect; quantitative traits are controlled by many loci of small effect.

How does measuring plant height in discrete categories versus centimetres alter the detected genetic architecture?

Categorizing as tall/dwarf reveals major single genes; measuring continuous centimetres reveals multiple quantitative trait loci (QTLs).

How are genes and repetitive sequence distributed relative to centromeres on tomato chromosomes?

Genes are concentrated at the distal ends of arms, while repetitive sequences accumulate heavily in pericentromeric regions.

What mechanism distinguishes DNA transposons from LTR retrotransposons?

DNA transposons move via a cut-and-paste mechanism; retrotransposons move via a copy-and-paste mechanism using an RNA intermediate.

Why are SINEs dependent on LINEs for movement within a genome?

SINEs are non-autonomous and lack transposition machinery, so they appropriate the enzymes produced by active LINEs.

How does DNA methylation silence gene transcription?

It blocks transcription factor binding directly and recruits methyl-CpG binding proteins that compact chromatin into an inaccessible state.

What is synteny?

The conservation of gene order along matching genomic regions across different species inherited from a common ancestor.

How do orthologs differ from paralogs?

Orthologs are homologous genes in different species separated by speciation; paralogs are homologous genes in one species separated by duplication.

What chromosomal event accounts for the difference between Przewalski's horse (66 chromosomes) and the domestic horse (64 chromosomes)?

A Robertsonian translocation fused two acrocentric chromosomes into the single chromosome ECA5.

Why is crossing over completely suppressed within a hemizygous chromosome region?

The hemizygous region lacks a sequence partner on the homologous chromosome, offering nothing to pair or align with.