Genetics and Molecular Biology Review: Inheritance, DNA Structure, and Biotechnology

Mendelian Genetics

• Learning goals recap:
  • Explain Mendel’s experimental approach
  • Describe monohybrid and dihybrid crosses and their outcomes
  • Explain the laws of segregation and independent assortment
  • Perform pedigree analysis
  • Identify Mendelian and non-Mendelian inheritance patterns

Mendelian genetics: basic concepts

• Heredity basics

  • Trait/character: heritable feature
  • True breeders: offspring have the same trait as the parent
  • Hybrids: offspring from genetically dissimilar parents

• Mendel’s experimental method (Practical steps)

  • Use true-breeding strains for each trait
  • Cross-fertilize true-breeding strain with alternate trait forms (reciprocal crosses)
  • Allow hybrid offspring to self-fertilize
  • Count offspring for each trait after generations

• Cross types and outcomes

  • Monohybrid cross: 1 gene, 2 alleles
  • Dihybrid cross: 2 genes, 4 alleles total considered in the cross
  • Punnett square used to predict offspring genotypes/phenotypes
  • Classic results:
  • Monohybrid F1 generation: all resemble one parent (no intermediates)
  • Monohybrid F2 generation: phenotypic ratio 3:1 (dominant:recessive), genotype ratio 1:2:1
  • Dihybrid cross: phenotypic ratio 9:3:3:1 for two genes in a classic Mendelian dihybrid cross

• Key terms and ideas

  • Allele: alternate forms of a gene
  • Homozygous: two identical alleles (PP or pp)
  • Heterozygous: two different alleles (Pp)
  • Dominant vs recessive: dominant allele’s trait appears in phenotype; recessive trait appears only when homozygous recessive
  • Alleles are discrete and do not blend in inheritance
  • Segregation: two alleles for a gene segregate into gametes, then reunite at fertilization

• Mendel’s Rules of Inheritance (summary)

  • Principle of Segregation
  • Parents have two alleles for a gene; each gamete gets one allele; fertilization reconstitutes the pair
  • Alleles: alternate forms of a gene; homozygous vs heterozygous
  • Dominance and recessivity: presence of an allele does not guarantee trait passage to offspring; dominance is about phenotype presentation, not allele passage
  • Genotypes: PP (homozygous dominant), Pp (heterozygous), pp (homozygous recessive)
  • Phenotypes reflect dominant vs recessive alleles in many cases

• Punnett square and allele notation

  • Gametes from a parent: $P$ or $p$ for a gene with two alleles
  • Cross example: Aa × Aa yields genotypes AA: Aa: aa = 1:2:1 and phenotypes 3:1 for dominant:recessive
  • Formulaic approach: for a gene with alleles A and a, cross between two heterozygotes yields:
  • Genotype ratio: 1:2:1
  • Phenotype ratio: 3:1 (dominant:recessive)

• Testcross: determining unknown genotype

  • Cross an individual with unknown genotype but dominant phenotype (A_) with a homozygous recessive (aa)
  • Purpose: reveal whether the dominant phenotype individual is AA or Aa

• Pedigree analysis (brief introduction)

  • Pedigrees track inheritance patterns in families; can reveal dominant, recessive, or sex-linked patterns
  • Useful for estimating disease risk and carrier status in humans

Extensions to Mendel (beyond simple dominance)

• Extensions acknowledge that most genes do not fit an ideal single-gene, two-allele, complete-dominance model.

• Major extensions include:

  • Polygenic inheritance: many genes influence a single trait, yielding continuous variation (e.g., height, skin color)
  • Pleiotropy: one gene influences multiple phenotypic traits (e.g., a gene with multiple effects like CFTR in cystic fibrosis can affect various organs)
  • Incomplete dominance: heterozygotes show an intermediate phenotype (e.g., red × white flowers yielding pink offspring)
  • Codominance and multiple alleles: both alleles in a heterozygote contribute to phenotype; ABO blood groups illustrate this with IA, IB, and i alleles
  • Phenotypic plasticity: environment influences gene expression (e.g., coat color in Siamese cats)
  • Epistasis: one gene’s product interferes with another gene’s expression (e.g., Labrador retriever coat color determined by pigment gene and distribution gene)

• Practical examples from the notes

  • Incomplete dominance example: red (CRCR) × white (CWCW) yields CRCW (pink) in heterozygotes; cross of pinks gives a 1:2:1 ratio (red:pink:white)
  • Codominance and multiple alleles example: ABO blood groups with IA, IB, and i; IA and IB are codominant to each other and dominant to i
  • Pleiotropy example: Cystic fibrosis has multiple organ effects due to a single gene defect
  • Polygenic trait example: human height; controlled by many genes, resulting in continuous variation
  • Epistasis example: Labrador coat color (pigment gene interacts with pigment distribution gene)

• Important notes on Mendelian deviations

  • Not all dominance is complete; some phenotypes are influenced by multiple genes or environmental factors
  • The Mendelian ratios (3:1, 9:3:3:1) are often perturbed in real-world scenarios due to these extensions

Chromosomal Basis of Inheritance and Human Genetics

• Chromosomal theory of inheritance

  • Genes reside on chromosomes; Morgan’s work with Drosophila supported this theory
  • Sex-linked traits are often inherited differently due to chromosome inheritance patterns

• X-linked inheritance and dosage compensation

  • X-linked traits show inheritance patterns distinct from autosomal genes
  • In humans, males have one X and one Y, so a single recessive allele on the X often manifests in males
  • Females have two X chromosomes; dosage compensation via X-inactivation balances expression
  • Barr body: an inactivated X chromosome in female cells, leading to genetic mosaics in heterozygous females (e.g., calico cats)

• Morgan’s X-linked eye color example in Drosophila

  • Parental cross: red-eyed male × white-eyed female (X-linked allele for eye color)
  • F1: all red-eyed
  • F2: red and white-eyed flies; all white-eyed individuals were male, establishing that the gene is on the X chromosome
  • Test cross revealed that white-eyed females are viable; thus eye color is X-linked

• Human X-linked disorders (examples)

  • Hemophilia: X-linked recessive disease affecting blood clotting protein
  • Royal family pedigree (illustrative) shows how X-linked traits can pass through generations and appear more in males

• Dosage compensation and X-inactivation in humans

  • In females, one X chromosome is randomly inactivated in each cell, creating genetic mosaics
  • Explains patchy phenotypes (e.g., calico cats; coat color mosaics in humans with X-linked genes)

• Human genetic disorders and chromosomal abnormalities

  • Autosomal disorders: often recessive (e.g., albinism) or dominant (e.g., juvenile-onset glaucoma)
  • Sickle cell disease: autosomal recessive; a single base mutation in HBB gene changes Glu to Val, causing abnormal hemoglobin structure
  • Down syndrome: trisomy 21; nondisjunction in meiosis leads to aneuploidy; incidence increases with maternal age
  • Nondisjunction and aneuploidy: too many or too few chromosomes; often inviable or lead to recognizable syndromes
  • Karyotype analysis used to diagnose chromosomal abnormalities

• Pedigrees as tools to study human inheritance

  • Pedigree analysis can identify autosomal dominant, autosomal recessive, or X-linked patterns
  • Carrier detection and risk assessment are possible with large family data

DNA: The Genetic Material and How Genes Work

• The genetic material must: replicate, store/express information, and vary to adapt to changes

• Historical identification of DNA as genetic material

  • Griffith’s transformation experiment (1928): S strain (virulent) and R strain (nonvirulent) show transformation when live R cells acquire virulence factors from dead S cells
  • Avery–MacLeod–McCarty (1944): purified DNA is the transforming material; proteins/RNA removal did not abolish transformation
  • Conclusion: DNA is the genetic material

• DNA structure and chemistry

  • Nucleotides: sugar (deoxyribose), phosphate, and nitrogenous base (A, T, C, G)
  • DNA is a double helix with antiparallel strands and a sugar-phosphate backbone
  • Base pairing: Adenine pairs with Thymine (A=T) via two hydrogen bonds; Guanine pairs with Cytosine (G≡C) via three hydrogen bonds
  • Chargaff’s rules: [A] = [T], [C] = [G]
  • Watson–Crick model (1953): two antiparallel strands form a right-handed helix; base pairs are central to genetic encoding
  • Major and minor grooves; base pairing forms the genetic code foundation

• DNA replication: semiconservative mechanism

  • Meselson–Stahl (1958) demonstrated semiconservative replication: each new double helix contains one old strand and one new strand
  • Replication requires a template, nucleotides (dNTPs), and DNA polymerase
  • Origin of replication: sites where replication begins; helicase unwinds the helix
  • Leading strand vs lagging strand synthesis; replication fork dynamics; DNA ligase joins fragments
  • In prokaryotes: single origin; in eukaryotes: multiple origins and more complex replication machinery

• Central dogma and RNA as intermediary

  • DNA -> RNA -> Protein; genetic code translates RNA into protein
  • Transcription: RNA polymerase reads the DNA template strand and synthesizes RNA
  • RNA types: mRNA, tRNA, rRNA, snRNA, miRNA/siRNA, etc.
  • Eukaryotic mRNA processing: 5' cap, 3' poly-A tail, intron removal via spliceosome; alternative splicing expands proteome
  • Prokaryotes: transcription and translation can be coupled; no extensive RNA processing

• Transcription details

  • Promoter: DNA sequence where transcription starts
  • Terminator: DNA sequence signaling transcription end
  • Transcription unit: region from promoter to terminator
  • mRNA processing in eukaryotes includes intron removal and exon joining

• Translation and the genetic code

  • Translation uses ribosomes and tRNA adapters to convert mRNA codons into amino acids
  • Codons: triplets of nucleotides in mRNA; code for amino acids or stop signals
  • Start codon: AUG (Met) initiates translation
  • Stop codons: UAA, UAG, UGA terminate translation
  • Anticodon on tRNA pairs with mRNA codon via complementary base pairing
  • Degeneracy: most amino acids are specified by more than one codon
  • The ribosome has A, P, and E sites for tRNA binding and peptide bond formation

• The genetic code in practice

  • Example codon table: UUU → Phe, UCU → Ser, UAU → Tyr, UGG → Trp, etc. (codons map to amino acids; most amino acids have multiple codons)
  • Start codon also sets reading frame; translation proceeds until a stop codon

• Mutations and their effects

  • Point mutations alter a single base; outcomes include
  • Silent mutation: same amino acid incorporated
  • Missense mutation: different amino acid incorporated
  • A classic disease example: sickle cell anemia caused by a single base change in HBB gene, replacing Glutamic acid (Glu) with Valine (Val)

• RNA processing and regulation

  • Eukaryotic transcripts may contain introns; exons encode protein
  • Alternative splicing generates multiple mRNA variants from a single gene
  • Small RNAs (miRNA, siRNA) regulate gene expression post-transcriptionally

Biotechnology and genetic engineering (Chapters 16-17 topics overview)

• Recombinant DNA and cloning

  • Restriction endonucleases cut DNA at specific recognition sequences, producing compatible ends
  • DNA ligase joins fragments to form recombinant DNA molecules
  • Vectors (e.g., plasmids) carry DNA inserts and replication origins; selectable markers (e.g., antibiotic resistance) enable identification of transformed cells
  • Creation of cDNA libraries from expressed genes via reverse transcription
  • Bacterial hosts amplify recombinant DNA via transformation
  • Applications include production of therapeutic proteins (e.g., insulin), gene function studies, and diagnostic tools

• Gel electrophoresis and DNA analysis

  • Gel electrophoresis separates nucleic acids or proteins by size; smaller fragments migrate faster
  • DNA visualization uses fluorescent dyes (e.g., ethidium bromide) under UV light
  • RFLP analysis detects polymorphisms by restriction enzyme digestion patterns; used in disease diagnosis and forensics
  • STRs (short tandem repeats) and VNTRs used for DNA fingerprinting and paternity testing

• Polymerase Chain Reaction (PCR) and RT-PCR

  • PCR rapidly amplifies specific DNA sequences in vitro using a heat-stable DNA polymerase (e.g., Taq polymerase)
  • Core steps per cycle: denaturation (~92–95°C), annealing (~50–60°C), extension (~72°C)
  • Each cycle doubles the amount of target DNA, yielding exponential amplification
  • RT-PCR converts mRNA to complementary DNA (cDNA) and then amplifies the cDNA; used to quantify gene expression

• DNA sequencing, microarrays, FISH, and gene chips

  • DNA sequencing determines the exact nucleotide order of DNA
  • Microarrays compare gene expression across many genes; cDNAs labeled with fluorescent dyes hybridize to a microarray to show up/down regulation
  • FISH (fluorescence in situ hybridization) uses fluorescent probes to detect specific DNA/RNA sequences in tissues or chromosomes; used to diagnose infections or chromosomal rearrangements
  • Gene chips assess expression patterns of thousands of genes simultaneously and identify SNPs

• Genome editing and RNA interference

  • RNA interference (RNAi): non-coding RNAs guide sequence-specific silencing of target mRNAs, reducing gene expression post-transcriptionally
  • CRISPR-Cas9: programmable genome editing that introduces mutations, deletions, or insertions at targeted DNA sequences guided by RNA
  • Both technologies enable functional gene studies and therapeutic strategies (with ethical and safety considerations)

• Practical applications and implications

  • Medical: diagnosis, personalized medicine, production of therapeutic proteins
  • Forensics: DNA fingerprinting for identity and paternity testing
  • Ethics and safety: gene editing raises concerns about off-target effects, germline modifications, and equitable access

Connections to foundational principles and real-world relevance

• Core genetic principles underpin medicine, agriculture, and forensic science
• Mendelian genetics provides a framework, but most traits involve polygenic and environmental factors; extensions like pleiotropy, epistasis, and incomplete/codominance explain deviations
• The chromosomal basis of inheritance links phenotype patterns to chromosome behavior, explaining sex-linked traits and dosage compensation in humans
• DNA as the genetic material unifies with the central dogma, tying sequence information to protein function and phenotype
• Modern biotechnology translates these concepts into practical tools for diagnosis, treatment, and biological research

Key formulas and numerical references (LaTeX)

• Monohybrid cross phenotypic ratio: 3:1
• Monohybrid cross genotype ratio: 1:2:1
• Dihybrid cross phenotypic ratio: 9:3:3:1
• Testcross design: cross with pp to reveal the genotype of an unknown dominant phenotype
• Chargaff’s rule (base composition): [A] = [T], \ [C] = [G]
• DNA strand orientation: 5' to 3' direction on one strand vs 3' to 5' on the complementary strand (antiparallel)
• Start codon: AUG; Stop codons: UAA, UAG, UGA
• Sickle cell mutation example (conceptual): single base change in gene HBB causing Glu to Val substitution; codon change from GAA (Glu) to GTA (Val) in the coding strand (illustrative; codon table maps changes to amino acids)
• Indicating the semi-conservative replication: each new double helix contains one old strand and one new strand (description rather than a numerical formula)

Note: The above notes reflect the breadth of topics in the transcript, including Mendelian genetics, extensions to Mendel, chromosomal inheritance, DNA structure and replication, the central dogma, gene expression, mutations, and foundational biotechnology methods such as PCR, cloning, and diagnostic technologies. For exam preparation, emphasize understanding of the processes, how to apply the Punnett square and pedigree analyses, and the connections between molecular mechanisms and phenotypic outcomes.