6.6 Genetics and DNA

Genetics and DNA revolutionized our understanding of life during the Modern Period. From discovering DNA's structure to unraveling inheritance patterns, these advances led to breakthroughs in medicine, agriculture, and biotechnology.

This topic explores the fundamentals of genetics, DNA replication, protein synthesis, mutations, and gene regulation. It also covers genetic engineering techniques, human genetics, population genetics, and evolutionary genetics, highlighting their impact on modern science and society.

Fundamentals of genetics

• Genetics revolutionized our understanding of heredity and biological variation during the Modern Period
• Advances in genetics led to breakthroughs in medicine, agriculture, and biotechnology
• Genetic discoveries shaped modern theories of evolution and the diversity of life

DNA structure and function

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• Double helix structure discovered by Watson and Crick in 1953
• Consists of nucleotide base pairs (adenine-thymine, guanine-cytosine) joined by hydrogen bonds
• Sugar-phosphate backbone forms the outer edges of the helix
• Stores and transmits genetic information through base pair sequences
• Undergoes replication to pass genetic material to daughter cells

Genes and chromosomes

• Genes defined as segments of DNA that code for specific proteins or RNA molecules
• Located on chromosomes composed of tightly coiled DNA and proteins
• Humans have 23 pairs of chromosomes (22 autosomes + sex chromosomes)
• Alleles represent alternative forms of a gene (dominant vs recessive)
• Gene expression influenced by regulatory sequences (promoters, enhancers)

Mendelian inheritance patterns

• Gregor Mendel's experiments with pea plants established fundamental principles of heredity
• Dominant and recessive alleles determine trait expression
• Monohybrid crosses involve one trait (3:1 phenotypic ratio in F2 generation)
• Dihybrid crosses involve two traits (9:3:3:1 phenotypic ratio in F2 generation)
• Punnett squares used to predict offspring genotypes and phenotypes
• Exceptions include incomplete dominance and codominance

DNA replication and repair

• DNA replication ensures genetic continuity between generations of cells
• Accurate replication critical for maintaining genome integrity
• Repair mechanisms evolved to correct errors and damage to DNA

Semiconservative replication process

• Each strand of DNA serves as template for synthesis of new complementary strand
• Results in two identical DNA molecules, each with one old and one new strand
• Begins at specific sequences called origins of replication
• Proceeds bidirectionally along the DNA molecule
• Requires unwinding of DNA helix by helicase enzyme

DNA polymerase and enzymes

• DNA polymerase adds nucleotides to growing DNA strand in 5' to 3' direction
• Primase synthesizes short RNA primers to initiate replication
• Ligase joins Okazaki fragments on lagging strand
• Topoisomerase relieves tension caused by unwinding of DNA
• Single-stranded binding proteins stabilize separated DNA strands

Proofreading and error correction

• DNA polymerase has 3' to 5' exonuclease activity for immediate error correction
• Mismatch repair system detects and corrects base-pairing errors after replication
• Nucleotide excision repair removes damaged DNA segments
• Base excision repair corrects chemically altered bases
• Double-strand break repair fixes breaks in both DNA strands

Protein synthesis

• Central dogma of molecular biology: DNA → RNA → protein
• Process of gene expression converts genetic information into functional products
• Crucial for cellular function and organism development

Transcription of DNA

• RNA polymerase synthesizes RNA complementary to DNA template strand
• Initiation begins at promoter sequence recognized by RNA polymerase
• Elongation proceeds as RNA polymerase moves along DNA, adding nucleotides
• Termination occurs at specific sequences, releasing newly formed RNA
• Post-transcriptional modifications in eukaryotes (5' cap, poly-A tail, splicing)

Translation of mRNA

• Occurs on ribosomes in cytoplasm or on rough endoplasmic reticulum
• Initiation complex forms at start codon (AUG) with initiator tRNA
• Elongation involves sequential addition of amino acids to growing polypeptide
• Termination occurs when ribosome encounters a stop codon (UAA, UAG, UGA)
• Newly synthesized proteins may undergo post-translational modifications

Genetic code and codons

• Triplet code: three nucleotides (codon) specify one amino acid
• 64 possible codons, 61 code for amino acids, 3 are stop codons
• Degeneracy: multiple codons can specify the same amino acid
• Start codon (AUG) initiates translation and codes for methionine
• Universal genetic code shared by most organisms with few exceptions

Genetic mutations

• Alterations in DNA sequence that can affect gene function and expression
• Source of genetic variation essential for evolution and adaptation
• Can be beneficial, neutral, or harmful to organisms

Types of mutations

• Point mutations: single nucleotide changes (substitution, insertion, deletion)
• Frameshift mutations: insertions or deletions that alter reading frame
• Chromosomal mutations: large-scale changes in chromosome structure
  • Inversions: segment of chromosome flips 180 degrees
  • Translocations: exchange of segments between non-homologous chromosomes
  • Duplications: repetition of chromosome segment
  • Deletions: loss of chromosome segment

Causes of mutations

• Spontaneous errors during DNA replication or repair
• Exposure to mutagens (physical or chemical agents)
  • Ionizing radiation (X-rays, gamma rays)
  • Ultraviolet light
  • Chemical mutagens (benzene, nitrous acid)
• Viral infections inserting genetic material into host genome
• Transposable elements moving within genome

Effects on protein synthesis

• Silent mutations: no change in amino acid sequence
• Missense mutations: change in single amino acid
• Nonsense mutations: premature stop codon, truncated protein
• Frameshift mutations: altered amino acid sequence, often nonfunctional protein
• Splice site mutations: abnormal mRNA processing, altered protein

Gene regulation

• Controls when and where genes are expressed in an organism
• Crucial for cellular differentiation and response to environmental stimuli
• Enables complex organisms to develop from a single fertilized egg

Prokaryotic vs eukaryotic regulation

• Prokaryotic regulation often involves operons (lac operon, trp operon)
• Eukaryotic regulation more complex, involves multiple levels of control
• Prokaryotes have coupled transcription and translation
• Eukaryotes have spatial and temporal separation of transcription and translation
• Eukaryotic regulation includes chromatin remodeling and nuclear transport

Transcription factors

• Proteins that bind to specific DNA sequences to control gene expression
• Activators enhance transcription by recruiting RNA polymerase
• Repressors inhibit transcription by blocking RNA polymerase binding
• Combinatorial control: multiple transcription factors work together
• Tissue-specific transcription factors determine cell type-specific gene expression

Epigenetic modifications

• Heritable changes in gene expression without altering DNA sequence
• DNA methylation typically represses gene expression
• Histone modifications (acetylation, methylation) affect chromatin structure
• Chromatin remodeling complexes alter nucleosome positioning
• Non-coding RNAs (miRNAs, lncRNAs) regulate gene expression post-transcriptionally

Genetic engineering techniques

• Revolutionized molecular biology and biotechnology in the Modern Period
• Enabled manipulation of genetic material for research and practical applications
• Raised ethical considerations regarding genetic modification of organisms

Recombinant DNA technology

• Involves combining DNA from different sources to create novel genetic sequences
• Restriction enzymes cut DNA at specific recognition sites
• DNA ligase joins DNA fragments with complementary ends
• Plasmid vectors used to introduce foreign DNA into host cells
• Bacterial transformation and selection for recombinant cells
• Applications include production of human insulin and growth hormone

CRISPR-Cas9 gene editing

• Precise genome editing technique adapted from bacterial immune system
• CRISPR RNA (crRNA) guides Cas9 nuclease to target DNA sequence
• Cas9 creates double-strand break at specific location
• Cell repair mechanisms used to introduce desired genetic changes
• Potential applications in treating genetic disorders and crop improvement
• Ethical concerns regarding human germline editing

Polymerase chain reaction (PCR)

• Amplifies specific DNA sequences exponentially
• Requires template DNA, primers, nucleotides, and heat-stable DNA polymerase
• Thermal cycling process: denaturation, annealing, extension
• Enables production of millions of copies from small amount of starting material
• Applications in diagnostics, forensics, and molecular biology research
• Variations include reverse transcription PCR (RT-PCR) for RNA analysis

Human genetics

• Study of inheritance patterns and genetic variation in humans
• Advances in human genetics led to improved understanding of diseases and traits
• Ethical considerations in genetic testing and counseling

Inheritance of traits

• Monogenic traits follow simple Mendelian inheritance patterns
• Polygenic traits influenced by multiple genes and environmental factors
• Codominance and incomplete dominance affect trait expression
• Sex-linked traits located on X or Y chromosomes (hemophilia, color blindness)
• Mitochondrial inheritance through maternal lineage
• Genomic imprinting affects gene expression based on parental origin

Genetic disorders

• Caused by mutations in one or more genes or chromosomal abnormalities
• Single-gene disorders (cystic fibrosis, sickle cell anemia)
• Chromosomal disorders (Down syndrome, Turner syndrome)
• Multifactorial disorders influenced by genes and environment (diabetes, cancer)
• Genetic testing used for diagnosis, carrier screening, and risk assessment
• Gene therapy approaches aim to treat genetic disorders at molecular level

Pedigree analysis

• Visual representation of family history and inheritance patterns
• Symbols indicate gender, affected status, and relationships
• Used to determine mode of inheritance (dominant, recessive, X-linked)
• Helps calculate probability of inheriting specific traits or disorders
• Valuable tool in genetic counseling and risk assessment
• Limitations include incomplete penetrance and variable expressivity

Population genetics

• Studies genetic composition and changes in populations over time
• Bridges gap between individual genetics and evolutionary processes
• Influenced by factors such as mutation, selection, and genetic drift

Gene pool and allele frequencies

• Gene pool represents all alleles present in a population
• Allele frequency measures proportion of specific allele in gene pool
• Genotype frequencies describe proportion of different genotypes
• Hardy-Weinberg principle used to calculate expected genotype frequencies
• Changes in allele frequencies indicate evolutionary processes at work

Hardy-Weinberg equilibrium

• Theoretical model describing genetic equilibrium in populations
• Assumes large population size, random mating, no selection or migration
• Represented by equation: $p^2 + 2pq + q^2 = 1$
• p and q represent allele frequencies for two alleles of a gene
• Deviations from equilibrium suggest evolutionary forces acting on population

Genetic drift and gene flow

• Genetic drift: random changes in allele frequencies, especially in small populations
  • Bottleneck effect: population size reduction leads to loss of genetic diversity
  • Founder effect: new population established by small number of individuals
• Gene flow: transfer of alleles between populations through migration
• Can introduce new alleles or change frequencies of existing alleles
• Counteracts effects of genetic drift and local adaptation

Evolutionary genetics

• Explores genetic basis of evolutionary processes
• Integrates principles of genetics with evolutionary theory
• Provides mechanistic understanding of adaptation and speciation

Natural selection at genetic level

• Differential survival and reproduction based on heritable traits
• Positive selection favors advantageous alleles
• Negative selection removes deleterious alleles
• Balancing selection maintains multiple alleles in population
• Molecular signatures of selection in genome (selective sweeps, reduced diversity)

Genetic basis of adaptation

• Adaptive traits arise from genetic variations in populations
• Standing genetic variation provides raw material for rapid adaptation
• De novo mutations can introduce novel adaptive traits
• Pleiotropy and epistasis influence complex adaptive traits
• Convergent evolution can result from similar genetic changes in different lineages

Speciation and genetic divergence

• Accumulation of genetic differences between populations leads to speciation
• Allopatric speciation: geographic isolation promotes genetic divergence
• Sympatric speciation: divergence without physical barriers
• Reproductive isolation mechanisms prevent gene flow between species
• Hybridization and introgression can blur species boundaries
• Genomic approaches reveal complex patterns of speciation and divergence

Modern applications of genetics

• Genetic knowledge transformed medicine, agriculture, and forensics
• Raised ethical and societal questions about genetic manipulation
• Continues to drive technological innovations in various fields

Personalized medicine

• Tailors medical treatments based on individual genetic profiles
• Pharmacogenomics optimizes drug selection and dosing
• Genetic testing identifies disease risk and guides preventive measures
• Cancer genomics informs targeted therapies and prognosis
• Challenges include data interpretation and ethical considerations
• Potential to improve healthcare outcomes and reduce adverse effects

Forensic DNA analysis

• Uses genetic markers to identify individuals or determine relationships
• Short tandem repeat (STR) analysis common in human identification
• Mitochondrial DNA analysis useful for maternal lineage tracing
• Y-chromosome analysis for paternal lineage and male identification
• DNA databases aid in solving crimes and identifying missing persons
• Raises privacy concerns and legal questions about genetic information

Genetically modified organisms (GMOs)

• Organisms with artificially altered genomes for desired traits
• Agricultural applications include pest resistance and improved nutritional content
• Medical applications involve production of vaccines and therapeutic proteins
• Environmental applications aim to address pollution and conservation issues
• Controversy surrounding safety, ecological impact, and labeling requirements
• Regulatory frameworks vary between countries and continue to evolve