Life Signs, DNA, and Genes

Signs of Life

• Living organisms share characteristics such as response to stimuli, active movement, growth & development, respiration, substance exchange, and reproduction & heredity.

Genetics vs Genomics

• Genetics studies heredity, focusing on how traits are passed between generations through genes.
• Genomics involves the study of an entire genome including its structure, mutations, and variations, to identify how all genes interact.

Gene vs Genome

• A gene is a DNA segment that codes for a specific protein or trait.
• A genome is an organism's complete set of DNA.

DNA Structure

• DNA consists of a sugar-phosphate backbone and nitrogenous bases: adenine (A), thymine (T), guanine (G), and cytosine (C).
• A-T and G-C are complementary base pairs.
• Its double helix structure features major and minor grooves.
• The backbone of DNA is hydrophilic, while the bases are hydrophobic.

DNA Denaturation

• High temperatures can break the hydrogen bonds in unzipping DNA.

Human Genome

• The human genome contains approximately 3 billion base pairs, totaling about 2 meters of DNA per cell.
• Humans have 23 pairs of chromosomes (46 total).
• Human gametes (egg/sperm) carry 23 chromosomes (haploid).
• Down syndrome results from trisomy 21, the presence of an extra copy of chromosome 21.

Proteins and Amino Acids

• Proteins, composed of amino acids, are functional molecules in the body
• Examples include actin and myosin in muscles, keratin and collagen in hair and skin, insulin as a hormone, pepsin and trypsin for digestion, antibodies for immunity, and hemoglobin for transport.

Central Dogma of Molecular Biology

• The flow of genetic information is DNA → RNA → Protein.
• Transcription occurs in the nucleus.
• Translation happens in ribosomes.

Mutation Types

• Silent mutations: Base change, same amino acid.
• Missense mutations: Base change, different amino acid.
• Nonsense mutations: Base change resulting in a stop codon.
• Frameshift mutations: Insertion or deletion that shifts the reading frame.

Degeneracy of the DNA Code

• Most amino acids are encoded by multiple codons.
• There is no start codon in terms of strict inheritance, but stop codons are present.

Cells and Domains of Life

• Prokaryotic cells (bacteria) are simple cells lacking a nucleus.
• Eukaryotic cells (animals, plants, fungi) are complex, containing a nucleus and organelles.

Bacteria

• Lactobacillus, Bacteroides, Bifidobacterium, and E. coli are beneficial bacteria.
• Clostridium, Campylobacter, and Staphylococcus are harmful bacteria.

Mitochondria

• Mitochondria originated from engulfed bacteria about 1.5–2 billion years ago.
• They perform cellular respiration for energy production.
• Mitochondria contain their own circular DNA (mtDNA).

Mitochondrial DNA (mtDNA)

• mtDNA is inherited solely from the mother.
• It contains 37 genes, totaling about 16,000 bases.
• mtDNA is used in forensics and ancestry studies.
• Mutations commonly occur in non-coding hypervariable regions.

Historical Case: Louis XVII

• mtDNA analysis confirmed the death of Louis XVII during the French Revolution by matching mtDNA from a preserved heart with that of his maternal relatives.

Stem Cells and Tissue Differentiation

• Cells have semi-permeable membranes.
• Stem cells can differentiate into any other cell type.
• Cells form tissues, such as muscle, nerve, bone, and fat.

Genotype vs. Phenotype

• Genotype is the genetic information of an organism.
• Phenotype refers to observable traits.

Phenotype Examples

• Fun phenotypes include dimples, eye color, hair texture, freckles, and unibrows.
• Medical phenotypes include cleft palate and early hair loss.

Mendel's Principles

• Mendel studied sweet peas.
• The principle of dominance says that one allele may mask the effect of another.
• Each organism inherits two alleles, one from each parent.
• Variants of a gene are called alleles.

Allelic Status

• Homozygous: Same allele from both parents.
• Heterozygous: One normal, one mutant allele.
• Mutant: Carries the altered gene.

Autosomal and X-linked Disorders

• Autosomal dominant disorders require only one mutant allele (e.g., Huntington's).
• Autosomal recessive disorders require two mutant alleles (e.g., cystic fibrosis).
• X-linked disorders are passed via the X chromosome (e.g., hemophilia, color blindness).

Blood Groups

• Blood groups are determined by the ABO gene.
• Blood groups are inherited in Mendelian patterns.

Genetic Studies

• Linkage studies: Large families.
• Association studies: Population-level.
• GWAS: Identifies small variations in the genome.

Twin Studies

• Monozygotic twins: Identical DNA, used to research environmental effects.
• Dizygotic twins: Shared environment, show genetic differences.

Mutation vs. Polymorphism

• Mutation, rare (less than 1% of population), often harmful, and may cause disease.
• Polymorphism: Common, usually harmless, contributes to variation (e.g., eye color).

Mutation Examples

• Mutations in clotting factor genes → Hemophilia.
• Hereditary thrombophilia: Factor V Leiden, Prothrombin gene mutation.

Evolution and Adaptation

• Variation enables survival.
• Natural selection: Traits that improve survival are passed on.
• Green anole lizards adapted to invasive species in Florida.

Mutation Types by Scale

• Chromosomal mutations (e.g., aneuploidy like Trisomy 21).
• DNA point mutations: Silent, Missense, Nonsense, and Frameshift (insertion/deletion).

Causes of Mutations

• Spontaneous mutations occur from errors in replication, transcription, or translation.
• Induced mutations are caused by external mutagens like chemicals, preservatives, radiation, viruses, or smoking.

Chemical Reactions on DNA

• Deamination: Loss of amino group.
• Oxidation: Adds oxygen, alters base.
• Methylation: Adds methyl group, may silence gene.

Mutation Origins

• Germline mutation: Inherited, present in every cell.
• Germline de novo: New mutation in egg/sperm or fertilization.
• Somatic mutation: Acquired during life, present in specific tissues.

Mutation Frequency

• RNA has a mutation rate of 1 in 100,000 (10^-5).
• DNA has a mutation rate of 1 in 1 billion (10^-9).
• Mutation is more common in regenerating cells (e.g., skin) than non-regenerating cells (e.g., heart).

Recombination and Meiosis

• Recombination: Exchange of DNA between homologous chromosomes.
• Meiosis: Cell division in gametes → halves chromosome number.
• Average 1–2 recombination events per chromosome.
• Measured in centiMorgans (genetic distance).

Gene Expression

• Genotype and environment determine an organism's Phenotype.
• Gene → Trait: A gene codes for a protein that contributes to a trait

Alleles and Phenotypes

• Variations in SLC/HER genes affect skin, hair, and other traits.

Mendelian Inheritance

• Homozygous dominant/recessive, heterozygous.
• Punnett squares visualize genotype ratios.

Inheritance Patterns

• Autosomal dominant: Huntington’s, familial hypercholesterolemia.
• Autosomal recessive: Cystic fibrosis, sickle cell anemia, albinism.
• X-linked dominant: Fragile X syndrome.
• X-linked recessive: Hemophilia A, red-green color blindness.

Carrier Status

• Females can be carriers of X-linked disorders.
• Males affected due to having their single X chromosome.

Predicting Offspring

• Punnett squares show probability of inheritance.
• Carrier parents can have affected, carrier, and unaffected children.

Tracing Studies

• Linkage studies: Use large families to find inherited traits.
• Association studies: Compare affected/unaffected in a population.
• Twin studies: Separate effects of genes vs environment.

GWAS (Genome-Wide Association Studies)

• Identify small variations associated with traits or diseases.

Genetic Diversity

• Every egg/sperm is genetically unique.
• Caused by recombination, mutations, and random assortment.

Point Mutations

• Silent: No change in protein.
• Missense: One amino acid changes.
• Nonsense: Premature stop codon.
• Frameshift: Reading frame shifts due to insertion or deletion.

Origin of Mutations

• Spontaneous: DNA replication errors.
• Induced: Environmental exposure (chemicals, UV, radiation).

Mutation Impact

• Some mutations cause disease.
• Some are neutral or beneficial.

Mutation Types by Origin

• Germline: Passed to offspring, in all cells.
• De novo germline: New mutation in sperm/egg.
• Somatic: Occurs after fertilization, affects only some cells.

Mutation Rates

• RNA: 10^-5 (1 in 100,000).
• DNA: 10^-9 (1 in 1 billion).
• Higher in dividing cells (e.g., skin).

Recombination

• During meiosis, chromosomes exchange segments
• Increases genetic diversity.

DNA Extraction and Analysis

• Break cells open with detergent.
• Add salt solution.
• Precipitate with ethanol.
• Clean and re-dissolve with buffer.

Electrophoresis

• DNA moves through gel under electric current.
• Smaller fragments move faster.
• Allows size estimation and DNA detection.

PCR (Polymerase Chain Reaction)

• Used to amplify DNA.
• Cycle: Denature → Anneal → Extend (repeated ~30 times).
• Uses Taq polymerase (heat-stable enzyme).

DNA Sequencing

• Sanger method: Older, chain-termination.
• NGS: Newer, faster, high-throughput.
• Applications:
  • Identify mutations
  • Compare genomes
  • Disease diagnosis

Frequencies in a Population

• p² + 2pq + q² = 1
• p + q = 1
• Can be used to estimate carrier and disease frequencies

Assumptions

• No mutation, migration, selection
• Random mating
• Large population

Real-World Use

• Public health: estimate genetic disease frequency
• Identify non-equilibrium in evolving populations