Principle of Variation in Evolution

Variation and Evolution

• Variation is crucial for understanding Darwin's theory, occurring both between and within species.
• There are two levels of variation: phenotype (observable characteristics) and genotype (set of genetic variants).

Cellular Structure

• Cells consist of different types, including eukaryotes (animals and plants with nuclei and mitochondria) and prokaryotes (bacteria).
• Cells are made of various chemical compounds, including proteins that give cells shape and structure, connect tissues, function as hormones and antibodies, and control chemical reactions.

Proteins and Amino Acids

• Proteins are made up of amino acids, with 20 types in total.
• The sequence of amino acids determines the properties of the protein.
• Phenotype is determined by the properties of proteins in cells, which are determined by the sequence of amino acids.

Genetics

• Genes encode the amino acid recipes for particular proteins.
• Genes come in alternate forms called alleles.
• Individuals have two copies of each gene, one from each parent.
• Genes have two functions: influencing physical characteristics and replicating themselves to produce new cells or individuals.

Central Dogma

• Changes in DNA sequence can lead to changes in proteins, but not vice versa.
• Alterations in the genotype lead to alterations in the phenotype, but not vice versa.
• The flow of information is one-way, and characteristics acquired in a lifetime are not genetically transmittable.

Somatic and Germ Lines

• Somatic cells make up the body, while germ lines produce new individuals (gametes).
• Mitosis is the normal cell division process that produces daughter cells genetically identical to the parent cell.
• Meiosis is the special cell division process that produces haploid gametes from diploid cells.

Molecular Genetics

• Genes are made of DNA, which contains the instructions for making proteins.
• DNA is a long, double-stranded molecule with a sugar-phosphate backbone and nitrogenous bases.
• The sequence of nitrogenous bases determines the genetic code.

Genetic Code

• The genetic code maps codons (triplets of bases) to amino acids.
• The code is almost identical across all living beings.
• Codons are read in sequence to assemble proteins.

Genome

• The genome is the complete set of genetic material in an organism.
• Most DNA is not genes, but rather non-coding regions.
• Non-coding DNA includes transposable elements, pseudogenes, and regulatory sequences.

Evolution of Genome Size

• Genome size tends to rise with phenotypic complexity.
• Polyploidy and regulatory sequences may contribute to increased genome size.

Mitochondrial DNA

• Mitochondria have their own small genomes.
• Mitochondrial DNA is haploid and asexually transmitted from the mother.

Evidence for DNA as the Genetic Material

• Prior to the 1950s, it was known that DNA is a polymer of nucleotides.
• Base composition of DNA varies between species.
• Chargaff's rules describe the base composition of DNA.

Human Genome

• The human genome consists of 3 billion base pairs and about 25,000 protein-coding genes.
• One-third of these genes are expressed only in the brain.

Chromosomes

• Human chromosomes are similar to those of great apes.
• Chromosomes have centromeres, which are regions without genes where the chromosome is attached to its new copy during cell reproduction.

Protein Function and Structure

• Proteins create the skeletal system, muscles, endocrine system, immune system, and nervous system.
• Protein shape can be altered through posttranslational changes, affecting function.

Microbiome and Epigenome

• The microbiome refers to the genomes of microbes that live on and in the body.
• The epigenome refers to chemical marks on DNA that may play a part in how the human genome functions and contributes to health, behavior, and disease.### Transcription and Translation
• Transcription: the process of creating an RNA molecule from a DNA template
• Translation: the process of creating a protein from an RNA molecule
• Importance of transcription and translation:
  • Carry genetic information from DNA to proteins
  • Essential for gene expression and regulation

Transposable Elements

• Ability to copy themselves into different parts of the DNA
• Prone to mutations
• Examples: Simple sequence repeats, microsatellites, and minisatellites

mRNA Synthesis and Translation

• Spliceosomes remove introns to create mRNA (messenger RNA)
• mRNA carries genetic message from DNA to protein-synthesizing machinery
• Translation: the process of creating a protein from an RNA molecule
• Change in language: monomers are amino acids rather than nucleotides

The Genetic Code

• Codons: triplets of nucleotides that code for amino acids
• 64 possible codons (4^3)
• The genetic instructions for a polypeptide chain are written in the DNA as a series of non-overlapping, three-nucleotide words
• For each gene, only one of the two DNA strands is transcribed (template strand)

Regulation of Gene Expression

• Gene expression is regulated at many stages, including transcription, translation, and post-translation
• Regulation is essential for cell specialization and adaptation to environmental changes
• Errors in gene expression can lead to diseases, including cancer

Epigenetic Inheritance

• The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
• Chromatin modifications, such as histone modifications and DNA methylation, can be passed on to future generations
• Important for gene regulation and cellular differentiation

Post-Transcriptional Regulation

• Mechanisms that operate after transcription, including RNA processing, mRNA degradation, and translation initiation
• Allow for fine-tuning of gene expression in response to environmental changes

Genetic Variation

• Types of mutations:
  • Point mutations (single-base substitutions)
  • Frameshift mutations (insertions or deletions)
  • Simple sequence repeat expansions and contractions
  • Transposable element insertions and segmental duplications
  • Whole-genome duplication
• Mutations can be silent, missense, or nonsense
• Mutagens: physical and chemical agents that interact with DNA and cause mutations

Effects of Genetic Variation

• Most genetic variation has no phenotypic effect
• Reservoir of genetic variation from which phenotypic variation may result
• Where mutations do have a phenotypic effect, they are usually deleterious
• Occasional mutations can arise that improve biological performance### Genetic Mutations and Natural Selection
• Rare advantageous mutations are spread by natural selection, which leads to a change in the genotype to phenotype.
• A new non-synonymous mutation in a gene's coding sequence can result in a distinct allele, producing a different amino acid chain and protein.

Single-Gene Characteristics and Diseases

• Single-gene characteristics are determined by which allele an individual has at a single genetic locus.
• Examples of single-gene diseases include cystic fibrosis (chromosome 7) and Rhesus factor.

Gene Hunting

• Linkage studies are used to localize genes underlying single-gene traits using a small number of genetic markers.
• Association studies are powerful but require many genetic markers per chromosome, and can be used to identify genes involved in polygenic characteristics.

Polygenic Traits

• Polygenic traits are variations in phenotype related to which allele is present across multiple genes.
• Examples of polygenic traits include height, and they are hard to detect using linkage and association studies.

Genes for Physical Characteristics

• Huntington's disease is a single-gene disease caused by a disease-causing allele of a gene on chromosome 4, leading to a protein that helps keep cells alive.
• An association study on dogs found a strong association between a gene on chromosome 15 and size.

Genes for Behavior

• A study on prairie voles found that a hormone arginine vasopressin causes a pair bond to form, and a gene that produces a receptor for this hormone is involved in this behavior.
• A study on humans found that a gene involved in regulating serotonin (mood states) is associated with conduct disorder.

Epigenetics

• Epigenetics is the study of mechanisms that change gene expression by modifying DNA without modifying its sequence.
• Epigenetic mechanisms, such as DNA methylation and histone modification, can explain how early life experiences can influence behavior and physical health later in life.

Epigenetic Mechanisms

• DNA methylation is the tagging of specific points in the DNA molecule with a methyl group, silencing genes.
• Histone modification is the chemical modification of histone proteins that DNA winds around, changing how tightly or loosely the DNA is wound.
• DNA methylation and histone modification interact with and depend on each other.

Importance of Nurturing

• The way a rat mother nurtures her pups influences how they respond to stress in later life.
• Less nurturing leads to increased methylation of the gene for BDNF (neural growth factor) and reduced glucocorticoid receptors.

Epigenetics and Development

• Epigenetics can explain how early life experiences can influence behavior and physical health later in life.
• Epigenetic mechanisms, such as DNA methylation and histone modification, are involved in development and can be influenced by nutrition.

Antisocial Behavior

• Antisocial behavior is influenced by genetic and environmental factors.
• Specific genes, such as MAOA, are associated with antisocial behavior.
• Brain impairments, such as reduced volume of the amygdala, anterior cingulate, and orbitofrontal cortex, are associated with antisocial behavior.
• Environmental influences, such as child abuse, can interact with genetic factors to predispose to antisocial behavior.