Mendel's Laws and Linked vs Unlinked Traits

• Mendel studied flower color and seed shape in pea plants
• He discovered these traits were inherited independently
• This led to Mendel's Law of Independent Assortment
• Different traits are passed down separately from one another

Unlinked Traits Study

• Mendel was able to clearly see the pattern of trait inheritance because the genes were unlinked
• Unlinked genes are located on different or far apart chromosomes
• Because of this, the genes were randomly shuffled when pea plants made gametes
• This lead to different combinations in the offspring

Linked Traits Study

• Things would have been more complicated if Mendel had chosen linked traits
• Linked genes are close together on the same chromosome
• Linked genes tend to be inherited together, rather than independently
• Some trait combinations would have appeared together more often than expected
• If genes for flower color and seed shape were linked, Mendel might have noticed certain combinations occurring more frequently
• This may have confused his results and he may not have been able to develop his law of independent assortment

Importance

• Because Mendel's traits were mostly unlinked, so he could correctly figure out how traits are passed down from parents to offspring
• If he had worked with linked traits, his findings might have been unclear
• It would have taken much longer for scientists to understand inheritance

Mendel's Success

• Mendel was lucky because the traits he studied were inherited independently
• This made it easier to see clear patterns
• If he had studied linked traits, his results would have been confusing
• He might not have discovered the law of independent assortment

Mendel's Experiments and Law of Segregation

• Mendel studied pea plants and focused on different traits, like flower color (purple vs white)

True Breeding Plants

• Mendel started with true-breeding plants
• These are plants that always produce offspring with the same trait

First Generation

• Mendel crossed a purple parent (PP) with a white parent (pp)
• All offspring (F1) had purple flowers

Second Generation

• When F1 plants were self-fertilized, purple and white flowers appeared in a 3:1 ratio

Hidden White Trait

• Even though the F1 plants all looked purple, they carried the hidden white trait

Mendel's First Law: The Law of Segregation

• Each organism has two gene copies (one from each parent) that separate when forming gametes
• Each gamete gets only one copy
• Some traits are dominant (purple), and some are recessive (white)

The Law of Independent Assortment

• Mendel also studied other traits, like seed shape (round vs wrinkled), at the same time as flower color
• Mendel found that flower color and seed shape were inherited independently
• Led to Mendel's Second Law: The Law of Independent Assortment
• Genes for different traits are inherited separately if they are unlinked (on different chromosomes)

Linked Genes

• If genes are close together on the same chromosome, they don't assort independently
• Instead, certain combinations of traits are inherited together more often

Revolutionary Work

• Before Mendel, scientists thought inheritance was like mixing paint
• A red and white flower would make a permanent pink flower
• Mendel showed that inheritance is particulate (like mixing colored filters, not paint)
• Traits can reappear later, even if they seem to disappear in one generation
• Mendels work explained how variation in a population is maintained, solving a problem in Darwin's theory of evolution

Importance For Evolution

• Darwin's theory of natural selection needed genetic variation to work
• Mendel showed that genes remain distinct, allowing new traits to persist and evolve
• If traits blended permanently, variation would disappear over time

Key Takeaways

• Law of Segregation is where each organism gets two gene copies, but only one is passed to offspring
• The Law of Independent Assortment states Genes for different traits are inherited separately (unless linked)
• Inheritance is particulate, not blended, which helps explain how new traits can evolve

Transmission Genetics

• Transmission Genetics explains how DNA Controls Traits

DNA

• DNA (Deoxyribonucleic Acid) carries genetic instructions and is the genetic material
• It is made of four building blocks (nucleotides): Adenine (A), Thymine (T), Cytosine (C), Guanine (G)
• DNA is shaped like a double helix (twisted ladder) according to these rules: A always pairs with T, C always pairs with G

Chromosomes

• DNA is packaged into chromosomes, there are 23 pairs of chromosomes (46 total) in humans
• Haploid organisms (like bacteria) have one copy of each chromosome
• Diploid organisms (like humans) havIng two copies of each chromosome

DNA to Proteins

• Traits are expressed when DNA makes proteins in two steps:

Transcription

• 1st step is transcription (Making RNA) where:
• DNA is copied into messenger RNA (mRNA)
• RNA is similar to DNA but uses Uracil (U) instead of Thymine (T)
• The enzyme RNA polymerase binds to a gene and copies its instructions into mRNA

Translation

• 2nd step is translation (Making Proteins) where:
• mRNA is read by a ribosome in triplets of nucleotides called codons
• Each codon codes for a specific amino acid (building blocks of proteins)
• Transfer RNA (tRNA) brings the correct amino acids to build the protein
• The protein folds into its final shape and determines the trait (phenotype)

Genes and Mutations

• A gene is a section of DNA that codes for a protein
• In eukaryotic cells, genes have exons (coding sections) and introns (non-coding sections that are removed)
• Mutations (changes in DNA) can affect protein production, potentially leading to new traits or diseases

Key Takeaways

• Mendel's Laws Explain How Traits Are Passed Down
• Law of Segregation is where each parent passes only one allele, and Law of Independent Assortment explains traits are inherited separately if genes are on different chromosomes
• DNA is made of four nucleotides (A, T, C, G), and genes are sections of DNA that provide instructions for proteins

Proteins

• Proteins Determine Physical Traits
• Transcription (DNA → RNA) and Translation (RNA → Protein) turn genetic code into traits
• Proteins do everything from building structures to regulating functions in cells

Mutations and Evolution

• Mutations Drive Evolution
• Mutations can create new traits and natural selection chooses the best traits for survival

Alleles and Genotypes

• Alleles are variants of the same gene. Locus is the specific location of a gene on a chromosome.
• Genotype is the combination of alleles an organism has at a locus.

Homozygous and Heterozygous

• Homozygous have two identical alleles at a locus (AA or aa), while Heterozygous organisms have to different alleles at a locus (Aa)

Dominant Versus Recessive

• A Dominant allele (A) is expressed in both AA (homozygous) and Aa (heterozygous)
• A Recessive allele (a): Only expressed in aa (homozygous recessive)

Incomplete Dominance

• Neither allele is completely dominant in Incomplete Dominance
• The heterozygote (Rr) has an intermediate phenotype; for example Red (RR) × White (rr) = Pink (Rr)

Punnett Squares

• A Punnett Square is a tool to predict offspring genotypes and phenotypes
• The example looks at a cross of Tt (tall) × tt (short) that has 50% Tt (tall) and 50% tt (short) offsprings
• The ratio is 1:1 tall to short

Regulatory Elements and Gene Expression

• Genes do not always turn on/off by themselves, they are controlled by regulatory elements
• Enhancers increase gene expression, while silencers decrease gene expression

Epigenetic Inheritance

• Epigenetic Inheritance is Gene Expression Without DNA Changes
• Epigenetics are heritable changes that affect gene expression without changing the DNA sequence
• Chromatin: DNA is wrapped around histone proteins
• Tightly packed chromatin = gene OFF (not expressed). Loose chromatin = gene ON (expressed)

Key Epigenetic Mechanisms

• DNA Methylation: a methyl group is added to DNA (C-G pairs), so more methylation = gene turned OFF. An example is Cavefish losing their eyes due to increased methylation in eye-development genes
• Histone Modification: Acyl groups → Open chromatin → Gene ON
• Methyl groups → Closed chromatin → Gene OFF
• X-Chromosome Inactivation where In female mammals (XX), one X chromosome is turned off to balance gene expression

Epigenetics and Health

• Epigenetic changes can be inherited across generations
• Prenatal environment influences gene expression (e.g., diet affects risk for diabetes)
• Epigenetic drugs are being developed to treat diseases

Key Takeaways on Alleles, Traits and Inheritance

• Alleles determine traits, and dominant/recessive rules explain inheritance
• Punnett squares predict offspring traits
• Regulatory elements control when genes turn on/off
• Epigenetics modifies gene expression without changing DNA
• Methylation and histone changes play a huge role in development and disease

Genetic Variation

• Genetic variation is essential for natural selection, which is the driving force of evolution
• New genetic variation enters a population in four ways: mutation, recombination, migration, and lateral gene transfer

Source Focus

• This section focuses on mutation and recombination, which create variation within a population

Mutation

• A mutation is a change in an organism's DNA sequence and the primary source of new genetic variation

Mutation Types

• Somatic Mutations happen in body cells and affect only that individual without being passed on to offspring(cancer being an example)
• Germ-line Mutations occur in reproductive cells (sperm or egg), can be inherited, and can contribute to evolution

Mutation Effects and Changes

• Single Base Changes (Point Mutations) are mutations where one base in the DNA sequence is changed: Transitions & Transversions

Effect on Proteins (Synonymous vs Nonsynonymous Mutations)

• Mutations can have three effects
• Synonymous (Silent) Mutation does not affect the amino acid sequence
• Nonsynonymous Mutation alters the amino acid sequence, which can change how the protein works (Bar-headed geese that migrate over the Himalayas)
• Nonsense Mutation creates a stop codon, which cuts the protein short, leading to loss of function

Insertions and Deletions

• With Insertions extra DNA bases are added, with Deletion DNA bases are removed
• If the insertion/deletion happens in multiples of three, it doesn't shift how the gene is read (in-frame mutation)
• If the insertion/deletion does not happen in multiples of three, it shifts the entire reading frame (frameshift mutation)

Larger-Scale Mutations

• Mutations can also affect entire genes or chromosomes
• Gene Duplications are where a whole gene gets duplicated, creating extra copies resulting in a primate species (douc langur) evolving to digest certain foods

Chromosomal Rearrangements

• Duplication is where A section of a chromosome is copied
• Deletion is where A large section of a chromosome is lost
• Inversion is where A section of a chromosome flips 180°
• Translocation is where A piece of one chromosome moves to another, and helped Codfish evolve the antifreeze glycoprotein gene

Changes in Ploidy

• Sometimes, an organism loses entire sets of chromosomes, which can cause the frog population to change
• Some frog species are diploid (2 sets of chromosomes), while others are tetraploid (4 sets.)

Key Takeaways on mutations

• Mutation is the main source of new genetic variation
• Not all mutations are created equally, Germ-line mutations matter for evolution while somatic do not.
• Point mutations can be silent (synonymous) or change proteins (nonsynonymous or nonsense.)
• Insertions and deletions can cause frameshift mutations, which dramatically change proteins.
• Large-scale mutations: gene duplications, chromosomal rearrangements, and chromosome # changes some mutations provide evolutionary advantages

Genetic Variation in Sex

• Unlike asexual reproduction offspring are clones of the parent
• Creating offspring with a mix of genes from two parents leads to genetic variation

Chromosomes and Homologous Pairs

• Each cell with a chromosome has a fixed number of chromosomes
• Chromosomes come in homologous pairs, which are pairs of chromosomes that contain the same genes (loci) but can have different versions (alleles) of those genes
• Each individual gets one chromosome of each homologous pair from each parent

How Are Gametes Made?

• To create sex cells (gametes), organisms go through a special type of cell division called meiosis.
• Diploid cells (cells with two sets of chromosomes) undergo one round of DNA replication
• This is followed by two rounds of cell division, resulting in four haploid gametes (each containing only one set of chromosomes)
• In animals Eggs come from the mother, while sperm come from the father, so when fertilization happens and there is egg to fusing restores the diploid state in the offspring

Recombination

• During meiosis, a process called crossing-over occurs
• Crossing-over is when homologous chromosomes physically exchange segments of DNA and creates new combinations of alleles that were not present in the parents
• The process of crossing over helps increase genetic diversity

Process Generation

• New allele combinations didn't exist in the parents, contributing to genetic diversity in a population

Why Does This Matter?

• Recombination increases genetic variation, which helps populations adapt to environmental changes
• Without recombination, offspring would inherit chromosomes exactly as they are from their parents, limiting diversity
• The process plays a major role in evolution by shuffling existing genetic traits, leading to new combinations that may be beneficial for survival

Mutation Variation Takeaways

• Mutations are random, not directed by an outside source
• Can be Harmful, neutral, or benificial
• Natural selection acts on random mutation and picks the most advantageous traits

Mutation And Their Roles

• Mutation is the source of genetic variation, which is essential for natural selection
• In humans, the mutation rate is about 10-8 mutations per nucleotide per generation
• Humans have 2 copies of each gene so mutations present in ofspring that are not found the parents is >100

Mutation Variation

• Muation is not the same across all organisms
• RNA mutates are more volitile as compared to DNA because of its unique property

Mutation Effects on Fitness

• Mutations can be good bad or neutral, and will affect an organisms ability to evolve

Measuring effects of mutations

• Mutations impact a living oranisms reprocution or survival
• The best way to measure such studies and variables is through the use of virus bacteria etc

Comparing Mutation

• Patterns across species tend to be the same, mutations will be most effective on more complex living organisms

Genetics, insights

• Understanding mutation rates and their impact on fitness allows to explore more about the population it affect along with the genome of the ecosystem itself

Population Thinking in Genetics

• There differences across genetics from a individual to a population

Population Genetics

Studies how gene frequencies change across generations in a population

Evolution

• Evolution is how that gene can shift and evolve in a organisem

Key Terms for Genetics

• Equilibrium means a system has reached a steady state where it doesn't change unless some external force acts on it