Meiosis, Inheritance, and Gene Expression: Comprehensive Notes

Meiosis and Sexual Life Cycles

• Genes and Genomes
  • Blueprints: Physical structures composed of DNA.
  • Genes: Segments/regions within genomes that encode something (i.e., they can be read or "transcribed" to make mRNA).
  • Genome Contents:
    • Coding: Genes (~2% of human genome).
    • Non-coding: 'Junk,' viruses, repeat sequences, transposable elements.
  • Genome Types:
    • Prokaryotes and viruses: Bacterial and viral (DNA or RNA) genomes.
    • Eukaryotes:
      • Nuclear genome (located in the nucleus).
      • Organelles: Mitochondrial and chloroplast genomes (located in mitochondria and chloroplasts).
  • Chromosomes:
    • Long DNA molecule.
    • Part or all of the genetic material of an organism (i.e., a genome is made up of one or more chromosomes).
    • Contains coding (genes) and non-coding DNA.
  • Genomes: An organism's complete set of DNA (or RNA in many viruses).
    • Full set of chromosomes.
    • Each genome contains all the information (genes) needed to build and maintain an organism.
  • Genomics: Investigate the properties of a genome, often in comparison with genomes of other species (comparative genomics).
  • Genetics: Investigate properties of one or more genes to understand heredity and variation.
  • Human Genome:
    • 22 paired chromosomes plus X and Y (=46 total).
    • 3 billion base pairs.
    • Coding sequence = 2%; non-coding = 98%.
  • Genes: Molecular unit of heredity.
    • Region of DNA that encodes for a functional RNA or protein product.
    • Every person has two copies of each gene, one inherited from each parent.
    • Alleles: Tens of same gene with small differences in DNA sequence.
      • Differences contribute to unique physical features.
    • Genes specify proteins via transcription and translation.
  • Evolution of Genetic Code:
    • Genetic code is nearly universal; all living things have DNA (RNA for some viruses).
  • Heredity: Transmission of genes from one generation to the next.
  • Variation: Differences in offspring from parent and siblings.

Reproduction

• Asexual Reproduction: Single individual passes its genes to its offspring.
  • Clone: Group of genetically identical individuals.
• Sexual Reproduction: Two parents give rise to offspring having unique combinations of genes inherited from parents.
  • Gamete: Cell that fuses with another cell to form a new organism.
    • Contains a single set of chromosomes → haploid (n).
      • Unfertilized egg (ovum): Sex chromosome is X.
      • Sperm cell: Sex chromosome can be X or Y.
  • Somatic Cell: Any cell other than a gamete.
    • Humans have 46 chromosomes in each cell → called diploid (2n) (n=23; 2n=46).
  • Karyotype: An ordered display of chromosome pairs from a cell.
    • Human somatic cells have 23 chromosome pairs.
      • Two chromosomes in each pair are homologous.
    • Sex Chromosomes: Determine the sex of individual (X and Y).
      • Human females: Homologous pair of X chromosomes (XX).
      • Human males: One of each (XY).
    • Autosomes: Non-sex chromosomes

Gametes

• How they are made
  1. Interphase: Chromosomes duplicate forming sister chromatids.
  2. Meiosis I: Homologous chromosomes pair up and separate → two haploid daughter cells containing replicated chromosomes.
  3. Meiosis II: Sister chromatids separate → four haploid daughter cells containing un-replicated chromosomes.

Meiosis I

1. Prophase I: Chromosomes condense, homologous chromosomes loosely pair up, homologous chromosomes physically connect and exchange information (synapsis and crossing over).
2. Metaphase I: Paired homologs line up at the metaphase plate with one chromosome facing each pole; microtubules (spindle fibers) from the poles attach to each pair.
3. Anaphase I: Pairs of homologous chromosomes separate, chromosomes move toward each pole; sister chromatids remain at the centromere and move as one unit to the pole.
4. Telophase I and Cytokinesis: Each half of the cell has a haploid set of chromosomes → cell division usually occurs simultaneously → 2 haploid daughter cells.

Meiosis II

1. Prophase II: Early → spindle apparatus forms; late → chromosomes move towards the metaphase plate.
2. Metaphase II: Sister chromatids arrange at the metaphase plate, no longer identical; sister chromatids attach to spindle fibers from opposite poles.
3. Anaphase II: Sister chromatids separate and move as 2 new individual chromosomes towards opposite poles.
4. Telophase II and Cytokinesis: Chromosomes arrive at opposite poles, nuclei form and chromosomes de-condense, cytokinesis separates the cytoplasm → each daughter cell is distinct from the others and the parent cell.

Mitosis

• Cells replicate themselves.
• Results in the production of two genetically identical daughter cells.

Mitosis vs. Meiosis

• Mitosis: Conserves the number of chromosome sets, producing cells that are genetically identical to the parent cell.
• Meiosis I: Reduces the number of chromosome sets in half, producing cells that differ genetically from each other and the parent cell.

Genetic Variation

• Mutations: Changes in organism's DNA.
  • Original source of genetic diversity.
  • Create different versions of genes (alleles).
  • Reshuffling of alleles during sexual reproduction produces genetic variation.
  • Single-nucleotide polymorphism (SNP): Substitution of a single nucleotide at a specific position in the genome.
  • Homeotic genes → control pattern formation
    • Bicoid gene → after front half of body → Supernodulation
    • Nodule number regulated by host plant → balance need for nitrogen vs. ability to expend energy.
    • Mutations in key genes in the autoregulation pathway lead to loss of modulation control and supernodulation phenotype.
    • Clubbed thumb → mirrored organs
• 3 Main Mechanisms Contributing to Genetic Variation
  1. Independent Assortment of Chromosomes
     • Homologous pairs of chromosomes orient randomly at metaphase I.
     • The number of combinations is 2^n.
  2. Crossing Over
     • Combines DNA inherited from each parent.
     • Begins very early in prophase I.
     • Homologous portions of two non-sister chromatids trade places.
  3. Random Fertilization
     • Any sperm can fuse with any ovum.
     • The fusion of two gametes produces a zygote with any of 70 trillion diploid combinations.
• Evolutionary Significance
  • Natural selection results in the accumulation of genetic variations favored by the environment.
  • Sexual reproduction contributes to genetic variation in a population, which originates from mutations.

Mendel and the Gene Idea

• Laws of Inheritance
  • Mendel discovered principles of heredity by breeding garden peas.
  • Mendel's Experiments
    • Only tracked characteristics that occurred in 2 distinct forms.
    • True-breeding → produced offspring of the same variety when self-pollinated.
    • Hybridization → mated two contrasting, true-breeding varieties.
    • Observed purple flower color was dominant; white was recessive.
    • ‘Heritable factor’ → now called gene.
  • Concept One
    • Alternative versions of a gene account for variations in inherited factors.
    • Alternative versions of a gene → now called alleles.
  • Concept Two
    • For each characteristic, an organism invents two alleles, one from each parent.
    • Two alleles may be identical (true-breeding) or they may differ.
  • Concept Three
    • The dominant allele determines the organism's appearance, and the recessive allele has no noticeable effect.
  • Concept Four
    • Two alleles separate (segregate) during gamete formation.
    • An egg or a sperm only gets one of the two alleles that are present in the parent organism.
• Punnett Square
  • Shows possible combinations resulting from sperm and egg.
  • Capital = dominant allele.
  • Lowercase = recessive allele.
  • Homozygous = 2 identical alleles (true-breeding).
  • Heterozygous = 2 different alleles.
  • Monohybrid = heterozygous for only one character/gene.
  • Law of Independent Assortment = each pair of alleles segregates independently of the others.
    • Crossing F1 dihybrids → phenotypic ratio = 9:3:3:1

Complex Genes

• Non-Mendelian Inheritance

  • When alleles are not completely dominant or recessive.
  • A gene has more than two alleles.
  • When a gene produces multiple phenotypes.

• Degrees of Dominance

  • Complete dominance: Phenotype of heterozygote and dominant homozygote are identical.
  • Incomplete dominance: F1 hybrid phenotype is somewhere between the phenotypes of the two parents.
  • Co-dominance: Two dominant alleles affect the phenotype in separate, distinguishable ways.
  • Pleiotropy: One gene influences multiple, seemingly unrelated phenotypic traits.
  • Epistasis: One gene alters the phenotypic expression of another gene.

Chromosomal Inheritance

• Locating Genes Along Chromosomes

  • A gene's location can be seen by tagging isolated chromosomes with fluorescent dye.

• Morgan's Experiments

  • Chromosomes contain Mendel's heritable factors (genes).
  • Traits alternative to wild type (normal) are called mutant phenotypes.

• Sex-Linked Genes

  • Genes located on sex chromosomes.

• Recombination

  • Generates new allele combinations.
  • Genes that are far apart on the same chromosome can have a recombination frequency of nearly 50%.

• Nondisjunction

  • Homologous chromosomes do not separate normally during meiosis.
  • One gamete receives two of the same chromosome.

• Aneuploidy

  • Fertilization of gametes where nondisjunction occurred.
  • Offspring have an abnormal number of a particular chromosome.
    • Monosomic zygote: Has only one copy of a particular chromosome.
    • Trisomic zygote: Has three copies of a particular chromosome.

• polyploidy

  • Organism with two or more complete sets of chromosomes.
    • Triploidy (3n) → 3 sets of chromosomes
    • Tetraploidy (4n) → 4 sets of chromosomes
    • Hexaploidy (6n) → 6 sets of chromosomes

• Alteration of Chromosomes

  • Deletion: Removes a chromosomal segment.
  • Duplication: Repeats a segment.
  • Inversion: Reverses the orientation of a segment within a chromosome.
  • Translocation: Moves a segment from one chromosome to another.

Gene Expression

• Transcription and Translation

  • Info in DNA is in the form of specific nucleotide sequences → code for RNA (typically encode for synthesis of proteins (made of amino acids))
  • Proteins link genotype and phenotype
  • Transcription → synthesis of RNA (e.g., mRNA (messenger RNA)) under the direction of DNA
    1. Initiation
    2. Elongation
    3. Termination
       • Promoter → DNA sequence where RNA polymerase attaches
       • Transcription factors mediate the binding of RNA polymerase and initiation of transcription
  • Translation → synthesis of a protein under the direction of mRNA
    • tRNA → carries a specific amino acid on one end and has an anticodon on the other → pairs with a complementary codon on the mRNA
      1. Initiation
      2. Elongation
      3. Termination
  • Ribosomes → translate mRNA into proteins
    • Facilitate the coupling of tRNA with mRNA colons

• Genetic Code

  • During transcription → one of two DNA strands (template strands) provides the template for mRNA synthesis
  • During translation → mRNA base triplets (codons) are read in the 5' to 3' direction for protein synthesis
  • Each codon specifies the amino acid to be placed along the polypeptide
  • DNA bases → adenine (A), cytosine (C), guanine (G), thymine (T)
  • RNA bases → adenine (A), cytosine (C), guanine (G), uracil (U)

DNA Tools and Biotechnology

• Biotechnology Tools

  • PCR - Polymerase Chain Reaction
    • Rapid and relatively inexpensive
    • Amplifies DNA and determines presence/absence
    • Generates large volumes of target sequence
    • Uses thermal cycling
  • cDNA Synthesis - Complimentary DNA
    • Very stable compared to mRNA
    • Coding sequence of the gene without introns
  • Real-Time PCR
    • Determines transcript abundance
    • Combines amplification and detection
  • Next-Gen Sequencing
    • Sequences genomes or RNA (RNAseq)
  • Gene Cloning
    • Amplifies sequence of interest

• Bioinformatics

  • Heaps of programs and bioinformatics tools are available to identify genes, genome and gene structures, introns, promoter regions, establish and visualize gene expression profiles.