Chapter 5 - Raw material: heritable variation among individuals

  1. 5.1 Evolutions Molecules: Proteins, DNA, and RNA
  2. Proteins are chains of amino acids (Fig. 5.2)
    1. Amino acids from Kimball's Biology Pages
    2. Polypeptides from Kimball's Biology Pages
    3. Proteins from Kimball's Biology Pages
    4. Rules of Protein Structure from Kimball's Biology Pages
      1. primary
      2. secondayy
      3. tertiary
      4. quaternary
    5. Enzymes from Kimball's Biology Pages
  3. DNA codes for protein (Fig. 5.3)
  4. DNA-the Double Helix from Kimball's Biology Pages
    1. Double helix with sugar-phosphate backbone and paired bases (Fig. 5.3)
    2. Nucleotides from Kimball's Biology Pages  
      1. 5 carbon sugar: deoxyribose  
      2. phosphate group  
      3.  nitrogenous base (nucleobase)
        1. purine: single ring
          1. cytosine, thymine  
          2. in RNA, uracil replaces thymine
        2. pyrimidine: double ring
          1. adenine or guanine  
      4. ATP from Kimball's Biology Pages
    3. Chemical Structure
      1. 3' C of one sugar is joined to the 5' phosphate of another
      2. X-Ray diffraction (Rosalind Franklin)  
      3. hydrogen bonds link complimentary strands
      4. Chagaff's rules (1949):  
        • A = T; G = C
        • purines (A + G) = pyrimidines (T + C)  
    4. How is the DNA Molecule Duplicated  
    5. (Fig. 5.3)
      1. Meselson and Stahl:  Replication is Semiconservative  
        1. each new double helix contains one parental strand  
      2. DNA helicase enzymes unwind helix during replication
      3. DNA synthesis requires an RNA primer  
      4. DNA polymerase: catalyzes polymerization of nucleotidess
      5. DNA replication is bidirectional
      6. DNA synthesis is always in a 5' to 3' direction  
      7. Synthesis of the leading strand is continuous; lagging strand is discontinuous  
      8. DNA ligases connect sections of nucleotides
    6. Mutation: any change to the genomic sequence
  5. Box 5.1 Prokaryotic DNA (p. 138)
    1. Plasmids
    2. Box 5.1 Genes and Heredity in Prokaryotes (Box Fig. 5.12 )
      1. vertical gene transfer
      2. horizontal gene transfer
  6. Eukaryotic DNA is organized into chromosomes (Fig. 5.4)
  7. Ploidy can vary (Fig. 5.5)
    1. Ploidy: Number of copies of unique chromosomes in a cell
      1.  Triploids (3N) - 3 sets of chromosomes
      2. Tetraploids (4N) - 4 sets of chromosomes, (etc.)
      3. Polyploid individuals are usually genetically isolated from parents
    2. Mechanisms: errors in meiosis form diploid gametes (mainly autopolyploidy)
      1. direct route": diploid gametes yield tetraploid offspring, which can self-fertilize
  8. Dioloid chromosomes come in homologous pairs (Fig. 5.6)
    1. Autosomes
    2. Sex chromosomes
  9. The "central dogma"
    1. Transcription
    2. Translation
  10. Production of protein from DNA  (Fig. 5.7)
    1. Gene expression: process by which information from a gene is transformed into product
  11. Ribosomes translate mRNA into protein  using tRNA(Fig. 5.7)
    1. The Central Dogma: information flows from DNA to RNA (transcription) to proteins (translation)
    2. The Genetic Code [Fig. 5.8]
  12. Gene expression can be regulated in a number of ways (5.9)
    1. transcription factors: proteins that bind to specific DNA regulatory regions and activate or deactivate genes
    2. Histone winding and unwinding
  13. Micro RNA (Fig 5.10B)
    1. Bind to complimentary sequences on mRNA
    2. Enhance or silence transcription
  14. MicroRNA can affect phenotypes (Fig. 5.10)
  15. Epigenetics
  16. RNA splicing can create multiple proteins from a single gene (5.11)
    1. Introns, Exons and alternative splicing
  17. Regulation of gene expression is flexible (Table 5.1)
  18. Non-coding regions make up most of the genome (Fig. 5.12)
    1. Non-coding regions include
      1. RNA genes (transfer, ribosomal, micro)
      2. Pseudogenes: often form from gene  duplication
      3. Mobile genetic elements ('jumping genes')
  19. Variation in genome size and complexity (Table 5.2)

5.2 Mutations: Creating Genetic Variation

  1. Key Concepts
    1. Most proteins function in four ways:
      1. Enzymes;
      2. Cell-cell signaling;
      3. Receptors;
      4. Structural elements
    2. Mutations are the raw material for evolution
    3. In diploid organisms, deleterious mutations may be masked by a functional gene copy
    4.  
    5. All cells use mRNA to carry genetic information
    6. Some viruses use RNA instead of DNA for the genome
    7. Non-coding RNA plays critical roles in gene regulation
  2. Types of mutation (Fig. 5.13)
    1. Point Mutations: base pair substitutions
      1. new alleles
      2. Causes of Point Mutations
        1. errors during DNA synthesis (assembly and proofreading)
        2. errors during repair of DNA damage
      3.  Classification of Point Mutations 
        1. transitions
          1. a purine (A or G) is substituted for another purine
          2. a pyrimidine (T or C) is substituted for another pyrimidine
        2. transversions
          1. a purine (A or G) is substituted for a pyrimidine (T or C) (or vice versa)
          2. transitions are >2X more common
        3. replacement: changes the amino acid specified by the mRNA
          1. missense and nonsense
        4. silent: no change (but still an allele)
      1. Insertion
      2. Deletion
    2. Gene duplications: new genes
    3. Chromosome inversion: tighter linkage
    4. Chromosome fusion and fission
    5. Aneuploidy: chromosome loss or duplication
    6. Genome Duplication (Polyploidization): new species
  3. Different types of mutation can alter the phenotype (Table 5.3)
  4. Examples of point mutations (Fig. 5.14)
  5. 5.3 Heredity
  6. Box 5.1 Genes and Heredity on Prokaryotes
  7. Germ line mutations are heritable
    1. Somatic mutations: affect cells in the body of an organism; not heritable
    2. Germ-line mutations: affect gametes; heritable and relevant to evolution
  8. Key Concepts
    1. Changes in coding sequences and gene expression are heritable
    2. Gene expression changes can affect when, where, and how much a gene is expressed
  9. Recombination (crossing over) generates variation (Fig. 5.15)
  10. Independent assortment ensures novel combinations of alleles (Fig. 5.16)
  11. Key Concepts
    1. Meiosis generates considerable genetic variation: Recombination & Independent assortment

5.4 The Link between Most Phenotypes and Genotypes is Complex p. 145

  1. Linking genotype and phenotype
    1. Genotype: the genetic make-up of an individual
    2. Phenotype: an observable measurable characteristic of an organism
  2. Simple polymorphisms can produce differences in phenotype (Fig. 5.18)
  3. Box 5.2 Mendelian Genetics
  4. The NATURE of QUANTITATIVE TRAITS
    1. qualitative traits
      1. characters that show discrete variation (Fig. 5.18)
    2. Sometimes a single genotype can produce multiple phenotypes 
      1. Polyphenic trait:  single genotype produces multiple phenotypes depending on environment
      2. Phenotypes may be discontinuous 
        1. Horned and hornless males of the dung beetle (Fig. 5.19)
  5. Quantitative traits influenced by genes and the environment
    1. Francis Galton (Fig. 5.20)
    2. Quantitative traits influenced by multiple genes; generate a normal distribution  (Fig. 5.19)
      1. show continuous variation e.g., human height [5.20], like many quantitative traits, has a normal distribution
      2. result of combined effect of many loci plus the environment
      3. The same genotype can express various phenotypes depending on environmental condition.
      4. The more genes influencing a given trait, the more continuous/quantitative the trait.
    3. the first step in quantitative genetics is to partition phenotypic variation into environmental and genetic components
    4. quantitative genetics measures and studies heritability, the strength and direction of selection, and the response of populations to selection
  6. Human height has genetic and environmental components  (Fig. 5.21)
  7. QTL analysis can help discover genes influencing quantitative traits  (Fig. 5.22)
    1. Quantitative Trait Loci is dscussed in chapter  7.
  8. Key Concepts
    1. Polyphenisms often result from a developmental threshold mechanism
    2. Continuously varying traits are called quantitative traits
  9. Evolutionary biologists study variation in the expression of phenotypic traits: Caused by genetic and environmental factors

5.5 How do Genes Respond to the Environment? p. 152

  1. Environmental influences on gene expression
    1. Phenotypic plasticity: changes in phenotype produced by a single genotype in different environments: Tailors organism to environment Discuused in Chapter 7
  2. Key Concept
    1. Gene expression often influenced by signals from the environment: Allows match to environmental circumstances

 

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