1. Sources of Variation:
Genetics Review
Mutation
Recombination

2. DNA, RNA, and Proteins
A. Proteins
1. Amino Acids

4. DNA, RNA, and Proteins
A. Proteins
1. Amino Acids
2. Polymerization

6. DNA, RNA, and Proteins
A. Proteins
1. Amino Acids
2. Polymerization
3. Levels of Structure

8. DNA, RNA, and Proteins
A. Proteins
1. Amino Acids
2. Polymerization
3. Levels of Structure
4. Functions

9. Structural
- actin (cytoskeleton, muscle)
- elastin
- collagen
Enzymatic
Trypsin
Salivary amylase
DNA polymerase II
Responsible for making all other types of biomolecules
Transport
Protein channels in membranes
Hemoglobin
Immunity
- Antibodies
Communication
- Hormones (insulin)
Regulatory
- Transcription Factors

10. DNA, RNA, and Proteins
B. DNA
1. Nucleotides

12. DNA, RNA, and Proteins
B. DNA
1. Nucleotides
2. Polymerization

13. 5’ 3’

14. DNA, RNA, and Proteins
B. DNA
1. Nucleotides
2. Polymerization
3. Double Helix and Genes

15. Antiparallel
Complementary
Purine
Pyrimidine

16. “Split-gene” structure of eukaryotic genes

17. DNA, RNA, and Proteins
B. DNA
1. Nucleotides
2. Polymerization
3. Double Helix
4. Eukaryotic Chromosome

18. 1.2 % of human genome codes for proteins

20. DNA, RNA, and Proteins
B. DNA
1. Nucleotides
2. Polymerization
3. Double Helix
4. Eukaryotic Chromosome
5. Chromosomes, sister chromatids, homologous chromosomes

21. A a A A a a

22. DNA, RNA, and Proteins
B. DNA
1. Nucleotides
2. Polymerization
3. Double Helix
4. Eukaryotic Chromosome
5. Chromosomes, sister chromatids, homologous chromosomes
6. Genomes

24. Ophioglossum vulgarum
1024 chromosomes

25. DNA, RNA, and Proteins
C. RNA
1. Nucleotides – 2 diff’s with DNA

26. DNA, RNA, and Proteins
C. RNA
1. Nucleotides

27. DNA, RNA, and Proteins
C. RNA
1. Nucleotides – 2 diff’s with DNA
2. Types and Functions

28. TRANSCRIPTION

31. DNA, RNA, and Proteins
D. Gene Regulation

32. Regulation of Transcription
TATA Binding Proteins bind to Promoter – enhance binding of Polymerase
Activators (transc. factors) bind to enhancers – increase expression
Repressors – bind to silencers, activators, promoters and decrease expression

33. Regulation of RNA Processing

34. Regulation of Translation
Micro-RNA’s block translation of other m-RNA’s… turns gene expression ‘off’

35. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
A. Types:

36. Loss or gain of a chromosome

37. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
A. Types:
B. Effects

38. Can affect the timing of gene action, the quantity of protein product,
and/or the type of protein produced…. or not!

39. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
A. Types:
B. Effects
C. Frequency

40. Point mutations are rare (1/million cell divisions), but with 6 billion base pairs in the human genome, they are actually abundant.
But mutations that affect whole chromosomes, while very rare, affect more base pairs when they happen.

41. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
A. Types:
B. Effects:
C. Somatic vs. Germ Line
Somatic affect body tissues (like cancers)
Germ Line (affect egg or sperm) - heritable

42. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
A. Types:
B. Effects:
C. Somatic vs. Germ Line
D. Causes

43. Point Mutations, Insertions, Deletions: DNA Replication Errors

44. Gene Duplication and Inversions: Error in Crossing-Over:
Unequal crossing over leads to gene duplication and deletion A B a b

45. Gene Duplication and Inversions: Error in Crossing-Over:b B

46. Gene Duplication and Inversions: Error in Crossing-Over:b B

47. deletions are usually bad – reveal deleterious recessives
i. Unequal Crossing-Over
a. process:
b. effects:
- can be bad:
deletions are usually bad – reveal deleterious recessives
additions can be bad – change protein concentration

48. deletions are usually bad – reveal deleterious recessives
i. Unequal Crossing-Over
a. process:
b. effects:
- can be bad:
deletions are usually bad – reveal deleterious recessives
additions can be bad – change protein concentration
- can be good:
more of a single protein could be advantageous
(r-RNA genes, melanin genes, etc.)

49. deletions are usually bad – reveal deleterious recessives
i. Unequal Crossing-Over
a. process:
b. effects:
- can be bad:
deletions are usually bad – reveal deleterious recessives
additions can be bad – change protein concentration
- can be good:
more of a single protein could be advantageous
(r-RNA genes, melanin genes, etc.)
source of evolutionary novelty (Ohno hypothesis )
where do new genes (new genetic information) come from?

50. Gene A
Duplicated A
generations
Mutation – may even render the protein
non-functional
But this organism is not selected against, relative to others in the population that lack the duplication, because it still has the original, functional, gene.

51. Gene A
Duplicated A
generations
Mutation – may even render the protein
non-functional
Mutation – other mutations may render the protein functional in a new way
So, now we have a genome that can do all the ‘old stuff’ (with the original gene), but it can now do something NEW. Selection may favor these organisms.

52. If so, then we’d expect many different neighboring genes to have similar sequences. And non-functional pseudogenes (duplicates that had been turned off by mutation).
These occur – Gene Families

53. And, if we can measure the rate of mutation in these genes, then we can determine how much time must have elapsed since the duplication event…
Gene family trees…

54. Gene Duplication and Inversions: Error in Crossing-Over:
Inversions occur when a chromosome crosses-over with itself:

55. Loss or gain of a chromosome occurs by Error in Meiosis: non-disjunction

56. Fusion occurs by translocation:

58. Genome duplication (polyploidy) occurs by failure of meiosis or failure of mitosis in tissues that produce gametes:

59. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
a. Autopolyploidy: production of a diploid gamete used in reproduction within a species.
Failure of meiosis I or II
2n gamete
3n zygote
Correct meiosis in other parent
1n gamete

60. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
a. Autopolyploidy: production of a diploid gamete used in reproduction within a species.
Errors in mitosis can also contribute, in hermaphroditic species

61. 2n
1) Consider a bud cell in the flower bud of a plant.

62. 2n 4n
1) Consider a bud cell in the flower bud of a plant.
2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell.

63. 2n 4n
1) Consider a bud cell in the flower bud of a plant.
2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell.
3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG

64. 2n
1) Consider a bud cell in the flower bud of a plant. 4n
2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell.
3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG
4) If it is self-compatible, it can mate with itself, producing 4n zygotes that develop into a new 4n species.
Why is it a new species?

65. How do we define ‘species’?
“A group of organisms that reproduce with one another and are reproductively isolated from other such groups”
(E. Mayr – ‘biological species concept’)

66. How do we define ‘species’?
Here, the tetraploid population is even reproductively isolated from its own parent species…So speciation can be an instantaneous genetic event… 4n 2n
Gametes
Zygote 1n 3n
Triploid is a dead-end… so species are separate

67. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
a. Autopolyploidy: production of a diploid gamete used in reproduction within a species.
b. Allopolyploidy: fusion of gametes from different species (hybridization). These are usually sterile because the chromosomes are not homologous and can’t pair during gamete formation. BUT… if the chromosomes replicate and separate without cytokinesis, they create their own homologs and sexual reproduction is then possible.

70. X Spartina alterniflora from NA colonized Europe
Spartina maritima native to Europe
Sterile hybrid – Spartina x townsendii
Allopolyploidy – 1890’s
Spartina anglica – an allopolyploid and a worldwide invasive outcompeting native species

71. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
2. Frequency:
Polyploidy is common in plants; 50% of angiosperm species may be the product of polyploid speciation events.

72. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
2. Frequency:
Polyploidy is common in plants; 50% of angiosperm species may be the product of polyploid speciation events.
In vertebrates, polyploidy decreases in frequency from fish to amphibians to reptiles, and is undocumented in birds. There is one tetraploid mammal. (Red viscacha rat).

73. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
2. Frequency:
3. The effect of hermaphrodism:

74. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
2. Frequency:
3. The effect of hermaphrodism:
- when the sexes are separate, the rare, random mutation of producing a diploid gamete is UNLIKELY to occur in two parents simultaneously. So, the rare diploid gamete made by one parent (karyokinesis without cytokinesis doubling chromosome number in a cell) will probably fertilize a normal haploid gamete. This produces a TRIPLOID… which may live, but would be incapable of sexual reproduction. 2n 3n 1n

75. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
2. Frequency:
3. The effect of hermaphrodism:
- unless…. the new organism could ALSO produce eggs without reduction..clonally… and these are the rare animals that we see – triploid ‘species’ that are composed of females that reproduce asexually. (Some may still mate with their diploid ‘sibling’ species so that the sperm stimulated the egg to develop – but without incorporation of sperm DNA.)
Like this Blue-spotted Salamander A. laterale,
which has a triploid sister species, A. tremblayi

76. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
2. Frequency:
3. The effect of hermaphrodism:
SO! Polyploidy may be more frequent in plants because they are hermaphroditic more often than animals; especially vertebrates. Most cases of polyploidy in animals is usually where triploid females survive and reproduce asexually.
Also, simpler development in plants means they may tolerate imbalances better.

77. Mutations I: Changes in Chromosome Number and Structure
A. Polyploidy
1. Mechanisms:
2. Frequency:
3. The effect of hermaphrodism:
4. Evolutionary Importance:
- obviously can be an instant speciation event
- polyploidy is also a mechanism for “genome doubling” or “whole genome duplication”
- this duplication allows for divergence of copied gene function and evolutionary innovation. Eventually, the copies may be so different that they don’t really represent duplicates any more… resulting in “diploidization”.

79. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
Sources of Variation:
A. Mutation - change to the genome
B. Recombination
- new genes

80. Recombination can produce new genes
Crossing over WITHIN a gene, in introns, can recombine exons within a gene, producing new alleles.
EXON 1a
EXON 2a
EXON 3a
Allele “a”
EXON 1A
EXON 2A
EXON 3A
Allele “A”
Allele “α”
Allele “ά”

81. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
Sources of Variation:
A. Mutation - change to the genome
B. Recombination
- new genes
- new genotypes

82. Without crossing over:
2n = 4, gametes = 4
2n = 6, gametes = 8
n = x, gametes = 2x
2n = 46, gametes = 8,388,608

83. 70 trillion combinations
Without crossing over:
2n = 4, gametes = 4
2n = 6, gametes = 8
n = x, gametes = 2x
2n = 46, gametes = 8,388,608
Two reproducing humans:
Any of the 8 million sperm could fertilize any of the 8 million types of eggs, creating:
70 trillion combinations

84. “Hey!! That solves my dilemma about how new variation is produced each generation!!
Too bad I’m dead!

85. DNA, RNA, and Proteins
II. Mutation: A change in the genome of a cell
Sources of Variation:
A. Mutation - change to the genome
B. Recombination – new genes and genotypes
C. The environment