1. B. The trp Operon in E. coli
This operon is responsible for making proteins that PRODUCE the amino acid tryptophan.
If [trp] is low, then genes are on
And trp is made
As [trp] increases, it binds to repressor, ACTIVATING the repressor so that it can bind to the operator – turning genes OFF.
This regulation is also mediated through stem-loop formation in the ‘leader-attenuator’ region of the m-RNA product.

2. B. The trp Operon in E. coli
m-RNA
B. The trp Operon in E. coli
This regulation is mediated through stem-loop formation in the ‘leader-attenuator’ region of the m-RNA product.
If [trp] is low:
Ribosome read to the double trp codons, but [trp] is low, so they are slow to add into the ribosome… so translation stalls in the 1 region; so 2 binds with 3. The 2-3 loop forms does not destabilize transcription – transcription continues and the rest of the m-RNA is made, and translation continues, also....
GENES ON for trp SYNTHESIS
…m-RNA

3. B. The trp Operon in E. coli
m-RNA
B. The trp Operon in E. coli
This regulation is mediated through stem-loop formation in the ‘leader-attenuator’ region of the m-RNA product.
If [trp] is high:
Ribosome read through the trp codons, adding trp amino acid to the protein chain and preventing the 2-3 loop. 3 binds with 4, forming the loop that terminates transcription even before [trp] is high enough to activate the repressor. Transcription is terminated in the attenuator region.
…m-RNA

4. XII. Gene Regulation
The lac Operon in E. coli
B. The trp Operon in E. coli
C. Regulation in Eukaryotes
Regulation in eukaryotes is more complex, as it regulates the specialization of different tissues, the developmental changes of organisms over time, and genetic responses to the environment.
As such, it is not surprising that the patterns of regulation are much more complex; often as a consequence of greater structural complexity of chromosomes and genes.

5. C. Regulation in Eukaryotes
- Histones affect accessibility of a gene

6. C. Regulation in Eukaryotes
- Histones affect accessibility of a gene
- Methylation causes condensation of genes and chromosomes
Imprinting
Heterochromatin (highly repetitive DNA)
Barr Bodies (X inactivation)

7. C. Regulation in Eukaryotes
- Histones affect accessibility of a gene
- Methylation causes condensation of genes and chromosomes
- Transcription is regulated by transcription factors that increase (enhancers) or decrease (silencers) the ability of the RNA polymerase to bind to the promoter and begin transcription.
Because genes are regulated by multiple transcription factors, it means one gene can be turned on by many different signals – and become associated with many enzymatic pathways in a cell/organism. And, binding can be modulated – not just on/off but on by degrees

8. C. Regulation in Eukaryotes
- Histones affect accessibility of a gene
- Methylation causes condensation of genes and chromosomes
- Transcription is regulated by transcription factors that increase (enhancers) or decrease (silencers) the ability of the RNA polymerase to bind to the promoter and begin transcription.
They tend to have particular structures that bind DNA in specific ways: helix-turn-helix, zinc fingers, leucine zippers

9. C. Regulation in Eukaryotes
Transcription can also be regulated by small pieces of RNA called “si-RNA” (small interfering RNA) and mi-RNA (microRNA). These molecules are short RNA sequences that bond with m-RNA and either cleave it (si-RNA) or just bind to it and block translation (mi-RNA). They can also initiate methylation of promoters and turn genes off.
This process is called RNA interference or RNAi

10. High resolution image (pdf 2,5 Mb) 
C. Regulation in Eukaryotes
Fire and Mello (Nobel in Phys or Medicine 2006)
RISC = “RNA-induced Silencing Complex”
Binds to m-RNA and splices it.

11. High resolution image (pdf 2,5 Mb) 
C. Regulation in Eukaryotes
There are two ways that double-stranded RNA’s naturally occur – through viral infection or transcription of mi-RNA “genes”.
Unclear whether this evolved first as a mechanism to regulate gene production, or as an adaptation to resist viral infection.

12. C. Regulation in Eukaryotes
RITS target promoters of specific genes or larger regions of chromatin. Remodeling of chromatin turns genes off, often by inducing methylation.
Important in imprinting
Both pathways can inhibit production of transcription factors, too, and affect other regulatory pathways.
RITS = “RNA induced initation of transcription silencing complex”

13. C. Regulation in Eukaryotes
- Alternate Splicing Pathways, regulated by intronic ribozymes and spliceosomes, can make different protein products
A calcium regulator in the thyroid
A hormone made in the brain

14. C. Regulation in Eukaryotes
- The initial polypeptide product can be spliced differently, too, to produce different functional proteins from the same initial polypeptide. And the methionine is cleaved and it is coplexed with other molecules (quaternary protein, lipoprotein, glycoprotein, riboprotein).

15. Chromatin remodeling
Polymerase binding
transcription
M-RNA processing
translation
Post-translational modifications

16. zygote
mitosis

17. Heredity, Gene Regulation, and Development Mutation
A. Overview

18. Mutation
A. Overview
1) A mutation is a change in the genome of a cell.

19. Mutation
A. Overview
1) A mutation is a change in the genome of a cell.
2) Some mutations occur during DNA repair, or after DNA is damaged by a mutagen. These changes may affect how that particular cell works. When/if that cell divides, then this defect will be propagated to the daughter cells in that body tissue. These are somatic mutations.

20. Mutation
A. Overview
1) A mutation is a change in the genome of a cell.
2) Some mutations occur during DNA repair, or after DNA is damaged by a mutagen. These changes may affect how that particular cell works. When/if that cell divides, then this defect will be propagated to the daughter cells in that body tissue. These are somatic mutations.
3) Some errors occur in DNA replication that precedes cell division; these changes are passed to the daughter cells in that body tissue. These are somatic mutations, too.

21. Mutation
A. Overview
1) A mutation is a change in the genome of a cell.
2) Some mutations occur during DNA repair, or after DNA is damaged by a mutagen. These changes may affect how that particular cell works. When/if that cell divides, then this defect will be propagated to the daughter cells in that body tissue. These are somatic mutations.
3) Some errors occur in DNA replication that precedes cell division; these changes are passed to the daughter cells in that body tissue. These are somatic mutations, too.
4) Some mutations occur during meiosis, and produce mutant gametes. These are the heritable mutations that we will focus on.

22. VI. Mutation Overview A change in the genome
Occurs at four scales of genetic organization:
1: Change in the number of sets of chromosomes ( change in ‘ploidy’)
2: Change in the number of chromosomes in a set (‘aneuploidy’)
3: Change in the number and arrangement of genes on a chromosome
4: Change in the nitrogenous base sequence within a gene

23. Some triploid babies are born alive, but die shortly after.
VI. Mutation
Overview
Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Triploidy occurs in 2-3% of all human pregnancies, but almost always results in spontaneous abortion of the embryo.
Some triploid babies are born alive, but die shortly after.
Syndactyly (fused fingers), cardiac, digestive tract, and genital abnormalities occur.

24. VI. Mutation Failure of Meiosis I 2n = 4 Gametes: Overview
Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Mechanism #1: Complete failure of Meiosis
- if meiosis fails, reduction does not occur and a diploid gamete is produced. This can occur because of failure of homologs OR sister chromatids to separate in Meiosis I or II, respectively.
Failure of Meiosis I
2n = 4
Gametes:

25. VI. Mutation Failure of Meiosis II 2n = 4
Overview
Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Mechanism #1: Complete failure of Meiosis
- if meiosis fails, reduction does not occur and a diploid gamete is produced. This can occur because of failure of homologs OR sister chromatids to separate in Meiosis I or II, respectively.
Failure of Meiosis II
2n = 4
Normal gamete formation is on the bottom, with 1n=2 gametes. The error occurred up top, with both sister chromatids of both chromosomes going to one pole, creating a gametes that is 2n = 4.

26. VI. Mutation Overview Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Mechanism #1: Complete failure of Meiosis
- if meiosis fails, reduction does not occur and a diploid gamete is produced. This can occur because of failure of homologs OR sister chromatids to separate in Meiosis I or II, respectively.
- this results in a single diploid gamete, which will probably fertilize a normal haploid gamete, resulting in a triploid offspring.
negative consequences of Triploidy:
1) quantitative changes in protein production and regulation.
2) can’t reproduce sexually; can’t produce gametes if you are 3n.

27. Like this Blue-spotted Salamander A. laterale,
VI. Mutation
Overview
Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Mechanism #1: Complete failure of Meiosis
negative consequences of Triploidy:
1) quantitative changes in protein production and regulation.
2) can’t reproduce sexually; can’t produce gametes if you are 3n.
3) but, some organisms can survive, and reproduce parthenogenetically (mitosis)
Like this Blue-spotted Salamander A. laterale,
which has a triploid sister species, A. tremblayi
A. tremblayi is a species that consists of 3n females that reproduce clonally – laying 3n eggs that divide without fertilization.

28. VI. Mutation Overview Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Mechanism #1: Complete failure of Meiosis
Mechanism #2: Failure of Mitosis in Gamete-producing Tissue

29. 2n
1) Consider a bud cell in the flower bud of a plant.

30. 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.

31. 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

32. 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?

33. 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’)

34. 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

35. Polyploidy occurs here; creating a cell with homologous sets
VI. Mutation
Overview
Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Mechanism #1: Complete failure of Meiosis
Mechanism #2: Complete failure of Mitosis
Mechanism #3: Allopolyploidy - hybridization
Polyploidy occurs here; creating a cell with homologous sets
Black Mustard
gametes
2n = 16
n = 8
n = 17
2n = 34
2n = 18
n = 9
Fertilization produces a cell with non-homologous chromosomes
New Species
Cabbage

37. 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

38. VI. Mutation
Overview
Changes in Ploidy
- These are the most dramatic changes, adding a whole SET of chromosomes
Mechanism #1: Complete failure of Meiosis
Mechanism #2: Complete failure of Mitosis
Mechanism #3: Allopolyploidy - hybridization
The Frequency of Polyploidy
For reasons we just saw, we might expect polyploidy to occur more frequently in hermaphroditic species, because the chances of ‘jumping’ the triploidy barrier to reproductive tetraploidy are more likely. Over 50% of all flowering plants are polyploid species; many having arisen by this duplication of chromosome number within a lineage.