1. LECTURE 23: DISSECTION OF GENE FUNCTION I: GENETIC FINE STRUCTURE
chapter 16
bead theory
phage cross
gene = unit of structure?
gene = unit of change?
gene = unit of function?
summary
problems

2. BEAD THEORY bead theory: chromosome = linear (1-D) array of genes
genes are defined by mutant alleles that ...
affect single characters / traits
map to single locus on chromosome
result in mutant phenotypes when individuals are homozygous recessive
show Mendelian ratios in progeny of crosses

3. BEAD THEORY testable bead theory hypotheses:
1. gene as fundamental unit of structure... indivisible by crossing over
2. gene as fundamental unit of change... mutations change alleles from one form to another; there are no smaller units within genes that can change
3. gene as fundamental unit of function... parts of genes cannot function alone in tests of complementation

4. PHAGE CROSS
Benzer (50’s) studied rII gene of T4 bacteriophage infecting E. coli hosts to test the bead theory...
began as physicist (like Delbrück, Brenner & others)
looking for physical properties unique to living matter
most important & influential geneticist (personal bias)
rigorous reductionist approach from physics
made most important link between classical / Mendelian genetics & modern molecular biology
now looks for genes to extend lifespan (in flies)

5. PHAGE CROSS
Benzer (50’s) studied rII gene of T4 bacteriophage infecting E. coli hosts to test these hypotheses...

6. PHAGE CROSS
Benzer (50’s) studied rII gene of T4 bacteriophage infecting E. coli hosts to test these hypotheses...
rII mutants are conditional... grow in E. coli B
 B is permissive host

7. PHAGE CROSS
Benzer (50’s) studied rII gene of T4 bacteriophage infecting E. coli hosts to test these hypotheses...
rII mutants are conditional... grow in E. coli B but not K
 B is permissive host, K is restrictive host

8. PHAGE CROSS
Benzer (50’s) studied rII gene of T4 bacteriophage infecting E. coli hosts to test these hypotheses...
large, round
small, ragged

9. GENE = UNIT OF STRUCTURE?
hypothesis #1: gene is fundamental unit of structure... indivisible by crossing over ?

10. GENE = UNIT OF STRUCTURE?
hypothesis #1: gene is fundamental unit of change... indivisible by crossing over ?
PFU on B = total, PFU on K = ½ of recombinants
recomb. frequency (RF) = 2(PFU on K) / PFU on B

11. GENE = UNIT OF STRUCTURE?
hypothesis #1: gene is fundamental unit of structure... indivisible by crossing over ?
PFU on B = total, PFU on K = ½ of recombinants
recomb. frequency (RF) = 2(PFU on K) / PFU on B

12. GENE = UNIT OF STRUCTURE?
what is the smallest unit of recombination detectable?
phage system can detect 1 mutation in 109 progeny
recombination frequency (RF) = 1 x 10–9
 smallest distance = 1 x 10–7 cM
if 1 cM  5 x 105 bp (on average, in flies)
 bp are separated by 2 x 10–6 cM
phage system ~20x more powerful than needed to detect smallest possible distance (which we now know is adjacent base pairs)
phage is the ultimate genetic system ... resolution!!

13. GENE = UNIT OF STRUCTURE?
hypothesis #1: gene is fundamental unit of structure... indivisible by crossing over ? ... 

14. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
same experimental protocol as for #1

15. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
same experimental protocol as for #1

16. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
same experimental protocol as for #1
mutants from #1 were deletions when they did not ...
recombine with some other mutants
ever revert back to wild type
deletions used to map positions of mutational sites

17. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
all survive on...
B only

18. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
4 +
+ 5

19. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
4 +
+ 5

20. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
4 5
survive on...
B only
K & B
+ +

21. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
4 +

22. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
4 +
survive on...
B only
K & B

23. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
4 +

24. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
4 +

25. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?
no recombination
4 +
survive on...
B only

26. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ? D1 D2 D3 D4

27. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ? D1 D2 D3 D4
A B C D E F G

28. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ?

29. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene ? ... 

30. GENE = UNIT OF CHANGE?
hypothesis #2: gene is fundamental unit of change... mutations change alleles from one form to another; there are no smaller mutable units within a gene... 
point mutations (= revert to wild type at low frequency) mapped to regions defined by deletion mutations
point mutations in the same regions that did not recombine with each other were identical sites
distribution of rII point mutations was not random...

31. GENE = UNIT OF CHANGE?
distribution of rII point mutations was not random...
hot spots & cold spots

32. GENE = UNIT OF CHANGE?
Poisson distribution predicted missed cold spots
observed hot spots (e.g.)
site = nucleotide base pair

33. GENE = UNIT OF CHANGE?
summary of fine structure mapping of rII region in T4

34. GENE = UNIT OF FUNCTION?
hypothesis #3: gene is fundamental unit of function... parts of genes cannot function in complementation tests ?

35.  GENE = UNIT OF FUNCTION?
hypothesis #3: gene is fundamental unit of function... parts of genes cannot function in complementation tests ?...
mutants fell into two functional groups... 2 genes
mutations fail to complement others in the same group 

36. SUMMARY complementation or recombination ? complementation...
protein level, mixing of gene products
no change in genotypes relative to parents
requires 1 generation of crosses to investigate
recombination...
DNA level
results in new genotypes relative to parents
requires 2 generations of crosses to investigate

37. SUMMARY complementation or recombination?
test single phage from E. coli K lysate (F1) for infection on E. coli B & E. coli K (F2)

38.  SUMMARY if you are dealing with complementation (only)...
or high F count
no F1
all F1 F2 plaques on E. coli B
but all still mutant,  no F1 F2 plaques on E. coli K

39. but all recombinant F1 F2 plaques on E. coli B
SUMMARY
if you are dealing with recombination (only)...
low F1 count
but all recombinant F1 F2 plaques on E. coli B

40. only ½ recombinant F1 F2 plaques on E. coli K
SUMMARY
if you are dealing with recombination (only)...
low F1 count
only ½ recombinant F1 F2 plaques on E. coli K

41. all F1 F2 plaques on E. coli B
SUMMARY
reality... recombination & complementation ... 
or high F count
low F1
all F1 F2 plaques on E. coli B

42.  SUMMARY reality... recombination & complementation ...
or high F count
low F1
all F1 F2 plaques on E. coli B
only ½ recombinant F1 F2 plaques on E. coli K

43.     SUMMARY testable bead theory hypotheses:
1. gene as fundamental unit of structure... indivisible by crossing over
2. gene as fundamental unit of change... mutations change alleles from one form to another; there are no smaller units within genes that can change
3. gene as fundamental unit of function... parts of genes cannot function alone in tests of complementation   

44. PROBLEMS
stay tuned...