How Do Genes Work

1
Chapter 1

• How Do Genes Work?

2
Chapter 11
3
Are Genes Composed of DNA or Protein?

• Proteins are more variable in structure than DNA,
  whichwas not thought to be sufficiently complex
  to code for allthe operations of a cell.

4
Are Genes Composed of DNA or Protein?

• Transformation experiments provide the first
  evidence that genes are DNA.
• Griffith material from dead virulent
  Streptococcus can transform benign Streptococcus
  into a virulent strain.
• Avery et al. extracted material from dead
  virulent Streptococcus and treated it with
  enzymes to destroy either DNA or RNA or proteins.
  Only DNA-destroying enzymes prevented
  transformation, hence DNA is the genetic
  material.

5
Figure 11.1a
There are two strains of Streptococcus pneumoniae.
ROUGH COLONY (R)
SMOOTH COLONY (S)
S strain is virulent (Polysaccharide
capsule prevents detection by hosts immune
system)
R strain is benign (Lacking a protective capsule,
it is recognized and destroyed by hosts immune
system)
6
Figure 11.1b
7
Figure 11.2
DETERMINING THAT DNA IS THE HEREDITARY MATERIAL
1. Remove the lipids and carbohydrates from a
solution of heat-killed S cells. Proteins, RNA,
and DNA remain.
Heat-killed S cells
Lipids
Carbohydrates
2. Subject the solution to treatments of enzymes
to destroy either the proteins, RNA, or DNA.
3. Add a small portion of each sample to a
culture containing R cells. Observe whether
transformation has occurred by testing for the
presence virulent S cells.
8
Are Genes Composed of DNA or Protein?

• Transformation experiments provide the first
  evidence that genes are DNA.
• Griffith material from dead virulent
  Streptococcus can transform benign Streptococcus
  into a virulent strain.
• Avery et al. extracted material from dead
  virulent Streptococcus and treated it with
  enzymes to destroy either DNA or RNA or proteins.
  Only DNA-destroying enzymes prevented
  transformation, hence DNA is the genetic
  material.

9
Are Genes Composed of DNA or Protein?

• T2 virus convinces skeptics that DNA is the
  genetic material since the material injected by
  the virus into host cells is DNA, not protein.

10
Figure 11.3
Virus protein coat
Host cell membrane
Virus DNA
2. Virus DNA directs the production of new virus
particles.
1. Start of infection. Virus DNA enters
host cells. Protein coat does not.
3. End of infection. New generation of virus
particles burst from host cell.
11
Essay 11.1, Figure 1
HOW DO VIRUSES WORK?
Free particles in tissue or enviroment
4. Particles assemble inside host, then burst or
bud to exterior.
12
How Do Genes Produce Traits?

• Garrod first to connect genes to metabolism by
  analyzing inherited genetic diseases responsible
  for "inborn errors of metabolism".
• A defective gene produces a defective enzyme.
• Without the enzyme, the substrate of the enzyme
  accumulates, producing the disease.

13
Figure 11.4a
A metabolic pathway
Enzyme 1
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
When enzyme 5 is not available, substrate E will
accumulate
14
Figure 11.4b
One metabolic pathway studied by Garrod
O
O
O
H
H
HO
CH2
COO-
OH
- OOC
CH2
C
HO
COO-
CH2
C
C
C
C
Enzyme
Enzyme
4-Maleylacetoacetic acid
CH2 COO
p-Hydroxyphenylpyruvate
Homogentisic acid
15
How Do Genes Produce Traits?

• Beadle and Tatum created mutants in the
  arginine biosynthesis pathway of Neurospora, and
  from them, formulated the one gene - one enzyme
  hypothesisgenes code for proteins, most of
  which are enzymes. Phenotype results from the
  combination of proteins thatare present.

16
Figure 11.5a
1. Expose bread mold to X-rays to
generate mutations. Different mutations will
occur in different individuals.
ISOLATING KNOCK-OUT MUTANTS FOR ARGININE
X-rays
Neurospora crassa
2. Place offspring of different mutagen- ized
individuals in hundreds of culture tubes with
complete medium. Result all offspring grow
to maturity.
Minimal medium
Complete medium (contains amino acids)
3. To find mutants, grow sample of each culture
on minimal medium. Result about 2 are
mutant (cannot grow on minimal medium).
Minimal medium (contains no amino acids)
Minimal medium plus arginine
4. To find which mutants are arginine mutants,
test on minimal mediumplus arginine.
17
Figure 11.5b
Hypothesized pathway for arginine synthesis
Ornithine or citrulline
Ornithine or citrulline
Precursor
Arginine
Enzyme 1
Enzyme 2
Other enzymes
18
Figure 11.5c
Locating arg mutants within arginine pathway
Minimal Medium Ornithine
Minimal Medium Citrulline
Minimal Medium Arginine
Minimal medium
Result
Conclusion
Mutant arg1 can grow if given either precursor.
Mutation must debilitate an enzyme earlyin the
arginine pathway.
arg1 mutant
Mutant arg2 can grow if given citrulline but
not if given ornithine
Mutation must debilitate an enzyme
between ornithine and citrulline in the pathway.
arg2 mutant
arg3 mutant
Mutation must debilitate an enzyme that creates
arginine at the end of the pathway
Mutant arg3 can grow if given arginine.
19
Figure 11.5d
THE ONE GENE-ONE ENZYME HYPOTHESIS
Hypothesis Beadle and Tatum proposedthat each
gene in an organism is responsible for making a
different protein, most of which function
as enzymes.
Ornithine
Precursor
Citrulline
Arginine
Enzyme 3
Enzyme 2
Enzyme 1
arg1 mutants havea nonfunctional enzyme 1
arg2 mutants havea nonfunctional enzyme 2
arg3 mutants havea nonfunctional enzyme 3
20
The Genetic Code

• The nucleotide sequence of DNA is a code DNA is
  an information-storage molecule without enzymatic
  capabilities(F. Crick).
• Hypothesis each of the 20 amino acids in
  proteins is specified by one or more 3 base
  codons (Gamow).

21
Figure 11.8
There are 4 RNA bases (U, C, A, G) and they must
specify 20 amino acids.
How many bases specify a single amino acid?
G
G
A
U
C
C
G
A
A
U
G
C
C
G
G
U
C
A
A
U
mRNA
G
A
A
U
U
C
C
G
A
A
A
A
U
U
G
A
C
C
C
C
C
G
G
C
U
C
C
C
1 Base?
2 Bases?
3 Bases?
4 Bases?...
A triplet code could specify a maximum of 4 x 4 x
4, or 64 amino acids.
A doublet code could specify a maximum of 4 x 4
or 16 amino acids.
U
U
U
U
U
C
A
G
U
U
U
U
U
U
U
U
U
C
A
G
G
C
A
U
2
2
3
4
1
1
3
4
1
2
3
4
C
C
C
C
C
C
C
C
U
C
A
G
U
C
A
G
C
C
C
C
4 lt 20 Not enough
5
6
7
8
6
5
7
8
A
A
A
A
A
U
C
A
G
A
A
Since there are only 4 bases, a singlet
code could onlyspecify 4 amino acids.
A
A
A
U
C
A
G
A
A
9
9
10
11
12
10
11
12
G
G
C
A
G
G
G
U
G
G
G
U
C
A
G
G
G
etc...
14
14
13
15
16
13
15
16 lt 20 Not enough
64 gt 20 More than enough
22
The Genetic Code

• Single or double nucleotide additions or
  deletions cause nonsense mutations in genes, but
  additions or deletions of3 nucleotides maintain
  the reading frame. Conclusion the code is
  composed of triplets of nucleotides. (F. Crick
  et al.).

23
Figure 11.9ac
(a) Single deletion or addition of base
A
A
T
A
A
T
A
A
T
A
A
T
A
A
T
Original DNA sequence
-
A
A
T
A
A
T
A
T
A
A
T
A
A
T
Incorrect registration
1 deletion mutation
A
A
T
A
A
T
A
T
A
A
A
T
A
A
T
G
Incorrect registration
1 addition mutation
(b) Combination of deletion and addition
Correct registration restored
A
A
T
A
A
T
A
T
A
A
T
A
A
T
G
-
1 deletion mutation 1 addition mutation
(c) Multiple deletions or additions
Correct registration restored
A
T
A
A
T
A
T
A
A
A
A
T
-
-
-
3 deletion mutations
Correct registration restored
A
A
T
A
A
T
A
A
T
A
A
A
A
T
T
G
G
C
3 addition mutations
Conclusion The code is read in triplets of
bases, not singlets or doublets.
24
The Genetic Code

• Nirenberg and Matthaei and others decipher the
  amino acidsthat are specified by different
  triplets using a special RNA polymerizing enzyme
  and probability theory.

25
Table 11.1
26
Figure 11.10
Second base
U
C
A
G
UUU
UCU
Phenyl- alanine
UAU
UGU
U
U C A G
Tyrosine
Cysteine
UUC
UCC
UAC
UGC
Serine
UCA
UUA
Stop codon
UAA
UGA
Stop codon
Leucine
UCG
UUG
Tryptophan
UAG
UGG
Stop codon
CGU
CCU
CUU
CAU
U C A G
C
Histidine
CGC
CAC
CCC
CUC
Leucine
Proline
Arginine
CGA
CCA
CUA
CAA
Glutamine
First base
CUG
CGG
CCG
CAG
Third base
AUU
AGU
U C A G
AAU
ACU
Asparagine
Serine
AUC
AGC
ACC
Isoleucine
A
AAC
Theronine
AUA
ACA
AGA
AAA
ACG
Lysine
Arginine
Methionine start codon
AUG
AGG
AAG
GGU
Aspartic acid
GUU
GCU
U C A G
GAU
GGC
G
GUC
GCC
GAC
Valine
Alanine
Glycine
GGA
GUA
GCA
GAA
Glutamic acid
GGG
GUG
GCG
GAG
27
The Central Dogma Information Flows from DNA to
RNA to Proteins (F.Crick)

• Hypothesis RNA acts as an intermediary between
  DNAand proteins. (Jacob and Monod).

28
Figure 11.6
DNA
Nucleus
mRNA
Cytoplasm
mRNA
Ribosome
Protein
29
The Central Dogma Information Flows from DNA to
RNA to Proteins (F.Crick)

• Hurwitz and Furth confirm the existence of
  messenger RNA and identify an RNA polymerase that
  copies DNA into RNA. The RNA is then translated
  into a specific sequence of amino acids, thus
  linking DNA to RNA to proteins.

30
Figure 11.7
ISOLATING RNA POLYMERASE
1. Purify and separate theproteins froma
culture ofE. coli cells.
Can one of these proteins catalyzethe formation
of RNA?
2. In each of many tubes put - proteins -
radioactive ribonucleotides
3. RNA polymers, formed by thepresence of
RNpolymerase, will precipitate in anacidic
solution. Ribonucleotide monomers willremain
solublein an acidic solution.
RNA polymerase present
31
The Central Dogma Information Flows from DNA to
RNA to Proteins (F.Crick)

• Viruses that have RNA genomes contradict the
  centraldogma, but all cells conform to it.