1. Mutations

2. What is a gene? Prokaryotic Genes PROMOTER 3’ 5’ 3’ (-35) (-10)
antisense
---TTGACAT------TATAAT AT-/-AGGAGGT-/-ATG CCC CTT TTG TGA
---AACTGTA------ATATTA TA-/-TCCTCCA-/-TAC GGG GAA AAC ATT
sense 3’
(-35)
(-10)
RIBOSOME
BINDING
SITE 5’ 5’ 3’
U-/-AGGAGGU-/-AUG CCC CUU UUG UGA
Met Pro leu leu stp
When all of these rules are satisfied then A segment of DNA will generate an RNA which will then be read by a ribosome and be translated into a protein.

3. Reading the genetic code
A T G
T T T
A A A
T A G
C C C 5’ 3’
C A T
A A A
T T T
C T A
G G G 5’ 3’
A T G
T T T
A A A
T A G
C C C 5’ 3’ 5’ 3’
A U G U U U A A A U A G C C C 5’ 3’
C A T
A A A
T T T
C T A
G G G
A U G
U U U
A A A
U A G
C C C 5’ 3’
U A C
Met
A A A
Phe
U U U
Lys
S T P

4. No Gaps
A U G
U U U
A A A
U A G
C C C 5’ 3’
U A C
Met
A A A
Phe
U U U
Lys
S T P
A U G
U U U
A A A
U A G
C C C 5’ 3’
U A C
Met
A A U
Asn
U U A
Leu

5. No overlaps
A U G
A A A
C C C
U A G 5’ 3’
U A C
Met
U U U
Lys
G G G
Pro
S T P
A U G
A A A
C C C
U A G 5’ 3’
U A C
Met
U U U
Lys
U G G
Trp

6. The GENETIC CODE The code is a three letter code. Second letter U C A
UUU
UUC
UUA
UUG
CUU
CUC
CUA
CUG
AUU
AUC
AUA
AUG
GUU
GUC
GUA
GUG
UCU
UCC
UCA
UCG
CCU
CCC
CCA
CCG
ACU
ACC
ACA
ACG
GCU
GCC
GCA
GCG
UAU
UAC
UAA
UAG
CAU
CAC
CAA
CAG
AAU
AAC
AAA
AAG
GAU
GAC
GAA
GAG
UGU
UGC
UGA
UGG
CGU
CGC
CGA
CGG
AGU
AGC
AGA
AGG
GGU
GGC
GGA
GGG U C A G
Phe
Tyr
Cys U
Ser
STOP
STOP
Leu
Trp
His C
Arg
Pro
Leu
Gln
First letter
Third letter
Asn
Ser
Ile A
Thr
Lys
Arg
Met
Asp G
Val
Ala
Gly
Glu

7. The Genetic Code Properties of the Genetic code:
1- The code is written in a linear form using the nucleotides
that comprise the mRNA
2- The code is a triplet: THREE nucleotides specify
ONE amino acid
3- The code is degenerate: more than one triplet specifies
a given amino acid
4- The code is unambiguous: each triplet specifies only
5- The code contains stop signs- There are three different stops
6- The code is comma less
7- The code is non-overlapping

8. xxxxxx

9. Mutations
Most mutations are harmful in their effects; only rarely are mutations beneficial.
A gene with one wild-type allele is monomorphic; a gene with two or more wild-type alleles is polymorphic.
The vast majority of mutant traits are determined by alleles of more than one gene. This means that most traits are multifactorial traits.
A Heterogeneous Trait is one that may be caused by mutations in more than one gene.
Human deafness is an example of a heterogeneous trait: Mutations in any of at least 50 genes lead to deafness.
An important class of mutations are conditional mutations- (Environment affects Phenotype). Conditional mutations are those that express their associated phenotype only under some conditions (restrictive conditions) and not others (permissive conditions).
Conditional lethal mutations are common.
Temperature-sensitive conditional mutations are invaluable in genetic research.

10. Generation of mutations
Spontaneous mutations
Replication induced mutations of DNA
Usually base substitutions (Most errors are corrected)
Meiosis- segregation defects or defects during crossing over can induce mutations
Small additions and deletions AND Large changes as well
Environment induced changes
Exposure to physical mutagens - Radioactivity or chemicals
Depurination (removal of A or G)
Repair results in random substitution during replication
Deamination (removal of amino group of base) (nitrous acid)
Cytosine--uracil--bp adenine--replication--
Oxidation (oxoG)
guanine--oxoguanine--bp adenine--replication --
Base analog incorporation during replication BU-T
Intercalating agents

11. Methods used to study mutations
Gross chromosomal changes-
deletions, insertions, inversions, translocations
Cytology- microscopy- karyotype
Small mutations
Small deletions, insertions and point mutations
Recombinant DNA technologies

12. Missense mutations UUU UUU UGC UUU UUU WT Phe Phe Cys Phe Phe
Missense mutations alters ONE codon so that it encodes a different amino acid
UUU UUU UGC UUU UUU WT
Phe Phe Cys Phe Phe
UUU UUU UGG UUU UUU mut
Phe Phe Trp Phe Phe

13. Consequences of Missense Mutations
Missense mutations alter one of the many amino acids
that make a protein
Its consequences depend on which amino acid is altered
Conservative mutations: K to R
Nonconservative mutations: K to E
Surface Vs buried
Mutations in globular domains Vs unstructured tails
Silent mutations
Mutations in non-coding regions
Nonsense mutations

14. NNN UGG CGA UGG CGA UGG CGA UGG CGA NNN
Frameshift mutations
A single base-pair deletion or insertion results in a change
in the reading frame
NNN UGG CGA UGG CGA UGG CGA UGG CGA NNN
Trp Arg Trp Arg Trp Arg Trp Arg
Delete A
NNN UGG CGU GGC GAU GGC GAU GGC GAN NN
Trp Arg Gly Asp Gly Asp Gly
Insert A
NNN UGG CGA AUG GCG AUG GCG AUG GCG ANNN
Trp Arg Met Ala Met Ala Met Ala

15. NNN UGGCGAUGGCGAUGGCGAUGGCGA NNN ... TrpArgTrpArgTRpArgTrpArg …
Frameshift mutations
A single base-pair deletion or insertion results in a change
in the reading frame
NNN UGGCGAUGGCGAUGGCGAUGGCGA NNN
... TrpArgTrpArgTRpArgTrpArg …
.... GlyAspGlyAspGlyAspGlyAsp
..... AlaMetAlaMetAlaMetAla
Delete A
UGG CGU GGC GAU GGC GAU GGC GANN
Trp Arg Gly Asp Gly Asp Gly
Insert A
UGG ACG AUG GCG AUG GCG AUG GCG ANN
Trp Thr Met Ala Met Ala Met Ala

16. Frameshift mutations- Deletion
Base-pair deletion or insertion results in a change
in the reading frame
AUG UUU AGC UUU AGC UUU AGC
Met Phe Ser Phe Ser Phe Ser
Delete C
AUG UUU AGU UUA GCU UUA GC
Met Phe Ser Leu Ala Leu
Delete GC
AUG UUU AUU UAG CUU UAG C
Met Phe Ile Stp
Delete AGC
AUG UUU UUU AGC UUU AGC
Met Phe Phe Ser Phe Ser

17. Frameshift mutations-Insertion
Base-pair deletion or insertion results in a change
in the reading frame
AUG UUU AGC UUU AGC UUU AGC
Met Phe Ser Phe Ser Phe Ser
Insert C
AUG UUU AGC CUU UAG CUU UAG C
Met Phe Ser Leu STOP
Insert CC
AUG UUU AGC CCU UUA GCU UUA GC
Met Phe Ser Pro Leu Ala Leu
Insert CCC
AUG UUU AGC CCC UUU AGC UUU AGC
Met Phe Ser Pro Phe Ser Phe Ser

18. AUG UUU AGC UUU AGC UUU AGC WT Met Phe Ser Phe Ser Phe Ser
Silent Mutations
Silent mutations do not alter the amino acid sequence!
The Genetic code is degenerate!
AUG UUU AGC UUU AGC UUU AGC WT
Met Phe Ser Phe Ser Phe Ser
AUG UUC AGC UUU AGC UUU AGC Mut
Mutations that occur within introns are often silent but mutations at splicing junctions have effects
Mutations that occur in non-genic regions are often silent except when they occur in regulatory sequences

19. Mutations in non-protein coding regions
Mutations in the promoter, splicing junction or ribosome binding site are also mutagenic
Reduced expression of mRNA might result in reduced levels
of proteins OR
Increased expression of mRNA might result in increased levels of protein
Mutations in splicing junctions may also be mutagenic improperly spliced mRNA will result in the intron being translated
Mutations in tRNA or aminoacyl-tRNA synthase are mutagenic

20. UUU UUU UGC UUU UUU Phe Phe Cys Phe Phe UUU UUU UGA UUU UUU
Nonsense mutations
Nonsense mutations alter one codon so that it now encodes
for a STOP codon
UUU UUU UGC UUU UUU
Phe Phe Cys Phe Phe
UUU UUU UGA UUU UUU
Phe Phe STOP
Nonsense mutations insert a stop codon which results in
premature termination
Truncated polypeptide usually results in loss of function
for polypeptide

21. A U G U A C A A A U A G C C C 5’ 3’ U A C Met A U G Trp U U U Lys
There are NO tRNAs in wildtype cells with anti-codons that recognize STOP codons in mRNA
What happens if there is a mutation in the anti-codon loop of a specific tRNA Gene that allows a tRNA to recognize a stop codon
A U G
U A C
A A A
U A G
C C C 5’ 3’
U A C
Met
A U G
Trp
U U U
Lys
S T P

22. Nonsense suppressor mutations!
These are the result of a mutation in the anti-codon loop of
a specific tRNA Gene
It allows the tRNA to recognize a nonsense codon and base
pair with it.
DNA
Gene encoding tRNATRP
Point mutation occurs in the anticodon loop OF THE tRNA
This allows this tRNA to base pair with a stop codon and ?
AUG
Trp
AUG
Trp
AUC
Trp
5---UAC---UAG---UAA3’
5--UAC---UAG---UAA3’
Normal tRNA
Mutant tRNA

23. Nonsense suppressor --- UUU UUU UAG UUU UUU ----- --- Phe Phe STP
Trp-tRNA has mutation in anticodon. This allows it to pair with a stop codon
5’--- UUU UUU UAG UUU UUU UAA-----3’
AUC
Trp
AAA
Met
Ala
Phe
--- Phe Phe Trp Phe Phe |
A mutant protein that is larger than normal will be synthesized!!

24. Nonsense and Nonsense suppressor
--- UUU UUU CAG UUU UUU -----
--- Phe Phe Gln Phe Phe ---
Nonsense mutation
--- UUU UUU UAG UUU UUU -----
--- Phe Phe STOP
AUC
Trp
---UAG---
What will happen if an individual carries both a nonsense mutation in a gene and a nonsense suppressor mutation in the anticodon loop of one of the trp-tRNA genes.
5’--- UUU UUU UAG UUU UUU ’
AUC
Trp
AAA
Met
Ala
Phe
Phe Phe Trp Phe Phe

26. Methods used to study mutations
Gross chromosomal changes-
deletions, insertions, inversions, translocations
Cytology- microscopy- karyotype
Small mutations
Small deletions, insertions and point mutations
Recombinant DNA technologies