Mutations

Genetic Code Chapter 17: page 306-309

Mutations Chapter 17: page 322-325
Transposons Chapter 19: page 360-361
 The Genetic Code is Universal

 All living things use the

same 4 bases
 All living things use the
same code: codons code
for the same amino acid
no matter what the
organism
The Genetic Code is Redundant
 64 different codons on
mRNA
 But only 20 different
amino acids
 Conclusion?

More than one codon

can code for the
same amino acid.
The Genetic Code is Redundant
 64 different codons on
mRNA
 But only 45 different
tRNA molecules
 Conclusion?

Some tRNAs recognize

more than one codon.

Fig. 17.4
 Wobble Hypothesis

 Base pairing rules are

flexible in the wobble
position
 Wobble position: third base
of the mRNA codon and its
corresponding tRNA
anticodon

Fig. 17.4
Inosine in the wobble position
 Inosine:
 a modified form of adenine that is found in tRNA
(anticodon)
 can form H bonds with U, C, or A on the mRNA

Inosine Adenosine

From http://bio.winona.msus.edu/berg/ChemStructures/Inos-ade.gif
Inosine in the wobble position

Example:
 tRNA anticodon CGI
 Can bind to codons
GCU, GCC and GCA
 All result in the addition
of the amino acid
alanine

Fig. 17.4
Reading the Genetic Code
Characteristics of the Code
 Degenerate / Redundant
 There are 64 codons, but only 20 amino acids
 The same amino acid may be coded by more than one
codon
 E.g. GCU and GCC both specify alanine
 No ambiguity
 Each codon only specifies one amino acid
 Marshall Nirenberg (1961)
 Deciphered first codon
 Awarded Nobel Prize in
1968 for the interpretation
of the genetic code
 Discovery Channel 100
Greatest Discoveries –
History of Genetics
(Nirenberg @ 25:25-28:49)
http://www.youtube.com/w
atch?v=0qgMd0obEkc

http://upload.wikimedia.org/wikipedia/commons/thumb/1/10/Marshall_Nirenberg_performing_experiment.jpg/481px-Marshall_Nirenberg_performing_experiment.jpg
http://profiles.nlm.nih.gov/ps/access/JJBBWR.jpg
Nirenberg’s Experiment
 Synthesized artificial mRNA with identical RNA
nucleotides
 E.g. UUUUUUUUUUUUUUU
 Thus only 1 type of codon (e.g. UUU)
 Resulted only in one type of amino acid in the
polypeptide (e.g. phenylalanine)
 Repeated with other nucleotides
 Other techniques used to decode mixed triplets
Tutorial: Reading the Genetic
Code
 http://learn.genetics.utah.edu/units/basics/transcribe/
Mutation
 a change in the genetic material of an organism
 genetic disorder or hereditary disease: harmful
mutations in gametes that are passed onto the
next generation
Origin/Cause of Mutation
 Spontaneous:
 errors in the genetic machinery during DNA
replication
 due to enzymes
 Induced: arising from exposure to mutagenic
agents
 Transposable elements:
 errors during recombination (crossing over)
 transposons
Mutagen
 a substance that can cause mutations
 Physical mutagen
 Radiation, UV light, x-rays
 Chemical mutagen
 Base analogues:
 chemical similar to normal DNA bases but pair
incorrectly during DNA replication
 e.g. used in a drug for treating HIV
 Distort DNA helix interfering with replication
 e.g. ethidium bromide, used in gel electrophoresis for
visualizing DNA
 Changing pairing properties in bases
Effect of Mutations
Affects 3 levels:
 RNA codons:
 Point mutation
 Frameshift mutation
 Amino acid sequence on polypeptide:
 Missense
 Nonsense
 Silent
 Protein function
 Negative
 Positive
 Neutral
Types of Mutations
 Point mutations
 Frameshift mutations
 Chromosomal mutations
 Point Mutations: Substitution

 a small change in a DNA

basepair where one
nucleotide is replaced
with another
Frameshift Mutation:
Insertion & Deletion
 Reading frame: triplet grouping (codons) of a genetic
message
 Frameshift mutation: number of nucleotides added/lost
is not a multiple of 3 thus altering the reading frame
 Insertion: addition of one or more nucleotide pairs in a gene
 Deletion: loss of one of more nucleotide pairs in a gene
 No frameshift: number of nucleotides added/lost is a
multiple of 3
 Leads to extra or missing amino acid
Frameshift
Mutations

 Frameshift deletion

 Frameshift insertion

 No frameshift

Fig. 17.24
Effects of mutations on polypeptide

 Missense mutation:
 altered codon codes for a different amino acid
 May or may not have an effect on protein function
 Nonsense mutation:
 changes an amino acid codon into a stop codon
 Results in truncated protein. Most are digested by the cell.
 often lethal at the embryonic stage
 Silent mutation:
 altered codon codes for same amino acid
 No effect on protein function
 Missense Mutation

Fig. 17.4 Fig. 17.24

Example: Sickle Cell Anemia
 Substitution missense: A  T changes amino acid
glutamine to valine
 Nonsense Mutation

Fig. 17.4 Fig. 17.24

 Silent Mutation

Fig. 17.4 Fig. 17.24

Wild Type:
Two men sat and had hot tea
Mutations
 Two men Sat and had hot tea
 Two men sat and had hot sea
 Two me.
 Two men sat and had hot tte a
 Two mes ata ndh adh ott ea

Missense Frameshift Insertion

Silent Nonsense Frameshift Deletion
Point/Frameshift Mutation
Summary

Types Missense effect Nonsense effect Silent

Point Mutation
Substitution

Frameshift
Insertion or
Deletion

No Frameshift
Insertion or
Deletion
Point/Frameshift Mutation
Summary

Types Missense effect Nonsense effect Silent

Point Mutation
  
Substitution

Frameshift 
Insertion or  
Deletion extensive

No Frameshift 
Insertion or (extra or missing  
Deletion amino acid)
Effect of mutation on protein
function / organism
 Negative mutations
 Changes protein function to make it detrimental to the organism
 From missense or nonsense mutations
 Example: most molecular biological research is related to this idea
 Positive mutations
 Changes protein function to benefit the organism
 From missense mutations
 Example: back mutations / reversions that restore original sequence
 Example: antibiotic resistance
 Neutral mutations
 Silent mutations: no change in amino acid
 Sometimes missense: change in amino acid without changing protein
function
 Example: mutations in introns doesn’t affect expressed protein
HW Question
 The genetic code is redundant but not ambiguous.
Explain what that means.
MaCS Enrichment
 The topic of transposons is for MaCS enrichment
only
Transposons
 DNA segments that naturally move around the
genome
 Transposable elements
 Mobile genetic elements
 Transposons

 Barbara McClintock was

awarded the Nobel Prize in 1983
for her discovery of transposons
in maize (corn)
 Discovery Channel 100 Greatest
Discoveries – History of Genetics
(McClintock @ 11:18-16:10)
http://www.youtube.com/watch?
v=0qgMd0obEkc

http://profiles.nlm.nih.gov/ps/access/LLBBQQ.jpg
Transposon in humans
 Almost half the human genome consists of
transposons:
 Retrotransposons accounting 42%
 DNA transposons (most if not all are inactive)
accounting for 2-3%
 Reference: http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

 No known function. Junk DNA.

Types of Bacterial Transposons
 Insertion sequence
 Composite transposon
Insertion Sequence
 Simplest type of bacterial transposon
 Consists only of DNA needed for the act of transposition
 Transposon contains:
 gene for transposase
 Transposase: enzyme that catalyzes movement of
transposon
 Inverted repeats
 at ends of transposons
 where transposase binds

Fig 18.16
Insertion Sequence Effect
 Can cause mutations when they land in DNA
region that regulates gene expression or the
coding region of a gene
 Mutation due to insertion sequence is rare (1 in 10
million generations)
 No known benefit
Composite Transposon
 Longer transposon and more complex
 Contain genes other than transposase
 Beneficial in bacterial reproduction
 confer antibiotic resistance

Fig 18.18
Mechanism of Transposition
 DNA transposon
 Transposition by cut-and-paste mechanism
 Transposition by replicative mechanism
 Retrotransposon
 Transposition by an RNA intermediate
 Uses reverse transcriptase
Animation
Transposons “Shifting Segments of the Genome”
 http://highered.mcgraw-
hill.com/sites/dl/free/0072556781/192785/anim0039.swf

Simple Transposition (cut-and-paste)

 http://highered.mcgraw-
hill.com/sites/0072995246/student_view0/chapter23/simple_transposition.ht
ml

Mechanism of Transposition: Replicative

 http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?
it=swf::535::535::/sites/dl/free/0072437316/120082/bio36.swf::Mechanism
%20of%20Transposition
 Mechanism of Cut-and-Paste
Transposition
 Transposase bind to
both inverted repeats
and target site
 Cut out transposon
 Cut open the target site
 Join transposon to
target site
 Reseal DNA

http://www.chrisdellavedova.com/wp-content/uploads/2008/01/transposons1.jpg
Mechanism of Replicative
Transposition
 transposon replicated
at original site
 copy inserts into new
site
 original transposon
still at original site
Retrotransposon
 Transposons that transpose through an RNA
intermediate
 Abundant in plants (e.g. maize = corn)
Mechanism of Retrotransposon
Movement

http://www.bio.miami.edu/~cmallery/150/gene/c7.19.16b.transposon.jpg
Mechanism of Retrotransposon
Movement
1. Retrotransposon RNA produced during
transcription
2. Translation of RNA makes:
 Reverse transcriptase: enzyme that converts RNA
 DNA
 Enzymes that catalyze insertion of retrotransposon
into target site
3. Retrotransposon DNA synthesized by reverse
transcriptase action on RNA
4. DNA inserted into target site