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Mutation. Timothy G. Standish, Ph. D. The Modern Synthesis.

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mutation

Mutation

Timothy G. Standish, Ph. D.

the modern synthesis
The Modern Synthesis
  • Charles Darwin recognized that variation existed in populations and suggested natural selection as a mechanism for choosing some variants over others, resulting in survival of the fittest and gradual changes in populations of organisms.
  • Without a mechanism for generation of new variation, populations would be selected into a corner where only one variation would survive and new species could never arise.
  • The Modern Synthesis combines the mechanism of mutation in DNA to generate variation with natural selection to produce new species.
mutation1
Mutation
  • Mutation = Change
  • Biologists use the term “mutation” when talking about any change in the genetic material. Not all result in a change in phenotype.
  • There are two major types of mutations:
  • Macromutations - Also called macrolesions and chromosomal aberrations. Involve changes in large amounts of DNA.
  • Micromutations - Commonly called point mutations and microlesions.
macromutations
Macromutations
  • Four major types of Macromutations are recognized:

1 Deletions - Loss of chromosome sections

2 Duplications - Duplication of chromosome sections

3 Inversions - Flipping of parts of chromosomes

4 Translocations - Movement of one part of a chromosome to another part

macromutation deletion

Chromosome

Centromere

Genes

A B C D E F G H

A B C D G H

E F

Macromutation - Deletion
macromutation duplication

Chromosome

Centromere

Genes

A B C D E F G H

A B C D E FE F G H

E F

Duplication

Macromutation - Duplication
macromutation inversion

Chromosome

Centromere

Genes

A B C D EF G H

A B C D F E G H

Inversion

Macromutation - Inversion
macromutation translocation

Chromosome

Centromere

Genes

A B C D E F G H

A B E F C D G H

Macromutation - Translocation
micro or point mutations
Micro or Point Mutations
  • Two major types of Macromutations are recognized:

1 Frame Shift - Loss or addition of one or two nucleotides

2 Substitutions - Replacement of one nucleotide by another one. There are a number of different types:

    • Transition - Substitution of one purine for another purine, or one pyrimidine for another pyrimidine.
    • Transversion - Replacement of a purine with a pyrimidine or vice versa.
frame shift mutations

Met

Thr

Cys

Gly

Ser

3’AGTTCAG-TAC-TGA-AAC-CAT-CAA-CTG-ATCATC5’

Met

Thr

Leu

Val

Val

Val

Frame Shift Mutations

3’AGTTCAG-TAC-TGA-ACA-CCA-TCA-ACT-GATCATC5’

5’AGUC-AUG-ACU-UGU-GGU-AGU-UGA-CUAGAAA3’

5’AGUC-AUG-ACU-UUG-GUA-GUU-GAC-UAG-AAA3’

Frame-shift mutations tend to have a dramatic effect on proteins as all codons downstream from the mutation are changed and thus code for different amino acids. As a result of the frame shift, the length of the polypeptide may also be changed as a stop codon will probably come at a different spot than the original stop codon.

substitution mutations

Transition

Met

Met

Thr

Thr

Cys

Cys

Gly

Gly

Ser

Ser

5’AGUC-AUG-ACU-UAU-GGU-AGU-UGA-CUAGAAA3’

Pyrimidine to

Pyrimidine

Met

Thr

Gly

Ser

Tyr

5’AGUC-AUG-ACU-UGU-GGU-AGU-UGA-CUAGAAA3’

Transversion

5’AGUC-AUG-ACU-UUU-GGU-AGU-UGA-CUAGAAA3’

Purine to

Pyrimidine

Phe

Met

Thr

Gly

Ser

Substitution Mutations

3’AGTTCAG-TAC-TGA-ACA-CCA-TCA-ACT-GATCATC5’

5’AGUC-AUG-ACU-UGU-GGU-AGU-UGA-CUAGAAA3’

3’AGTTCAG-TAC-TGA-ATA-CCA-TCA-ACT-GATCATC5’

3’AGTTCAG-TAC-TGA-ACA-CCA-TCA-ACT-GATCATC5’

3’AGTTCAG-TAC-TGA-AAA-CCA-TCA-ACT-GATCATC5’

transitions vs transversions
Transitions Vs Transversions
  • Cells have many different mechanisms for preventing mutations
  • These mechanisms make mutations very uncommon
  • Even when point mutations occur in the DNA, there may be no change in the protein coded for
  • Because of the way these mechanisms work, transversions are less likely than transitions
  • Tranversions tend to cause greater change in proteins than transitions
the genetic code
The Genetic Code

Neutral Non-polar

Polar

Basic

Acidic

S E C O N D B A S E

U

C

A

G

UUU

UUC

UUA

UUG

UCU

UCC

UCA

UCG

UAU

UAC

UAA

UAG

UGU

UGC

UGA

UGG

F

I

R

S

T

B

A

S

E

U

U

C

A

G

T

H

I

R

D

B

A

S

E

Phe

Tyr

Cys

Ser

Stop

Leu

Stop

Trp

CUU

CUC

CUA

CUG

CCU

CCC

CCA

CCG

CAU

CAC

CAA

CAG

CGU

CGC

CGA

CGG

C

U

C

A

G

His

Leu

Pro

Arg

Gln†

AUU

AUC

AUA

AUG

ACU

ACC

ACA

ACG

AAU

AAC

AAA

AAG

AGU

AGC

AGA

AGG

U

C

A

G

A

Asn†

Ser

Ile

Thr

Lys

Arg

†Have amine

groups

Met/

start

GUU

GUC

GUA

GUG

GCU

GCC

GCA

GCG

GAU

GAC

GAA

GAG

GGU

GGC

GGA

GGG

U

C

A

G

G

Asp

Val

Ala

Gly*

*Listed as

non-polar by

some texts

Glu

the sickle cell anemia mutation

Normal b-globin DNA

Mutant b-globin DNA

C

T

T

C

A

T

G

A

A

G

U

A

mRNA

mRNA

Normal b-globin

Mutant b-globin

Glu

Val

O

O

H2N

H2N

C

C

C

C

OH

OH

H

H

CH2

CH

CH3

H2C

H3C

OH

C

Neutral

Non-polar

Acid

O

The Sickle Cell Anemia Mutation
sickle cell anemia a pleiotropic trait

Mutant b globin is produced

Breakdown of

red blood cells

Accumulation of sickled

cells in the spleen

Red blood cells sickle

Anemia

Clogging of small

blood vessels

Pain and

fever

Spleen damage

Tower skull

Heart failure

Weakness

Brain

damage

Damage to other organs

Infections

especially

pneumonia

Impaired

mental function

Paralysis

Rheumatism

Kidney

failure

Sickle Cell Anemia:A Pleiotropic Trait

Mutation of base 2 in b globin codon 6 from A to T

causing a change in meaning from Glutamate to Valine

the likely and the unlikely
The Likely and the Unlikely
  • Arguments about evolution frequently revolve around probability. Meaningful complexity is unlikely to result from random events. Organisms are meaningfully complex. Some claim that natural selection overcomes much of this problem as, while change (mutation) may be random, selection is not.
  • Science is about predicting what is likely and what is unlikely. Everyone is in agreement that the events leading to production of living organisms are unlikely.
in a long time and big universe
In a Long Time and Big Universe
  • It has been argued that given massive lengths of time and a universe to work in, the unlikely becomes likely:
  • Given infinite time, or infinite opportunities, anything is possible. The large numbers proverbially furnished by astronomy, and the large time spans characteristic of geology, combine to turn topsy-turvy our everyday estimates of what is expected and what is miraculous.

Richard Dawkins. 1989. The Blind Watchmaker: Why the evidence of evolution reveals a universe without design. W.W. Norton and Co. NY, p 139.

little or big changes
Little or Big Changes?
  • Not all mutations improve fitness, they may:
    • Improve the fitness of an organism (very unlikely)
    • Be neutral, having no effect on fitness
    • Be detrimental, decreasing an organisms fitness (most likely)
  • The bigger the change the more likely it is to be significantly detrimental
  • Darwin argued that evolution is the accumulation of many small changes that improve fitness, big changes are unlikely to result in improved fitness.
  • “Many large groups of facts are intelligible only on the principle that species have been evolved by very small steps.”
    • The Origin of Species, Chapter VII, under “Reasons for disbelieving in great and abrupt modifications”
understanding complexity allows better estimates of probability
Understanding Complexity Allows Better Estimates of Probability
  • From Darwin’s time until the molecular revolution in biology, his explanation for the origin of organisms seemed reasonable as their complexity was not understood fully.
  • “First simple monera are formed by spontaneous generation, and from these arise unicellular protists . . .”

The Riddle of the Universe at the Close of the Nineteenth Century by Ernst Haeckel, 1900.

behe s insight

Board

Trigger

Staple

Cheese

Bait holder

Hammer

Spring

Behe’s Insight
  • Michael Behe contends that when we look at the protein machines that run cells, there is a point at which no parts can be removed and still have a functioning machine. He called these machines “irreducibly complex.”
  • We encounter irreducibly complex devices in everyday life. Behe used a simple mousetrap is an example of an irreducibly complex device:
irreducibly complex protein machines
Irreducibly Complex Protein Machines
  • Cells are full of irreducibly complex devices - Little protein machines that will only work if all the parts (proteins) are present and arranged together correctly.
  • Natural selection does not provide a plausible mechanism to get from nothing to the collection of parts necessary to run a number of irreducibly complex protein machines needed to have a living cell
  • Evolution of these protein machines must occur in single steps, not gradually, as to be selected a protein must be functional in some way. Each protein machine is fairly complex, thus evolution in a single step seems unlikely.
how can irreducibly complex protein machines be made
How Can Irreducibly Complex Protein Machines be Made?
  • The evolution model suggests two mechanisms:
  • Mechanism 1
    • Random events produce proteins with some minimal function
    • These proteins mutate and less functional variants are removed by natural selection
    • Some of these proteins cooperate with one another to do tasks
    • From this, emergent properties of the system come about, these only occur when all the components are present
  • Note that this mechanism only works if each protein involved has individual properties conferring added fitness
what if proteins have no independent function
What If Proteins Have No Independent Function?
  • Evolutionary Mechanism 2:
  • If the function of each protein in an irreducibly complex protein machine is completely dependent on the other proteins, then the only way to select them would be if the machine was already functional.
  • Getting a functional machine would require that all the components come together by chance
  • This seems unlikely
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