topic 5 (chapters 8 + 18)

Mutations

Changes in dna sequences that are inheritable by cells or organisms

Importance of mutation

1. Necessary for evolution as a source of genetic variation

2. Cause of many diseases and disorders

3. Can be used to genetically dissect biological systems

Two classes of mutations

• somatic

• Germline

Somatic mutations

Arise in somatic tissues which do not produce gametes

• the mutation is passed to identical cells created by mitosis

• Some have no obvious effect on phenotype or immediately stimulate cell death, but some divide more

Germ line mutations

Arise in cells that produce gametes

• can be passed to future generations

• Offspring carry the mutation in all their somatic and germline cells

Two major categories of mutations

• gene

• Chromosomal

Gene mutations

Usually only affect a single gene

• base substitutions

• Insertions and deletions

• Expanding nucleotide repeats

Chromosomal mutations

• mutations affecting chromosome structure or number

• Large scale genetic alteration

Base substitution

The alteration of a single nucleotide in dna

• transition

• Transversion

Transition base substitution

A purine is replaced by a purine

A pyramidine is replaced by a pyrimidine

Trans version base substitution

A purine is replaced by a pyrimidine or vice verse

• Less common but results more possibilities

Three causes of base substitution

1. Spontaneous replication error

2. Spontaneous chemical changes

3. Mutagens

Types of spontaneous replication error

• Tautomeric shift

• Wobble

Types of spontaneous chemical changes

1. Depurination

2. Deamination

Tautomer

Distinct rare form of each base with altered position of hydrogen

• usually moves from a functional group outside of ring to N inside ring or vice versa

Tautomeric shift

When hydrogen shifts to another position creating a new tautomer form of a molecule

• this allows for different base pairing (bases that originally only formed two H-bonds now form three and vice versa)

Wobble pairing

Flexibility in dna structure allows for mispairings of bases

depurination

the loss of a purine base from a nucleotide

• happens when the covalent bond between purine and sugar backbone is broken producing an apurinic site which cannot act as a template for a complementary base

steps of depurination

1. the apurinic site cannot provide a template for a complementary base on the newly synthesized strand

2. a nucleotide with the incorrect base is incorporated into the newly synthesized strand (usually A)

3. at the next round of replication, this incorrectly incorporated base will be used as a template

4. the mutation becomes permanent

deamination

loss of an amino group from a base spontaneously or by chemical mutagen

• alters base pairing properties (eg. cytosine deaminated is uracil)

insertion and deletion mutations

the addition or removal of one or more nucleotide pairs caused by strand slippage or unequal crossing over

strand slippage

• when the newly synthesized strand loops and an additional nucleotide is added

• when the template strand loops and a nucleotide is omitted

unequal crossing over

one of the causes of insertion and deletion mutations by the misalignment of homologous chromosomes

• results in one crossover product with an insertion and one with a deletion

expanding nucleotide repeats

when the number of copies of a set of nucleotides increases

ALS

amyotrophic lateral sclerosis

• caused by expanding nucleotide repeats

process of nucleotide repeat mutations forming during replication

1. strands separate and replicate as normally

2. during replication, a hairpin forms on new strand

3. the part included in the hairpin is replicated twice

4. the two strands separate but one contains more repeats

5. the strand with extra repeats is now a template strand, and new dna is longer

three types of mutations caused by base substitutions

• missense

• nonsense

• silent mutations

missense mutation

base substitution results in a different amino acid in the protein

nonsense mutation

changes the codon from coding an amino acid to coding for a termination amino acid

silent mutations

caused by base substitutions in which the new codon encodes for the same amino acid so their is no change in protein sequence

types of mutations caused by insertions and deletions

• frameshift

• in-frame mutations

frameshift mutations

changes in the reading frame of the gene from insertions and deletions, usually altering all amino acids encoded by the nucleotides following the mutation which will have a drastic effect on the phenotype

• might also introduce premature stop codons which will terminate the protein early

in-frame mutations

caused by insertions and deletions consisting of a multiple of three nucleotides that leave the reading frame intact

• may still affect phenotype

forward mutation

original mutation changing phenotype away from wild-type

• new phenotype

reverse mutation

a second mutation that reverses the original mutation site back and returns the phenotype back to wild-type

• phenotype is mutated and then reversed

suppressor mutation

a second mutation that reverses the phenotype back to wild-type by mutating a different site of the dna. therefore, hides the effect of another mutation

• phenotype is mutated and then reversed

• can be intragenic and intergenic

intragenic suppressor mutation

occur within the same gene containing the original mutation being suppressed

intergenic suppressor mutation

when suppressor mutations occur on a separate gene

types of chromosome mutations

1. rearrangements

2. aneuploidy

3. polyploidy

chromosome rearrangements

chromosome mutations that change the structure of individual chromosomes due to crossover errors or double stranded dna breakse

• duplications

• deletions

• inversions

• translocations

chromosome duplication and deletion

mutation in which part of the chromosome has been doubled

• chromosomes do not align properly resulting in unequal crossing over. One chromosome ends with double (duplication), one ends with none (deletion)

example of chromosome duplication

red/green colour blindness

• red opsin and green opsin gene. unequal crossing over causes deletion of green opsin resulting in colour blindness

• men are affected more frequently than women

detection of duplications and deletion of chromosomes

In prophase I the normal chromosome will loop out in order for the homologous sequences of the chromosome to algn

• if you see this loop, it is evidence of duplication/deletion

problems caused by chromosome duplications

Some genes will have extra copies which alters the relative amounts of interacting materials (unbalanced gene dosage)

• if the amount of one product increases and one stays the same, some developmental problems may occur

problems caused by chromosome deletions

deletions can be homozygous or heterozygous

• homozygous → lethal

• heterozygous

  • if centromere deleted, whole chromosome is lost

  • recessive mutation on homologous chromosomes become unmasked

  • haploinsufficiency

haploinsufficiency

some genes need two copies to function. haploinsufficiency means that one gene is enough

• causes issues when chromosome deletions occur

two types of chromosome inversions

• paracentric (next to centromere)

• pericentric (around/include the centromere)

chromosome inversions

a chromosome segment is turned 180 degrees changing the gene sequence

effects of chromosome inversions

• chromosomes break during inversion which may occur within a gene or its regulatory region and disrupt gene function

• position effect → expression may be altered as much of regulation is based on their position on a chromosome

inversions in meiosis

heterozygous inversions result in different orders on the two homologs so homologous sequences can only align and pair if the two chromosomes form an inversion loop. crossing over within the inversion loop creates unusual chromosomes

• the resulting recombinant gametes will be nonviable because they are missing some genes

chromosome inversions and evolution

inversions are frequent across plants and animals and may play a role in evolution

• eg) Human and Chimpanzee chromosomes 4 differ by a pericentric inversion

translocations

the movement of genetic material between non-homologous chromosomes

effects of translocation of chromosomes

• disrupt gene function by breaking a gene or regulatory region

• change expression because of positional effects

heterozygous translocations during meiosis

• in prophase I, a cross like configuration must form for homologous sections to align

• In anaphase I, there are three ways the chromosome can separate (cross, up/down T, sideways T)

• viable gametes exist from crossed chromosomes because they have one of each copy

• non-viable gametes exist from T chromosomes because they have too many or no copies

aneuploidy

a change in the number of individual chromosomes

causes of aneuploidy

• deletion of centromere during mitosis and meiosis resulting in loss of chromosomes

• nondisjunction during mitosis and meiosis

nondisjunction

failure of homologous chromosomes or sister chromatids to separate in meiosis/mitosis

trisomic

one additional chromosome (2n +1)

monosomic

one less chromosome (2n - 1)

nondisjunction in meiosis I

results in two trisomic cells and two monosomic cells

• after meiosis I, two homologous chromosomes are in one cell, and no chromosomes are in the other

• fertilization by a normal gamete results in three or one chromosomes

nondisjunction in meiosis II

results in one trisomic cell, one monosomic cell, and two normal diploid cells

• after meiosis II, nondisjunction occurs in one of the two cells so two are normal and two have either two copies of no copies

• after fertilization by a normal gamete, an additional chromosome is added to each

down syndrome

caused by aneuploidy of chromosome 21

• spontaneous disjunction (not heritable)

• most often 3 copies of the chromosome

nondisjunction in mitosis

leads to two cells with one and three chromosomes. after cell proliferation, somatic clones are monosomic and trisomic

genetic mosaicism

produced by nondisjunction in mitosis

• regions of tissues with different chromosome constitutions (eyes different colours)

polyploidy

an increase in the number of chromosome sets

• autopolyploidy

• allopolyploidy

autopolyploidy

caused by accidents in mitosis or meiosis that produce extra sets of chromosomes, all derived from a single species

• cytokinesis failure in mitosis leads to nondisjunction and new cells autotetraploid

• cytokinesis failure in meiosis I leads to nondisjunction and 2n gametes fertilized with 1n gametes to be autotriploid

allopolyploidy

arises from hybridization between two species giving a sterile hybrid plant. Then embryo had nondisjunction at early mitotic cell division and doubled chromosome number making the gametes allopolyploid and viable

• most common exampling is modern wheat which results from two hybridizations and two mitotic disjunctions in the past involving early wheat and wild grass.

benefits of polyploidy in plants/food

• increase in cell size

• larger plant attributes

• gives rise to new species

proofreading

first level of DNA repair by 3’-5’ exonuclease activity of DNA polymerase during replication

mismatch repair

occurs soon after replication as enzymes detect and correct single base pair mismatches and unpaired loops by cutting out the errors in the newly synthesized strand of DNA and replace it with new nucleotides

steps of mismatch repair complex repairing DNA

1. dna is nicked near newest methyl group

2. dna is looped to mismatch site is adjacent to the nearest methyl group

3. complex degrades the new strand between the mismatch and the nick

4. dna polymerase fulls gap from 3’ end to 5’ end

5. dna ligase ligates it to new corrected strand

direct repair of dna

restores the chemical structure of mutated/altered nucleotides

• differs from mismatch because there is no removal and adding of a different basebas

base excision repair of dna

a modified base is exised and then the entire nucleotide is replaced

• glycosylases cleave 1’ bond on sugar molecule and creates an apurinic or apyrimidinic site

• AP endonucleases cut phosphodiester bond

• DNA polymerase adds new nucleotides into the exposed group

• DNA ligase seals the nick in the backbone

nucleotide excision repair of dna

removes bulky dna lesions that distort the double helix

• enzyme complex scans for distortions

• enzymes separate dna strands and single stranded binding proteins stabilize singe strands

• sugar phosphate backbone of damaged strand is cleaved on both sides of damage

• damaged strand is peeled away by helicase

• gap is filled in by dna polymerase and sealed by dna ligase

two repair pathways for repairing double stranded breaks in dna

1. homology directed repair (HDR)

2. Nonhomologous end joining (NHEJ)

causes of double stranded breaks

• ionizing radiation

• oxidative radicals

• other dna damaging agents

homology directed repair

used to repair double stranded breaks

• some nucleotides removed from both strands

• use identical or nearly identical dna molecule as template

• strand invasion

• dna polymerization

• eventual cleavage to separate double stranded molecules

nonhomologous end joining

repair mechanism for double stranded breaks that does not require a homologous template

• proteins bind to double stranded ends and rejoin them