L10- DNA mutation + Repair

Gene mutations can be classified at diff levels such as

• DNA

• Protein

• Chromosome

• Phenotype

Mutation

• The process by which the sequence of base pairs in a DNA molecule is changed

• (Change in DNA sequence)

Germ line mutation can be transmitted

• in gametes

Somatic mutation

• only individual is affected

Mutation rate

• Probability gene undergoes mutation

  • typically per generation

  • “mutation hot spots”→ certain areas more prone to mutation (allow more diversity in bacteria)

• In sperm pt mutations increases w/ paternal age

Protein fx mutations

• mutation →Loss of function (null)

• Mostly recessive(2 copies need to be mutated)

• dominant exceptions

  • Haploinsufficiency→ 1 null other working, null has biggest effects (even w/ 1 working get problem)

  • Dominant negative→ A mutant protein(that lost its fx) joins the normal protein in a complex (like a dimer) and blocks it from working, so the mutation acts dominant.

Protein fx mutations

• gain of function is usually

• dominant

Base pair substitutions/pt mutations

• (one base swapped for another) change from 1 bp to another

transition type→ 1 pyr-pur pair to the other (A-T→ G-C)

• Purine ↔ Purine or Pyrimidine ↔ Pyrimidine.

Transversion→ from pyr-pur to pur-pyr (C-G to G-C)

• Purine ↔ Pyrimidine

• family change

DNA mutation

Other type of mutation in addition to bp sub/pt mutation

• Indels

• add/remove nucleotide

DNA mutation

Protein mutations

• Missense mutation

• Change from 1 aa to the other

• ex) AT→ GC transition mutation changes codon from lysine→ glutamic acid

Nonsense mutation

• Change from aa to a stop codon

• ex) AT→ TA transversion mutation changes codon from lysine to STOP codon (UAA)

Neutral mutation

• Change from 1 aa to another aa w/ similar chemical properties

Silent mutation

• Change in codon s.t same aa specified

  • due to redundancy of genetic code

Frameshift mutation (still protein)

• Indels (Addition/deletion) of 1 or a few bps leads to change in reading frame

Which type of protein mutation most detrimental?

• nonsense (he said)

• Both: loss of protein fx

• frameshift

  • changes the reading frame→ producing a completely different + often nonfx protein, usually with an early stop codon.

• nonsense

  • bc protein dramatically shorter (lacks essential fx domains)

• missense not AS bad

  • only change 1 aa, new aa may have similar chem properties so protein can still fx normally, if change occurs in non critical region its not detrimental

Forward mutations

• Changes wt→ mutant

2 classes of pt mutations based on how they affect a mutant phenotype

1. Reverse mutations

• Change mutants back to wt

• occurs at SAME site as initial mutation

• True (go back to exact codon) vs partial reversion (back to similar enough codon-aa)

2. Suppressor mutation

• Diminishes/abolishes the effect of a mutation

• occurs at a DIFF site than initial mutation

  • WILL NOT restore the original DNA seq

ex) frameshift mutation originally, then take out a base (reverse it) restore reading frame closer to wt

Intragenic supressors

• suppressor mutation occurs w/in same gene (as og mutation)

• It compensates for the defect by restoring the protein’s structure or reading frame.

• Example: a second insertion that restores a frameshift caused by an earlier deletion in the same gene.

Intergenic supressors

• suppressor mutation occurs w/in diff gene

• restores fx indirectly by affecting another molecule involved in the process

• ex) tRNA genes

Endogenous mutations

• Naturally occurring

• no specific agents responsible

• can occur anytime during cells life

• ex) cell metabolism, DNA rep

Exogenous mutation

• external materials interact w/ DNA causing mutation

• natural/artifical agents

• ex) UV, xrays etc

Tautomeric shifts

• Base changes tautomeric forms

  • keto to enol

  • amino to imino

• lead to mismatches

(struc isomers of DNA bases)

Slippage

• leads to indels

• Looping out of template/new strand→ indels (loop out part doesn’t get replicated or its replicated 2x)

  • more common in repeat regions

  • trinucleotide repeat amplification→ DNA pol has hard time copying repeat regions which get worse each generation (hard aligning template and nascent strand in repeat regions→ indels)

Depurination and deamination

Depurination

• loss of purine

  • most common event in cell

• Bond bw ribose and purine less stable than rib-pyr

Deamination

• loss of amino group from base

  • leads to conversion to another base

ex) C deam→ U

ex) C meth→ deam→ T (harder to detect mistake bc it’s a base in DNA)

• This can cause base pair transition C-G→ A-T because repair system doesn’t know which strand is “wrong”

• Hence, DNA doesn’t have Uracil so the system can distinguish it and repair it.

ex) A deam→ hypoxanthine→ diff interaction properties than A, bps w/ C can lead to permanent transition changes

Oxidative damage done by

• byproducts of normal cellular processes + exposure to high energy radiation

• Superoxides (O2-)

• OH radicals

• H2O2

can interact + mutate DNA

(endogenous)

Transposons

• mobile genetic elements that can move w/in or b/w genomes

  • integrations into new genomic locations can act as naturally occurring mutagens

• endogenous

Radiation can occur from.. (ionizing and non)

• from natural/man made sources

• Ionizing radiation→ energy sufficient to knock e- out of atomic shell

  • x Rays, cosmic, creates free radicals, effects cumulative

• Non ionizing radiation→ doesn’t induce mutation

  • except UV light

• ex) incidence of thyroid cancers in Belarus increases

UV light

• increases the chemical energy of pyrimidines in DNA

  • formation of bonds b/w adjacent molecules on same strand= pyrimidine dimers

Chemical mutagens

• Base analogs

• Similar to those found in normal DNA

• can replace regular bases

• have normal + tautomeric states

• Can lead to transition mutations

  • mimic one base but occasionally pair like another chemically similar base.

• ex) 5BU, 3AP

Base modifying agents

• Modify chemical structure and properties of bases

  • alkylating agents→ add alkyl group to amino/keto groups in nucleotides

  • hydroxylating agents→ donate OH to ““

  • Adduct forming agents→ bind DNA and change its conformation therefore interfering w/ replication + repair

Intercalating agents

• Insert themselves b/w adjacent bases

• distort and unwinds DNA

• Can lead to indels

• ex) EtBr (allows visualization of DNA in electrophoresis)