Genetics Exam 4

genetic material requirements

• effective transfer between generations (heritable)

• ability to store vast amounts of information

• effective replication/high fidelity

• information can be changed/mutable

types of point mutations

1. substitutions

2. insertions/deletions

3. functional mutants

types of substitution

1. transition mutant

2. transversion mutant

transition mutant

• type of substitution mutation

  • exchange of a purine for a purine or a pyrimidine for a pyrimidine

  • occurs more often due to switching for bases with similar structure

transversion mutation

• type of substitution mutation

  • exchange nucleotides outside of nucleotide family; exchange a purine for a pyrimidine

types of insertions/deletions

• silent mutations

• missense mutations

• nonsense mutations

silent mutation

• type of insertion/deletion

  • changing one codon to a synonymous codon causing no change in the amino acid sequence of the protein

    • “degeneracy of the genetic code”

    • generally, a change in the third nucleotide of a codon causes no change in the amino acid coded for; “a change in genotype causes no change in phenotype”

missense mutation

• type of insertion/deletion

  • changing one codon to a different codon resulting in a change in amino acid sequence of the protein

    • first position change of a codon will most likely cause a change in the amino acid

    • ex: sickle cell anemia- caused by a single base mutation

nonsense mutation

• type of insertion/deletion

  • changing one codon to a “STOP” codon resulting in premature stoppage of translation

  • stop codons: UAG, UGA, UAA

    • products become abnormal → sometimes lethal

  • ex: cystic fibrosis

  • duchenne muscular dystrophy

cystic fibrosis

• caused by a type of nonsense mutation

  • approximately 10% of all cases worldwide is caused by a nonsense mutation in the CFTR protein resulting in nmCF

duchenne muscular dystrophy

• caused by a type of nonsense mutation

  • approximately 15% of cases are the result of the absence or very low levels of the dystrophin protein caused by a premature STOP codon

frameshift mutation

• gain or loss of a nucleotide (or nucleotides) that result in change in the reading frame of the codon

  • everything downstream of deletion will be changed

  • ex: Chrons Disease

Crohns disease

• caused by a frameshift mutation

• a form of inflammatory bowel disease. symptoms include abdominal pain, fever, and weight loss. affects .3% of people in Europe and North America

  • insertion of the NOD2 gene at Cytosine 3020

  • insertion that causes a nonsense mutation

in-frame mutation

• type of insertion/deletion mutation

• gain or loss of a nucleotide or trinucleotide set that does not change the reading frame of the codon

  • ex: a missense mutation

types of general mutants

• loss of function mutation

• gain of function mutation

• lethal mutation

loss of function mutation

• results in a gene product with little or no functionality

  • amorphic- complete loss of gene function

  • most of the time, these phenotypes are recessive

gain of function mutation

• results in a gene product that has gained a new and abnormal function

  • neomorphic- a new or different function from normal

  • these mutations are typically dominant

lethal mutation

• mutation that leads to the death of the organism carrying the mutation

somatic cells

• non-sex cells

• mutations range from mild to severe

  • not passed to next generation (cannot be inherited)

germ cells

• sex cells/gametes

• typically, more severe manifestation passed along to offspring

• ex: CF, Sickle Cell Anemia

  • present in sperm and eg

  • cause cancer family syndrome

  • can be inherited

mechanisms of mutations

1. spontaneous

2. induced

spontaneous mutations types

• replication errors

• chemical changes

spontaneous mutations

• any mutation where no artificial factor or external regulator causes the mutation

  • you will only see the mutation when it occurs on a gene

  • 120,000 mistakes

spontaneous mutation types

• replication errors

• chemical changes

replication errors

• type of spontaneous mutation type

• includes:

  • wobble

  • slipped strand mispairings

wobble

• type of spontaneous mutation

  • non-complimentary bases can pair due to the flexibility of DNA double helix which can accommodate slightly misshaped pairings

  • typically, are fixed with exonuclease activity → but when they are not, incorporated in genome

slipped strand mispairing

• type of spontaneous mutation

  • involves denaturation and displacement of DNA strands that results in mispairing of complimentary bases

chemical changes

• type of spontaneous mutation

  • mutations caused by normal chemical reactions that occur in the cell

  • includes:

    • depurination

    • deamination

depurination

• type of chemical change

  • a chemical reaction in which a beta-n-glycosidic bond is cleaved by hydrolysis causing the release of an adenine or guanine from a DNA strand

  • losing a purine

  • the “A-rule” — will typically add an A to the apurinic site (can sometimes add C, G, T)

deamination

• type of chemical change

  • the hydrolytic removal of an amine group from a nucleotide releasing ammonia and converting the nucleotide to another molecule

  • most common: 5-methylcytosine → thymine

environmental factors

• type of mechanism of induced mutations

  • free radicals

free radicals

• very unstable and quick reacting molecule that “steals” electrons from nearby stable molecules

  • can occur due to: UV light, metabolism, ionizing radiation, smoking, air pollution, inflammation

antioxidants

• help reduce free radicals

  • very electron rich (can donate electron to free radical) turns free radicals to normal

  • ex: vitamin C and vitamin E (work with uric acid in our blood)

UV light

• causes pyrimidine dimers by the formation of covalent linkages localized on cysteine double bonds

  • causes a bulge in DNA (DNA polymerase cant read over it)

  • pyrimidine dimers are the primary cause of melanomas in humans

types of non-point mutations

• chromosome mutations

• transposable elements

chromosome duplication

• type of chromosome mutation

  • duplication of a region of DNA that contains a gene

  • causes: recombination

    • can be homologous or non-homologous

chromosome deletion

• type of chromosome mutation

  • small deletions- less likely to be deleterious

  • medium deletions- responsible for a number of genetic disease

  • large deletions- often fatal

• can be inframe or frame shift

in-frame deletion

• type of deletion

• downstream is not affected

frame shift deletion

• type of deletion

• downstream is affected

• worse affect

transposable elements

• “jumping genes” or transposons

• sequences of DNA that move (or jump) from location in the genome to another

  • originally thoughts of as “junk DNA,” not believed to make up close to 40% of the human genome

  • widely believed to carry out some biological function, most likely a regulatory gene

• often generate some type of mutation when they move from one location to another on a chromosome and in evolutionary, can increase the size of the genome

• their impact depends on where it lands: gene (can result in mutation); non-coding region (not much impact)

Barbara McClintock

• 1950: discovered the concept of transposition using maize. initially her work was met with skepticism

• 1960: with the description of the lac operon system, her work was finally accepted

• 1983: Nobel Prize in Medicine and Physiology for the discovery of the “mobile genetic element”

• discovery:

  • studied 4 genes

  • C’/C’- dominant colorless/color

  • Bz/bz- dominant purple/brown

  • Ds- dissociator (breakage of DNA- allows for transposon to cleave itself and move) actual transposon

  • Ac- activator (impacts of expression of Ds)- needs to be active to allow dissociator to move)

  • phenotype was dependent on when transposon actually moved

types of transposons

• class 1

• class 2

class 2 transposons

• do NOT require transcriptase in order to transpose [DNA transposons]

  • all DNA transposons encode

  • move throughout the genome in a “cut and paste” mechanism

  • less than 2% of the human genome is composed of DNA transposons [much more prevalent in prokaryotes/viruses]

• include

  • terminal inverted repeats

  • flanking direct repeats

terminal inverted repeats

• part of class 2 TEs

  • inverted compliments of 9-40 base pairs located at the both ends of the TE

  • recognized by the transposase (help us to identify the end of the TE)

flanking direct repeats

• adjacent to class 2 TEs

  • not a direct part of the TE but play a role in insertion that the TE back in the genome

  • provides a marker for the excision site once a TE has moved

  • not a part of the transposon

class 2 transposon mechanism

1. the transposan is removed form the DNA sequence by transposase

2. TE/transposase

3. staggered cuts are made in the target DNA by transposase

4. the TE inserts itself into another location in the DNA

5. staggered cuts leave short, ssDNA pieces

6. replication of the ssDNA creates the flanking DR

7. DNA where TE was located is ligated together

class 1 transposon

• require reverse transcriptase (the transcription of RNA into DNA) in order to transpose [RETROTRANSPOSONS]

  • function through the action of RNA intermediates

  • DO NOT encode transposase

  • produce RNA transcripts and rely on reverse transcriptase to reverse transcribe the RNA into DNA sequences prior to insertion into target DNA

  • move throughout the genome in a “copy and paste” mechanism

• includes: long terminal repeats and non-long terminal repeats

long terminal repeat transposon

• type of class 1 transposon

  • characterized by the presence of LTR on each end of the transposon

non-long terminal repeat transposons

• type of class 1 transoson

  • no LTR present

  • the ONLY active class of transposons in humans

• types:

  • autonomous

  • non-autonomous

autonomous non-LTR

• class 1 TE type of non-LTR

  • capable of moving on their own as they make their own

  • reverse transcriptase required to move

• Long Interspersed Elements

• DNA sequences that range in length from a few hundred to as many as 9,000 base pairs

• function L1 elements are about 6,500 bp in length and encode proteins, including an endonuclease that cuts DNA and a reverse transcriptase that makes a DNA copy of an RNA transcript

• most L1 elements are not functional, they may play a role in regulating the efficiency of transcritpion of the gene in which they reside

non-autonomous non-LTR

• short interspersed elements

  • short DNA sequence (100-400 base pairs) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase 2

  • represent some 10% of our total DNA

  • the most abundant SINEs are the Alu elements consisting of a sequence that contains a site that is recognized by the restriction enzyme Alu1

retrotransposition mechanism

1. reverse transcriptase made in the cell by normal machinery

2. the retrotransposon sequence is transcribed to RNA

3. retrotransposon sequence undergoes reverse transcriptase to produce dsDNA

4. staggered cuts are made in the target DNA

5. the retrotransposon integrates into the new site in the host DNA

6. replication fills in the gaps at the site of insertion creating FDR

• COPY and PASTE