Genetics Chapter 15

Gametic Mutations

Mutation Rate: 1 x 10-6 Number of genes: 50,000 (= 5 x 104) (1 x 10-6) (5 x 104) = 5 x 10-2 = 0.05 5% or 1 in 20 gametes carries a new mutation Both sperm and eggs have same chance Chances for a child/offspring: (product of 2 gametes) 0.05 x 2 = 0.1 10% chance of a new mutation in any child

Frameshift mutation

- a mutational event leading to the insertion or deletion of a number of base pairs in a gene that is not a multiple of three. This shifts the codon reading frame in all codons that follow the mutational site -reading codon shift with the addition of nucleotide (insertion), --Insertion --Duplications- nucleotides repeated tandemly over and over again --Deletions -shift will change primary polypeptide you make

Measuring Mutation Rates

-Direct Measurement: Dominant alleles Unique phenotype Fully expressed, penetrant Clear paternity No phenocopies Single locus Dominant Mutation: Achondroplasia Phenotype: Dwarfism, short arms, legs, enlarged skull. Survey of 242,257 births 7 mutations found 7/484,514 1.4 x 10-5 = Mutation Rate

Detecting Mutations

-Dominant Mutations Pedigree Analysis -X-Linked Mutations Pedigree Analysis -Autosomal Recessive Mutations ? -Most analysis on pedigree analysis -Mutations may occur within: o Can occur within anything other than a gene o Hard to track if you don't have a phenotype o Many deletion and mutations that occur with non-coding sequences of genome that associate with phenotype of mental retardation

Deletions and Insertions

-Emerging as major cause of mutation in human genetics -Produces Frameshifts

Mutations may occur within

-Gene coding sequences (exons) -Non-coding sequences (introns) -Regulatory sequences (promoters, enhancers) -mutations can occur in somatic cells or within germ cells --those that occur in germ cells are heritable and are the basis for the transmission of genetic diversity and evolution, as well as genetic diseases --those that occur in somatic cells are not transmitted to the next generation but may lead to altered cellular function or tumors

Somatic mutations vs. Germ-line mutations

-Mutations in somatic cells are not transmitted to future generations -Somatic mutations will have greater impact if they are dominant or, in males, if they are X-linked -Gametic mutations have higher impact because they are transmitted to offspring as part of germ line

Unscheduled DNA synthesis

-cells form xeroderma pigmentosum (XP) patienrs are deficient in DNA synthesis other than that occurring during chromosome replication -it is elicited in normal cells by UV radiation -thought to represent the activity of DNA polymerization during NER

Pyrimidine Dimers

-chemical species consisting of two identical pyrimidines--particularly ones consisting of two thymine residues --they distort the DNA conformation and inhibit normal replication

Free Radicals

-chemical species containing one or more unpaired electrons -can directly or indirectly affect the genetic material, altering purines and pyrimidines in DNA

Intercalating Agents

-chemicals that have dimensions and shapes that allow them to wedge b/w the pairs of DNA

Polygenic

-disease caused by variations in several genes

Monogenic

-even a single base-pair change in one of the approximately 20,000 human genes can lead to a serious inherited disorder -can be caused by many different types of single-gene mutations

Reactive oxidants

-generated by exposure to high-energy radiation, can produce more than 100 different types of chemical modifications in DNA, including modifications to bases, loss of bases, and single-stranded breaks

Ionizing radiation

-happens when x rays, gamma rays, and consmic rays are more energetic than UV radiation -they penetrate deeply into tissues

Loss of function mutation

-has an effect on the phenotype -mutation no longer confers activity of that protein/gene product

Silent Mutation

-if the point mutation alters a codon but does not result in a change in the amino acid at that position in the protein (due to degeneracy of the genetic code), it can be considered a _________

Mismatch repair

-in the ________, the mismatches are detected, the incorrect nucleotide is removed, and the correct nucleotide is inserted in its place --discrimination is important b/c if discrimination does not occur, the excision will be random, and the strand bearing sequence will be cut out 50%

SOS repair system

-in the presence of a large number of unrepaired DNA mismatches and gaps, bacteria can induce the expression of about 20 genes whose products allow DNA replication to occur even in the presence of these legions -DNA synthesis becomes error-prone, insertng random and possibly incorrect nucleotides in places that would normally stall DNA replication --as a result, SOS repair itself becomes mutagenic

DNA Polymerase III

-major DNA synthesizing enzyme in bacteria that makes error once every 100,000 insertions --however, it proofreads each step, catching 99% of those errors -if an incorrect nucleotide is inserted during polymerization, the enzyme can recognize the error and "reverse" its direction --it behaves as a 3' to 5' exonuclease, cuttng out the incorrect nucleotide and replacing it with the correct one

Dominant negative mutation

-may directly interfere with the function of the product of the wild type allele

DNA Repair

-Our DNA is exposed to physical and chemical agents, both environmental and intracellular, that directly or indirectly modify DNA. -These include: --sunlight (ultraviolet radiation) -- X-rays --food mutagens (99% of which are natural) --reactive chemical species (free radical by-products of ATP production) -Errors are introduced during DNA replication and imperfect recombination. These temporary modifications can lead to permanent changes in our DNA. -Such mutagenic events can lead to cell death or dysfunction, and ultimately, cancer. -To cope with DNA damage, organisms have evolved an elaborate array of repair systems that maintain genetic integrity. These systems must: --recognize specific forms of DNA damage --remove this damage --replace the aberrant segment with a normal piece of DNA -Such processes involve highly integrated pathways of several protein factors.

Mutation Rates

-Spontaneous or Adaptive -Rate of spontaneous mutation is low for all organisms -Rate of spontaneous mutation differs between organisms --May be due to each organisms efficiency of proofreading and repair systems -Rate of spontaneous mutation varies from gene to gene -Number of Mutated alleles/locus/generation 4 of 100,000 births show mutation from recessive - dominant 200,000 copies of gene involved Rate is: 4/200,000 2/100,000 or 2x 10-5/allele/generation

Repair of thymine dimers in photoreactivation repair

-Thymine Dimers generated by exposure to UV light -Repaired by DNA photolyase, activated by visible light -in the presence of visible light, the enzyme catalyzes chemical cleavage of the dimer, thereby restoring normal base pairing and repairing the DNA

Adductforming agents

-a DNA _______ is a substance that covalently binds to DNA, altering its conformation an interfering with replication and repair

Base Analogs

-a category of mutagenic chemicals that can substitute for purines and pyrimidines during nucleic acid biosynthesis

Point mutation/base substitution

-a change of one base pair to another in a DNA molecule

Missense mutation

-a change of one nucleotide of a triplet within a protein-coding portion of a gene may result in the creation of a new triplet that codes for a different amino acid in the protein product -Change AA1 --> AA2 -if you change amino acid on primary peptide to make a different amino acid -Substitutes one amino acid for another

Neutral Mutation

-a mutation that can occur either in a protein-coding region or in any part of the genome, and its effect on the genetic fitness of the organism is negligible

Lethal Mutations

-a mutation that may adversly affect a gene product that is essential to the survival of the organism

Excision Repair

-a number of light-independent DNA repair systems exist in all prokaryotes and eukaryotes -the basic mechanisms in these repairs are referred to as ________ or cut and paste mechanisms -STEPS: 1) the distortion or error present on one of the two strands of the DNA helix is recognized and enzymatically clipped our by an endonuclease. Excisions in the phosphodiester backbone usually include a number of nucleotides adjacent to the error as well, leaving a gap on one strand of the helix 2) A DNA polymerase fills in the gap by inserting nucleotides complementary to those on the intact strand, which it uses as a replicative template. The enzyme adds these nucleotides to the free 3'-OH end of the clipped DNA 3) DNA ligase seals the final "nick" that remains at the 3'-OH end of the last nucleotide inserted, closing the gap -includes base excision and nucleotide excision repair

Nonsense mutation

-a second possible outcome in which the triplet will be changed into a stop codon, resulting in the termination of translation of the protein -Changes codon --> termination codon

Double-strand break repair (DSB repair)

-a specialized form of DNA repair, these pathways, are activated and are responsible for reattaching two broken DNA strnds

Nucleotide Substitutions

-a type of mutation -Point mutations- nucleotide substitutions --Ex) replace guanine with cytosine or thymine Local environment may introduce these mutations -includes nonsense, missense, and sense mutations

Regulatory mutations

-affect the regulation of gene expression -a mutation in the regulatory gene or a gene control region can disrupt normal regulatory processes and inappropriately activate or inactivate expression of a gene

Deanimation

-an amino group in cytosine or adenine is converted to a keto group --in these cases, cytosine is converted to uracil, and adenine is changed to hypopoxanthine --the major effect of these changes is an alteration in the base-pair specificities if these two bases during DNA replication

Endonuclease

-an enzyme that creates a nick in the backbone of unmethylated DNA strand, either 5' or 3' to the mismatch

Beta-thalassemia

-an inherited autosomal recessive blood disorder resulting from a reduction of absence of hemoglobin -most common single-gene disease in the world -caused by mutations in the Beta-globin gene (HBB gene)

Postreplication repair

-another DNA system, called ________ responds after damaged DNA has escaped repair and has failed to be completely replicated -occurs if DNA replication ha skipped over a lesion such as a thymine dimer. Through the process of recombination, the correct complimentary sequence is recruited from the parental strand and inserted into the gap opposite the lesion. The new gap is filled by DNA polymerase an DNA ligase --after DNA polymerase skips over the lesion, it leaves an unreplicated gap on the newly synthesized strand ---to correct the gap, the RecA protein directs a recombinational exchange with the corresponding region on the undamaged parental strand of the same polarity ("donor" strand) ---when the undamaged segment of the donor strand DNA replaces the gapped segment, a gap is created on the donor strand. The gap can be filled by repair synthesis as replication proceeds

Mutagens

-any agent that causes an increase in the rate of mutation -have the potential to damage DNA

Conditional Mutations

-are present in the genome of an organism but can be detected only under certain conditions -Temperature-sensitive mutation --Only expressed if your at the proper temperature

Myotonic Dystrophy

-most common of muscular distrophy -A major pathogenic event in DM is the disruption of regulation of pre-mRNA alternative splicing. Pre-mRNAs from at least six genes undergo mis-regulated alternative splicing in DM tissues and splicing reverts to patterns observed in embryonic tissues. -These pre-mRNAs are targets for specific trans-acting factors and splicing of other pre-mRNAs is not affected. - The working hypothesis is that the expanded repeat RNA has a trans-dominant effect on a subset of alternatively spliced exons by disrupting the regulatory functions of these proteins. -Inappropriate expression of embryonic proteins is responsible for at least two major symptoms of DM

Visible mutations

-mutations affecting a morphological trait -recognized by their ability to alter a normal or wild-type visible phenotype

Somatic mutations

-mutations occurring in any cell in the body except germ cells

Autosomal mutations

-mutations within genes located on the autosomes -will not be passed to offspring

Haploinsufficiency

-occurs when the single wild-type copy of the gene does not produce enough gene product to bring about a wild-type phenotype

Depurination

-one of the most common causes of spontaneous mutations of DNA base damage -the loss of one nitrogenous bases in an intact double helical DNA molecule

Homologous recombination repair

-one pathway involved in double-strand break repair -1) break detected and 5' ends of break digested -2) 3' end invades homolgous region of sister chromatid -3) DNA synthesis across damaged region -4) heteroduplex resolved and gaps filled by DNA synthesis

Nucleotide excision repair (NER)

-pathways repair "bulky" lesions in DNA that alter or distort the double helix --these lesions include the UV-induced pyrimidine dimers and DNA adducts -one group of genes designated uvr (ultraviolet repair) and included uvrA mutations, etc. --the uvr gene products are involved in recognizing and clipping out lesions in the DNA ---usually, as specific number of nucleotides is clipped out around both sides of the lesion. The repair is then completed by DNA polymerase I and DNA ligase. The undamaged strand opposite the lesion is used as a template for the replication, resulting in repair

Tautomers

-replication errors due to mispairing predominantly lead to point mutations --the fact that bases can take several forms, known as ______, increases the chance of mispairing during DNA replication

Null mutation

-result in complete loss of function

Dominant gain-of-function mutation

-results in a gene product with enhanced, negative, or new functions

Dominant mutation

-results in a mutant phenotype in a diploid organism, even when the wild-type allele is also present

Trinucleotide repeat sequences

-specific short DNA sequences repeated many times -individuals with over 20 different human disorders appear to have abnormally large numbers of repeat sequences -Unstable Genomic Regions -Illustrate the dynamic nature of mutations -Change from generation to generation, causing earlier onset of symptoms, called anticipation.

Tautomeric Shifts

-the biologically important tautomers are the keto-enol forms of thymine and guanine and the amino-imino forms of cytosine and adenine --these shifts change the bonding structure of the molecule, allowing hydrogen bonding with noncomplementary bases ---hence, ________ may lead to permanent base-pair changes and mutations -a mutation occurs during DNA replication when a transiently formed tautomer in the template strand pairs with a noncomplementary base --in the next round of replication, the "mismatched" members of the base are separated, and each becomes the template for its normal complementary base. The end result is a point mutation

Gene Mutations

-the mutations occurring primarily in the base-pair sequence of DNA within individual genes

Recessive mutation

-they are most of loss-of-function mutations -results in a wild-type phenotype when present in a diploid organism and the other allele is wild type

Photoreactivation Repair

-this enzymes mode of action is to cleave the bonds b/w thymine dimers, thus directly reversing the effect of UV radiation on DNA STEPS: 1) DNA is damaged so a dimer is formed 2) the bond creating the thymine dimer is cleaved by the photoreactivation enzyme (PRE), which must be activated by blue light in the visible spectrum 3) Normal repair is restored

Transposons

-transposable genetic elements -DNA elements that can move within, or b/w, genomes -if moving to a new location they insert themselves into the coding region of a gene, they can alter the reading frame or introduce stop codons -can create chromosomal damage -IN BACTERIA --IS elements Transposase ITRs Tn elements Larger than IS Contain protein-encoding genes May contain IS within them -IN HUmans --Families: LINES SINES "jumping" DNA Frameshift mutations

Exonuclease

-unwinds and degrades the nicked DNA strand, until the region of the mismatch is reached

Transversion

-used to describe one type of base substitution --if a purine replaces a pyrimidine, or vice versa

Transition

-used to describe one type of base substitution --when a pyrimidine replaces a pyrimidine or a purine replaces a purine

Ames Test

-uses a number of different strains of bacterium salmonella typhimurium that have been selected for their ability to reveal the presence of specific types of mutations

Factors Affecting Mutation Rate

1) Size of the gene: --Larger the gene/ higher the rate --NF1: >300,000 base pairs --DMD: > 2,000,000 base pairs 2) Nucleotide Sequence: --Instability in gene --The composition sequence, not the size, matters 3) Spontaneous chemical changes --Some genes are more susceptible to environmental factors/changes ---Will effect those genes more than normal genes --Sometimes one gene can code for multiple traits

Base Excision Repair

1) involves the recognition of the altered base by an enzyme called DNA glycosylase 2) DNA glycosylases first cut the glycosidic bond b/w the base and the sugar, creating an apyrimidinic or aprunic site 3) the sugar with the missing base is then recognized by an enzyme called AP endonuclease 4) AP endonuclase makes a cut in the phosodiester backbone at the apyrimidinic or aprunic site 5) Endo nucleases then remove the deoxyribose sugar, and the gap is filled by DNA polymerase and DNA ligase

New Mutations

3,800,000 children born per year 10% = 380,000 new mutations Most are recessive Recessive mutations highly heterozygous More likely that wo alleles will not be identical Deleterious mutations does not pass on by homozygotes Mutation may have no phenotypic impact

Sense Mutations

Change Termination codon --> codon