Genetics Exam 4

Cystic Fibrosis

• Genetic disorder that causes mucuos build up in the lungs

• Caused by mutation in the CFTR (cycstic fibrosis transmembrane regulator) protein

• Autosomal In-frame germ-line deletion mutation

• likely arose from a rare 3 bp strand slippage is either egg or sperm (germline)

Mutation

alteration in the sequence of a gene

Somatic mutation

• mutations in cells that do not produce gametes

• mutant and wild type cells during mitosis = mosaicism

Germ Line Mutation

• in gametic cells during meiosis

• lead to inherited mutations in all offspring

Forward Mutation

changes in the wild-type mutant

Reverse Mutation

changes a mutant back to wild-type

Neutral phenotypic mutation

• no change in function of the mutation

• same aa coded for, replaced aa is the same charge/size/polarity

Loss of function phenotypic mutation

• creates a nonfunctional protein

Gain of function phenotypic mutation

• the protein produced is not normally present

Base substitutions

• alters a single nucleotide

Transition substitution mutation

• type of base substitution

• purine —> purine or pyrimidine —> pyrimidine

Transversion substitution mutation

• type of base substitution

• purine —> pyrimidine or pyrimidine —> purine

Missense mutation

• type of base mutation

• base substitution produces a different amino acid

• this may lead to coding of a different protein and gain, loss, or neutral function

Nonsense Mutation

• type of base mutation

• base substitution that produces a stop codon

• leads to loss of function

Silent mutation

• base substitution that produces the same amino acid

• usually neutral

• may alter translation and mRNA splicing

Indels

• insertions/deletions

• additions or removal of one or more nucleotides

In-frame

• indels that do not change the reading frame (usually needs to be an entire codon)

Frameshift

• indels that alter the reading frame downstream of the mutation (usually 1 or 2 bp)

expanding nucleotide repeats

• an increase in number of nucleotide repeats within a gene —> replication continues past hairpin and replicated the repeat again

• caused due to hairpin formation

  • more repeats = more hairpins = more repeats

Supressor Mutations

• mutations that supress the effect of another mutation but do not change the original mutation

Intragenic mutation

supressor mutation that occurs within the same gene as the original mutation

intergenic mutation

supressor mutation that occurs outside the original gene

Transposable Elements

• DNA sequences that can move around in a genome

• double stranded DNA is cut to create sticky ends —> matching transposable element is inserted in place

• may be replicated or excised and inserted (replicative vs nonreplicative)

Spontaneous mutations: tautometric shifts and DNA wobbling

• base mispairing

• tautometric shifts: rare forms of nitrogenous bases may bind with alternate nucleotides

• DNA wobbling: pronated forms of nitrogenous bases may wobble with other bases

Spontaneous mutations: strand slippage and unequal crossing over

• Insertions and Deletions:

• strand slippage: nucleotides loop out of DNA strand

  • insertions of new strand and deletion of template strand

• unequal corssing over: misallignment of chromosomes during meiosis prophase

  • one chromosome contains insertion and one contains deletion

Spontaneous mutations: depurination and deanimation

• depurination: loss of purine and empty bp slot is erroneously paired with another nitrogenous base

• deamination: loss of an amine group —> enzyme is needed to restore function to the nitrogenous base

Induced: Base analogs

chemicals with similair structure to nitrogenous bases pair in place of usual bases and alter structure and binding properties

• does not have any DNA function — cannot be replicated or transcribed

induced: akylating and deaminating

• add methyl or ethyl groups —> methylation of DNA —> less likely to be expressed

• both C/G —> T/A and T/A —> C/G mutations

induced: hydroxylamine

• Change from amino group to hydroxyl group

• C/G - T/A mutation

induced: oxidative radicals

• reactive oxygen derived from cellular metabolism (ROS damaging DNA)

• C/G - T/A mutation

induced: intercalating agents

• sandwich between nitrogenous bases in DNA

• cause insertions and deletions with frameshift

induced: radiation

• forms pyrimidine dimers that block replication and DNA repair

• thymine binds vertically with itself instead of horizontally with adenine

DNA Repair: mismatch repair

• enzymes detect incorrectly paired BPs and/or loops and cut section of new strand to replace using template strand

• for transition, transversion, or tautomeric shift (one bp is not where it should be)

DNA repair: direct repair

• fixes altered bases by restoring correct structures

• restorinf OG nucleotide function (removing methyl, adding amine, etc)

DNA repair: base excision repair

• replacement of the entire nucleotide or nitrogenous base

DNA repair: nucleotide excision repair

• removal of entire lesions such as pyrimidine dimers

• cuts our bound tymine (when removing >1 nucleotide, mutations are more likely to occur)

DNA repair: double strand break

• most common after radiation exposure

• Homology directed:

  • sister chromatid used as template to repair broken DNA (S, G2)

• Nonhomologous endjoining:

  • proteins recognize broken ends of DNA and rejoin them

  • may be joiined via random insertions or transposable elements

  • does not repair missing nucleotides and leads to massive insertions and deletions

DNA methylation and histone: epigenetics

• addition of methyl groups to nucleotide bases

• methyl groups supress transcription and leads to no gene expression

• histones may be methylated or acetylated

Gene silencing: Cell Differentiation

• pluripotency- stem cells express all genes: once fated, silence genes unecessary to their cell type

  • induced pluripotenet stem cells (iPSCs) reactivate genes and may revert to active stem cells

Gene Silencing: imprinting

• One allele, maternal or paternal, is silenced and result in either mutant or wild-type offspring

• insert only one functional copy (other copy is methylated)

• maternal imprinting- paternal gene is expressed

• paternal imprinting- maternal gene is expressed

Gene Silencing: X-chromosome inactivation

• inactivated X-chromosome unable to transcribe due to noncoding RNA

• RNA methylated histones to prevent transcription

Paramutation epigenetics

• interaction of two alleles lead to a change in expression of another allele

• only in plants

Behavioral epigenetics

• environmental conditions may affect how DNA is methylated/acetylated and histones are modified, either in an individual or in the gametes

Dutch-Hunger Winter

• The children and grandchildren of the war famine survivors had an increased risk of diabetes, obesity, and cardiovascular disease

• Behavioral DNA methylation in the gametes of affected individuals

• Thrifty phenotype hypothesis: conditions present during lifetime are likely to persist in children/granchildrens lifetimes

• Genetic Conflict: males and females favor different traits

Embryonic homologies

traits/phenotypes shared amongst related embryos that may disappear later in development

• gills, post anal tail, notochord, nerve cord, webbing

How embryonic homologies disapear during development

• gene regulation: silencing of certain genes (stem cells) that fate cells for a certain type

• regulated apoptosis: webbing in fingers should undergo apoptosis in humans and adjacent non webbed animals

pathway or embryonic development

• blastula: fluid filled cavity with cells around the outer edge

  • patterns dorsal/ventral and anterior/posterior (axis patterning)

• gastrulation: folds the embryo into distinct sections

• germ layers (ecto meso endo) will differentiate into distinct tissues once stem cells are fated

axis patterning genes location

• cytoplasm of the egg

• sperm entry also dictates some body axis patterning (either d/v or a/p depending on the species

Dorsal

• cactus binds dorsal in teh cytoplasm to prevent dorsal from moving into the nucleus

• dorsal in the cytoplasm

ventral

• toll binds cactus to degrade cactus and allow dorsal to enter the nucleus

• dorsal in the nucleus

anterior patterning

• bicoid expressed at anterior end and forms a gradient down the embryo

• bicoid + hunchbak = head and neck

posterior patterning

• nanos inhibits hunchback = posterior end

• hunchback expressed throughout the embryo

  • low concentration of bicoid (in middle of embryo) does not signal for head

  • low concentration of nanos (in middle of embryo) does not inhibit and turn into butt specifically

flow of segmentation

gap genes —> pair rule —> segment polarity

segmentation genes

• gap: give general areas for development

• pair rule: pairs of segments (bilateral would like to have 2 of some things and one of others)

• segment polarity: futher identifies segments of embryo

  • gap says head —> pair rules says upper head, middle head, lower head —> segment polarity says eyes, nose, mouth

Hox Genes

• expressed in the embryo in the order they appear in the genome (transcribed in the order of the segments)

  • labial (lab) expressed first

  • abdominal b (Abdb) is expressed last

How Hox genes are conserved amongst species

• same hox genes patteren all organisms

• duplications, insertions, deletions lead to differences in expression

Hox Gene related to developmental complexity

• the more hox genes, the more complex structures —? more dev. genes = more things develop

ectoderm, mesoderm, endoderm

• ectoderm: skin, nerves, skin appendages

• mesoderm- heart, muscle, kidney

• endoderm- lungs, gut tissues, etc goop

reciprocal signaling

• germ layers release signals that develop other layers

model organisms

• correlate phenotype to genotype

  • if two trairs are seen in a model organism and a human (large jaw, incorrect formation of the heart or the stomach or etc goop) then becuase developmental genes are conserved, likely the same pathway controls both phenotypes

    • only works if you are looking at the same trait in both organisms

SNPs

• more SNPs = less related

• if phenotype is conserved, SNPs can be used to indentify less likely genes that control phenotype

exon shiffling

• arrangement of exons in mature mRNA that gives a gene a distinct function from another gene with a different arrangement

  • post-transcriptional modification

gene duplication and multigene families

• duplicated genes can lead to multigene family

• duplicated genes that have acquired mutations give them different functions

genetic map

• describes the location of genes and chromosome variation

• measured in centimorgans (cM)

• estimates the probability of a recombination event —> genes being separated during crossing over

physical mapping

• measured in megabases (Mb) ~ 1 million bases

• physical distance between the loci

• not a direct a correspondance to cM

Cytogenic map

• P- short arm

• Q- long arm

• Naming: chromosome —> arm —> region —> band —> sub-band

recombination frequency

• cM measures the frequency of crossing over

• 1cM = 1% recombination frequency

Karyotype

• arrangement of chromosomes to identify breakage, insertions, deletions, and translocations

• identification of anueploidy and polyploidy

Trisomy 21

• down syndrome

• caused by nondisjunction event during meiosis

anueploidy and polyploidy

• anueploidy: monosome (2n-1) = missing one chromosome

• polyploidy: trisomy (2n+1) = having an extra chromosome

Familial down syndrome

• translocation of chroosome 21 to chromosome 14

balanced translocation in familial down syndrome

• one normal copy of 14 and 21

• one copy of 14/21 translocation

• carrier

unbalanced translocation in familial downsyndrome

• trisomy 21 (or 14):

  • two normal copies of 21

  • one copy of 14

  • one copy of 14/21

• Monosomy 21 (or 14):

  • two copies of normal 14

  • one copy of 21

Quantitative genetics

• looks at continous genetics

  • triats with carying degrees of phenotypes

  • may be influenced by other genes or the encironment

population genetics

• measurement of variation within a population

• calculation of allele frequencies

genotypic frequencies f(AA) f(Aa) f(aa)

• proportion of genotypes within a population

  • F(AA)= # of AA individuals/N = p²

  • f(Aa)= # of Aa individuals/N = 2pq

  • f(aa)= # of aa individuals/N = q²

allele frequencies

• proportion of alleles within a population

• p = f(A) = (2nAA+nAa)/2N

• q = f(a) = (2naa + nAa)/2N

Hardy-Weinburg Law

• If a population is:

  • large

  • experiencing random mating

  • not affected by mutation, migration, or natural selection

• Then:

  • the allele frequencies of a population do not change

  • teh genotypic frequencies will not change after one generation