Genetics 1- 10 Flashcards
Sildenafil (Viagara) works by
blocking the enzyme PDE5, which relaxes arteries & results in increased blood flow
Transformation
ability to deliver foreign DNA to cells, both prokaryotic and eukaryotic
Plasmid
Autonomously replicating DNA molecule; single origin of replication & can replicate itself in bacterial cells
Restriction endonucleases (enzymes)
molecular scissors to selectively cut DNA
Selection
methods to rapidly select those host cells that contain recombinant DNA
Personal genomics
branch of genomics where the genotyping stage employs single-nucleotide polymorphsm (SNP) analysis (0.2%of genome) or partial/full genome sequencing
Kinetochore
repeated sequence known as alpha satellite DNA
Telomere length is controlled by
erosion and addition
Chronic myeloid leukemia (CML)
malignant transformation of hematopoietic stem cells; accounts for 20% of all adult leukemias
caused by translocation between chromosomes 9 and 22 (BCR-ABL oncogene creation). Philadelphia chromosome!
CML is classified into three phases
chronic phase (less than 10% blasts), accelerated phase (10-20% blasts), and blastic phase (20% or more). These phases are based mainly on the number of immature white blood cells, myeoblasts, seen in the blood or bone marrow
Chronic is the most treatable phase
Philadelphia Chromosome
a reciprocal translocation between chromosomes 9 and 22
The ABL1 proto-oncogene encodes a cytoplasmic and nuclear protein tyrosine kinase; it is moved adjacent to BCR (breakpoint cluster region protein) on chromosome 22
BCR-ABL is a mutant tyrosine kinase that stimulates uncontrolled cell division of abnormal blood cells by the bone marrow
Epigenetics
heritable alternations in gene expression, which are not due to structural changes in the DNA; induced spontaneously
Methylation (turns gene off)
Acetylation (turns gene on)
Phosphorylation (positive and negative consequences)
Ubiquination (targets histones for degradation)
Sumolaytion (promotes gene silencing by affecting histones)
Functions of DNA methylation in mammals
Transcription gene silencing
genome stability
chromatin compaction
X chromosome inactivation (females)
Etopside (VP-16)
derivative of podophyllotoxin from the mandrake plant
etopside inhibits the re-ligation of the strands resulting in the accumulation or irreversible double strand breaks lethal to cells
snRNA
small nuclear RNAs, complexed with protein in the nucleus, invovled in RNA splicing
snoRNAs
small nucleolar RNAs, used to process and chemically modify rRNAS
Spinal Muscular Atrophy (SMA)
Second most-common recessive human disorder and the most common inherited cause of infant mortality
Mutations in the SMN1 encoding the survival motor neuron (SMN) protein cause SMA
SMN is needed in pre-RNA splicing
SMN2 is already damaged in us so it can’t make up for a errors in SMN1
Cryptic splice site
a randomly occurring site in the genome that contains a consensus sequence for 5’ or 3’ intron splicing but is not normally used for that purpose, until mutated
ex: progeria
Hutchinson-Gilford progeria syndrome (HGPS)
a point mutation activates a cryptic splice site and thus leads to the production of a mutant prelamin A protein, progerin. An internal cleavage site is removed, and the progerin protein is never properly cleaved (leaving it permanently farnesylated and carboxymethylated)
ncRNA (non-coding RNA)
a functional RNA molecule that is not translated into a protein
ex: rRNA, tRNA, snoRNA, microRNA, siRNA, piRNA, and long ncRNAs
Xist
non-coding RNA gene on the X chromosome that participates in X chromosome inactivation
miRNA
post-transcriptional regulators that bind to complementary sequences in multiple target mRNAS, usually resulting in translation repression or target degradation and gene silencing
(Dicer chops it up and then miRNA complexes with the RISC complex to attack mRNA)
siRNA
Small Interfering RNA - double-stranded RNA molecules that can be chemically synthesized and are used in therapeutic gene silencing (similar function to miRNA)
Gene drive
genetic systems that circumvent the traditional rules (50% chance of inheriting genes from either parent); they greatly increase the odds that the drive will be passed onto offspring
“Cas9 to the nth degree,” “eliminating Mendellian genetics”
circular RNA
ciRNAs might modulate RNA polymerase II in cis and thereby alter the expression of their gene.
ciRNAs also accumulate in the nucleus and can be localized to their sites of transcription
function as an miRNA sponge?
centimorgan (cM)
the genetic distance between two loci that yields recombination in 1% of gametes
LOD score
statistical measure of the likelihood of odds that the observed marker is indeed linked and not inherited with disease by chance
SNVs
single nucleotide variation seen in a single family or individual
CNVs
copy number variations - duplications or deletions, often 1000 to several million bp
Genome-Wide Association Study (GWAS)
how we map for polygenic traits
compare 100,000s of polymorphisms between cases and controls and identifies SNPs frequently associated with case
Levels of gene expression control in eukaryotes
- Chromatin structure
- Epigenetics control
- Transcriptional initiation
- Transcript processing and modification
- RNA transport
- Transcript stability
- Control of transcript mRNA levels by non-coding RNAs
- Post-translational modification
- Protein transport
- Control of protein stability
Regulation of transcriptional activators
- Phosphorylation stimulates cytoplasmic proteins to move to the nucleus
- Ligand binding increases or decreases affinity for DNA
- Some are already bound to their target site but remain inactive until they are stimualted
3 parts of a nuclear hormone receptor
- AD - activation domain
- DBD - DNA binding domain
- LBD - ligand binding domain
Burkitt Lymphoma
A very fast growing version of non-Hodgkin’s lymphoma. Caused by reciprocal translocation of the c-Myc locus on chromosome 8 with iG enhancer on chromosome 14.
Three clinical variants of Burkitt lymphoma
- Endemic - equatorial Africa along with Epstein-Barr virus
- Sporadic - outside Africa
- Immunodeficiency - usually associated with HIV or in post-transplant patients
Penetrance
the percentage of individuals of a specific genotype showing the expected phenotype
can be fully penetrant (always expressed) or incompletely penetrant (only shown sometimes)
Expressivity
measures the extent to which a given genotype is expressed in the phenotype (variability of a trait based upon a specific genotype)
Roberts syndrome (RBS)
caused by a mutation in ESCO2, a human homolog of yeast ECO1, that is essential for the establishment of sister chromatid cohesion
RBS cells have too few or too many chromosomes that ultimately lead to aborted cell divisions
Present with hands and feet attached to abbreviated arms and legs (phocomelia)
Phocomelia
congenital malformation in which hands and feet are attached to abbreviated arms and legs
Seen in Roberts Syndrome (RBS)
Harlequin ichthyosis (HI)
severe, often fatal congenital ichthyosis with an autosomal recessive inheritance pattern caused by a defect in the ATP-binding cassette transporter ABCA12
presents with hyperkeratosis, ectropion, and eclabium
hyperkeratosis
thickening of the stratum corneum, the outermost layer of the epidermis (fissures all over the body)
ectropion
lower eyelid turns outward
eclabium
the lips turn outward
“Second hits” in retinoblastoma
non-disjunction, non-disjunction reduplication, mitotic recombination, gene conversion, deletion, and point mutation
genetic imprinting
differential expression of a gene or chromosome region, according to the parent-of-origin of the allele
one parent’s allele is selectively silenced
“functional hemizygosity”
hydatiform mole
two sets of paternal chromosomes only
ovarian teratoma
two sets of maternal chromosomes only
Prader-Willi Syndrome (PWS)
Paternal-only genes on chromosome 15 fail to be expressed
Angelman Syndrome
Maternal-only gene UBE3A on chromosome 15 fails to be expressed
Four genetic mechanisms to PWS & Angelman
- Deletion (usually in a long-copy repeat area)
- Uniparental disomy (two copies of the chromosome from one parent)
- Mutation (more common in Angelman than PWS)
- Imprinting defect
Epigenotype
epigenetic parent of origin information
typically reprogrammed between generations
Myotonic Dystrophy Type 1 is caused by
Expanded CTG repeats in the 3’ UTR. Mild affect is 50-80 repeats. Severe is over 2000 repeats. CTG repeat length correlates with age of onset (more repeats, earlier age)
These CTG repeats are transcribed into CUG repeats. The CUG RNA sequesters RNA binding proteins like MBNL.
MBNL can now no longer perform its alternative splicing function, and muscle cells revert to fetal-like muscle cells which causes rigidity and myotonia
cytogenetics
brand of genetics focused on the structure and function of chromosomes
G-banding detects the following cytogenetic anomalies:
- Deletions > 5Mb
- Some translocations
- Aneuploidy
- Mosaicism
- Ring, marker, and isochromosomes (fragments)
Acrocentric chromosomes
13, 14, 15, 21, and 22
Aneuploidy
abnormal number of chromosomes
Edward’s Syndrome
Trisomy 18
rare to survive until 6 months, often stillborn. Low birth weight, cleft palate, heart & kidney defects, irregularly shaped head
Triploidy
three sets of chromosomes
85% are diandric (2 paternal). These fetuses are near normal size.
15% are digynic (2 maternal). These fetuses have intrauterine growth retardation.
Unbalanced translocations
Arise from fertilization of a gamete with a balanced translocation
Result may be 46 chromosomes but monosomy and trisomy for some segments
80-90% are usually normal, whereas theoretical outcome would be 25%
Robertsonian translocations
Between acrocentric chromosomes
Breakpoints at or near centromere and yield a metacentric or submetacentric chromosome (often dicentic)
Creates one giant chromosome and then a fragment piece thats usually lost
Paracentric inversion
within one arm of chromosome
risk for liveborn children is low (but 50% are often not viable due to acentricity or dicentricity)
Pericentric
inversion involving the centromere
risk for offspring is similar to balanced translocation
often less severe than paracentric because all chromosomes end up with a centromere
Primary mechanism of duplications and deletions
nonallelic recombination between low copy repeats
Marker chromosome
structurally abnormal chromosome often of unknown origin
ex: Cat Eye Syndrome
Isochromosome
Separation along the wrong axis in anaphase creates a chromosome that is p/p or q/q
ex: Pallister-Killian Syndrome is a isochromosome tetrasomy of 12p
Ring chromosome
Breaks on both p and q arms, ends fuse
Mitotically unstable
Yields a “dynamic mosaicism”
Heritable
ex: 6% of Turner syndrome cases are due to a ring X chromosome [ 46,X, r(X) ]
Mosaicism
individual with 2 or more genetically different cell varieties; cell types differ due to mutation or nondisjunction
Cytogenetic technologies
FISH
Microarray
SNP microarray
MS-MLPA
FISH
Fluorescence in situ hybridization
Clinical applications: aneuploidy, microdeletions and duplications, marker chromosome, and to refine breakpoints of insertions, deletions, translocations, etc
Benefits: rapid analysis for high risk pregnancies
Limitations: may not detect low-level mosaicism or structural chromosome anomalies (only sees region complementary to probe)
Charcot-Marie Tooth Type 1A
LCR-mediated duplication on chromosome 17
Demyelinating peripheral neuropathy, progressive distal muscle weakness and atrophy, sensory loss and slow nerve conduction
Comparative Genome Hybridization (CGH)
Chromosome microarray where subject DNA is hybridized with reference DNA and applied to an array. You compare and can tell if there is an extra copy or missing copy.
Great for high resolution of location/breakpoints of deletions or duplications
Will NOT detect balanced translocations
Chromosome microarray - SNP array
Detects variants (consanguinity) and copy number. The resolution is determined by the density of SNPs
Benefits of microarrays
high resolution, objectivity, nondividing tissue, detect several disorders at one time
Limitations of microarrays
Does not detect balanced rearrangements or point mutations; detects copy number variation of uncertain signifigance
isodisomy
two copies of the same homolog from one parent
Heterodisomy
two different homologs from one parent
Factors affecting pathogenicity of anomalies
Extent of genome affected, location in genome, inherited vs. de novo
DNA primase does what?
Makes RNA primer that initiates DNA replication
Components of a human gene
Exons, Introns, a transcription start site, a promoter (base or core promoter AND an “upstream” promoter), TATA Box (positions RNAPII) and enhancers
Factors influencing penetrance
- modifier genes
- Response to DNA damage
- Epigenetic factors: DNA methylation
- Age-related penetrance
Types of nonmendelian inheritance
triplet repeats, genomic imprinting, mosaicism, mitochondrial inheritance
Chromosomes are always named after what?
The source of the centromere
Unbalanced translocations arise from what?
The fertilization of a gamete with a balanced translocation
Limitations of microarrays?
Do not detect balanced rearrangements or point mutations
Detects copy number variations of uncertain significance
