MCB 3rd Unit 2 Flashcards
What gene mutation results in sickle cell disease? What mutation does this cause?
A->T transversion in HBB beta globin encoding gene
Causes missense mutation E6V
Amino acid 6: glutamic acid (E) -> Valine (V)
What mutation causes cystic fibrosis?
Delta F508
A process used for detecting DNA bands of a specific sequence and determining their size is:
Southern blotting
In Southern blotting, DNA fragments are separated based on ___ and detected by ____.
Size, hybridization
What does RFLP stand for?
Restriction Fragment Length Polymorphism
What process can be used to discriminate between alleles if a mutation/polymorphism changes the size of the DNA fragments?
Southern blotting
What is a RFLP?
A polymorphism that results in a change in size of a restriction fragment. A subset of SNP’s that happen to fall within a restriction site (create or destroy)
What are SNP’s?
Single-Nucleotide Polymorphisms
Besides SNP’s, what other ways can RFLP’s be formed?
Chromosomal rearrangement, Deletion/insertion between two restriction sites,
Full gene deletion
What is the mode of inheritance of hemophilia?
X-linked recessive
Hemophilia A is a defect in factor ___
VIII (F8 gene)
Hemophilia B is a defect in factor ___
IX (F9 gene)
~40% of hemophilia A cases are caused by____ which changes the distance between restriction sites, thus changing the fragments on Southern blot.
Inversion d/t homologous recombination of repetitive elements near the F8 gene
If all exons are present, can standard PCR tests detect a chromosomal inversion?
No
Nail-Patella syndrom is a result of what gene mutation?
LMX1B
What is the mode of inheritance of NPS?
Autosomal dominant
What can be used to track a mutation in a family?
RFLP’s
What is ASO hybridization?
Allele-Specific Oligonucleotide Hybridization
What is ASO hybridization used for?
Detecting sequence variants
How specific is ASO hybridization?
Can discriminate between sequences differing by a single base
ASO hybridization can be automated, and is useful in screening for mutations that are:
Frequent, such as CF and beta-thalassemia
What probe is used for ASO hybridization?
Oligonucleotides, one for each variant (wt and m)
What is the mode of inheritance for DMD and BMD?
XR
More residual protein function leads to more/less severe disease
Less
What is the mode of inheritance for Nail-Patella Syndrome?
AD
RFLP uses the principle of ____ to track mutations near a restriction site in a family
Linkage
The linkage tracked in an RFLP is ___ specific
Family
In ASO Hybridization, do we need to know the mutation?
Yes
Which type of diagnostic test uses dot blots?
ASO Hybridization
Why are only short ASO probes used?
Increase specificity, decrease mismatches which would be more stable with a long probe
What is the mode of inheritance for PKU
AR
In vitro exponential amplification of specific DNA sequences is called:
PCR
What is Taq
A Thermostable DNA polymerase
The three steps of a PCR cycle are:
Denaturing
Extension
Annealing
The upper limit of PCR in diagnostic labs is:
~1kb
A patient with sickle cell disease will have ___ reticulocytes and ___ hemoglobin
high, low
Southern Blot, RFLP, FISH, PCR, and CGH all rely on the principle of:
Hybridization
What is the inheritance pattern of sickle cell disease?
AR
Hemolytic anemia and swelling of the hands and feet are symptoms of:
Sickle cell disease
Sickle cell trait is displayed by people who are:
Heterozygotes/carriers
Most cases of Turner syndrome are due to a loss of a chromosome before/after fertilization (mosaicism)
after
A PCR based alternative to ASO hybridization
Allele-specific PCR
What type of PCR can be used to scan for commonly deleted exons?
Multiplex PCR
Define MLPA
Multiplex Ligation-dependent Probe Amplification
What is MLPA used for?
Detecting copy number variation
Give two examples of what MLPA can be used to detect
Deletions in DMD
Duplications in Down Syndrome
What are four advantages of MLPA?
High-throughput
Quantitative
Fast
Cost-effective
What can Southern blot identify that MLPA and CGH cannot?
Balanced chromosomal rearrangements (such as F8 in hemophilia A)
What three sequences are necessary for a MLPA probe?
Exon complimentary
Stuffer
Standard PCR binding sites
In an MLPA, the number of probe ligation products is a measure of the number of:
Target sequences
What does “FISH” stand for?
Fluorescence In-Situ Hybridization
What technique(s) is/are useful in detecting small deletions?
ASO
PCR
What technique(s) is/are useful in detecting medium deletions
PCR
Southern blotting
MLPA
CGH
What technique(s) is/are useful in detecting large deletions?
Southern blotting
MLPA
CGH
What technique(s) is/are useful in detecting very large deletions
FISH
What is the target of FISH?
Cellular chromosomal DNA
What is the probe used in FISH?
BACs
FISH is useful for detecting:
Known chromosomal rearrangements
What process can be used to detect unknown chromosomal rearrangements?
Spectral Karyotyping (SKY)
22q11 deletion syndrome, also called ___, results in “CATCH22” symptoms
DiGeorge Syndrome
What are the CATCH22 symptoms?
Cardiac defects Abnormal facies Thymic hypoplasia Cleft palate Hypocalcemia from parathyroid aplasia 22nd chromosome
What does CGH stand for?
Comparative Genome Hybridization
What is the gold standard for mutation identification and should identify any single base substitution?
DNA sequencing
Beta thalassaemia is due to what type of mutation in the beta-globin gene?
Null
Tandem repeats are also called:
Satellite DNA
Backwards slippage of a tri-nucleotide repeat causes an:
Insertion
Forward slippage of a tri-nucleotide repeat causes a:
deletion
Slippage of a non triple codon causes a:
Frameshift
Premature Termination Codons (PTC’s) result in:
RNA degradation (null mutation) *Truncated in USMLE*
The presence of ___ indicate that the ribosome is stalled at a PTC and Nonsense Mediatedd Decay machinery scans the 3 end and triggers RNA degradation
Exon Junctional Complexes (EJC’s)
Splice sites always start at __ and end at __
GT, AG
The rate at which new diseases occur is:
Incidence
The proportion of the population affected is:
Prevalence
Most diseases which involve enzymes and transporters are:
Recessive
Most diseases which involve structural proteins and transcription factors are:
Dominant
Variation in a trait or clinical presentation of a disease is called:
Phenotypic (clinical) heterogeneity
What are the two types of genetic heterogeneity (which may cause phenotypic heterogeneity)?
Allelic and locus heterogeneity
What is the term describing when a variety of mutations occuring on the same gene cause the same disease?
Allelic heterogeneity
What is the term describing when the same mutation within a variety of genes may cause the same disease?
Locus heterogeneity
Gower’s maneuver, calf pseudohypertrophy, and high creatine kinase are typical signs of:
DMD
One way to distinguis BMD from DMD at a young age is:
Ability to elevate head
The inheritance pattern and mutations resulting in DMD and BMD are:
X-linked recessive, dystrophin
A disease caused by enzyme deficiency is called an:
Enzymopathy
What are the two causes of disease in enzymopathies?
Substrate accumulation, product deficiency
What is an AR form of hyperphenylalaninemia involving a deficiency of PAH resulting in intellectual disability?
Phenylketonuria (PKU)
How many clinical variants of PKU exist?
3, Classic, variant, and non-PKU hyperphenylalaninemia
What type of heterogeneity does PKU express?
Allelic
In some cases of PKU, ___ supplementation is necessary to create neurotransmitters and prevent mental retardation
BH4
General hyperphenylalaninemia expresses what type of heterogeneity?
Locus:
PAH (PKU)
2 genes for BH4 synthesis, 2 genes for BH4 recycling
What is the mode of inheritance for Oculocutaneous albanism?
AR
What is the mechanism for oculocutaneous albanism?
OCA1 gene: tyrosinase deficiency
OCA1B gene: milder
What is the mode of inheritance for maple syrup urine disease?
AR
What is the mechanism for maple syrup urine disease?
Deficiency of BCKDC, defective metabolism of branched chain amino acids (Val, Leu, Ile)
The three mechanisms of dominance are:
Haploinsufficiency
Gain of function mut.
Dominant negative mut.
In the mechanism ____, expression from one copy of an allele is not enough to meet physiological requirements and produce a normal phnotype
Haploinsufficiency
Loss-of-function
What is the mutated transcription factor resulting in NPS?
LMX1B
What is defined as the probability that an individual carrying a disease-causing mutation will present with that disease?
Penetrance
“All-or-none”
What is defined as the probability that individuals carrying the same mutation may present with different phenotypes
Variable expressivity
NPS has ___ penetrance and variable expressivity
Complete
FGFR3 encodes a:
TKR
Achondroplasia is a ___ mutation in FGFR3
G380R
Mutation for sickle cell?
E6V
Mutation for cystic fibrosis?
Delta F508
G380R mutation causes:
Achondroplasia
The G380R mutation results in a _-of-function
Gain
Mutation resulting in cleidocranial displasia is:
Runx2
What is the function of cystein that no other amino acids have?
Formation of disulfide bonds
When the mutant gene product interferes with the function of the normal gene product the mutation is called:
Dominant negative
The best example of dominant negative mutations involve ___ proteins
Structural
The a.a. triplet that forms collagen involves glycine and usually:
Proline and hydroxyproline/lysine
Hydroxylation, glycosylation, and triple helix winding of collagen occurs in the:
ER/Golgi
Propeptide cleavage to tropocollagen and fibril assembly of collagen occurs in the:
ECM
Formation/winding of collagen occurs ___ to ___.
C terminus to N terminus
What mutation type leads to type I OI?
Null mutation d/t haploinsufficiency
What mutation type leads to type II-IV OI?
Missense, Dominant negative
Which type of OI is the most mild? The most severe?
I, II
OI usually involves substitutions of which amino acid?
Glycine
AD polydactyly (as well as holoprosencepahly) is caused by mutations in:
SHH
AD polydactyly is linked to an insertion in the intron of ___ in SHH, which is an enhancer in the gene.
LMBR1
A mutation in Sox9 will lead to an AD disease called:
Campomelic dysplasia
Symptoms of campomelic dysplasia include:
Skeletal abnormalities, 46XY karyotype with female genitalia
Lactose intolerance (as well as campomelic dysplasia and AD polydactyly) is caused by a mutation in the ___ section of a gene
Enhancer
A deletion syndrome involving 7q11.23 and multiple genes including Elastin (ELN) is:
Williams, or Williams-Beuren Syndrome (WBS)
If different missense mutations yield distinct phenotypes, then the mutation must be ___-of-function
Gain
