Genetics Flashcards
Name four types of genetic disease
- chromosomal defects (Down syndrome)
- Single gene defect (sickle cell anemia)
- Multifactorial/polygenic (diabetes)
- Mitochondrial disorder (LHON)
A phosphate group binds to which end of a sugar (nucleotide)?
5’
A hydroxyl group binds to which end of the sugar (Nucleotide) ?
3’
DNA replication occurs in what direction?
5’ to 3’
What is the makeup of a nucleosome?
8 histone subunits around which 146bp DNA is wrapped
What are chromatin fibers?
Coiled nucleosomes
Describe an acrocentric chromosome
P arms contain satellites which, when stained, do not have bands
Xq27.3 describes what area of a chromosome?
X chromosome, q arm, region 2, band 7, sub-band 3
Trisomy describes what chromosomal condition? What causes this?
3 copies of a chromosome
caused by nondisjunction by gametes, an existing chromosomal recombination, or by mitotic recombination in a germ line following fertilization
Down syndrome is caused by what genetic disorder?
Trisomy 21, or three copies of chromosome 21
What is the function of telomerase?
Regulates the length of telomeres by adding repeat sequences to the 3’ end of chromosomes
Ensures complete replication at the ends of chromosomes and prevents both degradation of the chromosome and unintended binding of chromosomes
Name three types of tandem repeats and their usual locations
Satellite DNA - main component of centromeres
Minisatellite DNA - at or near telomeres
Microsatellite DNA - dispersed throughout chromosome
Describe the concept of Copy Number Variation (CNV)
large, repeated segments of DNA that are polymorphic in length
Contrast Alu and L1 repeats
Alu repeats are non-autonomous, 10% of genome (SINES)
L1 (LINES) repeats are autonomous and, when expressed, can code for reverse transcriptases, propagate and reinsert into DNA
Contrast euchromatin and heterochromatin
Euchromatin - active,extended form, easily transcribed
Heterochromatin - condensed and compact, trancriptionally inactive
Contrast constitutive and facultative heterochromatin
constitutive - always inactive
facultative - either inactive or active (X inactivation)
Where does methylation occur?
at CpG dinucleotides and histone tails
At what position of cytosine does methylation occur?
the 5 position of the base
Describe post-transcriptional RNA processing
5’ cap is added to beginning of mRNA sequence
poly A tail is added to end of mRNA via poly A polymerase
5’ Cap and Poly A tail help prevent degradation in cytoplasm
Describe the formation of the lariat complex during RNA splicing
snRNP’s bind to 5’ GT and 3’ AG and physically pull the two ends of the intron together, forming the complex
intron is cleaved and removed
Describe the splice donor site, branch site and splice acceptor site
Splice donor: GT at 5’ end of intron
Branch site: signals proximity of splice acceptor (<20 nucleotides away, repeated (CCCCCCCCCCC)nAG)
Splice acceptor: AG at 3’ end of intron
Describe translational degeneracy
3rd position of codon loosely associates with tRNA so nucleotide variation at the 3rd position doesn’t necessarily code for a different amino acid
What is alternative splicing?
Different splicing patterns on a single gene that result in different translational products
Certain splicing patterns may be tissue specific or developmental stage specific
>50% genes show alternative splicing
What is the role of a locus control region?
Involved in differential gene expression via the recruitment of gene expression modifiers (transcription factors, coactivators, etc.)
Gene expression can vary by tissue or developmental stage
What is the significance of heteroplasmy in mitochondrial disease?
Different cells/tissues may have varying numbers of mutant mtDNA
Due to random skewing, these mutations and, consequently, mitochondrial diseases may be more or less severe
What is the significance of X-inactivation in regard to genomic disorders?
One x chromosome will be inactivated in females
Which chromosome is inactivated is random between cells
If random skewing results in a majority of cells with an active, mutated chromosome, that genetic disorder would be more severe than, say, an individual with a 50-50 split
XIST gene produces protein that coats the INACTIVATED Chromosome
In what scenario would you want to use PCR/RT-PCR vs. Southern blotting/northern blotting, and vice versa?
PCR - Amplify and have abundance of target gene, can then sequence, clone, etc. A lot of manipulation is possible
Blotting - Good when sequencing is not necessary, just want to see if gene is present, duplicated, absent, expanded, etc.
What is an advantage of northern blotting in regards to investigating splicing irregularities?
You are blotting RNA so the introns have been removed
If splicing was successful and went as expected, you will see target gene of an expected size on gel
If not, you know that splicing resulted in not enough or too much of the gene being removed
Describe the process of PCR amplification
Denature target DNA
Add primer sequences that target flanking regions around target gene
Lower temp. to promote synthesis
Repeat
What is a conservative mutation?
Replacement of a wobble base, ultimately codes for same amino acid
What is a missense mutation?
Replacement of a nucleotide with another nucleotide, results in codon for a different amino acid
What is the consequence of a nonsense mutation?
Prematurely stops transcription of mRNA due to unexpected stop codon
Consequent presence of exon junction complexes lead to mRNA being marked for destruction
What is a splice site mutation and what can result from it?
Point mutation in either the donor site (GT) or the acceptor site (AG)
Can result in exon skipping, or the splicing of an exon
What is a length variation mutation and after what event can this occur?
Change in length of a sequence; duplication, deletion, expansion, insertion
Common after a mismatched recombination
What are triplet repeat expansions?
Expansions of naturally occurring triplet repeats
Explain genetic anticipation in regards to repeat sequences
Repeat sequences are unstable and can increase in length in successive generations
Greater length and severity of disorder will result in earlier onset in successive generations, aka genetic anticipation
Example: myotonic dystrophy
Describe the function of base excision repair? When can this process be complicated?
The deamination of cytosine will result in a uracil
Uracil is easily recognized as improperly located in DNA and is excised
Deamination of a methylated cytosine (common for CpG) results in a thymine, which is not recognized as needing repair and is therefore a very common mutation
What is the function of nucelotide excision repair?
Removal of thymine dimers that result from UV damage
What is the advantage of SNP microarray analysis and FISH karyotyping?
Microarray analysis - looking for microdeletions, won’t be able to detect visually on chromosome, evidenced by SNP dosage
FISH - using probes to look for chromosomal microdeletions, duplications of chromosomes, etc., evidenced by the presence or lack of fluorescent hybrid visualization
What are some limitations of SNP microarray analysis?
Cannot detect balanced translocations
Cannot detect low level mosaicism
Could show variants of unknown clinical significance
What is Robertsonian translocation? What chromosomes can be involved? What are possible consequences?
Translocation involving acrocentric chromosomes where long arms are fused and satellite arms are lost
Acrocentric chromosomes 13, 14, 15, 21 and 22 are involved
Can result in unbalanced gametes and, consequently, trisomic or monosomic zygotes
Can microdeletions be inherited?
Yes, both deletions and duplications can be inherited
However, microdeletions are often due to some new recombination mutation and not inherited
Define digenic inheritance
AKA triallelic inheritance
Disease requires two mutant alleles in one gene + one mutant allele in another gene
Chargaff Rule
The amount of Cytosine = Guanine Adenine= Thymine
Okazaki Fragment
Separate fragmented strands that represent the lagging strand. Will need to be glued together
Aneuploidy
# of chromosome not divisible by 23 Caused by non-disjunction
Genetic Imprinting
Epigenetic Inheritance: One copy of a gene is silenced depending on parent of origin. Methylation of DNA
Prader Willi Syndrome : maternal imprint + Father deletion
Angelmon Syndrom : Paternal imprint + maternal deletion
Mediated RNA decay
Premature stop codons (Nonsense mutation) inserted into mRNA strand. First ribosome binds and removes EJs (Exon Junctions). Ribosome falls of at Stop codon. The remaining EJs mark mRNA for destruction
Fragile X
Promoter shut off due to methylation (5’UTR)
Via naturally occurring repeats
Huntington Disease
Toxic polyglutamine tract added (Exon)
Via naturally occurring repeats
Friedreich Ataxia
Inhibition of transcription (Intron)
Via naturally occurring repeats
Myotonic Dystophy
Abnormal interaction w/ RNA binding protein (3’UTR)
Via naturally occurring repeats
Define monoallelic expression
One allele is active while the other is silenced or imprinted
Haploinsufficiency
(Loss of function)
One healthy allele is not sufficient in order to produce the necessary amount of protein for proper function
Dominant-Negative Effect
The mutant protein produced interferes with function of normal proteins
Gain of Function
Mutant protein gains a new function
Mutations to a signaling protein causes the signal to always be on
Define uniparental disomy. What are possible consequences?
Individual inherits both copies of an allele/part of a chromosome from a single parent
Can inherit an AR disorder w/ only one carrier parent (Cystic Fibrosis)
Imprinting disorders (40% of PWS due to maternal UPD)
Describe monosomy rescue
If one gamete (usually an egg) is trisomic, another must nullisomic for the same chromosome
Fertilization of this nullisomy egg would normally result in monosomy (fatal)
If a duplication of the chromosome occurs in the germline, it is viable and there is uniparental disomy for that chromosome
Non-Allelic Homologous Recombination (NAHR)
- Areas of high recombination are flanked by unique low copy repeats
- Low Copy repeats cause the chromatids to misalign during recombination in meiosis
- This leads to non-homologous recombination and unequal crossover
Polygenic/Polygenic Traits
Multiple genes/Traits are continuous and quantitative (Blood pressure, Height)
Empiric Risk
Multifactorial Traits Risk
- Closeness of affected relative
- Number of affected relative
- Disease severity
- Sex
Concordance
If one person has it then the other will
ex. Huntington Monozygotic 100% concordance, Dizygotic 50% concordance
Describe trisomy rescue in relation to gene imprinting
Trisomy is most often caused my maternal nondisjunction
If a parental chromosome is inactivated, maternal UPD occurs
If a maternal chromosome is inactivated, normal phenotype occurs
If no chromosome is inactivated, trisomy occurs
What Hardy-Weinberg variable represents the frequency of affected males for an X-linked recessive disorder? Male carriers? Affected females? Female carriers?
q = affected males
No male carriers (only one X)
p-squared = affected females
2pq = female carriers
Recombination
- Meiosis I - Prophase 1 Recombination/crossing over happens easier from spread out genes.
- Recombination frequency is a measure of genetic distance
- Genetic linkage - closely positioned loci less likely to be separated by recombination
- Conserved haplotypes indicate linkages
Sanger
- Dideoxynucleotide/ddNTP “Terminator”
- Binds to C3 of sugar (Needs -OH group to have more nucleotides added
- ddNTP bind only -H at the C3 position stopping the chain and sequencing one at a time
