Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
170 Cards in this Set
- Front
- Back
What are the three (3) major, related mechanisms of epigenetic inheritance?
|
1. Covalent histone modification
2. DNA methylation/demethylation 3. Silencing/activation of chromatin |
|
What are the three (3) major inherited epigenetic diseases?
|
1. Praeder-Willi syndrome
2. Angelman syndrome 3. Beckwith-Wiedmann syndrome |
|
T/F: Many cancer genes are incorrectly methylated/demethylated.
|
True
|
|
How does methylation silence genes?
|
Attracts silencing complexes...
Regulatory proteins guide methyltransferases Same regions attract proteins that confer transcriptional activity |
|
What is the 'nerdy' name for demethylation?
What are its two pathways? |
5mC erasure
1. Passive: 5mC -> 5hmC -> Cyt 2. Active: 5mC -> many intermediates (inc Thy) -> Cyt |
|
Define imprinting.
|
Selective silencing of ONE parent's genes
|
|
What is the #1 force holding together DNA?
Describe the other components as well. |
*Base stacking* (VdW, h-phobic interactions)
-Main free E store Base pairing - minimal free E Plectomeric coil into double helix (unwind, not pull - ladder) |
|
Describe the significance of the major/minor grooves.
|
DNA recognition by proteins
|
|
What are the three (3) physical factors of DNA stability and duplex formation?
|
1. Tm (environment)
2. Base composition (exploited for probes) 3. Ionic strength |
|
What is Tm?
|
Midpoint temperature where DNA is stable
|
|
What are the three (3) major, related mechanisms of epigenetic inheritance?
|
1. Covalent histone modification
2. DNA methylation/demethylation 3. Silencing/activation of chromatin |
|
What are the three (3) major inherited epigenetic diseases?
|
1. Praeder-Willi syndrome
2. Angelman syndrome 3. Beckwith-Wiedmann syndrome |
|
T/F: Many cancer genes are incorrectly methylated/demethylated.
|
True
|
|
How does methylation silence genes?
|
Attracts silencing complexes...
Regulatory proteins guide methyltransferases Same regions attract proteins that confer transcriptional activity |
|
What is the 'nerdy' name for demethylation?
What are its two pathways? |
5mC erasure
1. Passive: 5mC -> 5hmC -> Cyt 2. Active: 5mC -> many intermediates (inc Thy) -> Cyt |
|
Define imprinting.
|
Selective silencing of ONE parent's genes
|
|
What is the #1 force holding together DNA?
Describe the other components as well. |
*Base stacking* (VdW, h-phobic interactions)
-Main free E store Base pairing - minimal free E Plectomeric coil into double helix (unwind, not pull - ladder) |
|
Describe the significance of the major/minor grooves.
|
DNA recognition by proteins
|
|
What are the three (3) physical factors of DNA stability and duplex formation?
|
1. Tm (environment)
2. Base composition (exploited for probes) 3. Ionic strength |
|
What is Tm?
|
Midpoint temperature where DNA is stable
|
|
What effect does the addition of positive ions have on Tm?
|
Decreased Tm because backbone (-) charges neutralized
|
|
How can forensic scientists perform unambiguous DNA identification?
|
PCR
Run PCR products on gel for VNTR's (hypervariable forensic sequences) Compare VNTR configuration 18-20 genomic region |
|
What is the (+1) nucleotide?
|
a) First nucleotide of RNA transcript
b) where transcription starts Upstream: (-1), not 0 |
|
"Write a sequence"
|
All gene regulation signals: top (coding) [AUG, TATA, A2UA3]
|
|
What is a gene?
|
DNA segment coding a functional RNA transcript
coding RNA: mRNA -> ptn ncRNA: many types |
|
What is a promoter?
|
Txn start site - Guides RNAP
|
|
What is a terminator?
|
Txn stop site - Guides RNAP
|
|
What is a start codon?
|
AUG
Translation start in cytoplasm |
|
What are the three stop codon sequences? What are their functions?
|
UAA/UAG/UGA
Translation stop (in cytoplasm) |
|
What is an ORF?
|
Open reading frame
|
|
What are RNA processing signals?
|
Sites for intron splitting and polyadenylation
|
|
What are the two (2) main mechanisms of mRNA processing?
|
1. 5` cap addition
2. 3` Poly-A tail addition |
|
Describe 5` cap addition.
a) linkage b) function c) when added |
a) 5`-5` linkage
b) Stability (protects 5` from ez's) Transport (first to enter cytoplasm) Translation (ribosome uses it to get onto mRNA) c) Co-transcriptionally (requires Carboxyterminal domain [CTD] of Large RNAP |
|
True or false: Exon order is retained from DNA -> RNA?
|
True
|
|
Describe the translation process
|
1. 40S SMALL subunit joins 5` cap
2. 40S continues down 5` -> 3` until AUG it "likes" 3. 60S joins 40S -> 80S 4. 80S goes 3nt at a time, inserts aa 5. 80S hits stop codon, complex dissociates |
|
True or false: the "stop" codon (UGA/UAG/UAA) codes for an amino acid.
|
False
|
|
True or false: Most disease-causing gene mutations are located in coding regions.
|
False... promoter, exons, introns, UTR's
|
|
What are the four specific types of mutations?
|
1. Point mutation
-Missense -Nonsense -> "nonsense-mediated decay" 2. Deletion/inversion/insertion -Disrupt reading frame -Usually premature stop -> truncated ptn 3. Expansions EX: Huntingtons 4. Xsomal reciprocal/nonreciprocal translocations |
|
How can transcription be exploited to yield breast/colon cancer prognosis or diagnosis?
|
Oncotype-DX: profiles mRNA in tumor cells
|
|
Describe the three steps of transcription.
|
1. Initiation
RNAP binds DNA RNAP conformation change opens dsDNA in bubble 2. Elongation 3. Termination RNAPII - preceded by poly-A cleavage Releases small RNA fragment between cleavage and Poly-A |
|
What is the primary RNA polymerase of eukaryotes?
|
II: mRNA, snRNA (splicing), miRNA
|
|
What are the three components of the promoter region?
|
1. Core promoter
2. Proximal control region 3. Distal control regions + Enhancers |
|
Describe the core promoter:
-Relationship to start site -Regulatory regions -"Other" |
Between 5` (-35) and 3` (+35) of start site
Regulatory regions: -3 to +5 Multiple conserved sequence elements |
|
Describe the multiple conserved sequence elements of the core promoter.
|
Initiator region: -2 to +4
-In every promoter -Can be 2+ (allows 2+ transcripts from one gene) TATA box -Binds TFIID, which allows RNAP "landing" -Then, other factors solidify -> txn initiation BRE/DPE |
|
What is the function/location of the proximal control region?
|
Binds gene-specific transcription factors
-35 to -100 |
|
What is the function/location of the distal control region + enhancers?
|
Binds tissue-specific transcription factors
1000's of bp's away from start site |
|
What are the binding domains for gene-specific transcription factors and what are their functions?
|
DBD- DNA binding domain
-Prox/dist to promoter TAD - transactivation domain -Interacts w/ basal txn apparatus via DNA looping (RNAP, mediator, TF) DD - Dimerization domains -Interacts w/ TF's - Homo/heterodimers |
|
Name the sites which activate core promoters 1000's of bp's away.
|
Enhancer sites
|
|
How does the enhancer binding protein work to initiate transcription?
|
Binds TF, reaches out to general TF complex
|
|
When does capping/splicing occur?
|
Co-transcriptionally as RNA emerges from RNAP
|
|
What allows TF's to recognize specific bp sequences?
|
DNA binding and dimerization domains
|
|
How do glucocorticoids (in ex) stimulate transcription?
|
-Binds glucocorticoid receptor
-Binds GRE (glucocorticoid response element in promoter) -Reaches out and touches basal cell transcription apparatus -Has Zn fingers (get into DNA, look for specific seq in binding) |
|
What do TF's recognize?
|
Patterns of H-bond donors/acceptors in major/minor grooves
|
|
Describe the mutation in Duchenne muscular dystrophy.
-Gene -Inheritance pattern -Mutation mechanism |
Dystrophin gene (-> skeletal/cardiac muscle)
XR Splice site mutations |
|
What are the differences between Duchenne v. Becker muscular dystrophies? What do they share?
|
Duchenne
Mxn: COMPLETE elimination -Nonsense (early stop), frameshift, splicing, large deletion Sy: EARLY onset, more severe Prog: Nonambulatory by teens, early death ---------- Becker Mxn: PARTIALLY defective -Point mxn, in-frame deletion (still make ptn, larger), rearrangements, deletions Sy: LATER onset, slow progression Prog: Nonambulatory in 20's live til 30's-50's --------------- Both: Cause of death = dilated cardiomyopathy |
|
How do you determine the exact nature of a genetic defect?
|
Multiplex PCR: across all introns/exons
-Use all primers -Generate PCR products from all regions, find missing ones |
|
What are the six (6) mechanisms that can produce multiple proteins from the same gene?
|
1. Alternate transcription start sites (promoters)
2. ** Alternative splicing (70% all genes) 3. Alternative use of tln start/stop codons 4. "Slippery regions" change frame 5. Alternative Poly-A (extra exons) 6. Post-translational processing -> breakdown into smaller peptides |
|
What are the three critical regions for splice signals of mRNA introns, which are highly-conserved?
|
1. 5` splice junction
[E1] AG | GU [INTRON] 2. 3` splice junction [INTRON] AG | G [E2] 3. UACUAAC box In intron, contains "branch point A" |
|
Describe the process of mRNA splicing.
|
-Cut @ 5` splice, 3` splice
-Lariat intermediate (loop w/ A branch point) -Intron spliced out (spliceosome [snRNP's] -Exon ligation |
|
What components make up the spliceosome?
|
snRNP's:
U1 - 5` splice junction U2 - A branch point U4/5/6 - Knock off U1 |
|
What is the purpose of the long nose of RNAPII? (3)
|
1. Landing site: Poly A, splicing/capping factors
2. Allows orderly, sequential splicing 3. Splicing factors there, ready to jump on splice sites and begin splicing DURING transcription |
|
Describe how the two (2) tissue-specific regulatory proteins control use of splice sites, independent of transcription.
|
1. Repressors: negative control, no splicing
2. Activators: positive control, splicing |
|
True or false: the First and Last exon HAVE to be exons in alternative splicing.
|
True. There cannot be introns at 5` or 3` end.
|
|
What is the modified scanning hypothesis?
|
40S subunit stops at first AUG it "likes"
|
|
What are the 2 pathways for mRNA degradation?
|
1. Decay pathways
2. Regulation pathways |
|
What is the Decay pathway of mRNA degradation?
|
Degrade from 3` UTR and 5` end
|
|
What is the regulation pathway of mRNA degradation?
|
NLS: Nuclear localization signal
-Binds adaptors for nuclear import -Block: prevents protein influx for translation |
|
What are the three (3) trisomy disorders from Week 1?
|
1. Trisomy 21 (Down's)
2. Trisomy 18 (Edwards) 3. Trisomy 13 (Patau) |
|
What are the manifestations of Edwards syndrome (trisomy 18)?
|
"Fawn-like ears"
Clenched hand, returns if pulled out Genital hypoplasia Foot missing digits Short sternum Cardiac/renal defects Facies |
|
What are the manifestations of Patau syndrome (trisomy 13)?
|
"Rocker bottom" feet
Holoprosencephaly Micropthalmia Cleft Polydactyly Cryptorchidism Cardiac defect |
|
What is the common cause of triploidy?
What is the most common triploid karyotype? |
Dispermy (2 sperm fertilize egg)
69, XXX (usu extra maternal Xsomes) |
|
What are the four (micro)deletion deletion syndromes we discussed in Week 1?
|
1. 5p Syndrome (cri-du-chat)
2. Williams syndrome (elf) 3. DiGeorge/VCF 4. WAGR syndrome |
|
What is the deletion in cri-du-chat syndrome?
|
5p
|
|
What are the manifestations of 5p deletion?
|
Cri-du-chat cry
Single palmar creases |
|
What is the deletion of Williams syndrome?
|
Elastin on X7
2 common deletions, spontaneous |
|
What are the manifestations of Williams syndrome?
|
Elf....
Triangular face Small Outgoing/happy Hypercalcemia MR |
|
What is the deletion of DiGeorge/Velocardiofacial syndrome?
What is the common cause? |
22q11.2 - TBX1 gene
Bad recombination of LCR's (low copy repeats) |
|
What are the manifestations of DiGeorge/Velocardiofacial syndrome?
|
Facial dysmorphology (cleft)
Thymus deficiency VSep defects Slow growth |
|
What is the deletion in WAGR syndrome? What genes are affected?
|
11p13
PAX6: Eye (aniridia) WT1: Tsg, kidney/male genitals |
|
What are the clinical manifestations of WAGR syndrome?
|
Aniridia - blindness/glaucoma
Kidney dysfunction Undescended testes / small phallus Wilms tumor |
|
What are the 4 sex chromosomal disorders we discussed during Week 1?
|
1. Klinefelter's (extra X('s))
2. Extra Y 3. Turner's syndrome (X absence) 4. SRY deletion/crossover |
|
What are the two common Klinefelter karyotypes?
|
47, XXY
48, XXXY |
|
What are the clinical manifestations of Klinefelter's syndrome in:
-47, XXY -48, XXXY (severe) |
47,XXY
-Small testes, tall/thin -Gynecomastia -Hypogenitalism/azospermia 48, XXXY - Severe -Genu valgum (knock kneed) -Short stature -Motor delay -MR |
|
What is the most common "NOS" (extra Y karyotype)?
|
47, XYY
|
|
What are the manifestations of 47, XYY?
|
No phenotype, normal fertility
Conduct disorder, LD's Bite knuckles |
|
What are the 4 variants of Turner's syndrome karyotypes?
|
1. 45, X
2. Mosaic (may include Y) 3. X-deletions 4. Deletions/rings/isochromes |
|
What are the manifestations of Turner's syndrome in:
-newborn -adolescent |
Newborn:
-Web neck / space suit edema -Aortic coarctation Adolescent: -Lack of puberty -Short |
|
What are the manifestations of SRY deletion/crossover?
|
No ovarian maintenance
Streak gonads |
|
What is the inheritance pattern of retinoblastoma?
|
AD
|
|
T/F: Retinoblastoma is a "2-hit" disease (i.e. before problems)
|
True
|
|
What is the inheritance pattern of neurofibromatosis?
|
AD
|
|
What are the manifestations of neurofibromatosis?
|
Cafe-au-lait spots
Lisch nodules in eye |
|
What gene is deleted in Marfan syndrome?
|
FBN1 (fibrillin protein)
|
|
What is the inheritance pattern of Marfan syndrome?
|
AD
|
|
What are the diagnostic criteria for Marfan syndrome?
|
Pectus carinatum/excavatum
Dec upper/lower body size Whirl/thumb signs Reduced elbow extension |
|
What are the manifestations of Marfan syndrome?
|
"Spider fingers"
Ectopia lentis (vision impairment) Dilated aortic root Skeletal dysmorphia |
|
What are the five biochemical laboratory tests Heidenreich discussed?
|
1. AA quant (Phe in blood)
2. Urine OA (methylmalonic acid) 3. Carnitine / acylcarnitine analysis: FA oxidation 4. Ammonia/BUN: Urea cycle defects 5. Urine mucopolysaccharides / VLCFA's: Zellwegger syndrome |
|
What is the main AA metabolism disorder?
|
PKU
|
|
What is the problem in PKU?
|
-Can't metabolize Phe, accumulates
-Essential - can't synthesize -Eat excess -> tyrosine (catabolic) |
|
What are the manifestations of PKU?
|
Dev delay @ 3-4 months if untreated
Born normal - Mom "takes care of Phe" Seizures, autistic features |
|
What is the mechanism of PKU?
|
SEE PICTURE
|
|
What is the tx for PKU?
|
Low-protein diet
Can improve neurological f(x) |
|
What is the main organic acid metabolism disorder?
|
Methylmalonic aciduria
|
|
What is the problem in methylmalonic aciduria?
|
Can't convert methylmalonyl-CoA into succinyl-CoA (for Kreb's)
-Lack of methylmalonyl-CoA mutase MMA produced in many catabolic reactions (aa's, chol, odd-chain FA's) |
|
What is the manifestation of methylmalonic aciduria?
|
Week 1 - Severe acidosis
|
|
What is the tx for methylmalonic aciduria?
|
Low protein diet
Liver transplant to prevent acidotic episodes later in life Potential bone marrow |
|
What is the mechanism of methylmalonic aciduria?
|
SEE PICTURE
|
|
What is the main peroxisomal disorder?
|
Zellwegger syndrome
|
|
What is the inheritance pattern of metabolic disorders (except Zellwegger)?
|
AD
|
|
What is the problem in Zellwegger Syndrome?
|
Can't form peroxisomes
|
|
What are the manifestations of Zellwegger syndrome?
|
Large head
Flat nasal bridge Hypotonia |
|
How is Zellwegger syndrome diagnosed?
|
Biochemical test: Inc VLCFA, abnormal bile acid
Prenatal dx |
|
What is the tx for Zellwegger syndrome?
|
None effective
|
|
What are the three lysosomal storage diseases Heidenreich discussed?
|
1. Tay-Sach's
2. Gaucher's 3. Hurlers/(Hunters?) syndrome |
|
What is the problem in Hurler's syndrome?
|
Can't metabolize mucopolysacharrides (MPS)
-MPS's compose ground substance b/w collagen + fibrinogen of skin -During growth, MPS's accumulate -> dysmorphia |
|
What is the presentation of Hurler's syndrome?
|
Macrocephaly
Upturned nose / flat nasal bridge Short Hepatosplenomegaly |
|
What treatment is available for Hurler's syndrome?
|
Enzyme replacement (aldurazyme)
-Weekly infusion into blood stream (not BB barrier) -Ports into ventricles -> directly infuse brain w/ enzyme |
|
What is the mineral disorder Heidenreich discussed?
|
Menke's disease
|
|
What is the problem in Menke's disease?
|
Can't absorb Cu2+ across intestinal epi -> severe deficiency
|
|
What is the inheritance pattern of Menke's disease?
|
XR (mostly males)
In females... -Consanguinity -Turner's -X translocation, autosomal comes back to X -Skewed inactivation |
|
What is the manifestation of Menke's disease?
|
"Kinky hair"
Neurodegeneration |
|
What is the tx of Menke's disease?
|
Copper histidinate infusion under investigation
|
|
What is the vitamin disorder Heidenreich discussed?
|
Biotinidase deficiency
|
|
What is the problem in biotinidase deficiency?
|
Biotinidase defect: Can't recycle/reclaim biotin
F(x): performs -COOH reactions |
|
What is the manifestation of biotinidase deficiency?
|
Alopecia
Dermatitis Deafness Seizures / neurodeterioration @ 4-6 months |
|
What is the mechanism of biotinidase deficiency?
|
SEE PICTURE
|
|
What is the treatment for biotinidase deficiency?
|
Biotin supplementation -> cure
|
|
What are the three main FA oxidation disorders we discussed in class?
|
1. MCAD (most common, AR)
2. FAD 3. "Rest" (VLCAD, often cardiac/hepatic pblms) |
|
What is the problem in MCAD?
|
Deficiency: medium chain acyl-CoA dehydrogenase deficiency
|
|
What is the manifestation of MCAD?
|
-Lethargy/vomiting child after fasting
-Hypoketotic hypoglycemia -Possibly asymptomatic |
|
What is the tx for MCAD deficiency?
|
Avoidance of fasting (cake frosting)
Rapid tx of hypoglycemia |
|
What is the purine/pyrimidine disorder Heidenreich talked about?
|
Lesch-Nyhan
|
|
What is the problem in Lesch-Nyhan syndrome?
|
HGPRT mutation - purine reclamation
|
|
What is the inheritance pattern in Lesch-Nyhan syndrome?
|
XR (males)
|
|
What is the manifestation of Lesch-Nyhan syndrome?
|
Neurological dysfunction [basal ganglia disorders]
Self-mutilation Inc uric acid -> gout |
|
What is the tx for Lesch-Nyhan syndrome?
|
Low purine diet
Allopurinol Medications for neurologic signs |
|
What is the carbohydrate disorder Heidenreich talked about?
|
hereditary fructose intolerance
|
|
What is the problem in hereditary fructose intolerance?
|
Aldolase B (fructoaldolase) defect
Normal: Converts fructose to glucose So, nursing babies get no fructose |
|
What is the manifestation of hereditary fructose intolerance?
|
Acute ingestion: vomiting/hypoglycemia
Chronic ingestion: hepatomegaly / renal dysfunction |
|
What is the mechanism of hereditary fructose intolerance?
|
SEE PICTURE
|
|
How is hereditary fructose intolerance diagnosed?
|
Apple juice -> "Boom! Coma"
Molecular analysis of fructoaldolase |
|
What is the tx for hereditary fructose intolerance?
|
Restrict fruit/veg/corn syrup/table sugar
|
|
What is the problem in a urea cycle defect?
|
Ammonia buildup... can't convert ammonia to urea
|
|
What is the most common ez deficiency in urea cycle defect?
|
OTC (ornithine transcarbamylase)
Also: NAGS, CPS, ASA, As, Arginase |
|
What are the manifestations of a urea cycle defect?
|
Presents as severe hyperammonemia
Neuro damage if no rapid tx |
|
What is the mechanism of a urea cycle defect?
|
SEE PICTURE
|
|
How is a urea cycle defect diagnosed?
|
BUN
Inc ammonia, diag aa |
|
What is the tx for a urea cycle defect?
|
Dialysis in babies
Dietary restiction (low protein) Ammonia scavenger medications Pxl liver transplant - lots of urea cycle in liver |
|
What is the difference between sex-limited, -influenced, and -linked?
|
Sex-limited: only expressed in one sex
Sex-influenced: influenced by sex hormones (i.e. male pattern baldness) |
|
What is male hemizygosity?
|
Males express all X genes
|
|
What is X inactivation? (aka Lyonization)
|
Inactivation event - "dosage compensation" (dec expression to 1 allele)
|
|
What is the pseudoautosomal region?
|
X&Y have "Par" @ talomeres
-Crossing over here b/w X&Y -Stays active w/ X inactivation |
|
What is the name of the inactivated X chrosome?
|
Barr body
|
|
Describe hypohidrotic ectodermal dysplasia.
-Inheritance -Manifestation (female/male) |
X-linked
Female: missing teeth / anhydrosis patches Male: no teeth, total agenesis, sparse hair |
|
What is the function of the SRY gene? What happens when it is absent?
|
Testicular development
Female phenotype (XX,male) w/ ambiguous genitalia |
|
What genes allow spermatogenesis?
|
Yq genes
|
|
The inheritance pattern of sex-linked disorders is always ___ and usually ___.
|
X-linked; recessive
|
|
Why aren't Y-related disorders relevant?
|
Would cause infertility -> mnot inherited
|
|
What is the 1 dominant sex-linked disorder we talked about?
|
Incontinentia pigmenti
|
|
What are the 3 recessive sex-linked disorders we talked about?
|
Duchenne
Hemophilia Red/green colorblindnes |
|
What is the inheritance pattern of incontinentia pigmenti?
|
Dominant sex-linked
|
|
What is the genetic defect in incontinentia pigmenti?
|
NEMO gene
|
|
What are the manifestations of incontinentia pigmenti?
|
Redness/blisters
Thick skin Neurologically normal (i.e. not herpes) |
|
True or false: incontinentia pigmenti is only present in females.
|
True
|
|
What is the genetic defect in hemophilia?
|
Reduced clotting factor 8(A) or 9(B)
|
|
Why are the clinical manifestations of hemophilia so variable?
|
Different mutations in same gene = allelic heterogeneity
|
|
What is the inheritance pattern of hemophilia?
|
X-linked recessive
|
|
What is the genetic defect and mutation locus of Duchenne muscular dystrophy?
|
Deletion/mxn of dystrophin gene @ Xp21
|
|
What are the clinical manifestations of Duchenne muscular dystrophy?
|
Normal @ birth -> muscle weakness -> wheelchair @ 10yo -> death
Pseudohypertrophy (Gower's sign) Respiratory insufficiency |
|
What are the manifestations of Duchenne muscular dystrophy in a carrier female?
|
None - asymptomatic
|