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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