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Mitosis/Meiosis - ugh > DNA > Flashcards

DNA Flashcards

1
Q

sequence repeated at telomeres

A

TTAGGG

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2
Q

how long are telomeres?

A

10-15 kb

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3
Q

kinetochore

A

Protein scaffold where spindle fibers attach

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4
Q

primase

A

synthesizes rna primers during DNA replication, since DNA polymerase can’t start from nothing

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5
Q

telomerase extends the (leading/lagging?) strand

A

lagging (template)

because that’s the one that has issues with okazaki fragments.

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6
Q

telomerase - how does it extend the lagging strand?

A

by using its RNA component as a template to add TTAGGG to the end of the lagging strand, thus giving more space for synthesis of another okazaki fragment

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7
Q

replication on the lagging strand involves

A

primase (lays down primer)
polymerase
splicing
ligase

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8
Q

what direction does DNA proofreading go?

A

3’ to 5’ - done by “exonuclease proofreading” function of DNA polymerase

opposite direction of DNA replication. Polymerase senses error (a bubble that doesn’t pair properly) and its exonuclease component goes to excise the incorrect base to fix the problem; correct base is inserted via polymerase.

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9
Q

mismatch repair proteins - mechanisms of action? at what point do they go in?

A

MMR proteins go in if proofreading fails, and there’s a mismatch “bubble”

MMR binds bubble, also binds the nicked strand (NEW DNA is kNicked to “mark” it as being freshly-made). MMR scans along the nicked strand until it gets to the bubble, then fixes it by:

excising wrong base on both sides
polymerase inserts correct bases
ligase

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10
Q

xeroderma pigmentosum – defect in what?

A

nucleotide excision repair (big, bulky problems, like two bases dimerized by UV)

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11
Q

Damage within ONE strand of DNA fixed by one of 4 mechanisms ?

A

Proofreading
Mismatch repair
Nucleotide excision repair
Base excision repair

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12
Q

double strand break:

homologous can lead to –

A

translocation (wrong ends joined)

deletion/duplication (missing bp’s at joining)

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13
Q

double strand break:

NON-homologous ?

A

“eating away” a bigger portion at the double stranded breakpoint on the chromosome to reveal overhangs

overhangs help sister chromatid be used as template during repair

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14
Q

BRCA - mechanism broken?

A

double strand break repair – homologous

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15
Q

MUTYH - mechanism broken?

A

BASE excision repair

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16
Q

Lynch - mechanism broken?

A

mismatch repair

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17
Q

RISC -
stands for what?
function?

A

RNA-induced silencing complex

either brings RNA template to SILENCE mRNA
or
DOWNREGULATES TRANSLATION (incomplete RNA template match to mRNA)

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18
Q

carrier rate for Fragile X

A

1 in 150 females

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19
Q

affected male rate for Fragile X

A

1 in 4,000

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20
Q

what’s more common, Fragile X or Noonan?

A

Noonan is more than twice as common

FraX = 1 in 4,000

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21
Q

FraX CGG repeat cutoffs

A

45-54 = “gray zone”
next generation at risk for:
premutation
POI - premature ovarian insufficiency
tremor/ataxia (FXTAS)
56-200 = premutation; maternally only
at risk for POI, FXTAS
if female, at risk for kids with FraX
230+ = affected

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22
Q

mitigating factor in CGG repeats in FraX

A

AGG repeats every 10 or so repeats - helps prevent slippage (FMR1 promoter region)

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23
Q

FraX mechanism

A

expansion of CGG (mitigated by AGG every 10 or so)
increased methylation of CpG
turning off tx of FMRP = fraX protein

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24
Q

Huntington - mechanism?

A 
CAG repeats (glutamine)
within HTT (huntingtin gene) - within exon
expand paternally

mechanism of toxicity not understood; potentially glutamine can aggregate in neurons

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25
Q

Huntington - repeat cutoffs

A 
27-35 = at risk for child with HD
36-39 = reduced penetrance alleles
40+ = full penetrance

^ repeat length –> lower age at onset, but hard to predict

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26
Q

myotonic dystrophy - mechanism?

A

repeat expansion in 3’ UTR (polyglutamine)
loss of RNA processing factors
50+ repeats = pathogenic

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27
Q

polyglutamine repeat disorders (2)

A

Spino-Cerebellar Ataxia (SCA)

Huntington

28
Q

Friedrich Ataxia - mechanism?

A

trinucleotide repeat disorder
RECESSIVE

gene: FXN / GAA repeat

29
Q

sensitivity
specificity
PPV
NPV

analytic validity
clinical validity
clinical utility

A

Disease Disease
+ -
Test + – PPV CLINICAL VALIDITY
Test - – NPV + penetr + heterog
| |
sensitivity specificity

          ANALYTIC VALIDITY

clinical validity is PPV/NPV, the pentrance of condition, and whether it’s genetically heterogeneous: ability to predict phenotype based on test

analytic validity is sensitivity/specificity for mutation(s) of interest

clinical utility: if know genotype, how useful is it for patient care?

30
Q

analytic validity
clinical validity
clinical utility

A

analytic validity –> is mutation there?
clinical validity –> predict pheno?
clinical utility –> useful to patient if know mutation?

31
Q

CLIA

A

Clinical Laboratory Improvement Amendments

  • equipment
  • turn around time
  • personnel
  • validation
  • regular quality control
  • interpretation !!
  • comments on patient-specific results

outside US and research labs – not CLIA-certified

32
Q

HexA - purpose

A

HexA enzyme is defective in Tay-Sachs.

Ashkenazi population has founder mutation(s?). Thus, DNA testing will pick it up 97% of time.

If person is non-AJ, may beed to do HexA enzyme testing, instead.

33
Q

FraX – preferred test?

A

Southern Blot – because can visualize BIG del/dups

34
Q

frequent/recurrent mutations in e.g., CF, sickle cell – assess by which testing technique, frequently?

A

oligo binding assay

    • oligo to mutation binding
    • oligo to normal sequence binding
    • measure amount of bound DNA by ligating both oligos to addiitonal oligo. One of two will not ligate together properly. Then can assess differences in size between final oligos.
35
Q

histones wraps ? bp of DNA as part of nucleosome

A

histone = 146 bp of DNA = beads on a string

36
Q

nucleosome made up of —

A

146 bp of DNA,

2x ( H2A, H2B, H3, H4,) …. +H1

37
Q

what modifications are added to histones as part of gene regulation? Do these modifications increase or decrease transcription?

A

acetyl groups, or methyl groups are added to Lysines of histones

acetyl groups increase transcription, methyl groups can decrease it

38
Q

after beads -on-a-string, what is next level of DNA compaction? how wide is it?

A

fiber.

30 nm.

(each nucleosome is 11 nm)

39
Q

after 30 nm fiber, the next sized DNA coil structures are are –

A

300 nm extended chromatin coil,
followed by
700 nm condensed (ready for mitosis)

40
Q

3 checkpoints and what they monitor in Mitosis

A

G1/S - DNA integrity, cell size
G2/M - DNA synthesis/damage
M - spindle formation/attachment to kinetochore

41
Q

cyclins/cyclin-dependent kinases - function? mechanism?

A

regulate cell cycle.

  1. cyclins - made and destroyed
  2. cdks - active only when cyclins around

cycles of phosphorylation/dephosphorylation of proteins necessary for various stages of cell cycle

42
Q

tumor suppressor genes - mechanism?

A

regulate cell cycle

initiate apoptosis if errors

43
Q

crossing over occurs during __ phase of Meiosis __

A

Prophase I of Meiosis I (not metaphase!!)

44
Q

amino acid - parts?

A 
amino group (NH3)
carboxyl group (COOH)
central carbon
R group (H or bigger)
45
Q

characteristics of genetic code

A 
degenerate
non-overlapping
unambiguous e.g., AUG always met
universal
   -- minor variation in prokaryotes, and within MITOCHONDRIA!!! e.g., AGA/AGG = Arg in nuclear, but STOP in mitochondria.
46
Q

rRNA - significance, cytogenetic location

A

rRNA makes up the ribosomes (60S and 40S subunits)

located on short arms of acrocentric chromosomes

5S (subunit of ribo) rDNA is in tandem array on chr 1. (2,000 copies!)

47
Q

Translation initiation

A

small ribosomal subunit (40S) loaded with:

  • initiator t-RNA - met (distinct from other met tRNA)
  • GTP
  • initiation factors (eIFs) – can also act as helicases

complex binds 5’ cap of mRNA, scans till AUG codon

@AUG, eIFs leave/ large 60S subunit binds - ready for protein synthesis.

48
Q

Translation - what happens at EPA sites?

A

A - “charged” tRNA enters with amino acid
P - existing aa – forms peptide bond with aa at A site, as everything shifts toward E
E - exit site - “uncharged” tRNA (with its aa detached) sits

49
Q

is there a start tRNA? is there a stop tRNA?

A

yes start - met tRNA - it’s specific to start, and initiates translation

no stop tRNA - instead, a “release factor” goes into A site, and releases nacent polypeptide chain

50
Q

non-sense mediated decay - function? mechanism?

A

degrades prematurely truncated proteins due to non-sense mutation (premature stop codon)

exon junction complexes (EJC) remain on mRNA after splicing out introns. typically, ribo comes across a few before reaching stop. yet if there is premature stop, a part of the ribo contacts the next EJC, and unleashes a clipping of the 5’ cap, thus leading to degradation of the mRNA.

51
Q

purpose/structure of cap of mRNA

A

methyl group
GMP (via 5’ - 5’ bond; unusual)
phosphate group removal

function:
to mark mRNA as “eukaryotic” vs prokaryotic
stability
recruitment/transport to ribosome

52
Q

function of 2’ hydroxyl (OH) group of RNA is –

function of 3’ OH, later –

(vs DNA is de-oxy…)

A

used during splicing of introns

splicing is via TWO consecutive transesterification reactions

  1. 2’ OH of conserved A on intron attacks 3’ end of left exon (exon junction) –> this forms lariat
  2. 3’ OH of this left exon then attacks 5’ end of right exon
  3. Exon Junction Complex (EJC) marks splice site as “complete”
53
Q

CFTR - what is splicing-related mechanism, and how does it modify CF/symptom severity?

A

exon 9 splicing depends on length of U prior to it. Can have 7xU, 9xU, or 5xU. If have 5 U’s (aka 5T), this exon likely to be skipped and gives non-functional CFTR protein.

5T prevalence is 10%.

Alone, unlikely to cause disease, but if homozygous can cause male infertility. In combination with mild CF mutation, can act as severe mutation. 5T in combination with severe mutation may have CF symptoms.

54
Q

alternative way of producing shorter protein, other than gene splicing

A

substitution editing (!!)

C–>U change ONLY in the RNA that produces a premature stop codon. Can be specific to organ system. e.g., ApoB is shorter in gut, vs liver.

A–> I (inosine, deaminated): I is read as G. – happens to 1,000 genes!

55
Q

3’ processing

A

cleavage of some RNA off the end

capped by PAB protein –> signals “maturity” of mRNA

56
Q

chance of a complex disease in a first degree relative = (rule of thumb)

risk to third degree relatives?

A

square root of population frequency

e.g., schizophrenia is 1% prevalence
thus, risk to FDR is sq rt (0.01) = 0.10 = 10%

which is true. Risk to FDRs for sz is 10-15%.

third degree relatives =~ population risk

57
Q

3 factors that affect complex disease risk in a family

A
  1. age-at-onset (earlier than average?)
  2. less commonly-affected sex (females are less commonly affected than males)
  3. severity of condition
58
Q

Cornelia de Lange - prevalence, features

A

CNS, facial (synophris) + arched, limb/bone defects, microcephaly, diaphragmatic hernia on ultrasound, GERD, short neck, cystic hygroma, low posterior hairline, hypertrichosis, long philtrum, thin upper lip, downturned corners, midface hypoplasia, 20% cleft palate, cryptorchidism, cesicoureteral reflux, micropenis, hearing loss, myopia, LONG eyelashes, LIMB ABNORMALITIES

check for: heart defects, gastrointestinal abnormalities

NIPTBL - chr5q - majority
SMC1A - X
SMC3 - chr10

almost 100% de novo; autosomal dominant

male to female ratio 1:1.3

59
Q

McCune Albright - features, inheritance

A
  • -one-sided cafe au lait spots, with ragged edges (vs smooth like in NF1)
  • -fibrous dysplasia of bones, – many bone fractures
  • –osteomas (1%)
  • -endocrine features (thyroid)

due to somatic MOSAICISM, thus NOT INHERITED

60
Q

Rett syndrome - features, inheritance

A
  • almost exclusively affects girls, 1 in 12,000
  • HAND-WRINGING/hands-to-mouth
  • autism-like (social/emotional)
  • random grimace/facial exressions
  • inconsolable crying
  • bouts of pain
  • REGRESSION at ~18 months
  • seizures (80%)
  • microcephaly
  • breath holding
  • absent speech

often confused with Angleman, autism

MECP2 gene, X-linked, 95% de novo!!

61
Q

Bardet-Biedl syndrome

A

rare 1 in 140,000

polydactyly
obesity
retinitis pigmentosa (one of first symptoms, in childhood)
hypogonadism
renal failre
intellectual disability

14 genes - BBS10
autosomal recessive

62
Q

derive heritability from disease concordance rates of MZ and DZ twins, if
MZ = 0.40
DZ = 0.25

A

Heritability = TWICE the difference of concordances

MZ=0.40
DZ=0.25
Heritability = (0.4-0.25)2 = 0.152 = 0.30 = 30%

63
Q

heritability definition

A

portion of phenotypic variability that is attributed to genetics

e.g., phenotypic variability is 100
and genetic variance is 40
then heritability is 0.40 (40/100)

64
Q

LD is NOT important in assessing linkage studies, but IS important for assessing association studies (T/F)

A

True. LD is NOT important in assessing linkage studies, but IS important for assessing association studies

Thus stuff like population substructure, admixture, etc, only influences association, but not linkage.

If find linkage signal, but NO association, maybe the linked marker is NOT in LD with the true locus. It can still be co-inherited, but it won’t be associated on a GWAS.

65
Q

family studies good for –

A

estimating heritability

66
Q

if marker is 3 cM from disease locus, and person does NOT inherit marker – chance of having inherited the disease locus (and thus having had a recombination event between locus and marker)?

A

0-3%

Mitosis/Meiosis - ugh (2 decks)

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