DNA

Question 1

sequence repeated at telomeres

Answer 1

TTAGGG

Question 2

how long are telomeres?

Answer 2

10-15 kb

Question 3

kinetochore

Answer 3

Protein scaffold where spindle fibers attach

Question 4

primase

Answer 4

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

Question 5

telomerase extends the (leading/lagging?) strand

Answer 5

lagging (template)

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

Question 6

telomerase - how does it extend the lagging strand?

Answer 6

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

Question 7

replication on the lagging strand involves

Answer 7

primase (lays down primer)
polymerase
splicing
ligase

Question 8

what direction does DNA proofreading go?

Answer 8

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.

Question 9

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

Answer 9

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

Question 10

xeroderma pigmentosum – defect in what?

Answer 10

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

Question 11

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

Answer 11

Proofreading
Mismatch repair
Nucleotide excision repair
Base excision repair

Question 12

double strand break:

homologous can lead to –

Answer 12

translocation (wrong ends joined)

deletion/duplication (missing bp’s at joining)

Question 13

double strand break:

NON-homologous ?

Answer 13

“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

Question 14

BRCA - mechanism broken?

Answer 14

double strand break repair – homologous

Question 15

MUTYH - mechanism broken?

Answer 15

BASE excision repair

Question 16

Lynch - mechanism broken?

Answer 16

mismatch repair

Question 17

RISC -
stands for what?
function?

Answer 17

RNA-induced silencing complex

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

Question 18

carrier rate for Fragile X

Answer 18

1 in 150 females

Question 19

affected male rate for Fragile X

Answer 19

1 in 4,000

Question 20

what’s more common, Fragile X or Noonan?

Answer 20

Noonan is more than twice as common

FraX = 1 in 4,000

Question 21

FraX CGG repeat cutoffs

Answer 21

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

Question 22

mitigating factor in CGG repeats in FraX

Answer 22

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

Question 23

FraX mechanism

Answer 23

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

Question 24

Huntington - mechanism?

Answer 24

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

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

Question 25

Huntington - repeat cutoffs

Answer 25

``` 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

Question 26

myotonic dystrophy - mechanism?

Answer 26

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

Question 27

polyglutamine repeat disorders (2)

Answer 27

Spino-Cerebellar Ataxia (SCA) | Huntington

Question 28

Friedrich Ataxia - mechanism?

Answer 28

trinucleotide repeat disorder RECESSIVE gene: FXN / GAA repeat

Question 29

sensitivity specificity PPV NPV analytic validity clinical validity clinical utility

Answer 29

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?

Question 30

analytic validity clinical validity clinical utility

Answer 30

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

Question 31

CLIA

Answer 31

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

Question 32

HexA - purpose

Answer 32

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.

Question 33

FraX -- preferred test?

Answer 33

Southern Blot -- because can visualize BIG del/dups

Question 34

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

Answer 34

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.

Question 35

histones wraps ? bp of DNA as part of nucleosome

Answer 35

histone = 146 bp of DNA = beads on a string

Question 36

nucleosome made up of ---

Answer 36

146 bp of DNA, | 2x ( H2A, H2B, H3, H4,) .... +H1

Question 37

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

Answer 37

acetyl groups, or methyl groups are added to Lysines of histones acetyl groups increase transcription, methyl groups can decrease it

Question 38

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

Answer 38

fiber. 30 nm. (each nucleosome is 11 nm)

Question 39

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

Answer 39

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

Question 40

3 checkpoints and what they monitor in Mitosis

Answer 40

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

Question 41

cyclins/cyclin-dependent kinases - function? mechanism?

Answer 41

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

Question 42

tumor suppressor genes - mechanism?

Answer 42

regulate cell cycle | initiate apoptosis if errors

Question 43

crossing over occurs during __ phase of Meiosis __

Answer 43

Prophase I of Meiosis I (not metaphase!!)

Question 44

amino acid - parts?

Answer 44

``` amino group (NH3) carboxyl group (COOH) central carbon R group (H or bigger) ```

Question 45

characteristics of genetic code

Answer 45

``` 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. ```

Question 46

rRNA - significance, cytogenetic location

Answer 46

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!)

Question 47

Translation initiation

Answer 47

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.

Question 48

Translation - what happens at EPA sites?

Answer 48

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

Question 49

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

Answer 49

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

Question 50

non-sense mediated decay - function? mechanism?

Answer 50

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.

Question 51

purpose/structure of cap of mRNA

Answer 51

methyl group GMP (via 5' - 5' bond; unusual) phosphate group removal function: to mark mRNA as "eukaryotic" vs prokaryotic stability recruitment/transport to ribosome

Question 52

function of 2' hydroxyl (OH) group of RNA is -- function of 3' OH, later -- (vs DNA is de-oxy...)

Answer 52

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"

Question 53

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

Answer 53

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.

Question 54

alternative way of producing shorter protein, other than gene splicing

Answer 54

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!

Question 55

3' processing

Answer 55

cleavage of some RNA off the end | capped by PAB protein --> signals "maturity" of mRNA

Question 56

chance of a complex disease in a first degree relative = (rule of thumb) risk to third degree relatives?

Answer 56

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

Question 57

3 factors that affect complex disease risk in a family

Answer 57

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

Question 58

Cornelia de Lange - prevalence, features

Answer 58

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

Question 59

McCune Albright - features, inheritance

Answer 59

- -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

Question 60

Rett syndrome - features, inheritance

Answer 60

- 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!!

Question 61

Bardet-Biedl syndrome

Answer 61

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

Question 62

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

Answer 62

Heritability = TWICE the difference of concordances MZ=0.40 DZ=0.25 Heritability = (0.4-0.25)*2 = 0.15*2 = 0.30 = 30%

Question 63

heritability definition

Answer 63

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)

Question 64

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

Answer 64

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.

Question 65

family studies good for --

Answer 65

estimating heritability

Question 66

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)?

Answer 66

0-3%