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Biochem Flashcards

1
Q

Which is active: Heterochromatin or Euchromatin?

A

Heterochromatin –> this is what a Barr Body is
–>More condensed = transcriptionally inactive

Activated into Euchromatin by Histone Acetylation

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2
Q

Which bases are methylated in DNA replication and why

A

Adenosine and Cytosine
allows mismatch repair enzymes to distinguish old from new

Note: Dna methylation at CpG islands = repress transcription

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3
Q

Cytosine to Uracil via

A

Deamination

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4
Q

Carbamoyl Phosphate is involved in 2 cycles

A

Urea Cycle

Pyrimidine synthesis

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5
Q

5-FU

6-Mercaptopurine

A

5-FU blocks Thymidylate Synthase (Fuck Fresh Thyme) = can’t make T (Pyridmidine)

6-MP blocks Purine Synthesis (blocks PRPP–>IMP–>AMP and GMP).

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6
Q

Ribonucleotide reductase blocker and Dihydrofolate REductase

A

RR: Hydroxyurea (can’t make pyrimidines)
DHFR: Methotrexate/Trimethoprim (can’t make T)

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7
Q

Adenosine Deaminase def

A

SCID

Can’t make DNA = decreased lymphocyte count

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8
Q

Lesch Nyhan: Purine or Pyrimidine?

A

Defective PURINE SALVAGE pathway b/c no HGPRT

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9
Q

Ribose-5-P —–>PRPP

A

enzyme: PRPP Synthetase (phosphoribosyl pyrophosphate)

–>De novo Purine and pyrimidine synthesis

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10
Q

Features of Genetic Code

A

Unabmbiguous (each codon only 1 aa)
Degenerate (1 aa coded by multiple codons)
No commas/overlap
Universal (conserved through evolution EXCEPT mito)

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11
Q

Create single or double stranded break in the helix to add/remove supercoils

A

Topoisomerase (includes Gyrase)

inihibited by fluoroquinolones

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12
Q

DNA Pol I vs DNA Pol III

A

Both are Prokaryotic
Pol 1: Degrades RNA primer, so has unique 5’->3’ Exonuclease activity (only 1 polymerase can take out rna primer)

Pol 3: elongates leading and lagging strand. has 3’->5’ proofreading activity.

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13
Q

Dna Ligase

A

phosphodiester bonds –> joins the Okazaki fragments (so the the 2 daughter strands i.e. leading and lagging will differ MOST in LIGASE activity)

also repairs ss breaks in dsDNA

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14
Q

RNA-dependent DNA polymerase found only in Eukaryotes, adds DNA at 3’ endto avoid loss of gnetic material

A

Telomerase (not reverse transcriptase son even though same activity)

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15
Q

Leading/lagging strand synth relative to replication fork

A

Leading: synth continuously toward replication fork
Lagging: the 5’ is next the rep fork so grows discontinously away from it

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16
Q

Deletion or insertion by # of nucleotides thats not divisible by 3

A

Frameshift mutation i.e. Duchenne’s

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17
Q

Lac operon = classic example of a _______ response to a ______ change

A

Genetic response to environmental change

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18
Q

Lac Operon activity

A

Glucose inhibits AC. when its absent, cAMP stimulates CAP to increase transcription on lac operon

High Lactose takes (unbinds) repressor protein away from the operator site = increase transcription

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19
Q

Whats the genetic problem in Ataxia Telangiectasia and Fanconi Anemia?

A

Problem in repair of ds-DNA

–>Nonhomologous End Joining (NHEJ)

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20
Q

is mRNA read 5–>3 or 3–>5

A

5–>3

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21
Q

RNA Pol 2 (mRNA)

A

Binds to Promotor (TATA)

“I RAN TWO the PROMOTION to buy a TATA BOX, but i couldn’t go because i had MUSHROOMS”

(amanitin/aminita phalloides inhibits RNA Pol 2)

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22
Q

Rifampin vs Actinomycin D RNA Polymerase inhibition

A

Rifampin: Prokaryotes only
Actinomycin D: Both P and E

Dactinomycin is a anti-tumor drug (DNA Intercalator) for childhood tumors (Ewing, Rhabdomyosarcoma, Wilms)

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23
Q

Initial transcript = heterogenous nuclear RNA (hnRNA). What are the post-transcriptional modifications that make it mRNA?

A
  1. 5’ cap (7-methylguanosine)
  2. 3’ Polyadenylation ( Poly A tail)–>no template req
  3. SPLICING introns

mRNA is transported out into the cytosol where it is translated

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24
Q

Antibodies to spliceosomal snRNPs

A

Anti-Smith –>SLE

25
Q

Introns are noncoding segments of ________ (DNA or RNA?) and absent in ______

A

DNA DUDE DNA DUE DNA DUDE

absent in cDNA (mRNA –RTase –>cDNA)

26
Q

Intracellular protein that helps/maintains protein folding i.e. heat shock preoteins expressed at high tepm to prevent protein denaturing

A

Chaperone protein

27
Q

PCR amplifies

A

DNA. Denature, Anneal, Elonagate

28
Q

Best measure of Gene expression (SNoW DRoP)

A

look at mRNA for gene expression!!!

So Northern Blot

29
Q

Southwestern blot

A

DNA-binding proteins aka TRANSCRIPTION FACTORS

So these proteins that can bind DNA = TF’s, Steroid , Thyroid proteins, Vit D receptor, Retinoic Acid-R.

30
Q

Used to assess single nucleotide polymorphisms (SNP) and copy number variants (CNV)
also
Used to profile gene expression levels of thousands of genes simultaneously

A

Microarrays (DNA or RNA probes hybridized to chip)

31
Q

Southern blot: visualizes ____ DNA

A

Double stranded!

Cleave–>Electrophoresis –> Denaturant –>Radiolabeled probe –>Anneal to complementary strand

32
Q

Used to detect specific antigen or antibody in patient’s blood sample

A

ELISA (she’s a private investigator looking for specific shit)
Direct: Antibody is added to detect antigen

33
Q

Not all people with mutant genotype show mutant phenotype i.e. BRCA mutation but not cancer

vs

Phenotype varies among two people with same genotype i.e. 2 ppl with NF2 with dif severity

A

Incomplete penetrance

Variable expressivity

34
Q

Phenomenon seen in TUMOR SUPPRESSORS but not oncogenes

A

Loss of heterozygosity (2 hit hypothesis i.e. RB. inherit one mutated allele, still need another mutated)

35
Q

Hardy Weinberg Caveat: X-linked niggas

A

In X linked disorder, fequency of the recessive allele is unique:
males = q
females = q^2

36
Q

Angelman and Prader Wili. Imprinting does what?

A

Imprinting = INACTIVATED by METHYLATION

So Prader Wili = Maternal Imprinting –> Maternal is not expressed.

  • ->Get disease when you inherit mutated/deleted gene
  • ->1/4 from maternal UDP (get 2 copies of maternally imprinted aka silenced genes)
37
Q

No Male–>Male transmission

A

X-linked recessive (can skip generations)

38
Q

Transmitted by both parents
Fathers: all daughters get it but no sons
Mothers: half of boys and girls get it

A

X-linked dominant

39
Q

Transfers CO2 groups with the help of _______ = Carboxylase

A

Biotin

40
Q

Require Thiamine as cofactor (deficient in alcoholics)

A

TRANSKETOLASE

Pyruvate Dehydrogenase, alpha-ketoglutarate Dehydroganse

41
Q

NAD+

NADPH

A

NAD+ for catabolic process (carry reducing equiv away from NADH)

NADPH = anabolic process (steroid/FA synth) as suppl of reducing equivalents

42
Q

Used in Anabolic processes, Cyt p450, Glutathione reductase, respiratory burst

A

NADPH

43
Q

Hexokinase/Glucokinase location

A

Hexo: Most tissues, except for liver and pancreas

Gluco: Liver, beta cells of pancreas
glucose sensor for insulin

44
Q

Hexo/Gluco: Induced by insulin?

A

Hexo: Nope
Gluco: YES –> its a glucose sensor for insulin

45
Q

Hexo/Gluco: affinity/capacity

A

Hexo: Lower Km=higher affinity. Lower Vmax = lower capacity

Gluco: Higher Km=decreased affinity; Higher Vmax = higher capacity

46
Q

Hexo/Gluco: Neg feedback by G-6-P

A

Hexo: Yes
Gluco: NOOOOOO

47
Q

FBPase2 and PFK2 are bifunctional enzyme

A

Fasting state: increase glucagon = increase cAMP/PKA:
FBPase2 –>fructose before phosphate (gluconeo)

Fed sate: increase insulin = decrease cAMP/PKA:
PFK2 –>Poop for kicks (glycolysis favored)

48
Q

Garlic breath/rice-water stools

A

Arsenic poisoning –> blocks Lipoic acid (one of the cofactors for Pyruvate DHase)

49
Q

Pyruvate Dehydrogenase deficiency (X-linked) causes Pyruvate to get shunts to production of ________ and _______

A

Lactate (via LDH) with byproduct of NAD+

Alanine (ALT)

50
Q

Lactic acidosis
Neuro Deficits
Increased alanine in infancy

A

Pyruvate Dehydrogenase Deficiency (cant do Pyruvate —>Acetyl CoA)

51
Q

Cyanide blocks _____ transport

A

electron transport (oxidative phosphorylation). Blocks Complex 4 (mito mem)

52
Q

How can aspirin cause fever after overdose?

A

it can work as Uncoupling agent (just like brown fat aka thermogenin) –> increase mem permeability. ATP synth stops but electron transport continues = heat

53
Q

These are irreversible enzymes for which process?

Pyruvate Carboxylase (biotin)  Pyruvate -->Oxaloacetate
PEP Carboxykinase        (req GTP)   oxalacetate -->PEP
F-1, 6, BPase                                        (citrate stimulates)
Glucose-6-Phosphatase                       (Endo reticulum)
A

Gluconeogenesis Irreversible Enzymes
(muscle cannot do gluconeo because lacks Glucose-6-phosphatase)

Odd chain FA can go to TCA and make glucose
Even chain FA can’t produce new glucose (only acetyl CoA equivalents)

54
Q

HMP Shunt aka Pentose Phosphate Pathway: All in Cytoplasm

A

Provides NADPH source from Glucose-6-P
–>needed for REDUCTION rxns (glutathione reduction in rbc, FA and cholesterol synth)

also makes ribose for nt synth

55
Q

Enzymes in HMP Shunt aka PPP

A

G6P DH; Transketolase (and phosphopentoseisomeras)

56
Q

What goes wrong in G6PD def

A

Glutathione needed to detoxify free radicals/peroxidase

NADPH required to keep glutathione reduced and able

G6PDH generates NADPH (from Glucose 6-P)

57
Q

Essential fructosuria vs fructose intolerance

A

Fructosuria : Fructokinase def

Fructose intolerance: Aldolase B def. this is more relevant. Hypoglycemia, jaundice, cirrhosis, vomiting

Urine dipstick - (only tests for glucose)

Fructose –Fructokinase–>F1P –Aldolase B–>Glycolysis

58
Q

Galactokinase def vs Classic Galactosemia

A

Cataracts from Galactitol from Galatokinase def (failure to track objects or develop a social smile)

Absent Galactose-1-P Uridyltransferase: cataracts, jaundice, hepatomegaly, E coli sepsis, avoid galactose and lactose (galactose + glucose)

Galactose–Galactokinase–>Gal1P–Uridyltransferase–>Glucose-1-P

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