Biochem

Question 1

Which is active: Heterochromatin or Euchromatin?

Answer 1

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

Activated into Euchromatin by Histone Acetylation

Question 2

Which bases are methylated in DNA replication and why

Answer 2

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

Note: Dna methylation at CpG islands = repress transcription

Question 3

Cytosine to Uracil via

Answer 3

Deamination

Question 4

Carbamoyl Phosphate is involved in 2 cycles

Answer 4

Urea Cycle

Pyrimidine synthesis

Question 5

5-FU

6-Mercaptopurine

Answer 5

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

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

Question 6

Ribonucleotide reductase blocker and Dihydrofolate REductase

Answer 6

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

Question 7

Adenosine Deaminase def

Answer 7

SCID

Can’t make DNA = decreased lymphocyte count

Question 8

Lesch Nyhan: Purine or Pyrimidine?

Answer 8

Defective PURINE SALVAGE pathway b/c no HGPRT

Question 9

Ribose-5-P —–>PRPP

Answer 9

enzyme: PRPP Synthetase (phosphoribosyl pyrophosphate)

–>De novo Purine and pyrimidine synthesis

Question 10

Features of Genetic Code

Answer 10

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

Question 11

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

Answer 11

Topoisomerase (includes Gyrase)

inihibited by fluoroquinolones

Question 12

DNA Pol I vs DNA Pol III

Answer 12

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.

Question 13

Dna Ligase

Answer 13

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

Question 14

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

Answer 14

Telomerase (not reverse transcriptase son even though same activity)

Question 15

Leading/lagging strand synth relative to replication fork

Answer 15

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

Question 16

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

Answer 16

Frameshift mutation i.e. Duchenne’s

Question 17

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

Answer 17

Genetic response to environmental change

Question 18

Lac Operon activity

Answer 18

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

Question 19

Whats the genetic problem in Ataxia Telangiectasia and Fanconi Anemia?

Answer 19

Problem in repair of ds-DNA

–>Nonhomologous End Joining (NHEJ)

Question 20

is mRNA read 5–>3 or 3–>5

Answer 20

5–>3

Question 21

RNA Pol 2 (mRNA)

Answer 21

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)

Question 22

Rifampin vs Actinomycin D RNA Polymerase inhibition

Answer 22

Rifampin: Prokaryotes only
Actinomycin D: Both P and E

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

Question 23

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

Answer 23

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

Question 24

Antibodies to spliceosomal snRNPs

Answer 24

Anti-Smith –>SLE

Question 25

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

Answer 25

DNA DUDE DNA DUE DNA DUDE absent in cDNA (mRNA --RTase -->cDNA)

Question 26

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

Answer 26

Chaperone protein

Question 27

PCR amplifies

Answer 27

DNA. Denature, Anneal, Elonagate

Question 28

Best measure of Gene expression (SNoW DRoP)

Answer 28

look at mRNA for gene expression!!! So Northern Blot

Question 29

Southwestern blot

Answer 29

DNA-binding proteins aka TRANSCRIPTION FACTORS So these proteins that can bind DNA = TF's, Steroid , Thyroid proteins, Vit D receptor, Retinoic Acid-R.

Question 30

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

Answer 30

Microarrays (DNA or RNA probes hybridized to chip)

Question 31

Southern blot: visualizes ____ DNA

Answer 31

Double stranded! Cleave-->Electrophoresis --> Denaturant -->Radiolabeled probe -->Anneal to complementary strand

Question 32

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

Answer 32

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

Question 33

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

Answer 33

Incomplete penetrance Variable expressivity

Question 34

Phenomenon seen in TUMOR SUPPRESSORS but not oncogenes

Answer 34

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

Question 35

Hardy Weinberg Caveat: X-linked niggas

Answer 35

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

Question 36

Angelman and Prader Wili. Imprinting does what?

Answer 36

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)

Question 37

No Male-->Male transmission

Answer 37

X-linked recessive (can skip generations)

Question 38

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

Answer 38

X-linked dominant

Question 39

Transfers CO2 groups with the help of _______ = Carboxylase

Answer 39

Biotin

Question 40

Require Thiamine as cofactor (deficient in alcoholics)

Answer 40

TRANSKETOLASE | Pyruvate Dehydrogenase, alpha-ketoglutarate Dehydroganse

Question 41

NAD+ | NADPH

Answer 41

NAD+ for catabolic process (carry reducing equiv away from NADH) NADPH = anabolic process (steroid/FA synth) as suppl of reducing equivalents

Question 42

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

Answer 42

NADPH

Question 43

Hexokinase/Glucokinase location

Answer 43

Hexo: Most tissues, except for liver and pancreas | Gluco: Liver, beta cells of pancreas glucose sensor for insulin

Question 44

Hexo/Gluco: Induced by insulin?

Answer 44

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

Question 45

Hexo/Gluco: affinity/capacity

Answer 45

Hexo: Lower Km=higher affinity. Lower Vmax = lower capacity Gluco: Higher Km=decreased affinity; Higher Vmax = higher capacity

Question 46

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

Answer 46

Hexo: Yes Gluco: NOOOOOO

Question 47

FBPase2 and PFK2 are bifunctional enzyme

Answer 47

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)

Question 48

Garlic breath/rice-water stools

Answer 48

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

Question 49

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

Answer 49

Lactate (via LDH) with byproduct of NAD+ Alanine (ALT)

Question 50

Lactic acidosis Neuro Deficits Increased alanine in infancy

Answer 50

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

Question 51

Cyanide blocks _____ transport

Answer 51

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

Question 52

How can aspirin cause fever after overdose?

Answer 52

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

Question 53

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) ```

Answer 53

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)

Question 54

HMP Shunt aka Pentose Phosphate Pathway: All in Cytoplasm

Answer 54

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

Question 55

Enzymes in HMP Shunt aka PPP

Answer 55

G6P DH; Transketolase (and phosphopentoseisomeras)

Question 56

What goes wrong in G6PD def

Answer 56

Glutathione needed to detoxify free radicals/peroxidase NADPH required to keep glutathione reduced and able G6PDH generates NADPH (from Glucose 6-P)

Question 57

Essential fructosuria vs fructose intolerance

Answer 57

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

Question 58

Galactokinase def vs Classic Galactosemia

Answer 58

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