Biochem Flashcards
Which is active: Heterochromatin or Euchromatin?
Heterochromatin –> this is what a Barr Body is
–>More condensed = transcriptionally inactive
Activated into Euchromatin by Histone Acetylation
Which bases are methylated in DNA replication and why
Adenosine and Cytosine
allows mismatch repair enzymes to distinguish old from new
Note: Dna methylation at CpG islands = repress transcription
Cytosine to Uracil via
Deamination
Carbamoyl Phosphate is involved in 2 cycles
Urea Cycle
Pyrimidine synthesis
5-FU
6-Mercaptopurine
5-FU blocks Thymidylate Synthase (Fuck Fresh Thyme) = can’t make T (Pyridmidine)
6-MP blocks Purine Synthesis (blocks PRPP–>IMP–>AMP and GMP).
Ribonucleotide reductase blocker and Dihydrofolate REductase
RR: Hydroxyurea (can’t make pyrimidines)
DHFR: Methotrexate/Trimethoprim (can’t make T)
Adenosine Deaminase def
SCID
Can’t make DNA = decreased lymphocyte count
Lesch Nyhan: Purine or Pyrimidine?
Defective PURINE SALVAGE pathway b/c no HGPRT
Ribose-5-P —–>PRPP
enzyme: PRPP Synthetase (phosphoribosyl pyrophosphate)
–>De novo Purine and pyrimidine synthesis
Features of Genetic Code
Unabmbiguous (each codon only 1 aa)
Degenerate (1 aa coded by multiple codons)
No commas/overlap
Universal (conserved through evolution EXCEPT mito)
Create single or double stranded break in the helix to add/remove supercoils
Topoisomerase (includes Gyrase)
inihibited by fluoroquinolones
DNA Pol I vs DNA Pol III
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.
Dna Ligase
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
RNA-dependent DNA polymerase found only in Eukaryotes, adds DNA at 3’ endto avoid loss of gnetic material
Telomerase (not reverse transcriptase son even though same activity)
Leading/lagging strand synth relative to replication fork
Leading: synth continuously toward replication fork
Lagging: the 5’ is next the rep fork so grows discontinously away from it
Deletion or insertion by # of nucleotides thats not divisible by 3
Frameshift mutation i.e. Duchenne’s
Lac operon = classic example of a _______ response to a ______ change
Genetic response to environmental change
Lac Operon activity
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
Whats the genetic problem in Ataxia Telangiectasia and Fanconi Anemia?
Problem in repair of ds-DNA
–>Nonhomologous End Joining (NHEJ)
is mRNA read 5–>3 or 3–>5
5–>3
RNA Pol 2 (mRNA)
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)
Rifampin vs Actinomycin D RNA Polymerase inhibition
Rifampin: Prokaryotes only
Actinomycin D: Both P and E
Dactinomycin is a anti-tumor drug (DNA Intercalator) for childhood tumors (Ewing, Rhabdomyosarcoma, Wilms)
Initial transcript = heterogenous nuclear RNA (hnRNA). What are the post-transcriptional modifications that make it mRNA?
- 5’ cap (7-methylguanosine)
- 3’ Polyadenylation ( Poly A tail)–>no template req
- SPLICING introns
mRNA is transported out into the cytosol where it is translated
Antibodies to spliceosomal snRNPs
Anti-Smith –>SLE
Introns are noncoding segments of ________ (DNA or RNA?) and absent in ______
DNA DUDE DNA DUE DNA DUDE
absent in cDNA (mRNA –RTase –>cDNA)
Intracellular protein that helps/maintains protein folding i.e. heat shock preoteins expressed at high tepm to prevent protein denaturing
Chaperone protein
PCR amplifies
DNA. Denature, Anneal, Elonagate
Best measure of Gene expression (SNoW DRoP)
look at mRNA for gene expression!!!
So Northern Blot
Southwestern blot
DNA-binding proteins aka TRANSCRIPTION FACTORS
So these proteins that can bind DNA = TF’s, Steroid , Thyroid proteins, Vit D receptor, Retinoic Acid-R.
Used to assess single nucleotide polymorphisms (SNP) and copy number variants (CNV)
also
Used to profile gene expression levels of thousands of genes simultaneously
Microarrays (DNA or RNA probes hybridized to chip)
Southern blot: visualizes ____ DNA
Double stranded!
Cleave–>Electrophoresis –> Denaturant –>Radiolabeled probe –>Anneal to complementary strand
Used to detect specific antigen or antibody in patient’s blood sample
ELISA (she’s a private investigator looking for specific shit)
Direct: Antibody is added to detect antigen
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
Incomplete penetrance
Variable expressivity
Phenomenon seen in TUMOR SUPPRESSORS but not oncogenes
Loss of heterozygosity (2 hit hypothesis i.e. RB. inherit one mutated allele, still need another mutated)
Hardy Weinberg Caveat: X-linked niggas
In X linked disorder, fequency of the recessive allele is unique:
males = q
females = q^2
Angelman and Prader Wili. Imprinting does what?
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)
No Male–>Male transmission
X-linked recessive (can skip generations)
Transmitted by both parents
Fathers: all daughters get it but no sons
Mothers: half of boys and girls get it
X-linked dominant
Transfers CO2 groups with the help of _______ = Carboxylase
Biotin
Require Thiamine as cofactor (deficient in alcoholics)
TRANSKETOLASE
Pyruvate Dehydrogenase, alpha-ketoglutarate Dehydroganse
NAD+
NADPH
NAD+ for catabolic process (carry reducing equiv away from NADH)
NADPH = anabolic process (steroid/FA synth) as suppl of reducing equivalents
Used in Anabolic processes, Cyt p450, Glutathione reductase, respiratory burst
NADPH
Hexokinase/Glucokinase location
Hexo: Most tissues, except for liver and pancreas
Gluco: Liver, beta cells of pancreas
glucose sensor for insulin
Hexo/Gluco: Induced by insulin?
Hexo: Nope
Gluco: YES –> its a glucose sensor for insulin
Hexo/Gluco: affinity/capacity
Hexo: Lower Km=higher affinity. Lower Vmax = lower capacity
Gluco: Higher Km=decreased affinity; Higher Vmax = higher capacity
Hexo/Gluco: Neg feedback by G-6-P
Hexo: Yes
Gluco: NOOOOOO
FBPase2 and PFK2 are bifunctional enzyme
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)
Garlic breath/rice-water stools
Arsenic poisoning –> blocks Lipoic acid (one of the cofactors for Pyruvate DHase)
Pyruvate Dehydrogenase deficiency (X-linked) causes Pyruvate to get shunts to production of ________ and _______
Lactate (via LDH) with byproduct of NAD+
Alanine (ALT)
Lactic acidosis
Neuro Deficits
Increased alanine in infancy
Pyruvate Dehydrogenase Deficiency (cant do Pyruvate —>Acetyl CoA)
Cyanide blocks _____ transport
electron transport (oxidative phosphorylation). Blocks Complex 4 (mito mem)
How can aspirin cause fever after overdose?
it can work as Uncoupling agent (just like brown fat aka thermogenin) –> increase mem permeability. ATP synth stops but electron transport continues = heat
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)
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)
HMP Shunt aka Pentose Phosphate Pathway: All in Cytoplasm
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
Enzymes in HMP Shunt aka PPP
G6P DH; Transketolase (and phosphopentoseisomeras)
What goes wrong in G6PD def
Glutathione needed to detoxify free radicals/peroxidase
NADPH required to keep glutathione reduced and able
G6PDH generates NADPH (from Glucose 6-P)
Essential fructosuria vs fructose intolerance
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
Galactokinase def vs Classic Galactosemia
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
