Biochem FA - p34-45 Molecular Flashcards
What gives DNA negative charge?
phosphate groups
What gives histones a positive charge?
lysine and arginine
Methylation within gene promoter (CpG islands) does what?
typically represses (silences) gene transcription
How does histone acetylation activate DNA?
Removal of histone’s ⊕ charge –> relaxed DNA coiling –> inc transcription.
where is the triphosphate on the nucleotide?
5’ end
Difference between purines and pyrimidines?
PURines (A,G)—2 rings. PYrimidines (C,U,T)—1 ring.
Difference between C-G bonds and A-T bonds?
G-C bond (3 H bonds) stronger than A-T bond (2 H bonds). IncG-C content –> Inc melting temperature of DNA. “C-G bonds are like Crazy Glue.”
Amino acids necessary for purine synthesis?
Glycine Aspartate Glutamine (Cats purr until they GAG):
uracil + ___?___ = thymine?
Methylation of uracil makes thymine
What rx (-) orotic acid formation (pyrimidine synthesis)?
Leflunomide: inhibits dihydroorotate dehydrogenase [stops Carbamoyl phosphate + Asp –> orotic acid]
Rx that inhibit dihydrofolate reductase (dec deoxythymidine monophosphate [dTMP]) in humans?
Methotrexate (MTX)
Same mech as MTX but in bacteria / protozoa?
trimethoprim (TMP) for bacteria, and pyrimethamine for protozoa
Mech of 5-florouracil (5-FU)?
form 5-F-dUMP, which inhibits thymidylate synthase (decdTMP)
Rx that inhibit de novo purine synthesis?
6-mercaptopurine (6-MP) and its prodrug azathioprine
Mech of Mycophenolate and ribavirin?
inhibit inosine monophosphate dehydrogenase
Rx that inhibits both purine and pyrimidine synthesis? mech of action?
Hydroxyurea: inhibits ribonucleotide reductase
Where are the locations of CPS (Carbamoyl phosphate synthase) I & II?
CPS1 = m1tochondria (urea cycle) CPS2 = cyTWOsol
Rxs that inhibits Pyrimidine synthesis?
Leflunomide
Methotrexate (MTX), trimethoprim (TMP), and pyrimethamine
5-florouracil (5-FU) and its prodrug capecitabin
Rxs that inhibit Purine synthesis?
6-mercaptopurine (6-MP) and its prodrug azathioprine
Mycophenolate and ribavirin: inhibit inosine monophosphate dehydrogenase
Major cause of autosomal recessive SCID?
Adenosine deaminase deficiency
def of adenosine deaminase causes an issue with our immune system why?
The enzyme is used in purine salvage pathways to break down adenosine and dATP. Increased dATP = lymphotoxicity
deficiency of HGPRT leads to excess what?
uric acid production and de novo purine synthesis?
HGPRT def seen in what patient population? why?
male babies - bc it’s x linked recessive
Symptoms of HGPRT def?
Hyperuricemia Gout Pissed off (aggression, self-mutilation) Retardation (intellectual disability) DysTonia
Reaction catalyzed by HGPRT?
converts hypoxanthine to IMP and guanine to GMP
Mechanism of action of allopurinol? give another rx with same mech?
Competitive inhibitor of xanthine oxidase –> decconversion of hypoxanthine and xanthine to urate.
2nd line rx - Febuxostat
Sign of hyperuricemia in babies?
(orange “sand” [sodium urate crystals] in diaper
Which rx working on rasburicase will increase uric acid in urine/decrease it?
Probenecid stimulates rasburicase, thereby increasing uric acid in urine, Aspirin inhibits it
Another use of allopurinol other than gout?
used in leukemia/lymphoma to prevent tumor lysis syndrome
SE// of allopurinol/febuxostat
- Added toxicity with Azathioprine/6-mercaptopurine bc they are metabolized by xanthine oxidase
- DRESS symptoms (Drug Reaction with Eosinophilia and systemic symptoms - 2-8 wks post admin: fever, morbilliform rash, HS-IV rxn)
- Cutaneous small vessel vasculitis (7-10 d after = palpable purpura)
- Steven Johnson syndrome
SE// of probenecid
- can lead to uric acid calculi. (kidney stones)
- Is a Sulfa drug (DRESS sx, allergic rxn, Steven Johnson, etc)
Which two amino acids are coded by only one codon? What are their codons?
methionine (AUG) and tryptophan (UGG) encoded by only 1 codon.
UGG - I’m so full. Tryptophan, thanksgiving, yaadah yaadah
Which nucleotides are seen in origins of replication and promotors?
AT-rich sequences (such as TATA box regions) are found in promoters and origins of replication
what enzyme of DNA replication is deficient in Bloom syndrome?
Helicase.
Inhibitors of topoisomerases in eukaryotes?
In eukaryotes: irinotecan/topotecan inhibit topoisomerase (TOP) I, etoposide/teniposide inhibit TOP II.
inhibitors of topoisomerases in prokaryotes?
In prokaryotes: fluoroquinolones inhibit TOP II (DNA gyrase) and TOP IV.
Function of DNA polymerase I and III in prokaryotes?
DNA polymerase III has 5′ –> 3′ synthesis and proofreads with 3′ –> 5′ exonuclease, DNA polymerase I does the same thing + it cuts out the RNA primer with at 5’ –>3’ exonuclease
What sequence of nucleotides does telomerase add?
TTAGGG
Telomerase TAGs for Greatness and Glory.
Of all the DNA mutations - list in order from least damage to worst?
silent «_space;missense < nonsense < frameshift.
What’s a missense mutation? Example?
Nucleotide substitution resulting in changed amino acid (called conservative if new amino acid is similar in chemical structure).
Ex/ sickle cell disease (substitution of glutamic acid with valine).
Nonsense mutation? ex?
Nucleotide substitution resulting in early stop codon. Usually results in nonfunctional protein
ex/Duchenne Musc dystrophy (more often frameshift in a Q)
List the stop codons
UAG, UAA, UGA
U Are Gone
U Are Away
U Go Away
What’s a frameshift mutation? Ex?
Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream. Protein may be shorter or longer, and its function may be disrupted or altered.
Ex/
Duchenne & Becker muscular dystrophy, Tay-Sachs disease.
Ex of splice site mutation?
rare causes of cancers, dementia, epilepsy, some types of β-thalassemia.
What causes the lac operon to be turned on?
Glucose is the preferred metabolic substrate in E coli, but when glucose is absent and lactose is available, the lac operon is activated to switch to lactose metabolism.
How does the lac operon work?
Low glucose –> Incadenylate cyclase activity –> Inc generation of cAMP from ATP –>activation of catabolite activator protein (CAP) –> Inc transcription.
High lactose –>unbinds repressor protein from repressor/operator site –> Inctranscription.
When does nucleotide excision repair occur?
G1 phase of cell cycle
Which disease has defects in nucleotide excision repair? What does it have issues repairing?
Xeroderma pigmentosum, can’t repair DNA pyrimidine dimers caused by UV exposure
When does mismatch repair occur?
S phase of cell cycle
What disease is mismatch repair defective?
Lynch syndrome
Disease that has issues repairing double stranded breaks?
Ataxia telangiectasia
Which disease has issues fixing homologous DNA breaks?
Breast/ovarian cancer with BRCA1
Fanconi anemia
Prokaryotic start codon codes for? What does it cause in humans?
AUG codes for N-formylmethionine - stimulates neutrophil chemotaxis
Where does mRNA quality control occur?
cytoplasmic processing bodies - P bodies
Function of RNA polymerase I, II, III?
- RNA polymerase I makes rRNA, the most common (rampant) type; present only in nucleolus.
- RNA polymerase II makes mRNA (largest RNA, massive) and small nuclear RNA (snRNA). RNA polymerase II opens DNA at promoter site.
- RNA polymerase III makes 5S rRNA, tRNA (smallest RNA, tiny). No proofreading function, but can initiate chains.
Toxin that (-) RNA polymerase II
α-amanitin, found in Amanita phalloides (death cap mushrooms), inhibits RNA polymerase II.
(-) RNA polymerase in both prokaryotes and eukaroyotes?
Actinomycin D, also known as dactinomycin, inhibits RNA polymerase in both prokaryotes and eukaryotes.
what drug inhibits DNA dependent RNA polymerase in prokaryotes?
Rifampin
what is a microRNA?
MicroRNAs (miRNAs) are small, noncoding RNA molecules that posttranscriptionally regulate gene expression by targeting the 3′ untranslated region of specific mRNAs for degradation or translational repression
What nucleotides are at the 3’ end of tRNA ?
CCA - (5’-CCA-3’ is the amino acid acceptor site)
What is the T arm?
On tRNA, contains the TΨC (ribothymidine, pseudouridine, cytidine) sequence necessary for tRNAribosome binding. T-arm Tethers tRNA molecule to ribosome
What is the D arm?
contains Dihydrouridine residues necessary for tRNA recognition by the correct aminoacyltRNA synthetase.
D-arm Detects the tRNA by aminoacyl-tRNA synthetase
function of aminoacyl-tRNA synthase?
Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for the accuracy of amino acid selection.
Aminoacyl-tRNA synthetase matches an amino acid to the tRNA by scrutinizing the amino acid before and after it binds to tRNA. If an incorrect amino acid is attached, the bond is hydrolyzed.
What happens if a tRNA is mischarged?
A mischarged tRNA reads the usual codon but inserts the wrong amino acid.
List ribosomal subunits in eukaryotes and prokaryotes?
Eukaryotes: 40S + 60S –> 80S (Even)
Prokaryotes: 30S + 50S –> 70S (Prime)
Where does the energy for tRNA function come from?
ATP—tRNA Activation (charging).
GTP—tRNA Gripping and Going places (translocation).
List the active sites on tRNA?
A site = incoming Aminoacyl-tRNA.
P site = accommodates growing Peptide.
E site = holds Empty tRNA as it Exits.
Most amino acyl-tRNA binds to A site, except?
Aminoacyl-tRNA binds to A site - except for initiator methionine, which binds the P site
How is translation stopped?
Eukaryotic release factors (eRFs) recognize the stop codon and halt translation –> completed polypeptide is released from ribosome. Requires GTP.
Sx of Fanconi anemia
Short stature, café-au-lait spots, thumb/radial defects, incidence of tumors/leukemia, aplastic anemia
hnRNA is what?
Initial transcript is called heterogeneous nuclear RNA (hnRNA). hnRNA is then modified and becomes mRNA
