USMLE Step 1: Biochemistry & other

• Hydroxyurea: inhibits ribonucleotide reductase
• 6-mercaptopurine: blocks de novo purine synthesis
• 5-fluorouracil: inhibits thymidylate synthase (dTMP decreased)
• Methotrexate: inhibits dihydrofolate reductase (dTMP decreased)
• Trimethoprim: inhibits bacterial dihydrofolate reductase (dTMP decreased)

1. Inability to convert orotic acid to UMP
   1. due to defect in either orotic acid phosphoribosyltransferase or orotidine 5'-phosphate decarboxylase
   2. autosomal recessive
2. Findings
   1. increased orotic acid in urine
   2. megaloblastic anemia
   3. failure to thrive
   4. No hyperammonemia
3. Treament: oral uridine administration

• Adenosine deaminase deficiency
  • excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase –> prevents DNA synthesis and thus decreases lymphocyte count –> SCID (severe comined immunodeficiency disease)
• Lesch-Nyhan syndrome
  • absence of HGPRT –> excess of uric acid production & de novo purine synthesis
  • findings: retardation, self-mutilation aggression, hyperuricemia, gout, choreoathetosis
  • x-linked recessive

• Silent: same aa, often base change in 3rd position of codon
• Missense: changed aa (conservative - new aa is similar in chemical structure)
• Nonsense: change resulting in early stop codon (UAA, UGA, UAG)
• Frame shift: change resulting in misreading of all nucleotides downstream, usually resulting in a truncated, nonfunctional protein

1. Unwinds DNA template at replication fork
2. Create a nick in the helix to relieve supercoils created during replication
3. Makes an RNA primer on which DNA ppolymerase III can initiate replication
4. Prokaryotic only. Degrades RNA primer and fills in the gap with DNA
5. Prokaryotic only. Has 5' –> 30 synthesis and proofreads with 3' –> 5' exonuclease
6. Seals
7. Enzyme adds DNA to 3' ends of chromosomes to avoid loss of genetic material with every duplication

• Nucleotide exicision repair: mutated in xeroderma pigmentosum
  • specific endonucleases release the oligonucleotide-containing damaged bases
  • DNA polymerase and ligase fill and reseal the gap, respectively
• Base excision repair:
  • specific glycosylases recognize and remove damaged bases
  • AP endonuclease cuts DNA at apyrimidinic site
  • empty sugar is removed
  • gap is filled and resealed
• Mismatch repair: mutated in HNPCC
  • Unmethylated, newly synthesized string is recognized
  • mismatched nucleotides are removed
  • gap is filled and resealed

• Nonhomologous end joining: mutated in ataxia telangiectasia
  • brings together 2 ends of DNA fragments
  • no requirements for homology

1. AUG
   • Eukaryotes: codes for methionine
   • Prokaryotes: codes for formyl-methionine
2. UGA, UAG, UAA

1. Eukaryotes
   • RNA polymerase I makes rRNA
   • RNA polymerase II makes mRNA (opens DNA at promoter site); alpha-amanitin (death cap mushrooms) inhibits RNA polymerase II –> liver failure
   • RNA polymerase III makes tRNA
   • No proofreading function, but can initiate chains
2. Prokaryotes
   • 1 RNA polymerase (multisubunit complex) makes all 3 kinds of RNA

1. Capping on 5' end (addition of 7-methylguanosine occurs in cytosol)
2. Polyadenylation on 3' end (ca. 200 A's)
3. Splicing out of introns

       = mRNA

Lupus

when active, E. coli can metabolize lactose

• Lactose inhibits the repressor
• Glucose inhibits the activator

1. Structure
   • 75-90 nucleotides
   • secondary structure, cloverleaf form
   • anticodon end is opposite 3' aminoacyl end
   • all tRNAs have CCA at 3' end
   • aa is covalently bound to the 3' end of the tRNA
2. Charging
   • Aminoacly-tRNA synthetase (1 per aa, uses ATP)
   • aa-tRNA bond has energy for formation of peptide bond
   • a mischarged tRNA reads usual codon but inserts wrong amino acid

Tetracyclines bind 30S subunit, preventing attachment of aminoacyl-tRNA

1. Initiation
   • Activated by GTP hydrolysis
   • initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA
   • Ribosom: eukaryotes (40S + 60S –> 80S), prokaryotes (30S + 50S –> 70S)
   • ATP –> charging of tRNA; GTP –> tRNA gripping
2. Elongation
   1. Aminoacyl-tRNA binds to A site
   2. Ribosomal rRNA catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site
   3. Ribosome advances 3 nucleotides toward 3' end of RNA, moving peptidyl RNA to P site
3. Termination
   • Stop codon ist recognized by release factor, and completed protein is released from ribosome

• Aminoglycosides: binds 30S and inhibit formation of the initiation cpmplex and cause misreading of mRNA
• Chloramphenicol inhibits 50S peptidyltransferase
• Macrolides block translocation
• Clindamycin and chloramphenicol block peptide bond formation

• Trimming: removal of N- or C-terminal propeptides from zymogens to generate mature proteins
• Covalent alterations: phosphorylation, glycosylation, and hydroxylation
• Proteasomal degradation: attachment of ubiquitin to defective proteins to tag them for breakdown

1. Picture
2. Regulation
   • CDKs (Cyclin dependent kinases): constitutive and inactive
   • Cyclins: Regulatory proteins that control cell cycle events; phase specific; activate CDKs
   • Cyclin-CDK complexes: Must be both activated and inactivated for cell cycle to progress
   • Tumor suppressors: Rb and p53 normally inhibit G₁ to S progression; mutations in these genes result in unrestrained growth

• Permanent: remain in G₀, regenerate from stem cells.
  • Neurons, skeletal and cardiac muscle, RBCs
• Stable: enter G₁ from G₀ when stimulated.
  • Hepatocytes, lymphocytes
• Labile: never go to G₀, divide rapidly with a short G₁
  • _{Bone marrow, gut epithelium, skin, hair follicles}

• Site of synthesis of secretory proteins and of N-linked oligosaccharide addition to many proteins
• Nissl bodies (RER in neurons) synthesize enzymes and peptide neurotransmitters
• Mucus-secreting goblet cells of the small intestine and antibody-secreting plasma cells are rich in RER

• Site of steroid synthesis and detoxification of drugs and poisons
• Liver hepatocytes and steroid hormone-producing cells of the adrenal cortex are rich in SER

1. Golgi = distribution center
   • modifies N-oligosaccharides on asparagine
   • adds O-oligosaccharides on serine and threonine
   • adds mannose-6-P to proteins for trafficking to lysosomes
2.  
   • COP1: retrograde, Golgi –> ER
   • COP2: anterograde, RER –> cis-Golgi
   • Clathrin: trans-Golgi –> lysosomes, plasma membrane –> endosomes

• inherited lysosomal storage disorder
• failure of addition of mannose-6-P to lysosome proteins
• coarse facial features, clouded corneas, restricted joint movement, high plasma levels of lysosomal enzymes
• often fatal in childhood

membrane-enclosed organelle involved in catabolism of very long fatty acids and amino acids

Barrel-shaped protein complex that degrades damaged or unnecessary proteins tagged for destruction with ubiquitin

• Cylindrical structure composed of a helical array of polymerized dimers of alpha- & beta-tubulin
• Each dimer has 2 GTP bound
• involved in slow axoplasmatic transport in neurons
• Dynein: retrograde to microtubule (+ –> -)
• Kinesin: anterograde to microtubule (- –> +)

1. Mebendazole/thiabendazole (antihelminthic)
2. Griseofulvin (antifungal)
3. Vincristine/vinblastine (anti-cancer)
4. Paclitaxel (anti-breast cancer)
5. Colchicine (anti-gout)

• microtubule polymerization defect resulting in decreased fusion of phagosomes and lysosomes
• recurrent pyogenic infections, partial albinism, peripheral neuropathy

• 9+2 arrangement of microtubules
• Axonemal dynein-ATPase that links peripheral 9 doublets

• immotile cilia due to a dynein arm defect
• male & female infertility
• bronchiectasis, recurrent sinusitis
• associated with situs inversus

• asymmetric lipid bilayer
• contains cholesterol (ca. 50%), phospholipids (ca. 50%), sphingolipids, gylcolipids and proteins.
• high cholesterol or long saturated fatty acid content –> increased melting temperature, decreased fluidity

1. Vimentin
2. Desmin
3. Cytokeratin
4. GFAP
5. Neurofilaments

• Na⁺-K⁺ ATPase is located in the plasma membrane with ATP site on cytoplasmic side
• for each ATP consumed 3 Na⁺ go out and 2 K⁺ come in
• during cycle, pump is phosphorylated

1. inhibts by binding to K+ site
2. directly inhibits the Na⁺-K⁺ ATPase, which leads to indirect inhibition of Na⁺/Ca²⁺ exchange

1. Type I (90%): bone, skin, tendon, dentin, fascia, cornea, late wound repair
2. Type II: cartilage, vitreous body. nucleus pulposus
3. Type III (reticulin): skin, blood vessels, uterus, fetal tissue, granulation tissue
4. Type IV: basement membrane or basal lamina