USMLE step 1 genetics

Editor-In-Chief: C. Michael Gibson, M.S., M.D. [1] Mahshid Mir, M.D. [2]

DNA synthesis

Histone → Contain lysine and arginine

DNA is negatively charged because of the negatively charged phosphate groups

Cytosine minus aminogroup = Uracil (Deamination)

G-C : 3 Hydrogen bonds. Higher melting points

A-T: 2 Bonds

Purine synthesis:

• You need glycine, glutamine and aspartate + tetrahydrofolate (Folic acid) + CO2
• Rate limiting step : Glutamine PRPP amidotransferase
• Carbon sources:
  • CO2, glycine, tetrahydrofolate
• Nitrogen sources
  • Aspartate + Glutamine

Pyrimidines:

Aspartate + carbamoyl phosphate (1 carbon and 1 nitrogen [glutamine]) + ATP

• Carbamoyl phosphate → Has 1 carbon and 1 nitrogen
• You need aspartate + CO2 + glutamine + ATP (Last 3 come from carbamoyl phosphate)
• Carbamoyl phosphate synthetase 2 (RATE LIMITING STEP)
• Start with orotic acid then add a base
• Carbon sources:
  • Aspartate
  • CO2
• Glutamine → Gives nitrogen

CPS 1 + CPS 2

• CPS 1
  • Mitochondria
  • Urea cycle
  • Use nitrogen from ammonia
• CPS 2
  • Cytosol
  • Pyrimidine synthesis
  • Use nitrogen from glutamine

Orotic aciduria

• Deficiency of UMP synthase
• AR
• Elevated oritic acid
• Megaloblastic anemia
  • Not corrected with B12 or folic acid
• No hyperammonemia
• Treat with uridine

Ornithine Transcarbomylase Deficiency

• Causes hyperammonemia
• Elevated orotic acid
• Problem with urea cycle

Ribosomes are synthesized in the nucleus and transported into the cytoplasm.

Ribosomes are made of proteins and rRNA

• Eukaryotes → 60 and 40s = 80s
• Prokaryotes → 50 s and 30 s = 70 s
  • Have 23s in 50s

Translation

• Initiation
  • IF1, IF2, If3
    • Assist in assembly of smaller ribosomal subunit to first trna molecule
    • Methionine is always the start
    • f-Methionine in prokaryotes
    • IF-2 first binds to 30s and then to methionine tRNA. Then when 50s comes along, it hydrolyzes GTP on IF2 and allows 50s to attach to 30s
  • A site → Incoming aminoacyl TRNA binds
  • P site → Polypeptide binds (Growing chain)
    • First tRNA binds here
  • E site → Free tRNA (exit)
• Elongation
  • Incoming charged aminoacyl TRNA binds to A site
  • Elongation factor help incoming trna to bind to A site (Uses GTP)
  • 50s has peptidyl transferase transfers AA from p site to A site
    • In prokaryotes, activity is in 23s subunit of 50s rRNA
  • Translocation
    • Ribosome complex moves 3 nucleotides
    • tRNA + Peptide is moved from A site to P site
    • Newly uncharged tRNA from P side to E side
    • EF-G  → Eukaryotes
    • EF-2 in eukaryotes
      • Diptheria and exotoxin (Pseudomonas) inhibit this
• Termination
  • Stop codons
    • UGA, UAA and UAG
    • Signal to STOP
    • No new TRNA coming
    • Release factor binds to MRNA and hydrolyzes GTP and new polypeptide is released.
• Antibiotics
  • Aminoglycosides → Inhibit 30s subunit before initiation (No pairing with TRNA)
  • Linezolid → Inhibits initiation by binding to 50s subunit
  • Tetracycline
    • Bind to 30s subunit
    • Prevent aminoacyl TRNA from binding to A site
  • Chloramphenicol
    • Inhibits peptidyl transferase
    • Binds to 50s
  • Macrolides
    • Inhibits translocation by binding to 50s subunit
  • Clindamycin
    • Same as macrolides
  • Lincamycin
    • Bind to 50s and inhibit translocation
  • Streptrogranin
    • Bind to 50s and inhibit translocation
  • Buy AT 30 ,CCELL at 50
• Post translational modification
  • Trim terminals
  • Covalent modification
    • Glycosylation, hydroxylation, phosphorylation
    • Collagen → Hydroxylation of proline and lysine
  • Disulfide bonds
  • Protein folding
    • Primary structure → Chain
    • Secondary structure → Beta and alpha pleated
    • Tertiary structure

Purine synthesis: You need glycine, glutamine and aspartate + tetrahydrofolate (Folic acid) + CO2 Rate limiting step : Glutamine PRPP amidotransferase Carbon sources: CO2, glycine, tetrahydrofolate Nitrogen sources Aspartate + Glutamine Pyrimidines: Aspartate + carbamoyl phosphate (1 carbon and 1 nitrogen [glutamine]) + ATP Carbamoyl phosphate → Has 1 carbon and 1 nitrogen You need aspartate + CO2 + glutamine + ATP (Last 3 come from carbamoyl phosphate) Carbamoyl phosphate synthetase 2 (RATE LIMITING STEP) Start with orotic acid then add a base Carbon sources: Aspartate CO2 Glutamine → Gives nitrogen CPS 1 + CPS 2 CPS 1 Mitochondria Urea cycle Use nitrogen from ammonia CPS 2 Cytosol Pyrimidine synthesis Use nitrogen from glutamine Orotic aciduria Deficiency of UMP synthase AR Elevated oritic acid Megaloblastic anemia Not corrected with B12 or folic acid No hyperammonemia Treat with uridine Ornithine Transcarbomylase Deficiency Causes hyperammonemia Elevated orotic acid Problem with urea cycle Dantrolene → Prevents release of calcium from SR of skeletal muscle Inhibit reuptake of norepinephrine: Cocaine TCA Ribosomes are synthesized in the nucleus and transported into the cytoplasm. Ribosomes are made of proteins and rRNA Eukaryotes → 60 and 40s = 80s Prokaryotes → 50 s and 30 s = 70 s Have 23s in 50s Translation Initiation

IF1, IF2, If3

Assist in assembly of smaller ribosomal subunit to first trna molecule Methionine is always the start f-Methionine in prokaryotes IF-2 first binds to 30s and then to methionine tRNA. Then when 50s comes along, it hydrolyzes GTP on IF2 and allows 50s to attach to 30s A site → Incoming aminoacyl TRNA binds P site → Polypeptide binds (Growing chain) First tRNA binds here E site → Free tRNA (exit) Elongation Incoming charged aminoacyl TRNA binds to A site Elongation factor help incoming trna to bind to A site (Uses GTP) 50s has peptidyl transferase transfers AA from p site to A site In prokaryotes, activity is in 23s subunit of 50s rRNA Translocation Ribosome complex moves 3 nucleotides tRNA + Peptide is moved from A site to P site Newly uncharged tRNA from P side to E side EF-G → Eukaryotes EF-2 in eukaryotes Diptheria and exotoxin (Pseudomonas) inhibit this Termination Stop codons UGA, UAA and UAG Signal to STOP No new TRNA coming Release factor binds to MRNA and hydrolyzes GTP and new polypeptide is released. Antibiotics Aminoglycosides → Inhibit 30s subunit before initiation (No pairing with TRNA) Linezolid → Inhibits initiation by binding to 50s subunit Tetracycline Bind to 30s subunit Prevent aminoacyl TRNA from binding to A site Chloramphenicol Inhibits peptidyl transferase Binds to 50s Macrolides Inhibits translocation by binding to 50s subunit Clindamycin Same as macrolides Lincamycin Bind to 50s and inhibit translocation Streptrogranin Bind to 50s and inhibit translocation Buy AT 30 ,CCELL at 50 Post translational modification Trim terminals Covalent modification Glycosylation, hydroxylation, phosphorylation Collagen → Hydroxylation of proline and lysine Disulfide bonds Protein folding Primary structure → Chain Secondary structure → Beta and alpha pleated Tertiary structure