Biochemistry for the USMLE/COMLEX

  1. Replication
    the process by which DNA is duplicated
  2. Transcription
    Making RNA based off of the DNA
  3. Translation
    making protein based off the the RNA sequence
  4. Nucleic Acid structure
    DNA and RNA are made up of a 5 carbon sugar (ribose or deoxyribose), a nitrogenous base (purine or pyrimidine) and one or more phosphate groups

    • the phosphate groups are located at the 5' position
    • there is a free OH group located at the 3' position
  5. The cell cycle
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    • G1 phase: a period of cellular growth, precedign DNA synthesis
    • G0: a phase for cells that have stopped growing
    • S: synthesis phase, DNA replication occurs
    • G2 phase: a period of cellular growth after DNA synthesis has occurred, replicated DNA is checked for errors
    • M phase: mitosis, cell division
  6. Drugs that target the S phase of the cell cycle
    • methotrexate - a drug to treat cancer
    • 5-flurouracil - pyrimidine analog - to treat cancer
    • hydroxyurea - treats CML, ovarian cancer, sickle cell disease (during transfusion)
  7. Drugs that target the G2 phase of the cell cycle
  8. Drugs that target the M phase of the cell cycle
    • paclitaxel - cancer
    • vincristine - leukemia
    • vinblastine - several cancers including hodgkins lymphoma, lung cancer and testicular cancer
  9. Non-cell cycle specific drugs to treat cancer
    • cyclophsphamide
    • cisplatin - bind tightly to DNA and alter its structure
    • Daunorubicin and doxorubicin - intercelate within the DNA bases, and prevent topoisomerase II from working
  10. Purine
    • a 2 ringed nitrogenous base structure
    • adenine and guanine

    Purine metabolites: xanthine, hypoxanthine, and uric acid
  11. Pyrimidine
    • A single ring nitrogenous base structure
    • cytosine, thymine and uracil
  12. Nucleic Acids and Polymerization
    polymers of nucleotides hoind by a 3' - 5' phosphodiester bond

    the seqeunce is always specified as 5' to 3'

    the hydroxyl group on the 3' sugar of the polymer will attack the 5' phosphate group of the free sugar to form the bond
  13. DNA structure - features of double stranded DNA
    • the 2 DNA strands are antiparallel
    • the 2 strands are complementary (A pairs with T, by 2 H bonds, C pairs with G by 3 H bonds)
    • Chargaffs Principle - #A =#T, #C=#G
  14. DNA packaging in the nucleus
    • First order structure: DNA is wrapped around a histone complex. A histone complex is a octomer of histones consisting of 2 molecules of each histone, H2A, H2B, H3 and H4. A histone is a protein rich in lysine and arginine so it has a positive charge. The negatively DNA is wrapped around the histone complex 2x, (146bp). It appears to look like a beads on a string
    • Second Order structure(polynucleosome): individual nucleosomes are connected by the space histone, H1. it organizes the DNA into a polynucleosome or nucleofilament
    • Higher order structure:additional condensation of the DNA structure, to chromatin
  15. Chromatin
    • Chromatin is found in 2 forms
    • Euchromatin: a less condensed form, lighter on electron microscopy, transcriptionaly active
    • Heterochromatin: more condensed, dark on electron microscopy, transcriptionaly inactive
  16. Mitosis - phases
    • Prophase: DNA condenses and nuclear membrane dissolves
    • Metphase: condensed chromosomes line up in the center
    • Anaphase -chromosome migrate to either side of the cell
    • Telophase: chromsomes decondense, and a separate nuclear membrane is formed, 
    • cytokensis: plasma membrane pinches off leaving 2 daughter cells
  17. DNA replication - the phases
    • the newly synthesized strand is formed in the 5' to 3' direction, and is anti-parallel to the template strand, 
    • Unwinding:
    • - Helicase breaks the hydrogen bonds holding the DNA together
    • - Topoisomerase breaks the strands of DNA between nucleotides further downstream to prevent supercoiling (topoisomerase I is for single strand breaks, topoisomerase II is for double strand breaks)
    • - SSBs (single stranded binding proteins) keep the DNA separated and protects them from degradation by nucleases
    • RNA Primer synthesisPrimase synthesizes a short RNA primer in the 5' to 3' direction, begining at the origin on the parental strand, 
    • DNA polymerization: DNA polymerase begins to synthesize DNA in the 5' to 3' direction, if it can be made as one long piece it is called the leading strand, or as shorter pieces called okazaki fragments that have to be added together later, in the lagging strand
    • Degrading RNA primers: RNA primers are degraded by RNAase H, an exonuclease, and DNA polymerase fills in the gaps (in prokaryotes DNA polymerase I removes the primers and fills in the gaps) 
    • Ligation: DNA ligase fills in the nicks between the okazaki fragments, making it a continuous strand of DNA
  18. DNA replication: Origins of replication
    Locations where replication starts
  19. Polymersases
    enzymes that synthesize nucleic acids by forming phosphodiester bonds
  20. Nucleases
    • enzymes that hydrolyze phosphodiester bonds
    • Exonuclease: removes the nucleotides from the 5' or 3' end of the nucleic acid
    • Endonuclease: cut within the nucleic acid and release nucleic acid fragments
  21. Drugs that block topoisomerase
    • Quinolones: effective against aerobic gram-negative bacteria(gonorrhea and UTIs), levofloxacin, ciprofloxacin, moxifloxacin 
    • Nalidixic acid : kills bacteria by blocking DNA gyrase (a prokaryotic topoisomerase)
    • Etoposide/teniposide: cancer drugs, inhibits eukaryotic topoisomerases
  22. Telomeres
    • Long stretches of repetative DNA sequences at the end of DNA, they are made by telomerase
    • if they get to short, apoptosis occurs
  23. Reverse Transcriptase
    • RNA-dependent DNA polymerase - needs a RNA template to synthesize new DNA
    • Seen in reterovriuses such as HIV
    • lacks a proofreadign ability
  24. Nucleotide analoues
    • AZT - converted to a triphosphate derivitive, used as a viral substrate for the viral reverse transcriptase, 
    • replaces the normal hydroxyl group with an azide ,preventing further transcritpion

    DDI (2,3-dideoxyinosine, Didanosine), removes the 3' hydroxyl group

    Cytarabine (cytosine arabinoside) - changes the sugar to arabinose, inhibits DNA synthesis - used to treat cancer
  25. DNA Repair - Ways DNA can get damaged
    • Thiamine dimers - UV radiation
    • Mismatched base repair - DNA replication errors
    • Cytosine deamination - spontaneous heat
  26. Thaimine Dimer DNA repair
    • UV light causes dimerization of adjacent thymines. It interfers with DNA replication, and normal gene expression. 
    • Eliminated by exicision-repair mechanism - using Excision endonuclease, and DNA polymerase and ligase

    Issues with this repair mechanism causes the disease xeroderma pigmentosa
  27. Base excision repair
    • cytosien deamination - causes a cytosine to go to a uracil. 
    • it is recognized by a AP endonuclease, and it removes it from the sequence
    • DNA polymerase and ligase fill in the gap and close it
  28. Tumor suppressor genes and DNA repair
    DNA repair will not occur when certain tumor suppressor genes have been inactivated through mutation or deletion:

    • p53 - prevents a cell with damaged DNA from entering S phase, inactivation or deletion is associated with LiFrumeni Syndrome
    • ATM gene - encodes a kinase responsible for p53 activity. Inactivated in ataxic telangiectasia
    • BRCA1 and 2
    • Rb - retinoblastoma gene, negative regulator of the cell cycle, ability to bind to E2F and repress transcription of genes needed for S phase
  29. Diseases associated with DNA repair dysfunction
    • Xeroderma pigemntosa
    • Lynch Syndrome/Hereditary nonpolyposis colorectal cancer (HNPCC)
  30. Xeroderma Pigmentosa
    • Epidemiology: Autosomal Recessive, 
    • Etiology/pathogenesis:  Deficiency of the Excision endonuclease needed to repair thymine dimers

    Clinical Manifestations: extreme sensitivity to sunlight, skin freckling, ulcerations, and skin cancer. Carcinomas and melanomas appear early in life.

    • Diagnosis: measurment of the enzyme in white blood cells
    • Treatment: avoid exposure to UV light
  31. Hereditary nonpolyposis colorectal cancer (Lynch syndrome)
    • Epidemilogy:
    • Etiology/pathogenesis: mutation in a gene (hMLH1 or hMSH2) encoding enzymes that carry out DNA mismatch repair

  32. Types of RNA
    • Ribosomal RNA: structural component of a ribosome
    • Transfer RNA: carry amino acids to the ribosome
    • Messanger RNA: carries the information specifying amino acid sequence to the ribosome
    • hnRNA: precursor to mRNA
    • snRNA: participate in splicing of mRNA
  33. RNA polymerases
    • RNA Polymerase I: located in the nucleolus and synthesizes 28S, 18S, and 5.8S rRNA
    • RNA polymerase II: located in the nuceloplasm and synthesizes hnRNA/mRNA
    • RNA polymerase III: synthesizes tRNA, and 5S rRNA
  34. Production of mRNA
    • RNA polymerase II (with help from transcription factors) binds to the DNA, at the promoter region. The promoter region has 2 important areas the TATA box and the CAAT box
    • RNA polymerase II seperates the strands, and starts transcription, in the 5' to 3' direction. It ends when it reaches the termination seqeunce
  35. Processing mRNA
    A 5' methylguanosine cap is added, it is a ribosome binding site, and protects it from degredation

    a poly-A tail is added to the 3' end, to protect from degredation

    • Introns are removed by splicing with a snRNP
    • - the way the introns are removed and the exons kept can be done in multiple ways - called alternative splicing
  36. Ribosomal Structure
    Eukaryotes - made up of a 60S unit, and a 40S unit to make an 80-S ribosome
  37. Stop codons
    • UGA
    • UAA
    • UAG
  38. Types of mutations
    • Silent: no change in protein
    • Missense: new codon specifies a new amino acid
    • Nonsence: new codon is a stop codon
    • Frameshift: addition or deletion of bases, usually creates a nonfunctional or shoter protein
    • large segment deletion: loss of function 
    • triplet repeat expansion
  39. Beta-Thalassemia
    Deficiency of the beta-globin proteins,
  40. Huntingtons Disease
    • Autosomal Dominant disorder
    • Etiology: trinucleotide repeate expansion of CAG
    • Clinical: mood disturbance, impaired memory, hypereflexia, abnormal gait, chorea, dystonia, dementia, dysphagia
  41. Translation - the process
    the formation of an amino acid is between peptide bonds, is between the carboxyl group of one aa and the amino group of the other

    • initation: occurs when the small ribosomal subunit binds to the mRNA,  a charged tRNA binds to the AUG codon, and then the large subunit binds to the small subunit. 
    • Elongation: a 3 step cycle - the tRAN binds to the A site, a peptidyl transferase forms the peptide bond between the last amino acid and the new one, then the ribosome moves 3 codons down, and moves the growing peptide into the P site.
    • Termination: when a stop codon is reached, peptidyltransferase hydrolyzes the compelte protein,
  42. Inhibitors of protein synthesis
    Prokaryotic translation: streptomycin, erythromycin, tetracycline, chloramphenicol

    Eukaryotic translation: cyclohexamide, Diptheria and Pseudomonas toxins
  43. Grey Baby Syndrome
    Occurs in newborns who are given chloramphenicol

    Occurs because they do not have enough UDP-glycuronyl transferase activity to excrete the drug

    Leads to: cyansosi, death, low BP
  44. Proteasomes and Ubiqutin
    ubiquitin binds to proteins that are defective and brings them over to the proteasome to be degraded
  45. Cystic fibrosis
    deletion of the phenyalanine at 508 of the CFTR protein
  46. Post-translational modifications to proteins
    N-terminal hydrophobic seqeunce - to ensure translation on the RER

    phosphorylation of mannose - direct enzymes to a lysosome
  47. I-cell disease
    Lysosomal storage disease

    Clinical: course facial features, gingival hyeprpaslia, macroglossia

    secretions of active lysosomal enzymes into the blood and extracellular fluid
  48. Collagen
    • CollagenI: bundle of fibers, high tensile strengh, located in bone, skin and tendons
    • Type II: thin fibrils, structural, located in cartalige and vitrious fluids
    • Type 3: thin fibrils, pliable, blood vessels, and granulation tissue
    • type IV: amorphous, basement membranes
  49. Disorders of collagen biosynthesis
    • Scurvy
    • Osteogenesis imperfecta
    • Ehler-Danlos syndromes
    • Menkes disease
  50. Scurvy
    • deficent hydroxylation secondary to ascorbate deficency
    • Symptoms: petechiae, ecchymosis, loose teeth, bleeding gums, poor wound healing, poor bone development
  51. Osteogensis Imperfecta
    • miutations in collagen disease
    • Symptoms: skeletal deformaties, fractures, blue sclera
  52. Ehlers-Danlos syndromes
    Mutations in collagen genes and lysyl hydroxylase gene

    Symptoms: hyperextensible, fragile skin, hypermobile joints, dislocations, varicose veins, ecchymoses, arterial and intestinal ruptures
  53. Menkes Disease
    deficient cross-linking secondary to a functional copper deficency

    Symptoms: depigemnted hair, arterial tortuosity, rupture. cerebral degeneration, osteoporosis, anemia
  54. Gene regulation: enhancers
    binding sites for activator proteins
  55. Hydrophobic amino acids
    • phenylalaniene
    • tyrosine
    • tryptophan
    • valine
    • leucine
    • isoleucine
    • proline
    • glycine
    • alanine
  56. Hydrophilic amino acids
    • lysine
    • arganine
    • histidine
    • aspartate
    • glutamate
    • serine
    • threonine
    • cysteine
    • methionine
    • asparagine
    • glutamine
  57. Nitrogen balance
    nitrogen balance - when the ampount of nitrogen incoporaed int othe body equals the amount excreted

    Causes of a negative balance: protein malnutrition, dietary deficency of 1 aa, starvation, uncontrolled diabetes, infection

    Causes of a postive balance: growth, pregnancy,
Card Set
Biochemistry for the USMLE/COMLEX
Cards to study for the biochemistry portion of the USMLE/COMLEX