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Flashcards in First Aid: Molecular Biochem Deck (29):

Stop codons


mutation to any of these is a "nonsense" mutation


Telomere code



start codons + what they code for

usually AUG

rarely GUG

codes for Met in euk

for N-formyl Met in prok


Nucleotide excision repair


when it happens


  • endonucleases release the damaged bases; DNA polymerase and ligase repair
  • happens in G1
  • xeroderma pigmentosum


RNA polymerase types + inhibitors (4)

  1. RNAP 1 - makes rRNA; in nucleolus
  2. RNAP 2 - makes mRNA; alpha-amantin inhibits
  3. RNAP 3 - makes tRNA + 5s rRNA
  4. Prokaryotic RNAP - makes all kinds of RNA

rifampin inhibits DNA-dep RNAP in prokaryotes; actinomycin D inhibits RNAP in prok/euk


what 3 processes are done to hnRNA (heterogenous nuclear) in the nucleus before it becomes mRNA?

  1. 7-methylguanosine capping - 5' end
  2. polyadenylation - 3' end; ~200 As
  3. intron splicing


Base Excision Repair enzymes

what kind of damage do they repair + when?

what are they?

Repair spontaneous / toxic deamination throughout whole cell cycle

  • Glycosylase - removes altered base -> apurinic/-pyrimidinic site made
  • AP-Endonuclease - cleave 5' to remove 1+ NTs
  • Lyase - cleaves 3'
  • DNA-Polymerase-beta - fills gap
  • Ligase - seals
  • (mnemonic = GEL PLease)


Mismatch Repair Enzymes

how they work + when?

defective in what disease?

  • in S phase > recognize new strand, remove mismatched NTs, fill + seal gap
  • defective in Lynch Syndrome (Hereditary Nonpolyposis Colorectal Cancer, HNPCC)


Double stranded DNA repair types (2)

how they work + diseases in which they are defective

  1. NHEJ - brings together 2 ends of DNA fragments; no homology req; may lose DNA
    • def. in ataxia telangectasia + Fanconi anemia
  2. Homologous Recomb. - 2 homolog DNA duplexes > damaged dsDNA strand repaired using complementary strand from homolog; no loss of NTs
    • defective in BRCA1 mut. (breast/ovary cc.)


Missense mutation

what is it + ex of disease

  • mutation that changes an AA
  • "conservative" if new AA is similar structure
  • sickle cell anemia is Glu > Val missense


Diff btwn promoters + enhancers + silencers

  • Promoter - RNA pol II and TFs bind upstream from gene (AT-rich, TATA or CAAT box)
  • Enhancer/Silencer - activator/repressor proteins bind sites close to/far from/within intron of gene


RNA processing

3 processes (where?) 

initial hnRNA (heterogenous nuclear) is modified in nucleus to become mRNA

  1. 5' cap - with methyl-guanosine
  2. polyadenylation - 3' tail of ~200 As
  3. intron splicing


mRNA quality control

where + how?

at cytoplasmic processing bodies (P-bodies)

  • exonucleases, decapping enzymes and miRNAs
  • mRNA may then be degraded or stored in p-body for later translation


explain process of pre-mRNA splicing

3 steps

  1. Spliceosome formation - primary transcript combines with snRPs and other proteins
  2. 5' cleavage - 5' end of intron cleaved; forms looped intermediate
  3. 3' cleavage - releases intron loop + exon ends join


examples of diseases of abnormal alternative splicing


  1. beta thalassemia
  2. Gaucher disease
  3. Tay-Sachs disease
  4. Marfan  syndrome

as well as some cancers



what are they, what do they do, how do they affect disease

  • small, conserved, noncoding RNA
  • posttranscriptionally reg gene expression by targeting 3' UTR on some mRNAs for degradation and translation repression
  • abnormal expr. of miRNAs targeting tumor suppressor gene products > cancer


tRNA structure

  • 75-90 NTs, cloverleaf shape
  • anticodon on one end binds mRNA codon, 
  • 3' aminoacyl end opposite... with CCA acceptor stem + many chemically modified bases
  • T-arm - binds tRNA to ribosome with TPsiC (ribothymidine, pseudouridine, cytidine)
  • D-arm - has dihydrouridine residues needed for tRNA recognition by aminoacyl-tRNA synthetase


enzyme which binds AA to tRNA

what does it do + how?

aminoacyl-tRNA synthetase

  • "charges" tRNA with proper AA; there is 1 AA-tRNA synthetase per AA + it uses ATP to charge
  • "scrutinizes" AA before + after tRNA binding + hydrolyzes bond if it is wrong
  • formed AA-tRNA bond has the E necessary for later peptide bond formation


Protein synthesis

3 steps, what's the first one + its details?

Initiation, Elongation + Termination

  • euk. initiation factors (eIFs) identify 5' cap or internal ribosome entry site (IRES) located anywhere on mRNA, often 5' UTR
  • eIFs help assemble 40s with initiator tRNA + release when 60s assembles w/ complex
  • requires GTP!

(remember ATP for Activation / charging of tRNA and GTP for Gripping/Going places ... translocation)


how do euk and prok ribosomes differ?

what direction are proteins synth'd?

  • Euk = 40s + 60s forms 80s (Even)
  • Prok = 30s + 50s forms 70s (Odd)


  • synth'd N terminus to C terminus


2nd step of protein synth?

+ its details

Initiation, Elongation, Termination

  • Think "going APE"
    • A site - binds incoming AA-tRNA
    • P site - accomodates growing peptide
    • E site - holds empty tRNA as it exits
  1. AA-tRNA binds A site (exc. initiator Met) using EF and GTP
  2. rRNA "ribozyme" catalyzes peptide bond formation, transfers polypept to AA on A site
  3. Ribosome advances 3 NTs toward 3' end mRNA, moving peptidyl tRNA to P site ("translocation")


3rd step of protein synth?

+ its details

Initiation, Elongation, Termination

  • "release factor" recognizes stop codon (UAG, UAA, UGA) + halts translation
  • completed polypept is released from ribosome, requiring GTP


What are the 2 types of PTMs?

+ 6 examples of 1 type

  1. Trimming - removing N- / C-terminal propeptides from zymogen > mature protein (eg trypsinogen > trypsin)
  2. Covalent Alterations - P-ation, glycosylation, OH-ation, methylation, acetylation, ubiquitination (PUGHAM)


What 3 processes does the Golgi perform on AAs / proteins in its function as a "distribution center" for proteins/lipids from ER to vesicles/membrane?

  1. Modifies Asn N-oligosaccharides
  2. Adds O-oligosacchs to Ser / Thr
  3. Adds mannose-6-phosphate to proteins for trafficking to lysosomes


What are endosomes?

"sorting centers" for material from outside cell or from Golgi

send stuff to lysosomes for destruction, or back to membrane/Golgi for use


What is I-cell disease?

Inclusion Cell Disease / Mucolipidosis Type II

  • inherited lysosomal N-acetylglucosaminyl-1-phosphotransferase defect
  • Golgi can't P-ate mannose resiudes on glycoproteins > proteins secreted EC rather than sent to lysosome
  • Clinical: coarse face, gingival hyp., cornea clouding, restricted joints, claw hand, kyphoscoliosis, high plasma lysosomal enzymes ... often fatal in childhood


What is the "signal recognition particle" ?

SRP is an abundant cytosolic ribonucleoprotein that traffics proteins from ribosome to RER

if dysfunctional/absent, proteins accumulate in cytosol


What are the 3 vesicular trafficking proteins + their functions?

"II steps forward, I steps back"

  1. COP-I - retrograde thru Golgi, cis-Golgi to ER
  2. COP-II - ER to cis-Golgi anterograde
  3. Clathrin - trans-Golgi to lysosome; membrane to endosomes (as in R-mediated endocytosis, such as LDL-Rs)