First Aid: Molecular Biochem Flashcards
Telomere code
TTAAGGG
start codons + what they code for
usually AUG
rarely GUG
codes for Met in euk
for N-formyl Met in prok
Nucleotide excision repair
enzymes
when it happens
disease(s)
- endonucleases release the damaged bases; DNA polymerase and ligase repair
- happens in G1
- xeroderma pigmentosum
RNA polymerase types + inhibitors (4)
- RNAP 1 - makes rRNA; in nucleolus
- RNAP 2 - makes mRNA; alpha-amantin inhibits
- RNAP 3 - makes tRNA + 5s rRNA
- 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?
- 7-methylguanosine capping - 5’ end
- polyadenylation - 3’ end; ~200 As
- 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
-
NHEJ - brings together 2 ends of DNA fragments; no homology req; may lose DNA
- def. in ataxia telangectasia + Fanconi anemia
-
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
- 5’ cap - with methyl-guanosine
- polyadenylation - 3’ tail of ~200 As
- 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
- Spliceosome formation - primary transcript combines with snRPs and other proteins
- 5’ cleavage - 5’ end of intron cleaved; forms looped intermediate
- 3’ cleavage - releases intron loop + exon ends join
examples of diseases of abnormal alternative splicing
(4)
- beta thalassemia
- Gaucher disease
- Tay-Sachs disease
- Marfan syndrome
as well as some cancers
miRNAs
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
- AA-tRNA binds A site (exc. initiator Met) using EF and GTP
- rRNA “ribozyme” catalyzes peptide bond formation, transfers polypept to AA on A site
- 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
- Trimming - removing N- / C-terminal propeptides from zymogen > mature protein (eg trypsinogen > trypsin)
- 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?
- Modifies Asn N-oligosaccharides
- Adds O-oligosacchs to Ser / Thr
- 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”
- COP-I - retrograde thru Golgi, cis-Golgi to ER
- COP-II - ER to cis-Golgi anterograde
- Clathrin - trans-Golgi to lysosome; membrane to endosomes (as in R-mediated endocytosis, such as LDL-Rs)
