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Central Dogma
Abnormal Amnio Dentral Dogma lecture
139
Biochemistry
Professional
09/10/2012

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Term
Semi-discontinuous process
Definition
leading (one piece) + lagging strands
Term
DNA ligase
Definition
joins Okazaki fragments
Term
direction of REPLICATION (DNA Synthesis)
Definition
5'-->3'
Term
how is replication processive?
Definition
(done all at once, not in bit and pieces) sliding clamp, loader
Term
primosome
Definition
make RNA primer
Term
replisome
Definition
make DNA by elongating the primer
Term
prokaryotic primosome components
Definition
DnaA binds oriC, DnaB (helicase) melts dsDNA (needs DnaC for binding), Primase makes makes RNA primer
Term
prokaryotic Replisome components
Definition
POL 3 (the primary replicative polymerase) makes DNA; POL 1 removes primer
Term
POL3 functions (2)
Definition
5' to 3' polymerase activity; 3' to 5' exonuclease proofing activity
Term
POL1 function
Definition
5' to 3' exonuclease proofing
Term
Topoisomerases
Definition
cut and rejoin DNA to resolve supercoils
Term
prokaryotic Topoisomerase example & drug which targets it
Definition
gyrase; cipro
Term
DNA ligase
Definition
joins Okazaki fragments
Term
what are the diff. euk. POLs?
Definition
alpha, beta, delta, epsilon, gamma
Term
alpha POL
Definition
initiation; primase activity; 5'-3' polymerase
Term
beta POL
Definition
DNA repair; 5'-3' polymerase
Term
delta POL
Definition
elongation & repair; 5'-3' polymerase; 3'-5' exonuclease
Term
epsilon POL
Definition
elongation & repair; 5'-3' polymerase; 3'-5' exonuclease
Term
gamma POL
Definition
mitochondrial replication; 5'-3' polymerase; 3'-5' exonuclease
Term
what do Euk. have to replicate along w/DNA?
Definition
Nucleosomes (duplicated during DNA synthesis); histones (synthesized in S phase)
Term
Telomeres
Definition
chromosome ends; tandem repeats of a hexanucleotide sequence (AGGGTT); get shorter with each cell division
Term
ribonucleoprotein complex
Definition
telomerase (replaces lost telomere DNA); NOT present in most normal somatic cells
Term
Telomerase contains
Definition
RNA template for DNA synthesis; Protein polymerase (reverse transcriptase)
Term
Which end on which strand gets lengthened by telomerase?
Definition
3' end of the 5' to 3' strand (the already longer strand)
Term
Excision repair: how accomplished?
Definition
Recognition, removal, replacement, resealing
Term
MMR (mismatch repair):
Definition
eliminates errors missed by proofreading
Term
MMR in prok.
Definition
MUT proteins
Term
MUT-S
Definition
recognizes mismatched bases
Term
MUT-L
Definition
joins and recruits MUT-H
Term
MUT-H
Definition
cleaves (endonuclease)
Term
how is daugther strand recognized?
Definition
parental strand is DAM (DNA adenine methylation)
Term
Euk. MMR
Definition
homologous to prok. (MSH, MLH; no MHH) system except for strand ID (no DAM)
Term
defect in MMR causes
Definition
HNPCC (colorectal cancer)
Term
BER (base excision repair) acts on
Definition
modified bases, UMP
Term
BER action
Definition
glycosylases cleave glycosidic bond (b/t base and the sugar); “AP” site; Remove sugar; replace dNMP and ligate
Term
NER repairs
Definition
bulky lesions, pyrimidine dimers from UV
Term
protein in prok. NER
Definition
uvrABCD protein complex
Term
protein in euk. NER
Definition
XP proteins that recognize and remove
Term
xeroderma pigmentosum
Definition
deficiency in any of the XP proteins; photosensitivity & skin cancers
Term
Cockayne syndrome
Definition
Deficiencies in additional proteins required for
Term
Repair of ds breaks
Definition
some DNA is lost; repair by NHEJ (non-homologous end joining) or HR (homologous recombination)
Term
NHEJ (non-homologous end joining)
Definition
rejoin the ends without replacing the lost DNA
Term
HR (homologous recombination)
Definition
uses homologous DNA as a template for the replacement of the lost DNA
Term
Defects in homologous recombination leads to
Definition
cancer (ex is BRCA)
Term
RAD51
Definition
finds template in homologous recombination
Term
damage tolerance
Definition
special group of DNA POLs can bypass DS lesion and synthesize DNA in spite of the damage
Term
what does transcription lack?
Definition
primer; 3'-5' exonuclease (proofreading) activity
Term
mRNA is identical to
Definition
coding strand of DNA (except for U/T)
Term
prok. RNA polymerase composition
Definition
hexameric holoenzyme (includes sigma factor)
Term
sigma subunit in prok. RNA POL
Definition
recognizes and binds the promoter
Term
euk. RNA polymerase composition
Definition
3 different multisubunit RNA POLs
Term
euk. POL I
Definition
rRNA, nucleolus
Term
euk. POL II
Definition
mRNA
Term
Euk. POL III
Definition
tRNA, 5S rRNA
Term
Promoter
Definition
Region on the gene where RNA POL binds (sigma in prok and TFs in euk) to initiate transcription
Term
prok. promoter
Definition
-35 and -10 (TATAAT or Pribnow box) consensus sequences
Term
Euk. promoter
Definition
none universally found; examples are TATAAA (Hogness box) centered at ~ -25 and Inr
Term
prok. initiation
Definition
holoenzyme via sigma binds promoter, DNA melts, several abortive attempts---once past ~ 10 nt sigma leaves
Term
rifamycin
Definition
inhibits prok. initiation
Term
prok. elongation
Definition
RNA made 5'-3' with 3'-5' phosphodiester links
Term
actinomycin
Definition
inhibits prok. & euk. elongation
Term
prok. intrinsic or rho-independent termination
Definition
sequence in DNA causes stem-loop structure in the RNA that terminates transcription
Term
prok. rho-dependent termination
Definition
POL pauses at terminatino site, rho crawls up RNA using ATPase activity & when it encounters RNA/DNA hybrid it pushes DNA out of the way (helicase activity)
Term
main POL in euk. transcription (mRNA)
Definition
POL II
Term
alpha-amanitin
Definition
inhibits POL II
Term
TFIID
Definition
TBP (TATA binding protein) binds TATA sequence; TAFs (TATA associated factors) join in; analogous to sigma in prok.
Term
TFIIF
Definition
ferries POL II to TFIID/DNA
Term
TFIIH
Definition
unwinds helix using ATP hydrolysis; performs several abortive attempts; phosphorylates C-terminus of POL II; elongation begins
Term
STFs (specific TFs)
Definition
regulate when/where/how much RNA is made; 2 functional domains: DNA-binding & transcription activation
Term
DNA-binding domain
Definition
part of STF; binds to DNA sequence on response elements (RE), UAS
Term
transcription activation domain
Definition
part of STF; recruits and binds other proteins such as the GTFs, other STFs, co-activators
Term
Co-activators
Definition
some help solve the chromatin problem (chromatin to tightly bound to transcribe)
Term
HATs
Definition
histone acetyl transferase; acetylate histones to loosen chromatin & enhance transcription
Term
HDACs
Definition
histone deacetlases; repress transcription by de-acetylating chormatin (tightens it)
Term
Enhancers
Definition
position/orientation independent
Term
pre-tRNA processing
Definition
(prok. & euk.) cleaved at 5' end, CCA added to 3' end, many bases modified (e.g. U to T)
Term
euk. post-transcription processing
Definition
5' cap; 3' poly-A; intron splicing
Term
5' cap
Definition
7-methyl-guanine in 5'-5' linkage
Term
poly-A
Definition
3' end using ATP; mRNA first cleaved after AAUAAA signal then polyadenylated; not directed by DNA
Term
spliceosome
Definition
removes introns; composed of snRNP (small nuclear ribonucleoproteins) (eg. U1-U6); assembly requires ATP hydrolysis
Term
U1
Definition
binds 5' splice donor site in splicing
Term
U2
Definition
binds branch site A (in intron) in splicing
Term
U4-5-6
Definition
bind and the spliceosome is complete
Term
splicing process
Definition
exon 1 cut from intron & forms 2'-5' linkage w/intron (forming lariat); free exon OH attacks exon 2 & lariat is released
Term
tRNA activation/charging
Definition
linkage of tRNA w/amino acid; occurs in cytocol; requires aminoacyl tRNA synthetases & ATP (2 equivalents)
Term
aminoacyl tRNA synthetases
Definition
links tRNA to appropriate a.a.; requires ATP; can proofread
Term
translation Initiation
Definition
small subunit of ribosome binds mRNA & aminoacyl tRNA; large ribosome subunit joins; energy (GTP) required
Term
prok. ribosome subunits
Definition
30S + 50S = 70S
Term
euk. ribosome subunits
Definition
40S + 60S = 80S
Term
A site of ribosome
Definition
Aminoacylated tRNA binds here
Term
P site of ribosome
Definition
Peptide bond formed as tRNA held here
Term
E site of ribosome
Definition
Empty tRNA held here until it Exits
Term
Small subunit puspose
Definition
decodes genetic info.
Term
large subunit puspose
Definition
makes the peptide bond
Term
eIF2
Definition
binds w/met~tRNA & GTP
Term
eIF3
Definition
binds small ribosomal subunit to eIF2-GTP-met-tRNA (at P site); aided by eIF1
Term
eIF4f
Definition
5'cap- binding complex; joins to mRNA-PAB-protein, which joins to small ribosomal subunit & other eIFs; scans mRNA for AUG, using ATP
Term
eIF5
Definition
helps large subunit join small subunit complew w/help of GTP; Forces eIF3 & eIF1 to leave
Term
mRNA circularization
Definition
prep. for translation elongation in euk.; mediated by eIF4 family members & PAB protein
Term
eIF4 role in circularization
Definition
eIF4A uses ATP to find 1st AUG; eIF4E interacts w/5' End; eIF4G grabs onto E& PAB to hold RNA in circular form
Term
EF1alpha-GTP
Definition
brings all other aa~tRNAs to A site; GTP-->GDP
Term
EF1beta-gamma
Definition
reactivates EF1alpha-GTP
Term
peptidyl transferase
Definition
a ribozyme of the large subunit; forms the peptide bond between met_i and aa #2
Term
EF2-GTP
Definition
causes translocation as GTP-->GDP (what was in A [dipeptide] is now in P, so A is now empty)
Term
diphtheria toxin
Definition
ADP-ribosylation; inhibits EF2
Term
eRF1
Definition
(euk. release factor) recognizes stop codon at A; binds eRF3-GTP
Term
eRF1-eRF3-GTP complex
Definition
hydrolyzes peptide; GTP hydrolyzed
Term
ATP needed for translation?
Definition
euk. yes; prok. no
Term
GTP needed for translation?
Definition
euk. yes; prok. yes
Term
anti-bacterial translation inhibitors
Definition
streptomycin, tetracycline, erythromycin
Term
anti-euk. translation inhibitors
Definition
cyclohexamide, phosphorylation of eIF2, ADP-ribosylation of EF2 by diptheria toxin
Term
anti-euk. & - prok. translation inhibitors
Definition
puromycin, chloramphenicol
Term
Selenocysteine
Definition
(Sec): Ser modified to Sec & inserted into signals that allow for Sec placement into stop codon
Term
SECIS & SBP
Definition
help insert Sec into peptide chain
Term
ATP needed for initiation of translation?
Definition
prok. no; euk. yes
Term
targeting pathway of Secreted proteins
Definition
co-translational; N-terminal signal sequence recognized/bound by SRP; translation stops; goes to RER; SRP attaches to R (docking protein); moves to translocon (GTP-->GDP); translation resumes; peptide threaded into ER lumen; signal sequence removed; vesicles containing the nascent protein bud off from ER, go to Golgi then to cell membrane, and contents are secreted
Term
targeting for ER-retrieval/resident proteins
Definition
2nd signal KDEL (lys, asp, glu, leu) si retrieval signal (prevents secretion); co-translational
Term
targeting for membrane proteins
Definition
threading into ER lumen stops due to hydrophobic “stop transfer”; cell (plasma) membrane is default location
Term
targeting for lysosomes
Definition
protein gets N-glycosylated; TERMINAL MANNOSE GETS PHOSPHORYLATED AT C6 (Mannose-6-Phosphate)
Term
how is C6 on mannose phosphorylated for lysosome targeting?
Definition
Phosphotransferase adds GlcNac-P to C6 of the mannose; phosphoglycosidase removes GlcNAc so just the P is left
Term
I-cell disease
Definition
deficiency in phosphotransferase; leads to lysosomal acid hyrdolases in the blood
Term
targeting to nucleus
Definition
NLS recognized by importins; protein-importin complex enters through NPC (nucleus pore complex), binds Ran-GTP, protein released, importin-Ran-GTP leave nucleus, GTP-->GDP
Term
nuclear localization sequence
Definition
(NLS); short, basic, internal (not on terminal ends), not removed after targeted
Term
Swyer syndrome
Definition
due to defect in NLS of SRY; leads to female phenotype in XY
Term
amphipathic alpha-helix
Definition
Mitochondrial N-terminal matrix-targeting signal
Term
targeting to mitochondria
Definition
unfolded-protein/amphipathic alpha-helix complex moves laterally to TOM-TIM interface, entry requires proton-motive force, ATP; signal removed
Term
targeting to peroxisomes
Definition
PTS1 (C-terminal) or PTS2 (N-terminal); peroxins function as chaperones
Term
Zellweger syndrome
Definition
defects in peroxins; neurological impairment
Term
N-linked glycosylation
Definition
Ndoplasmic reticulum (ER) to amide N of asn; pre-formed oligosaccharide built on dolichol-P (lipid of ER membrane) is transferred en bloc to asn; trimmed in ER + Golgi; additional sugars added in Golgi
Term
CDG (congenital disorders of glycosylation)
Definition
result of defects in N-glycosylation
Term
O-linked glycosylation
Definition
in GOlgi to OH of ser/thr + hyl; sugars added 1 by 1
Term
Proteasomal degradation characteristics
Definition
highly selective; ATP-requiring; proteasome and Ub (ubiquitin)
Term
Proteasomal degradation pathway
Definition
Ub tags proteins w/E1, E2, E3 (ligase); proteasome removes/recycles Ub; protein degraded
Term
N-end rule and internal PEST
Definition
sequences which mark protein for Ub-mediated degradation
Term
triple helix of collagen
Definition
Three alpha chains of Gly-X-Y
Term
Intracellular collagen reactions
Definition
Cleavage of signal sequence; hydroxylation of propeptides by vitamin C-dependent hydroxylases; Triple helix formation; O-glycosylation of selected Hyp
Term
procollagen
Definition
triple helix made of 3 alpha chains
Term
Extracellular collagen reactions
Definition
Cleavage of N-and C-terminal propeptides (forming tropocollagen); Lateral association of tropocollagen (forming fibrils); Cross-linking of fibrils (forming mature collagen fibers)
Term
Ehlers-Danlos syndrome
Definition
stretchy skin from deficiency in lysyl oxidase
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