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Biochemistry - Molecular

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ibench85lbs's version from 2016-07-14 21:27

DNA

Question Answer
Describe "beads on a string" = Chromatin structureDNA wraps around +charge histone octamer (lysine/arginine, made of 2 sets of H2A, H2B, H3, H4) to form nucleosome bead, H1 ties beads together (H1 is not in nucleosome core!)
Hetero vs euchromatinheterochromatin is condensed and not transcribed; Euchromatin is less condensed and transcriped
Which nucleotides are methylated and why?cytosine & adenine to allow mismatch repair enzymes to distinguish b/t old & new strands
Hypermethylationinactivates transcription of DNA
Histone Acetylationrelaxes DNA coiling, allowing for transcription - adds (-) charge to (+) histones
Nucleotides and # of rings in structurepurines (A/G) have 2 rings, pyriamidines (C,T,U) have 1 ring
Deamination of cytosine?makes uracil
Which nucleotide-nucleotide bond is strongest?G-C has 3 H-bonds and is stronger than A-T (2 H bonds) - AT GC 2,3!!
higher G-C content indicates?higher melting temperature
AAs needed for purine synthesisglutamine, aspartate, glycine (GAG)
Nucleoside vs nucleotidebase+ribose (Side) vs base+ribose+phosphate (Tide) (linked by phosphodiester bond)
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Pyrimidine & Purine Synthesis

Question Answer
Purines made from what precursor?IMP
Purine synthesis pathwaystart with Ribose 5P-->PRPP--> --> --> --> IMP--> AMP or GMP
Purine synthesis requires what?glycine, aspartate, glutamine, and THF
Pyrimidine synthesis pathwaystart with carbamoyl phosphate--> --> -->orotic acid + PRPP---> UMP-->UDP-->dUDP + CTP--->dUMP-->dTMP, requires aspartate, thymidylate synthase, dihydrofolate reductase, ribonucleotide reductase
Orotic acid + PRPP --> UMPUMP Synthase
UDP --> dUDP enzymeRibonucleotide reductase
dUMP --> dTMP enzymeThymidylate synthase
DHF --> THF enzymeDHF reductase
Hydroxyureainhibits ribonucleotide reductase (no UDP-->dUDP)
Used for: Melanoma, Sickle cell disease (increases HbF)
S.E.: Myelosuppression
6-mercaptopurine6MP blocks de novo purine synthesis = Thiol analog
Used for: AML/ALL
S.E. increased toxicity w/ Allopurinol since 6-MP is metabolized by xanthine oxidase
6-thioguaninesame mechanism as 6MP - blocks de novo purine synthesis
Can be used w/ Allopurinol
5-fluorouracil5FU inhibits thymidylate synthesis (no dUMP--> dTMP
Used for: solid tumors (colon, breast, ovarian CA)
S.E.: irreversible myelosuppression --> give Thymidine; photosensitivity
Methotrexateinhibits dihydrofolate reductase so no dTMP
Used for: Liquid tumors (Leukemias); abortion, RA, psoriasis
S.E.: reversible myelosuppresion --> give Leucovorin (folinic acid); teratogenic
Trimethopriminhibits bacterial dihydrofolate reductase (less dTMP)
Use: UTI, PCP
S.E.: Megaloblastic anemia, Leukopenia, Granulocytopenia (give Leucovorin)
Carbamoyl phosphateinvolved in 2 pathways for de novo pyrimidine synthesis and urea cycle
Ornithine transcarbamoylase deficiency (OTC)involved in urea cycle = takes carbamoyl phosphate to citrulline so leads to an accumlation of carbamoyl phosphate, this is converted to orotic acid-->aciduria
Findings = increased orotic acid w/ hyperammonemia
Orotic aciduriano conversion of orotic acid--> UMP due to defect in orotic acid phosphoribosyltransferase or decarboxylase
autosomal recessive
Findings = orotic acid in urine, megaloblastic anemia (doesn't improve with B12 supplement), CRYSTALS IN THE DIAPER...NO hyperammonemia
treat w/ oral uridine
HGPRTenzyme for transferring guanine or hyoxanthine on to phosphoribose to form purine nucleotides in purine salvage
Adenosine deaminase deficiencyexcess ATP/dATP imbalances nucleotide pool via feedback inhibition of ribonuc reductase-->prevents DNA synth-->decreased lympho count, **1 of major causes of SCID**
SCIDcan be caused by adenosine deaminase deficiency - adenosine builds up and is toxic to WBCs
treated by gene therapy
Lesch Nyhan syndromeXR deficiency of HGPRT which converts hypoxanthine-->IMP and guanine-->GMP, excess uric acid production--> retardation (brain relies on salvage pathway), self mutilation, aggression, gout, choreoathetosis
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Genetic Codes and Mutations

Question Answer
Transition vs transversiontransItion (identical) is purine for purine substitution (or pyrimidine) whereas transVersion is conVersion between purine/pyrimidine
AUG codonstart- methionine in euks, f-MET in proks
Genetic code featuresunambiguous (1 codon=1 AA), degenerate/redundant (more than 1 codon may = same AA), non-overlapping (continous sequence of bases), universal (exceptions are mitochondria, archaebacteria, mycoplasma, some yeast)
unambiguous1 codon = 1 AA
degenerate/redundantmore than 1 codon may = same AA
non-overlappingcontinuous sequence of bases
universalgenetic code is conserved throughout evolution (exceptions are mitochondria, archaebacteria, mycoplasma, some yeast)
Silent mutationsame AA results, often the 3rd base in codon is changed (tRNA wobble)
Most dangerous mutationsframeshift>nonsense>missense>silent
Missense vs nonsense mutationchanged aa (conservative because new AA is similar in structure) vs. stop codon is created in nonsenses mutation
Frame shiftchange --> misread nucleotides downstream --> nonfunctional protein (# of BP's deleted are not a multiple of 3)
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DNA Replication & Repair

Question Answer
origin of replicationparticular sequence in genome where DNA rep starts, in euks there may be multiple but only one in proks
helicase vs ligaseunwinds DNA at rep fork vs seals okazaki fragments together
SSBP vs DNA topoisomerasessingle stranded binding proteins prevent strands from reannealing VS creating nicks in helix to relieve supercoils (ex dna gyrase)
fluoroquinolones"Floxacins" - inhibit DNA gyrase (specific prok topoisomerase II & IV)
Use: G(-) rods of UTIs, Nisseria
S.E.: damage to cartilage
DNA poly 3 vs 1both are prokaryotic, 3 elongates the leading strand by adding deoxynucs to 3' end (synthesis in 5'-->3'), 3'-->5' exonuclease activity proofreads each added nucelotide VS 1 degrades the RNA primer and fills in the gap with DNA, excision via 5'-->3' exonuclease
Nucleotide excision repairendonucleases release oligonucleotide containing damaged bases, DNA poly/ligase fill/seal the gap
Xeroderma pigmentosumrepair of thymine dimers is impaired because of mutated endonucleases that excise damaged bases
Due to exposure of UV light --> stay out of sunlight
Base excision repairglycosylases remove damaged bases
Mismatch repairunmethylated newly synthesized string is recognized and mismatched nucleotides are removed, mutated in HNPCC (hereditary nonpolyposis colorectal cancer)
HNPCChereditary nonpolyposis colorectal cancer, caused by error in mismatch repair
Drugs blocking DNA replicationoften have modified 3'OH preventing addition of next nucleotide (i.e. chain termination)
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Transcription = DNA --> RNA

Question Answer
Protein synthesis directionN-->C
rRNAmost abundant and is made by RNA poly 1; ribosomal component (rampant)
mRNAlongest and made by RNA poly 2; carries sequence info from DNA to ribosome to be translated (massive) = capped, tailed, & spliced transcript
tRNAsmallest and made by RNA poly 3; carries A.A. to ribosome for protein synthesis (tiny)
Start codonsAUG
euk = methionine
prok = f-Met
Stop codonsU Go Away, U Are Away, U Are Gone = UGA, UAA, UAG
Promoter regionRNA poly and other TFs bind to DNA upstream from gene locus, has AT-rich sequence and TATA box
Enhancer vs silencer regionsalters gene expression by binding TFs vs site where negative regulators or repressors bind, both can be close/far/in gene whose expression it regulates
alpha amanitininhibits RNA poly 2 and can cause liver failure if ingested, found in death cap mushrooms
RNA poly in proks vs euksprok = only 1 which makes all 3 kinds of RNA
euks - there are 3 (1- rRNA, 2- mRNA, 3- tRNA), RNA poly has no proofreading function in euks but can initiate chains
RNA processingonly in euks, occurs in nucleus after transcription, capping on 5' end with 7 methylguanosine, poly A tail on 3' end (doesn't require template), spliced out introns
pre-mRNAheterogenous nuclear RNA (hnRNA) destined for translation
Splicing of pre-mRNA1. primary transcript combines with snRNPs and other proteins to make spliceosome
2. lariate-shaped (loop) intermediate is made
3. lariat is released to remove intron precisely and join 2 exons
Lupus and splicingAbs against spliceosomal snRNPs
Apolipoprotein B & splicingsplices in different spots to get 2 different proteins depending on where it is located
B-thalassemia mutationdifferent exons are combined by alternative splicing to make unique proteins in different tissues
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Translation

Question Answer
tRNA wobbleaccurate base pairing for first 2 NTs of codon so 3rd wobble position may code for same tRNA/aa (degenerate code)
tRNA structuresecondary structure, cloverleaf, antidcodon end is opposite 3' aminoacyl end, 3' end contains CCA which Can Carry A.A.
tRNA chargingaminoacyl-tRNA synthase scrutinizes aa before/after it binds to tRNA, requires ATP, if incorrect then bond is hydrolyzed
Tetracyclinesbind 30s subunit prevent attachment of aminoacyl-tRNA = "Cyclines"
Use: Borellia, Mycoplasma, Chlamydia, Rickettsia
S.E.: teeth discoloration, (-) bone growth, photosensitivity, x pregnancy; Fanconi syndrome w/ expired meds - don't re"CYCL"e meds
ubiquitinattached to defective proteins to tag them for destruction
tRNA aminoacylation Energy requirements?ATP-->AMP (2 phosphoanyhdride bonds)
Total E expenditure for translation4 phosphoanhydride bonds (1 ATP-->AMP, 2 GTP-->GDP)
Initiation of translationactivated by GTP hydrolysis, initiation factors help assemble 40s ribosomal subunit with initiator tRNA
Eukaryote vs prokaryote ribosome subunits40S+60S-->80S (Eukaryotes even), 30S+50S-->70S (prOkaryotes odd)
Elongation in translationGoing "APE"
1. A site = incoming aminoacyl tRNA binds to A site
2. P site = accommodates growing Peptide - rRNA catalyzes peptide bond formation --> transfers growing polypeptide to A.A. in A site
3. E site = holds Empty tRNA as it Exits - ribosome advances 3 nucleotides toward 3' end of RNA moving peptidyl RNA to P site = translocation
Aminoglycosidesbinds 30S - inhibit formation of initiation complex and cause misreading of mRNA = bacteriocidal
= "Mycins"
S.E.: nephrotoxicity that is increased w/ cephalosporins, ototoxicity w/ loop diuretics, teratogen
Chloramphenicolinhibits 50s peptidyltransferase
Use: Meningitis (H. influenza, N. meningitidis, S. pneumoniae)
S.E.: aplastic anemia, gray baby syndrome (decrease glucoronyl transferase)
increase p450 via phenobarbital
Macrolidesbind 50S blocking translocation = "Thromycins" throw you into an arrhythmia
Use: G(+) & atypical pneumonias
S.E.: prolonged QT
decrease cyp3A4
Clindamycinbind 50S blocking translocation
Use: Anaerobes above the diaphragm
S.E. = C. diff infection --> psuedomembranous colitis
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