Biochemistry DNA and RNA

eesohbel's version from 2015-07-21 13:05

Cell Cycle

Question Answer
Mitosis phasesprophase - metaphase - anaphase - telophase
CDKscyclin-dependent kinases, constitutive and inactive - control cell cycle
Cyclinsregulatory proteins that control cell cycle events, phase specific, activate CDKs
Tumor suppressorsp53 and RB normally inhibit G1 to S progression
Li-Fraumeni Syndromemutation in p53
Retinoblastomamutation in Rb
Stable or quiescent cellsenter G1 from G0 when stimulated, ex hepatocytes and lymphos
Labile cellsNever go to G0, divide rapidly with short G1, ex BM, gut, epithelium, hair, skin
Permanent cellsremain in G0, regenerate from stem cells, ex neurons, skeletal/cardiac mm., RBCs


Question Answer
RERsite of exported or secretory protein synthesis
Free ribosomessite of sythesis of cytosolic & organellar proteins
Misfolded proteins remain here...ER
Added if want protein to remain in ERcarboxyl terminal sequence
Nissl BodiesRER in neurons, makes enzymes and peptide NTs
SERsmooth ER for making steroids and detox
golgi functiondistrubtion of proteins from ER to membrane/lysosome/vesicles, modifies N-oligosacchs on asparagine, adds O-oligos to serine/threonine, adds mannose6P to proteins destined for the lysosome
COP1vesicular trafficking protein that is retrograde from golgi-->ER
COP2anterograde vesicular transport from RER-->cis Golgi
Clathrinvesicular trafficking protein from trans Golgi-->lysosomes, also for receptor mediated endocytosis (plasma membrane-->endosome)
I-Cell diseaseinclusion cell disease, inherited lysosomal storage disease, failure to add mannose6P to lysosome proteins, therefore enzymes are secreted outside of the cell
Findings: coarse facial features, clouded cornea, restricted joint mvmt, high levels of plasma lyso enzyme, often fatal in childhood
peroxisome fxncatabolism of very long chain F.A. & A.A.
proteasome fxndegrades damaged proteins or proteins tagged for destruction w/ ubiquitin
MT structurepolymerized dimers of alpha/beta tubulin, each dimer has 2 GTP bound, incorporated into flagella, cilia, mitotic spindles, grows slowly/collapses quickly
Dynein vs kinesinretrograde to MT (+ to -) = Dine In vs anterograde (- to +) = middle --> periphery
Mebendazole/thiabendazoleantihelminthic that acts on MTs
Griseofulvinantifungal that inhibits MTs
Use: dermatophytes
S.E.: teratogenic, carcinogenic, increase p450 therefore increase warfarin metabolism
Vincristin/vinblastineanticancer that bind tubulin to inhibit MT formation; alkaloids
S.E.: peripheral neuropathy (cristine), BM suppression (blastine - blast BM)
Paclitaxelanti-breast cancer that inhibit MT disassembly; "taxols"
Cilia structure9+2 arrangment, axonemal dynein is an ATPase that links peripheral 9 doublets causing bending of cilium by differential sliding of doublets
Actin/myosin functionsmicrovilli, m. contraction, cytokinesis, adherens junctions
Intermediate filaments functionStructure. These include: vinmentin, desmin, cytokeratin, glial fibrillary acid proteins (GFAP), neurofilaments
Stains for what cell type? vinmentin, desmin, cytokeratin, GFAP, neurofilamentsconnective tissue, muscle, epithelial cells, neuroglia, neurons


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 transciptionally inactive; 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
Histone methylationinactivates 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)
Uracil vs. thiamineuracil found in RNA and thymine in DNA

Pyrimidine & Purine Synthesis

Question Answer
purinesA, G (2 rings)
pyrimidinesC, T, U (one ring)
Purines made from what precursor?IMP
Purine synthesis pathwaystart with Ribose 5P-->PRPP--> --> --> --> IMP--> AMP or GMP
Purine synthesis requires what?glycine, aspartate, glutamine, C02 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
Rate limiting enzyme of pyrimidine synthesiscarbamoyl phosphate synthetase II makes carbamoyl phosphate from glutamine and C02
Rate limiting enzyme of purine synthesisPRPP amidotransferase makes IMP from PRPP
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 aka the rate limiting enzyme PRPP amidotransferase
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)
S.E.: Megaloblastic anemia, Leukopenia, Granulocytopenia (give Leucovorin)
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 or Folate supplement), ...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--> HGPRT (Hyperuricemia, Gout, Pissed off, Retardation, DysTonia)

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)

DNA Replication & Repair

Question Answer
origin of replication in prokaryotes versus eukaryotessingle prokaryotes and multiple in eukaryotes
helicaseunwinds DNA template at replication fork
single-stranding binding proteinsprevents strands from reannealing
DNA topoisomerasecreates a single or double stranded break in the helix to add or remove supercoils
primasemakes an RNA primer on which DNA polymerase III can initiate replication (prokaryotic only)
DNA polymerase IIIprokaryotic only. Elongates leading and lagging strand
DNA polymerase Iprokaryotic only. Degrades RNA primer, replaces it with DNA
DNA ligasejoins Okazaki fragments
telomeraseRNA dependent DNA polymerase that adds DNA to 3' end of chromsomes to avoid loss of DNA material in eukaryotes only
DNA polymerase alphamakes own primer. Builds Okazaki fragments on lagging strand.
DNA polymerase deltabuilds leading strand.
DNA polymerase betaDNA repair (base excision)
DNA polymerase gammareplicates mitochondrial DNA
transitionpurine to purine or pyrimidine to pyrimidine
tranversionpurine to pyrimidine or pyrimidine to purine
nucleotide excision repairrepairs bulky helix distorting lesions. Endonucleases release oligonucleotides containing damaged bases; DNA polymerase and ligase fill and reseal the gap; repairs bulky-helix distorting lesions.
base excision repairglycosylases remove the altered base and create AP site. Nucleotides are removed by endonuclease. DNA polymerase B fills the gap. Remember beta (base excision repair)
mismatch repairnewly synthesized strand's mismatched nucleotides are removed.
HNPCCmismatch repair defect
Xeroderma pigmentosumnucleotide excision repair defect; cannot repair pyrimidine dimers which are created by UV light
replicates lagging strand in eukaryotesDNA polymerase alpha
synthesizes RNA primerDNA polymerase alpha
replicates mitochondrial DNADNA polymerase gamma
replicated leading strand DNADNA polymerase delta

Transcription = DNA --> RNA

Question Answer
Protein synthesis directionN-->C
rRNAmost abundant and is made by RNA poly 1
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)
prokaryotic RNA polymerase1 RNA polymerase, inhibited by rifampin
location of synthesis rRNAnucleolus
location of mRNA synthesisnucleoplasm
location of tRNA synthesisnucleoplasm
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. This is all referring to mRNA
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
TATA boxpromoter region that binds transcription factors and RNA polymerase II during intiation of transcription. It is located approximately 25 bases upstream from the coding region
CAAT boxanother promoter region that is located 60 to 80 bases upstream of the begining of the coding region


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
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 (except for the first tRNA carrying methionine)
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
Antibiotics that block prokaryotic ribosomeBuy AT 30 CCELL AT 50. aminoglycosides, tetracyclines, clindamycin, choraphenicol, erythromycin (macrolides), linezolid, lineomycin

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