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Molecular

First Aid - Biochem - Molecular

QuestionAnswer
chromatin structure DNA exists in the condensed chromatin form to fit into the nucleus -negatively charged DNA loops twice around positively charged histone octamer (2 sets of H2A, H2B, H3 and H4) to form a nucleosome bead -- HI ties nucleosome beads together in a string
heterochromatin condensed, transcriptionally inactive, and sterically inaccessible
euchromatin less condensed, transcriptionally active and sterically accessible
nucleotides PURe As Gold: purines = adenine and guanine CUT the PY = pyrimidines = cytosine and thymine ---deamination of cytosine = uracil (RNA) G-C (3 H bonds) stronger than A-T (2 H bonds), so ^ G-C content means a higher melting temperature
purine salvage deficiencies nucleic acids > GMP > guanosine >< guanine > xanthine > uric acid AMP > adenosine > inosine >< hypoxanthine > xanthine > uric acid
adenosine deaminase deficiency excess ATP and dATP imbalance makes due to feedback inhibition of ribonucleotide reductase > prevents DNA synthesis and decreases lymphocyte count > major cause of severe combined immunodeficiency disorder
lesch-nyhan syndrome defective purine salvage owing to absence of HGPRT, this converts hypoxanthine to IMP and guanine to GMP. results in excess uric acid production > retardation, self-mutilation, aggression, gout, hyperuricemia, choreoathetosis
Amino Acids - purine synthesis GAG = glycine, aspartate, and glutamine are all necessary -Purines are made from IMP precursor
Pyrimidine synthesis pyrimidines are made from orotate precursor, with PRPP added later -ribonucleotides are synthesized first and are converted to deoxyribonucleotides by ribonucleotide reductase
pyrimidine synthesis 2 carbamoyl phosphate involved in de no pyr. syn and urea cycle, ornithine transcarbamoylase deficiency leads to an accumulation of carbamoyl phopsphate > converted to orotic acid
drugs that interfere with nucleotide synthesis Hydroxyurea = inhibits ribonucleotide reductase, 6-mercaptopurine = blocks de novo purine syn ,5-fluorouracil - inhibits thymidylate synthase, Methotrexate = inhibits dihydrofolate reductase, Trimethoprin = inhibits bacterial dihydrofolate reductase) las3
salvage path - nucleoside and nucleotides salvage pathway = recover bases and nucleosides formed during DNA or RNA degradation, nucleosides (hypoxanthine, guanine, adenine) and nucleotides (IMP, AMP, GMP)
DNA replication - origin particular sequence in genome where DNA replication begins
DNA replication - replication fork Y shaped region along DNA template where leading and lagging strands are synthesized
DNA replication - helicase unwinds DNA template at replication fork
DNA replication - single-stranded binding proteins prevents strand from reannealing
DNA replication - DNA topoisomerases create a nick in the helix to relieve supercoils created during replication
DNA replication - primase makes an RNA primer to which DNA polymerase III can initiate replication
DNA replication - DNA polymerase III prokaryotic - elongates leading strand by adding deoxynucleotides to the 3' end -- elongates lagging strand until it reaches primer of preceding fragment. 3' exonuclease proofreads each nucleotide
DNA replicaiton - DNA polymerase I prokaryotic -- degrades RNA primer and fills in the gap with DNA
DNA replicaiton - DNA ligase seals the DNA
DNA rep - Step 1 helicases unwind the parental DNA double helix
DNA rep - Step 2 single strand binding proteins stabilize the unwound parental DNA
DNA rep - Step 3 the leading strand is syn continuously in the 5' - 3' by DNA polymerase
DNA rep - Step 4 lagging strand syn discontinuously - primase synthesize short RNA primers that is extended by DNA polymerase to form an Okazaki fragment
DNA rep - Step 5 RNA primer replaced by DNA by another DNA polymerase and DNA ligase puts together the Okazaki fragments to growing strand
Fluroquinolones inhibit DNA gyrase (a specific prokaryotic topoisomerase)
Methods of single strand DNA repair nucleotide excision repair, base excision repair, and mismatch repair
Methods of double strand DNA repair nonhomologous end joining
nucleotide excision repair specific endonucleases release the oligonucleotide containing damaged bases, DNA polymerase and ligase fill and reseal the gap, respectively
Xeroderma pigmentosum - nucleotide excision repair no nucleotide excision repair - prevents repair of thymidine dimers from UV light > results in dry skin with melanoma and other cancers
Base excision repair specific glycosylases recognize and remove damaged bases, AP endonuclease cuts DNA at apyrimidine site, empty sugar is removed, and the gap is filled and resealed
Mismatch repair unmethylated, newly synthesized string is recognized, mismatched nucleotides are removed and the gap is filled and resealed (mutated in HNPCC/Lynch) hMLH1 mutation (microsatellite instability)
Nonhomologous end joining brings together 2 ends of DNA fragments -- no requirement for homology (error prone - can lead to translocations and telomere fusions)
DNA/RNA/protein synthesis direction 5' - 3' / DNA syn requires a free 3' OH at add the next nucleotide -- drugs blocking DNA replication often have a modified 3' OH preventing addition of the next nucleotide (chain termination)
Functional organization of the gene 5' promoter, enhancer, promoter (TATA), transcription initiation site, Coding Region (exon/intron) , AATAAA 3'
Promoter site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA and CAAT boxes *mutation = dramatic decrease in amount gene transcribed
Enhancer stretch of DNA that alters gene expression by binding transcription factors - (enhancers and silencers may be located close to far from or even within (in an intron) the gene whose expression it regulates
Silencer site where negative regulators (repressors) bind
RNA processing Nucleus: after transcription 1. capping on 5' end (7-methylguanosine) 2. polyadenylation on 3'end 3. splicing out of introns *capped and tailed transcript = mRNA - transported out of nucleus (AAUAAA polyadenylation signal)
Introns Introns are intervening noncoding segments of the DNA - stay in the nucleus
Exons contain the actual genetic information coding for protein, exons exit and are expressed
Alternative splicing (ex. Beta-Thal mutations) different exons can be combined by alternative splicing to make unique proteins in different tissues (Beta-Thal mutations)
tRNA structure secondary structure, cloverleaf formation, CCA at 3' end along with high % of chemically modified bases - amino acid covalently bound to 3' end of tRNA
tRNA charging aminoacyl-tRNA synthestase examines aa before and after it binds, incorrect bond hydrolyzed, aa-tRNA energy for formation of peptide bond, mischarged tRNA reads usual codon but inserts wrong aa
Tetracyclines aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of aa selection - Tetracyclines bind 30s subunit preventing attachment of aminoacyl-tRNA
protein synthesis - initiation activated by GTP hydrolysis, initiation factors assemble 40S ribosomal subunit with initiator tRNA and released when mRNA and ribosomal subunit assemble with the complex
protein synthesis - elongation 1. aminoacyl-tRNA binds to A site 2. ribosomal rRNA catalyzes peptide bond formation transfers growing polypeptide to aa in A site 3. ribosome advances 3 nucleotides toward 3' end of RNA, moves peptidyl RNA to P site
protein synthesis - termination completed protein is released from ribosome through hydrolysis and dissociates
protein synthesis inhibitors Clindamycin = binds 50S blocking translocation
Posttranslational modifications trimming(removal of N or C terminal propeptides from zymogens to generate mature proteins), covalent alt(phosphorylation, glycosylation, hydroxylation), proteasome degradation(ubiquitin to defective proteins tagged for breakdown)
Created by: Smukadam