USLME - Biochemistry General Questions With Answers @ 2024

USLME - Biochemistry General Questions With Answers @ 2024 Histones are rich in what AAs? - Answer Lysine and arginine (both + charg e) When does histone synthesis occur? - Answer S phase (along with DNA ge tting synthesized) Heterochromatin is _________, euchromatin is _________ - Answer Inactive/conde nsed; active/accessible What allows mismatch repair enzymes to distinguish between old and new DNA strands in prokaryotes? - Answer Methylation; old/template strands ar e methylated, new/daughter strands are unmethylated (and might have error s) Methylated histones are _________ while acetylated histones are __________ - Answe r Inactive "Mute"; active How do you tell thymine and cytosine apart? - Answer THYmine has a m eTHYl group Which is stronger, CG or AT bonds? - Answer CG (three H bonds instead of 2); higher GC content leads to higher melting temp of DNA Amino acids necessary for purine base synthesis - Answer "GAG" = Glycine, Aspa rtate, Glutamine Nucleoside - Answer Base + sugar (nucleoSide = Sugar) Nucleotide - Answer Base + sugar + phosphate (nucleoTide = pho sphaTe) 2 components of a pyrimidine base synthesis - Answer Carbamoyl phosphat e, aspartate Purine synthesis starts with _________ and adds _________ - Answer Sugar/Pi; base Pyrimidine synthesis starts with _________ and adds _________ - Answer Base (orotic acid, later modified); sugar/Pi 2 pathways that involve carbamoyl phosphate - Answer De novo py rimidine synthesis; urea cycle 2 things that can cause orotic aciduria - Answer (1) Ornithine transcaramoylase deficiency (urea cycle), (2) UMP synthase deficiency (pyrimidine synt hesis; this one also has megaloblastic anemia) What is an exception to the genetic code being "commaless" or n onoverlapping? - Answer Some viruses What is an exception to the universality of the genetic code? - Ans wer Human mitochondria Single-stranded binding proteins - Answer Prevent DNA strand from rea nnealing during replication DNA gyrase - Answer Topoisomerase which creates single/double strand br eaks in the DNA to add/remove supercoils; inhibited by fluoroquinolone ABs Primase - Answer Makes an RNA primer on which DNA polymerase III can initiate replication; does this regularly for the lagging strand DNA polymerase III - Answer Prokaryotic polymerase which has 5' -> 3' syn thesis and 3' -> 5' exonuclease activity DNA polymerase I - Answer Prokaryotic polymerase which has 5' -> 3' synthe sis, 5' -> 3' exonuclease, and 3' -> 5' exonuclease activity Telomerase - Answer RNA-dependent DNA polymerase which adds DNA to t he 3' ends of chromosomes to avoid loss of genetic material with every duplic ation; upregulated in cancer cells to increase lifespan Transition mutation - Answer Purine to purine or pyrimidine to pyrimi dine Transversion mutation - Answer Purine to pyrimidine or vice-versa Silent mutation - Answer Codes for same AA (usually changes 3rd po sition of codon "wobble"); protein is same size Missense mutation - Answer Codes for a different AA (e. g. Sickel cell an emia); protein is same size Nonsense mutation - Answer Codes for a stop codon; results in a shor ter, nonfunctional protein Frameshift mutation - Answer Deletion or insertion or 1 or 2 n ucleotides, resulting in misreading of all downstream codons; usually results in shorter, nonfunct ional protein (e. g. DMD) What type of mutation is a conservative mutation? - Answer It is a t ype of missense mutation that codes for a similar AA, so there is no loss of protein foldin g and subsequent function Nucleotide excision repair - Answer Repair process for BIG DNA lesions; endonuc lease removes damaged bases, then DNA polymerase and ligase fill and reseal the gap; associated with xeroderma pigmentosum Enzyme order in nucleotide excision repair - Answer Endonuclease -> DNA polymerase -> ligase Base excision repair - Answer Repair process for SMALL (single base) DNA l esions; glycosylase creates apurinic/apyrimidinic site, endonuclease cleaves 1+ nucleotides from 5' end, lyase cleaves sugar/Pi from 3' end, DNA polymerase-beta fills th e gap, and DNA ligase seals it Enzyme order in base excision repair - Answer Glycosylase, endonuclea se, lyase, DNA polymerase, ligase Mismatch repair - Answer Newly synthesized strand is recognized, mismatched nucleotides are IDed and removed, and polymerase/ligase fill/reseal th e gap; associated with HNPCC Disorder which has defective nonhomologous end joining - Answer Ataxia telangiectasia How does radiation damage DNA? - Answer Double-stranded breaks DNA is synthesized __ to __, while proteins are synthesized __-terminus to __-t erminus - Answer 5'; 3'; N; C DNA is read __ to __; mRNA is read __ to __ - Answer 3'; 5'; 5'; 3' (since we're talking about "reading" the template DNA strand, on which new DNA and mRNA will be ba sed when they are built 5' -> 3') Which end of the DNA has the triphosphate which is the energ y source for the bond? - Answer 5' end Start codon - Answer AUG (codes for methionine in euks and formylm ethionine in proks) 3 stop codons - Answer UGA, UAA, UAG Promoter - Answer Site where RNA polymerase and other TFs bind DNA upstr eam from the gene; AT-rich upstream sequence has TATA and CAAT boxes What happens when you mutate a promoter? - Answer Dramatic de crease in the level of gene transcription Enhancer - Answer Stretch of DNA that alters gene expression by b inding TFs Silencer - Answer Stretch of DNA where negative regulators/represso rs bind