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WEEK 4:
Molecular Genetics 1:
| Question | Answer |
|---|---|
| describe how nucleotides join on carbon atoms | phosphate attaches to sugar hydroxyl (5'-3') read from left to right |
| describe phosphodiester bonds | polar, asymmetric, 5'-3' |
| what type of structure does DNA have | double helix, anti parallel |
| define pyrimidine | one ring |
| define purine | two rings |
| what bases are pyrimidines | cytosine, thymine, uracil |
| what bases are purines | adenine + guanine |
| base stacking | bases stacked like a ladder using hydrophobic interactions + each base rotates slightly in the double helix where 10 base pairs = 1 full turn |
| + strand | sense strand 5'-3' |
| - strand | template strand 3'-5' |
| what strand does mRNA bind to | - (template strand) |
| B form of DNA | most common form on DNA |
| when 2 DNA strands twist together what forms | major and minor grooves |
| what groove displays base edges better | major |
| why are the grooves important | important site for where protein binds to DNA bases |
| examples of chemical inserting between stacked bases | ethidium bromide + benzo[a]pyrene |
| why do chemicals insert between stacked bases | similar shape rings |
| what happens when chemicals like ethidium bromide insert between stacked bases | DNA damage |
| conservative replication | parent -> oldold + new new |
| semi conservative replication | each strand acts as a template (parent -> oldnew oldnew) |
| where are strands separated in eukaryotic chromosomal replication | at multiple points |
| how many origins of replication are in prokaryotes | one |
| replication fork | DNA unwinds halfway through into a Y shape |
| describe the direction of movement of replication forks | opposite directions |
| if two strands are separated and DNA cannot rotate what does this mean | remaining DNA becomes over wound creating supercoiling so DNA replication stops |
| how do cells stop DNA from supercoiling | topoisomerases |
| topoisomerases | enzymes which stop DNA supercoiling |
| prokaryotic topoisomerase example | gyrase (bacteria) |
| how is bacterial gyrase inhibited to stop bacterial replication + treat bacterial infections in humans | using nalidixic acid |
| what do DNA polymerases require | dATP, dCTP, dGTP + dTTP and a primer |
| primer | small, pre-existing strand of 20 base pairs of RNA, made by DNA primase (DNA dependent RNA polymerase) |
| describe DNA polymerase in E coli | 2 DNA polymerase III molecules at each fork moving in the same direction (5'-3') but strands are different polarities |
| problem with lagging strand | DNA replicated backwards (3'-5') in smaller pieces (okazaki fragments) that are later pieced together |
| solutions for lagging strand replication | has repeated initiation by primase (as needs to add a primer each time to being replication) + small polymerase runs across once primer is add to make small DNA strands (okazaki fragments) |
| examples of drugs that target replication | camptothecin + etoposide |
| camptothecin | DNA topoisomerase I poison (prevents DNA from resealing after cutting by forming non covalent complexes), causing strand to break/death with higher levels in cancers + analogs used to treat colon, ovarian + cervical cancer |
| etoposide | impacts topoisomerase II in late S& G2 phase, preventing DNA re-ligation (binding) triggering mutagenic/ cell death pathway, used in testicular, prostate, bladder, stomach + lung cancers |
| list the order of replication in the replication fork | helicase + topoisomerase/ DNA gyrase (bacteria), RNA primer removed, DNA polymerase, DNA ligase |
| what does helicase do | unzips DNA strands |
| what does DNA polymerase do | uses RNA primer as starting point to add DNA nucleotides in 5'-3' direction to make a new strand |
| what does DNA ligase do | joins okazaki fragments together creating complete DNA strand by forming phosphodiester bonds |
| analogs | compounds with similar structure but different chemical makeup |
| where does camptothecin derive from | camptotheca acuminate |
| where does etoposide derive from | podohyllum peltatum + podophyllum emodi |
| what is etoposide used for | used in testicular, prostate, bladder, stomach + lung cancers |
| what is camptothecin used for | analogs used to treat colon, ovarian + cervical cancer |
| compare half life in mRNA and DNA | mRNA has a short half life compared to DNA |
| mRNA half life in bacteria | minutes |
| mRNA half life in eukaryotes | hours |
| what does a longer mRNA half life mean | higher protein synthesis rate (for given mRNA production rate) |
| difference in RNA functionality in prokaryotes and eukaryotes | RNAs fully functional in prokaryotes after transcription but not in eukaryotes |
| describe mRNA positions in cellular locations | positioned near where the protein will be needed using 3' untranslated region (3' UTR) like a post code (non coding region that helps recognition to bind to mRNA), placed asymmetrically (one side) with translational control (only activated when needed) |
| describe the 5' end modification capping in eukaryotes | in eukaryotes, GMP (modified guanine) is added by 5'-5- triphosphate bond in RNA which helps with stability (protects RNA from exonuclease- enzymes that ruin RNA ends) |
| stop codons | UAA, UAG, UGA |
| reading frame | long line of bases where ribosome could begin anywhere so reading frame gives specific starting point to which codons are read first in mRNA in order to make the correct protein |
| start codon | AUG |
| ORF | region that gets translated into protein |
| 5' UTR | region of mRNA upstream of AUG in 5' direction that does not code for protein, allows translational repressor to bind so that ORF cannot be made into a protein as it is not needed |
| order of mRNA makeup | 5' cap, 5' UTR, start codon AUG, ORF, stop codon, 3' UTR |
| translational repressor | binds to 5' UTR to prevent coding of mRNA into protein as it is not needed |
| kozak sequence in eukaroytes | 5'-ACCAUGG-3' (start codon AUG surrounded by specific sequence to attract ribosome) |
| shine dalgarno sequence in prokaryotes | short sequence upstream of start codon AUG help attract ribosome |
| hyperferritinemia (case example) | excess ferritin (protein storing iron), caused by mutations within iron responsive element in 5' UTR of L- ferritin gene |
Created by:
kablooey
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