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28 Cards in this Set
- Front
- Back
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what is an interesting case of a polar bond?
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h3po4 because the charge is shared between all oxygen atoms
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which molecules can cross the Bio Membrane?
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uncharged, nonpolar, hydrophobic molecules, buffers usually can, except for Hepes - local charges
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what constitutes an amino acid?
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alpha carbon atom, nh2, cooh, h, R
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hydrophobic amino acids?
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alanine - small
tryptophan - big methionine - long and narrow |
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what determines whether a basic amino acid is charged?
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if it's strongly basic it will retain it's charge
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what are the 3 special amino acids and describe each one?
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cysteine - forms disulfide bridges when oxidized
proline - R group is fixed, ring glyceine - simplest and smallest |
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define transcription
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process by which the information stored in DNA is copied into RNA
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define translation
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process by which the information in RNA is used to create a protein of a specific amino acid sequence
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describe phosphodiester bonds
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they link the 3' hydroxyl group of one base to the 5' phosphate group of another, leaving a free 5' phosphate group at one end and a free 3' oh group at the other end
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How is DNA bended, where is bended and why is this done?
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it is bended by DNA bending proteins
bended around its long axis - no H bonds done so it can pack into chromatin |
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what is the Tm of DNA
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temperature at which half the bases aren't engaged
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how is torsional stress created in prokaryotes?
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circular DNA can be twisted onto themselves - supercoiling
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how is torsional stress relieved?
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topioisomerases 1 and 2, cleave one or two of the DNA strands to flatten the supercoiling
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describe what occurs during initiation - 3 parts
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- template strand has an initiation start site in the promoter region which positions the RNA polymerase (closed complex)
- RNA polymerase melts the DNA duplex near the start site (open complex) - RNA polymerase catalyzes the phosphodiester linkage for the two initial rNTPs |
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describe what occurs during elongation - 3 points
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- polymerase advances 3' to 5' down template melting DNA duplex and adding rNTPs
- polymerase reanneals DNA duplex behind it - elongating RNA strand has 5' end reeled out of hybrid region |
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describe what occurs during termination
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RNA polymerase reaches transcription stop site and releases the RNA molecule and dissociates from the DNA
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what is an operon and how is it transcribed?
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an operon is an arrangement of genes with a common function and it is transcribed on one mRNA from a single transcription initiation start stie
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describe the addition of the 5' cap structure of RNA processing
what is the purpose of this? |
7-methyl guanylate is added to the 5' terminal nucleotide by a 5'-5' linkage
it protects from deterioration, aids transport into the cytoplasm and recruits translation factors |
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describe the addition of the poly A tail of RNA processing
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polyadenylation in the 3'UTR adds 100-250 adenine residues by poly A polymerase
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how is the continuous mRNA as the final step of RNA processing?
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introns are removed and exons are spliced together, mRNA retain their UTRs at the 5' and 3' ends
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describe alternative splicing and what is its purpose?
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primary transcript swaps exons to produce alternative mRNAs that encode protein variants of the same gene - isoforms - diversity!
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what is the CTD and what role does it have in transcription?
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carboxy terminal domain - largest subunit of RNA pol II
when it's unphosphorylated it initiates transcription when it's phosphorylated transcription is active |
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describe the 6 steps in initiating transcription (forming pre-initiation complex)
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1 - TATA box is bound by TBP (part of TFIID) which binds to the minor groove of DNA, TFIIA is also required
2 - TFIIB binds to both DNA and TBP 3 - pre-formed complex of RNA pol II with CTD tail and TFIIFbinds next (RNA pol II does not binds precisely at TATA box) 4 - TFIIE binds - act as docking site for TFIIH 5 - TFIIH binds (pre-initiation complex complete) - has helicase and kinase activity - helicase unwinds DNA to form open complex (template strand) 6 - kinase activity phosphorylates CTD, promoting elongation all factors are released except TBP |
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what is the operator region? where would it be located?
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it is a region on n operon that recognizes transcriptional activators and repressors
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how is a transcription repressed in a lac operon?
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lac repressor binds to the operator and sterically overlaps RNA poll II and inhibits transcription
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how can transcription in an operon be derepressed?
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presence of lactose, binds to lac repressor and changes its conformation so it can't bind to the operator region
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how can transcription in an operon be activated?
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low glucose, high lactose, cAMP is synthesized and binds and activates CAP which binds to the CAP site and interacts with RNA poll II to stimulate transcription
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what is the purpose of a sigma factor?
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recruits RNA pol II and recognizes specific DNA sequences - necessary for transcription initiation in prokaryotes
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