CHEM BIO 2 Flashcards
(70 cards)
How does bacterial transcription differ from eukaryotic
bacteria is done next to ribosome translated
immediately,
bacterial 5’end is a triphosphate
eukaryotic - done in nucleus and transported out ,
2) it has introns to be removed or kept in,
3) has 5’ capping and
4) has poly a tail post transcriptionally
Why do we splice mRNA
biodiverstiy
What and why do we have a 5’ g cap
It is literally GTP applied to the 5 end - Protects the end, disguises it as a 3’ end , prevents degradation and is a (ESSENTIAL FOR LOADING) binding site for ribosome
Why do we have poly A tail
direct mRNA to ribosome - - comes from a POLY A polymerase binder - 50-200 A’s
Know RNA processing steps
draw it out - pol II binds , as soon as transcribed - cap installation - then splicing occurs at splice site - once released - poly A tail from polyemrase - then exported to ribosome - cap and poly a tail have protein protein interactions - then DECAP - marks it for degradation
What does ribonuclease H do
- removes RNA primers from DNA replications - recognizes RNA-DNA hybrid and cuts out RNA - high specificity - good in lab(eg if mRNA pathogenic - can bind antisense DNA and cut it out
Can phosphates be chiral
yeah
What reaction does the ribosom ecatalyze
aminolysis of alpha amino esters (SIMPLE KNOW HOW TO DRAW)
What catalyzes the aminolysis of alpha amin esters
Lone pair on N3 of adenine deprotonates amino group (pKa ~7.6, over 10,000x more basic than N3 of free A due to H-bonding
)
What is energy used for in protein synth
In moving them along the protein and fideltiy
Are amino acids checked?Relevance?
NOPE only based on codon anti codon - SO if can generate an amino acid with the right codon ou can stick whatever you want on there to be added
What is tRNA synthase responsible for
f9idletiy of translation - couplesATP to amino acylation and 2 active site can have different specificity - this ATP attachment is largely done by attaching AMP to something - it’s a good leaving group
Using ATP for an nufvaroable reaction - particular joining amino acid to trna
so ATP binds to amino acid but the pyrophosphate cleaves off - has AMP as a good leaving group so tRNA can attach 9know how to draw - tRNA synthase slide - in notes)
What is a riboswitch
regions on the nascent 3’ RNA THAT CAN BIND SMALL MOLECULES THAT AFFECT translationg - 2 important regions are the termination sequence and aptarmer site which is a ligand binding site - - can cause conformation changes to terminate transcription
t
are peptide sequences directional?
yeah
PRACTICE TELLING IS AN AMINO ACID IS CHARGED OR NOT GIVEN ITS PKA
Most important force for protein folding and name 3 examples
Non polar interactions such as arene-arene, cation pi, dispersive, much more common than H bonds and salt bridges
What are most often the conserved parts of protein structure
hydrophobic core
What are the general forces that control protein secondary and tertiary structure
H-bonds
Dipoles
Sterics
Hydrophobic effect
BUT sterics and dipoles real important
Go over the sterics/ and A12 vs A3 strain again
Know how to draw it - so the A13 comes from the phi bond on the next main oacid and A12 comes from the not phi strain of the same amino acid (can tell byh counting bonds A13 should have 4 bonds total, A12 3) and A13 is the one that is really defining the energy and shape of peptide
Go over the sterics/ and A12 vs A3 strain again
in notes
What is the arrangement for alpha helix in terms of h bonding and why (what are other possible(
i + 4 - most stable (h bond angle matters) i+3 makes a 3:10 helix and i + 2 makes a serpentine shape - gamma turn s- not often used
Alpha helix macrodipoles - describe them
From the N to C terminal have + to negative general macrodipole
amino acids with issues with alpha helix
Proline, glycine and beta branched hydrophobics
