UWorld mix Aug 7th Flashcards
isomers that differ in their connectivity are called
consitutuional isomers
isomers that can be the same with rotation around bond
conformational
isomers that you would need to break bond to ake the same
configurational
configurationa isomer that is due to resticted movment (ie doube bond)
geometric, cis-trans isomer
do conformational isomers fall under diasterosomers?
no, it goes constitutional or steriososmers
and then steriosomers can be conformational or configurational and the configurational can be geometic, diasteriomers or enantiomers
describe one way geometric isomers can be seperated?
by GC bc they have different bp’s
is proline polar or non-polar
non-polar
are the acidic and basic amino acids hydrophilic?
yes, they are charged
tyrosine and cystine are a point of confusion
they both have polar bonds,
on own polar (SH bond)
when cysteine is S-S bonded - hydrophobic
tyrosine hydrophobic is the consensus- but can kinda be both
methionine
non-polar bc methyl attached to it
tyrosine
kaplan says relativley polar bc OH
how to determine R and S if H is in line with plane (not out, not in)
- pretend you are looking at it from side ( see if can figure it out
- rotate it, when we rotate the outy- stays put - think like your holding the massage spide thing from the top and rotate the other 3 prongs
tryptophan
non-polar - funky one with 2 righgs, aromatic
phenols with strong oxidizing agent
turn into quinones ( which are phenols but with the H’s removed and double c=o bonds) and only 2 double bonds on the ring - so usually not aromatic
ubiquinone(electron carrier) can be reduced to
ubiquinol (has OH)
how can alcohols serve as protecting groups
by reacting them with aldehydes or ketones they turn them to ketals and acetals which will protect the aldyhede and ketones - to remove them react with acid
why react alcohol with mesylate or tosylate?
so they attach to OH and become a leaving group - used for Nu subsitution (bc Oh is normally not that great)
sketcher synth
aldehyde, NH4Cl, and CN
irreversible rxns tend to be under _______ control and these favour
kinetic, low temp and the most favourable product is the one with the lowest activation energy
- the lowest activation energy reaction will yeild the most productive
reversible rxns tend to be under ________ which favours
thermodynamic control, high temps
- under these conditions all products form readily, and the most stable product will be favoured
how do you determine the most stable product
the lowest delta G
at 298K which products would be favoured
this is a low temp = irreversible rxn under kinetic control (this was stated in the passage- I missed it ) —> the product that is favoured will be the one with the lowest activation energy
when passage reads the reaction is irreversible what can we infer
that they are under kinetic control, so when deciding which product is favoured - look for activation energies
unit reaction rate is measured in
concentration of reactants used up or concentration of products produced over time
so a high rxn rate = fast rate
how is rate constant k related to T and activation energy
with Arrenhius equation
k= Ae^-Ea/RT
but get rid of negative expo by putting it in the denominator
when temp increases what happens to k
k increases exponentially
when Ea decreases what happens to k
k increases exponentially
when catalyst is added what happens to k
lower Ea, lower denominator = greater k = faster rate
what is the relevance of an equivalence point
at this point exactly enough (equal molar quantity) of base has been added to completly neutralize acid
- so if 50ml of 0.1M H2CO3 t titrated with 2M NaOH, then the mols of acid are 0.005, meaning that we need 0.005 mols of acid at the first equivalence poiint
- we are told 2M NaOH is the titrant –> so need 0.025ml to make 0.005
adiabatic
no heat exange
interferon
peptide signal that interfers with virual replication
- they induce production of RNaseL which cleaves RNA in cels to reduce the ability for virus to replicate
how can the host stop viral replication
by stropping viral transcription and translation –> this is what interferons do
what enzyme synthesises new DNA strand in replication euk and prok?
pro- DNA polymerase III
euk - DNA polymerase a,g,e
what enzyme removes RNA primer?
pro- DNA polymerase 1
euk- RNase H
then filled with DNA polymerase 1 (pro) and DNA polymerase g (euk)
monocistronic vs polycistronic
eukaryotic mRNA is monocitronic meaning that each mRNA translates to only one protein
but in prokatyotes, DNA is polycistronic, so starting translating at different parts on mRNA molecule can result in dif proteins
what is eukaryotes mRNA
Monocistronic mRNA is a mRNA that encodes only one protein and all eukaryotic mRNAs are monocistronic
what enzyme activates tRNA
aminoacyl-tRNA synthetase (requires ATP)
what organic chem rxn happens when tRNA is activated
CA (on aminoacid) + OH on tRNA 3’ end = an ester!
sequence on the 3’ end of tRNA
CCA
the activated tRNA has stored energy in its eter bonf- what does this power
translater - peptide bond later on
where is rRNA synthesized
in the nucleolous
ribozymes
enzymes made of rna instead of proteins
ribozymes help catalyze peptide formation
how doe you read anticodond
5’ to 3’ but this looks backwards - so just be careful with these questions
how to remeber stop codons
U Are Annoying
U Go Away
U Are Gone
nonsense vs missense
this nonsense has to STOP
missense is one aa for another
in eurkaryotes what enzyme is the main player in RNA transcription
RNA polymerase II - binds to TATA
DNA polymerase III
in e.coli - primary enzyme for DNA replication (equivalent to DNA poly age in eukaryotes)
which RNA in eukaryotes transcribes mRNA
RNA poly II ( 1 synth rRNA, 3 synth tRNA and some rRNA)
differences in DNA polymerase and RNA polymerase (one MAIN one)
RNA does NOT proofread
also doesnt need an RNA primer … duh
antisense stranf vs sense strand terminology refers to
antisense is the template strand so antiparallel and complmentary
and the sense strand –> is identica to the mRNA (exept it has thyamine - mRNA has uracil ) but it doest do anything during transcription- just gets pulled apart and seperated
is uracil or thymine heavier
thymine- bc it has one extra methyl group
affliction
something that causes pain or suffering
the first base transcribed from DNA to RNA is denoted?
+1 ( there is no zero) - TATA is usually around -25
what is mRNA called before it is processed?
hnRNA -the primary transcript
before hnRNA can leave the nucleous what has to happen
3 things so that it can survive the cytoplasm and interact with ribosome
- poly A tail, 5’ cap and intron splicing
introns
stay in the nucleus
what enzymes splice
snuRPs/ snRNA complex
whats the 5’ cap
7-methylguanylt triphosphate cap - protect from degradation
poly A tail
like time bomb as sooon as it leaves the tail will start getting degraded so the longer the tail the better
what is still left at the end of hnRNA processing? why?
UTRs- untranslated regions of mRNA on both the 5’ and 3’ end
- bc ribosome initiated translation at the start codon and end at stop
- roles in stability, translation ect..
where does translation get its energy from
GTP is required for each step: initiation, elongation and temination
eukaryotes subunits
40S + 60S = 80S
prokaryotes subunits
50S + 30S = 70S
where does translation occur
in the cytoplasm
in pro where does small ribosome bind
Shine-Dalgarno sequence which is in the 5’ UTR
in euk where does the small ribosome bind
to the 5’ cap
RNA –> protein - what way does ribosome read the mRNA? how does this ocmpare to the reading of RNA polymerase
ribosome reads 5’ to 3’ —> synth protein from N to C terminal
whereas NA poly and DNA poly READ 3’ to 5’ bc they synthesize 5’ to 3’
whats in the A site
the next amino acid to be added (determined by the mRNA codon in the A site bottom
- order is APE
whats in the P site
the tRNA with the growing peptide chain
also where the first methionine binds
the polypeptide chain is passed from P to A with peptidyl transferase (GTP)
when ribosome comes across a stop codon
a release factor binds to A site – this causes a water molecule to be added chain to hydrolyze the chain from tRNA
prenylation
adding lipid groups to proteins
Alternative Splicing vs. Monocistronic
so eukarytes are monocisronic meaning that one gen codes for one primary hnRNA under control of one promotor - however alternative splicing can cause many different ISOFORMS of that protein to come about
whereas prokaryotes have many genes under the contro of one promotore (lac) byut dont have mRNA proccessing
does prokaryotic mRNA get processed
In prokaryotes, there is a little or no processing of mRNA transcripts. Prokaryotic mRNA is degraded very rapidly from 5′ end. Therefore, to rescue from degradation it is translated before being finally transcribed.
operator site
non-transcribable region of DNA that a repressor protein can bind
promotor region
for RNA polymerase to bind
reguator gene
code from protein known as repressor
inducible system
repressor bound tight to operator, negative control
need an inducer to remove the roadblock
example of an inducable system
lac operon –> repressor is bound but lactose can act as an inducer and remove the roadblock
with help of CAP ( a TF)
CAP
is a TF used in e.coli,
low glucose- need to use diff fuel source, low glucose= high cAMP which binds to CAP- change shape and it can now bind to the promoter region of gene- further increase transcription of lactase genes
CAP binding increases transcription - this is called positive control
repressible system
usually always on, but when corepressor binds, the repressor binds to the operator and stops transcription
- Trp operon
when tryptophan is high it acts as a corepressor and a binds to repressor causing it to bind to operant site and thus turns off cells own supply of tryptophan
histone acetylases
coactiators
open up DNA bc they add an acetyl group to lysine whihc decreases positive charge on protein- lessens its attraction to DNA so it open up
histone deacetylases
deactivate DNA (close it up)
DNA methylation
silencing
during development - methylation plays an important role in silencing genes that are no longer needed
