Final Flashcards
PTransM: function of enzyme peptidases or proteases
cleavage of peptide bond
PTransM: functions of disulfide cross linking
joining to Cysteine groups together S-S to make cystiene
Process of preproinsulin to insulin
after membrane transport (from ribosomes), the leader sequence is cleaved by protease then the resulting proinsulin is folding using disulfide bonds and lastly, the connecting sequence gets cleaved resulting in the final mature insulin
Does proinsulin or insulin run faster on polyacrmylamide gel?
insulin runs faster because it has a lower MW so it will be at bottom while the pro insulin will be at the top (heaviest MW)
PTransM: acetylation of histone tails
lysine w/ histone tail + Acetyl CoA + HAT = opening of the double helix which allows enzymes to come in for transcription
Reverse you use HDAC to put back together
PTransM: GPI anchors
GPI anchors proteins into the cell membranes at the C terminus
PTransM: Vit C Dependent
example being the hydroxylation Vit C (acts as an antioxidant) is required so it can convert Fe3+ to Fe2+ so it can be used in the proline --> hydroxylproline reaction (IMPORTANT in SCURVY disease, aka lack of vit C disease)
PTransM: function of kinases
phosphorylation of hydroxyl groups (SER, THR, TYR)
PTransM: function of phosphotases
removal of PO4 group from a phosphorylated side chain
PTransM: Phosphorylation of CTD in RNA 2 poly (EUK) is a form of PTM and regulation. What is the protein that acts as a kinase?
TFIIH
PTransM: N linked glycosylation
occurs on ASN side chains, occurs in ER during synthesis, occurs b/w the amide N of the ASN and the C-1 of the amino sugar residue
PTransM: O linked glycosyaltion
occurs on SER and THR side chains, bond occurs b/w OH of the SER and THR and the amino sugar of the sugar residue
PTransM: zinc finger
zinc finger is bound to 2 CYS and 2 HIS residues. ZFD interact with the major groove with 3 consecutive bases from one strand of B-DNA
PTransM: Chaperonin
assists in protein folding, have to have hydrolysis of ATP molecules
PTransM: Ubiquitin
mostly highly conserved protein known in PRO and EUK, last form of PTM used to degrade protein, requires energy and LYS in target proteins, proteasome recognizes the polyubiquitinated protein that catalyzes the degradation of that protein
Biotechnology: basic cloning process
mRNA + reverse trancriptase = cDNA which is joined to the plasmid, that newly synthesized plasmid is then inserted into the E coli
Biotechnology: basic step in recombinant DNA experiment
1) Preparation of DNA
2) Cleavage of DNA in particular sequences
3) Ligation of DNA fragments
4) Introduction of recombinant DNA into compatible host cells
5) Replication and expression of recombinant DNA in host cells
6) Identification of host cell that contain the recombinant DNA of interest
Biotechnology: endonucleases are needed for
for reconstruction, they have to cut vector and pop in the target of the gene to that region
Biotechnology: Ligase is needed for
joining the cDNA into the plasmid
Biotechnology: Restriction enzymes
cut DNA at highly specific sequences, they have to be palindromic sequences (inverted repeats)
Biotechnology: in order to replicate, a plasmid MUST be
circular AND must contain a replicon
Biotechnology: what do you NOT want to have in your target DNA?
you do NOT want to have introns, thats why you use cDNA
Biotechnology: preparation of cDNA
mRNA + oligo (T) primer + reverse transcriptase = cDNA and mRNA (next the mRNA is degraded and TTTT is attached at the 3’ end of the cDNA, next DNA poly is added and made into a double stranded cDNA, next you will insert that into vector into plasmid
Biotechnology: Are probes used to screen?
probes are used to scan cDNA library for particular DNA sequences
Biotechnology: 3 possibilities of the experiment findings
1) no transformation
2) blue colonies cells were transformed but they did not contain the inserts
3) white colonies cells were transformed and they DID contain the inserts
Biotechnology: ampicillin
cells that are resistant to this will be white or blue colonies
Biotechnology: Dideoxy method
contain an H at the 3’ position where there is normally a OH. These are chain terminators, if you incorporate one of these, it will not attack incoming nucleotides and will not create a phosphodiester bond, terminates at that point where this is incorporated, done through a machine, makes exponential copies of the target sequences.
Translation: initiation in PRO
recognized by shine delgrano’s sequence in mRNA by 16S rRNA
Translation: formulated MET
only found in PRO, this recognizes AUG (start codon)
Translation: methionine’s found in PRO
both formulated MET external (Fmet-tRNA) and regular MET internal
Translation: Methionine’s found in EUK
ONLY regular MET, no formulated MET
Translation: formylmethionyl
form of post translational modification, after tRNA gets transcribed, formyl group attaches to the amino group
Translation: Steps of initiation of PRO
30S will tract for AUG and position itself w/ 3 codons in place to position tRNA’s, anticodon will be complimentary of codon mRNA, 16S of the 30S will find the shine delgrano’s sequence, once found the IF’s come in and recruit 50S resulting in the whole 70S complex
Translation: Initiation factors in pro and euk
pro (3)
euk (8 or more)
Translation: Elongation factors (pro) and their process
EF-Tu: bring in amino acid and position on codon , GTP gets hydrolyzed to GDP
EF-Ts: recycle GDP and turn back into GTP so EF-Tu can use it again for another cycle
Peptidyl transferase comes in to attach the amino acids creating a peptide bond
EF-G: once created, EF-G will move peptidyl-tRNA to the P site and allow the A site to be open for another amino acid
Translation: peptidyl transferase
catalyzes peptide bond formation
Translation: 3 steps for chain elongation
1) positioning correct amino aicd tRNA in the A site
2) Formation of the peptide bond
3) Shifting mRNA by one codon
Translation: Termination are caused by what
Termination factors
Translation: Termination steps
e coli releases termination factors, the TF will come in and bind to stop codons (UAA, UAG, UGA), once bound the polypeptide chain will be released by activating hydrolysis of the peptidyl-tRNA
Translation: Differences b/w PRO and EUK, ribosomal structure
same process, PRO: 70S– 50S + 30S (16S recognizes shine delgrano)
euk: heavier in weight 40S + 60S = 80S
Translation: Differences b/w PRO and EUK, Initiator tRNA
pro: n-formylmethionyl-tRNA
euk: methionyl-tRNA, 5’ cap site is recognized as the origin of translation, 40S will find the cap, tracks for the 1st AUG, MET binds to the codon, recruting the 60S resulting in whole complex 80S
Translation: Differences b/w PRO and EUK, initiation factors
pro: IF 1, 2, 3
euk: 8 or more
Translation: Differences b/w PRO and EUK, Elongation
pro: EF-Tu, EF-Ts, EF-G (3)
euk: EF1 and EF-Ts (2)
Translation: Differences b/w PRO and EUK, Termination
pro: RF 1 and RF 2
euk: eRF1 (1)
Translation: Differences b/w PRO and EUK, mRNA
For EUK, the 5 capping and poly A tail aid in stability
Translation: Differences b/w PRO and EUK, Protein synthesis
pro: cytoplasm
euk: nucleus
Streptomycin
inhibits translation only attacks PRO system, treats bacterial infection
Purocycin
dont ever use to treat, kills protein synthesis
Genetic code:
overlapping or non-overlapping
punctuation or no punctuation
Degenerate or not?
non overlapping, NO punctuation, and DEGENERATE
Genetic code: How many different codons are there for 20 amino acids?
64 codons
Genetic code: Stop codons
UAA, UAG, UGA
Genetic code: Start codons
AUG which is the only codon for Methionine
Genetic code: Some tRNA molecules can recognize more than one codon. The recognition of the 3rd base in the codon by the anticodon is called
the wobble
Genetic code: On the CCA acceptor stem, there is an aminoacyl-tRNA attached via
ester linkage
aminoacyl-tRNA is an amino acid ester of tRNA
Genetic code: function of aminoacyl tRNA synthetase
attaches amino acid to CCA acceptor stem on tRNA
Genetic code: Aminoacyl-tRNA sythetase reaction, what does it have to have
needs ATP for reaction to occur
RNA processing: what are the 3 steps of EUK PTranscM
1) 5’ppp capping
2) poly A tail
3) splicing
RNA processing: For the capping of the 5’ end of euk mRNA, what is the linkage called b/w the GTP molecule and precursor mRNA?
5-5 triphosphate linkage
1 PO4 on the GTP and 2 PO4 on the precursor mRNA
RNA processing: function of S-adenosyl methionine
the enzyme that caps and methylates CAP 0 at N-7
RNA processing: What begins/synthesizes polyadenylation? And at what end of the mRNA precursor?
RNA poly 2!! and at the 3’ end of the mRNA precursor
RNA processing: CPSF forms a complex containing what enzyme? This helps catalyze the cleavage of the transcript downstream
RNA endonuclease
RNA processing: After the endonuclease dissociates, the new 3’ end of the precursor is polyadenylated with what enzyme?
poly A polymerase
which results in the polyadenylated mRNA precursor
RNA processing: What do the splice sites contain as well as the branch site? These splice sites are also called what?
5’ splice site is GU, branch site is an A, and the 3’ splice site is an AG
—introns
RNA processing: What is the spliceosome?
a RNA protein complex that catalyzes splicing reactions
RNA processing: During the removal of the intron, what group attaches the 2’OH group on the 5’ splice site?
the branch site, A
RNA processing: After the 2’OH group is attacked by the A, what is the resulting linkage called? what is this overall process called? How is the newly OH group oreinted?
2-5 phosphodiester linkage, transesterfication, hanging 3’ OH group from the 5’ splice site
RNA processing: The newly 3’OH group hanging off of the 5’ splice site attacks what next?
The 3’ splice site
RNA processing: After the 3’OH from the 5’ splice site attacks the 3’ splice site, what does it result?
mature mRNA and lariat shaped molecule
Thalassemia is caused by ______ mutation which causes degradation of the alpha and beta cells
splicing
tRNA processing: which endonuclease cleaves the primary transcript?
RNase P
tRNA processing: what enzyme adds the CCA sequence to the 3’ end
tRNA nucleotidyl transferase
Rifampicin
inhibits transcription by blocking the RNA poly from binding
Actinomycin
prevents DNA to be used as a template
Cisplatin
inhibitor of replication and transcription
