Protein synthesis, modification and targeting

Question 1

steps in leading from DNA to protein fro both eukaryotes and prokaryotes

Answer 1

prokaryotes, one compartment- trx and trn in same place
eukaryotes, trx in nucleus and trn in cytoplasm
introns removed in the nucleus, the remaining exons are polyA and 5’cap, and exported to the cytoplasm

Question 2

mRNA decoded in sets of 3 nucleotides

Answer 2

decode mRNA code like they used a typewriter to decode Uboats
codon is in triplet
degenerate code (more than one codon per AA)

Question 3

tRNA

Answer 3

t shaped molecule that have an anticodon, attach to codon on the mRNA
adds the peptide piece
T domain and D domain recognized by ribosomes
3’ end attached to the AA

Question 4

genetic code translated by means of two adaptors

Answer 4

act one after the other,

the AA attaches to the 3’ end of the tRNA, then it can bind to the codon in the mRNA

Question 5

ribosome

Answer 5

makes proteins, decodes message- has 3 sites APE
the sites made out of RNA
stuck on ER

Question 6

comparison of prok and eukar ribosomes

Answer 6

euk- more proteins involved
heavier
has an extra ribosomal RNA

Question 7

initiation of proteins synth in euks

Answer 7

small ribosomal subunit is carrying the tRNA to the site, polyA tail bound to elF4G
hydrolyze GTP
large subunit comes in and closes it, another tRNA enters A site, the two AA are joined together with a peptide bond, and the tRNAs move through ribosome

Question 8

translation and elongation in protein synthesis

Answer 8

ribosome picks a tRNA that matches the codon, trial and error, the correct tRNA comes in, GTP hydrolyzes, then it stays in ribosome, catalyzes the peptide bond, elongation factor T comes in, hydrolyzes the other GTP and moves the ribosome forward

Question 9

final phase of protein synthesis

Answer 9

binding of release factor to the A site
peptide is hydrolyzed and released
the ribosome dissociates

Question 10

polyribosome

Answer 10

(usually 20 seconds to several minutes to make a protein transcript)
multiple ribosomes on a transcript

Question 11

inhibitors of proks protein synthesis are useful antiobiotics

Answer 11

tetracycline- inhibit binding of aminoacyl tRNA to A site in ribosome
streptomycin- pevents transition from trnsl. initiator to chain along. and cause miscoding
actniomycin D- blocks RNA polymerase
side effects come from mitochondria

Question 12

binding sites for antibiotics on bacterial ribosome

Answer 12

bind to the subunits to make it difficult for the ribosome to move along the mRNA

Question 13

nonsense-medicated mRNA decay

Answer 13

messes up the splicing
splice sites are impt, but if something isn’t spliced out, the ribosome hits a stop codon in the intron and UpF proteins bind, stops the translation

Question 14

steps to create functional protein

Answer 14

folding and cofactor binding
covalent modifications (glyc, phosph, acety)
binding to other subunits

Question 15

posttranslational modifications

Answer 15

adding bch. fuxnl groups, changes nature of the protein
enzymatic and non enzymatic, 
add hydrophobic groups
cofactors
modifications of translation factors
add small chem groups

Question 16

cotranslational protein folding

Answer 16

folding occurs as the ribosome is making the protein (spontaneous)

Question 17

chaperone

Answer 17

protein that helps the protein fold correctly and bind to other correct proteins (use hsp70 and ATP), if it can’t, the misfolded protein is sent to a proteasome for destruction

Question 18

Hsp60 family chaperones

Answer 18

it pulls proteins into the chaperone, recognizes the hydrophobic domain, there is a protein cap that covers the top, there is a squished conformational change, refolds it correctly and releases the good protein structures

Question 19

proteasome

Answer 19

degrades misfolded protein that has polyubiquitin chain marker, degrades it processively

Question 20

ubiquination

Answer 20

monoubiquination- histone regulation
multiubiquination- endocytosis
polyubiquination-proteasomal degradation or DNA repair

Question 21

protein aggregation can make human disease

Answer 21

mutant can change the conformation of proteins and change their shape of future proteins, they aggregate together and they can’t be degraded properly
like turning into beta sheet structures or amyloid sheets
THINK PRIONS

Question 22

protein target and sorting

Answer 22

targeting signal- AA that directs protein to organelle
cytosol proteins- no sorting signal
nuc- have nuc loc. sig
mito- have sorting signal
resident ER proteins have KDEL sequence
lysosomal proteins tagged with mannos 6 phos
proteins cotranslated in ER have signal sequences to send to golgi, PM, lyso, or secretion

Question 23

micro RNA (miRNA)

Answer 23

powerful translational regulator
usually a hairpin
gene switches
bind to some mRNA and attract RISC complex for degradation or repression of the gene
some are created on one miRNA and are cleaved by Drosha, exported, Dicer cuts off the loop, and makes a mature miRNA

Question 24

miRome

Answer 24

the miRNA genome, there are 2588 in homo sapiens
4 in HIV
overall: 28645 miRNA for 233 species

Question 25

regulation of tumorigenesis by miRNA

Answer 25

up regulate the trx of tumor suppressing miRNA, try and bind to the oncogene supposed to only target the specific gene researchers found that some people have mutations in oncogenic miRNA, it won't bind to the tumor suppressor gene and the tumor won't grow

Question 26

miRNA and cancer cell regulation

Answer 26

depending on the miRNA, they can regulate at different stages of tumor growth. can try and inhibit cancer stem cell, the epithelial mesenchymal transition, and the tumor cell invasion

Question 27

miRNA based treatment

Answer 27

try and synthesize miRNAs that can target the genes that are oncogenic or virus or they can treat the creation of the miRNA so it won't bind (miravirsen)