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114 Cards in this Set
- Front
- Back
There are 3 sites on a ___S ribosome:
|
70S
A P E |
|
__-site: binds the incoming aminoacyl-tRNA
|
A-Site
|
|
__-site: binds peptidyl-tRNA
|
P-Site
|
|
______-___ = tRNA + growing
peptide chain |
Peptidyl-tRNA
|
|
__-site : transiently binds to outgoing deacylated tRNA
|
E-Site
|
|
______-___ = tRNA + amino acid
|
Aminoacyl-tRNA
|
|
There is a tunnel-like structure between the __ and __-sites where the growing polypeptide
leaves 70S ribosome. |
E + P
|
|
Two subunits on eukaryotic ribosomes:
|
40S + 60S
|
|
Eukaryotic __S rRNA contains _______ ______ (peptide bond formation)
|
28S
peptidyl transferase |
|
Protein synthesis proceeds from the __-terminus to the _-terminus.
|
N to C
|
|
mRNA is read in the __’ to __’ direction.
|
5' to 3'
|
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Codon-anticodon interaction is proofread by the ______
|
Ribosome
|
|
3 Initiation factors:
|
IF-1
IF-2 IF-3 |
|
Assists IF-3 in separating ribosome subunits by binding to 30S
|
IF-1
|
|
Bound to GTP, ____ binds fMet-tRNAfMet and then to P-site at start codon
|
IF-2
|
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____ assists in separating ribosome subunits by binding to 30S
|
IF-3
|
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Bound to GTP, _____ binds to aminoacyl tRNA (charged tRNA) and binds in A-site
|
EF-Tu
|
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_____ Recharges EF-Tu with GTP
EF-Tu GDP -----> EF-Tu GTP |
EF-Ts
|
|
Bound to GTP, _____ causes translocation of ribosome by one codon via the
energy from _____ hydrolysis to _____ |
EF-G
GTP’s GDP |
|
Bound to GTP, _____ assists in termination by binding to RRF at stop codon in
A-site and hydrolyzing its GTP to GDP to make everything dissociate from ribosome |
EF-G
|
|
Binds to stop codon (UAA and UAG) in P-site and induces conformational change
causing peptidyl transferase to hydrolyze the peptide from tRNA in P-site |
RF-1
(release factor) |
|
RF-2 binds to stop codons (___ + ___) in P-site: same function as RF-1
|
UAA
UGA |
|
Bound to GTP, ___ binds to RF-1 in A-site
● GTP hydrolysis to GDP causes RF-1 and ___*GDP to dissociate from A-site |
RF-3
|
|
Binds in A-site to stop codon after RF-3*GDP leaves and is then bound by EF-G*GTP to end translation
|
RRF
|
|
3’ end of ____ rRNA (in the 30S subunit) binds to the Shine-Delgarno sequence to help position the P unit of the ribosome at the start
codon |
16S
|
|
________________ = fMet
the amino acid required to start translation in prokaryotes. |
N-Formylmethionine
|
|
IF-2 GTP binds fMet-tRNAfMet, which is the only tRNA that binds to ____ ribosome
|
30S
|
|
Once IF-3 leaves, the ___ subunit rebinds forming the 70S initiation complex:
o Empty A-site o fMet-tRNAfMet bound in P-site |
50S
|
|
There are three main steps to elongation which occur many times per polypeptide:
|
Decoding
Transpeptidaion Translocation |
|
_________: Transfer of proper aminoacyl-tRNA from cytoplasm to A-site of ribosome
|
Decoding
|
|
Elongation:
__________: Covalent linkage of new amino acid to growing polypeptide chain. |
Transpeptidation
|
|
_________: Movement of tRNA from A-site to P-site and simultaneous movement of
mRNA by 3 nucleotides (1 codon) |
Translocation
|
|
Transpeptidation :nucleophilic attack from the __-_____ group of aminoacyl-tRNA in
the A-site to ____ _______ on peptidyl-tRNA in the P-site |
α-amino
carbonyl carbon |
|
Translocation involves what elongation factor?
|
EF-G GTP
|
|
Termination
After RF-1 or RF-2 bind to the stop codon and enter the __-site, peptidyl transferase (part of 23S rRNA) acts as a _______ and hydrolyze the peptide |
A-site
hydrolase |
|
Termination:
When the peptide is hydrolyzed _______ binds to RF-1 (or RF-2) in the A-site in order for RF-1 or 2 to leave. |
RF-3*GTP
|
|
Termination:
RF-3*GDP leaves the A-site. ____ then binds the stop codon and ______ binds RRF, is hydrolyzed and releases everything. |
RRF
EF-G*GTP |
|
_____ toxin is a large molecule which acts catalytically, deactivating many ribosomes at once. It acts on eukaryotic ___ ribosomes.
|
Ricin
80S |
|
antibiotics are small molecules which act specifically and _________ (1 molecule per 1 ribosome) on prokaryotic 70S ribosomes.
|
stoichiometrically
|
|
Puromycin resembles the 3’ end of ___________ tricking the bacteria into thinking it is a suitable aminoacyl tRNA for the A-site
|
Tyrosyl-tRNA
|
|
What type of bond is formed when puromycin enters the A-site, preventing translation.
|
Amide
|
|
Why is streptomycin injected rather than taken orally?
|
It is a β-glycoside, cannot be broken down to be absorbed through GI.
|
|
At low concentrations ___________ causes bacterial 70S ribosomes to misread pyrimidines in mRNA (C, U), which will result in the wrong amino acids being inserted into the protein.
This slows growth but does not cause cell death. |
Streptomycin
|
|
At higher concentrations (i.e. the therapeutic dose), streptomycin inhibits ____________, resulting in cell death.
|
initiation of translation
|
|
________ is an antibiotic which binds to the 50S ribosomal subunit near the A-site and inhibits the peptidyl transferase activity of the ___ rRNA.
|
Chloramphenicol
23S |
|
Why shouldn't puromycin and chloramphenicol be used simultaneously?
|
They will both compete for the A-site
|
|
Why is chloramphenicol only used in severe infections.
|
It will destroy mitochondrial ribosomes as it recognizes them as bacterial ribosomes.
|
|
_________ binds to the 30S ribosomal subunit and prevents aminoacyl-tRNA (charged tRNA) from binding to the A-site of the ribosome but still allows for the hydrolysis of EF-Tu*GTP to EF-Tu*GDP.
|
Tetracycline
|
|
What is the resulting protein called after treatment with tetracycline?
|
Truncated non-functional protein
|
|
______ is a toxic enzyme, specifically an N-glycosidase which cleaves N-glycosidic bonds. It was originally isolated from castor beans.
|
Ricin
|
|
Ricin binds to eukaryotic ___ ribosomes and removes a highly conserved ________ in 28S rRNA (the rRNA which contains peptidyl transferase).
|
80S
adenine |
|
Removal of adenine from the highly conserved sequence in 28S rRNA prevents ________
|
elongation
|
|
_________ ___ allows the insertion of a selected gene (cut with endonucleases) to be inserted into a plasmid
|
Recombinent DNA
|
|
What is responsible for the overall number of genes in the human genome?
|
Alternative Splicing
|
|
True or False
There are no operons in eukaryotes. |
True
|
|
Protein coding genes almost never exist in multiple copies with the exception of _________
|
Histones
|
|
A _____ _____ is a set of closely related genes that code for the same or similar proteins
and which are usually grouped together on the same chromosome. |
gene cluster
|
|
____ ____ drugs are used in gene therapy to target a specific protein in an effort
to treat a genetic disorder caused by one specific protein. |
“Magic bullet”
|
|
The changing of one nucleotide within a sequence of nucleotides in a group of similar genes is called a
|
single nucleotide polymorphism (SNP = snip)
|
|
______ drugs are used to target SNPs because they can be used to target a group of genes, making them more effective than the “magic bullet” drugs which can only target one specific
gene. |
"Dirty"
|
|
_______ _____ _____ are highly repetitive sequences of DNA.
|
Short tandem repeats (STRs
|
|
True or False
Trinucleotide repeats are harmless |
False
|
|
Explains why the severity of the disease increases with each
generation of passage = |
genetic anticipation
|
|
There are two types of regulatory proteins:
|
Repressors
Activators |
|
A negatively regulated gene is only transcribed in the absence of the _________.
|
repressor
|
|
A co-repressor is a ______ that binds to and activates repressors.
|
ligand
|
|
A ________ regulated gene is normally transcribed without the repressor bound to the
silencer site. |
negatively
|
|
An ________ is a ligand that binds to the repressor to inactivate it
|
inducer
|
|
Gene is normally transcribed with an activator bound to the enhancer site.
_______ Regulated |
Positively
|
|
_________ means that there is an operon which codes for more than one gene.
|
polycistronic
|
|
How does the lac repressor bind to the silencer sequence
|
inserting its α-helix into the
major groove of DNA via a helix-turn-helix motif |
|
What is the name of the inducer that binds to the lac repressor for dissociation
|
Allolactose
|
|
An activator makes the recognition of the lac promoter region stronger in the absence of glucose:
|
Catabolite Activator Protein
CAP / CRP |
|
In eukaryotes gene expression is mostly regulated through ___________ and_________, but some also use activators and repressors which are signaled via hormone levels
|
phosphorylation
dephosphorylation |
|
By binding to a specific transmembrane receptor, hormones initiate ______ _____ _______ within the cell, which affect the activity of activators and repressors.
|
signal transduction cascades
|
|
A signal cascade is also known as
|
amplification
|
|
The degradative metabolism
involving the release of energy and resulting in the breakdown of complex materials |
Catabolic metabolism
|
|
The constructive part of metabolism
concerned especially with macromolecular synthesis |
Anabolic metabolsim
|
|
A ______ is an enzyme which puts a phosphate group on an amino acid
|
kinase
|
|
There are two main types of receptors used in protein phosphorylation.
|
Receptor is associated with tyrosine kinase.
Receptor is tyrosine kinase |
|
True or False
Cytokine receptors are transmembrane |
True
|
|
When the cytokine receptors dimerize, _____ ______ (JAK, a tyrosine kinase) is
activated and it phosphorylates tyrosine residues on itself and the cytokine receptors. |
Janus kinase
|
|
Signal Transduction:
____ binds to the phosphorylated tyrosines through a ____ domain on its surface which specifically recognizes and binds to phosphorylated tyrosines. |
STAT protein
SH2 |
|
Signal Transduction:
How is STAT protein activated? |
JAK phosphorylates STAT bound to SH2 receptor.
STAT dissociates and dimerizes with SH2. |
|
Signal Trandsduction:
Activated STAT will then activate the cytokine genes by binding to its _______ site on DNA within the cell’s nucleus. |
enhancer
|
|
_____ is a tyrosine kinase inhibitor used to treat tumors associated with uncontrolled gene expression.
|
Gleevec
|
|
These antibiotics are ineffective after RNAP has left the promoter region:
|
Rifamycin B + Rifampicin
|
|
________ is found in the mushroom Amanita phalloides (the “death
cap”). |
α-amantin
|
|
dyhyrdouridine is found in what part of tRNA
(ribosomal recognition) |
D-arm (loop)
|
|
pseudouridine is found in the ______ arm of tRNA for ribosomal recognition.
|
T-psi-C arm (loop)
|
|
What part of tRNA carries the amino acid to attach to the new protein?
|
Acceptor Stem
|
|
The acceptor stem is the __' end of tRNA
|
3'
|
|
tRNA synthetase recognizes new amino acids based on: (3)
|
size, charge,
hydrophobicity |
|
Ribsomes:
30S subunit • __ proteins • ___ rRNA (establishes the reading frame in prokaryotic translation) |
21
16S |
|
Ribosomes:
50S subunit • __ proteins • 5S rRNA • ___ rRNA (catalyzes the formation of the peptide bond) |
31
23S |
|
Example: 70S
The unit S means _______ ____, a measure of the rate of sedimentation of a particle in a centrifuge, where the sedimentation rate is associated with the size of the particle. |
Svedberg units
|
|
40S subunit
o __ proteins o ___ rRNA |
33
18S |
|
60S subunit
o __ proteins o 5S rRNA o 5.8S rRNA o ___ rRNA contains peptidyl transferase (catalyzes peptide bond formation) |
49
28S |
|
1 molecule per 1 ribosome =
|
stoichiometrically
|
|
Regulatory proteins are often _______ proteins modified by ligand binding.
|
allosteric
|
|
HMG proteins =
|
high mobility group
(in gel electrophoresis) |
|
Epigenetics =
|
Post modification of protein, changes the way DNA is packaged.
|
|
If DNA is tightly bound to the histone octamer it is transcriptionally ________
|
inactive
|
|
_______ attaches to a lysine
residue on a membrane protein to mark it for endocytosis |
ubiquitin
|
|
Most epigenetic modifications of histones occur at the ________ terminus on __ and __
. |
carboxyl
H3 H4 |
|
Lys loses its positive charge when ________ which weakens histones bond to DNA.
|
acetylated
|
|
________ causes DNA to unbind
histone due to steric bulk hindering the histone-DNA binding. |
Trimethylation
|
|
Phosphorylated serine on histone becomes ______ charged causing DNA-histone to weaken or break.
|
negatively
|
|
Transcriptionally active (uncondensed chromatin = _____)
|
euchromatin
|
|
Transcriptionally inactive (condensed chromatin = ______)
|
heterochromatin
|
|
________ _______(HAT) acetylates (puts on –COCH3) Lys residues on histone
proteins bound to DNA in a specific order. |
Histone Acetyltransferase
|
|
HATs are usually part of a large oligomeric protein called ___________ _________
|
transcriptional coactivators
|
|
___________ _______ (HDACs) remove acetyl groups from Lys residues on histones.
condense chromatin promotes transcriptional repression and gene silencing |
Histone Deacetylases
|
|
________ _______(HMTs) methylate (add –CH3) to Lys and Arg residues on the carboxyl terminus of H3 and H4.
Strengthens DNA-histone bond ______ gene expression |
Histone Methyltransferases
silencing |