-
-
Ribose-phosphate backbone
-
-
-
hydrogen-bonded base pairs
-
-
-
The secondary structure of tRNAs exhibits a ________ pattern
cloverleaf
-
what are the four components of the secondary structure of tRNA?
- 3 stem-loop structures
- variable region
- An acceptor stem
- 3' single strand region
-
The actual three-dimensional or tertiary structure of tRNA involves....
additional folding of the secondary structure
-
In addition to the normal A, U, G and C nucleotides, tRNAs commonly contain...
modified nucleotides
-
More than ____ of modified nucleotides can be contained in tRNAs.
60
-
Where is the anticodon located in the tRNA?
in the second loop region.
-
where do amino acids become attached to tRNA?
the acceptor stem
-
The "I" modified base is?
Inosine
-
The "ml" modified base is?
methylinosine
-
The "T" modified base is?
ribothymidine
-
The "UH2" modified base is?
dihydrouridine
-
The "m2G" modified base is?
dimethylguanosine
-
The "Psi" modified base is?
pseudouridine
-
What attahces amino acids to tRNAs?
aminoacyl-tRNA synthetases
-
Aminoacyl-tRNA synthetases are...
The enzymes that attach amino acids to tRNAs
-
How many types of aminoacyl-tRNA synthetases are there?
20 types
- Why are there only 20 aminoacyl-tRNA synthetases?
- there is one for each amino acid
-
Aminoacyl-tRNA synthetases catalyze a two-step reaction involving what three different molecules?
Amino acid, tRNA and ATP
-
What are the three steps to the catalytic function of aminoacyl-tRNA synthetase?
- 1) An amino acid and ATP bind to the enzyme and AMP is covalently bound to the amino acid then pyrophosphate is released
- 2) The correct tRNA binds to the enzyme. The amino acid becomes covalently attached to the 3' end of the tRNA and AMP is released.
- 3) The "charged" tRNA is released
-
What group is at the 5' end of tRNA?
phosphate group
-
What three base pairs are at the 3' end in tRNA?
CCA
-
How many different base pairs are in the D loop?
4
-
How many different base pairs are in the T loop?
6
-
How many different base pairs are in the anticodon?
6
-
What is the order of the base pairs in the D loop?
A, G, UH2, C, G, G, UH2, A
-
What is the order of the base pairs in the T loop?
T, Psi, C, G, A, U, U
-
What is the order of the base pairs in the anticodon loop?
U, U, I, G, C, ml, psi
-
Positions 34 and 37 in the tRNA contain...
the largest variety of modified nucleotides.
-
poisition 34 in the first base in the anticodon that matches the third base in the codon of...
mRNA
-
what positions recognizes valine?
3 bases of anticodon
-
what positions recognizes methionine?
3 bases of anticodon
-
what positions recognizes phenylalanine?
- 3 bases of anticodon
- G20 in D loop
- A73 at terminus
-
What position recognizes isoleucine?
modification at C34 of anticodon
-
What position recognizes glutamine?
anticodon, especially central U
-
What position recognizes serine?
- G1+C72
- G2+C71
- AE+U70 in acceptor stem
- C11+G24 bp in D stem
- What position recognizes Alanine?
- G3+U70 bp in acceptor helix
-
Translation involves an interpretation of one _________ into another
language
-
In genetics, the nucleotide language of mRNA is translated into...
the amino acid language of proteins
-
Translation relies on...
the genetic code
-
the genetic info is coded within mRNA in groups of three nucleotides known as ...
codons
-
the genetic info is coded within ____ in groups of three nucleotides known as codons
mRNA
-
the genetic info is coded within mRNA in groups of three _________ known as codons
nucleotides
-
the genetic info is coded within mRNA in groups of ______ nucleotides known as codons
three
-
What helped to crack the genetic code?
RNA copolymers
-
What was the novel method to synthesize RNA?
- 1) Created short RNAs (2 to 4 nucleotides long) that had a defined sequence
- 2) These were then linked together ezymatically to create long copolymers
-
____________ were used in a cell-free translation system
copolymers
-
Copolymers were used in a _________ system
cell-free translation
-
synthetic RNA was made with the enzyme...
polynucleotide phosphorylase
-
____________ was made with the enzyme polynucleotide phophorylase
synthetic RNA
-
Synthetic RNA does not use a ....
template
-
In synthetic RNA, the order of nucleotides is random because...
it does not use a template
-
UAA is a ________ codon
stop
-
UAG is a _______ codon
stop
-
UGA is a ________ codon
stop
-
AUG is a _______ codon
start
-
AUG specifies ....
methionine
-
More that one codon can specify for...
for the same amino acid
-
In most instances, the third base is the ________ base
degenerate
-
when something is degenerate, it means that...
more than one codon can specify the same amino acid.
-
the third base is sometimes referred to as the _________ base
wobble
-
the codon possibilities for UC are...
UCU, CUC
-
the codon possibilities for AG are...
AGA, GAG
-
the codon possibilities for UG are...
UGU, GUG
-
the codon possibilities for AC are...
ACA, CAC
-
the codon possibilities for UUC are...
UUC, UCU, CUU
-
the codon possibilities for AAG are...
AAG, AGA, GAA
-
the codon possibilities for UUG are...
UUG, UGU, GUU
-
the codon possibilities for CAA are...
CAA, AAC, ACA
-
the codon possibilities for UAUC are...
UAU, AUC, UCU, CUA
-
the codon possibilities for UUAC are...
UUA, UAC, ACU, CUU
-
UCU codes for what amino acid?
serine
-
CUC codes for what amino acid?
leucine
-
AGA codes for what amino acid?
Arginine
-
GAG codes for what amino acid?
Glutamic acid
-
UGU codes for what amino acid?
cysteine
-
GUG codes for what amino acid?
valine
-
ACA codes for what amino acid?
Threonine
-
CAC codes for what amino acid?
Histamine
-
UUC codes for what amino acid?
Phenylalanine
-
AAG codes for what amino acid?
Lysine
-
CAA codes for what amino acid?
Glutamine
-
AAC codes for what amino acid?
asparagine
-
ACA codes for what amino acid?
threonine
-
UAU codes for what amino acid?
tyrosine
-
AUC codes for what amino acid?
isoleucine
-
CUA codes for what amino acid?
leucine
-
ACU codes for what amino acid?
threonine
-
UAC codes for what amino acid?
tyrosine
-
In the codon-anticodon recognition process, the first two position pair strictly according to..
the A-U/G-C rule
-
How can the third position in tRNAs tolerate certain types of mismatches?
they can actually wobble or move a bit
-
The wobble position occurs between...
The first base in the 5' to 3' direction in the anticodon and the third base in the mRNA codon
-
With the revised wobble rules the third nucelotides of codon for the G nucleotide of the anticodon is..
C,U
-
With the revised wobble rules the third nucelotides of codon for the C nucleotide of the anticodon is..
G
-
With the revised wobble rules the third nucelotides of codon for the A nucleotide of the anticodon is..
U
-
With the revised wobble rules the third nucelotides of codon for the U nucleotide of the anticodon is..
A, G
-
With the revised wobble rules the third nucelotides of codon for the I nucleotide of the anticodon is..
U,C,A
-
The universal meaning for AUA codon is...
isoleucine
-
The universal meaning for UGA codon is...
Stop
-
The universal meaning for CUU, CUA, CUC, CUG is...
Leucine
-
The universal meaning for AGA, AGG is...
Arginine
-
The universal meaning for UAA, UAG is...
Stop
-
The exception for AUA codon is...
Methionine in yeast and mammalian mitochondria
-
The exception for UGA codon is...
Tryptophan in mammalian mitochondria
-
The exception for CUU, CUA, CUC, CUG codon is...
Threonine in yeast mitochondria
-
The exception for AGA, AGG codon is...
Stop codon in ciliated protozoa and in yeast and mammalian mitochondria
-
The exception for UAA, UAG is...
Glutamine in ciliated protozoa
-
The sedimentation coefficient of a bacterial ribosomal small subunit is...
30S
-
The number of proteins in a bacterial ribosomal small subunit is...
21
-
The rRNA of a bacterial ribosomal small subunit is...
16S rRNA
-
The sedimentation coefficient of a bacterial ribosomal large subunit is ....
50S
-
The number of proteins in a bacterial ribosomal large subunit is...
34
-
The rRNA of a bacterial ribosomal large subunit is...
5S rRNA, 23S rRNA
-
The sedimentaiton coefficient of a bacterial ribosomal assembled ribosome is...
70S
-
The number of proteins in a bacterial ribosomal assembled ribosome is...
55
-
The rRNA of a bacterial ribosomal assembled ribosome is...
16S rRNA, 5S rRNA, 23S rRNA
-
S (Svedberg) units are not....
additive
-
The sedimentation coefficient of a eukaryotic ribosomal small subunit is...
40S
-
The number of proteins in a eukaryotic ribosomal small subunit is...
33
-
The rRNA of a eukaryotic ribosomal small subunit is...
18S rRNA
-
The sedimentation coefficient of a eukaryotic ribosomal large subunit is ....
60S
-
The number of proteins in a eukaryotic ribosomal large subunit is...
49
-
The rRNA of a eukaryotic ribosomal large subunit is...
5S rRNA, 5.8S rRNA, 28S rRNA
-
The sedimentaiton coefficient of a eukaryotic ribosomal assembled ribosome is...
80S
-
The number of proteins in a eukaryotic ribosomal assembled ribosome is...
82
-
The rRNA of a eukaryotic ribosomal assembled ribosome is...
18S rRNA, 5S rRNA, 5.8S rRNA, 28S rRNA
-
What are the three stages of translation?
- Initiation
- Enlongation
- Termination
-
Amino acids are _____ cells carried to other forms of life Except mammalian mitochondria and protozoa
progenitor
-
Amino acids are progenitor cells carried to other forms of life Except for...
mammalian mitochondria and protozoa
-
What does peptidyl transferase do?
takes two amino acids and makes a peptide bond between them
-
What did Harry Noller discover?
That not only are ribosomes made or protein, but that they are made of catalytic RNA too.
-
Because of Harry Noller discovery, a Ribosome can also be called a....
ribozyme
-
What is the fucntion of riboenzymes?
catalyzes bond formation
-
concerning peptidyl transferase, what is the job of protein?
Allow RNA to fold properly
-
What is the start codon on mRNA?
AUG
-
In addition to AUG, what can aslo be a start codon on mRNA?
GUG
-
In terms of a start codon, there may be many AUG codon but there is only one...
start codon
-
The decopin function of the ribosomes maintains what?
high fidelity
-
What is fidelity?
the accuracy of DNA replication
-
What can 16S rRNA detect?
when an incorrect tRNA is bound at the A site
-
The ribosome-binding site can also be called the...
Shine-Dalgarno sequence
-
The Ribosome-binding site or Shine-Dalgarno sequence is _______ to a sequence in the 3' end of the 16S rRNA of the 30S small ribosomal subunit.
complememntary
-
What helps the codon get placed properly in trnaslation?
the 16S rRNA of the 30S small ribosomal subunit
-
The Ribosome-binding site or Shine-Dalgarno sequence is complementary to a sequence in the ___ end of the 16S rRNA of the 30S small ribosomal subunit.
3'
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The Ribosome-binding site or Shine-Dalgarno sequence is complementary to a sequence in the 3' end of the ___ rRNA of the 30S small ribosomal subunit.
16S
-
The Ribosome-binding site or Shine-Dalgarno sequence is complementary to a sequence in the 3' end of the 16S rRNA of the ____ small ribosomal subunit.
30S
-
What is the consensous sequence in translation
5'- [AGGAGGU]-[7-12 bases]-[AUG] - 3' (mRNA)
-
How long is the Shine-Dalgarno sequence?
usually 9 nucletoides long
-
Do eukaryotes use the Shine-Dalgarno sequence?
NO!!!!!!
-
the eukaryotic equivalent of the Shine-Dalgarno sequence is...
The Kozak consensus sequence
-
Where is the 7-methylG cap located?
on the 5' end of RNA
-
What happens when a ribosome recognizes the 7-methylG cap?
runs down mRNA to find AUG to start transcription
-
What are the three steps of the initiation step of translation?
- 1) IF3 promotes binding of mRNA to 30S subunit. The SD sequence is complememntary to portion of 16S rRNA of 30S subunit.
- 2) tRNA f'met binds to P site on 30S subunit via IF2. will be removed from final product by post translation modification after translation is over.
- 3) IF2 and IF3 are released, 50S subunit associates and form 70s
-
the tRNA f'met is only used to do what in trnaslation?
inititate transcription
-
the tRNA f'met is an
initiator tRNA/methionine modified w/ formyl group.
-
in translation, when is tRNA f'met removed from the final product?
after translation is over
-
in translation, how is tRNA f'met removed from the final product?
by post translational modifcations
-
In the last step of translation initiation, the 50S subunit associates and forms...
70S
-
In the last step of translation initiation, the ____ subunit associates and forms 70S.
50S
-
Only the _____ enters through the P site in the initiation of translation.
tRNA f'met
-
All tRNA other then tRNA f'met eneter through the ___ site in the initiaiton of translation
A
-
What marks the end of the initiaiton step in trnaslation?
formation of 70S
-
What are the six steps of the enlongation step of translation
- 1) A correctly charged tRNA binds to the A site based on the pairings w/ codon.
- 2) Peptidyl transferase catalyzes bon formation between polypeptide and amino acid in the A site
- 3) Polypeptide is transferred to the A site
- 4) Ribosome translocates one codon to the right (tRNAs at the P and A sites, move to the E and P sites respectively
- 5) uncharged tRNA released from the E site
- 6) Process repeats until stop codon is reached
-
What are the four steps of the termination step in translation?
- 1) once STOP codon reaches the A site, a RELEASE FACTOR will bind to the A site
- 2) polypeptide is released from the tRNA in the P site and the tRNA is released
- 3) Ribosomal subunits, mRNA and release factor dissociate
- 4) ribosomal subunits and mRNA are recylced by the time translation is over; enzymes may be degraded
-
EF-Tu stands for...
Elongation factor
-
What is EF-Tu role in peptide bond formation (elongation in trnaslation)?
Brings amino-acyl tRNA to the ribosome
-
What does the EF-Tu hydrolyze to get energy to bring the amino-acyl tRNA to the ribosome?
Hydrolyzes GTP into GDP and inorganic phosphate.
-
How many release factors do bacteria have?
3 release factors
-
RF1 recognizes....
UAA and UAG
-
RF2 recognizes...
UAA and UGA
-
RF3 recognizes...
none of the three codons
-
what does the RF3 do?
Binds to GTP and helps facilitate the termination process.
-
What binds to GTP and helps facilitate the termination process?
RF3
-
RF3 Binds to ____ and helps facilitate the termination process.
GTP
-
RF3 Binds to GTP and helps facilitate the ________ process.
termination
-
how many release factors does eukaryotes have?
1
-
What is the release factor for eukaryotes?
eRF
-
eRF recognizes which stop codons?
all three
-
What is a polysome?
mRNA transcript that has many bound ribosomes in act of translation
-
Every one of the ribosomes of polysomes start at the...
SD sequence
-
During translation ______ can be degraded at the 5' end.
mRNA
-
During translation, mRNA can be degraded at the ___ end.
5'
-
What two things can work simultaneously at the same place and the same time in a bacterial cell?
Transcription and translation
-
Transcription and translation can work simultaneously at the same place and the same in a ______ cell.
bacterial
-
What is puromycin?
an antibiotic that kill bacteria
-
How does puromycin work?
Looks like an Amino acid on tRNA, but it's not. Fools bacterial ribosome to use peptidyl and cause premature termination.
-
What can cause premature termination in bacterial cells?
puromycin
-
What does it mean when we say that the genetic code is degenerate?
It means that more then one codon can code for the same amino acid
-
Explain the universality of the genetic code?
The genetic code is nearly unviersal because it is used in the same way by viruses, prokaryotes, fungi, plants and animals
-
what are the two things that are an exception to the "universiality" of the genetic code?
protists, yeasts and mammalian mitochondria
-
Phenylalanine's (Phe) 2 codons are...
-
Leucine's (Leu) 6 codons are...
-
Isoleucine's (Ile) 3 codons are..
-
Methionine's (Met) codon is...
AUG (also start codon)
-
Valine's (val) 4 codons are...
-
Serine's (SER) 6 codons are..
-
Proline's (Pro) 4 codons are...
-
Threonine's (Thr) 4 codons are...
-
-
Tyrosine's (Tyr) 2 codon are...
-
Histidine's (His) 2 codons are...
-
Glutamine's (Gln) 2 codons are..
-
Asparagine's (Asn) 2 codons are
-
Lysine's (Lys) 2 codons are...
-
Aspartic Acid's (Asp) 2 codons are..
-
Glutamic acid's (Glu) 2 codons are...
-
Cysteine's (Cys) 2 codons are..
-
Tryptophan's (Trp) codon is..
UGG
-
Arginine's (ARG) 6 codons are...
-
Glycine's (Gly) 4 codons are..
-
If a tRNA molecule carries a glutamic acid, what are the two possibleanticodon sequences that it could contain? Be specific aboutthe 5ʹ and 3ʹ ends.
-
Why has the function of aminoacyl-tRNA synthetase been described as the "second genetic code"?
This ability is sometimes described as the second genetic code becausethe specificity of the attachment is a critical step in deciphering thegenetic code.
-
Where does mRNA-tRNA recognition happen in translation.
on the surface of the 30S subunit and at the interface between the two subunits
-
Where does peptidyl transfer reaction occur?
within the 50S Subunit
-
Where does the exit of the polypeptide chain from the ribosome take place?
from the 50S subunit
-
Where does the binding of intiation factors IF1, IF2 and IF3 is located?
To the 30S subunit
-
Describe the sequence in bacterial mRNA that promotes recognition by the 30S subunit.
Most bacterial mRNAs contain a Shine-Dalgarno sequence, which is necessary for the binding of the mRNA to the small ribosomal subunit.
-
How does a eukaryotic ribosome select its start codon?
The ribosome binds at the 5' end of the mRNA and then scans in the 3' direction in search of an AUG start codon.
-
Describethe sequences in eukaryotic mRNA that provide an optimal context for a start codon.
Aside from an AUG start codon, two other important features are a guanosine at the +4 position and a purine at the −3 position.
-
Explain the functional roles of the A site during translation.
The A (aminoacyl) site is the location where a tRNA carrying a single amino acid initially binds.
-
Explain the functional roles of the P site during translation.
The growing polypeptide chainis removed from the tRNA in the P site and transferred to the amino acid attached to the tRNA in the A site.
-
Explain the functional roles of the E site during translation.
The ribosome translocates in the 3' direction, with the result that the two tRNAs in the P and A sites are moved to the E (exit) and P sites, and the uncharged tRNA in the E site is released.
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