[2S] UNIT 3.3 Translation Flashcards
Taking the mRNA utilize it as
a template to synthesize protein
Translation
Set of instructions and ingredients to make a particular protein. o Orientation 5’ methylguanosine cap to 3’ poly A Tail
Mature RNA
Sequence of nucleotide that come in triplet
Codons
All __ codons have been assigned meaning (see Table of Degenerative Genetic Code)
64
Number of codons coding for amino acids
61
Number of codons serving as the termination signals (nonsense codons)
3
3 nonsense codons
UGA
UAG
UAA
Carries the amino acid domain
CCA tail
GENETIC CODE CHARACTERISTICS
5 prime to 3 prime (mRNA)
Comma less
GENETIC CODE CHARACTERISTICS
tRNA is read through every codon
○ If two nucleotides occur between each codon they are not skipped
Comma less
GENETIC CODE CHARACTERISTICS
Translation occurs continuously from end to end
Comma less
GENETIC CODE CHARACTERISTICS
The ribosomes will always translate the mRNA by the codons and give 1 amino acid for it
Non-overlapping
GENETIC CODE CHARACTERISTICS
“Degenerate”
Redundant
GENETIC CODE CHARACTERISTICS
The ribosomes on the other hand won’t overlap the reading
Non-overlapping
GENETIC CODE CHARACTERISTICS
They only code for 1 amino acid “Serine”
Redundant
GENETIC CODE CHARACTERISTICS
2 exceptions of redundancy
AUG (Methionine)
UGG (Tryptophan)
A nucleoside that is derived from adenosine, consisting of the purine base hypoxanthine attached to a ribose sugar
Inosine
In the degenerate or redundant codons, the first
nucleotide in the corresponding sequence of the anticodon is?
WOBBLE EFFECT: Inosine
Decreases the rate of mutation
Inosine
Due to the versatility of _______ and the ________ ______, if just one nucleotide in the codon is changed, the amino acid will not change at all.
inosine; Wobble Effect
What effect?
Because the inosine nucleotide will give a leeway for a few sequence of nucleotides that gets to be changed during a mutation
○ Inosine = Adenine
○ Inosine = Uracil
○ Inosine = Cytosine
Wobble Effect
Part of tRNA molecule that acts as the amino acid domain where amino acids bind
CCA tail
PARTS OF TRNA
Attached to the 5’ end
Phosphate group
A prototype tRNA molecule is made up of ____ nucleotides
75-94
Gives the tRNA the ability to carry amino acids
CCA tail
PARTS OF TRNA
Attached to the 3’ end
Hydroxyl group
T/F: tRNA ends with a CCA tail
T
PARTS OF TRNA
It is called T because it contains modified nitrogenous bases in
the form of ribothymidine (T) and contains Pseudouridine (U)
T-Arm (T loop)
PARTS OF TRNA
It enables RNA to tether to the ribosome so it would not be shaky as the elongation process goes on.
T-Arm (T loop)
T-arm contains modified nitrogenous bases in
the form of _______ (T) and contains _________ (U)
Ribothymidine; Pseudouridine
PARTS OF TRNA
It has modified nitrogenous bases in the form of dihydrouridine
D-Arm (D loop)
PARTS OF TRNA
It enables aminoacyl-tRNA synthetase to recognize the tRNA molecule
D-Arm (D loop)
PARTS OF TRNA
Amino-acyl-tRNA synthetase
recognizes if a specific tRNA carries a different amino acid
D-Arm (D loop)
PARTS OF TRNA
Binding site of tRNA synthetase
D-Arm (D loop)
PARTS OF TRNA
It is the 34th to 36th sequence of nucleotides that make up the tRNA
Anticodon loop
PARTS OF TRNA
The attachment of the phosphate group in the 5’ carbon and attachment
hydroxyl functional group in the 3’ end carbon is universal to all nucleic acids whether it may be any type of DNA or RNA
Anticodon loop
tRNA CHARGING
T/F: On its own, tRNA does not carry amino acids
T
tRNA CHARGING
Start: _____ strand that carries start codon AUG
mRNA
mRNA carries AUG (AUG anticodon: UAC)
Where did the tRNA molecule with UAC anticodon get the methionine amino acid?
ATP → PP is cleaved away from its nucleotide = AMP → bonds w/ phosphate group (meth) = S-adenosylmethionine
A nucleoside monophosphate carrying an amino acid
Aminoacyl-tRNA
tRNA CHARGING
Generic name for the molecule
Amino Acyl AMP
It is called ____ since the amino acid that is bound to the nucleotide lacks 1 hydrogen atom
Acyl
tRNA CHARGING
Recognizes that the anticodon of the tRNA is complementary to the amino acid that it carries
Aminoacyl synthetase
tRNA CHARGING
After recognition, it would now charge the amino acid to the CCA tail of tRNA molecule
Aminoacyl synthetase
It can recognize the tRNA molecule through the D-arm
Aminoacyl-tRNA synthetase
Holds the aminoacyl AMP molecule
Aminoacyl-tRNA synthetase
tRNA CHARGING: AMINOACYL SYNTHETASE
T/F: The carboxyl end of the amino acid binds to the OH group of the CCA tail in the 5’ end of the tRNA molecule. This would liberate the AMP molecule at the same time
F; 3’ end
Has unique molecular configuration that enables it to check the anticodon that
corresponds to the amino acid that it carries
Aminoacyl-tRNA synthetase
Functions contribute in associating the amino acids utilized in the translation
process to the amino acid domain in the tRNA molecule
Aminoacyl-tRNA synthetase
Major/Main difference between Eukaryotic and Prokaryotic Ribosomes
Size
Similarities of eukaryotic and prokaryotic DNA
2 subunits (large & small)
Molecular composition (ribosomes)
EUKARYOTIC RIBOSOME
● Large Subunit size: __
● Small Subunit size: __
● Total size (Large and Small Subunits): ___
60S
40S
80S
We are expressing a rate of sedimentation
PROKARYOTIC RIBOSOME
● Large Subunit size: __
● Small Subunit size: __
● Total size (Large and Small Subunits): ___
50S
30S
70S
ODD ONE OUT: 30S INHIBITORS
Aminoglycosides
Tetracyclines
Chloramphenicol
Glycylcycline-Tigecycline
Chloramphenicol (50S) bsta TAG ang 30S
3 phases of translation
● Initiation
● Chain elongation
● Chain termination
INITIATION OF PROKARYOTES
GGAGGU sequence
Shine Dalgarno Sequence
INITIATION OF PROKARYOTES
Purine rich
Shine Dalgarno Sequence
INITIATION OF PROKARYOTES
It is a ribosome binding site by the base pairing of pyrimidine rich sequence (3’ end of the 60S prime end) - ribosomal RNA
Shine Dalgarno Sequence
INITIATION OF PROKARYOTES
Starts at 5’ prime
Shine Dalgarno Sequence
INITIATION OF PROKARYOTES
Complex made up of small ribosomal subunits and the mRNA (3-5)
Shine Dalgarno Sequence
INITIATION OF PROKARYOTES
Acts as the start (signal) of the translation process for prokaryotes
Shine Dalgarno Sequence
INITIATION OF PROKARYOTES
Binded by Initiation Factor-3 which strengthens the binding of mRNA to the 30S small ribosomal units
Shine Dalgarno Sequence
INITIATION OF PROKARYOTES
Prevents immature binding of the 50S subunit because we do not want the ribosomal 50S to be randomly pairing with the codons present in the mRNA strand
SHINE DALGARNO: Initiation Factor-3
INITIATION OF PROKARYOTES
Binds to the tRNA and carries with it GTP. It helps deliver the initiator tRNA to the ribosome.
SHINE DALGARNO: Initiation Factor-2
INITIATION OF PROKARYOTES
It ensures that the ribosome only accepts the correct initiator tRNA (which carries the first amino acid, methionine) and prevents the binding of other tRNAs that could lead to errors
SHINE DALGARNO: Initiation Factor-1
INITIATION OF PROKARYOTES
Binds to the initiator tRNA and helps it attach to the ribosome at the start codon (AUG)
SHINE DALGARNO: Initiation Factor-2
INITIATION OF PROKARYOTES
Binds to GTP, it provides the energy needed for the initiator tRNA to properly fit into the ribosome
SHINE DALGARNO: Initiation Factor-2
INITIATION OF PROKARYOTES
Comes in the picture and binds initiation factor-3 on the lower part and initiation
factor-2 at the top
SHINE DALGARNO: Initiation Factor-1
INITIATION OF PROKARYOTES
Carried by IF-2
GTP
INITIATION OF PROKARYOTES
Very highly energized
GTP
INITIATION OF PROKARYOTES
IF-1, IF-2, and IF-3 would break down GTP to
form ____ and _______ making lots of energy
GDP and Inorganic complex
INITIATION OF PROKARYOTES
T/F: After binding with the 3 IFs, the large ribosomal subunit needs more initiation factors
F; does not need
INITIATION OF PROKARYOTES
Modified form of the amino acid methionine
fMet (N-formylmethionine)
INITIATION OF PROKARYOTES
GTP Process Result: large ribosomal subunit, small
ribosomal subunit, tRNA molecule with the _________ bound with the start codon
(mRNA molecule)
n-formylmethionine (f-met)
INITIATION OF PROKARYOTES
ODD ONE OUT: GTP PROCESS RELEASES:
GDP
Inorganic Phosphate
GTP
IF-1
IF-2
IF-3
GTP
INITIATION OF PROKARYOTES
The first amino acid incorporated into newly synthesized proteins. It is the result of adding a formyl group to methionine.
fMet (N-formylmethionine)
INITIATION OF EUKARYOTIC CELL
Chain initiation of the eukaryotic translation
43S Preinitiation Complex
INITIATION OF EUKARYOTIC CELL
The formation of the 43s preinitiation complex starts with the ___ small ribosomal subunit
40s
INITIATION OF EUKARYOTIC CELL
ODD ONE OUT: 43S PREINITIATION COMPLEX
tRNA
Methionine
GTP
Eukaryotic Initiation Factors
40S Ribosomal Unit
50S Ribosomal Unit
50S Ribosomal Unit eukaryotic nga dba
INITIATION OF EUKARYOTIC CELL
4 types of eukaryotic initiation factors bind to
the 40s ribosomal subunit
IF-A1, IF-3, IF-2, eif2
INITIATION OF EUKARYOTIC CELL
Binds tRNA (that carries methionine and GTP)
Eukaryotic initiation factor 2
INITIATION OF EUKARYOTIC CELL
The 43S subunit and eukaryotic initiation factors
constitute?
48s preinitiation complex
INITIATION OF EUKARYOTIC CELL
GTP → broken down into GDP & Inorg Phosphate → creates energy → large ribosomal unit breaks it down one by one
48S Preinitiation Complex
INITIATION OF EUKARYOTIC CELL
Large ribosomal subunit and small ribosomal subunit -packages the mRNA molecule to the 5 prime to the 3’ prime -hammers them to the start of translation process
48S Preinitiation Complex
ELONGATION OF EUKARYOTIC CELL
3 Different sites found in the large ribosomal subunit
Aminoacyl site (arrival site)
Peptidyl site
Exit site
ELONGATION OF EUKARYOTIC CELL
At the start codon the large and small ribosomal subunit sandwiches the mRNA molecule to the ___ end
5’ to 3’
ELONGATION OF EUKARYOTIC CELL
tRNA that carries methionine
P-site
ELONGATION OF EUKARYOTIC CELL
we should bring tRNA molecule in this site but tRNA cannot just enter the
arrival site that’s why eukaryotic elongation factor 1 is needed as a helper molecule
A-site
ELONGATION OF EUKARYOTIC CELL
Rings tRNA to bind to the messenger RNA to the AUA codon
Eukaryotic elongation factor 1
ELONGATION OF EUKARYOTIC CELL
In the large ribosomal subunit, there are 2 amino acids seated closely
together ______ & ______ form a strong bond = ______ bond
Methionine & Isoleucine; Peptide
ELONGATION OF EUKARYOTIC CELL
The large ribosomal subunit would then again break down GTP into: GDP and inorganic phosphate which enables the _______ to make
an opening for the tRNA to bind to the mRNA within the large ribosomal subunit
Eukaryotic elongation factor 1
ELONGATION OF EUKARYOTIC CELL
In the large ribosomal subunit, the ___ is not needed anymore so it is
ticked off
eEF1
ELONGATION OF EUKARYOTIC CELL
Blocks methionine from tRNA
Peptidyl transferase
ELONGATION OF EUKARYOTIC CELL
T/F: A-site and P-site has peptidyl transferase
F; only A-site has this, P-site loses its amino acid
ELONGATION OF EUKARYOTIC CELL
PEPTIDYL TRANSFERASE: translocation then takes place but in order for translocation to occur, we
need energy; hence, we need _____ because this factor carries with it a GTP
molecule
eEFG2
ELONGATION OF EUKARYOTIC CELL
T/F: PEPTIDYL TRANSFERASE
GTP is broken down again into: GDP and inorganic phosphate. The energy produced would create a shift to the A site to the P site
T
Occurs in the ribosome in the stop codon (UAA) along the RNA molecule
Termination
T/F: In termination, there is no tRNA will be brought in the A-site once the ribosome hits stop codon
T
TERMINATION
_____ _____ jumps in the a-site, unique because they can read and recognize and bind to the stop codon
Release factor
Stops the translation process
Release factor
RER
A growing peptide, which has a series of 16-30 amino acid residues which are recognized by the Signal Recognition Protein (SRP)
Signal Sequence
RER
The signal sequence is recognized by this protein and would drag the ribosome and polypeptide complex to the outer membrane of the ER
Signal Recognition Protein (SRP)
How does the Release factor stop the translation?
○ Jumps to the A-site and binds to the stop codon
○ Stops the translation process
○ Releases the peptide in the P-site, the peptide would then be incorporated into
the cell membrane, secreted in the extracellular fluid, etc.
ODD ONE OUT: FREE RIBOSOMES
Cytosolic proteins
Nuclear proteins
Mitochondrial enzymes
Meroxisomal enzymes
Membrane proteins
Membrane Proteins
Free Rib: CNu c MiMer
ODD ONE OUT: RER
Lysosomal proteins
Nuclear proteins
Secreted proteins
Membrane proteins
Nuclear proteins
RER: LSM
PROTEINS FOUND IN THE CYTOPLASM
Ribosome and polypeptide
complex binds in ____
SRPR / Signal Recognition Particle Receptor
Proteins found in the cytoplasm
STS
1. Signal Recognition Particle Receptor
2. Translocon
3. Signal Peptidase
PROTEINS FOUND IN THE CYTOPLASM
The 2 GDP produced in this
process opens up the
_____ which allows the ribosome to sit on the rough ER giving its rough appearance
translocon
PROTEINS FOUND IN THE CYTOPLASM
TRANSLOCON: After energy is released, SRPR slams to the ribosome and sends growing polypeptide to the ____of the rough ER
lumen
PROTEINS FOUND IN THE CYTOPLASM
Lives under the rough ER
Signal Peptidase
PROTEINS FOUND IN THE CYTOPLASM
Cuts off the signal sequence,
liberates the peptide in the
lumen of the rough ER closes the translocon, and removes RNA in the top of rough er, RNA will eventually dissociates
Signal Peptidase
PROTEINS FOUND IN THE CYTOPLASM
This protein will be then
secreted into the extracellular fluid, incorporated as a structural proteins of the membrane or become a lysosomal protein
Signal Peptidase
