Term
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Definition
Translation is the production of a protein through the use of mRNA as the carrier of information.
It is carried out by the ribosome, a huge complex of proteins and integral RNA molecules (ribosomal RNA, or rRNA)
The ribosome uses activated amino acids as the substrate for polymerization
Amino acids are activated when they combine with transfer RNA (tRNA) for use in the ribosome |
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Term
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Definition
The mRNA is read as blocks of three sequential nucleotides (codon), which specifies a particular amino acid
-Codons do not overlap, no gaps
-Three possible reading frames, could start at any base
-Correct reading frame is specified by an initiation codon, generally AUG, as well as regulatory sites for correct positioning
-Wrong reading frame = wrong proteins |
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Term
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Definition
True translational molecule, having an activated amino acid on one side, and the matching anticodon on the other.
- 3 stem-loop patterns
- Altered bases created in nucleus
- Side loops have important functions |
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Term
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Definition
| needed for synthetase recognition |
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Term
| Aminoacyl-tRNA synthetase |
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Definition
| attaches AMP to the a.a., then a.a. to the 2' or 3' hydroxyl of the terminal adenine residue. Each a.a. has its own synthetase |
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Term
| Activation of Amino Acids |
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Definition
must be activated before they are polymerized into peptide chains. Activated by joining them to tRNA.
-First step is formation of a mixed anhydride link between the amino acid and AMP, giving an aminoacyl adenylate.
-Second step forms an aminoacyl-tRNA, a charged tRNA. This is the substrate for polymerization into a polypeptide chain. |
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Term
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Definition
Composed of several rRNA strands and many proteins.
-Ribosomal proteins are located mainly on the exterior surface of the ribosome, while RNA occupies the interior.
-Ribosomal RNA is folded into domains that contain a few hundred nucleotides. Domains are composed of helices, many terminating in hairpin turns, and with bulges or loops of unequal numbers of bases which introduce bends into the helix
- Many of the nucleotides are modified |
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Term
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Definition
Bacterial ribosome 70s
- 30S and 50s subunits
Eukaryotic ribosome: 80s
-60s and 40s subunits |
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Term
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Definition
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Term
| Comparing Prokaryotic and Eukaryotic Translation |
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Definition
Start codon: typically AUG
Prokaryotes use shine-dalgarno sequence to specify the position of the initiating codon.
Eukaryotes use the AUG codon nearest the 5' end of the mRNA
Bacteria and mitochondria start protein synthesis with a formylated methionine residue (fMEt), carried by a special tRNA
In protein synthesis at the endoplasmic reticulum in eukaryotes, the first amino acid incorporated into a nascent polypeptide chain willy typically aslo be methionine (but not fMet), which also is carried by a special intiating tRNA |
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Term
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Definition
Prokaryotes: Occurs in the cytosol
Eucaryotes: takes place mainly on the outer face of the membranes of the ER
-small amount takes place from free ribosomes int he cytoplasm
Three main stages to protein synthesis: intiation, elongation, termination. |
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Term
| tRNA Binding and Chain Initiation |
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Definition
Ribosome has large and small subunit.
3 Binding sites:
1) Aminoacyl (A)
2) Peptidyl (P)
3) Exit (3) for uncharged tRNA
When two charged tRNA occupy A and P sites, a peptide bond will be formed.
Nascent peptide chain exits through the bottom of the large subunit.
- In eukaryotes, usually an exit to the ER lumen |
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Term
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Definition
mRNA binds small subunit
-start codon of mRNA is positioned at the P site
-Initial charged tRNA binds to the start codon on the mRNA (usually methionine, fMet for bacteria)
-Large ribosomal subunit associates with the small subunit
+ This process is aided in Eu by proteins called initiation factors, and require GTP hydrolysis
- T loop of tRNA molecules is used to recognize the loading site on the ribosome |
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Term
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Definition
| used to recognize loading site on the ribosome |
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Term
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Definition
Ribosome moves along mRNA sequentially by codon, matching each with an anticodon.
-At each step, the discharged tRNA exits through the E site, and the next tRNA enters the A site.
-Peptide bond forms between the nascent peptide chain and the next amino acid
-Elongation factors and GTP hydrolysis is required
-Peptide chain growns in the amino-to-carboxy direction, as the ribosome reads the mRNA in 5'to 3' direction |
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Term
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Definition
EF-TU and EF-G in bacteria
EF1 and EF2 in eukaryotes
provide speed and accuracy |
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Term
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Definition
Elongation continues until finally a termination (stop) codon on the mRNA is reached.
-No tRNA added to the A site
-Instead, a release factor fills the A site
-The ribosome dissociates into small an dlarge subunits, and the mRNA and tRNA molecules dissociate from the ribosome.
-The protein is folded into its tertiary state, often with the help of chaperones |
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Term
| Characteristics of Eukaryotic Translation |
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Definition
Most ribosomes will dock at receptor on ER; the ribosome starts translation but pauses before docking.
-Signal recognition particle (SRP) attaches to the protein to help it find the ER site.
-Proteins that will be associated with a membrane will contain a special sequence to direct this process
-In the ER lumen, the protein folds and is modified. Transport vesicles then bud off the ER and carry proteins to the golgi for further processing, or to other compartments in the cell, or to the plasma membrane.
-Eukaryotes use signaling sequences to direct proteins to different cellular locations |
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Term
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Definition
Encoded by UGA (normally a stop codon)
A SECIS element (hairpin) in the mRNA allows its incorporation.
High reduction potential, found in enzymes involved in anti-oxidation
About 25 known human proteins with selenocysteine |
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Term
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Definition
The ribosome is a big target for antibiotics.
-Bacterial and eukaryotic ribosomes differ in structure and sequence, and these differences can be targeted for antibiotic action against bacteria.
-Drugs known to inhibit Eu translation: puromycin, cycloheximide, anisomycin |
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Term
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Definition
Interfere with decoding of mRNA by blocking tRNA from binding in the A site.
-Tetracycline, doxycycline, minocycline, tigecycline
-Broad spectrum
[Four rings with C2H6N) |
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Term
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Definition
Bind around exit tunnel on the large ribosomal subunit, blocking peptide elongation
-Erythromycin,azithromycin (Zithromax), clarithromycin (Biaxin)
Broad Spectrum |
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Term
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Definition
Interfere with chain translocation; they can also interfere with proofreading - leading to errors in amino acid incorporation in the polypeptide, which in turn can lead to non-functional (nonsense) proteins that are toxic to the cell
-streptomycin,kanamycin,tobramycin,gentamicin,amikacin,spectinomycin
Broad spectrum |
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Term
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Definition
Useful for UTIs caused by Gram (-) rods.
Weird pentose nitro things |
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Definition
Chloramphenicol interferes with peptide bond formation by blocking the A site.
Looks like a pikmin sitting down
-SIGNIFICANT TOXICITY = RARELY USED |
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Term
| Reverse Transcriptase Inhibitors |
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Definition
Azidothymidine (AZT) is an analog of thymidine, and is an effective inhibitor of HIV replication.
-Taken up by the cella nd converted to AZT triphosphate, which is a substrate for HIV reverse transcriptase
- Like acyclovir, AZT lacks a 3' OH , so if it is incorporated at the end of a growing strand of DNA< there is no way to extend the DNA chain past it. This will block DNA synthesis and inhibit viral replication. |
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Term
| Retroviruses and Reverse Transcriptases |
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Definition
| Carry RNA, not DNA and often one or more copies of an RNA-dependent DNA polymerase, or reverse transcriptase. Enzyme syntesizes DNA, forming hybrid duplex, reverse transcriptase then degrades the RNA strand and syntesizes new DNA strand. Viral DNA may insert into host genome, then be transcribed. |
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