Biochemistry Chapter 27 Flashcards
Name sub-cellular site of protein synthesis and associated organelles
Protein synthesis occurs in the ribosomes for synthesis and the cytoplasm for initiation
Explain the adaptor hypothesis
An amino acid and tRNA are combined, while the tRNA is the adaptor molecule.
tRNA uses anticodon to adapt to each new segment of codon that will be transcribed against.
Together, this allows the transcription of DNA
Name various components of protein synthesis process and how they interact
Components:
mRNA
Ribosomes
tRNA
All amino acids
Cellular enzymes
Specific cofactors
ATP/GTP
Understand and explain nature of genetic code and its specific properties
Consists of three bases for each AA
Is universal
Is degenerate
Is read as triplets in a specific reading frame
Is non-overlapping
Recognize codons specific for initiation and termination of protein synthesis
One specific codon for initiation is 5’ AUG, while for prokaryotes it uses formyl-Met and eukaryotes use Met for the amino acids
Specific codons for termination is UAA, UAG, and UGA using the release factors RF1, RF2, and RF3
RF1, 2, and 3 are found in the ribosome
Define a reading frame
Decided at beginning of protein synthesis, changes sequence of AA sequence if shifted.
When shifted, can be called frame-shift mutations
Name specific inhibitors of protein synthesis and their applications
Puromycin: Antibiotic that terminates protein synthesis before it finishes
Fusidic acid: Blocks the release of GDP, can not translocate in the ribosomes
Tetracycline: Blocks A site of the ribosome, prevents binding of aminoacyl-tRNA to the A site
Chloramphenicol: Inhibits peptidyl transfer in bacteria, mitochondria, and chloroplast
Cycloheximide: Inhibits eukaryotic protein synthesis by blocking 60S ribosome factor for elongation
Streptomycin: Binds to 16S rRNA and prevents release of polypeptide chain
Name specific sequences involved in protein targeting and their properties
Typical sequence is 10-15 hydrophobic AA, preceded by 1-2 basic AA and followed by a polar residue with a short side-chain
Can go to different locations in the cell based on signal sequence
ER lumen: Glycosylation
Golgi complex: Additional modifications and secretory proteins
Name factors involved in protein degradation and describe the process of protein degradation
Factors: Removing defective proteins, recycling amino acids, regulating function, controlling metabolism
Ubiquitin covalently attaches to a protein and marks it for degradation, degraded by proteasome
How does mRNA react in protein synthesis?
mRNA acts as the template for the tRNA to make the anticodons from the codon sections of the mRNA
Wobble hypothesis
First two bases of a codon form strong Watson-Crick base pairs with the corresponding base of the anticodon
How do ribosomes play into protein synthesis?
Acts as the hub for the synthesis of new proteins and helps with termination of synthesis
How does tRNA play into protein synthesis?
It acts as an adaptor, being able to copy and translate new proteins in the synthesis process
How do amino acids play into protein synthesis?
They activate tRNA and start the process of protein synthesis
How do cellular enzymes play into protein synthesis?
They are instrumental to the elongation process, allowing mRNA to stretch and allow translation of all of the different codons of the mRNA
How do specific cofactors play into protein synthesis?
They can hold onto ATP/GTP to allow the release of them at a later time to complete certain steps in the ribosome
How do ATP/GTP play into protein synthesis?
They are hydrolyzed to add energy to allow certain steps in the ribosome to happen
Explain how mutations may affect protein synthesis process and/or its product
Mutations in protein synthesis can cause malformation of the protein and cause unwanted effects in the synthesis process and the product
Protein synthesis stage 1: Amino Acid Activation and all of its parts
Two amino acids, specific tRNA, Mg2+, ATP
Product: H2O, Bonded AA and tRNA
Peptide bond is formed
Aminoacyl-tRNA synthetase specific to each AA and its tRNA catalyze the attachment of each AA to its specific tRNA at the end of the amino acid activation stage
Protein synthesis stage 2: Initiation and all of its parts
Need: AA/tRNA complex, Methionine, 5’ AUG codon, Initiation factors, Mg2+, GTP, and 30S and 50S ribosomal subunits
Product: GDP, Pi, IF-1, 2, and 3, and Initiation Complex (AA/tRNA + mRNA + Ribosomal subunits)
Protein synthesis stage 3: Elongation step 1
Need: EF-Tu, EF-Ts, GDP, aminoacyl-tRNA-AA2 complex, EF-Tu-GTP
End: Next section of amino acids to copy more of the mRNA strand using the codon builder
Protein synthesis stage 3: Elongation step 2
Need: Aminoacyl-tRNA, Met-tRNA, 23S rRNA subunit
End: Peptide bond formed between Met and aminoacyl group of other tRNA
Protein synthesis stage 3: Elongation step 3
Need: Dipeptidyl-tRNA, deacetylated tRNA, EF-G, translocase
End: Dipeptidyl-tRNA shifts from A to the P site, deacetylated tRNA shifts to the E site and is released. EF-G or translocase provides the energy for this movement.
Protein synthesis stage 4: Termination
Need: Stop codon UAA, UAG, or UGA, RF1, RF2, and RF3, synthesized polypeptide
End: One of the stop codons signals termination, RF1 or 2 occupies the A site. Finally, polypeptide is hydrolyzed in the P site and released into the cytoplasm
Protein synthesis stage 5: Posttranslational Processing
- Amino terminal removal: Removal of formyl group, f-Met, or other amino acids
- Glycosylation (Eukaryotes): Enzymatic addition of Asn-linked or Ser/Thr-linked sugars
- Isoprenylation: Addition of isoprenyl group to Cys
- Addition of prosthetic groups: Heme to Hb or Cyt
- Proteolytic processing: Chymotrypsinogen to chymotrypsin
- Formation of S-S bonds: Immunoglobulins, peptide hormones
- Phosphorylation: Phosphorylase B, kinases, cyclins
