Biochemistry Chapter 27

Question 1

Name sub-cellular site of protein synthesis and associated organelles

Answer 1

Protein synthesis occurs in the ribosomes for synthesis and the cytoplasm for initiation

Question 2

Explain the adaptor hypothesis

Answer 2

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

Question 3

Name various components of protein synthesis process and how they interact

Answer 3

Components:

mRNA

Ribosomes

tRNA

All amino acids

Cellular enzymes

Specific cofactors

ATP/GTP

Question 4

Understand and explain nature of genetic code and its specific properties

Answer 4

Consists of three bases for each AA

Is universal

Is degenerate

Is read as triplets in a specific reading frame

Is non-overlapping

Question 5

Recognize codons specific for initiation and termination of protein synthesis

Answer 5

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

Question 6

Define a reading frame

Answer 6

Decided at beginning of protein synthesis, changes sequence of AA sequence if shifted.

When shifted, can be called frame-shift mutations

Question 7

Name specific inhibitors of protein synthesis and their applications

Answer 7

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

Question 8

Name specific sequences involved in protein targeting and their properties

Answer 8

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

Question 9

Name factors involved in protein degradation and describe the process of protein degradation

Answer 9

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

Question 10

How does mRNA react in protein synthesis?

Answer 10

mRNA acts as the template for the tRNA to make the anticodons from the codon sections of the mRNA

Question 10

Wobble hypothesis

Answer 10

First two bases of a codon form strong Watson-Crick base pairs with the corresponding base of the anticodon

Question 11

How do ribosomes play into protein synthesis?

Answer 11

Acts as the hub for the synthesis of new proteins and helps with termination of synthesis

Question 12

How does tRNA play into protein synthesis?

Answer 12

It acts as an adaptor, being able to copy and translate new proteins in the synthesis process

Question 13

How do amino acids play into protein synthesis?

Answer 13

They activate tRNA and start the process of protein synthesis

Question 14

How do cellular enzymes play into protein synthesis?

Answer 14

They are instrumental to the elongation process, allowing mRNA to stretch and allow translation of all of the different codons of the mRNA

Question 15

How do specific cofactors play into protein synthesis?

Answer 15

They can hold onto ATP/GTP to allow the release of them at a later time to complete certain steps in the ribosome

Question 16

How do ATP/GTP play into protein synthesis?

Answer 16

They are hydrolyzed to add energy to allow certain steps in the ribosome to happen

Question 17

Explain how mutations may affect protein synthesis process and/or its product

Answer 17

Mutations in protein synthesis can cause malformation of the protein and cause unwanted effects in the synthesis process and the product

Question 18

Protein synthesis stage 1: Amino Acid Activation and all of its parts

Answer 18

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

Question 19

Protein synthesis stage 2: Initiation and all of its parts

Answer 19

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)

Question 20

Protein synthesis stage 3: Elongation step 1

Answer 20

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

Question 21

Protein synthesis stage 3: Elongation step 2

Answer 21

Need: Aminoacyl-tRNA, Met-tRNA, 23S rRNA subunit

End: Peptide bond formed between Met and aminoacyl group of other tRNA

Question 22

Protein synthesis stage 3: Elongation step 3

Answer 22

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.

Question 23

Protein synthesis stage 4: Termination

Answer 23

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

Question 24

Protein synthesis stage 5: Posttranslational Processing

Answer 24

1. Amino terminal removal: Removal of formyl group, f-Met, or other amino acids
2. Glycosylation (Eukaryotes): Enzymatic addition of Asn-linked or Ser/Thr-linked sugars
3. Isoprenylation: Addition of isoprenyl group to Cys
4. Addition of prosthetic groups: Heme to Hb or Cyt
5. Proteolytic processing: Chymotrypsinogen to chymotrypsin
6. Formation of S-S bonds: Immunoglobulins, peptide hormones
7. Phosphorylation: Phosphorylase B, kinases, cyclins