Proteins synthesis & genetic code 01

Question 1

How much energy in a cell accounts for protein synthesis?

Answer 1

80% of cell’s energy

Question 2

What is body wasting?

Answer 2

Muscle-wasting (glu, aa) and subcutaneous fat loss (FA, energy, metabolites)

Question 3

What is Marasmus starvation?

Answer 3

total calorie under-nutrition

Question 4

What is Kwashiorkor?

Answer 4

Protein malnutrition, only in children eating food ok or high in calories but low in protein.
-> distorted serum aa composition, distorted liver aa pools, B-lipoprotein, albumin (edema)

Question 5

What is are some common protein synthesis inhibitors /toxins?

Answer 5

1. Alpha amanitine: RNA Pol II inhibitor
2. Ricin: binding to the 60S subunit
3. Diphteria: catalyzes the ADP-ribosylation of, and inactivates eEF2
4. Trichothecene mycotoxins: problems w/rapidly growing tissues.

Question 6

What are the 2 biological languages?

Answer 6

1. The nucleotide language

2. The aa language

Question 7

What are 3 important implication of the protein postulates?

Answer 7

1. There is a genetic code
2. RNA copy (mRNA) carries the code
3. There is an apparatus (ribosome & tRNA) for translating the code.

Question 8

What is the nature of genetic code?

Answer 8

a. 4 nucleotides
b. 20 letters in amino acid code
c. continuous code, nonoverlapping

Question 9

What are the start and stop codons?

Answer 9

Start: AUG (Met)
Stop: UAA, UAG, UGA

Question 10

What are some important characteristics of the genetic code?

Answer 10

1. The code is triplet, non-overlapping
2. Unambiguous (1 specific codon = 1 specific aa)
3. Degenerate (1 specific aa = 1+ specific codons)
4. Not universal

Question 11

What are the 4 major steps of protein synthesis?

Answer 11

1. Initiation: ribosome is assembled on mRNA
2. Elongation: aa is brought to ribosome and it’s joined to nascent chain. Entire assembly then moves 1 position along mRNA
3. Termination: at stop codon, no aa to add. Polypeptide is released from ribosome
4. Disassembly: a special factor binds to the ribosome to release mRNA and tRNA.

Question 12

What are the 3 exceptions to the 1 codon = 1 aa rule?

Answer 12

AUG: Methionine and N-formyl methionine
UGA: selenocysteine and stop codon
UAG: pyrrolysine and stop codon

Question 13

How are selenoproteins synthesized?

Answer 13

A selenoprotein mRNA has a SECIS structure, selenocysteine insertion sequence, that adopts a stem-loop structure. This motif directs the cell to translate UGA codons as selenocysteines. Selenium is an essential trace element.
*Selenoproteins: antioxidant defense (glutathione peroxidase), thyroid hormone metabolism, lymphocyte activation, myocyte regeneration.

Question 14

What are the 2 exceptions to the code degeneracy rule?

Answer 14

Met and Trp are encoded by a single codon

*Degeneracy is only found in the 3rd nucleotide of the codon.

Question 15

Why is it said that the genetic code is not universal?

Answer 15

-Some of the code words are changed in some organisms, specially in the mitochondria. -Variations are consistent with view that mitochondria are ancient prokaryotic organisms. -Mitochondria protein synthesis is more simila to prokaryotic protein synthesis than eukaryotic.

Question 16

What did Crick proposed about tRNA:mRNA interaction?

Answer 16

• He proposed that the interaction at the 3’ mRNA position was unusually loose.
• Watson-Crick bp in first two positions, but third position allows to wobble off with a G-U bp.

Question 17

Where do we see ionsine “I”?

Answer 17

tRNAs often occurs in the anticodon of tRNAs. It can bp with U, C, and A in the wobble position.
->3' codon base /  5' anticodon:
           A     / U or I
           C    /  G or I
           G    /  C or U
           U    /  A or G or I

Question 18

What are the two rules about protein synthesis?

Answer 18

1. mRNA is translated from 5’ to 3’
2. Proteins are synthesized from N-terminus to the C-terminus
   * 5’ of mRNA encode the N-terminal part of the protein

Question 19

How is prokaryotic protein synthesis different from eukaryotic one?

Answer 19

In prokaryotes, protein synthesis is closely coupled to mRNA synthesis in space and time.
In eukaryotes, mRNA synthesis occurs in the nucleus and translation in the cytoplasm; they both occur in the cytoplasm in prokaryotes almost at the same time.

Question 20

What is the overall structure of the eukaryotic mRNA?

Answer 20

5' cap (recruits ribosome)
AUG start codon
ORF (monocystronic)
Stop codon
Poly-A tail- 3'

Question 21

What are the “ingredients” for protein synthesis?

Answer 21

1. Aminoacylated tRNAs
2. Ribosomes
3. mRNA
   * Ancillary protein “factors”
   * A special tRNA for initiation

Question 22

What is the structure of tRNA?

Answer 22

• Cloverleaf structure folded to yield an “L” shape
• Unusual nucleosides due to post-translational modificatiosn (pseudouridine, ribothymidine)
• Phosphorylated 5’ terminus
• 3’- OH-ACC, where amino acid is attached
• 3 nucleotides in bottom loop form the anticodon
• 4 loops: DHU, anticodon loop, variable, TΨC

Question 23

What is the ribosomal subunit fo euk/prokaryotes?

Answer 23

Each ribosome has 2 ribonucleoprotein subunits

a) Prokaryotes: 70S = 50S + 30S
b) Eukaryotes: 80S = 60S + 40S
- Small subunit: decoding center
- Large subunit: peptidyl transferease center

Question 24

How can ribosomal RNA be used for diagnosis of infections?

Answer 24

• Most abundant type of RNA in the cell
• While structure has been well preserved, there has been substantial divergence of 1ry sequence
• Using probes specific for the ribosomal RNA of pathogenic bacteria and fungi, it will soon be possible to improve differential diagnosis.

Question 25

What is the aminoacyl-tRNA?

Answer 25

tRNA to which its amino acid chemically bonded (charged). The aa-tRNA, along with some elongation factors, deliver the amino acid to the ribosome for incorporation into the polypeptide chain that is being produced