Protein synthesize

Question 1

How much energy does protein synthesis take from overall energy of the cell

Answer 1

90%

Question 2

What are the outcomes that protein synthesize is very energy demanding process

Answer 2

The number of protein copies made = number of proteins needed

Question 3

What is the method of regulation of proteins

Answer 3

Degradation

Question 4

After the synthesize of the protein is finished, ___

Answer 4

Post translational modifications take place, for example 3d structure of the protein

Question 5

Where do tRNA has AA and where is the part that recognizes mRNA

Answer 5

Adaptor site and 3’ end of tRNA, to which amino acid is bound to

Question 6

How many codons we have and are they nonoverlapping or overlapping?

Answer 6

we have 64 combinations

Nonoverlapping code, that is taken by one AA only

Question 7

The code ( codon) is written in ___ ( direction)

Answer 7

5’ to 3’

Question 8

Are all bases in codon important for binding

Answer 8

No, the first two are most important for tRNA

Question 9

First codon establishes ____ and why it is important

Answer 9

The reading frame

Important , because if it is thrown off by a base or two, all subsequent codons are out of order

Question 10

There are __ stop codons and they are

Answer 10

3 codons
UAA
UGA
UAG

Question 11

What is particular about AUG

Answer 11

It codes for both Methyanine and it is an initiation codone

Question 12

What AA have only one codon

Answer 12

Methionine

tryptophan

Question 13

Why mitochondria is so unique

Answer 13

It has its own ribosomes and 13-14 proteins it can synthesize by itself
UGA encodes tryptophan ( instead if stop)
AGA/AGG encode stop ( instead of Arg)

Question 14

How do we number codon and anticodon

Answer 14

In antiparallel fashion
Codon 123
Anticodon 321

Question 15

What base determines how many codones will be read by tRNA

Answer 15

3 base on codon

Question 16

describe five stages of protein synthesis

Answer 16

1 The tRNAs are aminoacylated. 2
Translation is initiated when an mRNA and an aminoacylated tRNA are bound to the
small ribosome. 3 When the first AA is brought ( Met)->large ribosome is brought .3.1In elongation, the
ribosome moves along the mRNA, matching tRNAs to each codon and catalyzing peptide bond formation. 4 Translation
is terminated at a stop codon, and the ribosomal subunits are released and recycled for another round of protein synthesis.
5 Following synthesis, the protein must fold into its active conformation and ribosome components are recycled.

Question 17

tRNa has __ arms

Answer 17

4 arms
D arm
Anticodon arm
TwC arm
Amino acid arm

Question 18

All tRNa has what sequence

Answer 18

CCA that is added in postranslational modification process at amino acid arm

Question 19

What is done to attach AA to tRNA

Answer 19

aminoacylation

Question 20

Describe aminoacylation

Answer 20

Carboxyl group of AA attacks Alpha phosphate group on ATP, forming 5' aminoacyl adenylate( aminoacyl-AMP)
Then the process divides into two parts -> class 1 aminoacyl-tRNA synthetases
and class II aminoacyl-tRNA synthetases

Question 21

The difference in class I and class II aminoacyl tRNA transferases

Answer 21

For class I enzymes, 2a the aminoacyl group is transferred first to the 2′-hydroxyl group of the 3′-terminal A
residue, AMP gives off AA and leaves

then from carbon 2’ to 3′-hydroxyl group by a transesterification reaction.

 For class II enzymes,  the aminoacyl group
is transferred directly to the 3′-hydroxyl group of the terminal adenylate.

Question 22

The first AA in protein synthesize is

Answer 22

Met, because AUG codes for the start codone as well

Question 23

What happens in mitochondria and prokaryotes with the first methionine

Answer 23

initiation tRNA inserts n-Formylmethionine (fMet) and the rest of AUGs will be normal Met

Question 24

Initiation of translation in eukaryotes

Answer 24

Initiation factors eIF1A and eIF3 ,eIF1 bind to the 40S subunit , blocking tRNA binding to the A site (eIF1A) and premature
joining of the large and small ribosomal subunits, respectively

The factor eIF1 binds to the E site.
The charged initiator( the first with Met) tRNA is bound by the initiation factor eIF2, which also has bound GTP.

2)eIF5B bonded to GTP also comes and everything together they bond. first tRNA come to P site, The only tRNA that comes there. Now it is called 43 S preinitiation complex

3)The mRNA binds to the eIF4F complex, which, in step , mediates its association with the 43S
preinitiation complex and brings to 43 S complex with the usage of ATP. Now it is called 48S complex

4)This complex scans the
bound mRNA, starting at the 5′ cap, until an AUG codon is encountered.

5) the next tRNA comes to A site
6) As soon as the first codon is bonded, the complex disassembles and the large subunit comes.

Question 25

How is the first peptide bond is created?

Answer 25

This occurs by transfer of the initiating N-formylmethionyl group from its tRNA to the amino group of the second amino acid, now in the A site . The α-amino group of the amino acid in the A site acts as a nucleophile, displacing the tRNA in the P site to form a peptide bond. This reaction produces a dipeptidyl-tRNA in the A site, and the now “uncharged” (deacylated) tRNAfMet remains bound to the P site. The tRNAs then shift to a hybrid binding state, with elements of each spanning two different sites on the ribosome. The enzymatic activity that catalyzes peptide bond formation has historically been referred to as peptidyl transferase and was widely assumed to be intrinsic to one or more of the proteins in the large ribosomal subunit. We now know that this reaction is catalyzed by the 23S rRNA

Question 26

What factors bring in aminoacyl tRNA to A site

Answer 26

EF-Tu-GTP

Question 27

What happens if the right tRNA has been brought

Answer 27

EF-Tu-GTP is hydrolized to EF-Tu-GDP and exits

Question 28

How does the tRNAs change places

Answer 28

the ribosome moves one codon toward the 3′ end of the mRNA . This movement shifts the anticodon of the dipeptidyl-tRNA, which is still attached to the second codon of the mRNA, from the A site to the P site, and shifts the deacylated tRNA from the P site to the E site, from where the tRNA is released into the cytosol.

Question 29

Who pushes dipeptidyl -tRNA to Psite

Answer 29

EF-G-GTP | When it pushes, it will exit as EF-G-GDP and then A site is empty to receive another aa-tRNA

Question 30

How is ther protein synthesis is terminated?

Answer 30

Synthesis is terminated in response to a termination codon in the A site. First, a release factor, RF (RF1 or RF2, depending on which termination codon is present), binds to the A site. This leads to hydrolysis of the ester linkage between the last added polypeptide and the tRNA in the P site and release of the completed polypeptide. Finally, the mRNA, deacylated tRNA, and release factor leave the ribosome, which dissociates into its 30S and 50S subunits, aided by ribosome recycling factor (RRF), IF3, and energy provided by EF-G– mediated GTP hydrolysis. The 30S subunit complex with IF3 is ready to begin another cycle of translation

Question 31

Some proteins require ___ before the fully active conformation is achieved

Answer 31

Modification

Question 32

Examples of post-translational modification

Answer 32

Enzymatic removal of formyl group from first residue, or removal of Met and sometimes additional residues - Acetylation of N-terminal residue - Remocal of some regions - Forming disulfide links - Attaching carbohydrates

Question 33

Half-life range of proteins is

Answer 33

from seconds to month

Question 34

Hmoglobin is ___

Answer 34

long-lived protein, 120 days

Question 35

Proteins for rapidly changing needs are ___, as well as defective proteins

Answer 35

Short-lived

Question 36

What is done recognize what proteins should be degraded

Answer 36

Adding polyUbiquitin to lysine

Question 37

How ubiquitin is added on proteins

Answer 37

First, the free carboxyl group of ubiquitin’s carboxyl-terminal Gly residue becomes linked to an E1-class activating enzyme wuth the hydrolyses of ATP to ADP. The ubiquitin is then transferred to an E2 conjugating enzyme. An E3 ligase ultimately catalyzes transfer of the ubiquitin from E2 to the target, linking ubiquitin ε-amino group of a Lys residue in the target protein