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MABS Biochemistry > Translation: Protein Synthesis > Flashcards

Translation: Protein Synthesis Flashcards

1
Q

what is the process that produces proteins?

A

translation

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2
Q

on what does translation occur on and where?

A

ribosomes and mRNA

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3
Q

the coding region of mRNA is read in _____?

A

codons

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4
Q

what are codons?

A

sets of three nucleotides that specify individual amino acids.

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5
Q

codons are read sequentially in which direction?

A

5’-to-3’ direction starting with 5’-AUG (“start” codon) that specifies methionine.

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6
Q

what is set up when the start codon is found?

A

The reading frame is set up from this point and translation ends when a “stop” codon is reached (UAG, UGA, or UAA)

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7
Q

what is the start codon?

A

AUG or methionine

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8
Q

what is the stop codon?

A

(UAG, UGA, or UAA)

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9
Q

how many total codons are there?

A

64

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10
Q

what are the three codons that terminate protein synthesis? what do the remaining 61 codons specify?

A

3 UGA, UAG, UAA
Stop or nonsense codons

20 amino acids

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11
Q

what two amino acids only have 1 codon?

A

AUG=Met

UGG=Trp

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12
Q

why is the code considered degenerate but unambiguous?

A

Because many amino acids are specified by more than 1 codon, the code is degenerate. However, since each codon only specifies 1 amino acid it is unambiguous.

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13
Q

what is the variation in the third base called?

A

wobble hypothesis

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14
Q

what is the one exception for the code almost being universal?

A

human mitochondrial mRNA

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15
Q

what do we mean when the code is non overlapping?

A

one codon, one AA, no mix and match

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16
Q

what is the reading frame?

A

the order in which the sequence of bases in the mRNA is sorted into codons.

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17
Q

what does the order of the codon in the mRNA determine?

A

it determines the linear sequence of amino acids in the protein

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18
Q

for any given mRNA, how many possible reading frames are there?

A

three

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19
Q

what codon sets the reading frame for translation?

A

AUG

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20
Q

how do mutations result?

A

from damage to DNA nucleotides or from unrepaired errors during replication

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21
Q

can mutations be transcribed into mRNA?

A

yes, resulting in the translation of a protein with abnormal amino acids sequence.

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22
Q

what are the six types of mutations?

A 
point
silent
missense
nonsense
insertion
deletion
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23
Q

what is a point mutation?

A

a single base change

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24
Q

what is a silent mutation?

A

a change that specifies the same amino acid

25
Q

what is a missense mutation?

A

a change that specifies a different amino acid

26
Q

what is a nonsense mutation?

A

a change that produces a stop codon

27
Q

what is a insertion mutation

A

an addition of one or more bases

28
Q

what is a deletion mutation?

A

a loss of one or more bases

29
Q

what is a frameshift mutation?

A

occurs when the # of inserted or deleted nucleotides is not a multiple of three.

The reading frame shifts at the point where the insertion or deletion begins changing the amino acid sequence of the protein.

30
Q

what is aminoacyl tRNA?

A

tRNA with a covalently attached amino acid to the 3’-end. It is said to be “charged”.

31
Q

what is aminoacyl-tRNA synthetase? how many exist? whats unique about them?

A

highly specific enzyme that attaches an amino acid to its respective tRNA; 20 different synthetases exist; Each synthetase recognizes a particular amino acid and all of the tRNAs that carry that amino acid. (Recall: Several amino acids have >1 codon)

32
Q

what are the steps in the formation of Aminoacyl-tRNA? 2 steps - energy requiring process

A

Amino acid is activated when its carbonyl group reacts with adenosine triphosphate (ATP) to form enzyme/aminoacyl-adenosine monophosphate (AMP) complex and pyrophosphate.

The activated tRNA is transferred to the 2’- or 3’ hydroxyl group of the ribose connected to the 3’-terminal adenine residue of the tRNA

33
Q

what do aminoacyl tRNA synthetase provide?

A

the 1st error-checking step in preserving fidelity of translation

use different nucleotide sequences within the tRNA as recognition sites to attach the correct amino acid

34
Q

what are the three steps of translation?

A

initiation
elongation
termination

35
Q

what is initiation phase of translation?

A

formation of the initiation complex

36
Q

what is elongation phase of translation?

A

series of repeated additions of amino acids

37
Q

what is termination phase of translation?

A

mRNA stop codon is reached, polypeptide chain is released

38
Q

what is initiation in the process of translation?

A

Steps:

Met-tRNAiMet initially forms a complex with protein eukaryotic initiation factor 2 (eIF2), which binds to guanosine triphosphate (GTP)

Met-tRNAiMet – eIF2-GTP complex binds to small (40S) ribosomal subunit with eIF3
eIF3 also prevents premature association of 60S ribosomal subunit.

5’-cap of mRNA binds to the eIF4 complex, eIF4F, known as the cap-binding complex

The mRNA is association with the cap-binding complex then binds to the eIFs-Met-tRNAiMet-40S ribosome complex. [ATP required]

This complex unwinds a hairpin loop in the mRNA and scans the mRNA until it locates the AUG start codon.

GTP is hydrolyzed, the initiation factors released, and the large ribosomal (60S) subunit binds.

39
Q

what is the Kozak consensus sequence in eukaryotes?

A

recognized by the ribosome as the translational start site to aid in defining the initial AUG codon for translation. (A or G – CCAUGG ; purine base is 3 bases upstream of initial AUG)

40
Q

in the process of translation: during initiation, what is the first amino acid acid for eukaryotes? prokaryotes?

A

methionine; formyl-methionine

41
Q

in the process of translation: during initiation, how many initiation factors are required for eukaryotes? prokaryotes?

A

elFs (12 or more); IFs (3)

42
Q

in the process of translation, during the intiation portion, what are the ribosomes for eukaryotes?prokaryotes?

A

80S (40S and 60S subunits); 70S (30S and 50S subunits)

43
Q

in the process of translation, how does the binding of mRNA to small ribosomal subunits happen in prokaryotes? eukaryotes?

A

Identification of the initiating AUG triplet in prokaryotes occurs when a sequence in the mRNA (known as theShine–Dalgarno sequence) binds to a complementary sequence near the 3′-end of the 16S ribosomal RNA (rRNA) of the small ribosomal subunit.

cap at the 5’-end of mRNA binds eIFs and 40S ribosomal subunit containing tRNA-met. mRNA is scanned for AUG start codon within the kozak consensus sequence

44
Q

how does elongation happen in the process of translation, name the steps?

A

1) Binding of aminoacyl-tRNA to the A site
2) Formation of a peptide bond
3) Translocation
4) Ejection of free tRNA from E site

45
Q

during elongation, in the process of translation, what is the purpose of peptidyltransferase in the formation of a peptide bond?

A

Peptidyltransferase (rRNA of the large ribosomal subunit) catalyzes the formation of the peptide bond

46
Q

what are the three nonsense (unrelatable to an amino acid) codons or stop codons (end fo message) in the termination phase of the process of translation?

A

UGA, UAG, UAA

47
Q

what happens in the termination phase of the process of translation?

A

No tRNAs with anticodons to pair with a stop codon exist

Release factors bind to the ribosome

Peptidyltransferase hydrolyzes the bond between the peptide chain and tRNA

Polypeptide is released from the ribosome

Ribosome dissociates into individual subunits, releasing mRNA

48
Q

what are the inhibitors of protein synthesis in prokaryotes?

A

streptomycin binds to the 30S ribosomal subunit of prokaryotes preventing the formation of the initiation complex; causes misreading of mRNA

tetracycline binds to the 30S ribosomal subunit and inhibits binding of aminoacyl-tRNA to the A site

chloramphenicol binds to the 50S ribosomal subunit and inhibits peptidyltransferase

erythromycin binds to the 50S ribosomal subunit and prevents translocation

49
Q

significance of the antibiotic drugs that affect bacterial protein synthesis

A

These steps are usually different from eukaryotic protein synthesis so that their use inhibits bacterial proliferation while having little to no effect on human cells.

50
Q

what is a polysome?

A

Many ribosomes simultaneously translating a single mRNA, forming a complex

51
Q

in terms of polysomes, how many nucleotides do you need to have an effective polysome?

A

80 nucleotides and covered at intervals of 100 nucleotides

52
Q

in the processing of proteins, what are chaperones?

A

proteins that bind to the nascent polypeptide chain and mediate the folding process by preventing improper interactions from occurring. They serve as heat shock proteins.

As the nascent polypeptide emerges from the ribosome, it begins to fold and refold into its 3-D confirmation.

53
Q

in post translational modifications, what are the types of post translational modifications?

A

Initial methionine is removed by proteases

Cleavages to convert proteins to active forms

Enzymatic modifications of amino acid residues

54
Q

what are other types of postranslational modifications?

A

Acetylation and methylation can alter the charge on the protein
Proline and lysine residues can be modified by hydroxylation. In collagen, this can lead to stabilization.
Carboxylations are important for the function of proteins involved in blood coagulation.
Fatty acids or other hydrophobic groups (i.e. prenyl groups) anchor proteins in membranes.
ADP-ribose group can be transferred from NAD+ to certain proteins.
The addition and removal of phosphate groups (bind covalently to Serine, Threonine, or Tyrosine) serve to regulate activity.
Glycosylation, the addition of carbohydrate groups, is a common modification that occurs on proteins that are destined to be secreted or incorporated into lysosomes.

55
Q

what is Diphtheria Toxin?

A

a highly contagious disease caused by a toxin secreted by the bacterium Corynebacterium diphtheriae, where the A-subunit catalyzes an ADP-ribosylation reaction; it interrupts post translational modification like shape and function

56
Q

what is the fate of proteins synthesized on cytosolic polysomes?

A

Remain in cytosol to carry out functions

Enter organelles (e.g. mitochondria or nuclei)

57
Q

what is the fate of proteins synthesized on ribosomes bound to rough endoplasmic reticulum (RER)?

A

Secretion

Incorporation into various subcellular organelles (e.g., lysosomes, endoplasmic reticulum, Golgi complex) or cellular membranes.

58
Q

what is the purpose for the targeting of proteins?

A

Mechanisms are present within cells to specifically target newly synthesized proteins to different compartments in the cell.

MABS Biochemistry (54 decks)

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