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2024 SEM 1 BIOCHEMISTRY (LEC) > translation > Flashcards

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1
Q

it is the site of protein synthesis

A

ribosomes

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2
Q

what are the steps involved in protein biosynthesis

A
  1. aa activation
    aa covalently bonded to tRNA = aminoacyl-tRNA
    enzyme responsible for the covalent bonding - aminoacyl-tRNA synthetase

inactivated tRNA: w/o aa

  1. chain initiation
    aminoacyl-tRNA bind to start site of ribosomes
  • if it is TATA-less - start at random points
  1. chain elongation
    form peptide bons btwn successive aa residues
  2. chain termination
    release of a newly formed protein from the ribosomes
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3
Q

what are the requirements for protein biosynthesis

A

ribosomes
mRNA
tRNA
protein factors

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4
Q

what are the characteristics of the genetic code

A

triplet

nonoverlapping
- no bases are shared btwn consecutive codon

commaless
- no interventing bases btwn codons exist

degenerate
- more than one triplet can encode the same aa

universal
- same in all organisms (prokaryotes, eukaryotes and viruses)
*some codons seen in mitochondria are diff from those seen in the nucleaus

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5
Q

how many sequence of bases is needed to specify one amino acids

A

three bases, called the codon
3 bases = 1 aa

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6
Q

why is the genetic code 4^3

A
  • If it took 1 base to make a codon: 4^1 = 4
  • If it took two bases to make a codon: 4^2 = 16

those are not enough. hence,
* For 3 bases, or a triplet: 4^3= 64
its okay if exceed basta nag cover lahat ang 20 aa

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7
Q

true or false:
Each amino acid may have more than one codon, but no codon can encode more than one amino acid

A

true

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8
Q

what are the meanings in the assigned 64 codons

A

61 codons code for aa
3 termination signals (UAG, UGA, UAA)

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9
Q

true or false:
ribosomes moves along the mRNA one at a time

A

false - it moves along 3 bases at a time rather than 1 or 2

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10
Q

what are the 2 amino acids that have only one codon each but the rest have more than one

A

tryptophan
methionine

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11
Q

what are the 2 amino acids that can have as many as 6 codons

A

leucine
arginine

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12
Q

true or false:
multiple codons for a single amino acid are not randomly distributed but have one or two bases in common

A

true

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13
Q

1st and 2 part of codon:
3rd part of codon:

A

1st and 2 part of codon:
fixed

3rd part of codon:
“wobble” base - allows “wiggle room” in matching the correct aa

*wobble base pairing provides flexibility, helps the genetic code tolerate small errors, and makes the process of translating DNA into proteins more efficient.

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14
Q

a mutation in the DNA that does not lead to a change in the amino acid translated

A

silent mutation

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15
Q

it acts as a buffer against deleterious mutations

A

degeneracy of the code

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16
Q

it reads codons and make proteins. since wobble base pairing, they are needed in fewer amts cause it can recognize and bind to multiple codons that differ only in the third base

A

tRNA

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17
Q

Sequence of three bases in tRNA that hydrogen-bonds with the
mRNA triplet that specifies a given amino acid

A

anticodon

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18
Q

are there 64 tRNAs as well as 64 codons

A

there are 64 possible codons, but not exactly 64 tRNAs.
there are fewer tRNAs than codon bcs of the “wobble” effect

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19
Q

which of the three bases in the anticodon is the wobble base

A

the wobble base of the anticodon is the one at 5’ end

20
Q

in the bases at 5’ of anticodon, what are the base at 3’ end of codon

A

bases at 5’ of anticodon
Inosine - A, C, U
Guanine - C, U
Uracil - A, G
Adenine - U
Cytosine - G

21
Q

what are the steps in amino acid activation and the formation of aminoacyl-tRNA

A

catalyzed by aminoacyl-tRNA synthetase

  1. aa forms covalent bond to adenine nucleotide = aminoacyl-AMP
    - ATP serve as energy source
    - aminoacyl part is transferred to the tRNA
  2. ester linkage is formed btwn aa and either 3’ hydroxyl or 2’ hydroxyl of the ribose at the 3’ end of tRNA
22
Q

they are enzymes that make sure the correct amino acid is attached to the right tRNA

A

aminoacyl-tRNA synthetases

class I enzymes:
attach aa to 2’ hydroxyl grp on tRNA

class II enzymes:
attach aa to 3’ hydroxyl group

22
Q

stages in prokaryotic translation

A

chain initiation
chain elongation
chain termination

23
Q

Synthesis of polypeptide chain starts at the N- terminal end

A

chain initiation
- chain grows from initial N terminal aa of all proteins in N-formyl methionine (fmet)

24
what are the 2 tRNAs for methionine in E. coli
tRNAmet ---> met-tRNAmet tRNAfmet ---> met-tRNAfmet
25
what is the specific sequence of a triplet that tRNAmet and tRNAfmet contain
3'-UAC-5' - it is the base pair with '5-AUG-3' in the mRNA sequence tRNAfmet: recognizes AUG when it occurs at the beginning of the mRNA sequence that directs polypeptide synthesis tRNAmet: recognizes AUG when it is found in an internal position in the mRNA sequence
26
what are the components that enter the initiation complex
initiation codon (AUG) of mRNA 30s and 50s ribosomal subunits fmet-tRNAfmet GTP (guanine based) T3 protein initiation factors, IF-1, IF-2, IF-3
27
translation needs this for initiation
shine-dalgarno sequence it is a purine-rich leader sequence (5'-GGAGGU-3') that precedes the start signal lies abt10 nucleotide upstream of the AUG start signal acts as a ribosomal binding site
28
in chain elongation, what are the 3 binding sites for tRNA that are present on the 50S subunits of the 70S ribosomes
P (peptidyl) site: binds tRNA that carries peptide chain A (aminoacyl) site: binds incoming aminoacyl-tRNA, which has to be added to the growing peptide chain E (exit) site: carries an undercharged tRNA that is abt to be releases from the ribosomes
28
the shine-dalgarno sequence (5'-GGAGGU-3') binds to
pyrimidine-rich sequence on the 16S ribosomal RNA part of the 30S subunit - aligns it for proper translation beginning with the AUG codon
29
what are the steps in chain elongation in prokaryotic
1. add second aa specified by the mRNA to the 70S initiation complex second aminoacyl-tRNA binds at the A site triplet of tRNA bases form hydrogen bonds with a triplet of mRNA bases (acceptor of tRNA ---> hydrogen bonding of codon and anticodon) - ribosomes move not mRNA 2. requires GTP [hydrolyzed] 3 protein elongation factors > EF-P bound adjacent to the P site and E site help catalyze the first peptide bond formed > EF-Tu (temp unstable) [dissociates] when the correct aa is bound to the correct tRNA, EF-Tu is efficient at delivering the activated tRNA to the ribosomes if tRNA and aa are mismatched, EF-Tu does not bind the activated tRNA very well a >EF-Ts (temp stable) 3. peptide bond is formed in a reaction catalyzed by peptidyl transferase 4. translocation: motion of the ribosome long the mRNA as the genetic message is being read - occurs b4 another aa can be added to the growing chain - uncharged tRNA moves from the P site to the E site, from which it is released - peptidyl-tRNA is translocated to the vacant P site from the A site EF- is required GTP is hydrolyzed to GDP and Pi
30
what are the requirements for the peptide chain termination
stop signals: UAA, UAG, UGA they r recognized by release factors release factors: RF-1 binds to UAA & UAG RF-2 binds to UAA & UGA GTP: bound to RF-3 it does not bind to any termination codon facilitates the activity of RF-1 and RF-2 conserved sequence of Gly-Gly-Gln for the hydrolysis reaction of the RF
31
what happens in the peptide chain termination
entire complex dissociates, setting free the release factors tRNA mRNA 30S and 50S ribosomal subunits
32
what has been replaced in the cysteine residue
S atom has been replaced by a Se atom - Only amino acid that lacks its own tRNA synthetase and is synthesized while bound to its tRNA - codon is UGA
33
Assemblage of several ribosomes bound to one mRNA
Polysomes (Polyribosome) - Each of these ribosomes bears a polypeptide in one of various stages of completion
34
Process in which a prokaryotic gene is being simultaneously transcribed and translated
Coupled translation - Result of a lack of cell compartmentalization
35
it is when the mRNA of eukaryotes are characterized by two major posttranscriptional modifications
Eukaryotic Translation * 5′ cap * 3′ poly A tail
36
what is the chain elongation in prokaryotic translation
uses the same mechanism of peptidyl transferase and ribosome translocation as prokaryotes Ribosome does not contain an E site * Contains only A and P sites Involves 2elongation factors * eEF1 - Contains two subunits - eEF1A (counterpart of EF-Tu) - eEF1B (counterpart of EF-Ts) * eEF2 - Counterpart to EF-G, which causes translocation Ribosomes encounter stop codons that are not recognized by a tRNA molecule Only one release factor binds to all three stop codons - Catalyzes the hydrolysis of the bond between the C-terminal amino acid and the tRNA Suppressor tRNA: Permits translation to continue through a stop codon Found in cells in which a mutation has introduced a stop codon
37
in Posttranslational Modification of Proteins, what other substances can be linked to the newly formed polypeptide
* Cofactors, such as heme groups, are added * Disulfide bonds are formed * Some amino acid residues are covalently modified (Example - Conversion of proline to hydroxyproline) * Other covalent modifications can occur (Example - Addition of carbohydrates or lipids to yield an active final form of the protein in question) * Proteins can also be methylated, phosphorylated, arginylated, and ubiquitinylated
37
in Posttranslational Modification of Proteins, how are newly synthesized polypeptides are frequently modified before they reach their final form where they exhibit biological activity
* N-formylmethionine in prokaryotes is cleaved * Specific bonds in precursors are hydrolyzed, as in the cleavage of preproinsulin to proinsulin and of proinsulin to insulin * Leader sequences are removed by specific proteases associated with the endoplasmic reticulum * Finished protein enters the Golgi apparatus, which directs it to its final destination
38
Proteins are in a dynamic state in which they are turned over often
Protein Degradation
39
what happens to the abnormal proteins that are formed from errors in either transcription or translation
they are degraded quickly
40
in protein degradation, what are some Pathways they are restricted to
* Subcellular organelles, such as lysosomes * Macromolecular structures called proteasomes
41
Process of binding the polypeptide ubiquitin to a protein to mark it for degradation
Ubiquitinylation
42
what are the 3 enzymes involved in Ubiquitinylation
Ubiquitin-activating enzyme (E1) ubiquitin-carrier protein (E2) ubiquitin-protein ligase (E3)
43
true or false: Misfolded proteins cannot be repaired by eukaryotic chaperones
false - can be repaired *Can be targeted for destruction by ubiquitination

2024 SEM 1 BIOCHEMISTRY (LEC) (19 decks)

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