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Biochem & Cell bio > Unit 11: Protein synthesis/translation > Flashcards

Unit 11: Protein synthesis/translation Flashcards

1
Q

Describe the genetic code

A
  • triplet code- each codon is 3 nucleotides long
  • non-overlapping- codes do not overlap
  • commaless or no punctation- codes are not spaced apart
  • (almost) universal - almost all organisms use this
  • degenerate- most amino acids can be coded for by more than one codon (aka synonyms)
  • unambiguous- each codon can code for only one amino acid
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2
Q

what is the start codon

A

AUG= Met

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3
Q

what is the direction of peptide synthesis

A

5’ to 3’

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4
Q

What is the open reading Frame (ORF)

A
  • the sequence from start to stop codon
  • the start frame is determined by the where the start codon (AUG) is
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5
Q

what does aminoacyl-tRNA synthetase do

A
  • it is the enzyme that connects an amino acid with a corresponding tRNA
  • uses ATP. converts to AMP and PPi.
  • activates AA and charges tRNA. AA is considered activated when connected to tRNA and tRNA is considered charged when connected to an AA
  • produces aminoacyl-tRNA
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6
Q

where is the amino acid attached on the tRNA?

A

it is attached to the 3’-OH of CCA end of the tRNA or acceptor arm

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7
Q

describe the shine-dalgarno sequence

A
  • is purine rich
  • found in prokaryotes translation start
  • base-pairs with rRNA small subunit.
  • helps orient the ribosome to align with start codon
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8
Q

describe the prokaryotic start signal vs. eukaryotic start signal

A

prokaryotic:
shine dalgarno sequences (this sequence base pairs with rRNA small subunit) followed by start codon AUG that codes for fMet

eukaryotic:
first AUG from 5’ end codes for H2N-Met

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9
Q

describe the polypeptide synthesis mechanism

A

synthesized from n-term to c-term.
- new AA is added to carboxyl terminus by peptide transferase function of ribosome
- amino acids react in activated form as aminoacyl-tRNA
- mRNA translated 5’ to 3’
- this allows the concurrent transcription and translation in prokaryotes

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10
Q

what are the stages of protein synthesis

A
  1. Activation of AA- activate carboxyl group of AA to allow formation of peptide bond linkage to tRNA. produces aminoacyl-tRNA
  2. Initiation
  3. elongation
  4. termination
  5. protein folding and post translational processing
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11
Q

where does activation of AA take place

A

cytoplasm

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12
Q

where does initiation, elongation, and termination take place

A

the ribosomes (found in the cytoplasm and ER)

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13
Q

where does posttranslational processing take place

A

cytoplasm, ER, and Golgi

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14
Q

What bonds anticodon to codon?

A

non-covalent interactions

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15
Q

what enzyme forms the high energy bond between tRNA and AA? what type of bond is it

A

aminoacyl-tRNA syntheses. there is one synthetase per amino acid and recognizes all tRNAs for that specific AA.
- most have proofreading capacity. only proofreading done in translation
- it is a thioester bond; a covalent bond. this stores the energy that makes peptide bonds possible

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16
Q

ways of altering mRNA sequence

A

point mutations- single base pair changes: giving silent mutation, missense or nonsense mutation

frameshift mutations: insertion or deletion of nucleotides within coding sequence leading to altered reading frame

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17
Q

what is a missense mutation vs. a nonsense mutation

A

their is a base pair change that results in a different amino acid

nonsense mutation is a base pair change that results in an early stop codon

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18
Q

how many codons are there

A
  1. but only 61 actually code for amino acids.
    3 are stop codons (UAG, UAA, UGA)
19
Q

What is the wobble hypothesis

A

1st and 2 codon position in codon and anticodon follow strict Watson-crick base pairing

3rd mRNA codon and 1st tRNA anticodon are flexible

  • reduces the number of tRNAs needed
20
Q

tRNA structure

A
  • secondary and tertiary are similar for all tRNAs
  • many modified bases
  • 50% of all bases are paired
  • stem-loop structures don’t pair and create structural diversity.
  • AA binds to the 3’ CCA on the acceptor stem
  • 5’ end usually G rich
21
Q

describe the thermodynamics of the aminoacyl-tRNA reaction

A
  • aminoacyl-tRNA synthetase requires ATP to produce the ester bond.
  • in the process 2 high energy bonds are consumed for AA activation.
  • AMP + PPi are produced
  • rxn is exergonic
22
Q

describe the aminoacyl-tRNA synthetase proofreading activity

A
  • a separate editing site.
  • only incorrectly bound amino acids fit into the site and the bond is hydrolyzed
  • it is used by most syntheses but not all need them
23
Q

what are isoaccepting tRNAs

A

tRNAs that recognize >1 codon for a specific AA

24
Q

describe the main structure and function of a ribosome

A
  • contains a small and large subunit.
  • 70s prokaryotes (50S and 30s)
  • 80s eukaryotes (40s and 60s)
  • made of protein and RNA. is a ribonucleoprotein complex
  • main catalytic function, peptide transferase activity, is performed by RNA specifically large subunit
  • can be found free in cytoplasm or bound to membranes ( such as the RER in eukaryotes)
25
Q

describe rRNA structure

A
  • it is specific 3D structure with extensive intra-chain base pairing
  • shape of rRNAs is highly conserved
26
Q

what does the small subunit do (40s)

A
  • binds mRNA and aminoacyl-tRNAs
  • locates AUG start codon on mRNA
27
Q

what does the large subunit do (60s)

A

binds to the small subunit after the start codon is located
has peptidyltransferase activity

28
Q

what is expressosome formation

A
  • prokaryotic translation
  • complex of RNAP, mRNA and ribosome
29
Q

what is the function of polysomes

A
  • increase efficiency in prokaryotic translation
  • are multiple ribosomes translating the same mRNA
30
Q

what do initiation factors do? explain how initiation works in prokaryotes

A

they are required to bind the mRNA and beginning methionyl-tRNA to the small ribosomal subunit (eukaryotes)

  • in prokaryotes the 30s subunit binds IF1 and IF3 then the mRNA
  • then IF2-GTP binds the 30s and recruits fmet=tRNAfmet , which base pairs with the start codon
  • the 50s subunit associates, IF2 hydrolyzes GTP, and IF1, IF2 and IF3 dissociate
31
Q

Steps of elongation in prokaryotes

A
  1. binding of aminoacyl-tRNA (second tRNA) at A site
    - GTP-EF-tu is attached. once proper base pairing is complete GDP-EF-Tu is released
  2. peptide bond formation. peptide attached to tRNA in A site
  3. translocation of the ribosome
    - EF-G (translocase) binds to A site, displaces tRNA with peptide into P-site, uncharged to E site
    - GTP hydrolysis (loss of Phosphate) induces conformational change and release of EF-G
    - mRNA shifted by one codon toward 3’ end
    - uncharged tRNA dissociates and acceptor site can accept a new charged tRNA
32
Q

describe termination in prokaryotes

A
  • signaled by a stop codon
  • no tRNA recognizing stop codons
  • stop codons are bound by specialized release factors (RF-1, RF-2)
33
Q

what do release factors in prokaryotes do?

A
  • facilitate hydrolysis of ester linkage and peptide release
  • release of uncharged tRNA in P-site
  • Dissociate ribosome
34
Q

eukaryotic translation vs. prokaryotic translation

A
  • eukaryotic ribosomes are larger than prokaryotic ribosomes
  • prokaryotes use no shine-dalgarno sequence, eukaryotes use Kodak sequence (ACCAUGG) includes most upstream AUG sequence after 5’
  • eukaryotes have more initiation factors than prokaryotes
  • special initiator tRNA does not use fmet. and met may be removed after
  • circularized mRNA
    -similar thermodynamics and reaction mechanism in elongation as in prokaryotes
35
Q

elongation in eukaryotes?

A
  • EF1-GTP brings in next codons (EF-Tu homolog)
  • EF1beta/gamma regenerate EF1-GTP (EF-T homolog)
  • EF2-GTP responsible for hydrolysis of phosphate for ribosome translocation (EF-G homolog)
36
Q

describe termination in eukaryotes

A
  • release factor eRF1 binds at A site
  • this recognizes all stop codons and initiates hydrolysis of bound GTP and peptide-tRNA cleavage
  • separation of mRNA and ribosome subunits done by ABCE1. requires ATP
37
Q

how are ribosomal subunits recycled in eukaryotes?

A

by eIFs (eukaryotic initiation factors)

38
Q

what does over expression of initiation factors in cancer cells do?

A

leads to gene amplification in human cancers

39
Q

how is the process of translation exploited clinically?

A
  • pharmaceuticals target prokaryotic translation inhibitors
  • Use of antimicrobial therapy with prokaryotic translation inhibitors
  • this exploits structural differences in eukaryotic and prokaryotic ribosomes.
40
Q

how many ATPs are required for activation

A

2

41
Q

how many ATPs are required for initiation

A

1

42
Q

how many ATPs are required for elongation (each step)

A

2
* remember to account for the AA already in the active site

43
Q

how many ATPs are required for termination

A

1

Biochem & Cell bio (20 decks)

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