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BIOL 0280 UNIT 4 > Lecture 21: Protein Metabolism > Flashcards

Lecture 21: Protein Metabolism Flashcards

(65 cards)

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1
Q

Translation Basics

Where does translation occur in Prokaryotes vs. Eukaryotes?

A

Prokaryotes Cells
- Transcription & Translation occur in the cytoplasm

Eukaryotic Cells
- Transcription occurs in the Nucleus
- Translation occurs in the cytoplasm

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2
Q

Genetic Code

How many nucleotides at a time does mRNA read?

A

3 nucleotides at a time

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3
Q

Genetic Code

How many different 3 letter combination possibilities are there?

How many possible reading frames are there

A

64 possible 3 letter combinations

3 possible reading frames

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4
Q

Genetic Code

What is a codon?

A

Triplet nucleotides that code for amino acid

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5
Q

Genetic Code

In what direction are codons read?

A

5’ -> 3’

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6
Q

Genetic Code

How many start codons are there?

Name them

A

1 - AUG

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7
Q

Genetic Code

How many stop codons are there

Name them?

A

3

UAA
UAG
UGA

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8
Q

Genetic Code

Is the genetic code universal?

A

Yes

It is universal among all living things with minor variations

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9
Q

Genetic Code

Is there redundancy present in the genetic code?

What is the purpose of redundancy?

A

Yes – Multiple different codons can encode the same AA
- Except for Met and Trp

The purpose of this is to minimize deleterious effects of mutations

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10
Q

Genetic Code

What is a frameshift mutation?

A

Deletions or insertions of 1 or 2 nucleotides

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11
Q

Genetic Code

What is the affect of a frameshift mutation

A

Changes the reading frame -> could be detrimental to protein function

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12
Q

Genetic Code

What are the essential components of translation?

A
  • Codon
  • tRNA
  • Ribosome
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13
Q

Ribosomes

What do ribosomes do?

A
  • Ribosomes are organelles found in all cells that synthesize proteins
  • They are responsible for translating the genetic code in messenger RNA into a string of amino acids
  • Those amino acids then form long chains that fold into proteins
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14
Q

Ribosomes

How do Ribosomes interact with tRNA?

A

Ribosomes have specific binding pockets for tRNA

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15
Q

Ribosomes

What are the binding pockets for tRNA?

A

EPA

E - Exit site
P - Peptidyl tRNA binding site
A - Aminoacyl- tRNA binding site

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16
Q

Ribosomes

How well are ribosome sequence and structure conserved?

A

Ribosome sequence and structure is highly conserved

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17
Q

Ribosomes

What are Eukaryotic Ribosomes made of?

A

80S subunit & 60S subunit

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18
Q

Ribosomes

What are Prokaryotic Ribosomes made of?

A

70S subunit & 60S subunit

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19
Q

tRNA

Describe tRNA in terms of it’s function in the translation process

A

tRNA is the adaptor molecule that reads and therefore decodes mRNA

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20
Q

tRNA

What does tRNA’s structure resemble?

What are the 4 arms on a tRNA molecule going clockwise

Which arms provide the backbone structure for the tRNA molecule itself?

A

it’s structure resembles a clover leaf

  • Amino Acid arm
  • T phi C arm
  • Antocodon arm
  • D arm

The T phi C arm and D arm

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21
Q

tRNA

What are anticodons?

What do they do?

A

The reverse complement of the mRNA strand

They base pair with the codons on the mRNA strand

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22
Q

tRNA

What occurs on the amino acid arm?
Where specifically are amino acids link to?

A

Specific amino acids are linked to the 3’ end

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23
Q

tRNA

What did Francis Crick notice that lead to the Wobble hypothesis

A

They noticed that the first two nucleotides in the codon: anti-codon predicted which amino acid would be coded

The tRNA did not fit perfectly – it wobbled

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24
Q

tRNA

What does the wobble hypothesis suggest?

A

It suggests that anticodon pairing isn’t completely precise
- If it was too specific -> protein synthesis would be too slow, dissociation not fast enough

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25
*tRNA* What does the wobble hypothesis say about how many unique tRNA are needed for all 61 coding codons
Only 32 unique tRNA are needed - Different tRNA are needed only if any of the two nucleotides in a codon are different
26
*tRNA* What are the 4 wobble pairs?
I-C I-U I-A G-U
27
*tRNA* How is I formed?
I is inosine and is formed from the deamination of adenosine
28
*tRNA* What is the relationship between wobble and specificity?
More wobble = less specific Less wobble = more specific
29
*Decoding mRNA* What does the first codon in a sequence do?
Establishes the reading frame
30
*Decoding mRNA* What is the importance of the AUG/start codon
Establishes the reading frame - Translation continues until it encounters a stop codon
31
*Mutations* What is a wild type?
The original/normal functional protein
32
*Mutations* What is a substitution mutation? What are the 3 types of substitutions?
A mutation that potentially leads to AA changes - Silent - Missense - Nonsense
33
*Mutations* Describe a silent mutation
no AA change due to wobble, retains function
34
*Mutations* Describe a missense mutation
Mutations that lead to mistakes in the AA sequence
35
*Mutations* Describe a nonsense mutation
Mutation that leads to premature termination, and no protein
36
*Mutations* What is a frameshift mutation?
An insertion or deletion that shifts the reading frame - Reading frame established by AUG start codon
37
*Steps of Translation* What are the 5 steps of translation?
1) AA Activation 2) Initiation 3) Elongation 4) Termination/ribosome recycling 5) Folding/post translational processing
38
*Steps of Translation* What is the main point of AA Activation?
tRNA are covalently linked to amino acids to for aminoacyl-tRNA
39
*Steps of Translation* What does Aminoacyl-tRNA synthetase do?
Catalyze the formation of specific amino acids to specific tRNA
40
*Steps of Translation* Describe Fidelity in the context of Translation
Nucleotides that are unique to a tRNA make specific contacts with a synthetase
41
*Steps of Translation* What is the mechanism of AA Activation?
1) Amino acid is activated via adenylation AA + ATP ⇌ Aminoacyl-AMP + PP 2) Aminoacyl-tRNA synthetase attaches AA covalently to tRNA
42
*Steps of Translation* What is essential in Aminoacylation?
Accuracy is essential since amino acid identity is not checked again
43
*Steps of Translation* Describe Class II synthetase that is utilized in AA Activation
3' –OH directly attacks amino acid
44
*Steps of Translation* Describe Class I synthetase that is utilized in AA Activation
2' –OH attacks amino acid, which is then transferred to 3' OH
45
*Steps of Translation* How does the ribosome start scanning in a Prokaryotic vs. Eukaryotic cell?
Prokaryotic - Shine-Dalgarno sequence on mRNA pairs w/ 16S rRNA and positions mRNA on ribosome - Polycistronic: translate multiple genes at once - Co-transcriptional (transcription and translation occur simultaneously) Eukaryotic - Ribosome scans staring from 5' cap to find start (AUG) codon - Monocistronic: translate one gene at a time - NOT co-transcriptional
46
*Steps of Translation* What are the steps of initiation in prokaryotes?
1) Small subunit (30S) and Initiation Factors (IF) assembles at the 5' end of mRNA 2) Shine-Dalgarno sequence pairs with 16S portion of the small subunit 3) fMet-tRNA (initiator) binds to AUG in P site 4) IFs dissociate and large subunit (50s) completes ribosome complex. (full ribosome complex with initiator tRNA in P site)
47
*Steps of Translation* What codes for fMet
Only initiator tRNA code for fMET, internal AUG utilize a different tRNA activated with MET
48
*Steps of Translation* What is different about the mRNA of Eukaryotes vs. Prokaryotes?
Eukaryotic mRNA is capped and tailed
49
*Steps of Translation* How is Initiation in Eukaryotes and Prokaryotes similar?
Small subunit and IFs bind at the 5' end of mRNA
50
*Steps of Translation* How is Initiation in Eukaryotes and Prokaryotes different?
- Initiator of tRNA binds and scans 5' -> 3' to find start codon (AUG) - Starts with Met, no fMet - No Shine-Dalgarno sequence
51
*Steps of Translation* What are the steps in the Elongation phase of translation?
1) tRNA binds in A site with EF-Tu (Elongation Factor)' - GTP hydrolysis causes conformational causing EF-Tu to dissociate 2) Peptide bond formation - Peptide chain now attached to tRNA in A site and grows out of the ribosome exit tunnel 3) Translocation - tRNA without AA dissociates from E site - tRNAs translocated/moved over via EF-G
52
*Steps of Translation* What steps occur in termination?
1) A release factor (RF) is recruited and binds to A site with a stop codon 2) Peptide/AA-tRNA link is hydrolyzed, AA chain leaves 3) Components dissociate via GTP hydrolysis
53
*Steps of Translation* What occurs in Folding and Post Translational processing
1) Unfolded is not yet functional, need to process and fold 2) Lots of processing/post-translational modifications possible 3) Folding happens spontaneously and co-translationally
54
*Toxins* What do toxins and antibiotics do?
They inhibit translational machinery
55
*Toxins* What are 3 toxins that inhibit protein synthhesis?
1) Puromycin 2) Tetracycline 3) Ricin
56
*Toxins* How does Puromycin work?
Binds to A site, forms peptide bond, causes dissociation instead of translocation
57
*Toxins* How does tetracycline work?
Also binds to A site but blocks tRNA binding
58
*Toxins* How does Ricin work?
- Toxic protein against eukaryotic large subunit - Depurates ribosome, destroys structure
59
*Signal sequences and localization* How is cellular localization for proteins determined?
Proteins contain signal sequences to determine cellular localization
60
*Signal sequences and localization* What are NLSs? What do they do? What type of cell might utilize them?
Some proteins contain nuclear localization signals (NLS), which directs their localization to the nucleus
61
*Signal sequences and localization* What do alpha and beta importins do?
They bind to NLS and direct translocation through nuclear pores
62
*Signal sequences and localization* What happens to Ran-GTP?
It is recycled due to GTP hydrolysis upon export
63
*Protein Degradation* Why are proteins degraded?
They are degraded for lots of reasons - only needed during specific times - damage
64
*Protein Degradation* What do bacteria, mitochondria, and chloroplasts utilize?
The Clp system, which uses ATP
65
*Protein Degradation* What is ubiquitin?
Ubiquitin is a small protein that is covalently linked to proteins to tag them for degradation The proteasome degrades ubiquinated proteins

BIOL 0280 UNIT 4 (6 decks)

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