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

Lecture 21: Protein Metabolism Flashcards

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
Q

tRNA

What does the wobble hypothesis say about how many unique tRNA are needed for all 61 coding codons

A

Only 32 unique tRNA are needed
- Different tRNA are needed only if any of the two nucleotides in a codon are different

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26
Q

tRNA

What are the 4 wobble pairs?

A

I-C
I-U
I-A
G-U

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27
Q

tRNA

How is I formed?

A

I is inosine and is formed from the deamination of adenosine

28
Q

tRNA

What is the relationship between wobble and specificity?

A

More wobble = less specific
Less wobble = more specific

29
Q

Decoding mRNA

What does the first codon in a sequence do?

A

Establishes the reading frame

30
Q

Decoding mRNA

What is the importance of the AUG/start codon

A

Establishes the reading frame
- Translation continues until it encounters a stop codon

31
Q

Mutations
What is a wild type?

A

The original/normal functional protein

32
Q

Mutations
What is a substitution mutation?
What are the 3 types of substitutions?

A

A mutation that potentially leads to AA changes
- Silent
- Missense
- Nonsense

33
Q

Mutations

Describe a silent mutation

A

no AA change due to wobble, retains function

34
Q

Mutations

Describe a missense mutation

A

Mutations that lead to mistakes in the AA sequence

35
Q

Mutations

Describe a nonsense mutation

A

Mutation that leads to premature termination, and no protein

36
Q

Mutations

What is a frameshift mutation?

A

An insertion or deletion that shifts the reading frame
- Reading frame established by AUG start codon

37
Q

Steps of Translation

What are the 5 steps of translation?

A

1) AA Activation
2) Initiation
3) Elongation
4) Termination/ribosome recycling
5) Folding/post translational processing

38
Q

Steps of Translation

What is the main point of AA Activation?

A

tRNA are covalently linked to amino acids to for aminoacyl-tRNA

39
Q

Steps of Translation

What does Aminoacyl-tRNA synthetase do?

A

Catalyze the formation of specific amino acids to specific tRNA

40
Q

Steps of Translation

Describe Fidelity in the context of Translation

A

Nucleotides that are unique to a tRNA make specific contacts with a synthetase

41
Q

Steps of Translation

What is the mechanism of AA Activation?

A

1) Amino acid is activated via adenylation
AA + ATP ⇌ Aminoacyl-AMP + PP

2) Aminoacyl-tRNA synthetase attaches AA covalently to tRNA

42
Q

Steps of Translation

What is essential in Aminoacylation?

A

Accuracy is essential since amino acid identity is not checked again

43
Q

Steps of Translation

Describe Class II synthetase that is utilized in AA Activation

A

3’ –OH directly attacks amino acid

44
Q

Steps of Translation

Describe Class I synthetase that is utilized in AA Activation

A

2’ –OH attacks amino acid, which is then transferred to 3’ OH

45
Q

Steps of Translation

How does the ribosome start scanning in a Prokaryotic vs. Eukaryotic cell?

A

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
Q

Steps of Translation

What are the steps of initiation in prokaryotes?

A

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
Q

Steps of Translation

What codes for fMet

A

Only initiator tRNA code for fMET, internal AUG utilize a different tRNA activated with MET

48
Q

Steps of Translation

What is different about the mRNA of Eukaryotes vs. Prokaryotes?

A

Eukaryotic mRNA is capped and tailed

49
Q

Steps of Translation

How is Initiation in Eukaryotes and Prokaryotes similar?

A

Small subunit and IFs bind at the 5’ end of mRNA

50
Q

Steps of Translation

How is Initiation in Eukaryotes and Prokaryotes different?

A
  • Initiator of tRNA binds and scans 5’ -> 3’ to find start codon (AUG)
  • Starts with Met, no fMet
  • No Shine-Dalgarno sequence
51
Q

Steps of Translation

What are the steps in the Elongation phase of translation?

A

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
Q

Steps of Translation

What steps occur in termination?

A

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
Q

Steps of Translation

What occurs in Folding and Post Translational processing

A

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
Q

Toxins

What do toxins and antibiotics do?

A

They inhibit translational machinery

55
Q

Toxins

What are 3 toxins that inhibit protein synthhesis?

A

1) Puromycin
2) Tetracycline
3) Ricin

56
Q

Toxins

How does Puromycin work?

A

Binds to A site, forms peptide bond, causes dissociation instead of translocation

57
Q

Toxins

How does tetracycline work?

A

Also binds to A site but blocks tRNA binding

58
Q

Toxins

How does Ricin work?

A
  • Toxic protein against eukaryotic large subunit
  • Depurates ribosome, destroys structure
59
Q

Signal sequences and localization

How is cellular localization for proteins determined?

A

Proteins contain signal sequences to determine cellular localization

60
Q

Signal sequences and localization

What are NLSs?
What do they do?
What type of cell might utilize them?

A

Some proteins contain nuclear localization signals (NLS), which directs their localization to the nucleus

61
Q

Signal sequences and localization

What do alpha and beta importins do?

A

They bind to NLS and direct translocation through nuclear pores

62
Q

Signal sequences and localization

What happens to Ran-GTP?

A

It is recycled due to GTP hydrolysis upon export

63
Q

Protein Degradation

Why are proteins degraded?

A

They are degraded for lots of reasons
- only needed during specific times
- damage

64
Q

Protein Degradation

What do bacteria, mitochondria, and chloroplasts utilize?

A

The Clp system, which uses ATP

65
Q

Protein Degradation

What is ubiquitin?

A

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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