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BIOL243 > Theme 2C > Flashcards

Theme 2C Flashcards

Protein Structure & Translational and Posttranslational Gene Regulation

1
Q

What are the three steps of translational regulation of gene expression?

A
  1. Initiation
  2. Elongation
  3. Termination
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2
Q

What is Translation?

A

assembly of amino acids into polypeptides

aa contain amino & carboxyl group bonded to central carbon (a) with a hydrogen and R group

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3
Q

Two amino acids are joined together by a covalent ________ bond between the ______ and ________ by a ____________

A

peptide; amino; carboxyl; dehydration reaction

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4
Q

Polypwptides are

A

linear chains of amino acids linked by peptide bonds

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5
Q

Type of Amino Acid

Non-polar Amino Acid

A

R groups usually contain -CH2 or -CH3

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6
Q

Type of Amino Acid

Uncharged polar amino acid

A

R groups usually contain oxygen (-OH)

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7
Q

Type of Amino Acid

Charged amino acid

A

R groups that contain acids or bases that can ionize

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8
Q

Type of Amino Acid

Aromatic amino acid

A

R groups contain a carbon ring with alternating single and double bonds

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9
Q

Special Functional amino acid

Methionine

A

first amino acid in polypeptide

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10
Q

Special Functional amino acid

Proline

A

causes kink in polypeptide chains

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11
Q

Special Functional amino acid

Cysteine (S-S)

What does the S-S contribute to?

A

disulfide bridge contributes to structure of polypeptides

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12
Q

Levels of protein structure

Primary amino acid sequence

what does it determine?

A

protein folding and 3-D structure which is critical for proper function

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13
Q

Levels of protein structure

2º Structure

what does it depend on?

A

hydrogen bonding in polypeptide backbone (a-helices & b-sheets)

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14
Q

Levels of protein structure

3 structure

A

3-D structure of a single polypeptide and is composed of interactions between amino acid side chains

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15
Q

Levels of protein structure

4 structure

A

are interactions between more than one polypeptide to form a multisubunit protein

(ie. hemoglobin)

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16
Q

Levels of protein structure

Protein folding is disrupted by ______ or ________

A

denaturation or mutations that change amino acid sequence

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17
Q

Levels of protein structure

Chaperones function to

A

protect slow-folding or denatured proteins by preventing their aggregation

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18
Q

tRNAs

A

adaptors between codons (mRNA) and amino acids

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19
Q

slide 6 - tRNA

2-D cloverleaf and 3-D L-shaped folded RNA molecule from

A

self complementarity

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20
Q

tRNA

Acceptor stem is

A

where the amino acid is attached and contains the sequence 5’-CCA-3’ at the 3’ end of the tRNA

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21
Q

tRNA

The anti-codon is the ________ loop of the cloverleaf and contains three nucleotide sequence that recognize the ___________ by _______________ with mRNA

A

bottom; codon; base pairing

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22
Q

What type of base pairing?

____________ base pairing between codon and anticodon in tRNA

A

antiparallel

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23
Q

Aminoacyl-tRNA charging

Aminoacyl-tRNA synthease adds

(charging) adding the amino acid to the tRNA

A

the amino acid to the acceptor stem of the correct tRNA

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24
Q

Aminoacyl-tRNA (Charging)

Charging Reaction (Aminoacylation)

What is the equation?

A

amino acid + tRNA + ATP –> aminoacyl-tRNA + AMP + PPi

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25
Q

The genetic code consists of

2 things

A

61 “sense” codons and amino acids specified by them

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26
Q

Genetic code

The codons are written

in what direction?

A

5’-3’, as they appear on mRNA

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27
Q

Genetic Code

AUG (Methionine)

What is it?

A

initiation (start) codon

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28
Q

Genetic code

UAA, UAG, UGA

are what type of codons?

A

termination (stop) codons

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29
Q

Genetic Code

The genetic code shows _________ in which an amino acid can be specified by _____________

A

degeneracy; more than one codon

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30
Q

Rules of the Genetic Code

In what direction are codons on mRNA read?

A

5’-3’ direction

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31
Q

Rules of Genetic Code

Codons are ______________________ and the message contains no __________

A

non-overlapping; gaps

32
Q

Rules of Genetic Code

The message is translated in a ________________ by the start codon

A

fixed reading frame

33
Q

Frames

Is it neccessary that translation always start at the start codon?

A

no

34
Q

What are the three reading frames

A

1+, 2+, 3+

35
Q

Why are there only three and not four frames?

A

Because 4+ would be the same as 1+

36
Q

What is the most likely frame that encodes for polypeptide

A

2+

37
Q

Are there 61 different tRNAs that bind to the 61 mRNA codons?

A

no

38
Q

There are less than 61 tRNAs because

A

tRNAs can read more than one codon

39
Q

Why can tRNAs read more than one codon?

A

Because base at 5’ end of anticodon can form H-bonds with more than one type of base located at the 3’ end of a codon “wobble”

40
Q

Is there wobble during pairing of the other two nucleotides in the anti codon with the codon

not the nucleotide at 5’ end

A

No

41
Q

Ribosome

(prokaryotes)

A

protein synthesis machinery

42
Q

Ribosome is composed of ___________________ made of a complex of ______________ and ________________

A

two subunits; proteins; rRNA

43
Q

Ribosomes (prokaryotes)

The large subunit (50S) is made of ________________ and contains _________________________ for _________________.

A

5S and 23S rRNA + 34 proteins; peptidyltransferase center; formation of peptide bonds

44
Q

Ribosomes (prokaryotes)

Small subunit (30S) is made of ________________ and contains ____________ where ____________________ & ________________.

A

16S rRNA + 21 proteins; decoding center; charged tRNAs read and decode the codon of mRNA

based on anti-codon codon binding through parallel complimentary base-pairing

45
Q

Ribosomes (prokaryotes)

S (svedberg unit)

A

measure of seidmentation velocity, and, therefore, mass

46
Q

Ribosomes (prokaryotes)

each subunit exists separately in the ___________ but the two join together on the __________ molecule

A

cytoplasm; mRNA

47
Q

tRNA binding sites of ribosomes

What are the three tRNA binding sites of ribosomes?

A
  1. Aminoacyl (A)
  2. Peptidyl (P)
  3. Exit (E)
48
Q

tRNA binding sites of ribosomes

P site (peptidyl)

A

binds to the tRNA attached to the growing peptide chain

49
Q

tRNA binding sites of ribosomes

A site (aminoacyl)

A

binds to the tRNA carrying the next amino acid to be added

50
Q

tRNA binding sites of ribosomes

E site (exit)

A

binds to the tRNA that carried the previous amino acid added

51
Q

Translation Initiation (eukaryotes)

An ______________________ containing the ribosome, mRNA, and the initiator tRNA bound to methionine is formed during translation initiation

A

initiation complex

52
Q

What are the steps for translation initiation in eukaryotes

A
  • initiator tRNA met is brought to the P-site of the small ribosome subunit (reaction requires GTP)
  • complex of initiator tRNAmet and small ribosomal subunit is recruited to the capped 5’-end of mRNA & scans along the mRNA in a 5’-3’ direction until it reaches the first 5’-AUG-3’ start codon
  • complimentary base pairing occurs between anticodon of initiator tRNAmet and start codon of mRNA
  • Large ribosomalsubunit binds to small subunit to form the initiation complex, which is now ready to accept the first tRNA in the A-site
  • GTP is hydrolyzed to GDP and translation begins
53
Q

Translation elongation: growth of the polypeptide

What are the steps?

4 steps

A
  1. correct aminoacyl tRNA is loaded to A site by Elongation Factor-GTP (tRNA anticodon is compliemntary to mRNA codon in the A-site)
  2. Peptidyl transferase in the large subunit forms a peptide bond between carboxyl group of growing polypeptide and the amino group of the amino acid in the A site (tRNA in P site is uncharged)
  3. Ribosome translocate in which the tRNA with the polypeptide shifts from A to P site, and uncharged tRNA shifts from P to E site where it is ejected
  4. The next codon of the mRNA is now A site and next aminoacyl tRNA can be loaded by EF-GTP
54
Q

The three stop codons are found at _________________

A

end of a protein coding sequence

UAA, UAG, UGA

55
Q

Stop codons are recognized by

A

proteins called release factor

56
Q

when ribosome reaches the stop codon, the release factor binds the A-site and stimulates __________________________________________ to _______________________________

A

peptidyl transferase; cleave polypeptide from P-site tRNA

57
Q

Part 2

Posttranslational Regulation of Gene Expression

3 STEPS

A
  1. Phosphorylation
  2. Ubiquitination
  3. Proteolysis
58
Q

Posttranslational regulation of proteins

Phosphorylation

A

addition of phosphate to proteins by kinases, which can activate or inhibit their activity

Example: CDK1 phosphorylates and activates MAP to promote spindle assembly and mitotic entry

59
Q

Posttranslational regulation of proteins

Ubiquitination

A

addition of ubiquitin molecules to proteins target them for destruction by the proteasome

Example: cylclin is destroyed at the end of mitosis to inactivate CDK1

60
Q

Posttranslational regulation of proteins

Proteolysis

A

specific cleavage of the protein can induce activity

done by enzyme protease

Example: proteolysis of viral envelope glycoprotein triggers maturation of HIV

61
Q

Epigenetics

A

posttranslational modification of histones that affect transcription

62
Q

Epigenetics

Changes in gene transcription occurs ______________________

A

without changes in DNA sequence

63
Q

Epigenetics

Modifications to ______________ on ______________________ affect transcription of genes (histone code). This is a translational/posttranslational event.

A

lysines; histone tails (have + charge); posttranslational

64
Q

Epigenetics

Histone acetyltransferase (HATs) that add _________________ to histone tails increase gene transcription by losening DNA binding! Why?

A

acetyl groups (CH3CO-); because histones negative and DNA is negative, so repulsive forces causes DNA to loosen

65
Q

Epigenetics

___________________ of histone tails can activate and repress transcription of genes

A

methylation

66
Q

Epigenetics

DNA can be _________________________ at ________________ close to promoter repressing transcription

A

methylated; CpG islands

67
Q

Epigenetics

______________________________ displaces nucleosomes from promoter regions (ATP-dependent) activating transcription

A

Chromatin remodelling complex

68
Q

Level of gene regulation

Translational regulation

A

control of protein synthesis (rate of trnaslation initiation or formation of the initiation complex)

69
Q

Level of gene regulation

Posttranslational regulation

A

control of protein abundance & activity

ie. availability of functional proteins

70
Q
A
70
Q

Level of gene regulation

Abundance of protein depends on its rate of _________________________ (translation initiation) and ____________________ (posttranslational)

A

synthesis; degradation

71
Q

Level of gene regulation

Activity of protein depends on ___________________________ and _____________________________ (cleavage)

A

posttranslational modifications; processing

72
Q

Level of gene regulation

The expression level of a specific gene depends on the ______________________ & ___________________

A

abundance of proteins; its activity

73
Q

rEVIEW

slide 20

A
74
Q

4 Levels

Levels of Eukaryotic Gene Regulation

A
  1. Epigenetics (Chromatin remodelling)
  2. Transcriptional (mRNA synthesis)
  3. Post-transcriptional (mRNA processing)
  4. Translation (protein synthesis)
  5. Post-translation (protein processing)
75
Q

Levels of Eukaryotic Gene Regulation

Changes at any level of gene regulation would potentially _______________

A

alter protein expression and cause variation in phenotype

BIOL243 (7 decks)

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