Theme 2C Flashcards

Protein Structure & Translational and Posttranslational Gene Regulation (76 cards)

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
The genetic code consists of | 2 things
61 "sense" codons and amino acids specified by them
26
# Genetic code The codons are written | in what direction?
5'-3', as they appear on mRNA
27
# Genetic Code AUG (Methionine) | What is it?
initiation (start) codon
28
# Genetic code UAA, UAG, UGA | are what type of codons?
termination (stop) codons
29
# Genetic Code The genetic code shows _________ in which an amino acid can be specified by _____________
degeneracy; more than one codon
30
# Rules of the Genetic Code In what direction are codons on mRNA read?
5'-3' direction
31
# Rules of Genetic Code Codons are ______________________ and the message contains no __________
non-overlapping; gaps
32
# Rules of Genetic Code The message is translated in a ________________ by the start codon
fixed reading frame
33
# Frames Is it neccessary that translation always start at the start codon?
no
34
What are the three reading frames
1+, 2+, 3+
35
Why are there only three and not four frames?
Because 4+ would be the same as 1+
36
What is the most likely frame that encodes for polypeptide
2+
37
Are there 61 different tRNAs that bind to the 61 mRNA codons?
no
38
There are less than 61 tRNAs because
tRNAs can read more than one codon
39
Why can tRNAs read more than one codon?
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
Is there wobble during pairing of the other two nucleotides in the anti codon with the codon | not the nucleotide at 5' end
No
41
Ribosome | (prokaryotes)
protein synthesis machinery
42
Ribosome is composed of ___________________ made of a complex of ______________ and ________________
two subunits; proteins; rRNA
43
# Ribosomes (prokaryotes) The large subunit (50S) is made of ________________ and contains _________________________ for _________________.
5S and 23S rRNA + 34 proteins; peptidyltransferase center; formation of peptide bonds
44
# Ribosomes (prokaryotes) Small subunit (30S) is made of ________________ and contains ____________ where ____________________ & ________________.
16S rRNA + 21 proteins; decoding center; charged tRNAs read and decode the codon of mRNA ## Footnote based on anti-codon codon binding through parallel complimentary base-pairing
45
# Ribosomes (prokaryotes) S (svedberg unit)
measure of seidmentation velocity, and, therefore, mass
46
# Ribosomes (prokaryotes) each subunit exists separately in the ___________ but the two join together on the __________ molecule
cytoplasm; mRNA
47
# tRNA binding sites of ribosomes What are the three tRNA binding sites of ribosomes?
1. Aminoacyl (A) 2. Peptidyl (P) 3. Exit (E)
48
# tRNA binding sites of ribosomes P site (peptidyl)
binds to the tRNA attached to the growing peptide chain
49
# tRNA binding sites of ribosomes A site (aminoacyl)
binds to the tRNA carrying the next amino acid to be added
50
# tRNA binding sites of ribosomes E site (exit)
binds to the tRNA that carried the previous amino acid added
51
# Translation Initiation (eukaryotes) An ______________________ containing the ribosome, mRNA, and the initiator tRNA bound to methionine is formed during translation initiation
initiation complex
52
What are the steps for translation initiation in eukaryotes
- 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
# Translation elongation: growth of the polypeptide What are the steps? | 4 steps
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
The three stop codons are found at _________________
end of a protein coding sequence ## Footnote UAA, UAG, UGA
55
Stop codons are recognized by
proteins called release factor
56
when ribosome reaches the stop codon, the release factor binds the A-site and stimulates __________________________________________ to _______________________________
peptidyl transferase; cleave polypeptide from P-site tRNA
57
# Part 2 Posttranslational Regulation of Gene Expression | 3 STEPS
1. Phosphorylation 2. Ubiquitination 3. Proteolysis
58
# Posttranslational regulation of proteins Phosphorylation
addition of phosphate to proteins by kinases, which can activate or inhibit their activity ## Footnote Example: CDK1 phosphorylates and activates MAP to promote spindle assembly and mitotic entry
59
# Posttranslational regulation of proteins Ubiquitination
addition of ubiquitin molecules to proteins target them for destruction by the proteasome ## Footnote Example: cylclin is destroyed at the end of mitosis to inactivate CDK1
60
# Posttranslational regulation of proteins Proteolysis
specific cleavage of the protein can induce activity | done by enzyme protease ## Footnote Example: proteolysis of viral envelope glycoprotein triggers maturation of HIV
61
Epigenetics
posttranslational modification of histones that affect transcription
62
# Epigenetics Changes in gene transcription occurs ______________________
without changes in DNA sequence
63
# Epigenetics Modifications to ______________ on ______________________ affect transcription of genes (histone code). This is a translational/posttranslational event.
lysines; histone tails (have + charge); posttranslational
64
# Epigenetics Histone acetyltransferase (HATs) that add _________________ to histone tails increase gene transcription by losening DNA binding! Why?
acetyl groups (CH3CO-); because histones negative and DNA is negative, so repulsive forces causes DNA to loosen
65
# Epigenetics ___________________ of histone tails can activate and repress transcription of genes
methylation
66
# Epigenetics DNA can be _________________________ at ________________ close to promoter repressing transcription
methylated; CpG islands
67
# Epigenetics ______________________________ displaces nucleosomes from promoter regions (ATP-dependent) activating transcription
Chromatin remodelling complex
68
# Level of gene regulation Translational regulation
control of protein synthesis (rate of trnaslation initiation or formation of the initiation complex)
69
# Level of gene regulation Posttranslational regulation
control of protein abundance & activity ## Footnote ie. availability of functional proteins
70
70
# Level of gene regulation Abundance of protein depends on its rate of _________________________ (translation initiation) and ____________________ (posttranslational)
synthesis; degradation
71
# Level of gene regulation Activity of protein depends on ___________________________ and _____________________________ (cleavage)
posttranslational modifications; processing
72
# Level of gene regulation The expression level of a specific gene depends on the ______________________ & ___________________
abundance of proteins; its activity
73
# rEVIEW slide 20
74
# 4 Levels Levels of Eukaryotic Gene Regulation
1. Epigenetics (Chromatin remodelling) 2. Transcriptional (mRNA synthesis) 3. Post-transcriptional (mRNA processing) 4. Translation (protein synthesis) 5. Post-translation (protein processing)
75
# Levels of Eukaryotic Gene Regulation Changes at any level of gene regulation would potentially _______________
alter protein expression and cause variation in phenotype