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Mcb1 > Protein Metabolism P2 > Flashcards

Protein Metabolism P2 Flashcards

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1
Q

What are the mRNA stop codons?

A 
UGA = U Go Away
UAA = U Are Away
UAG = U Are Gone
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2
Q

What contributes to making of each of the sites, A P and E on the ribosomal unit?

A

both large and small ribosomal subunits contribute to forming the A and P site

On the large subunit contributes to the E site

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3
Q

What rRNA is responsible for the riboenzymatic reaction (peptidyl transferase) in the 50S subunit?

A

23S rRNA

  • This is the done by the 28S rRNA in the 60S eukaryotic subunit)
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4
Q

What are the five major stages of protein synthesis?

A
  1. Activation of amino acids
  2. Initiation
  3. Elongation
  4. Termination and release
  5. Folding and posttranslational processing
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5
Q

What is the 16S rRNA crucial for?

A

Positioning of the ribosome. It’s the complement of Shine-Dalgarno sequence

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6
Q

What are the essential components of activation of amino acids (1st step in E. coli )?

A 
20 aa
20 aminoacyl-tRNA synthetases
32 or more tRNAs
ATP
*Mg^2+*
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7
Q

What are the essential components in initiation?(e coli)

A 
mRNA
N-Formylmethionyl-tRNA^fmet
Initiation codon in mRNA (AUG)
30s ribosomal subunit
50s ribosomal subunit
Initiation factors (IF-3, IF-1, IF-2)
GTP
*Mg^2+*
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8
Q

What are the essential components of Elongation?(e. Coli)

A

Functional 70S ribosome (initiation complex)
Aminoacyl-tRNAs specified by codons
GTP
Mg^2+

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9
Q

What are the essential components in termination and release? (E.coli)

A 
Termination codon in mRNA
Release factors (RF-1, RF-2, RF-3)
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10
Q

What are these components essential for? Components: specific enzymes, cofactors, and other components for removal of initiating residues and spinal sequences, additional proteolytic processing, modification of terminal residues, and attachment of phosphate, methyl, carboxyl, carbohydrate, or prosthetic group?

A

Folding and posttranslational processing (Step 5, E. coli)

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11
Q

What does streptomycin do?

A

Binds to 30S subunit and causes misreading of the genetic code and inhibits initiation of translation at higher concentrations

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12
Q

What does puromycin do?

A

Structurally similar to the 3’ end of aminoacyl tRNA: binds to the A site and participates in peptide bonding: peptidyl-puromycin (premature ending of synthesis)

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13
Q

What does tetracyclin do?

A

Blocks A-site

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14
Q

What does chloramphenicol do?

A

Binds to the large ribosomal subunit and blocks bacterial peptidyl transferase

Note: high levels may also inhibit mitochondrial protein synthesis
*famous

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15
Q

What does erythromycin do?

A

Binds the large ribosomal subunit but translocation is now blocked

*famous drug

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16
Q

What are the 50S ribosome inhibitors?

A

Erythromycin

Chloramphenicol

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17
Q

What are the 30S ribosome inhibitors?

A

Tetracyclin

Streptomycin

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18
Q

What has helps bacteria become resistant to antibiotics?

A

Plasmid encoding enzymes (alter the host)

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19
Q

How did Staphylococcal become resistant to erythromycin?

A

It’s the result of the conversion of a single adenosine in 23S rRNA to N6-dimethyladenosine, so that erythromycin can no longer bind

The conversion is mediated by a plasmid-borne RNA methylase

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20
Q

What is the ortholog of EF-Tu in eukaryotes?

A

eEF1

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21
Q

What is the eukaryotic ortholog of EF-G?

A

eEF2

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22
Q

What binds on the 5’ cap the mRNA in eukaryotes?

A

elF4E

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23
Q

What binds the ends of the mRNA together?

A

EiF4G binds both elF4E (binds 5’cap) and PABP (bound to 3’ end)`

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24
Q

In eukaryotes, is the initiator tRNA^Met formylated?

A

No, this is only in prokaryotes

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25
What is ricin?
Toxic protein from castors beans: it depurinates a specific adenosine reside in the 28S rRNA, thereby inactivating its peptidyl transferase activity
26
What is Diphtheria toxin?
Inactivates eukaryotic elongation factor 2 (eEF2, similar to bacterial EF-G) by modification of a histidine residue (by ADP-ribosylation). *clinical: an upper respiratory track illness
27
What does Elongation factor Tu (EF-Tu) do?
Directs charged tRNAs to the A site for protein elongation at the expense of the hydrolysis of one high energy phosphate bone
28
What recycle's EF-Tu?
The Ts protein | EF-Tu is charged with GTP
29
What forms the peptide bond?
23S rRNA in bacteria 28S rRNA in eukaryotes
30
What is structurally similar to EF-Tu-tRNA complex and induces translocation?
EFG (elongation factor G). IT does this by temporarily occupying the A-site
31
What is the full cycle for eukaryotic peptide bond formation and translocation? (Full)
1. A new aminoacyl-tRNA is brought into the A site by eEF-1A-GTP (if fit is correct GTP is split) 2. eEF-1A--GDP dissociates from the complex (analog to EF-Tu) 3. The 28S rRNA peptidyl transferase catalyzes the formation of new peptide bond (analog to 23S in pro) 4. eEF-2--GTP causes the translocation of the tRNA forward one site; powered by splitting the GTP (EF-G factor analog) 5. eEF-2 is released once translocation has occurred and GTP is split 6. General cycle repeats
32
What are the analog proteins in eukaryotes to prokaryotes in translation?
Eukaryote: Prokaryote 2. eEF-1A : EF-Tu 3. 28S rRNA : 23S rRNA 4. eEF-2--GTP : EF-G factor
33
Cycles of phosphorylation of amino acids with OH-group containing side chains followed by dephosphorylation is important for?
Modulation of protein activity
34
What are heat shock proteins? (Hsp aka Chaperones)
Act cotranslationally to help proteins fold correctly
35
When are Hsp created?
Synthesized upon cellular heat exposure
36
What do Hsp bind to in order to help proteins fold correctly?
Have affinity for exposed hydrophobic patches of incompletely folded proteins and use ATP to bind and release these patches Note: hydrophobic regions should be inside the protein in most cases
37
_____ and ____ systems use a lot of ATP to ensure correct protein folding.
Hsp 60 and Hsp 70 Note: this occurs within the "isolation chamber" of the Hsp60 Hsp 70 occurs cotranslationally
38
Where are Hsp's present?
Cytoplasm and inside organelles Note: Hsp are created when there is high heat and high heat denatures proteins.
39
What is the function of the modifying group of: Phosphate on Ser, Thr, or Tyr
Drives the assembly of a protein into larger complexes
40
What is the function of the modifying group: Methyl on Lys
Helps to create histone code in chromatin through forming either mono-, di-, or tri-methyl lysine to regulate interaction with other proteins I.e transcription factors
41
What is the function of the modifying group: acetyl on Lys
Helps to create histone code in chromatin to regulare interaction with DNA Note: this is similar to the methylation of Lys
42
What is the function of the modifying group: Palmityl group on Cys
This fatty acid addition drives protein association with membranes
43
The Formyl group (bacteria), the amino terminal methionine, and often additional amino terminal amino aids are removed in the formation of?
The final functional protein
44
In 50% of eukaryotic proteins, the main group of the N-terminal residue is?
N-acetylated
45
What end group is N- acetylated in 50% of eukaryotic proteins?
The amino group of the N-terminal Note: carboxy terminus may also be trimmed and modified
46
What are the proglucagon derivatives in the intestine/brain?
Glicentin Oxyntomodulin GLP-1 (diabetes and weight loss) GLP-2 IP2
47
What are the proglucagon derived peptides in the pancreas?
Glucagon | MPGF
48
What is a strong signaling molecule because it has a phenylalanine group?
Phosphotyrosine
49
How does chaperonin-mediated glycoprotein folding with a glycosidase sensor work?
1. Glucosidase I will take off 1 of the 3 glucose from the protein if folded correctly 2. Chaperone proteins will make sure the protein is folded correctly (quality control) 3. After quality control, glucosidase II will remove 2 glucose 4. Two things can happen. A. Goes to golgi. B. Glucosyl-transferase +UDP-glucose adds 3 glucose and it begins the cycle again if not correctly folded
50
What are the phosphorylated amino acids?
Phosphoserine Phosphotyrosine Phosphothreonine
51
How may a child receive protein, calcium and phosphate in the milk protein casein?
By the phosphorylation of serine which then the phosphoserine binds to the calcium ion
52
What does vitamin c deficiency cause?
Scurvy
53
Hydroxylation of proline is dependent on?
Vitamin C
54
Where is hydroxylated proline found?
In collagen Fibrillar collagen consist of repeating units of Gly-x-y ``` X= proline Y= Hydroproline ```
55
What does (Gly-X-Y)n form?
Strongly twisted alpha-chain that then associate in triple-stranded collagen fibril
56
What does the hydroxyl group in hydroxyporline do?
Involved in interchain H-bonding
57
What are the two types of oligosaccharide linkages found in glycoproteins?
N-linked sugar/oligosaccharide O-linked sugar/oligosaccharide
58
What is an n-linked sugar?
Carbohydrate side chain is attached to the amide nitrogen of an Asn residue
59
What is an O-linked sugar?
Carbohydrate side chain is attached to the hydroxyl group on Ser or Thr residues
60
To what aa reside are n and o linked sugars attached to?
N: Asn O: Ser or Thr
61
What kind of proteins carry oligosaccharide side chains?
Proteins that function extracellularly such as plasma proteins and lubricating proteoglycans
62
_________ regulates the interactions of histone with DNA. (Of lysine)
Acetylation
63
__________ regulates the interaction of histones with other proteins, in particular transcription factors. (Lysine)
Methylation
64
What does acetylation remove? ( of lysine)
The positive charge
65
Membrane protein attachment occurs by?
A. A fatty acid covalently linked to a N-terminal glycine B. Fatty acid chain covalently linked to a cysteine C. A phenyl group linked to a carboxy terminal cysteine
66
What activates chymotrypsinogen?
Trypsin
67
What activates trypsinogen?
Enteropeptidase
68
What makes pI-chymotrypsin autolytic? What's it called?
Removal of ser14-Arg15 and Thr147-Asn148 Alpha-chymotrypsin
69
The binding and tagging of a target protein is done by?
Ubiquitin ligase
70
How are target proteins for polyubiquitylation marked?
They are usually phosphorylated
71
How are proteins directed to the proteasome for degradation?
A polyubiquitin chain on a lysine residue
72
What is a proteasome?
A cylindrical ATP-dependent protease for degradation
73
What are some examples of diese caused by protease-resistant protein aggregation followed by cell/tissue decay?
Sickle cell anemia Alpha-1-antitrypsin deficiency For brain: Huntington's and Alzheimer's disease Note: often dominate diseases
74
What part of the body is sensitive to protein aggregates?
Brain
75
Protease-resistance protein aggregation diseases usually follow what kind of inheritance pattern?
Dominant
76
Changes in what structures of proteins cause resistance to proteolysis
Secondary
77
How are prion diseases caused?
By misfolding and aggregation of prion proteins
78
What is the mechanism by which prion diseases occur?
2 alpha hélices in the prion protein convert into four beta strands and the resulting beta sheets stack just as the cross beta filaments Note: the cross beta filaments cannot be digested by the proteasome
79
What are some examples of prions?
human: creautzfeldt-Jacob disease (CJD) Cattle: Bovine spongiform encephalopathy Sheep: Scrappie Note: prions have an "infectious" nature. Don't eat anything affected with prions
80
Protein domains cn fold themselves or with the help of specific ATP-dependent ______.
Chaperones
81
What heat shock proteins works cotranslationally and which uses a folding chamber?
70: cotranslationally 60: protein chamber
82
What terminus of a protein is frequently acetylted?
The N-terminus
83
What are some famous examples of proteins that are proteolytically processed into multiple products?
Proglucagon Procalcitonin Proinsulin
84
Phosphorylation of casein allows it to carry what ion?
Calcium
85
Protein ______ is a key regulation mechanism for protein functioning, in particular signaling.
Phosphorylation
86
What must be done to a glutamate residue in blood clotting factor proteins in order for them to properly clot blood?
Carboxylate the glutamate residue to properly from blood clots
87
_______ _______ is an important constituent of fibrillar collagen molecules
Hydroxylated proline (hydroproline)
88
Addition of fatty acids to amino terminal amino acids or cysteine groups do what?
Anchor proteins to membranes
89
What is the process called that activates some proteins because their precursors are broken down?
Proteolysis
90
Proteins find their end in the _____ after ________ of a lysine residue
Proteasome Ubiquitination
91
What is the accumulation of the protease-resistant protein aggregates called?
Amyloid I.e. Alzheimers Beta amyloid plaque
92
___ of total RNA is tRNA.
15%
93
What are the non-traditional base pairing in the wobble position? (Excluded traditional pairing)
G:U U:G I:A,U,C
94
What kind of mutations do not affect the amino coding sequence?
Silent mutations
95
What are the subunits of the 50s ribosomes?
``` 5s 23s rRNA( responsible for peptidyl transferase activity ) ```
96
In what ribosome subunit is the 16s rRNA found?
In the 30S ribosome subunit

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