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Protein Metabolism P2 Flashcards

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
Q

What is ricin?

A

Toxic protein from castors beans: it depurinates a specific adenosine reside in the 28S rRNA, thereby inactivating its peptidyl transferase activity

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26
Q

What is Diphtheria toxin?

A

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

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27
Q

What does Elongation factor Tu (EF-Tu) do?

A

Directs charged tRNAs to the A site for protein elongation at the expense of the hydrolysis of one high energy phosphate bone

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28
Q

What recycle’s EF-Tu?

A

The Ts protein

EF-Tu is charged with GTP

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29
Q

What forms the peptide bond?

A

23S rRNA in bacteria

28S rRNA in eukaryotes

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30
Q

What is structurally similar to EF-Tu-tRNA complex and induces translocation?

A

EFG (elongation factor G). IT does this by temporarily occupying the A-site

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31
Q

What is the full cycle for eukaryotic peptide bond formation and translocation? (Full)

A
  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
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32
Q

What are the analog proteins in eukaryotes to prokaryotes in translation?

A

Eukaryote: Prokaryote
2. eEF-1A : EF-Tu

  1. 28S rRNA : 23S rRNA
  2. eEF-2–GTP : EF-G factor
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33
Q

Cycles of phosphorylation of amino acids with OH-group containing side chains followed by dephosphorylation is important for?

A

Modulation of protein activity

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34
Q

What are heat shock proteins? (Hsp aka Chaperones)

A

Act cotranslationally to help proteins fold correctly

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35
Q

When are Hsp created?

A

Synthesized upon cellular heat exposure

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36
Q

What do Hsp bind to in order to help proteins fold correctly?

A

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

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37
Q

_____ and ____ systems use a lot of ATP to ensure correct protein folding.

A

Hsp 60 and Hsp 70

Note: this occurs within the “isolation chamber” of the Hsp60
Hsp 70 occurs cotranslationally

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38
Q

Where are Hsp’s present?

A

Cytoplasm and inside organelles

Note: Hsp are created when there is high heat and high heat denatures proteins.

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39
Q

What is the function of the modifying group of: Phosphate on Ser, Thr, or Tyr

A

Drives the assembly of a protein into larger complexes

40
Q

What is the function of the modifying group: Methyl on Lys

A

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
Q

What is the function of the modifying group: acetyl on Lys

A

Helps to create histone code in chromatin to regulare interaction with DNA

Note: this is similar to the methylation of Lys

42
Q

What is the function of the modifying group: Palmityl group on Cys

A

This fatty acid addition drives protein association with membranes

43
Q

The Formyl group (bacteria), the amino terminal methionine, and often additional amino terminal amino aids are removed in the formation of?

A

The final functional protein

44
Q

In 50% of eukaryotic proteins, the main group of the N-terminal residue is?

A

N-acetylated

45
Q

What end group is N- acetylated in 50% of eukaryotic proteins?

A

The amino group of the N-terminal

Note: carboxy terminus may also be trimmed and modified

46
Q

What are the proglucagon derivatives in the intestine/brain?

A

Glicentin
Oxyntomodulin
GLP-1 (diabetes and weight loss)

GLP-2
IP2

47
Q

What are the proglucagon derived peptides in the pancreas?

A

Glucagon

MPGF

48
Q

What is a strong signaling molecule because it has a phenylalanine group?

A

Phosphotyrosine

49
Q

How does chaperonin-mediated glycoprotein folding with a glycosidase sensor work?

A
  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
Q

What are the phosphorylated amino acids?

A

Phosphoserine
Phosphotyrosine
Phosphothreonine

51
Q

How may a child receive protein, calcium and phosphate in the milk protein casein?

A

By the phosphorylation of serine which then the phosphoserine binds to the calcium ion

52
Q

What does vitamin c deficiency cause?

53
Q

Hydroxylation of proline is dependent on?

54
Q

Where is hydroxylated proline found?

A

In collagen

Fibrillar collagen consist of repeating units of Gly-x-y

X= proline
Y= Hydroproline
55
Q

What does (Gly-X-Y)n form?

A

Strongly twisted alpha-chain that then associate in triple-stranded collagen fibril

56
Q

What does the hydroxyl group in hydroxyporline do?

A

Involved in interchain H-bonding

57
Q

What are the two types of oligosaccharide linkages found in glycoproteins?

A

N-linked sugar/oligosaccharide

O-linked sugar/oligosaccharide

58
Q

What is an n-linked sugar?

A

Carbohydrate side chain is attached to the amide nitrogen of an Asn residue

59
Q

What is an O-linked sugar?

A

Carbohydrate side chain is attached to the hydroxyl group on Ser or Thr residues

60
Q

To what aa reside are n and o linked sugars attached to?

A

N: Asn

O: Ser or Thr

61
Q

What kind of proteins carry oligosaccharide side chains?

A

Proteins that function extracellularly such as plasma proteins and lubricating proteoglycans

62
Q

_________ regulates the interactions of histone with DNA. (Of lysine)

A

Acetylation

63
Q

__________ regulates the interaction of histones with other proteins, in particular transcription factors.
(Lysine)

A

Methylation

64
Q

What does acetylation remove? ( of lysine)

A

The positive charge

65
Q

Membrane protein attachment occurs by?

A

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
Q

What activates chymotrypsinogen?

67
Q

What activates trypsinogen?

A

Enteropeptidase

68
Q

What makes pI-chymotrypsin autolytic?

What’s it called?

A

Removal of ser14-Arg15 and Thr147-Asn148

Alpha-chymotrypsin

69
Q

The binding and tagging of a target protein is done by?

A

Ubiquitin ligase

70
Q

How are target proteins for polyubiquitylation marked?

A

They are usually phosphorylated

71
Q

How are proteins directed to the proteasome for degradation?

A

A polyubiquitin chain on a lysine residue

72
Q

What is a proteasome?

A

A cylindrical ATP-dependent protease for degradation

73
Q

What are some examples of diese caused by protease-resistant protein aggregation followed by cell/tissue decay?

A

Sickle cell anemia

Alpha-1-antitrypsin deficiency

For brain: Huntington’s and Alzheimer’s disease

Note: often dominate diseases

74
Q

What part of the body is sensitive to protein aggregates?

75
Q

Protease-resistance protein aggregation diseases usually follow what kind of inheritance pattern?

76
Q

Changes in what structures of proteins cause resistance to proteolysis

77
Q

How are prion diseases caused?

A

By misfolding and aggregation of prion proteins

78
Q

What is the mechanism by which prion diseases occur?

A

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
Q

What are some examples of prions?

A

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
Q

Protein domains cn fold themselves or with the help of specific ATP-dependent ______.

A

Chaperones

81
Q

What heat shock proteins works cotranslationally and which uses a folding chamber?

A

70: cotranslationally
60: protein chamber

82
Q

What terminus of a protein is frequently acetylted?

A

The N-terminus

83
Q

What are some famous examples of proteins that are proteolytically processed into multiple products?

A

Proglucagon

Procalcitonin

Proinsulin

84
Q

Phosphorylation of casein allows it to carry what ion?

85
Q

Protein ______ is a key regulation mechanism for protein functioning, in particular signaling.

A

Phosphorylation

86
Q

What must be done to a glutamate residue in blood clotting factor proteins in order for them to properly clot blood?

A

Carboxylate the glutamate residue to properly from blood clots

87
Q

_______ _______ is an important constituent of fibrillar collagen molecules

A

Hydroxylated proline (hydroproline)

88
Q

Addition of fatty acids to amino terminal amino acids or cysteine groups do what?

A

Anchor proteins to membranes

89
Q

What is the process called that activates some proteins because their precursors are broken down?

A

Proteolysis

90
Q

Proteins find their end in the _____ after ________ of a lysine residue

A

Proteasome

Ubiquitination

91
Q

What is the accumulation of the protease-resistant protein aggregates called?

A

Amyloid

I.e. Alzheimers Beta amyloid plaque

92
Q

___ of total RNA is tRNA.

93
Q

What are the non-traditional base pairing in the wobble position? (Excluded traditional pairing)

A

G:U
U:G
I:A,U,C

94
Q

What kind of mutations do not affect the amino coding sequence?

A

Silent mutations

95
Q

What are the subunits of the 50s ribosomes?

A 
5s 
23s rRNA( responsible for peptidyl transferase activity )
96
Q

In what ribosome subunit is the 16s rRNA found?

A

In the 30S ribosome subunit

Mcb1 (13 decks)

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