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Flashcards in The life and death of proteins Deck (83):
1

What is the enzyme attaches an amino acid to a tRNA?

Amino-acyl-tRNA synthetases

2

True or false: the reaction of amino-acyl-tRNA synthetase is an ATP dependent one

True

3

Where does protein synthesis occur?

In the cytosol

4

True or false: mitochondria have their own ribosomes?

True

5

What are ribosomes composed of?

1-3 rRNA molecules, as well as dozens of proteins.

6

Why is the fact that bacterial ribosomes differ greatly from human ribosomes important?

Targeting by Abx

7

What is the structure responsible for rRNA synthesis?

Nucleolus

8

Where are ribosomal subunits made? How do they get rRNAs that are in the nucleus?

Cytosol
Transported in, then back out of the nucleus when they get their rRNA

9

Initiation requires what three components?

Ribosomal subunit
an mRNA
a bound tRNA

10

What is the aminoacid that usually begins every polypeptide?

M

11

What are the five steps of ribosomal initiation?

1. elF2a is activated by binding GTP
2. elf2a-GTP binds a Meth-tRNA to form a ternerary complex
3. The ternerary complex binds a small ribosomal subunit
4. mRNA binds the ternerary complex
5. A large ribosomal subunit binds, and elF2a is hydrolyzed.

12

What is EF-1 used for?

(elongation factor 1) helps the additional tRNA molecules bind to the M-tRNA initially-no longer needed after second tRNA has been added

13

What is EF-2 used for?

Used to move the ribosome one codon further on the DNA chain

14

What is selenocysteine? What is its purpose in translation?

A rare aminoacid that will is coded for by stop codons.

15

How does translation of a protein get terminated (Hint: there are four steps, last one is the separation of the ribosome).

1. stop site on mRNA is reached
2. eRF binds to the A site
3. eRF-bound GTP hydrolyzed and peptide is release
4. Ribosome separates

16

What is the action of streptomycin?

Binds to the small subunit of prokaryotic ribosomes and inhibits initiation.

17

What is the action of Neomycin and gentamicin?

Bind to prokaryotic ribosomes and cause mistranslation

18

What is the action of tetracycline?

Blocks prokaryotic, ribosomes' A site.

19

What is the action of chloramphenicol?

Prevents prokaryotic peptidyl bond formation

20

What is the action of Ricin?

it is a glycosidase that removes adenine bases from rRNA

21

What is the action of diptheria toxin?

inactivates EF-2 to prevent elongation

22

What are the two ways that translation is regulated?

1. Preventing recognition of the start codon by binding earlier in the mRNA
2. Phosphorylating initiation factors (e.g. eIF-2)

23

What are chaparones?

Proteins that aid in the correct folding of other polypeptides

24

What is Charcot Marie tooth disease?

A protein folding disorder caused by mutations in HSPs (heat shock proteins)

25

Proteins destined for secretion out of the cell are produced where?

In the ER

26

What are the steps involved in the synthesis of exported proteins (4)?

1. Signal sequence emerges from the ribosome
2. A signal recognition protein (SRP) binds the singal sequence and the complex moves to the ER
3. SRP dissociates and translation goes through the ER
4. Signal peptidase cleaves the signal peptide

27

When there are too many unfolded proteins in the ER due to excess cholesterol or starvation, the cell has three ways of dealing with this. What are they?

1. Inhibit protein translation
2. Introduce chaperones
3. Apoptosis

28

Why is the glycosylation of proteins important? (2 reasons)

1. Change physical characteristics (Increases solubility, stability, size)
2. Recognition sites

29

Where does glycosylation being and end? What class of enzymes catalze this reaction?

Starts in the ER, ends in the golgi
Glycosyltransferases (SUPER specific)

30

What is the amino acid involved in N-link glyslyation?

N

31

What are the three steps involved in the syntesis of N-linked oligosaccahides?

1. Synthesis of a dolichol phosphate in the ER
2. Transfer of a universal oligosaccharide to the nascent polypeptide chain
3. Specific modification of the universal oligosaccharide by the Golgi

32

The Golgi produces two types of N-link polysaccharides. What are they?

High mannose type
Complex type (contain mannose and other carbs)

33

O-linked glycosylation occurs only on folded or unfolded proteins?

Only on fully folded

34

What are the steps of O-linked glycosylation (2 steps)?

Golgi transfers an N-linked galactosamine to the protein
This is then added to by other enzymes

35

O-linked glycosylation is the basis for blood typing. The O antigen has no sugars added to the H antigen. What do A and B have?

A = N-acetylgalactose
B= Galactose

36

What is multiple sufatase deficiency cause by?

A failure to convert C to formylglycine

37

Where do GPI anchors attach to?

At the C terminus

38

What is the usual amino acid at the N terminus of a newly synthesized protein? How can this be modified?

M
Trim it off

39

What are the types of FAs that are linked to newly synthesized proteins?

Myristic acid
Palmitic acid
Isoprenoids

40

What happens to fully folded and modified proteins?

Packed into vesicles that move them to their final destination

41

How does targeting of new glycoproteins to lysosomes happen?

High mannose glycoproteins are phosphorylated by N-acetylglucosamine

42

Where are most mitochondrial proteins synthesized?

In the cytosol

43

Mitochondrial proteins are synthesized in the cytosol with a N-terminal presequence. How are they stabilized?

By chaperones

44

The presequences of the mitochondrial proteins react with a receptor on the outer side of the mitochondiral matrix. What is the name of the enzyme that transports the protein in the next step?

TOM to TIM

45

What happens to the mitochondrial preprotein/presequence complex once it is inside the mitochondria?

The presequence is cleaved off

46

Deafness-distonia syndrome is caused by what?

It is a mitochondiral disorder--a mutation in the TIM component that impair mitochondrial protein transport

47

Cystic fibrosis is the result of a deletion in the CFTR1 gene. What does this result in?

This deletion interferes with folding and glycosylation the protein, and the signal it expresses directs it to the cytosol (where it dies) rather than the plasmamembrane

48

What is I-cell disease?

The impairment of the transfer of a phosphate to mannose in the lysosomal signal pathway.
This leads to the accumulation of undegraded proteins in lysosomes

49

What are the two indications for I-cell disease?

1. Dense inclusion bodies present in lysosomes
2. Lysosomal proteins that did not reach their destination in the serum

50

What are the two mechanisms for protein degradation?

1. Lysosomal - nonspecific
2. Proteasome - cytoplasmic proteins

51

What does clathrin function in?

Coats extracellular proteins and directs it to the lysosome for destruction

52

Where are cytoplasmic proteins degraded? What marks them for destruction in this way?

Proteosomes
bound to ubiquitin

53

Ubitquitin (in the proteosome degradation pathway) is activated by what enzymes? Conjugated? Ligated?

E1, E2, E3 enzymes for activation, conjugation, and ligation respectively

54

True or false: a single ligation of ubiquitin will target the cell for proteosome destruction?

False--POLYubiquination is the signal

55

The lifespan of proteins is determined by what three factors?

1. Its conformation (incorrect folding = bye bye)
2. Its N-terminal residue (M or S = gone)
3. Other sequences (P-E-S-T sequence of amino acids)

56

What are the factors involved for initiation, elongation, and termination?

Initiation = eIF2a
Elongation = EF1 and EF2
Termination = eRF

57

What is the action of Diphtheria toxin?

Inactivates EF-2

58

eIF2a is inhibited in the regulation of initiation factors. What will this affect?

I will stop initiation by inhibiting the binding of meth tRNAs to the ribosome for ALL proteins

59

How does the cell stop the translation of a specific protein?

Bind proteins to a start codon in the 5' UTR

60

What are the steps in N-linked glycosylation?

1. Dolichol phosphate is produced
2. Dolichol is phosphorylated by UDP galactose
3. additional sugars are added
4. Reorientation so that the sugar face the inside of the ER
5. Additional sugar added (monoses and glucoses)
6. Protein is added to the saccharide

61

What is the core structure of the N-linked

2 GlcNAc +
9 mannoses +
3 glucoses

62

O-linked glysosylation utilizes what two amino acids?

S and T

63

What is the mechanism of CDG I?

Defective synthesis of lipid-linked oligosaccharides in N-link glycosylation

64

What is the mechanism of CDG II?

Defective trimming of oligosaccharides in N-link glycosylation

65

What process if the hydroylation of proline used in?

Forming collagen

66

What process is the acetylation of lysine used in?

HATs

67

*****What is the function of adding hydrophobic moieties or GPI anchors to proteins?*******

Adds hydrophobic regions so that proteins are tethered into cell membranes

68

Proline hydroxylation is involved in what process?

Collagen formation

69

Lysine acetylation is involved in what process?

HATs

70

Multiple sulfatase deficiency is what?

A lack of sulfatases. This leads to the accumulation of c-alpha-formylglycine precursors since the thiol group in cystine cannot be converted into an acetylaldehyde. These products accumulate in lysosomes

71

What are the components of the ternary complex in ribosome initiation?

Activated eIF2a, and a M-tRNA

72

What are the components of the pre-initiation complex in ribosome initiation?

Activated eIF2a, a M-tRNA, and the small ribosome subunit

73

What are the components of the completed initiation complex in ribosome iniation?

Activated eIF2a, an M-tRNA, and the small and large ribosomal subunits

74

What is the protein that helps ribosomes find the ER in order to insert the protein it is building through a translocon?

SRP

75

What are glycosyltransferases specific for? (hint, three things).

1. The sugar donor
2. The acceptor
3. Type of glycosidic bond formed

76

Where does N-linked glycosylation begin? End?

ER, golgi

77

What is myristic acid linked to in the protein?

N-terminal G

78

What is a palmitic acid linked to in proteins?

C residues throughout the protein

79

What are isoprenoids linked to in proteins?

C residues close to the C-terminus

80

Congenital disorders of glycosylation affect what type of glycosylation: N-linked or O-linked?

N-linked

81

CDG I is defective what?

Defective synthesis of the the core diloichol phosphate

82

CDG II is defective what?

Trimming of oligosaccharides

83

Glycoproteins that are apart of the ECM (recall these are the preteoglycans and glycoproteins) are the result of what type of glycosylation process, N-linked or O-linked?

O-linked