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BioChem > Lecture 9 part 2 > Flashcards

Lecture 9 part 2 Flashcards

1
Q

Direction of protein synthesis?

A

amino terminal to the carboxyl terminal

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2
Q

Why are there two types of methionine tRNAs?

A

One is used for the start codon only and the other for all internal methionines.

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3
Q

What is added to the methionine to make it the initiator tRNA in bacteria?

A

it is formylated (added a formaline)

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4
Q

What enzyme formylates the methionine in bacteria?

A

Met-tRNA-formaltransferase

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5
Q

What does N-formylmethionine do in bacteria? In humans?

A

in bacteria - used as the starting amino acid.

in humans - initiates an immune response.

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6
Q

What does the 30S ribosome bind to first in initiation?

A

binds to IF-1 (binds to the A site and prevents premature tRNA binding) and IF-3 (which prevents association with 50S until the right time). I

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7
Q

What guides mRNA to the correct location during initiation? And where does it go?

A

16S rRNA. To the Shine-Delgarno sequence and position the AUG in the P site.

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8
Q

What is the shine-delgarno sequence?

A

used to assure proper positioning of the AUG codon of the mRNA to the P site. Occurs in the 5’ untranslated region and will react by base pairing.

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9
Q

Start codon for lacI (repressor) gene?

A

GUG but F-Met tRNA will still bind to it when it is in theP site.

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10
Q

Where do aminoacyl-tRNAs enter in during protein synthesis?

A

The A site

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11
Q

What is the chaperone for fMet-tRNA? And what does it do?

A

IF-2. And when GTP bound it will bind with fMet-tRNA and help bind to the mRNA and ribosome complex.

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12
Q

When does the 50S subunit bind to the complex?

A

After IF-2 and fMet-tRNA bind. The large subunit will hydrolyze GTP on IF-2 and cause IF-1, 2, and 3 to released. Creating the 70S.

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13
Q

How many initiation factors in eukaryotes?

A

At least 9.

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14
Q

Initiation in eukaryotes

A

IF factors can tie the 5’ and the 3’ ends of the mRNA and then the 5’ end is scanned for the first start codon. No shine-delgarno sequence. And no polycistronic

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15
Q

What are the three elongation factors in bacteria?

A

EF-Tu (thermally unstable), EF-Ts (thermally stable), and EF-G

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16
Q

EF-Tu

A

acts as a chaperone and brings in the aminoacyl tRNA when GTP bound. Enters into the A site and samples the A codon (Kd). If low Kd, then will anchor the correct one down. GTP will get hydrolyzed and EF-Tu GDP bound will leave, leaving the amino acid in the A site

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17
Q

EF-Ts

A

will regenerate EF-Tu with GTP. EF-Ts has high affinity for EF-Tu GDP and will cause EF-Tu to get rid of GDP. EF-Tu and EF-Ts do not have high affinity anymore and GTP will kick out EF-Ts.

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18
Q

What catalyzes peptide bond formation in prokaryotes?

A

23S rRNA molecule.

19
Q

Peptide bond formation

A

deprotonation of the amine to get a nucleophile in the A site, attacks the carbonyl carbon (proximity effect) making a covalent bond. This kicks off the fMet-tRNA in the P site, attaching the amino acid to the A site residue’s amino acid

20
Q

Translocation of amino acids in ribosome

A

tRNA in A site moves to P site and tRNA in P site moves to E site, it is then released and a new tRNA comes into the A site.

21
Q

EF-G

A

required for movement of the ribosome along the mRNA molecule, using the energy of GTP hydrolysis.

22
Q

What site do eukaryotes not have?

A

an E site

23
Q

Termination

A

A termination codon recruits three release factors (RF1-3), these factors hydrolyze the terminal peptidyl-tRNA bond, release the free polypeptide and tRNA from the P site, and dissociate the 70S ribosome.

24
Q

RF2

A

self regulated by a frameshift

25
Q

Formation of each aminoacyl-tRNA requires how many high-energy phosphate groups? And where do they come from?

A

2 and they come from the adenylylation, 2 are release from ATP when AMP is added.

26
Q

How many GTPs are needed to add each amino acid?

A

4 GTP

27
Q

Puromycin

A

Inhibitor of protein synthesis. Mimics the 3’ end of a tRNA molecule and will insert itself into the A site and can form a peptide-puromycin bond that causes premature dissociation.

28
Q

Tetracycline

A

blocks the A site by binding to the ribosome

29
Q

Streptomycin

A

an aminoglycoside. causes misreading of the genetic code. At [low] it doesnt read the codons correct, at [high] it blocks the binding of fMet-tRNA

30
Q

Ricin

A

catalyzes depurination of a specific adenosine in the eukaryotic 60S ribosome, leading to a rapid and irreversible inactivation

31
Q

Where residues does phosphorylation typically occur?

A

Serine, Threonine, and Tyrosine

32
Q

Where would a posttranslational modification by adding an extra carboxyl group occur?

A

On glutamic acid

33
Q

Where would a posttranslational modification by methylation occur?

A

methylation of a lysine

34
Q

Where are signal sequences typically found on the protein?

A

at the N terminus. and are generally removed once they reach its final location.

35
Q

Typically how long are signal sequences and what is their make up?

A

13 to 36 residues long and contain 10 to 15 hydrophobic residues. 1 or more positively charged near the amino end, and a short, relatively polar sequence near the cleavage site

36
Q

How does a signal sequence work?

A

a signal recognition particle binds to the sequence, stops elongation, and directs the ribosome to the ER. This is delivered to a peptide translocation complex, and elongation resumes, putting the protein into the lumen.

37
Q

SRP (signal recognition particle) in eukaryotes

A

associates with the signal sequence and the ribosome and docks it on the ER.

38
Q

What cleaves the signal sequence?

A

signal peptidase cleaves the signal sequence and then transcription resumes.

39
Q

How many residues are in the core during a glycosylation event? And where is it transferred to?

A

14 residue core oligosaccharide is synthesized in the ER and then transferred from dolichol phosphate to a protein Asn residue.

40
Q

What happens to proteins in the golgi?

A

O-linked oligosaccharides are added and additional modificiations are made to N-linked oligosaccharides. Proteins are also sorted.

41
Q

Mitochondrial proteins

A

signal sequence is recognized by cytosolic chaperone proteins, which deliver the proteins to a protein channel in the mitochondria. Translocation through the channel happens via hydrolysis of ATP and GTP. Signal sequence is then removed.

42
Q

How to get a protein in the mitochondrial membrane?

A

a “stop transfer” sequence will stop the feeding of the protein through the channel, entrapping the protein within the membrane.

43
Q

Nuclear transport sequences

A

Nuclear proteins must retain their signal sequences so that they can always go back to the nucleus after mitosis causing lysing of the nuclear membrane.

BioChem (14 decks)

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