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Biochemistry > New: Mechanisms of Protein > Flashcards

New: Mechanisms of Protein Flashcards

1
Q

Most changes that affect disease don’t lie in the genes themselves; they lie in the _______

A

gene SWITCHES

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2
Q

In bacteria, transcription and translation are

A

coupled

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3
Q

gene is being transcribed

A

left to right

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4
Q

ribosomes bind to the

A

5’ end of mRNA

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5
Q

are transcription/translation coupled in eukaryotes?

A

NO occur in separate locations

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6
Q

polysome

A

mRNA translated by more than one ribosome at a time

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7
Q

the ribosome is a complex of ___ and ____

A

RNA and protein

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8
Q

______ is the site where genetic info (in the form of mRNA) is translated in to protein

A

ribosome

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9
Q

_____ is the key for ribosome to bind

A

5’ cap

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10
Q

protein synthesis is carried out by a complex composed of these 4 things:

A

ribosome; initiation factors; mRNA and charged tRNA molecules

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11
Q

Initiation complex assembles at first

A

mRNA codon

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12
Q

initiation complex disassembles at

A

termination step

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13
Q

ribosome complex moves 5’–>3’ along

A

template mRNA

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14
Q

polypeptide is synthesized in the

A

N–>C direction (amino –> carboxyl terminal)

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15
Q

ribosomes have ___ tRNA binding sites

A

3

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16
Q

3 binding sites of tRNA

A
  1. the A (aminoacyl) site binds the incoming tRNA
  2. the P (peptidyl) site binds the tRNA with the growing peptide chain
  3. the E (exit) site binds the uncharged tRNA before it leaves the ribosome
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17
Q

Aminoacylated ends of the tRNAs are positioned at the site of

A

peptide bond formation

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18
Q

ribosome must hold both

A

mRNA and growing polypeptide chain

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19
Q

ribosomes are composed of what 2 things

A

rRNA and protein

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20
Q

initiation of translation - translation complex is assembled at the beginning of the

A

mRNA coding sequence

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21
Q

translation complex consists of what 4 things

A

ribosomal subunits
mRNA template to be translated (5’ cap)
initiator tRNA molecule
protein initiation factors

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22
Q

the nucleotides between the 5’ end of the mRNA and the first codon translated are called the

A

untranslated region (UTR)

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23
Q

the untranslated region (UTR) contains a ______ _____ sequence

A

shine-delgarno

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24
Q

sequence that direct protein synthesis machinery to the start site

A

shine-delgarno

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25
Q

S-D sequence is ____-rich, about 10 bp upstream of the start site, and interacts with the 16s rRNA to correctly position the

A

purine; AUG codon in the A site

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26
Q

initiation complexes assemble only at

A

initiation codons

27
Q

in order to start initiation, ribosomes bust recognize protein synthesis start which is usually

A

AUG

28
Q

dsRNA structure binds _____ to the ribosome

A

mRNA

29
Q

because transcription and translation both occur in the 5’ - 3’ direction, bacterial protein synthesis begins before

A

transcription is complete

30
Q

bacterial protein synthesis is initiated by

A

formylmethionyl tRNA

31
Q

3 steps in chain elongation

A
  1. positioning the correct aa-tRNA in site A
  2. formation of a peptide bond
  3. shifting mRNA by one codon
32
Q

elongation factors dock an aminoacyl-tRNA in the ___ site

A

A

33
Q

bacterial elongation factor _______ helps the correct aa-tRNA insert into site A

A

EF-Tu

34
Q

one of the most abundant proteins in bacteria

A

EF-TU

35
Q

hydrolysis of GTP causes conformational change in EF-Tu which releases

A

aa-tRNA

36
Q

peptidyl transferase catalyzes

A

peptide bond formation

37
Q

responsible for formation of peptide bond once aa-tRNAs are positioned in P and A sites; activity is contained within the large ribosomal subunit

A

peptidyl transferase

38
Q

aminoacyl-tRNA synthetase

A

binds amino acid to tRNA

39
Q

translocation moves the ribosome by ___ codon

A

1

40
Q

translocation step:

A

the new peptidyl-tRNA is moved from the A site to the P site, while the mRNA shifts by one codon

41
Q

the deaminoacylated tRNA has shifted from the P site to the

A

E (exit) site

42
Q

elongation factor G uses the energy of ___ _____ to translocate the mRNA factor by one codon

A

GTP hydrolysis

43
Q

upon translocation, the peptidyl-tRNA is fully in the ___ site, the ___ site is vacant, and uncharged tRNA is in the __ site, disengaged from the mRNA

A

P site; A site; E site

44
Q

growing peptide chain extends from the peptidyl-tRNA (P site) through a tunnel in the

A

50s (large) subunit

45
Q

newly synthesized polypeptide does not begin to fold until it

A

emerges from the tunnel

46
Q

termination codons

A

UGA; UAG; UAA

no tRNA molecules recognize these codons and protein synthesis stalls

47
Q

E. coli release factors:

A

RF-1, RF-2 RF-3

48
Q

protein synthesis is energetically

A

expensive

49
Q

____ phosphoanhydride bonds are cleaved for each amino acid added to a polypeptide chain

A

4

50
Q

Amino acid activation takes 2 ATP —>

A

AMP + 2 Pi

51
Q

chain elongation takes 2 GTP –>

A

2 GDP + 2Pi

52
Q

erythromycin

A

binds to 50s portion, prevents translocation - movement of ribosome along mRNA

53
Q

streptomycin

A

changes shape of 30s portion causes code on mRNA to be read incorrectly

54
Q

protein initiation is the same for all organisms except for

A

eukaryotes

55
Q

how are eukaryotes protein initiation more complex? 6 ways

A
  1. ribosomes are larger - 40s and 60s subunits that form the 80s ribosome
  2. protein synthesis begins with a methionine rather than formylmethionin. A special initiator tRNA called Met-tRNAi is required (tRNA initiator)
  3. The initiator codon is always the first AUG from the 5’ end of the mRNA
  4. the mRNA is circular b/c of interactions between proteins that bind the 5’ cap and those that bind the poly A tail
  5. elongation and termination are similar except that bacteria have 2 release facors while eukaryotes have only 1
  6. eukaryotic protein synthesis occurs in the cytoplasm and utilized large complexed associated with the cytoskeleton
56
Q

mRNA use is subject to

A

regulation

57
Q

stability of ____ is also regulated

A

mRNA

58
Q

RNA interference (RNAi) leads to

A

mRNA degradation induced by the presence of double stranded RNA - likely a protective mechanism against viruses since dsRNA can be present during certain viral infections

59
Q

dicer, a ribonuclease, cleaves double stranded RNA into small fragments called

A

small interfering RNA (siRNA) that are bound by a class of proteins called Argonaute to form the RNA induced silencing complex

60
Q

RNA induced silencing comples located mRNA complementary to the

A

siRNA and degrades the mRNA

61
Q

microRNA are how long?

A

21 nucleotides long

62
Q

microRNA regulate

A

gene expression post-transcriptionally; mRNA stability and/or translation; may regulate as much as 60% of mammalia protein-coding genes

63
Q

some miRNAs promote

A

cleavage of specific mRNAs; translational repression or deadenylation of mRNAs

Biochemistry (6 decks)

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