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Molecular Biology - Jourdan > Chapter 8 > Flashcards

Chapter 8 Flashcards

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0
Q

Where does protein synthesis occur?

A

Ribosomes

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1
Q

What is used to synthesize a protein?

A

Information present in nucleotide sequence of mRNA

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2
Q

What direction is protein synthesized?

A

amino-to-carboxyl direction by the sequential addition of amino acids to the carboxyl end of the growing peptide chain

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3
Q

What is genetic code?

A

A set of rules that converts the nucleotide sequence of a gene into the amino acid sequence of a protein using mRNA as an intermediary

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4
Q

The sequence of nucleotides in the mRNA molecule is read consecutively in groups of ____

A

3

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5
Q

What is each group of 3 consecutive nucleotides in RNA called?

A

A codon

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6
Q

What does each codon specify?

A

Either one amino acid or a stop to the translation process

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7
Q

How many triplet codons code for the 20 known amino acids?

A

61 trip codons

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8
Q

The genetic code is ______ because 61 codons code for 20 AA

A

degenerative

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9
Q

What is the adaptor hypothesis?

A

Postulates that the genetic code is read by molecules that can recognize a codon and carry to corresponding amino acid

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10
Q

What serves as an adaptor that binds to a specific codon and brings in an amino acids for incorporation into the polypeptide chain?

A

tRNA

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11
Q

What is the general structure of tRNA

A

Cloverleaf secondary structure (3D)
4 short double-helical segments
two regions of unpaired nucleotides

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12
Q

What are crucial to the functions of tRNA? What are the functions of tRNA?

A

Two regions of unpaired nucleotides are crucial

  1. anticodon loop: a set of 3 consecutive nucleotides that pair with a complementary codon on mRNA
  2. 3’CCA terminal region which binds the amino acid that matches the corresponding codon
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13
Q

What is the wobble wobble hypothesis?

A

Some tRNAs require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch at the third position

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14
Q

What does the wobble base-pairing hypothesis explain?

A

Why so many of the alternative codons for an amino acid differ only in their third nucleotide

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15
Q

Recognition and attachment of the correct amino acid to the corresponding tRNA is catalyzed by what enzyme?

A

aminoacyl-tRNA synthetase

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16
Q

What does the aminoacyl-tRNA synthase covalently couple?

A

Amino acid to the 3’terminal ribose residue of its corresponding tRNA to form aminoacyl-tRNA

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17
Q

What drives the production of aminoacyl-tRNA?

A

ATP hydrolysis

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18
Q

True or False?

One type of aminoacyl-tRNA synthase exists for all tRNAs and corresponding amino acid

A

False

Most cells have a different synthetase enzyme for each amino acid

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19
Q

Why does aminoacyl-tRNA synthetase have high fidelity?

A

The enzyme contains highly discriminating amino acid activation sites

The correct amino acid has the highest affinity for the active-site pocket of its synthetase and therefore is favored.

Amino acids larger than the correct one doe not bind to active site

Also contains editing site for proofreading

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20
Q

What happens in the editing site of aminoacyl-tRNA synthetase?

A

In the editing (hydrolytic) site, it cleaves activated species that are smaller than the correct one

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21
Q

What does hydrolytic editing do for accuracy statistics?

A

Raises the overall accuracy of tRNA charging to approximately one mistake in 40,000 couplings

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22
Q

Ribosome:

A

Complex catalytic machine, consisting of two subunits

–each contains different ribosomal proteins and several ribosomal rRNAs

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23
Q

What determines the overall shape of the ribosome, its ability to position tRNAs on the mRNA, and its catalytic activity in forming peptide bonds?

A

rRNAs, not other proteins

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24
Q

Function of small subunit

A

Provides a framework on which the tRNAs are accurately matched to the codons of the mRNA

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25
Q

What is the function of the large subunit?

A

Catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain

26
Q

When are the subunits separate and when are they together?

A

The 2 ribosomal subunits are separate when not synthesizing proteins. They join together at the 5’ end of an mRNA and initiate protein synthesis

27
Q

What is the role of ribosomes?

A

Protein synthesis and ensures accuracy and maintains correct reading frame

28
Q

In what direction is the mRNA pulled through?

A

5’-3’

29
Q

When is the mRNA sequence translated into amino acid sequence?

A

When the codons enter the core of the ribosome and use tRNAs as adaptors to bring in corresponding amino acid

30
Q

When does the ribosome release the protein?

A

Encounter a stop codon

31
Q

How many binding sites does the ribosome contain for RNA?

A

4
3 for tRNA
1 for mRNA

32
Q

What are the three binding sites for tRNA?

A

A-aminoacyl
P-peptidyl
E-Exit

33
Q

Where are the APE sites formed?

A

on the large s.u

34
Q

Where is mRNA bound?

A

small s.u

35
Q

When can tRNA molecules be held in the A and P sites?

A

only if their anticodon forms base pairs with complementary codon on mRNA being threaded

36
Q

What does the fundamental reaction of protein synthesis form between amino acids?

A

peptide bonds

37
Q

Where do peptide bonds form?

A

Between the carboxyl group at the end of the polypeptide and an amino group of the incoming amino acid

38
Q

The protein is synthesized stepwise in its _______________

A

N-terminal to C terminal end

39
Q

Why is the site at which protein synthesis beings very crucial?

A

Determines the reading frame for the whole length of the message

40
Q

Was signal defines the beginning of each encoded polypeptide chain?

A

Initiation codon AUG

41
Q

What does the initiator tRNA carry?

A

methionine

42
Q

Where is the initiator tRNA loaded

A

P site of the small subunit

43
Q

When are other eukaryotic initiation factors added? (eIFs)

A

After initiator tRNA binds to P site

44
Q

How does the small ribosomal subunit recognize the 5’end of the mRNA where it will attach?

A

by the 5’ cap and the bound initiation factors eIF4E and eIF4G

45
Q

What is the recognition consensus site ahead of AUG?

A

5’-ACCAUGG-3’

46
Q

What happens immediately after initiation?

A

The factors drop off

the large subunit joins the small subunit and protein synthesis starts

47
Q

What makes translation more efficient and accurate?

A

Elongation factors

48
Q

What are the elongation factors in bacteria and eukaryotes?

A

EF-Tu and EF-G in bacteria

EF1 and EF2 in eukaryotes

49
Q

What does EF-Tu bind to? What is its purpose?

A

Binds to GTP and aminoacytl tRNA
Escorts it to the ribosome and checks whether the amino acid-tRNA match is correct
Monitors interaction between anticodon of incoming aminoacyl tRNA and the codon of mRNA

50
Q

What introduces critical proof-reading steps into protein synthesis?

A

EF-Tu, tRNA, and ribosome

51
Q

What brings about the conformational changes in ribosomes and increases efficiency greatly?

A

GTP hydrolysis

52
Q

What are the stop codons?

A

UAA, UAG, and UGA

53
Q

What are unique about stop codons?

A

They are not recognized by any tRNA and do not code for any amino acids
They instead signal ribosome to stop translation

54
Q

What are stop codons recognized by?

A

Release Factors (RFs), proteins that promote the release of the completed protein from the tRNA

55
Q

What binds to A site of ribosome containing the stop codon? What does it catalyze?

A

RFs bind to A site and catalyze the addition of a water molecule instead of an amino acid

56
Q

What does the reaction catalyzed by RFs do?

A

Reaction frees the carboxyl group of the polypeptide from tRNA

57
Q

Where is completed protein released from ribosome? What happens to protein?

A

The Cytoplasm; folds into 3-D structure

58
Q

What are inhibitors of protein synthesis?

A

Antibiotics

59
Q

What are many effective antibiotics made by?

A

Many are compounds made by fungi that inhibit bacterial protein synthesis

60
Q

What do antibiotic compounds exploit?

A

Structural and functional differences between bacterial and eukaryotic ribosomes

61
Q

What do many antibiotics do?

A

Bind to ribosomes and interfere with protein synthesis by blocking ribosomal function

62
Q

What are antibiotics used for?

A

Clinical purposes and for research

Molecular Biology - Jourdan (8 decks)

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