Lec 08- Transcription and Translation 2

Question 1

Where does protein synthesis occur?

Answer 1

on ribosomes

Question 2

In what direction is a protein synthesized?

Answer 2

in the amino-to-carboxyl direction

Question 3

What end of the growing peptide do amino acids add to?

Answer 3

the carboxyl end

Question 4

What kind of bond is formed when amino acids are added to the carboxyl end of the growing peptide?

Answer 4

dipepdityl bond

Question 5

What is the genetic code?

Answer 5

• a set of rules
• converts the nt sequence of a gene into the amino acid sequence of a protein
• uses mRNA as an intermediary

Question 6

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

Answer 6

4 nucleotides

groups of 3

Question 7

How many total codons are possible?

Answer 7

4^3 = 64

Question 8

How many of the codons are stop codons?

Answer 8

3 stop codons

Question 9

How many codons are there for the 20 amino acids?

Answer 9

61 codons

Question 10

What does the adaptor hypothesis postulate?

Answer 10

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

Question 11

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

Answer 11

tRNA

Question 12

What does the tRNA structure look like?

Answer 12

a cloverleaf

Question 13

tRNA folds up into a defined 3D structure and contains ____ short double-helical segments

Answer 13

4 short double-helical segments

Question 14

What are the 2 regions of unpaired nucleotides that are crucial to the functions of tRNA?

Answer 14

• Anticodon loop

- 3’ CCA terminal region

Question 15

What is the anticodon loop?

Answer 15

• set of 3 consecutive nucleotides

- pairs with a complementary codon in an mRNA molecule

Question 16

What is the 3’ CCA terminal region?

Answer 16

• region on the 3’ end

- binds the amino acid that matches the corresponding codon

Question 17

How many tRNAs are there for most amino acids?

Answer 17

more than 1 tRNA for most amino acids

Question 18

What is the wobble hypothesis?

Answer 18

• some tRNAs require accurate base-pairing only at first 2 positions of the codon
• can tolerate mismatch/wobble at the 3rd position

Question 19

What does the wobble base-pairing explain?

Answer 19

why so many of the alternative codons for an amino acid differ only in their 3rd nucleotide

Question 20

What catalyzes recognition and attachment of the correct amino acid to the corresponding tRNA?

Answer 20

aminoacyl-tRNA synthetases

Question 21

Where does the aminoacyl-tRNA synthetase covalently couple an amino acid to on the ribose residue of its corresponding tRNA? What does this form?

Answer 21

the 3’ terminal

Question 22

What is an aminoacyl-tRNA made of?

Answer 22

an amino acid covalently coupled to the 3’ terminal ribose residue of its corresponding tRNA

Question 23

What drives the process of aminoacyl-tRNA formation?

Answer 23

ATP hydrolysis

produces a high energy bond between tRNA and the amino acid

Question 24

Most cells have ____________________ for each amino acid.

Answer 24

a different synthetase enzyme

Question 25

Where does the editing (hydrolytic) site cleave?

Answer 25

cleaves activated species that are smaller than the correct one

Question 26

What is the result of hydrolytic editing?

Answer 26

raises the overall accuracy of tRNA charging to 1 mistake in 40,000 couplings

Question 27

What are the 2 adaptors that translate the genetic code?

Answer 27

- aminoacyl-tRNA synthetase | - tRNA molecule

Question 28

What kind of activation sites does aminoacyl-tRNA synthetases contain?

Answer 28

highly discriminating amino acid activation sites

Question 29

What has the highest affinity for the active-site pocket of the tRNA synthetase?

Answer 29

the correct amino acid -therefore favored over the other 19 amino acids

Question 30

Which amino acids of not bind to the active site of the tRNA synthetase?

Answer 30

amino acids that are larger than the correct one

Question 31

What does the aminoacyl-tRNA use for proofreading?

Answer 31

an editing site

Question 32

What are the general size differences between PRO and EUK ribosomes?

Answer 32

PRO = small subunit (70S) EUK = large subunit (80S)

Question 33

What is a ribosome and what does it consist of?

Answer 33

- a complex catalytic machine | - consists of 2 subunits

Question 34

What does each ribosomal subunit contain?

Answer 34

- different ribosomal proteins | - several rRNAs

Question 35

What is the function of rRNAs?

Answer 35

Determines: - overall ribosome shape - ability to position tRNAs on the mRNA - catalytic activity in forming peptide bonds

Question 36

What does the small subunit provide?

Answer 36

a framework on which the tRNAs are accurately matched to the codons of the mRNA (binding sire for mRNA strand)

Question 37

What does the large subunit do?

Answer 37

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

Question 38

Why does protein synthesis occur on the ribosome?

Answer 38

- ensures accuracy | - maintains correct reading frame

Question 39

When are the 2 ribosomal subunits separated?

Answer 39

when they are not synthesizing proteins

Question 40

Where do the 2 ribosomal subunits join together?

Answer 40

at the 5' end of an mRNA

Question 41

What initiates protein synthesis?

Answer 41

the 2 ribosomal subunits joining together at the 5' end of an mRNA

Question 42

What direction is the mRNA pulled through the ribosome?

Answer 42

5' >> 3' direction

Question 43

What happens to the mRNA sequence as the codons enter the core of the ribosome?

Answer 43

the mRNA sequence is translated into amino acid sequence using tRNAs as adaptors

Question 44

When does the ribosome release the protein?

Answer 44

when it encounters a stop codon

Question 45

How many binding sites for RNA does the ribosome contain?

Answer 45

4 binding sites

Question 46

What are the 4 ribosomal binding sites for RNA?

Answer 46

3 sites for tRNA: - A site = aminoacyl - P site = peptidyl - E site = exit 1 site for mRNA

Question 47

The rRNA from which subunit dorms the APE sites?

Answer 47

the rRNA of the large subunit

Question 48

Which subunit binds the mRNA?

Answer 48

the small subunit

Question 49

When are the tRNA molecules held in the AP sites?

Answer 49

only if their anticodon forms base pairs with complementary codon in mRNA threaded through the ribosome

Question 50

What is the fundamental reaction of protein synthesis?

Answer 50

formation of peptide bond between amino acids

Question 51

Where does the peptide bond occur?

Answer 51

between the carboxyl group at the end of the polypeptide and an amino group of the incoming amino acid CO-NH

Question 52

A protein is synthesized stepwise from its ______ terminal to its ______ terminal end

Answer 52

N-terminal to C-terminal end

Question 53

Steps of peptide bond formation

Answer 53

1) peptidyl-tRNA attached to C-terminus of the growing polypeptide chain 2) aminoacyl-tRNA 3) tRNA molecule freed from its peptidyl linkage 4) peptide bond formed 5) new peptidyl-tRNA molecule attached to C-terminus of the growing polypeptide chain

Question 54

What are the 4 steps of mRNA translation?

Answer 54

1) tRNA binding 2) peptide bond formation (peptidyl transferase) 3) large subunit translocation 4) small subunit translocation

Question 55

What is very crucial for EUK translation initiation?

Answer 55

the site at which protein synthesis begins

Question 56

What does the site of protein synthesis determine?

Answer 56

the reading frame for the whole length of the message

Question 57

What do all known mRNA molecules contain?

Answer 57

signals that define the beginning of each encoded poylpeptide chain

Question 58

What codon starts translation?

Answer 58

AUG (methionine)

Question 59

What carries the amino acid methionine?

Answer 59

a special initiator tRNA

Question 60

What is the initiator tRNA-methionine complex loaded onto?

Answer 60

the small subunit of ribosomes on the P-site

Question 61

What other things, besides the initiator tRNA-methionine complex, are added for EUK translation initiation?

Answer 61

EUK initiation factors (eIFs)

Question 62

What subunit binds to the 5' end of the mRNA?

Answer 62

the small ribosomal subunit

Question 63

How is the 5' end of the mRNA recognized?

Answer 63

- its 5' cap | - the bound initiation factors

Question 64

What are the 2 bound initiation factors to EUK mRNA?

Answer 64

eIF4E eIF4G

Question 65

What is ahead of the AUG of EUK mRNA?

Answer 65

a recognition consensus site 5'-ACCAUGG-3'

Question 66

What happens after EUK translation initiation?

Answer 66

- the factors drop off - the large submit joins the small subunit - protein synthesis starts

Question 67

What makes EUK translation more efficient and accurate?

Answer 67

elongation factors

Question 68

What are the 2 PRO elongation factors and 2 EUK elongation factors?

Answer 68

PRO = EF-Tu & EF-G EUK = EF1 & EF2

Question 69

What does EF-Gu bind to?

Answer 69

- GTP | - the aminoacyl-tRNA

Question 70

What does EF-Gu do after binding GTP and the aminoacyl-tRNA?

Answer 70

- escorts it to the ribosome | - checks whether the amino acid-tRNA match is correct

Question 71

What do elongation factors monitor?

Answer 71

interaction between anticodon of incoming aminoacyl-tRNA and the codon of mRNA

Question 72

What introduces critical proofreading steps into protein synthesis?

Answer 72

interactions of: - EF-Tu - tRNA - ribosome

Question 73

What brings conformational changes in the ribosomes to greatly increase efficiency?

Answer 73

GTP hydrolysis

Question 74

What are the 3 stop codons?

Answer 74

UAA UGA UAG

Question 75

What recognizes the stop codons?

Answer 75

release factors (RFs)

Question 76

What are release factors?

Answer 76

proteins that promote the release of the completed protein from the tRNA

Question 77

What happens when the RFs bind to the A site containing the stop codon?

Answer 77

- catalyzes the addition of a water molecule instead of an amino acid - frees the carboxyl group of the polypeptide from tRNA - completed protein released from ribosome into cytoplasm - protein folded into 3D structure

Question 78

What are many effective antibiotics made by?

Answer 78

fungi that inhibit bacterial protein synthesis

Question 79

What do antibiotics do?

Answer 79

exploit structural and functional differences between bacterial and eukaryotic ribosomes

Question 80

Where do many antibiotics bind?

Answer 80

to ribosomes

Question 81

What happens when antibiotics bind to ribosomes?

Answer 81

interfere with protein synthesis by blocking ribosomal function