Lecture 3

Question 1

protein synthesis goes in what direction

Answer 1

N terminal to C terminal

Question 2

what is the start codon

Answer 2

AUG (makes met)

Question 3

AUG/ met turns into what terminal of a protein

Answer 3

N terminal

Question 4

where will the peptide bond form between two AA

Answer 4

will lose H2O

Question 5

how long are tRNAs

Answer 5

70-90 nucleotides long

Question 6

what structure does tRNA have

Answer 6

2D structure resembling a cloverleaf

Question 7

what is the role of tRNA

Answer 7

• to act as an adaptor
• to bring the correct AA specified by the codon on the mRNA

Question 8

what does the trident mean here

Answer 8

• the location is “psi”
• this is the most common modification

Question 9

true/false the anticodon is complementary to the codon

Answer 9

true

Question 10

true/false the anticodon is the same sequence as the codon

Answer 10

false

Question 11

what loops are present on the cloverleaf structure of the tRNA

Answer 11

• T loop
• anticodon loop
• D loop

Question 12

true/false the accuracy of attaching AA to tRNA is very accurate

Answer 12

true

Question 13

what end is this

Answer 13

3’ end of tRNA

Question 14

the process of linking an activated AA to a tRNA is also referred to as what

Answer 14

tRNA charging

Question 15

the energy in this bond is used for what

Answer 15

• to incorporate the NEXT AA to the polypeptide chain
• not the current one

Question 16

how many aminoacyl-tRNA synthetases are there

Answer 16

• 20
• one for each AA

Question 17

how many subunits in ribosomes

Answer 17

2 (large and small)

Question 18

what does the small subunit of a ribosome do

Answer 18

binds the tRNAs and mRNA

Question 19

what does the large subunit of a ribosome do

Answer 19

• binds the tRNAs
• catalyzes peptide bond formation

Question 20

rRNAs are ______ (more/less) highly conserved than the ribosomal proteins

Answer 20

more

Question 21

what does SSu rRNAs stand for

Answer 21

small subunit rRNAs

Question 22

sequence comparison of SSu rRNAs from diff organisms are commonly used for what

Answer 22

construction of phylogenic trees

Question 23

how many binding sites are in the ribosome for mRNA

Answer 23

1

Question 24

how many binding sites are in the ribosome for tRNA

Answer 24

3

Question 25

how many tRNAs can be bound on the ribosome at the same time

Answer 25

2

Question 26

the tRNA that is connected to the polypeptide chain is at which site

Answer 26

P site

Question 27

what are the diff binding sites of the ribosome

Answer 27

EPA

Question 28

what are the steps included in translation of mRNA

Answer 28

- incoming Aminoacyl-tRNA binds to A-site - peptide bond forms with the AA in the P site (which is attached to the pre-existing polypeptide chain) - the large subunit moved over one codon. so now tRNA 3 is at hybrid site EP and tRNA 4 is at hybrid site PA - *basically the tRNAs stay in place, just the EPA binding sites move over one so they aren't in the spot they were before* - the large and small subunits are aligned anymore so the small shifts over to align with large - this means the ribosome is "reset" - now A site is free for a new tRNA

Question 29

when do tRNAs dissociate from the E-site

Answer 29

- once the small subunit shifts over, resetting the ribosome - when the tRNA goes from E/P hybrid site to just E

Question 30

**true/false** the ribosome picks which AUG is the right to follow the same way in prokaryotes and eukaryotes

Answer 30

- **false** - they're diff mechanisms

Question 31

how does the ribosome picks which AUG is the right to follow in prokaryotes

Answer 31

- usine shine-dalgarno sequence - should be about 10 nucleotides upstread of AUG - the other (wrong) AUGs won't have them, so the ribosome knows they're wrong

Question 32

how does the shine-dalgarno sequene work

Answer 32

its complementary to the 3' end of the 16s rRNA within the small subunit of the ribosome

Question 33

what are polycistronic mRNA

Answer 33

contains coding regions for diff proteins

Question 34

what is an example of polycistronic mRNA

Answer 34

the lac operon

Question 35

prokaryotic ribosomes assembling directly on AUG codon within interior of mRNA allows for translation of what

Answer 35

polycistronic mRNA

Question 36

what are added to eukaryotic mRNA post transcription

Answer 36

- 5' cap - 3' polyA tail

Question 37

how to ribosomes bind to eukaryotic mRNA

Answer 37

- small subunit binds to 5' cap - start scanning 5' to 3' until they reach the first AUG - 90% of the time, they start translation at this first AUG

Question 38

what is the preferred translation start in eukaryotic mRNA

Answer 38

ideally there will be a Kozak sequence surrounding the 1st AUG

Question 39

what happens in eukaryotic mRNA is a kozak sequence is missing

Answer 39

- **"leaking scanning"** - an AUG codon further downstream would be chosen for translation start

Question 40

where does "ribosome scanning" mechanisms occur

Answer 40

translation initiation in eukaryotes

Question 41

10% of the nucleotides within tRNA molecules are modified how

Answer 41

by covalent modifications

Question 42

how does covalent modifications done to nucleotides within tRNA affect it

Answer 42

- promotes intramolecular basepairings - this stabilizes tRNA structure - helps tRNAs recognize correct AA and mRNA codon

Question 43

what is important in wobble basepairing

Answer 43

isonine

Question 44

what is the difference between uridine and pseudouridine

Answer 44

modified nucleotide (Ψ) found in cellular tRNA (and rRNA, snRNA, snoRNA)

Question 45

what is the difference between pseudouridine and N1-Methylpesuedouridine

Answer 45

chemically modified pseudouridine in mRNA made for COVID vaccine

Question 46

what did the 2023 nobel prize in physiology or medicine do

Answer 46

- the use of pseudouridine to stabilize and reduce cellular toxicity of in vitro transcribed mRNA - tRNA will survive by mRNA won't, so they found the major difference was in the modification of uridine

Question 47

why do stop codons stop

Answer 47

- cause it doesn't have a complementary tRNA or antidocon - once it reaches there, they bring in water instead of tRNA cause there is no tRNA for it

Question 48

**true/false** the genetic code is redundant

Answer 48

true

Question 49

how many diff tRNAs are needed to recognize the 4 glycine codons

Answer 49

3

Question 50

how can a tRNA recognize more than one codon

Answer 50

through wobble base pairing

Question 51

how does wobble base pairing occur

Answer 51

- according to a list, for each nucleotide in the third position of the codon, there are possible *different* nucleotides that can be there that can still code for the same tRNA - this happens often with isonine - the bonds will be weaker than typical base pairs

Question 52

when does isonine form

Answer 52

the deamination of adenosine

Question 53

what is needed for the reaction in which two AA are attached to each other *(ie, if they're not there, AA cannot be added and proteins cant be formed)*

Answer 53

- 2 AA - ATP

Question 54

how are AA attached to tRNA

Answer 54

- ATP hydrolysis happens, producing energy - AA will be "activated" by attaching its carboxyl group to AMP - this makes an adenylated AA - the AMP then switches places kinda with the 3' end of the tRNA molecule - the AMP goes away