exam 3 (translation)

Question 1

what material does translation use to make protein

Answer 1

DNA-encoded info

Question 2

translation in what step of the central dogma

Answer 2

last step

Question 3

where are proteins synthesized

Answer 3

ribosomes

Question 4

describe the structure of a bacteria ribosome

Answer 4

• large subunit has a short and long strand of rRNA and proteins L1, L2, L3
• small subunit has strand of rRNA and proteins S1, S2, S3

Question 5

how many proteins are in the large subunit of a bacteria ribosome? how many are in the small subunit?

Answer 5

large- 36

small- 21

Question 6

how many proteins are in the large subunit of a eukaryotic ribosome? how many are in the small subunit?

Answer 6

large- 50

small- 33

Question 7

what results in loss of ribosome function in yeast

Answer 7

cells grow slowly, can’t complete well with wild-type strains

Question 8

what results in loss of ribosome function in Drosphila

Answer 8

a class of mutations (called minute)

Question 9

what is Diamond-Blackfan anemia (DBA) and what is it a result of?

Answer 9

lack of red blood cells and congenital abnormalities. caused by mutations in 10-15 diff ribosomal protein genes (RPS19)

Question 10

what is Treacher-Collins syndrome and what is it a result of?

Answer 10

craniofacial defects, hearing loss.

results from mutations of TCOF1, which participates in rRNA processing and genes that encode subunits of RNAPi

Question 11

what programs ribosomes for protein synthesis

Answer 11

mRNA

Question 12

mRNA is read in which direction

Answer 12

5’ –> 3’

Question 13

what are codons

Answer 13

triplets of bases in mRNA that specify which amino acids are a part of the protein strand

Question 14

what is the open reading frame (ORF)

Answer 14

portion of mRNA encoding a protein, that is a way the nucleotide sequence can be divided

Question 15

reading frames start with which codon

Answer 15

ATG (AUG) methionine

Question 16

what is the wobble in codon-anticodon pairing

Answer 16

the 5’ end of the tRNA anticodon can recognize multiple bases at the 3’ end of the codon

Question 17

what provides the greatest flexibility for codon-anticodon pairing

Answer 17

inosine

Question 18

what are the 3 codons that terminate translation

Answer 18

UAA
UAG
UGA

Question 19

which of the stop codons can be repurposed to incorperate nonstandard amino acids into proteins

Answer 19

UGA

UAG

Question 20

what is the 21st amino acids in proteins and is found in all domains of life

Answer 20

SEC- selenocysteine

Question 21

selenocysteine is encoded by what codon

Answer 21

UGA codon

Question 22

what is the function of the selenocysteine incorporation sequence (SECIS)

Answer 22

recoding of UGA as a U codon

Question 23

what is the 22nd amino acid found in proteins of bacteria and archea

Answer 23

pyrrolysine

Question 24

what is pyrrolysine encoded by

Answer 24

UAG

Question 25

what is the adapter hypothesis

Answer 25

proposed by francis crick states that there is some molecule that tells protein synthesis machinery which amino acids are specified by the mRNA was later discovered that tRNAs are the adapters

Question 26

what is the function of the acceptor stem on tRNA

Answer 26

responsible for the interaction with an amino acid

Question 27

what is the function of the anticodon on the tRNA

Answer 27

responsible for the interaction with the mRNA codon

Question 28

the anticodon of the tRNA pairs with what during translation

Answer 28

codon on mRNA

Question 29

what are aminoacyl-tRNA synthetases

Answer 29

attach amino acids to their cognate tRNA (called=charging) | must be able to discriminate between amino acids with similar side chains

Question 30

explain the proofreading process of aminoacyl-tRNA synthetases

Answer 30

double-sieve model to only allow isoleucine have course sieve on the activation site to reject larger amino acids have fine sieve on editing site to reject smaller amino acids

Question 31

what can cause tRNA recognition by aminoacyl synthetases to be altered

Answer 31

mutation of the identity element alters the specificity of the tRNA for the synthetase

Question 32

what are the 4 mechanisms of translation

Answer 32

initiation elongation chain termination recycling

Question 33

what other codons could start

Answer 33

GUG | UUG

Question 34

lacl has what starting codon

Answer 34

GUG

Question 35

lacA has what starting codon

Answer 35

UUG

Question 36

what is generally the first amino acid incorporated into a new protein

Answer 36

methionine | but can also occur in the middle

Question 37

what are the 2 methionine tRNAs in bacteria

Answer 37

initiator | elongator

Question 38

what hydrolyzes GTP to GDP during prokaryotic translation initiation

Answer 38

IF2

Question 39

what is the shine-dalgarno sequence

Answer 39

- observations made by john shine and Lynn Dalgarno - many bacterial ORFs have purine-rich consensus sequence, 5-7 nt upstream of initiating AUG codon - the 16S rRAN has a complementary pyrimidine-rich sequence near its 3' end

Question 40

how are eukaryotic translation initiation different that prokaryotic

Answer 40

- mRNAs are much more highly processed - no shine-dalgarno sequence - ribosomes bind to the mRNA and scnas for a proper AUG

Question 41

what is the Kozak sequence

Answer 41

sequence that has AUG embedded, to start

Question 42

describe the 3 sites of the ribosome

Answer 42

A site: entry point for a charged tRNA P site: where the peptidyl tRNA is located (tRNA is attached to the growing polypeptide chain) E site: exit point for an uncharged tRNA

Question 43

when does translation termination occur

Answer 43

when a termination codon enters the A site

Question 44

translation termination requires 3 release factors

Answer 44

- RF1 and 2 interact with the termination codon | - RF3 stimulates cleavage of the completed peptide from the last tRNA

Question 45

how does Diphtheria toxin target ribosomes

Answer 45

adds an ADP-ribose molecule to eEF2

Question 46

how does ADP-ribosylation and exotoxin A impair eEF2 function

Answer 46

inhibits protein synthesis

Question 47

What are and the functions of saponin, shiga toxin, adn ricin

Answer 47

they are ribosomal posions, of which each remove a single adenine base from the 28S rRNA

Question 48

where are many ribosomal toxins found

Answer 48

they are found in: staple crops--rice, maize, and barley because they aren't toxic to humans

Question 49

how are ribosomes used in cancer therapy

Answer 49

they are a part of "immunotoxin", where they are an antibody against cancer cell-specific proteins, where they inhibit protein synthesis

Question 50

what are chaperones

Answer 50

factors that mold disordered protein chains into proper shapes

Question 51

what is the bacterial chaperone's role in it exit of a ribosome

Answer 51

the trigger factor associates with the nascent polypeptide chain

Question 52

what is the signal hypothesis

Answer 52

- states that free and ER-asscoaited ribosomes are the same - it was originally hypothesized that all protein synthesis begins on free ribosomes and proteins were specifically functionized to be directed to ribosomes on the ER

Question 53

what is the function of proteasome

Answer 53

protein complex that gets rid of unnecessary/damaged proteins

Question 54

what is the structure of a proteasome

Answer 54

barrel-like structure that is capped by regulatory subunits

Question 55

explain the function of ubiquitin and ubiquitination with proteasomes

Answer 55

- proteins that are to be degraded are tagged with ubiquitin - ubiquitination targets the protein to the proteasome - proteasomes hydrolyze peptide bonds, chopping proteins into small fragments