Exam 4 Review Part 2

Question 1

Based on the amount of bases in the E. coli chromosome, it should take 40 minutes for the chromosome to replicate - so please explain why bacteria in a nutrient rich environment can replicate in 20 minutes

Answer 1

theta structure - can start the next round of replication before the previous round is complete

Question 2

Most plasmids will replicate using the ___________ method which is a very different process than what is known for the chromosome replication

Answer 2

rolling circle

Question 3

Compare Archaea, Bacteria, Eukarya: How many RNA polymerases?

Answer 3

B: 1
A: 1
E:3

Question 4

Compare Archaea, Bacteria, Eukarya: how many subunits does the RNA polymerase have?

Answer 4

B: 4-5
A: 11-13
E: 12+

Question 5

Compare Archaea, Bacteria, Eukarya: What finds the promoter for the RNA polymerase?

Answer 5

B: sigma factor
A: transcription factor
E: transcription factor

Question 6

Compare Archaea, Bacteria, Eukarya: What protein can be involved in termination of transcription?

Answer 6

E; Termination factor
B. intrinsic method/ rhoprotein method
A: inverted repeats followed by AT rich DNA sequence, Eta termination protein

Question 7

Is the following most likely true or false: the composition of the bacterial RNA polymerase is different between the initiation phase and most of the elongation phase of transcription. explain!

Answer 7

True - initiation requires a sigma factor, while elongation doesnt

Question 8

bacterial promoters consist of a consensus sequence, TATAAT, located ____ (#) bases upstream of the bacterial transcription start site is called the __________. a second consensus sequence ________ is located ____ (#) bases upstream of the bacterial transcription start site

Answer 8

10
pribnow box
TTGACA
35

Question 9

T/F: the average bacterial cell probably expresses over 1000 different sigma factors

Answer 9

False

Question 10

Explain three similarities between DNA polymerase and RNA polymerase

Answer 10

• catalyze phosphodiester bonds by using nucleotide triphosphates
• move in 5’ to 3’ direction
• require templates

Question 11

Explain three differences between DNA polymerase and RNA polymerase

Answer 11

• DNA polymerase requires a primer, RNA polymerase doesn’t (can start de novo)
• DNA polymerase has exonuclease activity
• DNA polymerase synthesize DNA, RNA polymerases synthesize RNA
• RNA polymerase does not require a promoter because of intrinsic helicase activity

Question 12

In Bacteria, the intrinsic method for the termination of transcription involves two components found within DNA. The first is the presence of ______________ within the DNA which when transcribed within RNA forms a _______ structure pausing further movement of RNA polymerase. What is the second component and what relationship does this cause with the RNA?

Answer 12

inverted repeats
stem-loop
string of adenines, pair with uracil causing the weakest interactions following the stem-loop structure allowing for termination and separation of RNA polymerase

Question 13

_________________ are the enzymes responsible for charging individual tRNA molecules with the appropriate amino acid. The amino acid is always added to the 3’ acceptor site consisting of three unpaired nucleotides with the sequence of __________

Answer 13

aminoacyl-tRNA synthetases
CCA

Question 14

T/F: 5.8S rRNA is found only in the large ribosomal subunit of prokaryotes

Answer 14

False

Question 15

Please explain why a chemical that binds to the 3’ end of 16S rRNA would be a good antimicrobial agent? Would there be any cross-reactivity with eukaryotic cells?

Answer 15

It would block the Shine-dalgarno sequence from pairing, thus there would be no start codon for recognition by tRNA. No, the binding site is distinct from that of eukaryotic cells

Question 16

please explain how the binding of the 50S large ribosomal subunit in the initiation of translation is controlled

Answer 16

IF-3 prevents the 30S subunit from binding to the 50S subunit, can only bind when IF-1 binds to the 30S subunit kicking IF-3 off and forming the 30S initiation complex

Question 17

________ is the primary start codon in all organisms. However, there is some discrepancy regarding what it codes for in each domain, please provide what it codes for in each domain

Answer 17

Bacteria: formyl-MET
Archaea: MET
Eukarya: MET

Question 18

Which of the following is not true of bacterial translation?
a. IF-2 requires GTP
b. the first tRNA is placed within the P site of the ribosome of the 50S subunit
c. 23S rRNA is the peptidyl transferase
d. fewer initiation/elongation factors are used compared to eukaryotes
e. all of the above are true
f. none of the above

Answer 18

a

Question 19

what is the function of EF-Tu in bacterial translation?

Answer 19

brings tRNA into A site

Question 20

what is the function of EF-Ts in bacterial translation?

Answer 20

removes GDP adds GTP

Question 21

what is the function of EF-G in bacterial translation?

Answer 21

ribosome translocation

Question 22

To terminate the bacterial translation process, a ________ binds instead of a tRNA molecule. There are __ (#) of these in bacteria and ____(#) in eukaryotes

Answer 22

release factor
2
3

Question 23

T/F: polysomes are observed in all three domains to improve efficiency of translation

Answer 23

True

Question 24

T/F: prokaryotic proteins rarely have sugars added to them

Answer 24

false

Question 25

In bacterial cells most proteins are aided in terms of folding by ______ and _______, which help to limit folding errors by _______________. if the protein is unable to fold properly, the protein will then be transferred to _______ and ________. T/F: both of these mechanisms require energy in the form of ATP

Answer 25

DNAK DNAJ slowing down the folding GroEL GroES True

Question 26

Which is not used at the post-translational level by covalent modification? a. ADP b. hydroxyl groups (OH) c. Phosphate (PO4) d. methyl groups (CH3) e. all of the above are used f. none of the above are used

Answer 26

B

Question 27

______________ is found within lipopolysaccharide, is not a typical glycerol lipid, instead it has two glucosamine sugar derivatives attached to either phosphate or pyrophosphate and then has three fatty acid chains extending from each sugar derivative

Answer 27

Lipid A

Question 28

bacteria within the clostridium genus are known to ferment _____________ in a series of steps known as the stickland reaction

Answer 28

amino acids

Question 29

exopolysaccharide coatings are common amongst bacteria categorizes as __________ in regard to their cardinal temperature range

Answer 29

extremophiles

Question 30

you provided an example of a regulatory nuclotide for catabolite repression - please provide another example of a regulatory nuclotide: ________

Answer 30

cGMP