Exam 4

Question 1

which is NOT true about plasmids?
a. They are usually circular
b. They can replicate independently of the chromosome
c. They can be present in different copy numbers
d. Their typical size is about 1/5 the size of an average bacterial chromosome
e. All of the above are true
f. None of the above are true

Answer 1

d. Their typical size is about 1/5 the size of an average bacterial chromosome

Question 2

Which of the following is not true about bacterial replication?
a. Replication is bi-directional from the replication fork
b. To maintain short generation times, multiple origins of replication are present
c. The next round of replication can occur before the previous round has been completed
d. There is both a lagging and leading strand
e. All of the above are TRUE
f. None of the above are TRUE

Answer 2

b. to maintain short generation times, multiple origins

Question 3

which of the following is NOT a similarity between the replicative DNA polymerase and the RNA polymerase used in transcription?
a. Both require nucleoside triphosphates
b. Both polymerize in the 5’ to 3’ direction
c. Both require templates
d. Both require primers to initiate new
strand synthesis
e. All of the above are traits of both
enzymes
f. None of the above are shared traits

Answer 3

d. Both require primers to initiate new
strand synthesis

Question 4

Which of the following is NOT TRUE of Bacterial translation?
a. The process is energy-demanding, but done more quickly compared to eukaryotes
b. The first tRNA is placed within the P site of the ribosome of the 505 subunit
C. 23S rRNA is responsible for catalyzing the transpeptidation
d. Fewer initiation/elongation factors are used compared to eukaryotes
e. All of the above are TRUE
f. None of the above are TRUE

Answer 4

e. all of the above are true

Question 5

True or False Topoisomerases are involved in both the initiation of bacterial replication and the termination of replication.

Answer 5

True

Question 6

True or False In Bacteria there tends to be one main sigma factor used for transcription but alternative factors are usually required for special circumstances.

Answer 6

True

Question 7

True or False ribosomes are observed in all three domains to improve efficiency of translation.

Answer 7

True

Question 8

Important to the DNA replication process is separating the two strands of the DNA chromosomes, please provide the 3 proteins within the replisome that are imperative in this role.

Answer 8

single stranded binding proteins, helicases/ helicase loaders
origin binding proteins

Question 9

In bacteria, how is DNA polymerase I different in enzymatic activity from DNA polymerase III?

Answer 9

DNA polymerase 1 uses 5’ to 3’ exonuclease activity

Question 10

Is the following statement most likely true or false?. The FtZ protein is found encoded on a common plasmid that is found in most Bacteria. Please defend your answer!

Answer 10

false,

Question 11

Plasmids replicate using the_________ _________ method.

Answer 11

rolling circle

Question 12

The consensus sequence, TATAAT, located_______(number) bases upstream of the Bacterial transcription start site is called the______________. A second consensus sequence,____________ is located 35 bases upstream of the Bacterial transcription start site.

Answer 12

10, promoter, TTGACA

Question 13

T/F Archaeal microorganisms contain these same promoter sequences for their transcriptional processes.

Answer 13

False

Question 14

In the intrinsic method of terminating transcription, the DNA at the end of the gene will be GC-rich and contain inverted repeats followed by a stretch of adenines - how do these sequences affect mRNA structure and contribute to the termination of transcription?

Question 15

One unique characteristic regarding Bacterial mRNA is that it is_____________
which means it contains multiple genes. Please explain how the eventual proteins are separated?

Answer 15

polycistronic,

Question 16

Please provide 3 characteristics that define mRNA Transcripts within eukaryotes but are NOT shared by Bacteria.

Answer 16

Eukarya
-3 RNA polymerases
-main RNA polymerase = RNAP 2
- about 12 subunits
- use transcription factors to bind to promoter site (can have multiple factors per site)
Bacteria
-1 RNA polymerases
-4-5 subunits
-use sigma factors to bind to promoter (one per site)

Question 17

___________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 which ends with the sequence ________

Answer 17

aminoacetyl tRNA synthetase ,CCA

Question 18

Provide one reason why tRNA is more stable than mRNA.

Answer 18

More stable because it has secondary structures making it not linear (ribonuclease is less likely to attack)

secondary structures are the modified bases add more stability bc by adding more units its less likely for ribonuclease to attack.

Question 19

Please answer the following questions regarding the Bacterial translation:
a. The Shine-Dalgarno sequence is located within the_______ _______ of the mRNA transcript at the_____ end.

Answer 19

leader sequence, 5’

Question 20

What does the Shine Dalgarno sequence specifically bind to?

Answer 20

the leader sequence found at the 5’ end at the AUG codon

Question 21

True or (False) The Shine Dalgarno sequence is uniquely found within prokaryotes.

Answer 21

True

Question 22

True or False IF-3 binds to the large ribosomal subunit to prevent it binding the small subunit too early.

Answer 22

False

Question 23

Please explain how tRNAs are brought into the A site during Bacterial translation. (You must provide the correct elongation factors and their roles to get full credit)

Question 24

True or False Bacterial proteins begin to fold before the peptide synthesis is complete while eukaryotes tend to wait until synthesis is finished.

Answer 24

false

Question 25

What happens if a protein cannot be folded after interacting with DnaK and DnaJ then proteins are shuttled to a system involving ________ and __________

Answer 25

Gro EL, Gro ES

Question 26

How is the secondary system provided in part b, structurally/ functionally different than the Dnak/DnaJ system?

Answer 26

DnaK and DnaJ act as clips and bite down while GroES will make proteins and Gro EL will use it .....

Question 27

what trait is shared by these folding systems? (GroEL and GroES)

Answer 27

Both use ATP

Question 28

Which of the following is NOT true of the negative control of transcription process of induction? a. Involves a DNA binding protein referred to as the repressor b. Usually regulates catabolic reactions V c. An inducer molecule would cause the DNA binding protein to bind to the DNA d. All of the above are true e. None of the above are true

Answer 28

c. An inducer molecule would cause the DNA binding protein to bind to the DNA

Question 29

Which of the following is NOT true of positive control of transcription? a. An activator protein must bind to DNA at the operator site b. Promoters tends to be weak in comparison to those used in negative regulation c. Binding of the activator protein can cause bending of the DNA d. Activator proteins may physically interact with the RNA polymerase e All of the above are true f. None of the above are true

Answer 29

a. An activator protein must bind to DNA at the operator site

Question 30

Which of the following is NOT true in regard to transformation? a. DNA binding complexes resemble a type IV pilus/fimbriae b. DNA is shortened during transport across the cell membrane c. Expression of single-stranded binding proteins is increased d. Bacteria exhibit variations in when transformation occurs and how much of the population that will be able to take up DNA e. All of the above are true f. None of the above are true

Answer 30

e. All of the above are true

Question 31

True or False A constitutive protein is only expressed at certain times during a bacteria's lifetime.

Answer 31

False

Question 32

True or false A riboswitch mechanism of regulation at the translational level usually mediates recognition of the Shine Dalgarno sequence by the small ribosomal subunit.

Answer 32

True

Question 33

True or False In a two-component regulatory system, the sensor kinase is an integral protein found in the cytoplasmic membrane and will undergo autophosphorylation at a specific histidine residue when its environmental cue is sensed.

Answer 33

True

Question 34

True or False A point mutation that changes a codon from CCU to GCU is likely a silent mutation.

Answer 34

false

Question 35

True or false Base analogs will only induce mutations when DNA is actively replicating.

Answer 35

True

Question 36

True or False Intercalating agents are more likely to result in frameshift mutations rather than a point mutation.

Answer 36

True

Question 37

True or False Bacteria within the Proteobacteria phylum are all Gram-negative.

Answer 37

True

Question 38

Though they occur at different levels, post-translation versus transcription respectively, what is a SIMILARITY in the mechanisms used in feedback inhibition and that used in the repression mechanism of negative control?

Question 39

Based on what you learned in class - Potterase, Cookase, and Gruwellase are examples of_______ which means__________________

Answer 39

isoenzymes,

Question 40

Is the following statement most likely true or false?: Both small regulatory RNAs and riboswitches involve a metabolite binding to the mRNA via complementary sequences. Please defend your answer!

Question 41

Based on what you learned in class, describe how proline can be regulated at the transcriptional level using an attenuation mechanism a. What would be necessary within the leader Sequence for this attenuation mechanism to work?

Answer 41

proline receptors and a continuous chain of the same amino acids

Question 42

When proline is in high concentrations - what sections will be involved in a secondary structure and what is the effect of the secondary structure?

Answer 42

C and D form a stem loop structure which will prevent the DNA polymerase from entering

Question 43

T/F Attenuation mechanisms are common in all three domains of life.

Answer 43

False

Question 44

Explain what would happen in a two component regulatory system if the phosphatase became mutated and could no longer functioned?

Answer 44

the system would never be able to shut down

Question 45

Provide TWO reason why mutations are easier to study in prokaryotes rather than eukaryotes.

Answer 45

faster generation time, no copies