DNA, RNA, Protein

Question 1

In what direction is DNA synthesized?

Answer 1

5’—->3’

Question 2

What enzyme catalyzes DNA synthesis?

Answer 2

DNA polymerase

Question 3

Is DNA conservative or semiconservative?

Answer 3

Semiconservative as each DNA strand serves as a template for synthesis of a new DNA strand

Question 4

Where does DNA replication occur and in what direction?

Answer 4

At the origin of replication and occurs bidirectionally

Question 5

What causes spontaneous mutations?

Answer 5

frequency of errors in DNA replication

Question 6

How does proof reading occur/ how is fidelity maintained during DNA replication?

Answer 6

3’—->5’ exonuclease activity of DNA polymerase

Question 7

What does DNA gyrase do?

Answer 7

Removes positive supercoils

Question 8

What are restriction enzymes?

Answer 8

They cut DNA producing a double strand break at a specific recognition sequence.

Question 9

Why do bacteria produce restriction enzymes?

Answer 9

To degrade invading DNA such as virus DNA

Question 10

How do bacteria protect their own DNA from restriction enzymes?

Answer 10

Methylation protects a bacterium’s DNA from its own restriction enzymes

Question 11

How is transcription different in eukaryotes vs. in bacteria?

Answer 11

-prokaryotes only have one RNA polymerase while eukaryotes have more than one.
–most bacterial mRNA are polycistronic(encodes more than one protein}
-bacterial genes have operons
-bacterial mRNAs have no introns, no polyA tails, no 5’ caps

Question 12

What is the role of a sigma factor?

Answer 12

Allows RNA polymerase to recognize specific promoters to initiate transcription

Question 13

What is rho- dependent termination?

Answer 13

-it involves the rho protein

Question 14

what is rho independent termination of transcription?

Answer 14

• involves an inverted repeat which forms a stem and loop structure in the RNA and a series of A residues that form weaker A-U basepairs which allows the transcript to be released

Question 15

Protein synthesis: Compared with elks, proks have;

Answer 15

-smaller ribosomes with different structure, fewer initiation factors
-coupling of transcription and translation
-polycistronic mRNA

Question 16

How is translation different in eukaryotes vs. in bacteria?

Answer 16

-fmet starting codon for bacteria
-Met starting codon for eukaryotes
-bacteria have shine delgarno ribosome binding site
-eukaryotes have kozak sequence

Question 17

What is a start codon?

Answer 17

its where translation begins
-AUG, UUG, GUG

Question 18

What is protein processing?

Answer 18

The process that converts polypeptides into a mature protein

Question 19

Examples of of covalent modifications

Answer 19

Cleavage, disulfide bond formation

Question 20

What are the role of GroEL and GroES?

Answer 20

Chaperone proteins involved in folding

Question 21

What is translocation?

Answer 21

The movement of molecule from one location to another

Question 22

What is protein export?

Answer 22

Translocation out of the cytoplasm

Question 23

What is protein secretion?

Answer 23

translocation through all membranes to extracellular environment

Question 24

What are signal sequences?

Answer 24

A sequence of 15-30 amino acids found at N-terminus of polypeptides destined for export from the cytoplasm
-are usually cleaved off when the protein is exported

Question 25

For some biotech drugs, companies engineer bacteria (such as E. coli) to
produce large quantities of a certain human protein (e.g. insulin or human
growth hormone). Reviewing what you have learned in this chapter, what are
possible obstacles to expressing functional human proteins in bacteria?

Answer 25

⇰ presence of introns in human genome-E.Coli doesn’t have a splicesome to deal w/ them
⇰ E. coli might not recognize Kozak sequence
⇰ E. coli strain might have restriction enzymes that would degrade the human protein
⇰ E. coli’s start codon is f-Met while human protein has Met
⇰ human protein would need a promoter that allows its transcription in bacteria
⇰ needs correct post-translational modifications

Question 26

How does a type III secretion system work? What is the destination and
function of effector proteins secreted by a type III secretion system? What
would happen to a bacterium if the genes encoding its type III secretion system
proteins were deleted?

Answer 26

-required for virulence
-type III secretion systems are activated upon contact with host cells
-delivers effector protein directly into the cytoplasm of eukaryotic host cells or into extracellular space
-function of the effector protein is to mimic the host proteins to control host cell function
-loss of genes encoding type III secretion system would prevent the bacteria from spreading virus

Question 27

Give a examples of how some type III secretion system
effectors work.

Answer 27

-Tir: improves E.coli adherence to intestinal cells
- YopT: cleaves isoprenyl groups from Rho CTPase, releasing them from their normal plasma membrane location, which then prevents phagocytosis by macrophages that normally clears Yersinia from the blood.
-SopE(salmonella): GEF that activates the small GTP binding proteins altering the cytoskeleton of the host cell so that normally nonphagocytic cells engulf the invading bacteria into the vacuole where they can grow

Question 28

What kind of secretion system do Agrobacterium tumefaciens use?

Answer 28

Type IV

Question 29

How does a type IV(4) secretion system work? How is a type IV secretion
system different from a type III secretion system? Explain how the type IV
secretion system helps Agrobacterium tumefaciens cause disease. Why is A.
tumefaciens often used in the genetic engineering of plants?

Answer 29

-related to bacterial conjugation system(transfer of DNA during conjugation)
-mediates protein and DNA translocation
-can transfer DNA, protein, and DNA-protein complexes
-transfers effector proteins directly into host or surrounding environments
-found in pathogens such as agrobacterium tumefaciens
-> a piece of Tsi plasmid, the tDNA is injected into host cells by the type IV secretion
-> T-DNA integrates into the chromosome of the plant and causes the cell to churn out plant growth hormones to form gall and to synthesize nutrients from the bacteria

Question 30

What is type VI(6) secretion?

Answer 30

-translocates toxin proteins to eukaryotic cells or other bacterias
-evolved from bacteriophages structures

Question 31

Describe the role of the Tse proteins, Tsi proteins, and T6SS of P.
aeruginosa. How does the T6SS provide a competitive advantage against other
nearby bacterial species?

Answer 31

-⇝ Tse1 and Tse3 are effector proteins sent to periplasm of recipient cells via T6SS to degrade peptidoglycan, thus killing the bacterial recipient
⇝ Tsei proteins are “immunity” proteins that bind to Tse1 and Tse3 in periplasm, protecting donor bacteria from self-intoxicating

Question 32

Imagine that you had a bag full of eukaryotic and bacterial cells in front of
you, and that you could reach in and pull out one of the cells. With the
“mystery” cell in hand, what questions would you like to ask (regarding its DNA
replication, transcription, translation, and protein processing) that would help you
decide whether the cell is eukaryotic or bacterial?

Answer 32

-how any RNA polymerase are there
- does it have a shine delgarno or kozak sequence
- are the chromosomes linear or circular
- are there histones or no histones
-what is the starting codon