DNA, RNA, Protein Flashcards
In what direction is DNA synthesized?
5’—->3’
What enzyme catalyzes DNA synthesis?
DNA polymerase
Is DNA conservative or semiconservative?
Semiconservative as each DNA strand serves as a template for synthesis of a new DNA strand
Where does DNA replication occur and in what direction?
At the origin of replication and occurs bidirectionally
What causes spontaneous mutations?
frequency of errors in DNA replication
How does proof reading occur/ how is fidelity maintained during DNA replication?
3’—->5’ exonuclease activity of DNA polymerase
What does DNA gyrase do?
Removes positive supercoils
What are restriction enzymes?
They cut DNA producing a double strand break at a specific recognition sequence.
Why do bacteria produce restriction enzymes?
To degrade invading DNA such as virus DNA
How do bacteria protect their own DNA from restriction enzymes?
Methylation protects a bacterium’s DNA from its own restriction enzymes
How is transcription different in eukaryotes vs. in bacteria?
-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
What is the role of a sigma factor?
Allows RNA polymerase to recognize specific promoters to initiate transcription
What is rho- dependent termination?
-it involves the rho protein
what is rho independent termination of transcription?
- 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
Protein synthesis: Compared with elks, proks have;
-smaller ribosomes with different structure, fewer initiation factors
-coupling of transcription and translation
-polycistronic mRNA
How is translation different in eukaryotes vs. in bacteria?
-fmet starting codon for bacteria
-Met starting codon for eukaryotes
-bacteria have shine delgarno ribosome binding site
-eukaryotes have kozak sequence
What is a start codon?
its where translation begins
-AUG, UUG, GUG
What is protein processing?
The process that converts polypeptides into a mature protein
Examples of of covalent modifications
Cleavage, disulfide bond formation
What are the role of GroEL and GroES?
Chaperone proteins involved in folding
What is translocation?
The movement of molecule from one location to another
What is protein export?
Translocation out of the cytoplasm
What is protein secretion?
translocation through all membranes to extracellular environment
What are signal sequences?
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
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?
⇰ 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
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?
-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
Give a examples of how some type III secretion system
effectors work.
-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
What kind of secretion system do Agrobacterium tumefaciens use?
Type IV
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?
-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
What is type VI(6) secretion?
-translocates toxin proteins to eukaryotic cells or other bacterias
-evolved from bacteriophages structures
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?
-⇝ 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
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?
-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
