Molecular Bio

Question 1

Plasmids

Answer 1

Double-stranded circular DNA molecules found in a cell, separate and apart from the chromosome of the cell
Many contain genes for antibiotic resistance

Question 2

Plasmids ori

Answer 2

Origin of replication
Allows them to replicate inside the cell
If source DNA were not joined to a DNA molecule with an ori (vector), the source of DNA would not be replicated in cell

Question 3

What makes a plasmid an attractive vector

Answer 3

If a plasmid can replicate to high copy number in a bacterial cell

Question 4

PCR

Answer 4

Polymerase Chain Reaction
a way to replicate DNA in a test tube
Uses heat rather than helicase to separate DNA strands
DNA primers elimintae need for primase
One enzyme used, DNA polymerase from a thermophilic bacterium. Because it will not denature at high temps
Repeated cycle of strand separation, primer annealing, and new strand elongation can amplify a billion fold

Question 5

Advantages of PCR

Answer 5

Ability to amplify tiny amounts of source DNA
Amplify a particular region of source DNA defined by the primers chosen
SPEEED

Question 6

Restriction enzymes

Answer 6

Cut large pieces of DNA into smaller fragments.
Double-stranded DNA-specific endonucleases
Bind to certain sites on double helix and break phosphodiester bonds linking nucleotides
Also, make a staggered cut in DNA

Question 7

Palindrome

Answer 7

Generally a 4-6 base sequence that a restriction enzyme recognizes and cuts

Question 8

XbaI

Answer 8

Recognizes TCTAGA in DNA. When it cuts it leaves 4 base, single stranded ends
Cuts on the 3’ side of the T in both strands
resulting in
5’T CTAGA 3’
3’ AGATC T 5’

Question 9

Sticky ends

Answer 9

Hydrogen bond to another identical sticky end by complementary base pairing
The two ends can then be covalently linked by DNA ligase

Question 10

DNA ligase

Answer 10

If a plasmid is opened by cutting with a restriction enzyme, a DNA fragment from another organism cut with the same enzyme can be pasted into it. The foreign DNA will be replicated with the plasmid

Question 11

Transformation

Answer 11

Only a few bacteria are naturally transformable. Most are not able to because cell membrane is impermeable to DNA
We use E. Coli as the recipient of our recombinant plasmit

Question 12

pGEM-3Z

Answer 12

Plasmid that carries a gene for ampicillin resistance (bla), transformed cells can be selected by growth on medium containing ampicillin. Cells without it will be killed

Question 13

Ampicillin

Answer 13

derivative of penicillin blocks synthesis of peptidoglycan, the main component of bacterial cell wall.

Question 14

B-lactamase

Answer 14

bla produces this enzyme, which breaks down ampicillin before it can interfere with cell wall synthesis

Question 15

MCS

Answer 15

Multiple cloning site
Present in pGEM-3Z
Region where a dozen different restriction enzymes have a unique cleavage site
MCS is near the start of the lacZ gene carried by the vector
Insertion of the foreign DNA in the MCS disrupts the lacZ gene and allows screening for reocmbinants by blue/white selection

Question 16

Outcomes of transformation
Cell does not take up plasmid
Cell takes up plasmid without gfp gene
Cell takes up plasmid with gfp gene inserted

Answer 16

Cell dies on Amp plate because no bla gene
Cell grows on Amp plate but does not glow
Cell grows and glows

Question 17

pGLO

Answer 17

Plasmid used as source for gfp, originally isolated from jellyfish
Modulates the green color of light

Question 18

GFP

Answer 18

gfp regulated by presence of the sugar arabinose
Downstream of an araC-dependent promoter.
Will not be made unless arabinose is present

Question 19

AraC protein

Answer 19

Made from a plasmid gene, serves as a repressor for GFP production in the absence of arabinose
When sugar is added to growth medium, AraC changes conformation and stimulates GFP synthesis

Question 20

What was our aim

Answer 20

Take the gfp portion of pGLO and move it into pGEM-3Z
Use PCR to selectively amplify an 831 base pair fragment,
Trim that down using XbaI, and drop it into XbaI site of pGEM-3Z
This would separate gfp from the promoter that controls its expression (pBAD, where AraC protein binds
Making GFP expression independent of arabinose

Question 21

Agarose gel electrophoresis

Answer 21

Helps predict the size of DNA fragments after being cut. Cast by melting agarose in buffer and pouring the warm liquid into a mold. Once the gel hardens, DNA samples can be loaded into wells at one end
An electric field is applied across the gel
DNA will migrate to the anode (positively charged electrode)
DNA must move through pores in the gel matrix
Short DNA fragments do this easier, so they migrate faster
Rate of migration is inversely proportional to the log of fragment length
Location of DNA in gel can be determined by staining gel with fluorescent dye that intercalate of the double helix
When UV light is shined on stained gel, DNA bands glow orange. The intensity of staining is proportional to the amount of DNA. Can tell concentration of DNA

Question 22

Gel concentrations

Answer 22

Higher 2% agarose concentrations, lead to smaller pores for small fragments 100-1500 BP
Lower concentrations (0.5%) best for large fragments (5,000-50,000)

Question 23

Column Chromatography

Answer 23

Separates and purifies proteins based on some property they possess
Size, charge, hydrophobicity, or binding specificity
Cell extract loaded on a column containing bead matrix
Some proteins stick to the beads, others pass.
In a second pass, conditions can be changed, so some proteins no longer stick to the beads and elute.
GFP is hydrophobic
Under salt conditions, GFP will fold so the hydrophobic residues face inward and do not interact with water.
High salt- proteins will denature
Result is that GFP residues will be exposed
If passed over a column with hydrophobic beads, then it will stick to them strongly
As lower salt concentration, GFP will become normal again and no longer stick to beads

Question 24

Column Chromatography Results

Answer 24

1. Binding buffer: 2M (NH4)2SO4——GFP denatured. Sticks to beads
2. Wash buffer 1: (NH4)2SO4—–GFP denatured. Sticks to beads
3. Wash buffer 2: 0.4M (NH4)2SO4—-GFP denatured. Sticks to beads
4. Elution buffer: 0M (NH4)2SO4—-GFP refolds. Washes off columns

Question 25

Calculating Transformation Efficiency

Answer 25

To naturally transform E. Coli, mix with DNA, heat shock at 42 degrees C, small % will take in DNA Our sample contains about 0.1 microgram of DNA

Question 26

Part 1

Answer 26

Given solution of pGLO DNA. Some for transforming cells, others serve as template in PCR reaction to amplify gfp. Premade PCR cocktail has enzyme, buffer, nucleotides, and primers

Question 27

Part 1 Transformation

Answer 27

Add 2 microliters pGLO DNA to 200 microliters competent HB101 cells in microcentrifuge tube. Ice for 20 minutes Transfer tubes to 42 degrees C water bath leave for 90 seconds. Put on ice for 90 seconds. Heat cold shock helps uptake of DNA Transfer 100 microliter cells to nutrients plate with ampicillin Spread remaining 100 microliter cells on plate with ampicillin and arabinose Incubate at 37 degrees C for one day and kept at 4 degrees C

Question 28

Part 1 PCR

Answer 28

Add 2 microliters pGLO DNA to 23 microliters premixed PCR cocktail in a sterile PCR tube. Put tube in thermocycler. Run for 25 cycles i) 1 minute at 95 degrees C to denature ii) 1 minute at 52 degrees C to let primers anneal iii) 1 minute at 72 degrees C for strand elongation Stored in fridge

Question 29

Part II PCR cleanup | Get ride of dNTPs, primers, etc may interfere with digestion

Answer 29

Add 125 microliters PBI buffer to PCR sample in PCR tube Put combined 150 microliters into spin column in a 2 ml collection tube Centrifuge for 1 minute at max speed. Linger fragments will remain bound to matrix while primers, nucleotides, etc will flow through Discard liquid, keep tube Wash column by adding 750 microliters PE buffer. Centrifuge for 1 min at max speed Discard flow through and put column back Centrifuge for 1 minute at max speed, ensuring dryness Put column in clean 1.5 ml centrifuge tube. Discard collection tube Add 30 microliters elution buffer to column and sit for 1 minute. Longer fragments will be released from matrix Centrifuge for 1 min at max speed PCR product is liquid in tube

Question 30

Digestion

Answer 30

Dispense 16 microliters of cleaned PCR product into a microcentrifuge tube. Add 4 microliters of XbaI enzyme plus buffer mix Dispense 16 microliters pGEM-3Z vector into second tube Add 4 microliters XbaI enzyme plus buffer mix Incubate both at 37 degrees C for 45 minutes

Question 31

Heat inactivation of XbaI

Answer 31

Both digestion tubes in 65 degrees C for 10 minutes | Ensures ligation is not undone

Question 32

Ligation

Answer 32

``` Join fragment and vector Clean tube Transfer 8 microliter cut PCR product to tube Add 8 microliter cut vector DNA Add 4 microliter ligase and buffer mix Spin Incubate ```

Question 33

Transformation 2

Answer 33

Add 200 microliters competent HB101 cells to ligation mix Sit on ice 20+ minutes Heat shock at 42 C for 1 minute Transfer 100 microliters cells to Amp plate Incubate

Question 34

Purification of GFP

Answer 34

2 microcentrifuge tubes add 1 ml of pGLO to each Spin at 10k for 5 minutes Pour supernatant fluid in waste Resuspend each pellet in 125 microliter TE plus lysozyme Incubate at 37C for 15 minutes Quick freeze cells in dry ice Thaw in 37 C bath SPin for 10 minutes Combine supernatant fluid from both tubes Add 250 binding buffer Run whole volume through column and collect eluate in tube 1 Add 250 wash buffer 1 over column, collect in tube 2 Add 250 wash buffer 2, collect tube 3 Add 500 elution buffer, collect tube 4 Cap bottom, add 1ml equilibration buffer, cap top Use UV light to see which has GFP

Question 35

Assay for beta-lactamase

Answer 35

Transfer 100 microliters eluate from tubes to new tubes. Put 100 microliters DI water in 5th tube Add 100 microliters indicator solution to each tube/ Vortex Check for clearing