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Microbiology Y2S1 > Genetic Engineering > Flashcards

Genetic Engineering Flashcards

0
Q

Give 2 ways in which an oligohistidine tag be added to a protein?

A

1) cloning the protein coding sequence in-frame in an expression vector with an oligohistidine tag coding region
2) adding the coding region by PCR before cloning into vector

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1
Q

What is the name of a feature that can be associated with a recombinant protein that allows purification?

A

Oligohistidine tag

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2
Q

What is the type of chromatography used to purify an oligohistidine tagged protein?

A

Affinity

Immobilised, Ni-NTA

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3
Q

How does the resin in affinity chromatography allow protein purification?

A

Resin bind ps diva lent metal ions

Histidines coordinate to free positions on metal ions

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4
Q

How can a protein be eluted from a chromatography column using a histidine tag?

A

Use imidazole

Has structure similar to histidine = competition

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5
Q

How would you check whether your protein is pure?

A

Use SDS-PAGE to check molecular mass and any contaminating proteins

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6
Q

What is a fluorescent molecule?

A

Absorbs light at shorter wavelengths and emit at longer wavelength

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7
Q

What is labeled with a fluorophore during immunofluorescence?

A

Antibody, by cross-linking

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8
Q

3 advantages of fluorescent proteins in cellular imaging

A 
Used in live cells
Multiple colours
Genetically encoded
Intrinsic fluorophore
Can be used as tag for other proteins of interest
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9
Q

Disadvantages of fluorescent protein?

A

Low brightness
Complex photo physics such as dark states
Large size
PH sensitivity

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10
Q

You have purified the regulatory protein ‘X’, thought to bind to upstream regulatory region of ‘Y’ gene, the nt sequence of which is known.
What reagents do you need to perform a gel shift experiment to confirm this interaction?

A

Labelled ‘Y’ gene regulatory sequence
Purified ‘X’ protein

OR!!!
Cell fractions and antibody to ‘Y’

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11
Q

What does a DNA footprint analysis show?

A

Nt region where a protein binds to a regulatory gene

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12
Q

What reagents are required for DNA footprint analysis?

A

Radio labelled regulatory region
Your protein of binding
DNase I

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13
Q

Described the steps in immunoprecipitation using an antibody against a protein of interest

A

1) Treat living cels with cross linking agent, formaldehyde
- -> this will cross link the regulatory region with the protein
2) lyse the cells
3) sonicate DNA to shear into fragments
4) use antibody to co-ppt your protein bound to target sequence
5) remove protein using protease
6) sequence DNA (binding site will be common to all purified fragments)

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14
Q

State the fuels needed for successful Quikchange mutagenesis

A

At least 25nt long
Ideally G or C at 3’ ends
High Tm phosphorylation

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15
Q

Using NaOH raises pH, does this degradation RNA or DNA?

A

RNA

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16
Q

What’s the function of Bal31

A

Removes nucleotides from both 5’ and 3’ ends of a double stranded DNA molecule

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17
Q

What is the function of exonuclease

A

To remove nucleotides from the 3’ end of DNA molecules

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18
Q

What are isochizomers?

A

Restriction enzymes from different bacteria capable of recognising the same restriction site

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19
Q

What is the purpose of high stringency conditions in terms of nucleic acid hybrids?

A

To destabilise less stable nucleic acid hybrids

Include a low salt concentration and a temperature close to the Tm

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20
Q

Briefly describe the process of nick translation

A

DNase I used to introduce single stranded breaks into DNA at random sites
Exploits 5’-3’ Pol activity and 5’-3’ exonuclease of E. coli DNA Pol

1) Enzyme binds to nicks created by DNase I
2) removes nts and replaces with labelled nts

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21
Q

What’s the relationship between E. coli Klenow fragments and random hexanucleotide primers?

A

Random hexanucleotide primers are used in different labelling procedure called random primer method using the Klenow fragment of E.coli DNA polymerase

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22
Q

What do you need to do first before cloning DNA?

A

Purify it

1) grow cells in culture
2) spin cells down
3) lyse cells
4) apply to affinity column (usually silica)

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23
Q

What is the purpose of an oligodT column?

A

To separate mRNA from other RNAs

mRNAs possess polyA tail which binds to strings of T residues

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24
Q

What are the initial steps in cloning for purifying vector DNA?
What about for target DNA (genomic, cDNA, silico sourced)

A

Vector

1) digest circular plasmid with restriction enzymes
2) alkaline phosphatase treat to remove 5’ Ps

Target DNA
Either
— digest DNA with restriction enzyme
— PCR amplify fragment with carefully designed primers and digest

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25
Q

What steps follow in basic cloning after genome purification?

A

1) ligate digested Vector and target DNA
- –> gives mixture of vector and recombinant a
2) transform into E. coli
3) plate onto agar with antibiotic
4) only cells containing the plasmid will grow
5) get a clone through replication colonies
6) screen colonies to identify those with recombinant clone
7) colony PCR or plasmid isolated & restriction digest

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26
Q

Outline PCR

A

Add template, nts, polymerase, buffer and primers
95 — 55 — 72
Denature the DNA
Allow binding of primers
Allow thermos table polymerase to copy DNA between primers

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27
Q

Why should you avoid complementary primer sequences

A

Production of primer dimers
Get no replication of DNA as a result
Appear as thick band at bottom of agarose

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28
Q

Primer sequences don’t need to be perfectly complementary
But why should they be at the 3’ end
Why is that advantageous for the 5’ end?

A

Region of extension
Need to ensure specificity of annealing to correct target sequence

Can add different sequences for mutagenesis, recombination, manipulation, addition of Restriction enzyme

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29
Q

What is the purpose of the origin of replication

A

To allow autonomous replication from the genome

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30
Q

Why would you add restriction sites to a clone

A

To allow insertion into a vector, e.g. pET28

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31
Q

What does the reaction vessel for PCR contain?

A

0.2-0.5ml of polypropylene

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32
Q

How would you analyse the DNA fragments from a PCR reaction?

What kind of fragments would move fastest/slowest?

A

Agarose gel electrophoresis
Supercoil will most fastest bc compact

Introduce a nick produces open circular = significantly slower

Second strand break produces linear = quicker than open circular

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33
Q

What are the 3 types of ends produced by restriction enzymes

A

5’ overhang = EcoRI
Blunt end = Pvu II
3’ overhang = Kpn I
Some enzymes recognise different sites but generate the same sticky ends

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34
Q

Why is alkaline phosphatase used to treat the plasmid vector before inserting your DNA?

A

Removes 5’ phosphates to prevent self ligation

Mixture need inactivation first at 37 for 30 mins to prevent insert from being dephosphorylated as well

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35
Q

How are vector and insert DNA joined?

A

Ligase buffer containing ATP and DNA ligase

Cells repair missing phosphate in vector

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36
Q

Following a ligation reaction of your insert into a plasmid vector, what steps follow next?

A

1) Aliquot transformed into E. coli cells
2) treated with CaCl2 to disrupt cell walls
(Frozen stored at -80)
3) then thawed on ice adding 40-50ng DNA
4) heat shocked for 1-2 mins at 42 to take up DNA

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37
Q

What is another method apart from antibiotic resistance to show the presence of the recombinant plasmid?

A

LacZ blue white selection

White colonies indicate the presence of an insert in lacZa which disrupts beta galactosidase formation

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38
Q

What are the advantages and disadvantages of using a prokaryotic expression system?

A

Advantages

  • large quantities
  • numerous expression systems can be tested
  • high throughput

Disadvantages

  • poor functional expression of eukaryotic proteins
  • problems with solubility of multi domain proteins
  • little post translational modification
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39
Q

What are the advantages and disadvantages of eukaryotic expression systems?

A

Advantages

  • good functional expression if eukaryotic proteins
  • expressed proteins have native fold
  • post translational modification (glycosylation)

Disadvantages

  • small quantities
  • limited number if expression systems
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40
Q

Give examples of prokaryotic and eukaryotic expression systems

A

Prokaryotic
Yeast cells - saccharomyces
Prokaryote - e.coli

Eukaryotic
Mammalian cells - HEK293
Insect cells - DES S2
Fungal cells - aspergillus

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41
Q

What are the advantages and disadvantages of using E. coli as an expression system?

A

Advantages

  • simple and rapid culture
  • easy to transform
  • well characterised
  • range of vectors/markers

Disadvantages

  • requires cDNA (no introns)
  • lacks much lost-translational processing
  • possible protein stability/solubility/toxicity issues
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42
Q

Why do you need to optimise codon usage within an expression organism?

A

1) E.g. certain E. coli strains have additional tRNA genes to enhance expression
2) mutate critical codons to more commonly used codons
3) Re synthesise the complete gene to reflect codon usage

Some codons in heterologous genes may inhibit protein synthesis as they are rarely used by the expression host

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43
Q

3 examples of promoters that could be used in expression systems

A

Tac
Arabinose
T7

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44
Q

What role does IPTG play in T7 system

A

Causes induction of T7 RNA polymerase to act on the polymerase to product large amounts of recombinant protein
Cells enter stationary phase with no continued growth

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45
Q

Explain the process of autoinduction for glucose and lactose

A 
Cells grow on glucose to high cell density
Glucose depletes
Cells use lactose
Convert to allolactose
Switches on gene expression
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46
Q

Why can secondary mRNA structures affect translation

A

Prevent efficient translation initiation and access to RBS or initiating ATG

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47
Q

How can we improve translation and subsequent product expression

A

Introduction of N terminal silent mutations into first 6 codons preventing mRNA secondary structure around the ATG

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48
Q

How could we increase transcription of a fungal enzyme galactose oxidase when expressed in E. coli?

A

N-terminal silent mutation enhances expression in VITRO by preventing mRNA secondary structure around ATG
Silent mutations in first 6 codons
‘GO’ construct in Bl21 Star (DE3)
Mutation in rne gene (rne131) = an RNAse responsible for mRNA degradation

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49
Q

What is Strep tag affinity purification?

A

Use of streptactin binding to protein of interest

Trp-ser-his-pro-gln-phe-glu-lys

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50
Q

What are the advantages of using yeast as an expression system?

A 
Flexibility
Some eukaryotic post translational modifications
Maintenance of multiple plasmids
Cheap and easy to grow
Well characterised

However DOES NOT work with all proteins

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51
Q

Describe Pichia pastoris

A 
Methylotrophic yeast
AOX1 promoter produces up to 5% mRNA
Yields 30% total cell protein
Genetically similar to saccharomyces
Low transformation efficiency
Not identical glycosylation to mammals
Potentially very high yields:
1) 2.5g/l soluble/secreted
2) 1.3g/l cytoplasmic
3) 1mg/l membrane
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52
Q

In terms of expression from a vector, what are the differences between saccharomyces and Pichia?

A

Saccharomyces = autonomous or integration into genome
Pichia = must integrate into genome to be expressed
(Either by single or double cross-over event)

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53
Q

What does real time PCR entail?

A

Measuring the amount of amplified DNA by measuring fluorescence emitted during each cycle rather than at a fixed endpoint
Simple and sensitive

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54
Q

How does SYBR green work and why would you use it in preference to ethidium bromide?

A

Bind to double stranded DNA and fluoresces
Ratio between ds and ss is much higher than EB
Fluoresces much brighter than ethidium bromide

SYBR green doesn’t bind ssDNA

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55
Q

What two probes can be used in real time PCR?

Briefly describe how they work

A

Hydrolysis based probes
— e.g taqman (5’-3’ exonuclease, digests end of probe to release reporter group)
Use reporter quencher system, when separated fluoresces

Hybridisation based probes
E.g. Beacons and fret probes
Base pair with DNA changing their 3D structure
FRET = fluorescence resonance energy transfer
Uses 3’ donor fluorophore and 5’ acceptor fluorophore
When brought in close proximity 5’ fluoresces (occurs only after hybridisation)

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56
Q

What is the cycle threshold in RTPCR?

A

When the PCR mixture fluorescence exceeds the threshold fluorescence
(Baseline produced with no template)
Use these values to creates melting curve to assess DNA quality
Plot change in fluorescence against temp

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57
Q

Give 3 applications of RTPCR

A

Quantification of infectious agents (HIV, HPV)
Analysis of gene expression at mRNA level
Genotyping

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58
Q

Why is traditional OCR only semi-quantitative?

A

Insensitivity of ethidium bromide

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59
Q

Name 4 methods for quantification of mRNA

A

Northern blotting
Ribonuclease protection assay
In situ hybridisation
Reverse transcription PCR

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60
Q

Why is RTPCR a good technique to use for quantification of mRNA?

A

Most sensitive of all techniques
Discriminates between closely related mRNAs
Technically simple
Only requires small amount of mRNA

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61
Q

How do you calculate the ratio of target transcript in experimental and control samples from a northern blot?

A

(Fold change in target transcript) / (fold change in reference transcript)

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62
Q

In RTPCR what criteria should ‘standards’ fulfil?

A

Same copy number in all cells
Expressed in all cells
Expression doesn’t change when conditions of cell growth are changed
Medium copy number = correct more accurate

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63
Q

Give some examples of commonly used standards in RTPCR

A 
Glyceraldehyde-3-phosphate dehydrogenase mRNA
Beta-actin mRNA
MHCI mRNA
Cyclophilin mRNA
mRNAs for certain ribosomal proteins
(RPLP0)
28S or 18S rRNA
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64
Q

What is the importance of controls in RTPCR?

A

Negative (no DNA) = checks reagents for contamination
No reverse transcriptase control = detects if signal from contaminating DNA
Positive = checks reagents/primers working (especially important for showing absence of gene)

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65
Q

On a graph of RTPCR, where should the threshold value be overlapping?

A

Should be in the linear part of the reaction

Should be high enough for showing reactions due to amplification and not noise

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66
Q

What would a standard curve graph show for series 10 fold dilutions in RTPCR?

A

CT values for dilutions against concentration
Linear graph
Excellent correlation coefficient, >0.99

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67
Q

What is the efficiency deltadeltaCT method?

A

Approximation method
Assumes:
1) minimal correction for standard gene
2) standard and target have similar efficiencies
2deltadeltaCT value assumes efficiencies at 100%

DeltaCT = target - ref
Difference = deltaCT(control) - deltaCT(experimental)
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68
Q

Name 4 techniques used to detect protein

A

Immuno dot blots
Western blot analysis
Immuncytochemistry
Immunoprecipitation

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69
Q

What technique is used to detect protein DNA interactions?

A

Chromatin Immunoprecipitation

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70
Q

What technique is used to detect protein-protein interactions?

A

Co Immunoprecipitation

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71
Q

What’s the difference between monoclonal and polyclonal antibodies?

A 
Poly = recognise different regions, have different affinities for protein
mono = only one region (produced using clonal cell line)
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72
Q

What are 2 ways in which proteins can be labelled directly?

Give 2 pros and cons of this

A

Radioactive
Fluorescent (FITC green or rhodamine red)

Pros: convenient, simple
Cons: health risk, potential poor signal

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73
Q

What does indirectly antibody labelling entail?

A

Secondary antibody that recognises constant region of primary antibody
Secondary antibody linked to fluorophore or fluorescence releasing enzyme (e.g horseradish peroxidase)

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74
Q

Describe the process of chromatin Immunoprecipitation

A

Determines DNA sequences bound by specific proteins or modified histones

1) cross link DNA and proteins and isolate chromatin
2) sonicate or digest chromatin
3) immunoprecipitate, reverse cross link and purify DNA
4) PCR amplify target sequences

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75
Q

Name 4 ways in which you can analyse ChIP products and describe what they reveal

A

1) PCR - does the protein bind
2) qPCR - quantify level of protein binding
3) microarray - determine if protein binds to large no. Of different sequences and its relative affinity
4) ChIPSeq - determine all sequences bound by protein

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76
Q

Describe the 3 steps in immune cytochemistry

A

1) FIX cells with formaldehyde = crosslinks protein and preserves structures
2) PERMEABILISE cells using detergent
- e.g. Triton X-100 or methanol/acetone = puts holes in membrane
3) VISUALISE using secondary antibody with fluorescence of enzyme reaction

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77
Q

What is immunohistochemistry used for?

Describe the steps involved

A

Measures rate of protein synthesis/degradation

1) incubate cells with 35S Met for set time (pulse)
2) incubate cell with excess unlabelled Met (chase)
3) make protein extracts at several time points
4) immunoprecipitate with antibody
5) run on SDS-PAGE
6) quantify 35S label in protein

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78
Q

What is immunocyto- and immunohistochemistry used for?

A

Protein localisation and co-localisation

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79
Q

What proteins are used in Immunoprecipitation for recovery of poly and monoclonal antibodies?
How do they facilitate this process?

A

Protein A and G
Type G Streptococci
A from staphylococcus aureus

Both bind constant region of IgG
Both can be linked to agarose/magnetic beads/solid supports

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80
Q

What does in VITRO protein synthesis complement?

A

Co-Immunoprecipitation

1) take wheat germ or reticulocytes
2) lyse cells
3) spin to remove nuclei, mitochondria and plasmids
4) products can be used in GST pull-down experiments

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81
Q

What do GST pull down assays detect?

A

Detect protein-protein interactions in VITRO

1) express GST-fusion of protein in E. coli
2) purify via GST beads
3) in VITRO transcribe and translate prey protein

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82
Q

Name 3 essential features of vectors

A

Ability to :

1) replicate in host cell
2) be readily introduced into host cell
3) readily insert foreign DNA into vector

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83
Q

Why are plasmids not the vector of choice for cloning gene clusters or making genomic libraries?

A

Gene clusters from humans have larger genomes which exceed max. packaging limit

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84
Q

Name 3 features of bacterial host needed for efficient transformation

A

1) host deficient in natural restriction modification systems
e. g. E. coli B instead of K intrinsically have less protease activity (from deletion of hsdR gene)
2) required stable maintenance of transformed DNA = avoid rearrangements by using mutants in recombination genes (recA or recF)
3) disabled host for safety reason = auxotophic on metabolite only produced in lab to prevent growth if accidentally released

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85
Q

Give 4 features of natural plasmids

A

1-100kb
1-1000 copies per cell
Replicate independently of chromosome
Carry e.g. Antibiotic resistance

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86
Q

What are the essential features in a plasmid for use as a vector?

A

ORI (15-20 per cell)
Selectable marker
Suitable region for DNA insertion (restriction sites)
Suitable size

87
Q

Give an example of a typical plasmid cloning vector

A 
pUC19
2686 bp
>500 copies per bacterial cell
Possess lacZ gene
Contains poly linker = multiple restriction sites
88
Q

Name 2 ways for plasmid uptake into bacteria

A

Chemical transformation - CaCl2 and heat shock

Electroporation

89
Q

What is the genome size for insertion into bacteria?

Why is this a problem for creating genomic libraries?

A

0 to 10kbp
Eukaryotic genes are much larger
Size limitation and poor transformation efficiency for making genomic library, construction tricky

90
Q

Describe genome organisation in bacteriophage lambda

A

Genome 49kb
Linear double stranded DNA, present in phage particles
Single stranded complementary termini of 12nt called cohesive ends

91
Q

What is the purpose of cohesive ends in the bacteriophage lambda genome?

A

Allows recircularisation which initiates replication

Site of joining is called a cos site, producing a circular concatemer

92
Q

What are the 2 life cycle stages of bacteriophage lambda?

A

Lysis
DNA replication, phage product synthesis, phage release
Lysogeny
Integration of lambda into host genome

93
Q

Briefly describe the Lytic pathway in lambda phage

What kind of replication

A

Rolling circle mechanism
Replication starts at ORI
Produces long catenane, cut at cos sites to produce whole genome fragments
Head and tail assembled separately

94
Q

Describe the process of concatenation packaging into phage prehead

A

Concatenation cleaved at cos site packaging into pre head
(Phage encoded endonuclease)
Fixed length is always packaged (packaging constraint)

95
Q

Name 4 different methods of distinguishing an ‘empty’ vector (no insert) from a recombinant molecule (insert present)

A

1) differential antibiotic resistance (plasmids such as pBR322)
2) lacZ complementation (plasmids and phage)
3) Spi selection (specific for lambda replacement vectors)
4) ci selection (insertion and replacement vector)

96
Q

Describe the lacZ gene

A

Encodes beta-galactosidase
N terminal 146 AA portion inserted into cloning vector (promoter and alpha-peptide)
This region is inactive
Vector contains regulatory sequences to bind repressor = repressed

97
Q

How and what visual changes occur during lacZ complementation to identify plasmid uptake into E. coli cells

A

Plasmid engineered to produce n terminus alpha peptide
Vector engineered to produce c terminus beta peptide

Add IPTG (lacZ inducer) and X-gal (chromogenic substrate)
Active beta gal by alpha complementation produced
Observe blue colonies

98
Q

Poly linker cloning site of parent vector is situated within the middle of the lacZa gene. Does this affect its synthesis
What happens if foreign DNA is inserted into this site?

A

No

Disrupts alpha peptide production
Therefore no beta gal formed
White colonies or plaques

99
Q

Chemical transformation of phage DNA into E. coli is inefficient
How is it inserted?

A

Using normal phage infectivity

100
Q

Describe the packaging constraints of phage lamba

A

Cannot exceed 50kb
Only DNA molecules of 78-105% of wild type (48kb) can be packaged
gt10 = commonly used vector
contains unique EcoRI site within cl gene encoding Lytic gene repressor = inactivation means no lysogen formation = plaques are clear not turbid

101
Q

How would you make phage lamba accept larger inserts?

A

Remove DNA for non-essential lytic growth
20kb of integration and excision
gt10 vector contains 43.8kb genome, therefore takes up 9kb
CHARON series vectors can take up 22kb

102
Q

What is the lower packaging limit in phage?

A

Limit otherwise cannot be propagated

Cannot delete more than 25% wild type

103
Q

What does the Klenow fragments of E.coli DNA polymerase lack compared to the wild type?

A

5’ to 3’ exonuclease activity

104
Q

What does formamide do to the Tm of nucleic acid hybrids?

A

Lowers it

105
Q

Give four facts regarding illumina sequencing

A

Based on reversible cycle-terminators technology
Is a massively parallel sequencing technology
Clinical amplification of DNA fragments occurs on a surface
Sequencing of bacterial chromosomes to detect chromosomal mutations is now routine

106
Q

Cells from the liver express a different set of genes compared to cells from the brain. What techniques can be used to measure these differences?

A

Microarray analysis
Western blot
Northern blot
2D gel electrophoresis

107
Q

What kind of vectors are usually used for cloning cDNA?

A

Lambda replacement vectors

108
Q

What two purposes does production of a fusion protein have in bacteria

A

Improve stability of foreign protein

Assist purification of the foreign protein

109
Q

does GFP require cofactors of substrates in order to produce fluorescence?

A

No

110
Q

What does sanger sequencing require and how does it separate fragments?

A

Dideoxynucleotides
Radioactively or fluorescently labelled deoxynucleotides

Separates by size

111
Q

Vectors containing specific promoters such as phage T6 or SP7 promoter can be used to do what?

A

Generate riboprobes

112
Q

What does cassette mutagenesis involve?

A

Replacing a restriction fragment with a synthetic DNA region containing appropriate mutations to be studied

113
Q

What does the Quikchange system for high efficiency mutagenesis use DpnI for?

A

Digest the original wild type template DNA

114
Q

In gel shift analysis, what does the addition of an excess of unlabelled DNA sequence do?

A

Decrease the mobility of the radio labelled DNA-protein complex

115
Q

DNaseI can be used for what?

A

Foot printing the protein binding sites of a promoter

116
Q

Which is more stable, RNA/RNA or DNA/RNA hybrids

A

RNA/RNA

117
Q

When using biotin as a non-radioactive label for probes, what reagents can be used to carry out detection of the probe

A

Avidin

Biotin-conjugated alkaline phosphatase

118
Q

Describe creation of a replacement vector

A

To create a vector, central non essential region is substituted with stuffer fragment
Approx. same size as wild type
Stuffer contains restriction sites for cutting itself into small pieces to prevent its own reinsertion during cloning
Replaced during cloning, designed to carry larger DNA, up to 22kb

119
Q

In VITRO packaging what happens?

A

Introduce recombinant concatemer into e. Coli by in VITRO packaging into phage particles
Will package any molecule so long as has cos sites separated by 37-50 kb

120
Q

Steps to making a cosmic library

A

Propagate cosmic vector as a plasmid

Cleave with restriction enzymes, add foreign DNA and ligate to form concatemer

121
Q

Why can a recombinant cosmic not initiate the Lytic cycle

A

Lacks gene required for lambda particle production
Instead produce colonies on ampicillin plates
Acts as plasmid in e.coli

122
Q

Briefly describe bacteriophage M13

What is the advantage of these in terms of size of insert

A

Filamentous phage
Single stranded DNA, 6.4kb
No head particle, just gets longer
Problem with large inserts = prone to rearrangements

123
Q

How does M13 phage infect e. Coli for delivery of insert DNA?

A

Usually used for phage display
Male specific phage
Host needs to contain f plasmid to produce f pilus
M13 binds to F pilus, internalised
Converted to dsDNA and purified like a plasmid

124
Q

How do you clone using M13 to produce plaques?

A

Mix transformed e.coli with non-infected e. Coli
Add too agar
Infected cells release more phage = infect neighbours
Produce slow growing plaque of uninfected cells
M13 does not kill the host

125
Q

With plaques of e. Coli and M13 containing an insert, what steps follow for isolation of this DNA?

A

Inoculate e. Coli culture with plaque of infected cells
Grow liquid culture
Pellet bacteria
Either:
1) isolate ds recombinant DNA using regular plasmid prep
2) isolate ss recombinant DNA from released phage in supernatant

126
Q

Why would we need to use cloning by expression and/or functional assays?

A

When no DNA or AA sequence available but have clearly defined functional property/antibody to protein
Functional assay in e. Coli or mammalian cell
Make library in expression vector

127
Q

Describe the process for gene cloning by expression in e.coli

A

Transfer plaques expressing fusion protein to nitrocellulose filter
Incubate filters with available antibody to desired protein
Antibody binds to plaque with protein
Secondary antibody could with dye-based detection
Western blot reveals location

128
Q

Name three ways in which you could detect a protein expressed in e. Coli and identify which clones contain these

A

Antibody labelling
Isolation of clones by membrane hybridisation (autoradiography and radiolabelled probe)
Degenerate oligonucleotide hybridisation marking

129
Q

How can we make use of degenerate oligonucleotides for hybridisation to identify a clone containing a protein

A

For a 6 amino acid protein partial sequence

1) Make oligonucleotide mixture
2) Comprises 8 different oligos containing all possible DNA sequences that can encode all six amino acids
3) one of the oligos will be fully complementary to gene

Or could make guessmer based on known preference of codon usage in organism

130
Q

How could you isolate clones containing your protein using membrane hybridisation?

A

Nitrocellulose/nylon filter make copy of plate
Treat filter to denature DNA (NaOH, bake)
Hybridise with radio labelled probe (65)
Wash off unhybridised probe (65)
Perform autoradiography
Signal appears over colony/plaque complementary to probe

131
Q

Name 3 requirements of genomic DNA a when preparing for insert
What size fragments are usually inserted into replacement and Cosmid vectors

A

Pure, high MW, free of nicks

Replacement = 20-25kb
Cosmid = 40kb

Avoid complete digestion otherwise fragments are too small

132
Q

What kind of enzymes can you use to partially digest genomic DNA

A

EcoRI (GAATTC) = once per 4096bp
BamHI (GGATCC) = once per 4096bp
Sau3A (*GATC) = once per 256bp

133
Q

How would we use the DNA of a whole genome in separate phage to reconstruct the genome?

A

Align the sequences and look for the same sequences at the start and end and match up

134
Q

Briefly describe the sanger/dideoxy method of sequencing

A

Enzymatic approach
Extend a primer strand against a template strand
4 reactions, each terminated by different dideoxy analogue
ddNTP lacks 3’OH
Strand elongation is not possible is 3’OH is missing

135
Q

What 3 activities does E. Coli DNA polymerase possess?

A

5’-3’ exonuclease (repair)
5’-3’ DNA synthesis
3’-5’ exonuclease (proof-reading)

136
Q

What 2 assays can be used to test for lambda growth?

A

Liquid culture assay
— add phage stock to bacteria, culture
— lysogenisation goes from milky to clear beer
Plaque assay
— add aliquot of mixture to ‘top agar’ and pour onto agar
— turbid plaques

137
Q

What can peptide mass fingerprinting facilitate the identification of?

A

Gene that encodes a protein that has been separated when using 2D SDS-PAGE

138
Q

How would you digest a genomic library for insertion into a vector

A

Partially digest
Frequently cutting restriction enzymes
E.g. Sau3A
Purify fragments within desired size range (20-25kb) by gel electrophoresis or sucrose gradient centrifugation
Once packaged into phage, each one contains distinct piece of genomic DNA

139
Q

For insertion of target DNA into a cloning vector, what should the ligation reaction mixture contain?

A

Suitable buffer
Plasmid and insert DNA
DNA ligase
ATP, energy for formation of phosphodiester bond between nt strands

140
Q

What are some non-radioactive labels used in nucleic acid hybridisation?

A

Biotin
— fluorescently labelled streptavidin
— alkaline phosphatase linked streptavidin
Digoxigen
— using primary anti- and secondary antibody
— direct binding to anti-DIG antibody
(Both fluorescently labelled)

141
Q

What are some of the uses of nucleic acid hybridisation?

A

Analysis of gene expression/complex restriction maps
Screening gene libraries
Identifying mutations/mRNs size and conc
Identifying restriction fragments carrying target gene

142
Q

Give some examples of uses of in situ hybridisation

A

Detecting:

1) infectious agents
2) mRNA temporal/spatial gene expression
3) gene expression in diagnostics
4) genetic defects/chromosome mapping

143
Q

Give an example of a well known proto-oncogene and its analysis by in situ hybridisation and treatment regime

A

HER2 (ERBB2) - encoding 185kDa transmembrane tyrosine kinase receptor
Promotes cell division/survival, inhibits apoptosis
Herceptin - humanised monoclonal antibody has positive outcome for breast cancer treatment

144
Q

Give four uses or site directed mutagenesis

A

Creating desired sequence changes
Investigating role of DNA/RNA
Understanding protein structure/function relationships
Creating new proteins

145
Q

What were some of the problems with early site directed mutagenesis approaches? How were they solved?

A 
Poor ligation (phosphorylate primer, improve conditions)
Strand displacement (T4/7 pol)
Mismatch repair (mutL/S
Mutant recovery often less than 0.1%
146
Q

What is the general principle of high efficiency mutagenesis approaches?

A

Once template has been used to copy mutant strand it is of no further use and can only reduce mutant recovery

147
Q

What is the purpose of an amber stop codon

A

Read as a stop codon or glutamine in different e. Coli stains

148
Q

What is the limited size of synthetic oligonucleotides that can be made for site directed mutagenesis?

A

About 60nt

149
Q

What is the purpose of fusion tags?

A

Easy identification and purification of protein
Improved stability/folding
Added N or C terminal of in-frame

150
Q

What needs to be removed when adding first a C terminal fusion tag and secondly an N terminal fusion tag

A 
C = stop codon to create fusion with tag
N = start codon so that fusion tag is not missed
151
Q

2 ways to detect tagged protein

Recombinant protein expression

A

Coomassie stained gel

Western blot detection of 6His tag

152
Q

Why may we want to remove a fusion tag in recombinant protein expression? How can this be done?

A

Purposes of crystallising the protein
Or when protein is large (e.g. maltose binding protein)

At gene cloning stage, incorporate site for protease cleavage enzyme
After purification, protein passed through column again and enzyme added to remove fusion tag

153
Q

How would you add a promoter in recombinant protein expression?

A

Usually provided by the vector

Can put in during PCR

154
Q

Name 2 ways in which protein expression can be switched on during recombinant protein expression

A

Tac
pBad
Lac

155
Q

Describe how the tac promoter works in recombinant protein expression

A

Lac repressor binds to operator preventing RNA polymerase binding
Induced upon addition of IPTG or autoinduction

156
Q

Describe how pBAD promoter works in recombinant protein expression

A

Arabinose or ramnose utilisation operon respond to increasing concentrations of their corresponding compound in growth medium

157
Q

Describe show the lac promoter is used in recombinant protein expression

A

IPTG induction
Autoinduction
IPTG binds to repressor molecule allowing e. Coli RNA pol to transcribe T7 RNA polymerase
IPTG has also bound to repressor on other operator
T7 RNA pol can transcribe gene of interest

158
Q

How may we improve the translation of proteins when designing a gene for recombinant protein expression?

A

Insert a signal sequence after the ATG to cause secretion into periplasm
Periplasm is an oxidising environment = favours formation of disulphide bonds

159
Q

What kind of promoter causes constitutive activation for expression of RNA transcription?

A

CMV promoter

160
Q

Name four types of expression and how they are activated

A

Constitutive - permanently active promoter e.g. CMV
Inducible - hormone/drug/metabolite-dependent binding
Transient - short period when no selection for vector in expression cell
Stable - permanent expression by the host cell

161
Q

How are eukaryotic cells grown by tissue culture?

A

Sterile flask (25-300cm2)
Contain necessary nutrients and bicarbonate buffer
Incubators - 37 degrees, O2/N2/CO2
Mostly cancer cells - immortalised/rapid growth/amenable to vector introduction

162
Q

Name 4 ways to get foreign cDNA into a eukaryotic cell cultured in vitro

A

Lipofection (DNA/lipid complex
Electroporation
Spontaneous uptake using Ca2+ complex or polycationic carrier
Successful only for small proportion of cells
Use viruses to deliver DNA

163
Q

Give examples of viral and mammalian promoters that can be used within mammalian expression systems

A

Viral - SC40, CMV, MMTV

Mammalian - actin, heat shock protein

164
Q

Name the components of a typical mammalian expression system and the use of each component

A

PCMV & polyA - drive mRNA transcription
PS40, NeoR & polyA - selection in stable transformed cells
AmpR & ORI - drive replication and allow antibiotic selection in e.coli

165
Q

How does the tet-on system function in mammalian expression systems

A

Engineered transcription activator protein binds to tetracycline response element only in the presence of antibiotic (tetracycline-like doxycycline)

166
Q

Describe the tet-off system in mammalian expression systems

A

Transactivator is modified to normally bind to promoter allowing transcription
Addition of antibiotic prevents Transactivator binding to promoter = transcription terminates

167
Q

What is the function of the 2 plasmids required for tet-on/off systems in mammalian expression systems?

A

1) contains cDNA for protein of interest downstream of promoter
2) drives expression of Transactivator and contains selectable marker

168
Q

Briefly describe the natural life cycle of baculoviruses spodoptera

A

1) viral particles with polyhedron coat protein digested
2) alkaline gut pH dissolves particle, capsids released
3) capsids taken up by epithelial cells
4) replicate using host cell machinery
5) bud off from infected cell using gp64

169
Q

In which 2 ways can a recombinant baculoviruses genome be created?

A

Double cross-over recombination

Transposons-mediated recombination

170
Q

For organisation of baculoviruses vectors, what components are required for replication in e. Coli and independently integration with baculoviruses DNA to create backed DNA

A

E.coli
— lacZ, f1region, AmpR, ORI

Integration
— Tn7L&R, GenR, pPolh, MCS, SV40 polyA

171
Q

What are the reported yields for insect cell expression in both baculovirus sf9 cells and drosophila S2 cells

A

Baculovirus
Soluble: intracellular = 10-25mg/l, secreted 18-40 mg/l
Histamine receptor/substances P receptor: total protein = 0.1-3.9 ug/mg

Drosophila
Soluble (dopamine hydroxylase): 16mg/l secreted
Glucagon receptor: 12ug/mg total protein
Dopamine receptor: 200ng/mg total protein

172
Q

How would using viruses other than baculoviruses in mammalian expression systems be advantageous?

A

Lentivirus - good for transfecting ‘difficult’ cells e.g. Primary cells
Adenovirus - gives potentially higher expression levels

Special containment needed even though not component in autonomous replication

173
Q

Briefly describe lentivirus structure

A 
RNA
E.g. VSV
Core shell, p24
Surrounded by membrane envelope overlying matrix protein
Contains gp41 and gp120
174
Q

Briefly describe the lentivirus life cycle in 293T cells

A

1) host transfected with virus and packaging mix of helper plasmids for replication and assembly
2) viral RNA transcribed, exported from nucleus
Recognised by psi sequence and new virus cores assemble
3) virus core binds to virally encoded envelope glycoproteins at inner plasma membrane

175
Q

What components would a lentiviral expression plasmid need to contains? (Lenti-X)

A 
3' and 5' LTRs
Psi viral packaging protein recognition
RRE, WPRE - RNA stability/nucleus export
cPPT - increased infectivity
PCMV - target transcription promoter
PPGK - constitutive expression promoter of antibiotic marker
176
Q

Name and briefly describe the 4 steps required for turning siRNA into a drug

A

1) sequence selection
- – Bioinformatics and in VITRO screening for cytotoxicity on off-target cells
2) synthesis and modifications
- – Chemical stabilisation - methylation may change specificity
3) packaging and delivery
- – Eliminates off target effects/deals with immune response/cytotoxicity/clearance from organism/accumulation in unwanted tissues
4) targeting
- – recognition of specific cells

177
Q

How can you study differential gene expression

A

Measuring mRNA abundance

Looking at protein abundances (IEF and 2D separation)

178
Q

What animal model is frequently used for studying gene expression

A

Nematode worms
C. Elegans
80% of animals on earth and these
899 cells

179
Q

Briefly describe 3 experiments of showing that genes are not lost during differentiation

A

Adult frog and unfertilised egg - egg nucleus destroyed and injected with adult nucleus, normal embryo and tadpole form

Carrot section - proliferating cell mass - separate in liquid medium - single cell - organised clone of diving cells - young embryo - carrot

Cows
Epithelial cells from oviduct fused with unfertilised egg with removed meiosis spindle and associated chromosomes
Reconstructed zygote and embryo eventually form young calf

180
Q

Give 2 examples of changes in gene expression caused by gene amplification
Very rare

A

2 chorion genes in drosophila
Structural protein for eggs shells
Amplified 16 or 64 fold

Xenopus egg rRNA genes
Needed in massive amounts
Excised to form circular plasmids to allow 3000x amplification

181
Q

Name 4 methods for direct detection of transcripts via hybridisation

A

Northern blot
In situ hybridisation
Quantitative PCR
Microarrays

182
Q

What kind of reporters could you use to detection of a protein?

A

Fluorescence (GFP)

Enzymatic (beta-gal, beta-glucuronidase, luciferase)

183
Q

Briefly describe GFP

A 
Natural product of aequorea victoria
238 aa long
11 strand beta barrel
Central chromosohore
No required cofactors of substrates
1hour time lag
184
Q

For enzymatic reporters, where would each one typically be used and what changes would be detected

A

Beta galactosidase
Not in plants as beta-gal is naturally high
Blue colour

Beta glucuronidase
Blue colour

Luciferase
Photinus pyralis or renilla
Needs luciferin substrate

185
Q

What is cassette mutagenesis used for?

A

Inserting DNA fragments of up to 100bp between restriction sites

186
Q

What is PCR mutagenesis used for?

A

Removes the limitation of length from cassette mutagenesis

187
Q

What is sticky feet mutagenesis used for?

A

Insertion of fragments above 100bp to several kbp

188
Q

Is there a limit of how big a deletion can be made in deletion mutagenesis?

A

No

189
Q

What is saturated mutagenesis used for?

A

Random mutagenesis throughout the sequences

Generates all possible mutations are a specific site in a narrow gene region

190
Q

Briefly describe affinity chromatography

A 
Specific binding of protein due to tag
Load NTA resin with nickel divalent ions
Load lysate with tagged protein
Wash off any unspecific binding 
Eluted with imidazole having competitive binding with his tag
Pure protein is eluted
191
Q

Briefly describe streptag streptactin purification

A

Similar principle as hexa histidine purification
Collect cells and lyse
Centrifuge and purify supernatant with your recombinant tagged protein
Binds to streptactin via streptag (mimics biotin)
Competitive binding with desthiobiotin
Pure protein eluted

192
Q

Briefly describe the tet on and tet off systems

A

Tet-on
Engineered transcription Activator protein binds tetracycline responsive element upstream of DNA only in presence of antibiotic
Tet-off
Modified Transactivator Constitutively binds to promoter to allow transcription
Antibiotic added prevents this = no transcription of gene

193
Q

Briefly describe the steps in baculovirus as a vector

A

Gene of interest subcloned into transfer vector
Second vector contains parts of baculovirus particle
Both recombine in specially engineered e.coli cells to form bacmid DNA by recombination between tn7 sites of transfer and compatible bacmid site
Introduce bacmid DNA into sf9 or sf21 insect larval cells

194
Q

What steps would you take to ensure successful transfection of your insert into the vector

A

Recover your bacmid DNA
Check for insert using PCR not electrophoresis bc too big
Transfect insect cells
Recover recombinant virus produce from strong polyhedrin promoter
SDS-PAGE and immunoblotting for time-post infection

195
Q

Briefly describe the process of RNA interference

A

Binds to DICER (endonuclease) = fragments approx. 21nt
Short fragments bind to argonaut protein
Guide strand selected, other degraded
Forms RISC complex (RNA induced silencing complex)
siRNA directs RISC to mRNA binding through complementarity
Argonaut catalyses cleavage of mRNA which is degraded

196
Q

Briefly describe the process of miRNA

A

Processed in nucleus by drosha/pasha complex
Binds to DICER
Then argonaut
The ‘seed’ guides RISC
Imprecise pairing with mRNA allows targeting of hundreds of endogenous mRNAs
RNA degradation of translation inhibition

197
Q

Briefly describe quantitative PCR

A

Reverse transcribe mRNA in cDNA
PCR with fluorescently labelled primers of dye that binds dsDNA
Fluorescence emitted when product made
Rate of product appearance relates to concentration of mRNA

198
Q

What is the even skipped gene (Eve) required for and in what organism

A

Drosophila
Essential gene
Defines body segment formation
Discrete stripes, well characterised

199
Q

What causes eve expression?

A

Long upstream region 7.3kb
Controls:
1) switching on of expression
2) defining where eve is expressed (stripe 1-7)

200
Q

How could we define the eve gene sequence?

A

Substitute eve ORF for a reporter ORF and see where the gene is expressed
Make random deletions to the regulatory region
Introduce altered genes into eggs
Does expression still occur?

201
Q

What 3 ways could deletions be made to a regulatory region to define it?

A

Restriction enzyme digestion
Nucleases digestion
Site directed mutagenesis

202
Q

Explain briefly the use of restriction enzyme digestion for analysing use of a gene

A

Make first set of deletions
Look for expression
Make smaller deletions in critical region

203
Q

Describe briefly the use of nuclease digestion in elucidating gene use

A

Restriction digest
Exonuclease III digest 3’ termini of exposed DNA duplex
Ligate back together
Make bigger deletions for time course

No need to multiple restriction sites
Don,t depend on position of enzyme site
Can rapidly introduce variety of deletions

204
Q

What 4 methods could be used for studying protein?
2 for what proteins binds
2 for where they bind

A

Gel mobility. Shift assay
Affinity chromatography

DNA footprint analysis
Chromatin Immunoprecipitation

205
Q

Briefly describe gel mobility shift assay

A

Make ‘hot’ DNA fragment
Fractionated cell proteins by centrifugation
Mix fractions with “hot’ DNA
Find which cell proteins bind to ‘hot’ regulatory region
Use antibody to elucidate protein

Relies of DNA movement slower when bound to protein
DNA moves in proportion in size on gel

206
Q

Describe the use of DNA affinity chromatography

A 
Make DNA fragment of regulatory region
Attach to solid matrix and line on column
Add protein, only protein binds to DNA
Eluted with salt
Defines which proteins bind
207
Q

Briefly describe DNA footprint analysis

A 
Purify your protein
Make 'hot' regulatory region
Bind DNA and protein
Add DNase I
Protein protects binding site
Run hot DNA fragments on gel with control
208
Q

Briefly describe chromatin Immunoprecipitation

A

Treat living cells with formaldehyde to crosslink
Extract genomic DNA protein complex
Cleave in 300 bp fragments
Some will contain bound protein - purify with antibody
Remove protein using nuclease
Determine nucleotide sequence of bound proteins

209
Q

How could you arrange the expression of the eve reporter in all cells of the drosophila embryo

A

Introduce plasmid by injection into G0 embryo
Transposons integrates into nuclei at embryo pole
Pole nuclei become pole cells (form germline)
Foreign genes now in germline
Transgenic organisms are the offspring of these modified organisms

210
Q

How do you get a reporter gene construct to express in other higher organisms?
And how would you screen for the gene?

A

Pronuclear micro injection of 200-300 gene copies to the fertilised egg before fusion of the nuclei
fertilised eggs divide forming early embryo
Embryo implanted into uterus of surrogate mother developing as normal
Time consuming - wait for 3 weeks for birth
Insertion random, success rate low

211
Q

How would you get a reporter gene construct to express in other higher organisms using embryonic stem cell transfection?

A 
Transgene introduced into stem cells, grown to colonies
Combine with early embryo
Forms hybrid embryo
Hybrid incubated in female mouse
Screen offspring
No need for intita, microinjection
Screening doesn't involve live animal
212
Q

How could you use gene transfer in plants?

A 
Agrobacterium tumefaciens
Mediated by natural plasmid called Ti
Use T-DNA repeat for transfer of gene
Gene of interest flanked by T-DNA repeat
Bacterium infects plants
Grow into crown gall and plant
Antibiotics used to select for transgene recipients
213
Q

How do you get plasmids into cells for expression of your protein?

A

Transfection:
1) liposomes - cationic detergents, high efficiency
2) calcium phosphate - low efficiency, unknown mechanism
Electroporation
(placed in electric field, pore forms, DNA diffuses in, high efficiency)
Bombardment
(fires 0.3-1.6um gold particles, coated with DNA/RNA, used for gene delivery)

214
Q

What is another way to study the function of gene X or protein X other than altering its expression or looking for its expression in different cells etc.?

A

Prevents it correct expression
Knock out or knock in mutants
Replace functional gene with non functional gene using homologous recombination
Then infected stem cells, grow colonies, combine with early embryo = hybrid! incubated in female mouse! screen offspring

Microbiology Y2S1 (4 decks)

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