EXAM2_L20_Molecular_Bio_in_Medicine Flashcards Preview

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_________ are bacterial enzymes that cut ______DNA into smaller pieces. They cut in a ______specific and ____ specific manner.

What is an example? Where does it cut? what does it cut?

Restriction endonucleases cut DOUBLE STRANDED DNA


ie. ECOR1 cuts between G/A of sequences GAATTC


Cohesive/sticky ends
Blunt ends

sticky ends sometimes have 2-4ntds overhanging

DNA fragments made by SAME restriction enzyme an be joined together again by DNA ligase


Molecular Cloning-
3 parts needed for a vector

covalently binding recombinant DNA into a vector to make Copies

Vector is Circular dsDNA capable of auto replication inside a host cell.

1. Multiple Cloning Sites (one or more palindrome seq.)
2. Antibiotic resistance
3. Origin of Replication (for auto replicate of vector)


3 Steps to creating a recombinant DNA molecule

1. Vector cleaved w/ restriction endonuclease
2. Cleave foreign DNA with SAME Restriction Enzyme
3. Add DNA ligase to join DNA pieces covalently

Product (recombinant molecule) can be put in bacteria to make large amount of copies.


Gel electrophoresis
What does it do?
What gels used?

Separates DNA by its size
-Uses electricity (migrate to positive end)
-Smaller migrate further
AGAROSE- large pores (separates big differences in size)
POLYACRYLAMIDE- (Small pores- separates one base pair difference)


The Sanger Sequencing method: ddNTPs
(Dr. Fred Sanger)

This works because ddNTP's stop elongation at each A,T,G,C site and at each length.
Small pieces to large sequences will be plotted in the correct nucleotide channel to indicate the nucleotide, and the gel electrophoresis will separate pieces by size and indicates Where that (A,T,G,C) is in the sequence.

This allows us to get a perfect sequence of the template

dideoxyribonucleotides (ddNTPs)
- derivatives of dNTPs without the 3' OH group
-chain terminates w/o 3' OH

1. Template DNA to be sequenced is added to 4 flasks
2. Primer & dNTPs added to each flask equally
3. Radiolabeled ddNTP's added to each flask individually
(ddATP, ddTTP, ddCTP, ddGTP) *one in each flask
4. DNA polymerase added
5. Polyacrylamide electrophoresis run for each flask (A,T,G,C)
6. Sequence read for SIZE (bottom to top) to display sequence of the template.

The new sequence is IDENTICAL to the original strand that the template came from


Fluorescent DNA sequencing (automated)

Improved Sanger Method:
One tube One lane,
Each ddNTP labeled with different dye
Each color ID'd w/ laser & computer


4 components
3 steps
How many molecules per cycle?

1 tube, 4 components
1. dsDNA template
2. excess of 2 sets of DNA Primers (one for each strand)
3. excess dNTPs
4. DNApol (taq. poly)- heat stable

1. Denature (95C)- separates DNA
2. Anneal (55C)- primers bind each template strand
3. Elongation-synthesizes w/ DNApol

#molecules= 2^n (n= #of cycles)



makes DNA from mRNA (NEAT!)
1. mRNA converted to cDNA via reverse transcriptase
(copy of gene w/ EXONS only- lacks introns)
2. cDNA used as template for PCR (amplification)


Blotting & Hybridization
What 3 types of blots?
What material analyzed for each?
What do each detect?
What probe used for each?

Detecting Specific DNA, RNA, PROTEIN in a contaminated mixture
1. Southern (DNA)- detects #copies of a gene or to detect specific genes in DNA--- radioactive/floresc DNA label

2. Northern (RNA)- detects sizes & amounts of mRNA (transcriptional regulation)---radioactive/floresc DNA label

3. Western (Protein)-detects amount of Proteins & differences in post-translational modification
(translational regulation)--- enzyme-linked antibody


4 General steps of blotting?

1. Electrophoresis (separation by size) DNA,RNA,Protein
2. Transfer "blot" onto membrane
3. bind Labeled probe
4. Visualize by autoradiography or chemiluminescence


How do you detect specific nucleic acids?

What is in situ hybridization?

Base pairing between complementary strands of DNA or RNA.
- Denature at high temp
- re-anneal at low temp with hybrid label strands

In situ- detects DNA or RNA sequences in chromosomes or intact cells


DNA Microarrays "DNA Chips"

thousands of DNA sequences on a microchip
-each spot is a gene
1. genotyping (genetic testing) -Uses DNA
2. Gene expression profiling (genomic test)
- use mRNA converted to cDNA via RT-PCR
-detects how much mRNA being made


Two types of microarrays?

1. Genotyping (genetic test)- Seq of DNA- AMPLICHIP
(what type of protein being made?)

2. Gene expression profiling (genomic testing)
Type/quantity of mRNA
(how much mRNA is being made?) ie: cDNA microarray


Genetic vs genomic testing

Genotyping (genetic testing) - amplichip
-test sequence of DNA (what type of protein being made)

Gene expression profiling (genomic testing)
- How much mRNA is being made? (use cDNA microarray)


What type of test to use when trying to find out what type of proteins are being made?

What test used to find out how much mRNA being made?

type/seq. DNA- Genetic testing- amplichip

# mRNA (Genomic testing)- gene expression profiling- cDNA microarray


CYP (cytochrome P450)
What does CYP enzyme activity tell us?
How does it vary?
Why is this useful?
What does it help us avoid?

Enzymes that hydroxylate drugs

-CYP enzyme activity SHOWS how fast a drug will be metabolized

- Activity varies between genetic differences in each person

CYP genotype informs physicians how to adjust medication dosages and prevent adverse drug responses


AmpliChip CYP450
uses what?

What medications is this very useful for?

WBC blood sample, amplified by PCR, analyzed on microarray to determine CYP2D6, and CYP2C19 alleles

Psychotropic Medications
-commonly lack response or have adverse reactions
-phenotype specific dose adjustments could be helpful for these types of drugs


What 4 types of categories can amplichip450 put a person in?

Ultrarapid metabolizers, (need higher doses)
Extensive, intermediate (need decreasing doses)
Poor metabolizers (decrease dose/remove from medication)

if you metabolize the drug too fast, you need higher dosage (or else the drug won't work)

if you metabolize the drug too slow you need lower dosage (or else you can overdose)


How does CYP450 Enzymes work for prodrugs?
Opposite as normal activated drugs

A Pro-drug becomes active when metabolized:

Hypermetabolizers will have adverse affects (activation too fast)

Slow mebabolizers will not feel affects of drug (cant get activated)


Classes of metabolized drugs- % metabolized- polymorphisms

antidepressants, antipsychotics, beta blockers
~25% of all drugs metabolized
-5 major polymorphisms (27 detected by test)



Antidepressants, antiepileptics, proton pump inhibitors
-5% metabolized
-2 major polymorphisms (3 detected by test)


CYP3A4 (not amplichip)

analgesics, anticonvulsants, antidepressants, antihistamines, antipsychotics, local anesthetics
-40% metabolized
>70 known polymorphisms (rare, not on amplichip)