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41 Cards in this Set

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  • Back
Describe the four types of mutations causing activities.
1. tautomeric shift (TH: keto -> enol) (AD: amino -> imino)

2. ionizing radiation (xray, gamma ray -> one or two strand break)

3. uv radiation (pyrimidine dimers)

4. chemicals
- base analogs (5BRU)
- free radicals (O^3)
- deamination (ADENINE -> hypoxanthine)
- alkylation (methylbromide, ethylene oxide)
- intercalating agents (proflavin)
Describe some of the DNA repair mechanisms.
1. BER (incorrect base at a specific bp)

2. NER (lesions in the genome - could be small regions or entire chromosomes)

3. AP endonuclease (baseless / apurinic sites)

4. Post replication mismatch repair

5. 3' -> 5' exonculease activity (transcription - gene repair)

6. Repair of double-strand breaks
- homologous (good)
- non-homologous (bad, adds more mutations)
DNA glycosylase is specific for cleaving this mutation.
C -> U deamination -- specifically cleaves the uracil base but leaves the glycosidic bond in place but this too must be removed
If a base has been removed during the repair mechanism phase, what enzyme comes along and cleaves the glycosidic link?
AP endonuclease
How do the repair mechanisms distinguish an old strand from a new one?
Bacteria: The old strand has either pyrimidine dimers or has certain bases methylated

Humans: The new strand is the one with the nick and therefore mismatched base
This base is a mutational hotspot.
5-methyl-cytosine --- it is deaminated to thymine which causes an incorrect bp to form

C -> G [This no longer happens]
T -> A [This now happens after several replications]
What are four DNA repair defects and their diseases?
1. Xeroderma Pigmentosum
- autosomal recessive
- defect of genome-wide NER

2. Cockayne Syndrome
- autosomal recessive
- defect of transcription-coupled NER

3. HNPCC (non-polyposis colon cancer)
- autosomal dominant
- defect post-replication mismatch repair

4. Ataxia-telangiectasia
- autosomal recessive
- defect in PK involved in (non)-homologous end joining
Most DNA is 5 - 7% _______________.

Why is this important?
Negatively supertwised

This favors unwinding via Type I (swivelase) as it doesn't require ATP
Topoisomerase Type II is the target of _____________ and _______________.
Antibiotics and chemotherapy
What are some of the inhibitors of Type II Topoisomerase?

How do they work?
Ciprofloxin (prokaryotes)
Doxorubicin (eukaryotes)

The inhibitors cause strand breakage in the chromosome
What is the major functional difference between DNA polymerase I and III?

Why is this?
DNA polymerase III starts from where RNA primer left off and finishes to the end

DNA polymerase I remove the RNA primer and lays down DNA in its place
- It is the only one to have 5' -> 3' exonuclease activity
UV damage and repair is initiated by this complex.

- Make nicks before and after the area of damage
What are snRNA and what is their function?
snRAN are small RNA molecules found in the nucleus.

They are important in RNA splicing and telomere maintenance.

They are referred to as SNRNP (snurps) = spliceosome complex
What are the components of the RNA polymerase holoenzyme?
alpha, beta, beta prime, and sigma
Which component of the RNA polymerase first bind to the Shine-Dalgarno sequence?
Sigma subunit
What are the two types of transcription terminal signals?

Which one is used in emergency situations (e.g. cell low on energy)?
1. GC stem loop

2. Rho
- This is used in emergency situations as Rho can race down the mRNA strand and create a hairpin loop
Name two elongation factors tin both prokaryotes and eukaryotes where energy is spent.
EF-Tu (pro) & eEF-1A (euk) = bind all aminoacylated tRNAs, GTPase

EF-G (pro) & eEF-2 = translocation, GTPase
Achondroplasia (ACH) is a form of dwarifism. The mutation which causes this disease is a ______ which in turn causes this change to happen?
Single nucleotide polymorphism

- The codon for glycine (GLY) becomes changed and instead codes for arginine (ARG)
Restriction enzymes can leave two different types of ends. What are they and which one is better for integrating with a genome?
Blunt and sticky ends

- Sticky ends aid in genome integration because they have 1 or more bases protruding from each end
What are the steps and raw supplies needed for PCR?

Discuss what is needed at each step of the way.
* Require double stranded DNA
* Require two different RNA primers, one for each strand

Step 1: Heat solution to denature/de-anneal DNA strands

Step 2: Add RNA primer to the solution

Step 3: Cool down the solution to allow annealing of primer to DNA

Step 4: Increase temperature to allow thermo-stable polymerase to operate efficiently & optimally; don't forget the dNTPs

Which of the electrophoresis gels has a loose mesh and which one has a tight mesh?
Loose mesh: Agarose

Tight mesh: Polyacrylamide/bis-acrylamide
What is the major difference between gel electrophoresis and pulsed field electrophoresis?
Pulsed field electrophoresis can resolve a much larger size molecule.

This has definite uses in a hospital where it can be uses to track down different strains of illnesses.
High stringency of hybridization is made possibly by
* Increased temperature
* Decreased salt

For short probes:
* Decreased GC content
* Decreased length
What are the different kind of blots and what do they target?

Southern: DNA
Northern: RNA
Western: Protein
Dot Blot: DNA or RNA
True or false.

A Northern blot can use DNA or an oligo as a probe.
A cancer cell is reacting differently to a newly designed drug. You want to measure the level of transcription of a gene encoding a multidrug resistance transporter.

Which blotting method would you choose?
A cloning a glycoprotein will require the use of this cell line.
What is the difference between polygenic and multifactorial genetic disorders?
Multifactorial genetic disorders also include environmental causes into their understanding of the disease
General transcription factors are the sites of ____________
Promoters (CAAT, TATA, ...)
What are three ways that genomics aids in medical practice?
1. Identifying optimal patient-centered therapeutic dosages

2. Identifying optimal-patient centered therapies

3. Improvement of patient-centered long-term risk assessment
Are ALU repeats SINEs or LINEs?
How are minisatellites and microsatellites used in the world?
Minisatellites: DNA fingerpriting

Microsatellites: Tracking individual polymorphisms in individuals of a family -- establish kinship/parentage
Chromatin is made active by?

Chromatin is made inactive by?
* HAT (histone acetyl transferase) adds acetyl groups to lysine and thus 'opening up' DNA

* Histones can have methyl groups added to lysine and arginine

* Histones can phosphorylate serine, threonine, and lysine

- This increases rates of transcription and replication


Histones can be deactivated by HDAC (histone de-acetylation complex)

- This decreases transcription and replication rates
What are four types of DNA binding proteins?

Where do they bind to on the chromosome?
1. Helix Turn Helix

2. Helix Loop Helix

3. Leucine Zippers

4. Zinc Fingers

*** They all bind to the major groove of the chromosome
The toll-like receptor found on human immune cells senses this on bacterial cells.
What are three ways by which prokaryotes transfer genetic information?
1. Conjugation (F Plasmid)
2. Transduction (Viral infection)
3. Transformation (Pick up DNA from environment)
What is transcriptional silencing?
The hypermethylation of promoter CG islands by some cancers.
Which of the following mutations occurs at the promoter region and which acts farther away?

Cis-acting mutations occur at the promoter region
On a eukaryotic mRNA strand, what is the sequence of protein bindings and ribosome activation?
* TFIID binds to TATA
- TBD is a subunit of TFIID

* IIA, IIB, and IIH bind to TFIID

* IIH phosphorylates RNA Polymerase II

* RNA Polymerase II begins transcription
Translation initiation is dependent on these factors.
elongation factors (eEF-2, eEF-1a)
What toxin directly effects elongation factor 2 and disables protein translation?
Diphtheria toxin