Mini 1 General Review 2

Front 1

Describe the four types of mutations causing activities.

Back 1

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)

Front 2

Describe some of the DNA repair mechanisms.

Back 2

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)

Front 3

DNA glycosylase is specific for cleaving this mutation.

Back 3

C -> U deamination -- specifically cleaves the uracil base but leaves the glycosidic bond in place but this too must be removed

Front 4

If a base has been removed during the repair mechanism phase, what enzyme comes along and cleaves the glycosidic link?

Back 4

AP endonuclease

Front 5

How do the repair mechanisms distinguish an old strand from a new one?

Back 5

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

Front 6

This base is a mutational hotspot.

Back 6

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]

Front 7

What are four DNA repair defects and their diseases?

Back 7

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

Front 8

Most DNA is 5 - 7% _______________.

Why is this important?

Back 8

Negatively supertwised

This favors unwinding via Type I (swivelase) as it doesn't require ATP

Front 9

Topoisomerase Type II is the target of _____________ and _______________.

Back 9

Antibiotics and chemotherapy

Front 10

What are some of the inhibitors of Type II Topoisomerase?

How do they work?

Back 10

Ciprofloxin (prokaryotes)
Doxorubicin (eukaryotes)

The inhibitors cause strand breakage in the chromosome

Front 11

What is the major functional difference between DNA polymerase I and III?

Why is this?

Back 11

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

Front 12

UV damage and repair is initiated by this complex.

Back 12

uvrABC

- Make nicks before and after the area of damage

Front 13

What are snRNA and what is their function?

Back 13

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

Front 14

What are the components of the RNA polymerase holoenzyme?

Back 14

alpha, beta, beta prime, and sigma

Front 15

Which component of the RNA polymerase first bind to the Shine-Dalgarno sequence?

Back 15

Sigma subunit

Front 16

What are the two types of transcription terminal signals?

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

Back 16

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

Front 17

Name two elongation factors tin both prokaryotes and eukaryotes where energy is spent.

Back 17

EF-Tu (pro) & eEF-1A (euk) = bind all aminoacylated tRNAs, GTPase

EF-G (pro) & eEF-2 = translocation, GTPase

Front 18

Achondroplasia (ACH) is a form of dwarifism. The mutation which causes this disease is a ______ which in turn causes this change to happen?

Back 18

Single nucleotide polymorphism

- The codon for glycine (GLY) becomes changed and instead codes for arginine (ARG)

Front 19

Restriction enzymes can leave two different types of ends. What are they and which one is better for integrating with a genome?

Back 19

Blunt and sticky ends

- Sticky ends aid in genome integration because they have 1 or more bases protruding from each end

Front 20

What are the steps and raw supplies needed for PCR?

Discuss what is needed at each step of the way.

Back 20

* 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

[REPEAT]

Front 21

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

Back 21

Loose mesh: Agarose

Tight mesh: Polyacrylamide/bis-acrylamide

Front 22

What is the major difference between gel electrophoresis and pulsed field electrophoresis?

Back 22

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.

Front 23

High stringency of hybridization is made possibly by

Back 23

* Increased temperature
* Decreased salt

For short probes:
* Decreased GC content
* Decreased length

Front 24

What are the different kind of blots and what do they target?

Back 24

SNOW
DROP

Southern: DNA
Northern: RNA
Western: Protein
Dot Blot: DNA or RNA

Front 25

True or false.

A Northern blot can use DNA or an oligo as a probe.

Back 25

True

Front 26

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?

Back 26

Northern

Front 27

A cloning a glycoprotein will require the use of this cell line.

Back 27

Eukaryotic

Front 28

What is the difference between polygenic and multifactorial genetic disorders?

Back 28

Multifactorial genetic disorders also include environmental causes into their understanding of the disease

Front 29

General transcription factors are the sites of ____________

Back 29

Promoters (CAAT, TATA, ...)

Front 30

What are three ways that genomics aids in medical practice?

Back 30

1. Identifying optimal patient-centered therapeutic dosages

2. Identifying optimal-patient centered therapies

3. Improvement of patient-centered long-term risk assessment

Front 31

Are ALU repeats SINEs or LINEs?

Back 31

SINEs

Front 32

How are minisatellites and microsatellites used in the world?

Back 32

Minisatellites: DNA fingerpriting

Microsatellites: Tracking individual polymorphisms in individuals of a family -- establish kinship/parentage

Front 33

Chromatin is made active by?

Chromatin is made inactive by?

Back 33

* 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

Front 34

What are four types of DNA binding proteins?

Where do they bind to on the chromosome?

Back 34

1. Helix Turn Helix

2. Helix Loop Helix

3. Leucine Zippers

4. Zinc Fingers


*** They all bind to the major groove of the chromosome

Front 35

The toll-like receptor found on human immune cells senses this on bacterial cells.

Back 35

LPS

Front 36

What are three ways by which prokaryotes transfer genetic information?

Back 36

1. Conjugation (F Plasmid)
2. Transduction (Viral infection)
3. Transformation (Pick up DNA from environment)

Front 37

What is transcriptional silencing?

Back 37

The hypermethylation of promoter CG islands by some cancers.

Front 38

Which of the following mutations occurs at the promoter region and which acts farther away?

Cis-acting
Trans-acting

Back 38

Cis-acting mutations occur at the promoter region

Front 39

On a eukaryotic mRNA strand, what is the sequence of protein bindings and ribosome activation?

Back 39

* 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

Front 40

Translation initiation is dependent on these factors.

Back 40

elongation factors (eEF-2, eEF-1a)

Front 41

What toxin directly effects elongation factor 2 and disables protein translation?

Back 41

Diphtheria toxin