100% satisfaction guarantee Immediately available after payment Both online and in PDF No strings attached
logo-home
BCH5413 - 1 EXAM PREP WITH COMPLETE SOLUTION $13.49   Add to cart

Exam (elaborations)

BCH5413 - 1 EXAM PREP WITH COMPLETE SOLUTION

 2 views  0 purchase
  • Course
  • BCH5413 - 1
  • Institution
  • BCH5413 - 1

BCH5413 - 1 EXAM PREP WITH COMPLETE SOLUTION

Preview 4 out of 81  pages

  • September 1, 2024
  • 81
  • 2024/2025
  • Exam (elaborations)
  • Questions & answers
  • BCH5413 - 1
  • BCH5413 - 1
avatar-seller
hurryben
BCH5413 - 1 EXAM PREP WITH
COMPLETE SOLUTION
DNA structure - =- nucleic acid bases (purine (A,G) and pyrimidine (C,U,T))
- sugars (ribose, deoxyribose)
- sugars linked by phosphate groups (sugar-phosphate backbone)


*form antiparallel strands


In mammilian DNA, which base has various forms - =cytosine


Chargaff's rule - =A=T and C=G


Is DNA conservative or semi-conservative? - =semi-conservative
- parental sequence and daughter strand bind together


Alternative Double stranded DNA conformation
- A and Z DNA - =A DNA
- dehydrated form
- right handed helix
- 11 bp per helical
- bp tilted 19 degrees
- major groove narrow and deep
- found with dsRNA and RNA-DNA duplex


z-DNA
- >1% of cellular DNA

,- favored by G-C repeats and alternating purines-pyrimidines
- left handed helix
- 12 bp per turn
- bp tilted 9 degrees
- major groove flattened, nearly gone
- bound by poxvirus E3L virulence factor and down regulates apoptosis genes


Non-duplex DNA structures
- cruciform DNA - =- inverted repeat sequence
- favored by excessive negative supercoiling
- AT-rich cruciforms associated with 'fragile' DNA


Alternative modes of base pairing - =Watson Crick:
A--T and C---G
- adenine is at anti-conformation


Hoogsteen:
- adenine or guanine can be flipped to sin-conformation (different H-bonding)


Hoogsteen base pairing
- when can it occur - =- in triplex and quadruplex DNA structures


Triplex DNA - =- pyrimidine rich strand
- negative supercoiling


Chair DNA - =- two G-rich strands
- down regulation of c-myc transcription

,Intrinsic Bends in DNA - =- distortion of the ideal B-DNA conformation resulting from base
stacking in the nucleotide sequence
Eg. Adenine-tract DNA results in 20 degree bends


- also can be found in duplex-oligonucleotide model DNA
- causes 23 degree bend and mis-stacking of one GC
- DNA is not a uniform structure


Does B-DNA have a perfect structure? - =No
- sequence specific local variation in twist between paired bases, sugat conformation, tilt of
base pairs, rise distance, etc.


Supercoiled DNA
- negative v. positive - =- left handed under-twisted DNA is in a negative supercoil


- right handed over-twisted DNA is in a positive supercoil


*most is negatively supercoiled (topoisomerase releaves supercoiling)


Denaturation/Melting of DNA - =- separation of DNA strands
- can happen due to temp, salt concentration, G---C content, and length of DNA
(Hyperchromicity effect)
- as temp increases, absorption of light increases due to bases becoming less shielded when
they melt apart


The (greater/lower) the G+C content and the (higher/lower) the salt, the more stable the DNA
duplex - =greater G+C and higher salt

, What are higher stringency conditions - =high heat and low salt


What else can melt DNA? - =pH


DNA renaturing and hybridization - =- add complementary RNA and re-anneal by gradually
lowering temp.


Where are chemical groups present in the DNA - =major and minor groove


How do sequence specific DNA binding proteins bind in a sequence specific manner - =the
amino acids of sequence specific DNA binding proteins recognize the pattern of chemical
groups in the major/minor groove
- may interact through different bonding to permit sequence specific recognition


Zinc finger binding proteins - =- custom designed DNA binding proteins
- two beta sheets attached to an alpha helix coordinate by a zinc molecule
- triple zinc finger can bind in the major groove of DNA


Zinc finger custom design - =swapping the alpha helix domain and beta-hairpin segments allows
for different sequence specificity
*alpha helix domain determines sequence specificity


Zinc finger properties - =Crystallographic studies
- a single zinc finger protein can recognize 3bp of DNA


Zinc finger and DNA binding specifics - =- AA of zinc finger at position 6 recognizes first
nucleotide of DNA
- AA of zinc finger at position 3 recognizes second nucleotide of DNA
- AA of zinc finger at position -1 recognizes third nucleotide of DNA

The benefits of buying summaries with Stuvia:

Guaranteed quality through customer reviews

Guaranteed quality through customer reviews

Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.

Quick and easy check-out

Quick and easy check-out

You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.

Focus on what matters

Focus on what matters

Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!

Frequently asked questions

What do I get when I buy this document?

You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.

Satisfaction guarantee: how does it work?

Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.

Who am I buying these notes from?

Stuvia is a marketplace, so you are not buying this document from us, but from seller hurryben. Stuvia facilitates payment to the seller.

Will I be stuck with a subscription?

No, you only buy these notes for $13.49. You're not tied to anything after your purchase.

Can Stuvia be trusted?

4.6 stars on Google & Trustpilot (+1000 reviews)

80202 documents were sold in the last 30 days

Founded in 2010, the go-to place to buy study notes for 14 years now

Start selling
$13.49
  • (0)
  Add to cart