L14 Flashcards

(45 cards)

1
Q

Structure of DNA

A
double helix
can have A, B, Z conformations
DNA is a polymer of poly nucleotides, a huge polymer
Right handed
Major and minor grooves
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2
Q

Structure of RNA

A

polymer of polynucleotides

single strand with stem-loop

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3
Q

The conformational freedom of what is limited?

A

the glycosidic bond, ribose ring, and sugar phosphate backbone

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4
Q

What terms are super coiled DNA described in?

A

linking number, twist and writing number

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5
Q

What are topoisonmerases?

A

Used to cut one or both strands of DNA to add or remove supercoils

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6
Q

What does the genome comprise of?

A

Exons: part of the gene that gets expressed
Introns: rest of the gene

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7
Q

What is the central dogma of molecular biology?

A

DNA–transcription–> RNA —-translation–> protein

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8
Q

What’s the difference between nucleosides and nucleotide?

A

Nucleotide has a phosphate attached to it. While nucleosides are linked to sugar and pentose

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9
Q

What is the Chargaff’s rule?

A

Different organisms’ composition of bases have to be equal.

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10
Q

What is hybridization? What does it allow?

A

The pairing of two DNA or RNA strands that form non covalent duplexes.
It allows templated polymerization. The backbone is identical in each repeating unit. But the bases vary.

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11
Q

What do phosphodiester bonds link?

A

Nucleotide residues in DNA and RNA.

The H base paring provides specificity.

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12
Q

What carbon does the phosphodiester and glycosidic bonds stem off of?

A
phosphodiester (3'5')
glycosidic bond (1')
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13
Q

What is an A DNA conformation like?

A

scrunched with a fatter helix

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14
Q

What is Z DNA like?

A

Forms left handed double helix

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15
Q

What does an RNA look like when it forms a double helix?

A

It looks like DNA A form.

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16
Q

State for each A, B and Z, if its’ condensed or not.

A

A is un condensed and rest is condensed.

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17
Q

Glycosidic bond conformation for A, B, Z

A

Anti, Anti and for Z, it’s Anti for pyrimidines and syn for purines

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18
Q

What are the physical constraints of the nucleic acid structure? How many torsion angles?

A

The bond rotation of the nucleotide unit.

There’s seven torsion angle that dictates the conformation, 6 sugar phosphate and 1 glycosidic bond.

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19
Q

What are the syn and anti conformations?

A

syn conformation is base rotated out
anti conformation is base rotated in
remember how bases reaches in and rotates limits the constraints that happens in the backbone

20
Q

Ribose conformation: C3’ endo

A

5.9 A, less rotation than C 2

21
Q

Ribose conformations C2’ edo

A

7.0 A. How much rotation available dictates the conformation that pushes inside the constraint of the DNA.

22
Q

What does supercoiling help with?

A

It helps pack the DNA in the cell and protects it.

23
Q

What does the topological tension in DNA affect?

A

It affects normal gene regulation.

24
Q

Describe L = T +W

A

L= linking number: one DNA strand winds around another
T= Twist, complete rotation polynucleotide strand
W=Writing

25
What does spooling of DNA onto histones do to the L=T+W?
Spooling of DNA onto histones remove negative twist increases writhe
26
Describe topoisomerases Type IA
Breaks the phosphodiester bond and relaxes the DNA. Modifies linking number (L) does not need ATP interlink circles of ssDNA covalent intermediate: Tyr on Topo I linked to DNA through phosphodiester bond
27
Topoisomerases Type IB
``` relaxes highly coiled DNA Relaxes negative or positive coils does not interlink ssDNA cricles Controlled rotation mechanism, covalent intermediate iis same as Topo IA Does not need ATP ```
28
What are the differences between Type IA and Type IB topoisomerases?
Type IB does not interlink ssDNA and relaxes positive coils.
29
topoisomerase II
passes one strand of dsDNA through another Breaks and religates both streands of one duplex symmetric dimer consumes ATP, releases ADP and Pi Can interlink two dsDNA circles
30
What are inhibitors of topoisomerases?
antibiotics and anti cancer drugs
31
How does antibiotics work against bacteria without targeting mammalian cells?
Antibiotics selectively inhibit gyrase, but not Topo II in eukaryotic cells.
32
What are the important inhibitors for anti cancer drugs?
Topo II inhibitors
33
What are the forces that stabilizes DNA?
base pairing - Watson- Crick base pairs stacking from hydrophobic forces (Van der waals) ionic interactions DNA can be denatured and re natured
34
What stabilizing force is important for pair specificity?
It's the H bonds between Watson Crick base pairs. | But H bond do not provide the major energetics contribution for duplex formation.
35
What's the difference between AT and CG bonds?
There's 3 H bonds in CG
36
What is ssDNA
Single Stranded DNA
37
What is dsDNA
double stranded DNA
38
What is unique about the RNA variability?
It's highly variable, can form a lot of structures, intermolecular base pairing, Watson Crick pairing. RNA viruses has taken advantages of this flexibility, an example HPV
39
What is the eukaryotic chromatin structure like?
The DNA coils around histones. | Chromatin forms higher order structure
40
What are histones?
Histones are basic proteins form nucleosomes.
41
Histones are rich in what proteins?
Arg and Lys
42
How many genes does the mtDNA code for? Break it down.
37 genes. 13 are for proteins. 22 are tRNA 2 for small and large units of rRNA
43
About how many bp are in mtDNA?
16600 bp
44
Unique properties of mtDNA
has own DNA and polymerase to synthesize it.
45
What important processes are mtDNA genes involved in?
Complex I, Complex III, Complex IV, Atp synthase, transfer RNA, ribosomal RNA, control region of DNA.