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Flashcards in 432 Lecture 24/8 Deck (48):
1

What causes the Tautomerization of Nucleotides?

Higher pH. Affects H-bonding properties. Cytosine goes to imino form. Thymine goes to enol form.

2

How is the DNA nucleotide polymer linked?

Linked by 3' to 5' Phosphodiester bonds.

3

Polarity of ssDNA

Hydrophillic at the side of the phosphodiester side of DNA; Hydrophobic at the nitrogenous base side of the DNA

4

What role does the OH group play in RNA?

In basic solution, OH group rips H from OH on the 2' carbon, causing nucleophillic attack on a phosphate group on the 3' carbon. Causes the formation of 2',3' cyclic monophosphate derivatives leading to the formation of 2' or 3' -monophosphate derivatives by hydrolysis reactions. RNA is not as stable in a single strand.

5

Bonding Character of DNA bases

non-covalent hydrogen bonding

6

Bonding Bases

A-T (2 hydrogen bonds) ; G-C (3H-bonds)

7

What are the three energetically favorable arrangements in DNA?

1) hydrophobic interactions in the center away from hydrophillic center 2) hydrophillic interactions with the aqueous environment with the phosphodiester bonds and sugars 3) Van der Waals interactions between bases (very favorable).

8

Major Groove and Minor Groove coding for G-C pair.

Major groove - AADH
Minor groove - ADA
(A-Acceptor, D- Donator, M-methyl). Minor grooves are the same regardless of G-C, C-G arrangement. G-C (AADH); C-G (HDAA).

9

Major Groove and Minor Groove coding for A-T pair

(A-T) MG = ADAM (T-A) MG=MADA both minor grooves AHA!

10

A DNA

A: Right Handed, short and broad, pitch 2.3A, 11bp/turn (less salty

11

B DNA

Right Handed, longer, thinner, pitch 3.4A, 10 bp turn (Primary form of DNA) -normal.

12

Z DNA

Left handed, longest, thinnest, pitch = 3.8A, 12bp/turn. (Salty regions promote Z-DNA also methylation causes)

13

Gene

Segment of DNA that contains all the information needed for regulated synthesis of an RNA or protein product.

14

Genome

the entire DNA sequence content of an organism.

15

Negative super-coiling Inter-wound

Clockwise winding of the DNA, tending to separate the strands, leads to negative super-coiling.

16

Positive Super-coiling Inter-wound

Counterclockwise direction induces positive supercoiling (closes DNA)

17

Toroidal Super-coiling

1) Left handed turn around protein (negatively supercoiled) 2) Right handed turn around protein (Positive super coiling)

18

Linkage Number

(Lk) The number of times one strand of DNA wraps round the other, in relaxed B-DNA, one strand wraps round the other every 10.5 bp. Unwound Lk = 18 fixed for circular DNA.

19

Twist

(Tw) The number of turns in a fragment of DNA (1+ 360˚)

20

Writhe

(Wr) describes supercoiling closed circular DNA or constrained linear DNA. Positively Supercoiled DNA has Wr >0 Negatively coiled has Wr

21

Lk equation

Lk = Wr + Tw; Lk constant; negative super coiling = -

22

Topoisomerases

Enzymes that regulate the overwinding or underwinding of DNA; both have Tyrosine mediate breakage of DNA

23

Type I

relax DNA/remove supercoils (does not require ATP); cut ssDNA

24

Type II

Introduce negative supercoils (ATP dependent) make dsDNA cuts

25

Eukaryotic Type IIa Topoisomerase

Functions as a dimer; 1) binds segment of DNA 2) second segment bound at N gate 3) second segment trapped, while first segment is cleaved 4) second DNA passed through break. 5) Broken DNA is religated and the second DNA is released through the C gate.

26

What type of linkages are made after a segment of DNA is cleaved for Super-coiling?

Two 5' phosphotyrosyl linkages to the enzymes

27

DNA Gyrase

Topoisomerase II; The only enzyme that can introduce negative super coiling. Present in bacteria. Does not happen in Eukaryotes. Gyrase the only topoisomerase that can introduce negative super coils. other topoisomerases just remove positive or negative super coils.

28

What are two examples of antibiotics and anticancer drugs that inhibit topoisomerase?

Cipro- antibiotics camptothecin- anti-cancer

29

Nucleosome Histone core associations

H2A - H2B; H3-H4 (Nucleosomes introduce torroidal super coiling) histone cores protect regions of DNA from digestion from nucleases.

30

DNA-Histone Association

1) Called "DNA-Histone Association Complex" 2) A-T rich regions are associated with H3/H4 of complex 3) associates with minor groove of DNA 4) Mostly hydrophobic interactions, not covalently.

31

What two amino acids are critical in phosphate backbone interaction with histone proteins

Lysine and Arginine Basic/positively charged; make up tails of histone cores phosphodiester backbone is negatively charged

32

Chromatin changes regulating gene activity

1) Acetylation (lysine, negates positive charge) , methylation, phosphorylation and ubiquination of histone side chains.

33

10nm fiber

First level; nucleosome association with DNA; bead on a string appearance

34

30nm fiber

compacting of 10nm fiber

35

Histone (H1)

Histone protein, not in the HAC, Linker protein, associates with DNA and pulls DNA closer to the nucleosome, causes compaction of the chromatin.

36

Cellular Inter-phase

DNA Uncondensed; G1 (gap phase); S ; G2

37

G1

Gap phase

38

S phase

synthesis phase-DNA replicated

39

G2 phase

the replicated chromosomes, chromatids, cohere to each other

40

Mitosis

PMAT

41

Prophase

DNA undergoes condensation

42

Metaphase

chromosomes line up along the plane between the spindle poles

43

Anaphase

sister chromatids separate

44

Telophase

completion and partial decondensation

45

SMC proteins

Structural maintenance of chromosomes Cohesions and condensins

46

Cohesins

(SMC1/3) Cause sister chromatids to stick together. wrap around sister chromatids, during S phase, as soon as DNA is replicated; comes off before metaphase by separase

47

Condensin

(SMC 2/4) Condense chromosomes, function after G2, after DNA is replicated. come off after telophase.

48

Structure of SMC

Dimer; hinge; N-C and CN ATP binding sites, ATP binds, ATP hydroylzed, cause super-coiling.

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