Biochem PART II

Question 1

QUESTION 17: How do the chemical variables compromising the sugar rings of DNA an RNA differ from those of other organic molecules?
-They have ____ internal ____ ____
-What does this create?
-Which sugar ring is particularly distorted?

Answer 1

-distorted
-valence angles
-intrinsic stress in DNA
-5-membered ring

Question 2

QUESTION 18: To what do the terms C2’-endo and C3’-endo refer?
-DNA?
-RNA?

Answer 2

-C2’-endo, you can get a B-type helix
-C3’-endo, you can get a B-type helix

Question 3

QUESTION 19: What is meant by electronic fingerprint?
-It refers to the ____ electronic properties of what?
-What is this due to?

Answer 3

-unique; the bases
-different electronegativities

Question 4

QUESTION 19: What is meant by electronic fingerprint?
-It influences DNA’s ___ and ____
-It does this by creating what?

Answer 4

-function and interactions
-regions of excess electron build-up

Question 5

QUESTION 20: How do electronic fingerprints relate to DNA sequence and recognition?
-They help recognize what?
-How?

Answer 5

-DNA sequences
-by guiding ion buildup (cations accumulate)

Question 6

QUESTION 21: What is a helix from the perspective of chemistry?
-It is a ____ made up of what?

Answer 6

-polymer; identical repeating units

Question 7

QUESTION 22: How can one distringuish a right-handed from a left-handed helix?
-With a right-handed what do you do?

Answer 7

Match the spiral to your right hand with thumb up

Question 8

QUESTION 23: How does the chirality of the monomeric componenets relate to the handedness of a polypeptide or polynucleotide helix?
-It determines ____ handedness, leading to what kind of twist in what?

Answer 8

-helical
-right-handed twist in DNA and RNA

Question 9

QUESTION 24: Why are the grooves unevenly spaced in the classical DNA double helix?
-The _____ in the sugar-phosphate backbone creates what?
-What does it form?

Answer 9

-asymmetry
-unevenly spaced grooves
-major and minor grooves

Question 10

QUESTION 25: What chemical information led Watson and Crick to the idea that adenine paired with thymine and guanine with cytosine in their model of the double helix?
-They observed _____ of A always equals ___ and G equals ___, leading to the base-pairing hypothesis

Answer 10

-percentages
-T
-C

Question 11

QUESTION 26: What chemical information led to the idea that the base pairs should lie in the center of the double helix?
-Titration studies indicated that the sugar-phosphate backbone must lie on the ____ to protect what?

Answer 11

-outside
-the base pairs inside the helix

Question 12

QUESTION 27: How might Linus Pauling’s knowledge of proteins have influenced his early model of DNA as a triple helical structure with bases wrapped on the outside of the sugar-phosphate backbones?
-His understanding of ____ and their ____ helix structure may have led him to propose that DNA also had a ____ helix with bases on the ____

Answer 12

-proteins
-triple
-triple
-outside

Question 13

QUESTION 28: What are meant by the terms major-groove edge and minor-groove edge?
-Major-groove: Exposes the _____ edges of the ____ ____
-Minor-groove: Exposes the ____ edges of the ____ ____
-Which one is wider?

Answer 13

-upper; base pairs
-lower; base pairs
-Major-groove

Question 14

QUESTION 29: What is the Golden Ratio?
-What number is it?
-What does it reflect?

Answer 14

-1.618
-the ratio between the pitch and diameter of the double helix

Question 15

QUESTION 29: What is the Golden Ratio?
-What is the pitch?

Answer 15

The vertical distance it takes to complete a full turn

Question 16

QUESTION 30: How does DNA differ in the A, B, C, D, and Z forms?
-They differ in ___ ___ ___ ___
-How many are there in each?

Answer 16

-base pairs per turn
-A (11), B(10), C(9), D(8)

Question 17

QUESTION 30: How does DNA differ in the A, B, C, D, and Z forms?
-They also differ in ___ ___
-What are they?

Answer 17

-helical direction
-A, B, C, & D are right-handed, while Z-DNA is left-handed

Question 18

QUESTION 31: What happens to the major/minor grooves as DNA converts from the classical B form to the A or C forms?
-The major groove becomes ____
-The minor groove becomes ____
…this happens in A-DNA and C-DNA

Answer 18

-narrower
-wider

Question 19

QUESTION 32: In what ways does the chemical backbone accommodate the transitions of DNA from the B to A or C forms?
-Conversion from B-DNA to A or C-DNA involves changes in what?
-This changes reduces the distance between what?
-What does it reorient?

Answer 19

-sugar ring conformtion (C3’-endo to C2’-endo)
-phosphate groups
-the bases