DNA Lecture 5

Question 1

Any regular, stable structure adopted by the nucleotides in the nucleic acid

Answer 1

DNA Secondary Structure

Question 2

What is the shape of DNA?

Answer 2

Double Helix

Question 3

DNA is comprised of two complementary strands of

Answer 3

Polydeoxyribonucleotides

Question 4

What term describes how the opposite strands of DNA are arranged?

Answer 4

Anti-Parallel

5’—–>3’
(3’—–>5’)

Question 5

In DNA, the ratio of A/T and G/C is…

Answer 5

1:1

Question 6

How many base pairs per repeat were determined in the x-ray diffraction pattern produced by wet DNA fibers?

Answer 6

10 base pairs per repeat

Layer line spacing is 1/10 of the pattern repeat, 10 resides/turn

Question 7

These interactions are important to double helix stability

Answer 7

Base stacking interactions

Question 8

Base pairing is only possible if the major _____ forms are present. Other base pairs would form but they’re less favorable

Answer 8

Tautomeric

Question 9

The fact that strands are complimentary suggested a model for DNA replication.

In the replication process, base pairs are formed through _____

Answer 9

Hydrogen bonding

Question 10

A bonds to T through ___ H bonds

G bonds to C through ____ H honds

Answer 10

2

3

Question 11

Each stand can act as a template for a new complimentary strand, and two new daughter DNA molecules are formed which are identical in sequence to the parent molecule

Answer 11

!

Question 12

Are hydrophilic backbones of alternating deoxyribose and phosphate groups on the outside or inside of the double helix?

Purine and pyrimidine bases are on the outside or inside of the double helix?

Answer 12

Outside, facing water

Inside

Question 13

The furanose ring of each deoxyribose is in the _____ endo conformation

Answer 13

C-2’

Question 14

Hydrophobic and nearly planar rings are very close together and parallel/perpendicular to the long axis

Offset pairing of the two strands creates a major and minor ____

Answer 14

Perpendicular

groove

Question 15

The three types of DNA are..

Answer 15

A-DNA
B-DNA
Z-DNA

Question 16

This type of helix corresponds to the curvature of your left hand as you move along the helix in the direction of your thumb

This type is the opposite

Answer 16

Left Handed Helix

Right Handed Helix

Question 17

The sugar phosphate backbone forms a right handed helix in ______ DNA

In _____ DNA the sugar phosphate backbone forms a left-handed helix

Answer 17

A and B DNA

Z DNA

Question 18

Indicates the angle of rotation of one base pair relative tot he neighboring base either above or below it in the helix

If there are 10 steps per turn, then the rotation per step (base pair) is

Answer 18

Rotation per base

36 degrees

Question 19

This corresponds to the step height per nucleotide

Answer 19

Helical rise per base pair

Question 20

In B-DNA, the avg. rise is

In A-DNA, its

The rise corresponds mainly to the ___ of a pyrimidine or purine ring

Answer 20

0. 33nm
1. 23nm

Thickness

Question 21

Defined as the distance along the helix axis corresponding to one turn

Answer 21

Pitch

Question 22

Rotation about the C-N bonds (glycosidic bond) moves the base away from or on top of the deoxyribose ring. What is it called in both circumstances?

Answer 22

Anti - away from

Syn - On top of the deoxyribose ring

Question 23

In all nucleotides in DNA, four of the five atoms are in a single plane.

The fifth atom (C-2’ or C-3’) is on the same side of the plan relative to the C-5’, and this is called

When the fifth atom is on the opposite side of the plan relative to the C-5’, it is called

Answer 23

Sugar Pucker Confirmations

Endo

Exo

Question 24

The most stable structure for a random sequence DNA molecule under physiological conditions is..

It’s the form that Watson and Crick proposed

Answer 24

B-DNA

Question 25

In this DNA form the bases lie close to the helix axis (center of the helix) and the base pairs are approximately perpendicular to the helical axis The phosphate groups are on the surface of the helix. They will come into contact with the solvent

Answer 25

B-DNA

Question 26

The B-form has major and minor grooves. What do they result from? What does this allow for B-DNA, but not A-DNA?

Answer 26

The glycosidic bonds between the sugars and bases in a given base pair not being directly opposite one another B-DNA can accommodate a spine of water molecules lying in the minor groove

Question 27

This type of DNA is favored in many solutions which lack water

Answer 27

A-DNA

Question 28

What type of helix is A-DNA? Same as B-DNA. What's different?

Answer 28

Right handed 11 base pairs per turn (wider helix)

Question 29

In this form of DNA, the bases come out farther from the helix axis, and the plane of the base pairs is tilted about 20 degrees with respect to the helix axis. Does the A-form have grooves?

Answer 29

A-DNA Yes and they are equal in depth

Question 30

Is there evidence that A-DNA occurs in cells?

Answer 30

No.

Question 31

This type of DNA is a left handed double helix. It is more slender and elongated

Answer 31

Z-DNA

Question 32

How many base pair per helical turn in Z-DNA?

Answer 32

12

Question 33

Describe the appearance of Z-DNA

Answer 33

Zig-Zag

Question 34

Does Z-DNA have grooves?

Answer 34

One deep helical groove, it is the minor groove and is narrow and deep

Question 35

Certain ______ sequences fold in left-handed Z-helices

Answer 35

Nucleotide ex) Sequences with alternating pyrimidine and purine residues ----C&G, or 5-methyl C&G

Question 36

Is Z-DNA found in the cell?

Answer 36

Yes, short stretches in both prokaryotes and eukaryotes

Question 37

What role might the short tracts of Z-DNA play in prokaryotes and eukaryotes?

Answer 37

Regulation of gene expression or genetic recombination

Question 38

Structural variations have been detected with larger chromosomes which are sequence dependent, and the function and metabolism of DNA segments in their vicinity may be affected When ______ or more _____ residues appear sequentially in one strand, bends occur. This may be important for ________

Answer 38

4 or more adenine strands It may be important for protein binding

Question 39

A word or phrase that is spelled identically when read forwards or backwards, and is applied to regions of DNA with inverted repeats of base sequence What structures can result?

Answer 39

Palindromes Hairpin or cruciform

Question 40

When an inverted repeat occurs within each individual strand of DNA, a _____ is formed

Answer 40

Mirror Repeat

Question 41

In this type of position/pairing, the N-7, O6 and N6 of purines, the atoms that participate in hydrogen bonding are called The non-Watson-Crick pairing is called What can result?

Answer 41

Hoogsten positions Hoosten Pairing Triplex DNAs

Question 42

Four DNA strands can also pair to form a _____ if a very high proportion of____ residues is present

Answer 42

Tetraplex; guanine

Question 43

This type of DNA is found in polypyrimidine or polypurine tracts that also incorporate a mirror repeat

Answer 43

H-DNA