DNA Structure Flashcards by Darren Zhou

What is the name of a nucleotide?

2’-deoxyadenosine 5’-monophosphate

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What do nucleotides comprise of?

a base, a sugar, and phosphate

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What do nucleosides comprise of?

base+sugar

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What are the functions of nucleotides?

energy storage (ATP), enzymatic co-factors (NAD, NADPH)

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What sugar does RNA have?

ribose

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What is the structure of ribose?

five carbon atoms

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What sugar does DNA have?

deoxyribose

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What is the structure of deoxyribose?

lacks hydroxyl group at 2’ carbon

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What is a glycosidic bond?

in DNA/RNA, the base is attached to the 1’ carbon

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What joins the nucleotides together into a linear strand?

3’ and 5’ positions will form covalent bonds

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What are two types of bases in DNA and RNA?

purines and pyrimidines

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What are purines?

adenina, guanine

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What are pyrimidines?

cytosine, thymine, and uracil

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What is the nucleoside form of adenine?

adenosine

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What is the nucleoside form of guanine?

guanosine

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What is the nucleoside form of cytosine?

cytidine

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What is the nucleoside form of thymine?

thymidine

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What is the nucleoside form of uracil?

uridine

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How do purines make glycosidic bonds?

through the 9 position of the base to the 1’ carbon of the sugar

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How do pyrimidines make glycosidic bonds?

through the 1 position of the base to the 1’ carbon of the sugar

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What is the backbone of DNA or RNA?

repeating of sugar and phosphate

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How are nucleotides joined?

a phosphodiester bond between the 3’ hydroxyl of one sugar and the phosphate attached to the 5’ hydroxyl of the next sugar

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How are nucleic acid strands asymmetric?

one end has an exposed 3’ hydroxyl, the other end has an exposed 5’ phosphate

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What are nucleic acid sequences written?

in the 5’ to 3’ direction (the DNA strand to the right has the sequence: ATGC)

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How do DNA strands associate?

via non-covalent hydrogen bonds to form double-stranded DNA

How many H-bonds bond A and T?

2 H-bonds

How many H-bonds bond C and G?

3 H-bonds

What type of base pairs are AT and GC?

Watson-Crick base pairs

Why are strands complementary?

the sequence of one strand dictates the sequence of the other strand

What direction are two strands?

antiparallel - one strand runs from 5' to 3' while the other runs 3' to 5'

What is the most energetically favorable formation of double stranded DNA?

two strands to wind around one another in a right-handed double helix

What is the orientation of hydrophobic bases in the center of DNA?

cluster, away from the aqueous cellular environment

What is the orientation of hydrophilic sugar-phosphate backbone?

on the outside

What are base pairs?

planar molecules that are perpendicular to the axis of the helix and form a stack in the interior of the helix

What stabilizes the helix of DNA?

Van der Waals interactions between p-orbitals of the bases

What is the diameter of the helix?

~20 A

T or F: A-T and G-C base pairs have similar widths

true

What is the predominant configuration of DNA?

B-DNA

What is the frequency of B-DNA?

repeats every 10.5 base pairs, and base pairs are 3.4 A apart

What is the structure of B-DNA?

the helix forms a major groove (~13 A) and a minor groove (~9 A) accessible from the outside of the molecule

What governs the interactions between DNA and other molecules?

the shape and size of the major and minor groove

What nucleotides lead to more flexibility?

regions rich in A-T

T or F: the sequence of bases in DNA can influence structure

true

What exposes the genetic information in DNA?

major and minor grooves

What are exposed in the major and minor grooves of the DNA helix?

chemical groups of the bases

What do each base pair have?

a characteristic set of groups that is available for interaction

T or F: DNA-binding proteins recognize specific DNA sequences through the major and minor grooves by separating the two DNA strands

false, without separating the two DNA strands

What does B-DNA represent?

the prototypical or most common DNA conformation

What is A-DNA?

a right-handed helix with 11 base pairs per turn; grooves are more evenly sized. the A conformation can be induced by DNA binding proteins

What is Z-DNA?

a left-handed helix, favored by methylation of cytosine torsional stress, and high salt concentrations. its biological significance is unclear

How do DNA relieve tension?

twists into supercoils

What are relaxed DNA?

open, uncoiled circular DNA

What induces supercoiling?

untwisting or overtwisting

What initiates the overwinding or underwinding of a closed circular DNA molecule?

at least one strand of DNA must be cut, and the strands twisted relative to each other, and re-ligated together

Why does DNA supercoil?

1. changes the number of bases per turn 2. restores the preferred number of bases per turn

T or F: supercoiling can be positive or negative

true

When do linear segments of DNA supercoil?

if one end is immobile

What creates negative supercoils?

unwinding the DNA helix of a constrained DNA molecule creates negative supercoiling to compensate for the strain on the molecule

When do supercoils release?

if one of the DNA strands is cut or otherwise free to rotate

What are the names of supercoiled structures?

toroidal or interwound (plectonemic)

What stabilizes the structure of DNA?

stabilized by complementary base-pairing and the combination of many weak, non-covalent interactions

What makes DNA less reactive and more stable compared with RNA?

the absence of hydroxyl

Why can one strand carry the entire code necessary to restore the other strand?

complementary base-pairing

How can two strands be separated?

held together only by non-covalent interactions

How is base information chemically readable?

in the major and minor grooves even without separating the two strands

What is supercoiling due to?

due to over- or under-winding which are caused by molecular mechanisms of replication and transcription

What is linkage number?

the number of times one strand of DNA wraps round the other

How often does B-DNA wrap around each other?

every 10.5 base pairs

T or F: linkage number can change in a closed circular DNA

false

What is twist?

the number of turns in a fragment of DNA (+1 per 360 twist)

How often does B-DNA twist?

+1 for each repeat of the double helix

What does a positive number denote in twist?

a right-handed helix

What does a negative number denote in a twist?

a left-handed helix

What is writhe?

a supercoiling of closed circular DNA or constrained linear DNA

What is the writhe of a relaxed plasmid?

zero

What is the writhe of a positively coiled DNA?

Wr > 0

What is the writhe of a negatively coiled DNA?

Wr < 0

What is the formula for linking number?

Lk = Tw + Wr

DNA Structure Flashcards

(79 cards)