Chapter 6: DNA and RNA Structure

Question 1

Nucleotide

Answer 1

molecule consisting of heterocyclic base, 5-carbon sugar (pentose), and a phosphate group

Question 2

Heterocyclic Compound

Answer 2

cyclic compound with one or more ring structures that contain atoms of at least two different elements

Question 3

Nucleoside

Answer 3

a nucleotide without a phosphate group; heterocyclic base with a pentose

Question 4

Purine

Answer 4

nitrogenous base; adenine or guanine; slightly larger

Question 5

Pyrimidine

Answer 5

nitrogenous base; cytosine, thymine, or uracil; slightly smaller

Question 6

Glycosidic Bond

Answer 6

covalent joining of a base to a carbon on the pentose in nucleosides; loses molecule of water

Question 7

Ester Bond

Answer 7

phosphate group is covalently joined to the 5’ carbon of a pentose to form a nucleotide; loses molecule of water

Question 8

Deoxyribonucleotide

Answer 8

structural unit of DNA; made up of nitrogenous base, phosphate group, and deoxyribose sugar

Question 9

Ribonucleotide

Answer 9

structural unit of RNA; made up of nitrogenous base, phosphate group, and ribose sugar

Question 10

Phosphodiester Bond

Answer 10

5’-phosphate group of a nucleotide is linked to 3’ hydroxyl group of next nucleotide; loss of water

Question 11

Hydrophobic Stacking

Answer 11

important mode of interaction between bases in nucleic acids due to their hydrophobicity and cyclic nature; stabilizes 3D structure of nucleic acids and minimizes bases contact with water

Question 12

Base Pairing

Answer 12

important mode of base interaction in nucleic acids; results from H-bonding capacity of ring nitrogen, ring carbonyl groups, and exocyclic amino groups of pyrimidines and purines; H-bonds between bases permit complementary association of strands; A-T/U; G-C; permits duplication of genetic information

Question 13

Chargaff’s Rules

Answer 13

1. Base composition of DNA varies between species
2. DNA specimens from different tissues of same species have same base composition
3. Base composition of DNA in a species doesn’t change with age, nutritional state, or environment
4. A=T, G=C and A+G=T+C

Question 14

Antiparallel

Answer 14

the two strands of DNA run in opposite directions (5’->3’)

Question 15

Major Groove

Answer 15

larger surface caused by the twist of the helix of DNA

Question 16

Minor Groove

Answer 16

smaller surface caused by the twist of the helix of DNA

Question 17

B-DNA

Answer 17

Watson-Crick structure of DNA; most stable structure for a random sequence DNA molecule under physiological conditions; right handed

Question 18

A-DNA

Answer 18

common for RNA and certain DNA structures; more compact than B-DNA; major groove is deeper and minor groove shallower

Question 19

Z-DNA

Answer 19

forms only under high salt conditions or C-G rich DNA sequences; left handed; zigzag pattern backbone; less compact, with shallow major groove and narrow and deep minor groove

Question 20

Palindromes

Answer 20

regions of DNA where the two complementary strands have the same sequence when read 5’->3’ direction or 3’->5’ direction

Question 21

Inverted Repeats

Answer 21

complementary sequences that occur on same strand of DNA but in inverse direction (usually some interruption between repeats); can form hairpin or cruciform structure through base pairing between adjacent repeats

Question 22

Mirror Repeat

Answer 22

inverted repeat sequence is non-palindromic

Question 23

RNA Secondary Structure

Answer 23

enables RNA molecules to fold into many different shapes that lend themselves to many biological functions

Question 24

Ribonucleoproteins (RNPs)

Answer 24

complexes of RNAs that are folded into three dimensional structures in the presence of bound proteins

Question 25

Denaturation

Answer 25

the disruption of hydrogen bonding between paired bases and base stacking, causing DNA to unwind and form two single, separate strands; occurs at extreme pH or temperatures above 80C

Question 26

Annealing

Answer 26

unwound segments of two strands spontaneously rewind to form the intact initial duplex

Question 27

Hypochromic Effect

Answer 27

hydrogen bonding and base stacking in double helix limit resonance of aromatic rings, decreasing UV light absorption

Question 28

Hyperchromic Effect

Answer 28

increased absorption of single stranded DNA due to not being as constricted, thus allowing resonance

Question 29

Melting Point

Answer 29

the temperature at which half the DNA is denatured; higher contact of G-C bp, higher melting point

Question 30

Hybrid Duplexes

Answer 30

when segments of mouse DNA strand form base paired regions with segments of a human DNA strand; valuable tool to explore evolutionary relationships

Question 31

Probe

Answer 31

carefully chosen nucleic acid sequence complementary to the gene of interest; to be visualized in a lab, must be somehow labeled

Question 32

Gel Electrophoresis

Answer 32

used to separate DNA or RNA molecules by size; use agarose gel which allows smaller fragments to move more quickly when attracted to a voltage;

Question 33

Southern Blotting

Answer 33

method to detect DNA; first gel electrophoresis, then transferred to nitrocellulose membrane and hybridized with DNA or RNA probe

Question 34

Northern Blotting

Answer 34

method to detect RNA; first gel electrophoresis, then transferred to nitrocellulose membrane and hybridized with DNA or RNA probe

Question 35

Mutations

Answer 35

alterations in DNA structure that produce permanent genetic changes

Question 36

Deamination

Answer 36

nucleotide base’s spontaneous loss of exocyclic amino group