Structure of Nucleic Acids
I.
INTRODUCTION
A. Chromosomes are composed of chromatin
1. Chromatin is a combination of DNA and proteins
a) Proteins include histones and non-histone proteins
2. Only the structure of DNA will be discussed in this section
a) The structure of chromatin and chromosomes will be discussed later
B. Function
1. To be replicated
a) Copies are passed on from cell to cell and generation to generation
2. To determine phenotype
a) Nucleic acids determine our genetically encoded physical traits
II.NUCLEOTIDES
A. Nucleic acids are polymers of nucleotides
1. Composition of nucleotides
a) A pentose sugar
b) A nitrogenous base
c) Phosphoric acid
2. Nuclein
a) DNA was isolated in 1869 by Friedrich Miescher
(1) It was isolated from pus (leukocytes) from bandages
(2) He termed the substance nuclein
b) Nucleic acid is derived from that term
B. Pentose sugars
1. Types
a) Ribose and Deoxyribose
(1) Deoxyribose replaces the 2'-hydroxyl group found in RNA with a hydrogen
2. Numbering of carbons
a) Both ribose and deoxyribose are pentose sugars
b) Carbons are numbered 1' - 5'
(1) These are primed numbers so as not to confuse them with the ordinary
numbers used to label the nitrogenous bases
(2) 1' carbon is bound to the base
(3) 3' carbon is bound to phosphate of adjacent nucleotide
(4) 5' carbon is bound to phosphate in its nucleotide
C. Nitrogenous bases
1. Characteristics
a) Ringed structures
b) Contain nitrogen
c) Mostly hydrophobic
(1) This causes them to stack on top of each other (slightly staggered) rather than
facing out randomly from the sugar-phosphate backbone
d) Some groups capable of hydrogen bonding
2. Purines
a) These are derivatives of purine
(1) A double-ring structure
b) Includes guanine and adenine
c) The nitrogen and carbon atoms are numbered 1 - 9
(1) These are linked to sugars via a n-glycosidic bond
(a) The 1' carbon of the pentose is bonded to the 9 nitrogen of the base
3. Pyrimidines
a) These are derivatives of pyrimidine
(1) A single-ring structure
b) Includes thymine, uracil, and cytosine
(1) Uracil is found only in RNA and thymine only in DNA
c) The nitrogen and carbon atoms are numbered 1 - 6
(1) These are linked to sugars via a n-glycosidic bond
(a) The 1' carbon of the pentose is bonded to the 6 nitrogen of the base
4. Base pairings
a) Chargaff's rule states that purines always pairs with pyrimidines (equal
amounts)
(1) Thymine - Adenine
(a) 2 hydrogen bonds
(2) Cytosine - Guanine
(a) 3 hydrogen bonds
b) Base pairs have same size and shape (constant diameter)
c) Bases pair via hydrogen bonds
(1) Bases must be antiparallel for proper bonding
d) Denaturation studies can estimate the G + C content of DNA
(1) G - C pairs have more hydrogen bonds and therefore require higher
temperatures to denature
D. Phosphate
1. An ionized form of phosphoric acid
2. Negatively charged component of the sugar-phosphate backbone
3. Labeling in nucleoside triphosphates
a) The one attached to the sugar is labeled , the next , and the one farthest
from the sugar 
III.TERMINOLOGY
A. Nucleosides
1. Definition
a) Contains a base and sugar
(1) These are connected via a N-glycosidic bond
b) Deoxynucleoside
(1) Contains deoxyribose
c) Ribonucleoside
d) Contains ribose
B. Nucleotides
1. Definition
a) Nucleoside + phosphate(s)
b) Deoxynucleotide
(1) Contains deoxyribose
c) Ribonucleotide
(1) Contains ribose
2. Nucleotide monophosphates
a) Nucleoside plus one phosphate
(1) Includes ribonucleotide and deoxynucleotide monophosphates
3. Nucleotide diphosphates
a) Nucleoside plus two phosphates
(1) Includes ribonucleotide and deoxynucleotide diphosphates
4. Nucleotide triphosphates
a) Nucleoside plus three phosphates
(1) Includes ribonucleotide and deoxynucleotide triphosphates
b) Ribonucleotide triphosphates often used to drive endergonic reactions
(1) For example, the hydrolysis of ATP to drive flagella in eukaryotes
c) Only the nucleoside triphosphates can be used to make nucleic acids
(1) Cleavage of phosphates provides energy to drive nucleic acid synthesis
C. Types and abbreviations
1. Ribonucleotides includes
a) Ribonucleotide monophosphates
(1) Adenosine monophosphate (AMP), Cytidine monophosphate (CMP),
Guanosine monophosphate (GMP), and Uridine monophosphate (UMP)
b) Ribonucleotide diphosphates
(1) Adenosine diphosphate (ADP), Cytidine diphosphate (CDP), Guanosine
diphosphate (GDP), and Uridine diphosphate (UDP)
c) Ribonucleotide triphosphates
(1) Adenosine triphosphate (ATP), Cytidine triphosphate (CTP), Guanosine
triphosphate (GTP), and Uridine triphosphate (UTP)
2. Deoxyribonucleotides includes
a) Deoxyribonucleotide monophosphates
(1) Deoxyadenosine monophosphate (dAMP), Deoxycytidine monophosphate
(dCMP), Deoxyguanosine monophosphate (dGMP), and Deoxythymidine
monophosphate (dTMP)
b) Deoxyribonucleotide diphosphates
(1) Deoxyadenosine diphosphate (dADP), Deoxycytidine diphosphate (dCDP),
Deoxyguanosine diphosphate (dGDP), and Deoxythymidine diphosphate
(dTDP)
c) Deoxyribonucleotide triphosphates
(1) Deoxyadenosine triphosphate (dATP), Deoxycytidine triphosphate (dCTP),
Deoxyguanosine triphosphate (dGTP), and Deoxythymidine triphosphate
(dTTP)
IV.NUCLEOTIDE
- NUCLEOTIDE BONDS
A. Nucleotides are linked together via phosphodiester bond
1. Ester linkages
a) Esters are formed from the bonding of acids and alcohols
(1) Phosphoric acid bonds to the hydroxyl groups (which serves as an alcohol) of
ribose and deoxyribose sugars
2. Referred to as phosphoester linkages since they involve phosphorous
3. Referred to as a phosphodiester since the phosphate binds to two sugars in
nucleic acids
a) It binds to the 5' carbon of its sugar
b) It binds to the 3' carbon of the next nucleotide
B. Formation of the phosphodiester bond is a dehydration synthesis reaction
1. Breakage of the bond is referred to as hydrolysis
C. Nucleotides can only be added to the 3’ carbon of the previous nucleotide
V.
NUCLEIC ACID STRUCTURE
A. Overall structure
1. 2’-deoxyribonucleotides linked by phosphodiester bonds between the adjacent
3’ & 5’ sugar residues
B. Size of human genome
1. 2.8 X 109 base pairs split up between 23 chromosomes
a) Human chromosomes may contain 100s of millions of base pairs
b) Each base pair is about 660 Daltons
C. DNA is a double helix
1. Contains two strands of DNA twisted around each other
a) Natural DNA is found mostly as a right-handed helix
(1) It twists clockwise as it moves away from the observer
2. There is one right-turn of the helix for every 10.6 base pairs
3. The twisting of the double helix causes the formation of two grooves
a) The minor groove is between the backbone of the double helix
b) The major groove is between twists in the double helix
D. Antiparallel
1. One strand of DNA runs 5' - 3' while the other strand goes in the opposite
direction (3' - 5')
E. Sizes
1. Bases are flat molecules that are stacked slightly staggered on top of each other
a) The ring structure of bases are hydrophobic and tend to
react with other hydrophobic bases
(1)Each is rotated 34.6 to the next
b) Bases are 3.4 Å apart
(1)One turn of the double helix is 34 Å and includes 10.6
bases
2. Length
a) 1 m = 2 X 106 Daltons
b) Extremely fragile
(1) The average molecular weight of DNA isolated from Escherichia coli is 2.5 X
107, indicating the chromosome was broken into over 100 pieces during the
isolation procedure
3. Diameter
a) 20 Å
F. Chargaff's rule
1. The amount of A = T and G = C
2. The amount of purines = amount of pyrimidines
3. The percent G + C for higher eukaryotes is around 50%
a) Ranges from .49 to .51 for primates
b) Ranges from 27% (Clostridium) to 76% (Sarcina) in prokaryotes
c) Percent G + C can be determined by its thermal melting point and by CsCl
ultracentrifugation
G. Breathing
1. Definition
a) Breathing refers to the fact that the base pairs found in DNA are continually
breaking and reforming their hydrogen bond
(1) The DNA frequently opens to become a bubble
(2) This is important as it allows proteins to interact with certain nucleotide
sequences
(3) Breathing is more frequent in A-T rich areas than G-C rich areas
2. Experiment
a) Formaldehyde binds to amine groups of bases which prevents proper
hydrogen bonding between base pairs
b) The addition of formaldehyde results in a slow, non-reversible denaturation
of the DNA molecule
H. Base stacking
1. Due to their hydrophobicity, bases tend to stack (slightly staggered) on top of
each other to reduce contact with hydrophilic substances
2. Unstacking is more likely to occur at the ends of a DNA molecule
a) At the end, a base is only stabilized by one other base
b) In the middle, a base is stabilized by bases on each side
3. Larger molecules are more stable than small molecules in this regard
a) An average DNA molecule will have 7 base pairs at its end not bonded to
each other
(1) These are referred to as "frayed ends"
b) A DNA molecule shorter than 15 base pairs is not stable
VI.FORMS
A. A-form
1. Formed at 66% humidity
2. 11 base pairs per turn of helix
3. Bases tilted 20%
B. B-form
1. Formed at 92% humidity
2. 10 base pairs per turn of helix
3. Bases perpendicular to backbone
C. Left-handed (Z-form) helices
1. Formation
a) Formed with high salt and divalent cations
b) Alternating purines and pyrimidines will cause DNA to form left-handed
helices
2. Differences from right-handed helices
a) The sugar phosphate backbone with be in a zig-zag fashion
(1) Often referred to as Z-DNA
(2) It makes the molecule wavy
b) 12 base pairs per turn of the helix
c) Only has a single groove rather than the major and minor groove of B DNA
3. Z-DNA has been detected in supercoiled DNA at physiological salt concentration
a) Some proteins only bind to Z-DNA
VII.DIFFERENCES
BETWEEN RNA AND DNA
A. RNA is generally single-stranded
1. Some double-stranded RNA viruses
2. RNA may have some areas that are folded back on itself forming a local area of
double-strandedness
3. If double stranded, the strands must be antiparallel
B. RNA contains ribose; DNA contains deoxyribose
C. Solubility
1. RNA is more stable due to the 3'-OH group of ribose
D. Stability
1. RNA is less stable than DNA due to the 3'-OH group of ribose
E. Bases
1. DNA contains thymine but not uracil
2. RNA contains uracil but not thymine
VIII.SELECTED
CONTRIBUTORS
A. Know what the following persons contributed to the knowledge of the structure of
DNA and RNA
1.
2.
3.
4.
5.
6.
Friedrich Meischer
Leven and Jacobs
Linus Pauling
Maurice Wilkins and Rosalind Franklin
Erwin Chargoff
James Watson and Francis Crick