Nucleotides and Derivatives

Nucleotides and their derivatives participate in

Chapter 5: nearly all biochemical processes

Nucleic Acids, etc. (1) Monomeric units of nucleic acids

(2) Nucleoside triphosphates (ATP) are energy rich
end products of most energy-releasing pathways
AND are consumed in energy-requiring processes
(3) Regulators of metabolic pathways and metabolic
Voet & Voet: Sections 1 & 3 processes

Pages 80-82 & 85-88 (4) Required component of enzymatic reactions

(nicotinic adenine dinucleotide, flavin adenine
dinucleotide, coenzyme A)
Any introductory Biochemistry textbook will have (5) Catalytic activity (ie. ribozymes)
an introductory chapter on nucleic acids

Lecture 8 Biochemistry 2000 Slide 1 Lecture 8 Biochemistry 2000 Slide 2

Nucleic Acids Nitrogenous Base

Nucleotides are nucleoside phosphates
Nitrogenous bases are planar, aromatic molecules that are
(typically) derivatives of purine or pyrimidine

Nucleosides consist of a nitrogenous base covalently
attached via a glycosidic bond to the C1' of a five carbon Parent compounds for nucleic acid bases (nucleobases)
sugar (pentose)
All nucleotides contain a nucleoside
Not all nucleosides are nucleotides

glycosidic
bond

Lecture 8 Biochemistry 2000 Slide 3 Lecture 8 Biochemistry 2000 Slide 4

 -D-Ribose Phosphate
Riboses (or aldopentoses) are five carbon sugars with an aldehyde
Phosphate is covalently attached to the D-ribose via
functional group (linear form only; revisit during energetics)
phosphate ester bonds


Nucleic acids are composed exclusively of the -D stereoisomer of ribose (or
Phosphates are typically attached to the C5' (5'-nucleotide)
deoxyribose)


RNA (ribonucleic acid) contains -D-ribose and DNA (deoxyribonucleic acid)
In polymers, the phosphate is attached to both the C5' and C3'
contains -2'-deoxy-D-ribose Nucleic acids are acidic, polyanions due to the phosphate groups
of nucleotides

Lecture 8 Biochemistry 2000 Slide 5 Lecture 8 Biochemistry 2000 Slide 6

Nucleic Acid Nucleic Acid Polymer

Polymer
Nucleic acids have a 5' and 3' end

Schematic for (dAdTdCdG)p or d(ApTpCpGp)


Convention: Nucleic Acids are written from 5' to 3'

Tetranucleotide deoxyadenyl-3',5'-deoxythymidyl-3',5'-
deoxycytidyl-3',5'-deoxyguanyl-3'-phosphate

Nucleic acids are synthesized from 5'-nucleoside
triphosphates in a 5' to 3' direction
Commonly named using a one letter code
eg. RNA tetranucleotide (right)
Schematic representation of
(a) AUCGp assumes phosphate between nucleotides DNA structure
(b) ApUpCpGp all phosphates indicated with 'p'
Proper Name adenyl-3',5'-uridyl-3',5'-cytidyl-3',5'-guanyl-3'-
phosphate (only used for small or uncommon
oligonucleotides)

Note: dA, dT, dC, dG represent deoxyribonucleotides

Lecture 8 Biochemistry 2000 Slide 7 Lecture 8 Biochemistry 2000 Slide 8

 Summary Modified Bases

Similar to the case with amino acids, nucleic acid bases
X refers to :
also occur as modified forms of the standard bases
H
when naming base inevitably modified bases have functional consequences
ribose
when naming
nucleoside
ribose and phospate
Modified bases occur in DNA
when naming
and more commonly in RNA
nucleotide

Uracil occurs in RNA

and Thymine in
DNA

Lecture 8 Biochemistry 2000 Slide 9 Lecture 8 Biochemistry 2000 Slide 10

Base Tautomers

Each base has a tautomer

T and G tautomers are shown
Tautomeric forms of base display altered
hydrogen bonding patterns


Mechanism that can lead to spontaneous
mutation during transcription and
replication

C and A tautomers are between amine and
imine forms (not shown)

Lecture 8 Biochemistry 2000 Slide 11