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Chapter 8 Nucleotides and Nucleic Acids


Suggested reading: pg 281 302, 306 308
Problems: #2, 10, 12
NOTE: you are still responsible for this material (and the reading even though we will not be covering
it in class)!!

DNA genes codes for either a protein or an RNA molecule

RNA - different types of RNAs carry out different functions:


ribosomal RNA: components of ribosomes (where protein synthesis occurs)
messenger RNA: encode the amino acid sequence of one or more polypeptides. Sequence is
complementary to one of the DNA strands, and it carries the gene sequence from the
chromosome to the ribosome.
transfer RNA: read the mRNA sequence and transfer a specific amino acid to the growing
polypeptide chain during protein synthesis

both RNA and DNA are made up of nucleotides, which have three components:
1. a pentose (ribose or deoxyribose)
2. a phosphate
3. a nitrogenous base: either a purine or a pyrimidine (bound with a N--glycosyl bond to the
1 position of the pentose)

2 kinds of pentoses: the group at the 2


position is -OH in ribonucleotides and -H
in deoxyribonucleotides

purine bases:
a fused double heterocyclic aromatic ring structure
major types in both DNA and RNA: adenine (A) and guanine (G)
pyrimidine bases:
a 6-membered heterocyclic aromatic ring
cytosine (C): found in both DNA and RNA
thymine (T): found in DNA and uracil (U): found in RNA

SEE FIGURE 8-4 (STRUCTURES OF THE MAJOR BASES you are expected to know these for the exam,
and how they link together in a chain)

formation of DNA and RNA chains joined via phosphates, where the 5-phosphate group of one
nucleotide is covalently linked to the 3-hydroxyl group of another nucleotide (phosphodiester
linkage)
backbones: alternate between pentose and phosphate groups, and the side groups are
the nitrogenous bases
DNA or RNA sequence: read from the 5 to the 3 end (the 5 end has no nucleotide at 5
position, and the 3 end has no nucleotide at 3 position)
DNA:
5' End
O
O

T
O-

P
O-

5'

O
H

3'
O

P
O-

O5'

3'
O

H
3' End

properties:
backbones of DNA and RNA chains are hydrophilic
OH groups on the sugars H-bond with water
phosphates (pKa ~0): negatively charged at pH 7 (charges are neutralized by ionic
interactions with proteins, metal ions, etc)
pyrimidines and purines:
weakly basic
hydrophobic and mostly insoluble in water at neutral pH (under acidic or basic
conditions the bases become charged and a little more water-soluble)
engage in hydrophobic stacking interactions (planes of the rings are parallel),
mediated in part by van der Waals interactions. Stacking minimizes contact
between the bases and water (and stabilizes the double helix structure)
H-bonding between bases (i.e. base-pairing) allows for complementary association
between two strands of DNA or RNA.
most important base pairs: A=T and GC. There is a stronger interaction
between G and C due to three hydrogen bonds, compared to two between A
and T (or A and U). SEE FIGURE 8-11.

DNA double helix:


when two DNA strands interact: hydrophilic backbones face water and the hydrophobic
bases are stacked inside the helix. Most common double helix is the B-form (SEE FIGURE 813). Note major and minor grooves
the strands are anti-parallel (5 to 3 strand binds to 3 to 5 orientation)

DNA can also adopt unusual structures in regions of the sequence that are palindromes (inverted
repeats with symmetry over two strands):
since these regions are self-complementary, hairpin or cruciform structures can form SEE
FIGURES 8-18 and 8-19

RNA structure:
can form anti-parallel double helix with another RNA strand or with DNA.
single-stranded RNA can also form very complex structures with hairpin structures and
pairing of self-complementary sequences SEE FIGURE 8-24

double-helical DNA or RNA can be denatured


under extremes in temperature or pH the H-bonds between bases can be disrupted, causing
the helix to unwind (denature)
can renature the helix once the temp and pH returns to normal the helix will
spontaneously rewind (anneal) SEE FIGURE 8-26

mutations alterations to the nucleotide structure. Most common:


1. spontaneous:
depurination: hydrolysis of the base / pentose (N--glycosyl) bond
deamination in the bases SEE FIGURE 8-30a
deamination of cytosine results in a uracil base. This is why DNA contains
thymine and not uracil (because the DNA repair system will recognize that
uracil is a mutation and remove it).
2. caused by external forces:
UV light:
forces condensation of ethylene groups to form a cyclobutane ring. In DNA,
this causes the formation of cyclobutane pyrimidine dimers SEE FIGURE 831a
can also cause 6-4 photoproduct to form
ionizing radiation (x-rays, gamma rays) can cause ring opening and base
fragmentation, or breaks in backbone (causes ~10% of all DNA damage)
reactive chemicals:
deaminating agents (ex: nitrous acid, nitrites)
alkylating agents (which alter DNA bases)
oxidative damage from radicals, primarily hydroxyl radicals (cause a wide
variety of damage)
it is more important to maintain the DNA template without mutations than RNA or proteins
this explains why there are so many biochemical repair systems to recognize
mutations and fix DNA (and none for RNA or proteins)

other functions of nucleotides:


carriers of chemical energy ATP (adenosine 5-triphosphate) is the most common:

components of many enzyme cofactors: coenzyme A (assists in acyl group transfer


reactions), NAD+ (nicotinamide adenine dinucleotide, hydride transfers), FAD (flavin
adenine dinucleotide, electron transfers)
regulatory molecules acting as chemical signals. Example: cyclic AMP (adenosine 3,5cyclic monophosphate)

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