NUCLEOTIDES, NUCLEIC ACIDS, and HEREDITY The five principal bases of DNA and RNA

The Molecules of Heredity

• Each cell of our bodies contains thousands of
different proteins. All of these molecules are
made up of amino acids.
• How do cells know which proteins to
synthesize out of the extremely large number
of possible amino acid sequences?
o An individual gets the information
from its parents through heredity
o Heredity is the transfer of
characteristics, anatomical as well as
biochemical, from generation to
generation.
• From the end of the 19th century, biologists
suspected that the transmission of hereditary
information took place in the nucleus, more
specifically in structures called chromosomes.
• The hereditary information was thought to Bases: Purines and Pyrimidines which are components
reside in genes within the chromosomes. of nucleotides
o Genes are units of heredity DNA Purine
segments that code for one protein or • Bicyclic: 1 cyclohexane, 1 cyclopentane
one type of RNA • Adenine and Guanine
• Chemical analysis of nuclei showed Pyrimidine
chromosomes are made up largely of proteins • Unicyclic: cyclohexane
called histones and nucleic acids. • Cytosine, Thymine (DNA), Uracil (RNA)
• By the 1940s, through the work of Oswald Nucleosides
Avery, it became clear that deoxyribonucleic Nucleoside: A compound that consists of D-ribose or 2-
acids (DNA) carry the hereditary information. deoxy-D-ribose bonded to a purine or pyrimidine base
o Other work by George Beadle and by a b-N-glycosidic bond.
Edward Tatum, in the 1940s • Nucleosides: composed of a sugar and a base
demonstrated that each gene controls • b-N-glycosidic bond: bond between a sugar
the manufacture of one protein. and purine/pyrimidine base
o Thus, the expression of a gene in terms uracil O

of an enzyme protein led to the study HN

b-D-riboside 1
of protein synthesis and its control.
5' O N a b-N-glycosidic
Nucleic Acids HOCH2 O bond
1'
H H
• There are two kinds of nucleic acids in cells: 4'
H 3' 2' H anomeric
o Ribonucleic acids (RNA) carbon
HO OH
o Deoxyribonucleic acids (DNA) Uridine
• Both RNA and DNA are polymers built from Sugars
monomers called nucleotides. A nucleotide is • In DNA, 2-deoxy-d-ribose (hence the name,
composed of: deoxyribonucleic acid)
o A base, a sugar (monosaccharide), and o No oxygen on the 2nd carbon
a phosphate group • In RNA, d-ribose (hence the name, ribonucleic
acid)
o Hydroxyl (-OH) group on the 2nd
carbon
Nucleotides Another example:
Nucleotide: A nucleoside in which a molecule of
phosphoric acid is esterified with an -OH of the
monosaccharide, most commonly either at the 3’or
the 5’-OH.
• Sugar with base plus phosphate group
Naming Nucleotides
Remember the bases:

Sugar: Ribose
Base: Adenine
Phosphate group: 3 groups on 5th carbon
Name: adenosine-5’-tri-phosphate
Shortcut: adenosine triphosphate / ATP
TAKE NOTE: the term ‘ribose’ is not included in the
naming, only the sugar deoxyribose is indicated in
naming by using ‘deoxy’
Adenosine 5’-triphosphate (ATP) serves as a
common currency into which energy gained
from food is converted and stored.
Take this example: Summary
O Nucleoside – sugar + base
CH3
HN Nucleotide – sugar + base + phosphate
Nucleic acid – chain of nucleotides
5' O N
HOCH2 O DNA—Primary (1°) Structure
H H 1' • For nucleic acids, primary structure is the
H 3' H sequence of nucleotides, beginning with the
O H
nucleotide that has the free 5’ terminus.
O P O-
-
o The strand is read from the 5’end to
O

Determine: the 3’end.

• The sugar: no oxygen on 2nd carbon, therefore
a deoxyribose
• The base: in this case, a thymine
• The phosphate group: only 1 (mono)
phosphate group attached at the 3rd carbon or
3’
Following the order of naming: sugar, base, phosphate
• The name will be:
deoxythymine-3’-monophosphate
• The shortcut will be: dTMP
o Thus, the sequence AGT means that
adenine (A) is the base at the 5’
terminus and thymine (T) is the base at
the 3’ terminus.
o Lagging strand: 5’ to 3’
o Leading strand: 3’ to 5’
DNA—2° Structure
Secondary structure: The ordered arrangement of
nucleic acid strands.
• The double helix model of DNA 2° structure
was proposed by James Watson and Francis
Crick in 1953.
Double helix: A type of 2° structure of DNA in which
two polynucleotide strands are coiled around each
other in a screw-like fashion.
B-DNA. It is the most common and most stable
form. Distinguishing feature of major groove and
 minor groove which arise because two strands are • Transcription – DNA to mRNA
not equally spaced • Translation – mRNA to protein
Roles of different kinds of RNA
Base Pairing RNA type Size Function
• A and T pair by forming two hydrogen bonds. Transfer RNA Small Transports amino acids
(tRNA) to site of protein synthesis
G and C pair by forming three hydrogen
Ribosomal RNA Several kinds; Combines with proteins to
bonds. (rRNA) variable in size form ribosomes,
the site of protein synthesis.
• They are also called complementary base Messenger RNA Variable Directs amino sequence of
(mRNA) proteins.
pairs
Small nuclear Small Processes intitial mRNA to its
RNA (snRNA mature form in eukaryotes.
Superstructure of Chromosomes Micro RNA Small Affects gene expressions;
(miRNA) important in growth and
DNA is coiled around proteins called histones. development
• Histones are rich in the basic amino acids Lys Small intefering Small Affects gene expression ; used
RNA(siRNA) by scientists to knock out gene
and Arg, whose side chains have a positive being studied.

charge.
• The negatively-charged DNA molecules and
positively-charged histones attract one
another and form units called nucleosomes.

Nucleosome: A core of eight histone molecules around
which the DNA helix is wrapped.
• Nucleosomes are further condensed into
chromatin.
• Chromatin fibers are organized into loops, and
the loops into the bands that provide the
superstructure of chromosomes.
Summary
1. DNA is wrapped in histones forming a
nucleosome
2. Nucleosome will condense “bead on a string”
forming a chromatin
Clusters to six nucleosome per turn
forming a solenoid
3. Chromatin fibers organized into loops then
bands forming a chromosome
DNA and RNA
The three differences in structure between DNA and
RNA are:
1. DNA bases are A, G, C, and T;
the RNA bases are A, G, C, and U.
2. The sugar in DNA is 2-deoxy-D-ribose;
in RNA it is D-ribose.
3. DNA is always double stranded; there are
several kinds of RNA, all of which are single-
stranded.
Information Transfer
• Replication – 2 identical DNA molecules
Gene: A segment of DNA that carries a base sequence
that directs the synthesis of a particular protein, tRNA,
or mRNA.
• There are many genes in one DNA molecule.
• In bacteria, the gene is continuous.
• In higher organisms, the gene is
discontinuous.
Exon: A section of DNA that, when transcribed, codes
for a protein or RNA.
Intron: A section of DNA that does not code for
anything functional.
• Spliced out by ribozymes; functions as spacers
or enzymes catalyzing the splicing of exons into
mature mRNA
Satellites: DNA molecules in which short nucleotide
sequence are repeated hundreds or thousands of times
Mini-satellites/microsatellites: smaller repetitive
sequence, associated with cancer when they mutate
The DNA in the chromosomes carries out two
functions:
(1) It reproduces itself. This process is called
replication.
(2) It supplies the information necessary to
make all the RNA and proteins in the body,
including enzymes.
Gene - section of a DNA molecule containing a specific
sequence of the four bases (like amino acids to protein)
Base sequence - carries the information to produce
one protein molecule
 • If the sequence is changed into a different
molecule is produced, which might have an
impaired function
Replication begins at a point in the DNA called the
origin of replication or a replication fork
3’-5’ – leading strand
5’-3’ – lagging strand
Primer – pre-existing chain, made of RNA not DNA
Why do you think DNA needs to be replicated?
• Cells are constantly dying; the DNA has
mechanism to replicate without error to
produce cells that are similar to the old ones
DNA REPLICATION
The replication of DNA occurs in a number of distinct
steps.
1. Opening up of the superstructure of the
chromosomes.
• One key step is this process is acetylation-
deacetylation of lysine residues on histones.
This reaction eliminates some of the positive
charges on histones and weakens the strength
of the DNA-histone interaction
2. Relaxation of Higher-Order Structures of DNA.
• Topoisomerases (also called gyrases)
temporarily introduce either single-or double
strand breaks in DNA.
• Once the supercoiling is relaxed, the broken
strands are joined together and the
topoisomerase diffuses from the location of
the replication fork.
• DNA GYRASE - for bacteria
• Topoisomerases and Gyrases - only for
relaxation of coiled strands
3. Replication of DNA molecules starts with the
unwinding of the double helix which can occur at
either end or in the middle.
• Special unwinding proteins called helicases,
attach themselves to one DNA strand and
cause the separation of the double helix.
4. Primers/Primases
• Primers are short—4 to 15 nucleotides long—
RNA oligonucleotides synthesized from
ribonucleoside triphosphates. They are
needed to initiate the primase-catalyzed
synthesis of both daughter strands.
5. DNA Polymerase - key enzymes in replication
• Once the two strands are separated at the
replication fork, the DNA nucleotides must be
lined up. In the absence of DNA polymerases,
this alignment is extremely slow. The enzyme
enables complementary base pairing with high
specificity. While bases are being hydrogen
bonded to their partners, polymerases join the
nucleotide backbones
Along the lagging strand 3’—>5”, the enzymes
can synthesize only short fragments, because
the only way they can work is from 5’ to 3’.
These resulting short fragments consist of
about 200 nucleotides each, named Okazaki
fragments after their discoverer.
6. Ligation
• The Okazaki fragments and any nicks
remaining are eventually joined by DNA ligase.
HOW DO WE AMPLIFY DNA?
To study DNA for basic and applied scientific
purposes, we must have enough of it to work with.
• Millions of copies of selected DNA fragments
can be made within a few hours with high
precision by a technique called polymerase
chain reaction (PCR).
• To use PCR, the sequence of a gene to be
copied or at least a sequenced segment
bordering the desired DNA must be known.
• In such a case, two primers that are
complementary to the ends of the gene or to
the bordering DNA can be synthesized. The
primers are polynucleotides consisting of 12 to
16 nucleotides. When added to the target DNA
segment, they hybridize with the end of each
strand of the gene.
HOW IS DNA REPAIRED?
• Externally, UV radiation or highly reactive
oxidizing, such as superoxide, may damage a
base
• Errors in copying or internal chemical
reactions, such as deamination of a base, can
create damage internally
 • Deamination of cytosine turns it into uracil,
which creates a mismatch. The former C-G
base pair becomes a U-G mispairing that must
be removed

One of the most common base repair prepare means is

called BER, base excision pair
The BER pathway contains two parts:
1. A specific DNA glycolase recognizes the damaged
base
• catalyzes the hydrolysis of the N-C’ β-glycosidic
bond between uracil base and the
deoxyribose, then releases the damaged base
(uracil) completing the excision. The sugar-
phosphate backbone is still intact.
• At the AP site (apurinic or apyrimidinic site)
created in this way
o The backbone is cleaved by a second
enzyme, exonuclease.
o A third enzyme, endonuclease
liberates the sugar-phosphate unit of
the damaged site.
2. In the synthesis step, the enzyme DNA polymerase
inserts the correct nucleotide, cytidine
• the enzyme DNA ligase seals the backbone to
complete the repair

NER (Nucleotide excision repair) pathway

• involves whole nucleotide

Xeroderma pigmentosa - a condition in which an

enzyme in the NER pathway is missing or defective thus
having a greater risk of developing skin cancer