MT2112: BIOCHEMISTRY | LECTURE

Lesson 4: Nucleic Acid

the DNA and the ribosomes. The mRNA

sequence is then read to build proteins. The
OUTLINE:
progression from DNA to RNA to protein is the
I. Introduction "CENTRAL DOGMA" of molecular biology.
II. Nucleic Acid o CENTRAL DOGMA – Theory that
III. Nitrogen Bases states there is only one flow of genetic
a. Pyrimidines information. Starting from DNA to RNA
b. Purines then to proteins.
IV. Pentose Sugar
V. Nucleoside
NUCLEIC ACIDS
VI. Nucleotides
a. Formation of Nucleotides
• The nucleic acids DNA and RNA consist of
b. Nucleoside & Nucleotides with
monomers called nucleotides that consist of a:
Purines / Pyrimidines
o Pentose Sugar
VII. Structure of Nucleic Acids
▪ 5 carbon sugar
a. Example of RNA & DNA
o Nitrogen-Containing Base
structure
o Phosphate
b. DNA Double Helix
VIII. Complementary Base Pairs
IX. DNA Replication
X. RNA & The Genetic Code
XI. RNA
a. Transfer RNA
XII. Protein Synthesis
a. Replication
b. Transcription
c. Translations

NUCLEIC ACID
NITROGEN BASES
INTRODUCTION The nitrogen bases in DNA and RNA are:

• Nucleic acids DEOXYRIBONUCLEIC ACID • PYRIMIDINES

(DNA) and RIBONUCLEIC ACID (RNA), carry o Cytosine – DNA
genetic information which is read in cells to o Thymine – DNA
make the RNA and proteins by which living o Uracil – RNA
things functions. • PURINES
o PROTEIN – builds most of our body o Adenine – DNA
and needed to maintain the living cell. o Guanine – DNA
• Nucleic acids are macromolecules composed
of units called NUCLEOTIDES.
o Nucleosides – simpler; no phosphate
group just sugar and nitrogenous base
o Nitrogen Bases – simplest; ATGCU

• Many genes encode for specific sequences of

amino acids which then be converted into
proteins, but before this information can be
used for protein synthesis, an RNA copy
(transcription) of the gene must first be made.
• This type of RNA is called MESSENGER RNA
(MRNA), as it serves as a messenger between
 NUCLEOTIDES

• Is a nucleoside that forms a phosphate ester

with the C5' -OH group of a sugar (ribose or
PENTOSE SUGAR deoxyribose)
• The pentose (five-carbon) sugar • Is named using the name of the nucleoside
o In RNA is Ribose followed by 5'-monophosphate.
○ Single structure
○ Has oxygen
o In DNA is Deoxyribose with no oxygen
atom on carbon 2’.
○ Double helix
○ Having no oxygen on carbon 2’
o Has carbon atoms numbered with primes
to distinguish them from the atoms in
nitrogen bases.

FORMATION OF NUCLEOTIDE

• A nucleotide forms when the -OH on C5' of a

sugar bonds to phosphoric acid.

NUCLEOSIDE

• Has a nitrogen base linked by a glycosidic

bond to C1' of a sugar (ribose or
deoxyribose).
• Is named by changing the nitrogen base
ending to:
o -OSINE for purines
o -IDINE for pyrimidines

• Adenine to Adenosine
• Guanine to Guanosine
• Cytosine to Cytidine
• Thymine to Thymidine
 NUCLEOSIDES AND NUCLEOTIDES WITH
PURINES
• Nucleoside to Nucleotides
○ Addition of phosphate group
○ 5’-monophosphate
NUCLEOSIDES AND NUCLEOTIDES WITH
PYRIMIDINES
• Nucleoside to Nucleotides
○ Addition of phosphate group
○ 5’-monophosphate
NAMES OF NUCLEOTIDES AND
NUCLEOSIDES
PRIMARY STRUCTURE OF NUCLEIC ACIDS
• NUCLEIC ACIDS (polymer) is composed of
many nucleotides (monomer)
• In the primary structure of nucleic acids
• nucleotides are joined by phosphodiester
bonds.
○ PHOSPHODIESTER BONDS – link
one nucleotide to another nucleotide.
■ It is between ribose sugar and
phosphate group.
• The 3'-OH group (carboxyl) of the pentose
sugar in one nucleotide forms an ester bond
to the phosphate group on the 5'-carbon of
the sugar of the next nucleotide.
STRUCTURE OF NUCLEIC ACIDS
A NUCLEIC ACID:
• It has a free 5'-phosphate group at one end
and a free 3'-OH group at the other end.
o Read as 5’ to 3’ direction
• Is read from the free 5'-end using the letters of
the bases.
• This example reads:
o -A-C-G-T-
 EXAMPLE OF RNA STRUCTURE
THE PRIMARY STRUCTURE OF RNA:
• Is a single strand of nucleotides with bases A,
C, G, and U.
• Is linked by phosphodiester bonds between
ribose and phosphate.
EXAMPLE OF DNA STRUCTURE
• Nucleotides containing bases A, C, G, and T
are linked by ester bonds between
deoxyribose sugars and phosphate groups.
DNA DOUBLE HELIX
A DOUBLE HELIX:
• Is the structure of DNA.
• Has two strands of nucleotides that wind
together.
• Is held in place by 2 HYDROGEN BONDS that
form between the base pairs A-T.
• Is held in place by 3 HYDROGEN BONDS that
form between the base pairs G-C.
IN THE DOUBLE HELIX OF DNA:
• Two strands of nucleotides form a double helix
structure like a spiral staircase.
• Hydrogen bonds link bases A-T and G-C.
• The bases along one strand complement the
bases along the other.
• ANTI-PARALLEL – opposite running of 5’ and
3’ (salungat yung nitrogen bases)
• Phosphodiester bond – nucleotide to
nucleotide
• Hydrogen bond – nitrogen bases to nitrogen
bases
COMPLEMENTARY BASE PAIRS
DNA contains complementary base pairs in
which:
• ADENINE is always linked by two hydrogen
bonds with THYMINE (A-T)
• GUANINE is always linked by three hydrogen
bonds with CYTOSINE (G-C)
o Stronger and stable bond
DNA REPLICATION
IN DNA REPLICATION:
• Genetic information is maintained each time a
cell divides.
• The DNA strands unwind.
• Each parent strand bonds with new
complementary bases.
• Two new DNA strands form that are exact
copies of the original DNA.
 RNA AND THE GENETIC CODE
• Transcription – will use DNA as source of
information to produce a series of amino acids
that then converted into protein.
o Form a mRNA, that will undergo
translation to amino acids to protein.
RNA
• Transmits information from DNA to make
proteins.
• Has several types:
o Messenger RNA (mRNA) carries
genetic information from DNA to the
ribosomes.
o Transfer RNA (tRNA) brings amino
acids to the ribosome to make the
protein.
o Ribosomal RNA (rRNA) makes up 2/3
of ribosomes where protein synthesis
takes place.
• mRNA (5-10) – serves as a blueprint/floorplan,
has the code for amino acid that will eventually
form.
• tRNA (10-15) – links the ribosomes to the
mRNA to make protein, then transports it to the
ribosome for protein.
• rRNA (75) – for the formation of proteins.
TRANSFER RNA (tRNA)
EACH tRNA:
• Has a triplet called an anticodon that
complements a codon on mRNA.
○ CODON (code) – sequence of code
that is equivalent to specific amino acid.
• Bonds to a specific amino acid at the acceptor
stem.
PROTEIN SYNTHESIS
PROTEIN SYNTHESIS INVOLVES:
• TRANSCRIPTION – mRNA is formed from a
gene on a DNA strand.
• TRANSLATION – tRNA molecules bring amino
acids to mRNA to build a protein.
DNA – Replication (2 new strands) – Transcription
(form mRNA) – Translation (form amino acid to
protein)
TRANSCRIPTION: SYNTHESIS OF mRNA
DURING TRANSCRIPTION:
• A section of DNA containing the gene unwinds.
• One strand of DNA bases is used as a
template.
• mRNA is synthesized using complementary
base pairing with uracil (U) replacing thymine
(T).
• The newly formed mRNA moves out of the
nucleus to ribosomes in the cytoplasm.
RNA POLYMERASE
DURING TRANSCRIPTION:
• RNA polymerase (enzyme) moves along the
DNA template to synthesize the corresponding
mRNA.
• The mRNA is released at the termination point. AUG – start codon
UUA UAG UGA – stop codons

CODONS AND AMINO ACIDS

• Determine the amino acids from the following

codons in a section of mRNA.
o CCU - AGC - GGA - CUU -
• According to the genetic code, the amino acids
for these codons are:
o CCU = proline
o AGC = serine
PROTEIN SYNTHESIS: TRANSCRIPTION o GGA = glycine
o CUU = leucine
• This mRNA section codes for an amino acid
sequence of:
o - CCU - AGC - GGA - CUU -
o - Pro - Ser - Gly - Leu -

INITIATION OF PROTEIN SYNTHESIS

FOR THE INITIATION OF PROTEIN

SYNTHESIS:
• A mRNA attaches to a ribosome.
• The start codon (AUG) binds to a tRNA with
methionine.
• The second codon attaches to a tRNA with the
next amino acid.
• A peptide bond forms between the adjacent
GENETIC CODE amino acids at the first and second codons.

THE GENETIC CODE:

• Is a sequence of amino acids in a mRNA that TRANSLOCATIONS
determine the amino acid order for the protein.
DURING TRANSLOCATION:
• Consists of sets of three bases (triplet) along
• The first tRNA detaches from the ribosome.
the mRNA called codons.
• The ribosome shifts to the adjacent codon on
• Has a different codon for all 20 amino acids
the mRNA.
needed to build a protein.
• A new tRNA/amino acid attaches to the open
• Contains certain codons that signal the "start"
binding site.
and "end" of a polypeptide chain.
• A peptide bond forms and that tRNA detaches.
• The ribosome shifts down the mRNA to read
the next codon.
THE GENETIC CODES: mRNA CODONS o Ribosome recognize codons that are
found in mRNA.
 PEPTIDE FORMATION

PROTEIN SYNTHESIS

TERMINATION

IN THE TERMINATION STEP:

• All the amino acids are linked.
• The ribosome reaches a "stop" codon: UGA,
UAA, or UAG.
• There is no tRNA with an anticodon for the
"stop" codons.
• The polypeptide detaches from the ribosome.

SUMMARY OF PROTEIN SYNTHESIS

TO SUMMARIZE PROTEIN SYNTHESIS:

• A mRNA attaches to a ribosome.

• tRNA molecules bonded to specific amino
acids attach to the codons on mRNA. The
ribosome shifts to each codon on the mRNA
until it reaches the STOP codon.
• Peptide bonds form between an amino acid
and the peptide chain.
• The polypeptide chain detaches to function as
an active protein