Nucleic

Acids and
Protein
Synthesis
Nucleic Acids
Nucleic acids are unbranched polymers composed of repeating monomers called nucleotides.

1. DNA, deoxyribonucleic acid, stores the genetic information of an organism and transmits that
information from one generation to another.
2. RNA, ribonucleic acid, translates the genetic information contained in DNA into proteins
needed for all cellular functions.

Nucleic acids were first isolated in 1869 by Friedrich Miescher and so named because he found them
in the nuclei of leukocytes (pus cells) from discarded surgical bandages.
Structural Differences between DNA and RNA
Nucleotides: Structural Building
Blocks
for Nucleic Acids
A nucleotide is a three-subunit molecule in which a pentose
sugar is bonded to both a phosphate group and a nitrogen-
containing heterocyclic base.
Pentose Sugars
 Bases
Nucleic acid bases (nucleobases) –
nitrogen containing aromatic
compounds that make
up the coding portion of nucleic
acids

purine bases – nitrogen-containing

aromatic compounds that contain a
six-membered ring fused to a five-
membered ring; the parent
compounds of two nucleobases,
adenine and guanine

pyrimidine bases – nitrogen-

containing
aromatic compounds that contain a
six-membered ring; the parent
compounds of several nucleobases
PHOSPHATE
Nucleotides
Nucleotides are phosphoric esters of nucleosides
Nucleotide Formation
1. First, the pentose sugar and nitrogen-
containing base react to form a two-
subunit entity called a nucleoside.
2. The nucleoside reacts with a
phosphate group to form the three-
subunit entity called a nucleotide. It is
nucleotides that become the building
blocks for nucleic acids.
Nucleoside Formation
• A nucleoside is a two-subunit
molecule in which a pentose
sugar is bonded to a nitrogen
containing heterocyclic base.

Important characteristics of the nucleoside formation process of combining two molecules into one are:
1. The base is always attached to C1′ of the sugar (the anomeric carbon atom, which is always in a b-
configuration. For purine bases, attachment is through N9; for pyrimidine bases, N1 is involved. The bond
connecting the sugar and base is a b-N-glycosidic linkage.
2. A molecule of water is formed as the two molecules bond together; a condensation reaction occurs.
Naming Nucleosides
• Nucleosides are named as derivatives of the
base that they contain; the base’s name is RNA Nucleosides DNA Nucleosides
modified using a suffix. ribose–adenine deoxyribose–adenine
1. For pyrimidine bases, the suffix -idine is
ribose–cytosine deoxyribose–cytosine
used (cytidine, thymidine, uridine). ribose–guanine deoxyribose–guanine
ribose–uracil deoxyribose–thymine
2. For purine bases, the suffix -osine is used
(adenosine, guanosine).
3. The prefix deoxy- is used to indicate that
the sugar present is deoxyribose. No prefix
is used when the sugar present is ribose.
Naming Nucleosides
 Nucleotide Formation

Important characteristics of the nucleotide formation process of adding a phosphate group to a nucleoside are the ff:
1. The phosphate group is attached to the sugar at the C5 ′ position through a phosphoester linkage.
2. As with nucleoside formation, a molecule of water is produced in nucleotide formation. Thus, overall, two
molecules of water are produced in combining a sugar, base, and phosphate into a nucleotide.
Naming Nucleotides
Nucleotides are named by appending the term 5′-monophosphate to the name of the
nucleoside from which they are derived. Addition of a phosphate group to the
nucleoside adenosine produces the nucleotide adenosine 5′-monophosphate.
The Structure of DNA
PRIMARY NUCLEIC ACID STRUCTURE
Primary nucleic acid structure is the sequence in which
nucleotides are linked together in a nucleic acid
The Secondary Structure of DNA
In 1953, Watson and Crick proposed a model for the secondary
structure of DNA.
DNA’s Base Composition is Governed
by Chargaff’s Rules
The amount of adenine present in DNA
always equals the amount of thymine, and
the amount of guanine always equals the
amount of cytosine.

Two important findings from this work are

often called Chargaff’s rules:
1. The proportion of A always equals that
of T, and the proportion of G always
equals that of C, or: A = T, and G = C.
2. The ratio of G–C to A–T varies with
different species.
The DNA Double Helix
DNA consists of two polynucleotide strands that wind into a right-
handed double helix.

The antiparallel nature of the two polynucleotide chains in the DNA

double helix means that there is a 5’ end and a 3’ end at both ends of
the double helix.

The two strands of DNA in a double helix are complementary. This

means that if you know the order of bases in one strand, you can
predict the order of bases in the other strand.

The following two notations for a DNA base sequence have identical
meaning.
5 ’ A–C–G–T–T 3’
5’ ACGTT 3’
major groove the larger of two
empty spaces in an imaginary
cylinder that encloses the DNA
double helix

minor groove the smaller of two

empty spaces in an imaginary
cylinder that encloses the DNA
double helix
B-DNA the most common form of the
DNA double helix

A-DNA a form of a DNA double helix

characterized by having fewer residues
per turn and major and minor grooves
with dimensions that are more similar
to each other than those of B-DNA

Z-DNA a form of DNA that is a left-

handed helix, which has been seen to
occur naturally under certain
circumstances
Tertiary Structure of DNA
For nucleic acids, tertiary structure refers to
overall three-dimensional shape, including
the contribution of secondary structure.

DNA Supercoiling The majority of DNA

molecules inside a cell are folded up on
themselves to create a structure known as a
supercoil.
DNA Supercoiling
Three parallels between primary nucleic
acid structure and primary protein
structure.
1. DNAs, RNAs, and proteins all have
backbones that do not vary in structure.
2. The sequence of attachments to the
backbones (nitrogen bases in nucleic
acids and amino acid R groups in
proteins) distinguishes one DNA from
another, one RNA from another, and
one protein from another.
3. Both nucleic acid polymer chains and
protein polymer chains have
directionality; for nucleic acids there is
a 5 end and a 3 end, and for proteins
there is an N-terminal end and a C-
terminal end.
DNA REPLICATION
Replication – the process by which an exact
copy of a DNA molecule is produced.

Semiconservative replication – a replication

process that produces DNA molecules containing
one strand from the parent and a new strand that
is complementary to the strand from the parent.

Replication fork – a point where the

double helix of a DNA molecule unwinds
during replication.
RNA as the Intermediary between
Genes and Proteins
• The sugar is ribose.
• U (uracil) replaces T (thymine) as one of the
bases.
• RNA is single stranded.
FROM GENES TO PROTEINS
• Transcription is the process by which RNA is produced to carry genetic
information from the nucleus to the ribosomes. A short segment of the DNA
double helix unwinds, and complementary ribonucleotides line up to produce
messenger RNA (mRNA).

• Translation is the process by which mRNA directs protein synthesis. Each

mRNA is divided into codons, ribonucleotide triplets that are recognized by
small amino acid carrying molecules of transfer RNA (tRNA), which deliver the
appropriate amino acids needed for protein synthesis.
PROTEIN SYNTHESIS
Transcription: DNA to RNA
• The enzyme RNA polymerase binds to DNA during transcription and separates the DNA strands.
The template strand is the strand of DNA used for RNA synthesis. The informational strand (the
non-template strand) is the strand of DNA not used for RNA synthesis. RNA polymerase then uses
the template strand of DNA to assemble nucleotides into a complementary strand of RNA.
• RNA polymerase binds only to promoters, regions of DNA that have specific base sequences.
Promoters are signals to the DNA molecule that show RNA polymerase exactly where to begin
making RNA. Similar signals cause transcription to stop when new RNA molecule is completed.
• RNA may be edited before it is used. Portions that are cut out and discarded are called introns.
The remaining pieces, the exons, are then spliced back together to form the final mRNA
DNA TRANSCRIPTION

The genetic information in DNA is

replicated in cell division and used to
produce messenger RNA that codes for
amino acids used in protein synthesis at
the ribosomes.
DNA undergoes transcription when RNA polymerase makes a
complementary RNA copy of a gene using only one of the DNA
strands as the template.
THE GENETIC CODE
In 1954, George Gamow proposed that because
there are only four “letters” in the DNA alphabet
(A, T, G, and C) and because there are twenty
amino acids, the genetic code must contain
words made of at least three letters taken from
the four letters in the DNA alphabet.

The genetic code is a sequence of three

nucleotides (a triplet) codes for a specific amino
acid. Each triplet is called a codon.
CODONS AND ANTICODONS
The 3 bases of an anticodon are
complementary to the 3 bases of a codon

Example: Codon ACU

Anticodon UGA
RNA to Protein: Translation
• Messenger RNA is transcribed in the nucleus and then
enters the cytoplasm.
• On the ribosomes, translation begins at the start codon.
Each codon attracts anticodon, the complementary
sequence of bases on tRNA.
• Each tRNA carries one kind of amino acid. The match
between the codon and anticodon ensures that the
correct amino acid is added to the growing chain.
• The amino acids bond together, each in turn. The
ribosome moves along the mRNA, exposing codons that
attract still more tRNA with their attached amino acids.
• The process concludes when a stop code is reached.
The newly formed polypeptide and the mRNA molecule
are released from the ribosomes.
An activated tRNA: (a) general structure and
(b) a schematic representation