1. The genetic code is deciphered through research that matched codons (three-nucleotide sequences in mRNA) to their corresponding amino acids. It was discovered that 61 codons code for specific amino acids while 3 are stop codons. 2. tRNA molecules carry specific amino acids and have anticodons that are complementary to mRNA codons, allowing the correct amino acid to be added to the growing polypeptide chain via the ribosome. 3. Translation is the process of protein synthesis, directed by the mRNA template, where tRNA molecules bring amino acids to the ribosome according to codon-anticodon base pairing. The amino acids are linked together through the joining of peptide bonds.

2. THE GENETIC CODE
The nucleotide (base) sequence of an
mRNA molecule is the informational part
of such a molecule. This base sequence in
a given mRNA determines the amino acid
sequence for the protein synthesized
under that mRNA’s direction.

3. How can the base sequence of an mRNA
molecule (which involves only 4 different
bases—A, C, G, and U) encode enough
information to direct proper sequencing of 20
amino acids in proteins? If each base encoded
for a particular standard amino acid, then only
4 amino acids would be specified out of the 20
needed for protein synthesis, a clearly
inadequate number.

4. If two-base sequences were used to code
amino acids, and then there would be 42 = 16
possible combinations, so 16 amino acids
could be represented uniquely. This is still an
inadequate number. If three-base sequences
were used to code for amino acids, there
would be 43 = 64 possible combinations,
which is more than enough combinations for
uniquely specifying each of the 20 standard
amino acids found in proteins.

5. Research has verified that sequences of
three nucleotides in mRNA molecules
specify the amino acids that go into
synthesis of a protein. Such three-
nucleotide sequences are called codons. A
codon is a three-nucleotide sequence an
mRNA molecule that codes for a specific
amino acid.

6. Which amino acid is specified by which codon?
(We have 64 codons to choose from.)
Researchers deciphered codon–amino acid
relationships by adding different synthetic
mRNA molecules (whose base sequences were
known) to cell extracts and then determining
the structure of any newly formed protein. After
many such experiments, researchers finally
matched all 64 possible codons with their
functions in protein synthesis.

7. It was found that 61 of the 64 codons formed
by various combinations of the bases A, C,
G, and U were related to specific amino
acids; the other 3 combinations were
termination codons (“stop” signals) for
protein synthesis. Collectively, these
relationships between three-nucleotide
sequences in mRNA and amino acid
identities are known as the genetic code.

8. The genetic code is the assignment of the
64mRNA codons to specific amino acids (or stop
signals). The determination of this code during the
early 1960s is one of the most remarkable of
twentieth-century scientific achievements. The
1968 Nobel Prize in chemistry was awarded to
Marshall Nirenberg and Har Gobind Khorana for
their work in illuminating how mRNA encodes for
proteins.

9. 1. The genetic code is highly degenerate;
that is, many amino acids are designated by
more than one codon. Three amino acids
(Arg, Leu, and Ser) are represented by six
codons. Two or more codons exist for all
other amino acids except Met and Trp, which
have only a single codon. Codons that
specify the same amino acid are called
synonyms.

10. 2. There is a pattern to the arrangement of
synonyms in the genetic code table. All synonyms
for an amino acid fall within a single box, unless
there are more than four synonyms, where two
boxes are needed. The significance of the “single
box” pattern is that with synonyms, the first two
bases of the codon are the same— they differ only
in the third base. For example, the four synonyms
for the amino acid proline (Pro) are CCU, CCC,
CCA, and CCG.

11. 3. The genetic code is almost universal.
Studies of many organisms indicate that
with minor exceptions, the code is the
same in all of them. The same codon
specifies the same amino acid whether
the cell is a bacterial cell, a corn plant
cell, or a human cell.

12. 4. An initiation codon exists. The existence
of “stop” codons (UAG, UAA, and UGA)
suggests the existence of “start” codons.
There is one initiation codon. Besides coding
for the amino acid methionine, the codon
AUG functions as an initiator of protein
synthesis when it occurs as the first codon
in an amino acid sequence.

13. The Universal Genetic Code
The code is composed of 64 three-nucleotide
sequences (codons), which can be read from the
table. The left-hand column indicates the nucleotide
base found in the first (5’) position of the codon. The
nucleotide in the second (middle) position of the
codon is given by the base listing at the top of the
table. The right-hand column indicates the
nucleotide found in the third (3’) position. Thus the
codon ACG encodes for the amino acid Thr, and the
codon GGG encodes for the amino acid Gly.

15. ANTICODONS AND tRNA MOLECULES
The amino acids used in protein synthesis
do not directly interact with the codons of an
mRNA molecule. Instead, tRNA molecules
function as intermediaries that deliver amino
acids to the mRNA. At least one type of tRNA
molecule exists for each of the 20 amino acids
found in proteins. All tRNA molecules have the
same general shape, and this shape is crucial
to how they function.

16. The two-dimensional “cloverleaf” shape of a
tRNA molecule, a shape produced by the
molecule’s folding and twisting into regions
of parallel strands and regions of hairpin
loops. (The actual three-dimensional shape
of a tRNA molecule involves considerable
additional twisting of the “cloverleaf” shape.
Two features of the tRNA structure are of
particular importance.

17. 1. The 3’ end of the open part of the cloverleaf
structure is where an amino acid becomes
covalently bonded to the tRNA molecule through
an ester bond. Each of the different tRNA
molecules is specifically recognized by an
aminoacyl tRNA synthetase enzyme. These
enzymes also recognize the one kind of amino
acid that “belongs” with the particular tRNA and
facilitates its bonding to the tRNA.

18. 2. The loop opposite the open end of the
cloverleaf is the site for a sequence of
three bases called an anticodon. An
anticodon is a three-nucleotide
sequence on a tRNA molecule that is
complementary to a codon on an mRNA
molecule.

21. The interaction between the
anticodon of the tRNA and the
codon of the mRNA leads to the
proper placement of an amino
acid into a growing peptide chain
during protein synthesis.

22. TRANSLATION: PROTEIN SYNTHESIS
Translation is the process by which
mRNA codons are deciphered and a
particular protein molecule is synthesized.
The substances needed for the translation
phase of protein synthesis are mRNA
molecules, tRNA molecules, amino acids,
ribosomes, and a number of different
enzymes.

23. A ribosome is an rRNA–protein complex that
serves as the site for the translation phase
of protein synthesis. The number of
ribosomes present in a cell for higher
organisms varies from hundreds of
thousands to even a few million. Recent
research concerning ribosome structure
suggests the following for such structures:

24. 1. They contain four rRNA molecules and about 80
proteins that are packed into two rRNA-protein
subunits, one small subunit and one large subunit.
2. Each subunit contains approximately 65% rRNA and
35% protein by mass.
3. A ribosome’s active site, the location where proteins
are synthesized by one-at-a time addition of amino
acids to a growing peptide chain, is located in the
large ribosomal subunit.
4. The active site is mostly rRNA, with only one of the
ribosome’s many protein components being present.

25. 5. Because rRNA is so predominant at the
active site, the ribosome is thought to be a
RNA enzyme, that is, a ribozyme.
6. The mRNA involved in the translation phase
of protein synthesis binds to the small subunit
of the ribosome. There are five general steps
to the translation process: (1) activation of
tRNA, (2) initiation, (3) elongation, (4)
termination, and (5) post-translational
processing.

27.  Activation of tRNA
 There are two steps involved in tRNA
activation. First, an amino acid interacts with an
activator molecule (ATP) to form a highly
energetic complex. This complex then reacts
with the appropriate tRNA molecule to produce
an activated tRNA molecule, a tRNA molecule
that has an amino acid covalently bonded to it at
its 3’ end through an ester linkage

29. Initiation
The initiation of protein synthesis in
human cells begins when mRNA
attaches itself to the surface of a small
ribosomal subunit such that it’s first
codon, which is always the initiating
codon AUG, occupies a site called the P
site (peptidyl site).

30. An activated tRNA molecule with anticodon
complementary to the codon AUG attaches
itself, through complementary base pairing, to
the AUG codon. The resulting complex then
interacts with a large ribosomal subunit to
complete the formation of an initiation
complex. (Since the initiating codon AUG
codes for the amino acid methionine, the first
amino acid in a developing human protein
chain will always be methionine.)

31. Elongation
Next to the P site in an mRNA–
ribosome complex is a second binding
site called the A site (aminoacyl site).
At this second site the next mRNA
codon is exposed, and a tRNA with the
appropriate anticodon binds to it.

32. With amino acids in place at both the P and the A
sites, the enzyme peptidyl transferase effects the
linking of the P site amino acid to the A site amino
acid to form a dipeptide. Such peptide bond
formation leaves the tRNA at the P site empty and
the tRNA at the A site bearing the dipeptide. The
empty tRNA at the P site now leaves that site and
is free to pick up another molecule of its specific
amino acid. Simultaneously with the release of
tRNA from the P site, the ribosome shifts along
the mRNA.

33. This shift puts the newly formed dipeptide at
the P site, and the third codon of mRNA is now
available, at site A, to accept a tRNA molecule
whose anticodon complements this codon. The
movement of a ribosome along an mRNA
molecule is called translocation. Translocation
is the part of translation in which a ribosome
moves down an mRNA molecule three base
positions (one codon) so that a new codon can
occupy the ribosomal A site.

37. Now a repetitious process begins. The third
codon, now at the A site, accepts an incoming
tRNA with its accompanying amino acid; and
then the entire dipeptide at the P site is
transferred and bonded to the A site amino acid
to give a tripeptide. The empty tRNA at the P
site is released, the ribosome shifts along the
mRNA, and the process continues. The transfer
of the growing peptide chain from the P site to
the A site is an example of an acyl transfer
reaction.

39. Termination
The polypeptide continues to grow by way
of translocation until all necessary amino
acids are in place and bonded to each other.
Appearance in the mRNA codon sequence of
one of the three stop codons (UAA, UAG, or
UGA) terminates the process. No tRNA has an
anticodon that can base-pair with these stop
codons. The polypeptide is then cleaved from
the tRNA through hydrolysis.

40. Post-Translation Processing
Some modification of proteins usually
occurs after translation. This post-
translation processing gives the protein
the final form it needs to be fully
functional. Some of the aspects of post-
translation processing are the following.

41. 1. In most proteins, the methionine (Met)
residue that initiated protein synthesis is
removed by a specialized enzyme in a
hydrolysis reaction. A second hydrolysis
reaction releases the polypeptide chain from
its tRNA carrier.
2. Some covalent modification of a protein
can occur, such as the formation of disulfide
bridges between cysteine residues.

42. 3. Completion of the folding of polypeptides
into their active conformations occurs. Protein
folding actually begins as the polypeptide
chain is elongated on the ribosome. For
protein with quaternary structure, the various
components are assembled together. Recent
research indicates that there may be a
connection between synonymous codons
within the genetic code and protein folding.

43. It now appears that synonymous
codons, even though they translate into
the same amino acids during protein
synthesis, have an effect on the way
emerging proteins fold into their three-
dimensional shapes (tertiary structure)
as they elongate and then leave a
ribosome.

44. This means that two stretches of mRNA that
differ only in synonymous codons can
produce proteins with identical amino acid
sequences but different folding patterns.
Two differently folded proteins would be
expected to produce different biochemical
responses within a cell when interacting
with other substances; there is some
evidence, now, that this is the case.

45. Efficiency of mRNA Utilization
Many ribosomes can move simultaneously along a
single mRNA molecule. In this highly efficient
arrangement, many identical protein chains can be
synthesized almost at the same time from a single
strand of mRNA. This multiple use of mRNA
molecules reduces the amount of resources and
energy that the cell expends to synthesize needed
protein. Such complexes of several ribosomes and
mRNA are called polyribosomes or polysomes. A
polyribosome is a complex of mRNA and several
ribosomes.

47. MUTATIONS
A mutation is an error in base sequence in a gene
that is reproduced during DNA replication. Such
errors alter the genetic information that is passed
on during transcription. The altered information can
cause changes in amino acid sequence during
protein synthesis. Sometimes, such changes have a
profound effect on an organism. A mutagen is a
substance or agent that causes a change in the
structure of a gene. Radiation and chemical agents
are two important types of mutagens.

48. Radiation, in the form of ultraviolet light, X rays,
radioactivity, and cosmic rays, has the potential
to be mutagenic. Ultraviolet light from the sun is
the radiation that causes sunburn and can induce
changes in the DNA of the skin cells. Sustained
exposure to ultraviolet light can lead to serious
problems such as skin cancer. Chemical agents
can also have mutagenic effects. Nitrous acid
(HNO2) is a mutagen that causes deamination of
heterocyclic nitrogen bases. For example, HNO2
can convert cytosine to uracil.

49. Deamination of a cytosine that was
part of an mRNA codon would
change the codon; for example,
CGG would become UGG. A variety
of chemicals—including nitrites,
nitrates, and nitrosamines—can
form nitrous acid in the body.

50. The use of nitrates and nitrites as preservatives
in foods such as bologna and hot dogs is a
cause of concern because of their conversion to
nitrous acid in the body and possible damage to
DNA. Fortunately, the body has repair enzymes
that recognize and replace altered bases.
Normally, the vast majority of altered DNA
bases are repaired, and mutations are avoided.
Occasionally, however, the damage is not
repaired, and the mutation persists.

51. TYPES OF MUTATION
 Sickle-cell anemia – a substitution of a
single base pair in the gene that codes for
normal hemoglobin results in abnormally
shaped red blood cells.
 Albinism – is caused by a change in
nucleotide sequence of the gene that
codes for an enzyme necessary for pigment
production.

52.  Chromosome mutation – involves a change
in structure of an entire chromosome or
pieces of it.
 Germ mutation – mutations that occur in
the genes or chromosomes of reproductive
cells.
 Somatic mutations – occur in body cells
and are not passed to the offspring.