SUMMARY OF BIOCHEMICAL TESTS

Summary of Biochemical Tests

Tests used to
identify Gram Positive
Catalase Test Bacteria
Mannitol Salt Agar (MSA)
Blood Agar Plates (BAP)
Streak-stab technique
Taxos P (optochin
Taxos A (bacitracinsensitivity testing)
CAMP Test sensitivity testing)
Bile Esculín Agar
Nitrate Broth
Spirit Blue agar
Starch hydrolysis test
Motility Agar
Coagulase Test
Tests used to identify Gram
Oxidase Test
Sugar (egglucose) broth with
Negative Bacteria
Durham tubes
Methyl Red /
Voges-Proskauer (MR/VP)
Kliger's Iron Agar (KIA)
Nitrate Broth
Motility Agar
MacConkey agar
Simmon's Citrate Agar
Urease test
Sulfur Indole Motility Media (SIM)
 CHAPTERI

INTRODUCTION

1.1BACKGROUND
information encoded within
The genetic code is the set of rules by which genetic material
(DNA or mRNA sequences) is translated into proteins by living cells.
accomplished by the ribosome, which links amino acids in an order specified by
Translation is
mRNA, using
transfer RNA (tRNA)molecules to carry amino acids and to read the mRNA three nucleotidee at
a time. The genetic code is highly similar among all
organisms and can be expressed in a simple
table with 64 entries, The code defines how
sequences of nucleotide triplets, called codons.
specify which amino acid will be added next during
in a nucleic acid sequence
protein synthesis.A three-nucleotide codon
specifies a single amino acid. Because the vast
encoded with exactly the same code (see the majority of genes are
RNA codon table), this
referred to as the canonical or standard particular code is often
some variant codes have genetic code, or simply the genetic code, though in fact
evolved. For example, protein
differs from:the, standard synthesis human mitochondria relies
on a genetic code that in
determines a protein's amino acid genetic code.While th
these proteins are sequence, other genomic regions "genetic code"
produced according to a
multitude more complex "gene
of
determine when and where
Codon (genetic code) is a series of regulatory codes".
combi
to as a
nationof nucleotides in the
three-Thenucleotide sequence that encodes a particular amino
mRNA which consists of a
triplet codon.
sequence ATG amino acids encoded by acid, so often referred
are in an (AUG in RNA). Many the example of
methionine by the nucleotide
mRNA amino
the start codon molecule. Translation of
acids are encoded by more
than one codon. Codons
(AUG) and the final mRNA into
Codon in an mRNA codon (UAA, UAG,protein-coding is done on roads
flanked by
tRNA. Each mol ecule Can or UGA), these
called tRNA carries the exncode amino acids with the help of segments called genes.
anticodon that are in
amino acid corresponding to three or interpretation codon by
codon in the tRNA triplet nucleotide
mRNA. The
mRNA, so that
amino anticodon node. Anticodon binds sequence
genetic message acids brought by the tRNA in accordance withcompl e mentarily at
translation codon by codon in a way tRNA carriesexisting codon in
amino acids
corresponding anticodon complementary to a codon and
polypeptide chain. Ribosome adds cach amino acid ribosome connect amino acids into a
polipeptide chain. carried by tRNA to the end of the growing

The genetic code codes for

proteins. The information of the DNA is
chain of amino acids that forms a "translated' into a
protein. These proteins form the building blocks for
within the cells and ultimately the whole body. structures
Proteins also form enzymes and other chemicals
that perform various functions in the body. Each
gene can code for different proteins and thus the
number of proteins known to exist in the cells is more than the
number of genes. All genes are
not expressed or do not code for any protein. This
could be organ specific for example a liver
cell expresses different genes than kidney cells. The
environment also plays a role in determining
the ultimate trait. The phenotype of an organism thus depends on the interaction of
genetics with
the environment. The environment for example, has a role in effects of the human
genetic
disease phenylketonuria, The mutation that causes phenylketonuria disrupts the ability of the
body to break down the amino acid phenylalanine. This leads to toxic build-up of an intermediate
molecule leading to mental retardation and seizures. Persons with phenylketonuria mutation on a
strict diet that avoids this amino acid may remain normal and healthy.

1.2PROBLEM
1. What is the genetic code?
2. What are properties of the genetic code?
3. What is meant by the start codon and stop codon?
4. How the process of protein synthesis?
5. What are the functions of the genetic code?
genetic code?
6. What is relation between mutation and

1.3PURPOSE
1. To know the genetic code
genetic code
2. To know properties of the
the start codon and final codon
3. To know meant by
of protein synthesis
4. To know the process
2
 5. To know the functions of the genetic code in the body
6. To know therelation between mutation and genetic code

1.4BENEFIT
1. Giving additional
information topublic about genetic code
 CHAPTER II
CONTENT

2.1 DEFINITION OF GENETIC CODE

Genetic cole is the set of rules by which
informationencoded within genetic material
(DNA or mRNA sequences) is translated into protein by
living cells. This help in determining
the amino acid sequence used in the synthesis of an
organism proteins and it is universal in all
organism. Genetic code composed by codon, codon is a sequence of three DNA or RNA
nucleotides that corresponds with specific amino acid or stop signal during protein synthesis.

2.2 CHARACTERISTIC OF GENETIC CODES

Characteristic of genetic codes are:

Triplet code
core word. The codons.
The group bases specifying one amino acid is called a codon or
are strong evidences to prove that a
are formed using the bases available in mRNA. There
protein, the code is triplet.
sequence of three nucleotides code for one amino and
nucleotide bases (A, G, C, and U) in mRNA are used to produce the three base
The four There are
codons include the sense codons (codons that specify amino acid).
codons. The 64
amino acids, and since each codon code for only one amino
therefore, 64 codon code for the 30
are more than one code for the same amino acid.
this means that, there
acids
Commaless code
codon is immediately adjacent to the next,
There is no punctuation between; that is, each
nucleotides in between.
without any spacer
 Nonoverlapping code
nucleotide that forms part of a triplet
sequentially read in group of three. A direction so the first base is
The code is 5' ->3'
thenext triplet. Each triplet is read from
never forms part of 3' base.
middle base then the last base which is
5' base, followed by the

Examples:
5'-AUG3' codes for methionine

5'-UCU-3' codes for serine

5°-CCA-3' codes for proline

The coding dictionary

Second letter Key:

Als Alanine (A
UUU UCU UAU 1 UGU Arg Arginine (R)
UUG Ph UCC UAC TY UGG Cy
Ser
UAA 8TOP UGA STOR
Asn A^paragioe (N)
UUA LOu
UUG
UCA
UCG UAG STOP UGG Trp AspASpartate {D)
CysCystelne, (C)
Gln Glytamine (Q)
First
letter. CUU: CCU CAU ) CGU)
CUC CCC GAC His CGC
Gl Guamate (E)
CUA
Leu
CCA
Pro
CAA CGA Arg Gly Glycné (3)
CUG CCG CAG Gln CGG Nis Hlstidine (H).
lle soleucne 4)
AUU ACU AAU AGU Ly Leucdne (Ly
AUCe ACC AACIAsn AGC Ser Ly Lysine ()
AUA ACA AAA AGA 1.s Mot Mothionlne M)
AUG Mot ACG AAG Y AGGAg Phe Phenyalanine ()
Pro Poine )
GUU GCU) GAU GGT Ser Serino (3)
GUC GCC GACAp GOC Thr Threonino (T)
Val. Ala Gly Trp Typtophan (W)
GUA GCA GAA
GAG Gly GGA
GUG GCG 8GG TyrTyrosine (V)
Val Vaine (V1
Picture 1. The Codon Table

Degenerate code

Al amino acids except methionine (AUG) and tryptophan (UGG) are coded by several
codons: that is; some codons are synonyms. For example, theonine is coded by four codons
ACU, ACC, ACA and ACG.
 Universality of code
Genetic code is largely universal for all
living organisms and viruses.
exceptions are found in mitochondria, For example, However a few
human, is the code for tryptophan yeast in UGA, one of the termination codons in
mitochondria. Few other examples are stated below:
Non ambiguous code
The code is unambiguous under normal conditions, that means
that each codon specifics
the samne amino acid all the time.

Chain initiation codons

The initiation signal for the synthesis polypeptide chain is AUG

Chain termination codons

The termination, signal is provided by three codons UAG(Amber), UAA (0chre) and
UGA (opal). These chaintermination codons do not code for any amino acids and hence termed
as non sense codons.

Polarity
fixed direction, in the 5 to 3
The genetic code has polarity, the code is always read in
direction, it would specify 2 different
direction. It is apparent that if the code is read in opposite
protein.

2.3 GENE EXPRESSION

expression simply refers to the events that transfer the information

The process of gene Although there
gene into the production of a functional product, usually a protein.
content of the
is an RNA, inclåding the genes encoding the ribosomal
product
are genes whose functional majority of genes
transfer RNAS and certain other small RNAs, the vast
RNAS as well as the expression are as follows:
protein-encoding genes. Mechanismn of gene
within the cellare

6
 Transcription

expression is the transcription of the DNÁ molecule into an exact

Thà initial step in gene
copy. The transfer of infomation, to the ultimate synthesis of a protein, is accomplished
RNA
Via an RNA intermediate, the so-called nessenger RNA.
(mRNA), The mRNAmolecule contains
(with U substituted for T),.
the exact same sequence of nucleotides as found in the DNA molecule
This occurs through the process known as transcription and is carried out by an enzyme termed
DNA-dependent RNA polymerase. Transcription always proceeds in a 5' to 3' direction with
respect to polarity of the nucleotides in the RNA. Thus, an unmodified primary transcription
product would contain a 5' end with a triphosphate and a 3' end with a OH.

The polymerase must initiate transcription. This does not involve a primer molecule as is
the case for DNA synthesis but rather starts at a specific site in the gene. This site is dictated as a
result of the interaction of the RNA polymerase at a specific site, guided by the transcription
factors that have bound to the promoter and enhancer sequences. The polymerase must
complete
the transcription of the gene and then terminate transcription. In some cases, the
termination of
transcription is precise whereas in other cases it can occur heterogeneously over a broad region
of DNA.

Post-Transcriptional Eventutigvyels
Whereas the initial transcript of a bacterial gene is the actual
messenger RNA, the initial
transcript of a eukaryotic gene must be altered in a variety of ways before it can
function. Thus,
post-transcriptional processing and modification events are critical to the formation of a
eukaryotic mRNA. i6
RNA Modifications

In addition to the various steps that process the initial

primary transçript, the mRNA is
also modified in several ways. The 5'
terminus of the transoript is capped by the addition ofa
modified GTP residue that forms a 5-5' linkage. Internal
adenosine residues in the RNA are
modified methylation but the function of these modifications is not known.
by
 Nucleus-Cytoplasmic RNA Transport
Unlike bacteria, the eukaryotic cell is compartmentalized.
Therefore, the final processed
product (mRNA) must be transported through the nuclear envelope to reach the cytoplasm and
be engaged with the ribosomes for translation.

Translation

Translation is essentially the reading of the sequence in the mRNA to direct the synthesis
translation: Ribosome, a multicomponent.
of a unique protein. There are two components of
upon which protein synthesis takes place.
RNA-protein structure that serves as the framework
enzymatic activity for formation of the peptide bonds; and tRNA, a
and which also provides the tRNA carries the amino acid to the
small RNAs, each specific for a given amino acid. The
set of
growing polypeptide chain. The anticodon in the tRNA is
ribosome for insertion into the are synthesized from N terminus to C
mRNA, The proteins
complementary to the codon in the
elongation, and termination. none oe
terminus in 3 steps: initiation,
Initiation
recognition of a methionine codon (AUG) in the
synthesis involves that is used for
Initiation of protein methionyl tRNA
from the
special methionyl tRNA, different initiation factors
mRNA by a through the action of several
The initiation event is accomplished subunit, GTP, and the
initiator
elongation, small ribosomal
interaction of the mRNA with the mRNA is facilitated by the RNA
that allow codon in the
recognition of the initiating AUG subunit of the
met-tRNA. The interaction takes place, the large
surroundthe codon. Once the
sequences that
interacts and protein synthesis begins.
ribosome

b. Elongation appropriate amino acid

which carry the
are recognized by tRNAS, between the codon in
the
in the mRNA pairing
Codons
Codon recognition involves base ribosome that are
machinery. functional sites on the
to the translation tRNA. There are two (peptidyl) and the A
anticodon in the formation. The P site
mRNA and the peptide bond in the P site
that facilitate tRNA remaining
occupied by tRNA and formation of the peptide bond,
the
aminoacyl-tRNA, specified
Following A new
site (aminoacyl). complex moves to the P site. 8
tRNA-peptidyl
leaves and the
 the A site and peptide chain elongation continues. The
by the mRNA codon, then moves into
peptide bond formation is a function of the large ribosomal subunit. Very recent
catalysis of
Component of the large subunit that carries the
evidence indicates that it is the ribosomal RNA
nzymatic activity of peptidyl transferase.
C. Termination

thus
Three codons (UAG, UAA, and UGA) do not specify an amino acid-tRNA and
cause termination of translation. These codons signal the release of the peptidyl-tRNA complex
when recognized by termination factors. This results in the release of an uncharged tRNA
lacking an attached amino acid residue as well as the completed polypeptide chain. The
ribosome then disengages from the mRNA and the subunits dissociate, ready to start the cycle
over again.

V2.4 FUNCTION OF GENETIC CODES

Genetic codes play a role in synthesize of protein. Genetic code becomes a basic to
explain how abnormality of proteins can gave some effect such as genetic disorder and we can
uphold diagnosis and treatment that should given for genetics disorder. Genetic code that formed
by 64 codons, 61 codons bring information of amino acid and three codons induced termination
of protein synthesize. We all know that cach codon specifies one single acid(Picturel).
Previously we have discuss about characteristic of genetic code, especially every characteristic
of genetic code have their function, example to helps prevent effects of DNA mutations, most
amino acids have more than one codon, and it is unambiguous that means each codon has only
one meaning for one acid.

2.5 GENETIC CODES AND MUTATION.

As we know genetic code are composed by codon. Codon is a sequence of three base
DNA or RNA and we can also called it as triplet base.
 A
mutation is a change in genetic codes
material of life, such that the which we can fnd it in
genetic code differs from what is DNA, the hereditary
wrong genetic codes will occur the found in most people, so the
because it range in size; mutation. Mutations may or may not
cause health problem
they can affect anywhere from a
chromosome that includes multiple genes. DNA affects howbaseit pair to a large segment oI a
physiology. So a change in DNA can cause changes in all looks, how it behaves, and its
aspects of its life.
Mutations can be lassified in two major ways:
Hereditary mutations are inherited fromaparént and are present throughout a
persons life
in virtually every cell in the body. They are
presenting the parents egg or sperm cells,
which are also called germ cells.
Acquired/somatic mutations occur at some time during aperson life and are present only
in' certain cells. These changes caused by environmental factors or occur if a mistake is
made as DNA copies itself during cell division. Acquired mutations in somatic cells
cannot be passed'on to the next generation.

Mosaicsm is somatic mutation which the genetic changes are not presenting a parent's
egg or sperm cells,or in the fertilized egg, but happen when the embryo growth several cells. As
all the cells divide during growth and development, cells that occur from the cell with the altered
gene willhave the mutation, while other cells will not.Some genetic changes are very rare; others
are common in the population. Genetic changes that occur in more than 1% of the population are
called polymorphisms. They are common enough to be considered a normal variation in the
DNA. Polymorphisms are responsible for many of the normal differences between people such
as eye color, hair color, and blood type. Although many polymorphisms have no negative effects
certain
on a persons health, some of these variations may influence the risk of developing
disorder
person's
So as we describe above, the mutation of genetic codes may or may not effect
becomes UUC, because both of them
health, it will not damage for examples if the codon UUU
when it comes to a nonsense mutation it
will produce the same amino acid phenylalanine. But
codon that supposed to produce amino acid
may affected, nonsense mutation occur when a
into stop codon, it will cause some premature protein, which mean the protein is shorter
change
10
 these protein usually
than normal because it can't finish adding all the necessary amino acid and
Then what will happen if the ston
are not functional then it may caused many genetic disorder.
codon doesn't occur? These mRNA that lack of stop codon will cause the translation to continue
into the poly-A (lysine). Since there isno stop codon is present, the ribosome attached to the
mRNA,it willcause the activation ofa pathways known as non-stop decay.

The other changes of genetic code is present in the codon that produce amino acid, when
the genetic code is changed then it will produce the different amino acid which mean that the
protein are differs from the normal one and it may caused the health problem. There are 4
mutation that will changes the genetic code. Transvertion is the changes pirimidin becomes purin
for example if we had the DNA with base TAC it becomes GAC the problem is mRNA will
.transcript different code and it will leads to different protein. Transition is the change in genetic
code 'where the purin becomes purin and pirimidin becomes pirimidin. Deletion is a ch¡nge of
genetic code caused by deleted some base. And insertion is the change of genetiç code because
of additional base.
 CHAPTER III
SUMMARY
Genetic code is the set of rules by
(DNA or mRNA which information encoded within genetic material
sequences) is translated into
codon, codon is a sequence of three protein by living cells. Genetic code composed by
DNA or RNA nucleotides that
amino acid or stop signalduring coresponds with specific
protein synthesis.
There are shecific characteristics of genetic
codes, such as that a codon that are composed
of three nucleotide: bases, have a total of 64 for
30 amino acids,therefore there are more than
one code for the same amino acid with exception of
methionine(AUG)and tryptophan (UGG)
that only have one code for each. Another example is that genetic code has polarity and have a
main function in synthesizing of protein.

The process of gene expression simply refers to the events that transfer the information
content of the gene into the production of a functional product, usually a protein. The mechanisn
of gene expression are trarnscription, post-transcriptional event, RNA modification, nucleus
cytoplasmic RNA transport, translation. Meanwhile the process of protein synthesizing follow
the order of initiation, elongation, and
termination.

A mutation is a change in genetic codes which we can find it in DNA, the hereditary
most people. Mutation is
material of life, such that the genetic code differs from what is found in
mutation. In addition, there are
classified in two ways, heredity mutation and acquired/somatic
are transversion, transition, deletion
several types of mutations that change genetic codes. There
and insertion.
 REFERENCES

1. Voet Donald, Voet Judith G.,Prat Charlotte W. Fundamental of biochemistry: life at the
molecular level. 4h ed; 2006:814-817.
2. Nevins, Joe &West, Mike. Gene expression analysis. Durham: Duke University:
Durham; 2004:113-146.
3. Murray, Robert K,et al. Harper's Illustrated Biochemistry. 29"ed. New York: Mc-Graw
Hill; 2014:441.
4. What is mutation gene and how do it occur? [Internet]. 2016 [cited 3 December 2016].
Available from: https:llghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation
5. Mutation and health; 2016:3-7.
6. Jeraldo P. The genetic code; 2006.
7. Klauer and van HÍof. Degradation of mRNAs that lack a stop codon: A decade of
nonstop progress. Wiley Interdiscip Rev RNA; 2012 [cited 5 December 2016]:3:649-650.