Living Organisms are very complex.

All the activities of the body are carried out by hundreds of proteins inside every cell. These proteins specified for a particular function is controlled by a set of molecules called nucleic acids. Nucleic acids are very large molecules made up of a sugar backbone, phosphate molecule and nucleotide base. The genetic information of every living organism is stored inside these nucleic acid molecules. There are two types of nucleic acids namely: DNA- Deoxyribonucleic RNA - Ribonucleic acid. DNA- Deoxyribonucleic acid - In most living organisms (except for viruses), genetic information is stored in the form of DNA. DNA is present in the nucleus of every cell. The nucleotide bases present in the DNA are adenine (A), cytosine (C), guanine (G), and thymine (T). The original structure of the DNA molecule is a double helix. DNA is a double stranded structure. RNA- Ribonucleic acid forms the genetic material in smaller organisms namely viruses.RNA is important in the production of proteins in living organisms. RNA can move around in the cells of living organisms and serves as a genetic messenger, passing the information stored in the cell's DNA from the nucleus to other parts of the cell for protein synthesis. The 4 bases found in RNA are adenine (A), cytosine (C), and guanine (G), RNA does not contain thymine, instead, the fourth nucleotide present in RNA is the base uracil (U).RNA is a single stranded structure.

DNA & RNA

Difference between DNA & RNA

DNA
DNA is the molecule that is the hereditary material in all living cells. In 1953, two biochemists, James D. Watson and Francis H.C. Crick, proposed a model for the structure of DNA. DNA is present in chromosomes of nucleus. Genes are present on threadlike things called chromosomes. As proposed by Watson and Crick, deoxyribonucleic acid (DNA) consists of two long nucleotide chains. The two nucleotide chains twist around one another to form a double helix, a shape resembling a spiral staircase. Weak chemical bonds between the chains hold the two chains of nucleotides to one another.

DNA parts: A nucleotide in the DNA chain consists of three

a nitrogenous base, a phosphate group, and a molecule of deoxyribose. The nitrogenous bases of each nucleotide chain are of two major types: purines and pyrimidines. The two purine bases in DNA are adenine (A) and guanine (G). The pyrimidine bases in DNA are cytosine (C) and thymine (T). Purines and pyrimidine bases are found in both strands of the double helix. The phosphate group of DNA is derived from a molecule of phosphoric acid. The phosphate group connects the deoxyribose molecules to one another in the nucleotide chain. Adenine is always opposite thymine and binds to thymine. Guanine is always opposite cytosine and binds to cytosine. Adenine and thymine are said to be complementary, as are guanine and cytosine. This is known as the principle of complementary base pairing.

Nucleotide
The two nitrogenous bases are held together by weak hydrogen bonds. The nucleotide is formed of 3 components, namely a phosphoric acid, a deoxyribose sugar and a nitrogenous base. The nucleoside is formed of a base and a deoxyribose sugar.

Purines
A nitrogen-containing, double-ring, basic compound that occurs in nucleic acids. The purines in DNA and RNA are adenine and guanine. Adenine - Adenin is a purine base and base pair with A-T (adeninethymine) in DNA and A-U (adenine-uracil) in RNA. Guanine - Guanine is a purine base and base pair with G-C (guanine and cytosine).

Pyrimidines
A nitrogen-containing, single-ring, basic compound that occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine. The pyrimidines in RNA are cytosine and uracil.

Thymine - Thymine is a pyrimidine base and base pair with adenine in DNA.

Cytosine Cytosine is a pyrimidine base and base pair with guanine in DNA.

Pyrimidine
Uracil - Uracil is a pyrimidine base and base pair with adenine in RNA.

DNA Replication
The synthesis of new DNA molecules from pre-existing DNA is called replication. Replication of DNA begins at a specific point, called initiation point and is recognised by the initiator proteins. The mechanism of replication was one of three models originally proposed for DNA replication. 1. Semiconservative replication would produce two copies that each contained one of the original strands and one new strand. 2. Conservative replication would leave the two original template DNA strands together in a double helix and would produce a copy composed of two new strands containing all of the new DNA base pairs. 3. Dispersive replication would produce two copies of the DNA, both containing distinct regions of DNA composed of either both original strands or both new strands.

DNA Replication

DNA Replication
Semiconservative method - The process of DNA replication begins when specialized enzymes pull apart, or "unzip," the DNA double helix by breaking the hydrogen bond. As the two strands separate, the purine and pyrimidine bases on each strand are exposed. The exposed bases then attract their complementary bases. Deoxyribose molecules and phosphate groups are present in the nucleus. The enzyme DNA polymerase joins all the nucleotide components to one another, forming a long strand of nucleotides. Thus, the old strand of DNA directs the synthesis of a new strand of DNA through complementary base pairing. The old strand then unites with the new strand to reform a double helix. This process is called semiconservative replication because one of the old strands is conserved in the new DNA double helix.

Steps involved in DNA Replication

1. Initiation carried out by RNA primers synthesised by RNA primase. 2. Helicase unwinds double helix into two strands. 3. DNA Polymerase adds nucleotides to an existing strand. 4. Removal of RNA primer by Endonuclease. 5. Ligase brings together the Okazaki fragments.

DNA Replication
The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. The leading strand template is the strand of DNA being replicated continuously. The leading strand is formed as a polymerase "reads" the template DNA and continuously adds nucleotides to the 3' end of the elongating strand. The lagging strand grows in the direction opposite to the movement of the growing fork. It grows away from the replication fork and it is synthesized discontinuously. The RNA Polymerase reaches the origin of replication and stops replication until a new RNA primer is placed. These fragments of DNA produced on the lagging strand are called Okasaki fragments. Okazaki fragments are short molecules of single-stranded DNA that are formed on the lagging strand during DNA replication.

Genes
A gene is the fundamental unit of heredity. Gregor Mendel is the father of Genetics. Genes are found on chromosomes and are made of DNA. Small section of DNA are called genes. Different genes determine the different characteristics, or traits, of an organism. In the simplest terms one gene might determine the color of a bird's feathers, while another gene would determine the shape of its beak. Parents pass some of their characteristics on to you through genes. For example, if both of your parents have green eyes, you might inherit the trait of green eyes from them. Thus biological traits are passed on to successive generations.

Gene
Exon The segments of the genes code for amino acids. Intron - The segments of the genes does not code for amino acids.

Genetic Code
Genetic code is defined as the sequence of nitrogen bases in DNA or mRNA molecule which contains the information for the synthesis of protein molecules. Codon is defined as the sequence of nitrogen bases in mRNA which codes for a single amino acid. Triplet code It is the sequence of three nitrogen bases determining a single amino acid. Eg: GCU, GCC, GCA, GCG codes for the amino acid Alanine.

Genetic code
Initiation codon The synthesis of a polypeptide chain is initiated. Eg:AUG codes for the amino acid methionine. Termination codon - The synthesis of a polypeptide chain is completed. It does not code for any amino acid. Eg: UAA, UGA, UAG The triplet codons represented in terms of mRNA Language.

Gene Expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins. Gene expression is the most fundamental level at which the genotype gives rise to the phenotype. The genetic code stored in DNA is "interpreted" by gene expression, and the properties of the expression give rise to the organism's phenotype.

 Genetic material is packaged into DNA molecules. DNA molecules relay the inherited information to messenger RNA (mRNA) which, in turn, codes for proteins. This chain of command is represented as: DNA --> mRNA --> Protein. The flow of information from DNA to protein is known as the Central Dogma of molecular biology.

Transcription & Translation

Transcription
The coding strand contains the genetic information while non-coding strand serves as a blueprint for the production of RNA. The production of RNA copies of the DNA is called transcription and is performed by RNA polymerase, which adds one RNA nucleotide at a time to a growing RNA strand.

1.Template recognition One of the strand act as template. The template is determined by the specific sequence of DNA nucleotides called the promoter. RNA polymerase binds the promoter. 2.Initiation DNA is unwound at the promoter to form an open complex. Chains of 2-9 bases are synthesized and released. RNA polymerase joins ribonucleotides into a strand. 3.Elongation RNA polymerase synthesizes RNA. Transcription bubble moves along the RNA polymerase. RNA polymerase reaches the end of the gene. 4.Termination RNA polymerase ends the chain when it reaches a stop signal. Adenosine nucleotides called poly A tail is added to the transcribed RNA strand. The tail gives signal to move RNA out of the nucleus and then bind to ribosomes in the cytoplasm where protein synthesis occurs. RNA polymerase and RNA are released.

Transcription

Transcription

RNA
Ribonucleic acid is a long polymer of nucleotides found in the nucleus but mainly in the cytoplasm of a cell; it transmits genetic information from DNA to the cytoplasm and is involved with the synthesis of proteins that control chemical processes in the cell. RNA is made up of a long chain of components called nucleotides. The sequence of nucleotides allows RNA to encode genetic information.

RNA

Types of RNAs and Functions

Messenger RNA (mRNA): Carries the genetic information out of the nucleus into cytoplasm for protein synthesis. Transfer RNA (tRNA): Decodes the information in mRNA. It delivers amino acids to the ribosome. Ribosomal RNA (rRNA): It is involved in protein synthesis. It links amino acids together to form proteins.

Types of RNA
In the synthesis of protein, three types of RNA function. The first type is called ribosomal RNA (rRNA). This form of RNA is used to manufacture ribosomes. Ribosomes are ultramicroscopic particles of rRNA and protein. They are the places (the chemical "workbenches") where amino acids are linked to one another to synthesize proteins. Ribosomes may exist along the membranes of the endoplasmic reticulum or in the cytoplasm of the cell. A second important type of RNA is transfer RNA (tRNA). Transfer RNA exists in the cell cytoplasm and carries amino acids to the ribosomes for protein synthesis. The third form of RNA is messenger RNA (mRNA). In the nucleus, messenger RNA receives the genetic code in the DNA and carries the code into the cytoplasm where protein synthesis takes place. Messenger RNA is synthesized in the nucleus at the DNA molecules. During the synthesis, the genetic information is transferred from the DNA molecule to the mRNA molecule. In this way, a genetic code can be used to synthesize a protein in a distant location.

m RNA
mRNA- Messenger RNA - This carries information from the nucleus to the ribosomes which are sites for protein synthesis. The coding sequence on the mRNA determines the amino acid sequence in the protein. The mRNA is a straight molecule extends from the 5' to 3' end. It is transcribed from a DNA template. On the mRNA nucleotides are arranged into codons consisting of 3 bases eac. Each such codon specifies an amino acid. Role of mRNA in protein synthesis 1. Represents the sequence of codons (mRNA language) from the DNA strand. 2. Brings the sequence to the ribosomes (site of protein synthesis) in the cytoplasm. 3. Provides the sequence for the synthesis of specific protein from the amino acids (found in cytoplasm).

Processing Pre-mRNA
Also occurs in the nucleus Pre-mRNA made up of segments called introns & exons Exons code for proteins, while introns do NOT! Introns spliced out by splicesome-enzyme and exons re-join

End product is a mature RNA molecule that leaves the nucleus to the cytoplasm

pre-RNA molecule
exon intron
intron

exon

intron
intron

exon

exon
splicesome

exon
splicesome

exon

exon

exon

exon

Mature RNA molecule

Messenger RNA (mRNA)

Carries the information for a specific protein Made up of 500 to 1000 nucleotides long Sequence of 3 bases called codon AUG methionine or start codon UAA, UAG, or UGA stop codons
start codon mRNA

A U G G G C U C C A U C G G C G C A U A A
codon 1 codon 2
glycine

codon 3
serine

codon 4
isoleucine

codon 5
glycine

codon 6
alanine

codon 7
stop codon

protein

methionine

Primary structure of a protein

aa1 aa2 aa3 peptide bonds aa4 aa5 aa6

t RNA
tRNA:Transports amino acids floating in the cytoplasm to ribosomes for protein synthesis (So, it's function compares to a transport vehicle). The tRNA has a

clover leaf model with 5 arms each with a specific function. The tRNA also has an anticodon region that can base pair with the codon region on the mRNA.

 rRNA- This is the RNA. The rRNA is synthesized in the nucleolus. In the cytoplasm, ribosomal RNA and protein combine together to form a nucleoprotein called a ribosomes. The ribosomes and mRNA bind to carry out protein synthesis. The ribosomal RNAs form two subunits namely; the large subunit and small subunit. The rRNA forms complex with various proteins and make a structure called ribosome, and this complex reads the coded sequence in mRNA to link amino acids together into particular proteins.

r RNA Ribosomal

 The molecular factory synthesis and hence is called ribosimal (r) RNA. It is present in the cytoplasm and forms about 80% of the total RNA. The singlestranded molecule of rRNA is variously folded and twisted upon itself in certain regions forming a secondary structure. In such folded regions, complementary bases form pairs and are joined by hydrogen bonds. The secondary structure of rRNA is a complex pattern of short double-stranded stems, interspersed with unpaired single-stranded loops and bubbles. 1. It provides proper binding sites for the mRNA. 2. It orients the mRNA in such a way that its nitrogen base triplets or codons are properly read or translated. 3. It also releases tRNA after the transfer of activated amino acid to the ribosome complex. 4. It protects the mRNA strand from the action of enzymes (nucleases) which can destroy it. 5. It protects the growing polypeptide (protein) chain from proteolytic enzymes.

rin RNA involved protein

Protein synthesis

Ribosomes

P= Peptide site A= Amino acid site

Large subunit

P Site

A Site

mRNA Small subunit

A U G

A C U U C G

Protein synthesis
The sequence of amino acids in a protein is a type of code that specifies the protein

and distinguishes one protein from another. A genetic code in the DNA determines this amino acid code. The genetic code consists of the sequence of nitrogenous bases in the DNA. How the nitrogenous base code is translated to an amino acid sequence in a protein is the basis for protein synthesis. For protein synthesis to occur, several essential materials must be present, such as a supply of the 20 amino acids, which comprise most proteins. Another essential element is a series of enzymes that will function in the process. DNA and another form of nucleic acid called ribonucleic acid (RNA) are essential. RNA is the nucleic acid that carries instructions from the nuclear DNA into the cytoplasm, where protein is synthesized. For a cell to make protein, the information from a gene is copied, base by base, from DNA into new strands of messenger RNA (mRNA). Then mRNA travels out of the nucleus into the cytoplasm, to cell organelles called ribosomes. One of these active processes is protein synthesis, a universal function whereby mRNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA (tRNA) molecules to deliver amino acids to the ribosome, where ribosomal RNA (rRNA) links amino acids together to form proteins.

Translation
1. Initiation Initiation codon AUG codes for amino acid methionine. mRNA attaches with the small sub unit of ribosome. The initiation codon and small sub unit of ribosome are together called initiation complex. The amino acid methionine binds with tRNA. It again binds with the initiation complex. The large sub unit combines with the small sub unit. The entire complex is called ribosome mRNA amino acid tRNA complex. The second amino acid is attached to A site. tRNA released from P site. 2. Elongation Addition of amino acids at the P site lead to the formation of poly peptide chain. 3. Termination The synthesis of amino acid is stopped when it reaches the termination codon which does not code for any amino acid. The protein is released by peptidyl transferase.

Translation in a protein through the The genetic code is transferred to an amino acid sequence
translation process, which begins with the arrival of the mRNA molecule at the ribosome. While the mRNA was being synthesized, tRNA molecules were uniting with their specific amino acids according to the activity of Amnioacyl tRNA synthetases. The tRNA molecules then began transporting their amino acids to the ribosomes to meet the mRNA molecule. After it arrives at the ribosomes, the mRNA molecule exposes its bases in sets of three, the codons. Each codon has a complementary codon called an anticodon on a tRNA molecule. When the codon of the mRNA molecule complements the anticodon on the tRNA molecule, the latter places the particular amino acid in that position. Then the next codon of the mRNA is exposed, and the complementary anticodon of a tRNA molecule matches with it. The amino acid carried by the second tRNA molecule is positioned next to the first amino acid, and the two are linked. At this point, the tRNA molecules release their amino acids and return to the cytoplasm to link up with new molecules of amino acid. When it's time for the next amino acid to be positioned in the growing protein, a new codon on the mRNA molecule is exposed, and the complementary three-base anticodon of a tRNA molecule positions itself opposite the codon. This brings another amino acid into position, and that amino acid links to the previous amino acids. The ribosome moves further down the mRNA molecule and exposes another codon, which attracts another tRNA molecule with its anticodon.

Translation
One by one, amino acids are added to the growing chain until the ribosome has moved down to the end of the mRNA molecule. Because of the specificity of tRNA molecules for their individual amino acids, and because of the base pairing between codons and anticodons, the sequence of codons on the mRNA molecule determines the sequence of amino acids in the protein being constructed. And because the codon sequence of the mRNA complements the codon sequence of the DNA, the DNA molecule ultimately directs the amino acid sequencing in proteins. The primary "start" codon on an mRNA molecule is AUG, which codes for the amino acid methionine. Therefore, each mRNA transcript begins with the AUG codon, and the resulting peptide begins with methionine. The amino acids join together in peptide bonds, and the tRNA molecules are released to pick up additional amino acid molecules. After the protein has been synthesized completely, it is removed from the ribosome for further processing and to perform its function. After synthesis, the mRNA molecule breaks up and the nucleotides return to the nucleus. The tRNA molecules return to the cytoplasm to unite with fresh molecules of amino acids, and the ribosome awaits the arrival of a new mRNA molecule.

mRNA Codons Join the Ribosome

Large subunit

P Site

A Site
mRNA

A U G
Small subunit

A C U U C G

Initiation
aa1 aa2

2-tRNA 1-tRNA anticodon

hydrogen bonds

U A C A U G codon

G A U C U A C U U C G A
mRNA

Elongation
peptide bond aa1 aa2 aa3

3-tRNA 1-tRNA anticodon

hydrogen bonds

2-tRNA

G A A

U A C A U G codon

G A U C U A C U U C G A
mRNA

aa1

peptide bond aa3 aa2

1-tRNA

U A C
(leaves) 2-tRNA

3-tRNA

G A A

A U G

G A U C U A C U U C G A
mRNA

Ribosomes move over one codon

aa1

peptide bonds aa4 aa2 aa3

4-tRNA 2-tRNA 3-tRNA

G C U

A U G

G A U C U A

G A A C U U C G A A C U
mRNA

aa1

peptide bonds aa2 aa3 aa4

2-tRNA 4-tRNA

G A U
(leaves) 3-tRNA

G C U

A U G

G A A C U U C G A A C U
mRNA

Ribosomes move over one codon

aa1

peptide bonds aa2 aa3 aa4

aa5

5-tRNA

U G A
3-tRNA 4-tRNA

G C

G A A G C U A C U U C G A

A C U
mRNA

aa1 aa2

peptide bonds aa3

aa5

aa4

5-tRNA 3-tRNA

U G A A U A C U
4-tRNA

G A G C

G C U U C G A

A C U
mRNA

Ribosomes move over one codon

aa4

aa5
aa199 aa200

Termination

aa3 primary structure aa2 of a protein aa1

200-tRNA

terminator or stop codon

A C
mRNA

C A

U G U

U A G

End Product The Protein!

The end products of protein synthesis is a primary structure of a protein A sequence of amino acid bonded together by peptide bonds

aa2 aa1

aa3

aa4

aa5
aa199 aa200
48

Difference between Eukaryotic and Prokaryotic protein synthesis

S.No. Eukaryote Prokaryote

1. 2.

The ribosome is 80S.

The ribosome is 70S.

The ribosome has only two sites, The ribosome has three binding sites, namely A site and P site. The E site is namely A site, P site and E site. absent. The ribosome identifies the initiation The ribosome identifies the initiation codon by scanning the mRNA from codon by a leader sequence called 3end. shine-Dalgarno sequence. The rate of protein synthesis is very The rate of protein synthesis is high. low. The first amino acid methionine Methionine is formylated into N-formyl entering the ribosome is not methionine. formylated. Eukaryotic mRNA are very stable and The half life period of prokaryotic its half life is several hours to a few mRNA is short. days. The first mRNA codon interacting AUG is the main first codon. In few

3.

4. 5.

6.

7.