Unit-II Synthetic Biology: Protein Synthesis Synthetic Biology is - A) the design and construction of new biological parts, devices, and systems, and B) the re-design of existing, natural biological systems for useful purposes.

Protein Synthesis: Central Dogma DNA and RNA both are important in the protein- making process. In the cell, the DNA nucleotides are used as a genetic alphabet, arranged in sets of three (ATC,GGA,TCA) to form code words in DNA language. DNA and RNA both are important in the protein- making process. In the cell, the DNA nucleotides are used as a genetic alphabet, arranged in sets of three (ATC,GGA,TCA) to form code words in DNA language. It is the sequence of these code words in DNA that dictates which amino acids are used and the order in which they appear in proteins. It is the sequence of these code words in DNA that dictates which amino acids are used and the order in which they appear in proteins.

Steps of Protein Synthesis: 1 st Step- Transcription- Making RNA 1 st Step- Transcription- Making RNA 2 nd Step- Translation-Making Proteins 2 nd Step- Translation-Making Proteins

Transcription-Making RNA An enzyme, RNA polymerase, attaches to the DNA at the promoter sequence and reads the sequence of DNA nitrogenous bases and follows base-pair rule to build the new RNA molecule. An enzyme, RNA polymerase, attaches to the DNA at the promoter sequence and reads the sequence of DNA nitrogenous bases and follows base-pair rule to build the new RNA molecule. The strand of DNA that is directly read by the enzymes to synthesis RNA is called the template or non-coding strand. The strand of DNA that is directly read by the enzymes to synthesis RNA is called the template or non-coding strand. The other strand, complementary to the template strand is called the coding strand. The other strand, complementary to the template strand is called the coding strand.

The base-paired RNA nucleotides are linked together by RNA polymerase to form a new RNA molecule that is complementary to the DNA sequence. The base-paired RNA nucleotides are linked together by RNA polymerase to form a new RNA molecule that is complementary to the DNA sequence. The termination sequence signals the RNA polymerase to end RNA transcription. The termination sequence signals the RNA polymerase to end RNA transcription. Newly formed RNA is separated from the DNA molecule and is ready to leave the nucleus for 2 nd step. Newly formed RNA is separated from the DNA molecule and is ready to leave the nucleus for 2 nd step.

Types of RNA mRNA-Messenger RNA carries the blueprint for making the necessary protein. mRNA-Messenger RNA carries the blueprint for making the necessary protein. tRNA- Transfer RNA is used to read the mRNA. tRNA- Transfer RNA is used to read the mRNA. rRNA- Ribosomal RNA bring the amino acids together for assembly into a protein. rRNA- Ribosomal RNA bring the amino acids together for assembly into a protein.

2 nd step-Translation-Making Protein It is the process of using the information in RNA to direct protein synthesis by attaching amino acids to one another. It is the process of using the information in RNA to direct protein synthesis by attaching amino acids to one another. The mRNA read in sets of three nucleotides called codons.A codon is a set of 3 nucleotides that codes for specific amino acid. The mRNA read in sets of three nucleotides called codons.A codon is a set of 3 nucleotides that codes for specific amino acid.

These are common amino acids used in the protein synthesis.

The process of translation can be broken down into three basic steps- 1. Initiation-Protein synthesis begins. 1. Initiation-Protein synthesis begins. 2. Elongation-Adding amino acids. 2. Elongation-Adding amino acids. 3. Termination- Stop signal. 3. Termination- Stop signal.

Protein Synthesis

Initiation Ribosomes exist as two subunits-a large and a small subunit. Ribosomes exist as two subunits-a large and a small subunit. During initiation the two subunits combine and hold the mRNA between them. During initiation the two subunits combine and hold the mRNA between them. AUG is the initiation codon and is responsible for hydrogen bonding with the tRNA carrying the amino acids. AUG is the initiation codon and is responsible for hydrogen bonding with the tRNA carrying the amino acids.

Elongation The two tRNA’s align the amino acids so that they can be chemically attached to one another by forming a peptide bond. The two tRNA’s align the amino acids so that they can be chemically attached to one another by forming a peptide bond. Once the bond is formed, the first tRNA detaches from its position on the mRNA. Once the bond is formed, the first tRNA detaches from its position on the mRNA. The ribosomes moves down one codon on the mRNA. The ribosomes moves down one codon on the mRNA. The process continues with a new tRNA, a new amino acid, and the formation of a new peptide bond. The process continues with a new tRNA, a new amino acid, and the formation of a new peptide bond.

Termination The stop codons are- UAA, UAG or UGA, The stop codons are- UAA, UAG or UGA, When any of these codons appear during the elongation process, protein encounters a stop signal. When any of these codons appear during the elongation process, protein encounters a stop signal. When the protein releases, the ribosomal subunits separate and release the mRNA. When the protein releases, the ribosomal subunits separate and release the mRNA. The mRNA can be used to make another copy of the protein or can be broken down by the cell to prevent any more of the protein from being made. The mRNA can be used to make another copy of the protein or can be broken down by the cell to prevent any more of the protein from being made.

Basic Review If a DNA nucleotide sequence is TACAAAGCA, what is the mRNA nucleotide sequence that would base-pair with it? If a DNA nucleotide sequence is TACAAAGCA, what is the mRNA nucleotide sequence that would base-pair with it? How do tRNA, rRNA and,mRNA differ in functions? How do tRNA, rRNA and,mRNA differ in functions? List the sequence of events that take place when a DNA message is translated into protein. List the sequence of events that take place when a DNA message is translated into protein. How does the manufacture of RNA molecule differ from the DNA replication? How does the manufacture of RNA molecule differ from the DNA replication?

The Control of Protein Synthesis Cells have many protein-coding sequences. Cells have many protein-coding sequences. Gene expression occurs when a cell transcribes and translates a gene. Gene expression occurs when a cell transcribes and translates a gene. Cells do not make all their proteins at once. Cells do not make all their proteins at once. Cells can control which genes are used to make proteins. Cells can control which genes are used to make proteins. Cells use many ways to control gene expression in response to environmental conditions. Cells use many ways to control gene expression in response to environmental conditions.

Controlling Protein quantity The cell regulates the amount of protein (enzymes) that is made by changing how much mRNA is available for translation into protein. The cell regulates the amount of protein (enzymes) that is made by changing how much mRNA is available for translation into protein. Factors controlling protein quantity- Factors controlling protein quantity- DNA packaging-The genetic material consists of highly coiled condensed chromatin fiber known as chromosome. The degree to which chromatin is coiled provides a method for long term control of protein expression. In tightly coiled chromatin RNA polymerase cannot initiate transcription. DNA packaging-The genetic material consists of highly coiled condensed chromatin fiber known as chromosome. The degree to which chromatin is coiled provides a method for long term control of protein expression. In tightly coiled chromatin RNA polymerase cannot initiate transcription. Loosely packaged chromatin exposes the promoter sequence so that transcription can occur. Loosely packaged chromatin exposes the promoter sequence so that transcription can occur.

Enhancers and Silencers-Enhancers and Silencer sequences are DNA sequences that act as binding sites for proteins. Enhancer sequences increases protein synthesis where as silencer sequences decreases protein sysnthesis. Enhancers and Silencers-Enhancers and Silencer sequences are DNA sequences that act as binding sites for proteins. Enhancer sequences increases protein synthesis where as silencer sequences decreases protein sysnthesis. Transcription factors- transcription factors are proteins that control the availability of the promoter sequence for transcription. Transcription factors- transcription factors are proteins that control the availability of the promoter sequence for transcription. RNA degradation- Enzymes in the cell break down mRNA, so that it can no longer be used to synthesize protein. RNA degradation- Enzymes in the cell break down mRNA, so that it can no longer be used to synthesize protein.

Controlling Protein Quality Another way that cells can control gene expression is to change the amino acid sequences to form different versions of an enzymes. Another way that cells can control gene expression is to change the amino acid sequences to form different versions of an enzymes. In eukaryotic cells protein coding regions are scattered, the sequences that do not code proteins are called introns, the remaining coding sequences are called exons. In eukaryotic cells protein coding regions are scattered, the sequences that do not code proteins are called introns, the remaining coding sequences are called exons. After the protein coding region of a eukaryotic gene is transcribed into mRNA, the introns in the mRNA are cut out and exons are spliced together end to end to create shorter version of the mRNA. After the protein coding region of a eukaryotic gene is transcribed into mRNA, the introns in the mRNA are cut out and exons are spliced together end to end to create shorter version of the mRNA.