Protein Synthesis Process Guide PDF

## Steps Involved in Protein Synthesis - Information from DNA is used to direct the synthesis of proteins in two-step processes namely, transcription and translation. - **Transcription** is the synthesis of RNA from the information contained in DNA. - It is catalyzed by an enzyme RNA polymera...

## Steps Involved in Protein Synthesis - Information from DNA is used to direct the synthesis of proteins in two-step processes namely, transcription and translation. - **Transcription** is the synthesis of RNA from the information contained in DNA. - It is catalyzed by an enzyme RNA polymerase and occurs in the nucleus. - **Translation** is the actual synthesis of proteins. - tRNA and rRNA, together with proteins, use the nucleotide sequence in an mRNA molecule to synthesize the specific amino acid sequence of a protein. - Ribosomal RNA combines with dozens of proteins to form a complex structure called a ribosome. - Translation is catalyzed by ribosomes and occurs in the cytoplasm. ### Base Pairing - One strand of DNA: TAC CAT TTG AAT CCA GTT AAC ACG ATT - mRNA: AUG GUA AAC UUA GGU CAA UUG UGC UAA ### Diagram Description - The diagram shows a ribosome moving along a strand of mRNA. - The mRNA is being translated into a polypeptide chain. - tRNA molecules are bringing amino acids to the ribosome, where they are added to the growing polypeptide chain. - The anticodon of the tRNA is complementary to the codon on the mRNA. ## The mRNA - The mRNA is a single strand of linearly arranged nucleotides. - The nucleotides are read in threes. - Each triplet code makes up of a particular sequence of nitrogenous bases is called a codon. - The codon has its complement in an anticodon found in one of the three loops of the clover leaf-shaped tRNA. - A tRNA has an attachment site for a particular type of amino acid. - Proteins are made up of linearly arranged amino acids. - Each amino acid that will form the protein molecule to be synthesized is determined by the triplet code or codon on the mRNA. ## The Genetic Code Chart | First Base | Second Base | Third Base | Amino Acid | |---|---|---|---| | U | U | U | Phenylalanine | | U | U | C | Phenylalanine | | U | U | A | Leucine | | U | U | G | Leucine | | U | C | U | Serine | | U | C | C | Serine | | U | C | A | Leucine | | U | C | G | Leucine | | U | A | U | Tyrosine | | U | A | C | Tyrosine | | U | A | A | STOP | | U | A | G | STOP | | U | G | U | Cysteine | | U | G | C | Cysteine | | U | G | A | STOP | | U | G | G | Tryptophan | | C | U | U | Leucine | | C | U | C | Leucine | | C | U | A | Leucine | | C | U | G | Leucine | | C | C | U | Proline | | C | C | C | Proline | | C | C | A | Proline | | C | C | G | Proline | | C | A | U | Histidine | | C | A | C | Histidine | | C | A | A | Glutamine | | C | A | G | Glutamine | | C | G | U | Arginine | | C | G | C | Arginine | | C | G | A | Arginine | | C | G | G | Arginine | | A | U | U | Isoleucine | | A | U | C | Isoleucine | | A | U | A | Isoleucine | | A | U | G | Methionine | | A | C | U | Threonine | | A | C | C | Threonine | | A | C | A | Threonine | | A | C | G | Threonine | | A | A | U | Asparagine | | A | A | C | Asparagine | | A | A | A | Lysine | | A | A | G | Lysine | | A | G | U | Arginine | | A | G | C | Arginine | | A | G | A | Arginine | | A | G | G | Arginine | | G | U | U | Valine | | G | U | C | Valine | | G | U | A | Valine | | G | U | G | Valine | | G | C | U | Alanine | | G | C | C | Alanine | | G | C | A | Alanine | | G | C | G | Alanine | | G | A | U | Aspartic acid | | G | A | C | Aspartic acid | | G | A | A | Glutamic acid | | G | A | G | Glutamic acid | | G | G | U | Glycine | | G | G | C | Glycine | | G | G | A | Glycine | | G | G | G | Glycine | ## DNA and RNA - DNA and RNA differ in structure and other characteristics. - **DNA:** - Deoxyribonucleic acid - Deoxyribose - A, T, C, G - Single stranded - A-T, C-G - DNA, tRNA - **RNA:** - Ribonucleic acid - Ribose - A, C, G, U - Double stranded - A-U, C-G - mRNA, rRNA, tRNA ## Protein Synthesis - Francis Crick first proposed the idea that the sequence involved in the expression of hereditary characteristics is from DNA to RNA to protein. - This involves three processes namely, replication, transcription and translation. - These major critical components and processes form the basic storage, transmission and expression of hereditary information. ## The Genetic Code - The Genetic Code is written in the language of nucleic acids. - It is passed on from one cell to another, from one generation to the next when chromosomes are distributed from the parent cell to the daughter cells. - The genetic code is stored in DNA and may be expressed when copied in mRNAs. ## Ribonucleic Acid - Although DNA is the genetic material, it does not work alone. - Ribonucleic acid (RNA) plays an equally important role in the transmission of traits. - Ribonucleic acid is made up of ribose-phosphate backbone. Unlike DNA, it is made up only of a single strand of nucleotides and consists of nitrogen bases such as adenine, guanine, cytosine and uracil which replaces thymine in DNA. ### Types of RNA - **Messenger RNA (mRNA):** - A single strand linearly-arranged nucleotides which carries the code for a protein coding gene from DNA to ribosome. - This code is represented by triplet bases which is called codon. - **Ribosomal RNA (rRNA):** - Combines with proteins to form ribosomes, the structure that link amino acids to form a protein. - **Transfer RNA (tRNA):** - A clover leaf-shaped RNA with attachment site for a particular type of amino acid which it carries to the ribosomes during protein synthesis. - It contains anticodon which complements with the codon in mRNA during protein synthesis. ## Role of DNA, RNA and Proteins in the Transmission of Hereditary Traits - DNA performs important roles such as storing, transmitting and expressing genetic information. - Because of these functions, DNA must make a copy of itself for the organism to continuously pass its genetic information from generation to generation. - This process by which a DNA molecule makes an exact copy of itself is referred to as DNA replication. ## DNA Replication - DNA replication has the following steps: 1. **Helicase breaks the hydrogen bonds:** An enzyme called helicase breaks the hydrogen bonds that hold the double helix together, so the two DNA strands unwind and separate or split. 2. **Complementary nucleotides are added:** The bases attached to each other strand then pair up with the free nucleotides. The complementary nucleotides are added to each strand by DNA polymerases continuously in the leading strand and discontinuously in the lagging strand to form new strands. - In the lagging strand, an enzyme lays down RNA primer to start replication, then another enzyme adds free nucleotides to pair with the nucleotides in this strand. - This produces short DNA segments which are called Okazaki fragments. - Another enzyme replaces RNA primer with DNA. Finally the enzyme ligase links the pieces of Okazaki fragments in the lagging strands. 3. **Two new molecules are formed:** Two new molecules, each with a parent strand and each with a new strand, are formed. ## Simulation of DNA Replication - The diagram shows the process of DNA replication. - The parent DNA molecule is shown in the first panel. - In the second panel, the two strands of the DNA molecule are separated. - In the third panel, new strands of DNA are synthesized, using the parent strands as templates. - In the fourth panel, the two new DNA molecules are complete. ## Semiconservative Replication - In forming new DNA molecules, the process of DNA replication conserves one parental DNA strand (serve as pattern for the synthesis of new strand). - The process is called semiconservative replication. ## Most of the Cellular DNA is Stored Inside the Nucleus - DNA is a linear polymer. It is a polymer consisting of at least 3 billion nucleotides. - To fit inside the nucleus of a cell, DNA is packed using a multi-level packing system that involves coiling, folding and lots of proteins called histones. ## Chromosomes - When the cell is not dividing, DNA is extended into long thin strands called chromatin. - During cell division, these strands condense or thicken forming a chromosome. - Chromosomes are highly visible during the metaphase stage of the mitosis where they align at the metaphase plate. - Metaphase chromosomes are basically composed of arm (a long arm and a short arm) attached to a centromere. - During metaphase, all the DNA inside the cells condenses into 23 pairs of chromosomes. - Twenty-two pairs are called somatic chromosomes while the remaining pair is called the sex chromosome. - This chromosome determines the sex of the offspring. ## Chromosome Structure - Each cell in your body contains DNA. This molecule contains section with a specific sequence of nucleotides called genes. - Genes are particularly important since they contain all the instruction to code for proteins needed to perform various cellular processes. - The order of sequence of these nucleotide forms a genetic code that determines the type protein that will be produced in the process called protein synthesis. - This is the concept of the Central Dogma of Molecular Biology ## Central Dogma of Molecular Biology - Replication (DNA → DNA) - Transcription (DNA → RNA) - Translation (RNA → proteins) ## The Two DNA Strands are Composed of a Backbone Made Up Alternating Sugars and Phosphate Groups - The first phosphate group (P-1) is attached to carbon no. 5 of the first sugar (S-1) while the next phosphate (P-2) is attached to carbon no. 3 of the same sugar (S-1). - This pattern is evident all throughout that strand 1. - The opposite happens on (strand 2), the first phosphate (P-3) is attached to carbon no. 3 of the first sugar (S-3) while the next phosphate (P-4) is attached to the carbon no. 5 of the same sugar (S-3). - This orientation where one strand is running the opposite direction compared to the other strand is called an antiparallel orientation. ## The Complementary Base Pairing - Chargaff found out that the number of adenine is almost equal to thymine while cytosine is almost equal to guanine. - This gave him the idea that a purine is always paired with a pyrimidine. - This concept is now known as the Chargaff's rule. - The rule shows the complementary base pairing adenine to thymine and guanine to cytosine. - Hydrogen bond is formed between hydrogen and an electronegative atom like oxygen, nitrogen, and fluorine. ## Structure and Properties of the DNA - The structure of the DNA as we now know today is the result of various experimentations, analyses, and modelling. - Several scientists have devoted their scientific work in discovering the structure of the DNA and how its structure affects its role inside the cell. ## Nucleotide - Another component of a nucleotide are the nitrogenous bases. - Both the RNA and DNA contain these nitrogenous bases. - The main difference between purines and pyrimidines is the number of rings in each molecule. ### Purines - Guanine (DNA and RNA) - Adenine (DNA and RNA) ### Pyrimidines - Cytosine (DNA and RNA) - Thymine (DNA and RNA) - Uracil (RNA only) ## Nucleic Acid - In a cell, nucleic acid can either be in the form of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). - These are both Informational macromolecules since they carry set of codes for protein production. - DNA and RNA are both polymers. - The monomer of a nucleic acid is called a nucleotide. A nucleotide is mainly composed of a 5-carbon sugar, a phosphate group, and a nitrogenous base. ## The Hershey-Chase Experiment - Radioactive sulfur and phosphorus were used to trace the fates of protein and DNA in a bacteria-infecting virus called T2 bacteriophage. - Viruses are used in their experiment since they are composed of proteins and DNA. - It is known that viruses reproduced by injecting its DNA or RNA into its host cell and taking over the cellular processes. - The Hershey-Chase experiment confirms that viral DNA entered the cell, and not proteins. - The viral DNA can program the host cell by manipulating its DNA. - This proves that the nucleic acid and not the protein, functions as the genetic material of bacteriophages. ## Griffith's Experiment on Bacterial Transformation - In 1928, Frederick Griffith conducted an experiment on the process of bacterial transformation using two strains (R and S strains) of _Streptococcus pneumoniae_. - From his experiment, it was revealed that the genetic material of bacteria is DNA. - The diagram shows the bacterial transformation in _Streptococcus pneumoniae_. - The non-pathogenic R strain to cause the disease because of the unknown substance from the heat-killed S cells that was incorporated in the non-pathogenic R strain. - This process makes the R strain pathogenic. - He called this phenomenon transformation. - It was the experiment of Oswald Avery, Colin MacLeod, and Maclyn McCarty that confirmed that the DNA is the transforming substance in the Griffith's experiment. ## Experiments leading to the Discovery of the Nature of Genetic Material - The nature, role, and structure of the DNA as we know today is the product of a series of experiments conducted through the years. - It all started with the experiment of Gregor Mendel in early 1860s using pea plants (_Pisum sativum_). - From his experiment, he observed that certain traits of the parent plant are being transmitted to the offspring plant. - He later concluded that the characteristics are being directed by distinct units of inheritance in which he then called factors. - Today, we call these factors as genes. - In 1869, Friedrich Miescher discovered the first evidence of deoxyribonucleic acid or DNA in which he called it nuclein. - It was later realized that the nuclein he obtained from white blood cells collected from pus and from salmon sperm cell contains a crude sample of DNA and proteins. - Together with the rediscovery of Mendel's work in 1900s, the nature of these "factors" and "nuclein" will become the focus of numerous experiments. - Three leading experiments in the early 21st century confirms that the DNA functions as the genetic material.