DNA, RNA, and Protein Synthesis PDF

DNA _RNA & PROTEIN SYNTHESIS By: NURUL AINI AHMAD  Objectives Differentiates between DNA & RNA Explain the DNA replication Explain the synthesis of protein Identify and explain process transcription and translation DOUBLE HELIX DNA  DNA is made of chemical buildin...

DNA _RNA & PROTEIN SYNTHESIS By: NURUL AINI AHMAD  Objectives Differentiates between DNA & RNA Explain the DNA replication Explain the synthesis of protein Identify and explain process transcription and translation DOUBLE HELIX DNA  DNA is made of chemical building blocks called nucleotides. These building blocks are made of three parts: A phosphate group, A sugar group - deoxyribose and Four types of nitrogen bases To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating. Phosphodiester bonds connect the phosphate group to the DNA sugar. Hydrogen bonds connect bases to one another Glycosidic bonds occur between sugar group and the base groups. Telomere Region of repetitive DNA sequences at the end of a chromosome. Protect the ends of chromosomes from becoming frayed or tangled. Each time a cell divides, the telomeres become slightly shorter. Eventually, they become so short that the cell can no longer divide successfully, and the cell dies. Gene Unit of hereditary information that occupies a fixed position (locus) on a chromosome. Consist of nucleotides segment of DNA. Carries information of traits and codes for a protein. Codon A sequence of three successive nucleotides which ultimately code for a specific amino acid - the monomer of proteins. RIBONUCLEIC ACID (RNA) Consist of single polynucleotide strand of: ü ribose sugar ü phosphate ü nitrogenous base (A-U, G-C) Different between RNA and DNA: ü Second carbon of ribose bears a hydroxyl group, while the equivalent carbon of deoxyribose has a hydrogen instead. ü Thymine (DNA) – replace by uracil (RNA) Types of RNA Messenger RNA (mRNA) Made up of a single strand polynucleotide. Transcribe from DNA. Ribosomal RNA (rRNA) Provide the site where polypeptides are assembled. Transfer RNA (tRNA) Smallest RNA molecules containing 75 – 80 nucleotides. Different tRNAs to carry amino acid to the ribosomes for polymerization into polypeptide chains.  rRNA tRNA mRNA  A ribosome is composed of two subunits. The smaller subunit fit on the surface of the large one. The A, P and E sites of the ribosome, play key role in protein sysntesis. REPLICATION DNA DIRECTION DNA is read from the 5' to 3' end. The 5’ (five prime) carbon has a phosphate group attached to it. The 3’(three prime) carbon has a hydroxyl (-OH) group. The relative positions of genes or other sites along a DNA strand can be described as upstream (towards the 5' end) or downstream (towards the 3' end).  DNA Replication Enzyme DNA helicase unwinds the parental double helix DNA. The weak hydrogen bonds holding the base pairs break. Single stranded binding proteins stabilize the single strands (coiling/ degrade). The DNA templates are exposed to enable the assembly of new complementary strands.  FORMATION OF A LEADING STRAND Enzyme primase synthesis a short RNA primer about 10 nucleotide, a short segment of single-stranded RNA used as a binding site for DNA polymerase to initiate DNA replication. This enables the DNA polymerase to elongate the strand by adding new deoxyribonucleotides one by one from the nucleoplasm. For example, base adenine pairs with thymine and cytosine pairs with guanine. The complementary strand is called the leading strand and is formed continuously from 5’ to 3’, towards the replication fork. Complementary strands in DNA replication are new strands that are synthesized by DNA polymerases using the original strands as template. FORMATION OF THE LAGGING STRAND Topoisomerase also plays an important maintenance role during DNA replication by preventing the DNA double helix ahead of the replication fork from getting too tightly The lagging strand is formed discontinuously. wound as the DNA is opened up. Enzyme primase synthesises a short RNA primer. DNA polymerase adds nucleotides to the primer to form short Okazaki fragments. Enzyme ligase (enzyme that can catalyze the joining (ligation) of two molecules by forming a new chemical bond) joins the Okazaki fragments to form the lagging strand. When the replication is complete, two molecules of DNA a r e formed. Each DNA molecule has one parental and one new complementary strand. This replication of DNA is semi-conservative. Incorporation of nucleotide into a DNA strand PROTEIN SYNTHESIS  Central dogma : Information passed from the genes (DNA) to (RNA) and production of protein. DNA RNA PROTEIN  TRANSCRIPTION During transcription, the code for a protein (a chain of amino acids in a specific order) must be copied from the genetic information contained within a cell’s DNA. This initial protein synthesis step produces an exact copy of a section of DNA, known as messenger RNA (mRNA). A strand of mRNA produced is complementary to a strand of DNA called a gene. A gene can easily be identified from the DNA sequence. A gene contains the basic three regions, promoter, coding sequence (reading frame- contains codons), and terminator. This mRNA must then be transported outside of the cell nucleus before the next step of protein synthesis can begin. 1. Initiation: STEPS OF TRANSCRIPTION v RNA polymerase binds to the promoter region of the DNA molecule cause the DNA unwind. v The two strands of DNA are named based on whether they will be used as a template for RNA or not. v The strand that is used as a template is called the template strand, or can also be called the antisense strand. v The sequence of bases on the opposite strand of DNA is called the non-coding or sense strand. 2. Elongation: v RNA polymerase reads the DNA template strand and synthesizes a complementary RNA strand. v Adding RNA nucleotides to the growing mRNA strand. 3. Termination: v RNA polymerase reaches the end of the gene and detaches from the DNA molecule. v The result is a strand of mRNA that is nearly identical to the coding strand DNA. v The only difference is that DNA uses the base thymine, and the mRNA uses uracil in the place of thymine  PROCESSING mRNA The new mRNA is not yet ready for translation. At this stage, it is called pre-mRNA, and it must go through more processing before it leaves the nucleus as mature mRNA. These processes modify the mRNA in various ways. Such modifications allow a single gene to be used to make more than one protein. EXONS Coding sequences that contain the instructions for making proteins. Present in mRNA. Highly conserved and change little with time. INTRONS Non-coding sequences that don not code for anything. Present in DNA and are removed by RNA splicing before translation. Variable and change frequently with time.  PROCESSING mRNA SPLICING Removes introns from mRNA, regions that do not code for the protein. The remaining mRNA consists only of regions called exons that do code for the protein. Editing is also done and changes some of nucleotides accordingly. 5′ CAPPING Adds a methylated cap to the “head” of the mRNA. This cap protects the mRNA from breaking down, and helps the ribosomes know where to bind to the mRNA. POLYADENYLATION Adds a “tail” to the mRNA. The tail consists of a string of As (adenine bases) and the greater the length of poly – A tail, the more stable of mRNA molecule. It signals the end of mRNA and also involved in exporting mRNA from the nucleus as well as protects mRNA from enzymes that might break it down.  TRANSLATION The second protein synthesis step is translation, which occurs within a cell organelle called a ribosome. mRNA makes its way to and connects with the ribosome under the influence of ribosomal RNA and enzymes. Transfer RNA (tRNA) is a molecule that carries a single amino acid and a coded sequence that acts like a key. This key fits into a specific sequence of three codes on the mRNA, bringing the correct amino acid into place. Each set of three mRNA nitrogenous bases is called a codon. The result of protein synthesis is a chain of amino acids that have been attached, link by link, in a specific order. This chain is called a polymer or polypeptide and is constructed according to a DNA- based code.  STEPS OF TRANSLATION 1.Initiation: v The ribosome binds to the mRNA molecule at the start codon – AUG. v T h e AUG codon signals both the interaction of the ribosome with m R N A and also the t RNA with the anticodons (UAC). 2.Elongation: v The ribosome reads the mRNA codons and matches them with the appropriate AA (amino acid) of tRNA and attached to P site (peptidyl site). v Synthesis proceed when other tRNAs bind to A site (adjacent aminoacyl site) in order to elongate the peptide v As a tRNA moves into the ribosome, its AA is transferred to the growing polypeptide according to complementary base pairing between the codons on the mRNA and the anticodons on the tRNA. v Once this transfer is complete, the tRNA leaves the ribosome, the ribosome moves one codon length down the mRNA, and a new tRNA enters with its corresponding AA. v This process repeats and the polypeptide grows.  STEPS OF TRANSLATION 3.Termination: v At the end of the mRNA coding is a stop codon which will end the elongation stage. v Is signaled by one of the 3 stop codons (UAA, UAGor UGA). v The stop codon doesn’t call for a tRNA, but instead for a type of protein called a release factor, which will cause the entire complex (mRNA, ribosome, tRNA, and polypeptide) to break apart, releasing all of the components. v T h e peptide chain leaves the ribosome. v The N- formyl-methionine that was used to initiate the protein synthesis is also hydrolyzed from the completed peptide at this time. v The last AA is hydrolyzed from its tRNA and is dissociate from the ribosome. v The ribosome is now ready to repeat the synthesis several more times.  GENETIC CODE The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Each gene’s code uses the four nucleotide bases of DNA: v Adenine (A) v Cytosine (C) v Guanine (G) v Thymine (T) A 3-nucleotide code (triplet code) would give 64 different possibilities for all 20 amino acids. 2 amino acids are coded for by only one codon: v Methionine – AUG (start codon) v Tryptophan – UGG Other amino acids are coded for by M O R E t h a n 1 codon. Mostly differs in the 3rd base position of the triplet. v Stop codons: UAG, UAA and UGA (nonsense codons) 21 amino acid each is specified by a three-nucleotide sequence.