Central Dogma of Molecular Biology Lecture Notes PDF

FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Central Dogma of Molecul...

FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Central Dogma of Molecular Biology Lec Module 7 Far Eastern University IAS – Dept. of Mathematics Biochemistry Cluster 1 Outline Introduction to the Central Dogma RNA Transcription Genes: Prokaryotes vs Transcription Unit Eukaryotes RNA Transcription Introns & Exons Post-Transcription Modifications DNA Replication Translation Replisome Ribosome Leading vs Lagging Strand Genetic Code DNA Replication tRNA Protein Synthesis 2 1 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Introduction to the Central Dogma of Mol. Biology 3 Central Dogma of Molecular Biology The Central Dogma of Molecular Biology refers to the process of making copies of genetic information and its conversion into protein products, wherein DNA can be replicated, converted into RNA, and then into proteins. 4 2 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Genes Genes are nucleotide sequences that carry specific instructions for the cell. They are the smallest hereditary unit that can be passed from parent to offspring. The number and structure of genes an organism possesses greatly varies from organism to organism. The process of converting information in genes into a functional protein product is referred to as gene expression. 5 Genes In most cases, simpler organisms will have more genes within a given number of bases compared to more complex organisms. 6 3 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Genes: Prokaryotes vs Eukaryotes In prokaryotes, the entire gene codes for a protein or molecule. In eukaryotes, the gene consists of coding and non-coding regions. 7 Introns & Exons Introns are the non-coding regions of eukaryotic genes. Exons are the coding regions of eukaryotic genes. During transcription, introns are removed and exons are joined together to form the final mRNA product through a process called RNA splicing. 8 4 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Introns & Exons 9 Introns & Exons Only 3% of human DNA codes for proteins, but non-coding regions still play a role. Satellites are highly repetitive, non-coding DNA sequences that provide structural stability to chromosomes. Mini-satellites and microsatellites are shorter repeats, and are used to monitor mutations implicated in diseases, such as cancer. 10 5 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 DNA Replication 11 Introduction Replication is the process by which DNA makes copies of itself and takes place in the nucleus. Replication occurs in a semi-conservative manner, wherein one strand of the parent DNA becomes the template for the daughter strands. 12 6 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Introduction Replication starts at the origin of replication. This is where the double stranded DNA (dsDNA) begins to open to form the ‘replication bubble’. A chromosome can have multiple origins. The replication fork is where replication actively occurs. 13 Replisome The replisome is an assembly of proteins that facilitate DNA replication at the replication fork. 14 7 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Replisome Components of the replisome include: DNA Gyrase/Topoisomerase - prevents DNA from supercoiling by introducing breaks to relieve stress Helicase - breaks the H-bonds between base pairs to unzip the dsDNA Primase - synthesize primers for DNA polymerase 15 Replisome Components of the replisome include: Clamp Protein - keeps DNA polymerase in place DNA Polymerase (DNA Pol) - synthesizes new DNA strand - can only add to existing nucleotide chain and cannot initiate replication 16 8 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Replisome Components of the replisome include: DNA Ligase - joins Okazaki fragments in the lagging strand Single-stranded Binding Proteins (SSB) - stabilizes and protects the single stranded region of DNA during replication 17 Leading vs Lagging Strands Replication occurs on both strands of the DNA, and on both sides of the replication bubble. The newly synthesized DNA is called either the leading strand or the lagging strand. Leading Strand Synthesized using the template that runs 3’ to 5’ towards the replication fork Replication is continuous. 18 9 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Leading vs Lagging Strands Lagging Strand Synthesized using the template that runs 5’ to 3’ towards the replication fork. Replication is discontinuous. Forms Okazaki fragments that are joined together at the end 19 Leading vs Lagging Strands 20 10 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 DNA Replication in Brief 1. Opening of the DNA Superstructure. 2. DNA Relaxation via DNA gyrase. 3. DNA Unwinding via helicase. 4. Primer Synthesis via primase. 5. DNA Elongation via DNA Polymerase. 6. DNA Ligation via DNA ligase. 21 DNA Replication in Brief DNA Replication - https://www.youtube.com/watch?v=TNKWgcFPHqw 22 11 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 DNA Replication in Brief DNA Replication - https://www.youtube.com/watch?v=TNKWgcFPHqw 23 RNA Transcription 24 12 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Introduction Transcription is the process through which genetic information from DNA is converted into mRNA in the nucleus. This is the first step of gene expression. The resulting mRNA molecule is referred to as the transcript. 25 Introduction For transcription to take place, DNA must first be unwound and separated by proteins. The opening in the double helix where transcription takes place is called the ‘transcription bubble’. The separated DNA strands are then referred as: Template Strand Coding Strand 26 13 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Introduction Template Strand DNA strand that is transcribed; also called the (-) strand or antisense strand Coding Strand DNA strand that is NOT transcribed; also called the (+) strand or sense strand Coding Strand Template Strand 27 Introduction RNA Polymerase Enzyme responsible for RNA synthesis Reads template from 3’to 5’, synthesizes RNA from 5’ to 3’ RNA Pol II is used for mRNA Cannot recognize genes on their own, requires the help of transcription factors 28 14 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Transcription Unit A protein-coding gene, also referred to as a transcription unit, can be divided into the following components: Regulatory Regions – includes the promoter and terminator regions Structural Gene – contains the exons and introns 29 Transcription Unit Promoter Region Located upstream from the transcription site Identifies which DNA strand is the template Initial binding site of transcription factors, which then call RNA polymerase for binding 30 15 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Transcription Unit Promoter Region Consensus Sequence - identifies the precise nucleotide at which transcription begins - where the initial transcription factors bind - ex: TATA box Initiation Signal - gives RNA pol the signal when to start transcription 31 Transcription Unit Terminator Region Nucleotides at the end of a gene that signals RNA polymerase to end transcription 32 16 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 RNA Transcription in Brief 1. Initiation. Binding of transcription factors and RNA Polymerase to the promoter region. 2. Elongation. Addition of the appropriate complementary nucleotide to the growing transcript. 3. Termination. Release of the complete but non-functional transcript called the pre-mRNA upon transcription of the terminator region. 4. Post-Transcription Modifications. Processing of pre-mRNA into functional mature mRNA. 33 RNA Transcription in Brief 34 17 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 RNA Transcription in Brief RNA Transcription - https://www.youtube.com/watch?v=_Zyb8bpGMR0 35 RNA Transcription in Brief RNA Transcription - https://www.youtube.com/watch?v=_Zyb8bpGMR0 36 18 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Post-Transcription Modifications The pre-mRNA is the initial transcript formed, which still contains introns, the terminator region and other sequences not necessary for protein synthesis. Pre-mRNA must undergo additional changes before it can be considered a fully functional mRNA called the mature RNA. These processes are referred to a post-transcription modifications. 37 Post-Transcription Modifications 5’ Capping Addition of a methylated guanine group to the 5’ end Protects mRNA from exonucleases Aids in transport to the cytosol Allows for initiation of translation 3’ Polyadenylation Addition of several adenosine residues to the 3’ end, referred to as the poly(A) tail Protects mRNA from exonucleases 38 19 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Post-Transcription Modifications RNA Splicing Removal of the introns and joining of the exons Leaves behind the code for the amino acid sequence of a protein 39 Translation: Protein Synthesis 40 20 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Introduction Translation is the synthesis of proteins from a mature mRNA molecule which takes place in the cytosol. Ribosomes are the RNA-protein complexes that serve as the site for protein synthesis, found free in the cytosol or bound to the rough endoplasmic reticulum. 41 Ribosome Characteristics of a eukaryotic ribosome include: Is a ribozyme Has two (2) subunits: 60S and 40S Subunit is 65% rRNA and 35% protein Has four (4) rRNA molecules distributed between the subunits rRNA in the small ribosomal subunit acts as active site 42 21 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Ribosome There are three sites in the ribosome: A site – ‘attachment’ site for tRNAs P site – ‘polypeptide’ formation site E site – ‘exit’ site for the tRNA 43 Genetic Code The genetic code refers to the base sequence in mRNA that determines the amino acid sequence in protein synthesis. The genetic code is said to be: Triplet in nature – codons are three-nucleotide sequences. Degenerate – amino acids have multiple codons to minimize mutations Precise/Unambiguous – a codon corresponds to only one amino acid Universal – codons for human are the same for other organisms (with some exceptions) 44 22 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Genetic Code A codon is a three-nucleotide sequence in an mRNA molecule that codes for a specific amino acid. There are 64 codons in total: one (1) start codon – AUG for methionine three (3) termination (STOP) codons – UAG, UGA, UAA Each codon that corresponds to an amino acids has a complementary sequence in a tRNA molecule called the anticodon. 45 Genetic Code 46 23 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Transfer RNA (tRNA) Transfer RNAs (tRNAs) are the RNA responsible for carrying amino acids to the ribosome during translation. Anticodons are complements of codons. Each amino acid has a codon, and each codon has an anticodon. 47 Protein Synthesis in Brief 1. tRNA Activation. tRNAs are loaded with their corresponding amino acids. 2. Initiation. Ribosome detects start codon and Met-tRNA attaches to the P site. 3. Elongation. Bond between 1st and 2nd amino acid forms. First tRNA exits ribosome while next AA-tRNA enters. Cycle repeats. 4. Termination. Ribosome detects stop codon and a release factor binds to the A site to open ribosome and release the polypeptide. 48 24 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 Protein Synthesis in Brief Translation (Initiation) - https://www.youtube.com/watch?v=kAeLta-Bst0 Translation (Elongation & Termination) - https://www.youtube.com/watch?v=C4QiMqBSDe4 49 Protein Synthesis in Brief Translation (Initiation) - https://www.youtube.com/watch?v=kAeLta-Bst0 Translation (Elongation & Termination) - https://www.youtube.com/watch?v=C4QiMqBSDe4 50 25 FEU Biochemistry Property. All forms of replicatin are prohibited. Seek approval from Ms. Jessa Natividad and Ms. Erika Viloria 8/13/24 END! 51 26