BIOL 1005 Introduction to Biology Lecture Notes 2025 PDF

BIOL 1005 Introduction to Biology Lectures 2-3 Allen Cheung 15 Jan 2025 The central dogma of molecular biology History of RNA Discovered in 1868 by Friedrich Miescher, who called the material “nuclein” since it was found in the nucleus Nuclein was fou...

BIOL 1005 Introduction to Biology Lectures 2-3 Allen Cheung 15 Jan 2025 The central dogma of molecular biology History of RNA Discovered in 1868 by Friedrich Miescher, who called the material “nuclein” since it was found in the nucleus Nuclein was found to have acidic properties, hence nucleic acid As early as 1939, the role of RNA in protein synthesis was already suspected Severo Ochoa won the 1959 Nobel prize for his discovery of how RNA is synthesized In 1967, Carl Woese realized that RNA can be catalyzed and proposed that the earliest life forms relied on RNA to carry genetic information and carry biochemical processes In 1990, introduced genes can silence homologous endogenous genes in plants, now known as RNA interference In the same year, discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA = siRNA RNA 01 02 Ribose Ribonucleic acid Differs from DNA because of the sugar component used 03 04 A, U (!), C, G Structure In RNA, Thymine is replaced No base pairing by Uracil Single strand Adenosine Adenosine Uracil Thymine Cytosine Cytosine Guanine Guanine  RNA nucleotides Sugar = ribose No base pairing (single stranded) Structure of RNA ○ Found in the nucleus and cytoplasm ○ Contains the sugar, ribose & phosphates ○ Backbone is ribose sugar-phosphate ○ N-bases, adenine, uracil, cytosine and guanine ○ Forms alpha-helix (mostly) or 3D structures RNA folding Mostly linear (alpha-helix) But can fold upon itself to form 2-D and 3-D structures Influenza A viral RNA Scientific Reports volume 7, Article number: 15041 (2017)  Classic types of RNA 1. mRNA – messenger RNA 2. tRNA – transfer RNA 3. rRNA – ribosomal RNA Collectively, these function to make proteins after taking the instruction from cell/DNA Temporarily present in the cell  Single long chain of nucleotides A molecule of RNA encoding a chemical “blueprint” for a protein product Transcribed from the DNA gene template, and carries coding information Messenger RNA to the ribosomes for protein synthesis (mRNA) The genetic information is arranged into codons consisting of three bases each Each codon encodes for a specific amino acid, except the stop codon that terminates protein synthesis → After transcribed, mRNA moves out of the nucleus to find a ribosome mRNA in pro- and eu-karyote cells  (S=Svedberg units) rRNA is the central Two subunits component of ribosomes Prokaryote = 70S (50S + 30S) Found in >80% of cells Eukaryote = 80S (60S + 40S) Relatively G:::C rich Ribosomes Prokaryote Eukaryote 80S (60S and 40S) 70S (50S and 30S) 60S – 28S, 5.8S, 5S + 50 50S = 23S & 5S + 31 proteins proteins 40S – 18S RNA + 33 30S =16S + 21 proteins proteins rRNA structure  Ribosome function Found in cytoplasm Allows mRNA to be translated into proteins Requires tRNA during translation Base pairing Transfer RNA (tRNA) Smallest among the RNAs (75-93 nt) Recognizes codon on mRNA Shows high affinity to amino acids Carry amino acids to the site of protein synthesis tRNA is transcribed by RNA polymerase III tRNA genes also occur in repeated copies throughout the genome, and may contain introns Transcription and translation https://www.youtube.com/watch?v=gG7uCskUOrA Summary so far Nucleotides for RNA RNA structure RNA functions mRNA, rRNA, tRNA Proteins Proteins Composed of 20 amino acids Encoded by codons (AAs) A, U, C, G Structure determines function  AA → Protein Genetic code defines the protein DNA/genes/nucleotides DNA: ATCG RNA: AUCG 3 nt = one codon  Amino acids Full name → 3 letter short name → 1 letter symbol (Otsuka Jp)  Reading the encoded sequence DNA sequence TAC CCT ACC AAT ACT (T → U) mRNA sequence AUG GGA UGG UUA UGA Protein sequence Met Gly Trp Leu  Met Gly Trp Asn Protein sequence = MGWN e.g. Homo sapiens Insulin MALWMRLLPL LALLALWGPD PAAAFVNQHL CQSHLVEALY LVCGERGFFY TPKTRREAED LQVGQVELGG GPGAGSLQPL ALEGSLQKRG IVEQCCTSIC SLYQLENYCN  Short Exercise HIV nef gene sequence tac ccc ccg ttc acc agt ttt tca tcg tat … mRNA AUG GGG GGC AAG UGG UCA AAA AGU AGC AUA … Translated protein sequence Met Gly Gly Lys Trp Ser Lys Ser Ser Ile … MGGKWSKSSI … What is the point of understanding protein sequence? Sars-CoV-2 spike protein (Qu et al., Nat Comm 2020) *important for binding, find blockers/antibodies based on this information. (Shereen et al., J Adv Res 2020) Peptides Met Gly Trp Asn Short chain of (>2) amino acids Linked by peptide bonds  Polypeptides Generally >10 but 50 aa (amino arranged in secondary, acids) tertiary and quaternary structures Structure (conformation) provides the specific function, or protein-protein binding pair  Protein structure (SRMU) Shape of the protein is determined by the bonding interactions between the amino acids and the side chains Central Dogma Video https://www.youtube.com/watch?v=J3HVVi2k2No  Summary Amino acids → Peptides → Polypeptides → Protein Protein structure (1º, 2º, 3º, 4º) → correct shape give the function of the protein Stabilized by protein bonds Understanding the importance of knowing the protein structure and amino acids composition