Biology 1 – Cells, Molecular Biology and Genetics (Biol 1000) Winter 2025 PDF

Biology 1 – Cells, Molecular Biology and Genetics (Biol 1000) Professor: Dr. Michael Cardinal-Aucoin Winter 2025 Biol 1000 - Dr. M. Cardinal-Aucoin 2  Building Blocks of Life Chemistry of Life Biological Macromolecules Polymers Carbohyd...

Biology 1 – Cells, Molecular Biology and Genetics (Biol 1000) Professor: Dr. Michael Cardinal-Aucoin Winter 2025 Biol 1000 - Dr. M. Cardinal-Aucoin 2  Building Blocks of Life Chemistry of Life Biological Macromolecules Polymers Carbohydrates Lipids Proteins Nucleic Acids Biol 1000 - Dr. M. Cardinal-Aucoin 3  Review Chapter 2 Building Blocks Bonds Chemical Reactions Matter Ionic Reactants Element Covalent Products Atom ‒ Non-polar Reversible ‒ Neutron ‒ Polar Equilibrium Nucleus ‒ Electronegativity ‒ Proton Specificity ‒ Electron Hydrogen Atomic mass Van der Waal’s Properties of Atomic number forces water Isotope Polarity Valence electron Functional groups Cohesion Ion Adhesion ‒ Cation High specific ‒ Anion heat Biol 1000 - Dr. M. Cardinal-Aucoin 4  The Molecules of Life UNITY: All cells are made of 4 classes of biological macromolecules: 1. Carbohydrates 2. Lipids All have carbon 3. Nucleic acids skeleton. 4. Proteins DIVERSITY: infinite variety of ways in which they are built and combined. Biol 1000 - Dr. M. Cardinal-Aucoin 5  The Chemistry of Life About 20–25% of the 92 elements are essential to life. Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter. Most of the remaining 4% consists of calcium, phosphorus, potassium, sulfur, sodium, chlorine and magnesium. Biol 1000 - Dr. M. Cardinal-Aucoin 6 Can you think of examples of how cells use these elements? Biol 1000 - Dr. M. Cardinal-Aucoin 7  Water and Life Water is the biological medium on Earth; life evolved in the ocean and only a few groups of organisms have become fully terrestrial. All living organisms require water more than any other substance. Most cells are surrounded by water, and cells themselves are about 70–95% water. Cells = bag of molecules dissolved in water. The abundance of liquid water is the main reason the Earth is habitable. Biol 1000 - Dr. M. Cardinal-Aucoin 8  Summary The 4 emergent properties of water are mainly due to its polarity and the formation of hydrogen bonds. These properties are critically important to life on Earth: 1. Expansion upon freezing; 2. Cohesion/Adhesion 3. Moderation of Temperature; 4. Versatility as a Solvent. The pH of water is tightly regulated in living systems. Biol 1000 - Dr. M. Cardinal-Aucoin 9  Water Hydrogen Oxygen Your single proton Most of me is you. fundamental, essential. I strive for independence, Water. Life. Starfuel. fail with every breath. Water Simple and complex, polarity defines you. The birthplace of life. Biol 1000 - Dr. M. Cardinal-Aucoin 10  The Backbone of Life Living organisms consist mostly of carbon-based compounds. Carbon is unparalleled in its ability to form large, complex, and diverse molecules AND it is extremely abundant in the cosmos. Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds. Biol 1000 - Dr. M. Cardinal-Aucoin 11  A note about formulae Aspartic acid is an amino acid, one of the building blocks of proteins. Chemical formula: C4H7NO4 Skeletal formula: Condensed structural formula: Carbon atom (2 H’s missing) NH2CH(CH2COOH)COOH Lewis diagram: Free pairs of Double bond.. valence electrons are sometimes Single bond.. illustrated. This nitrogen is emerging above the plane. Each vertex represents a carbon atom. Single bond Double bond H atoms attached to carbons left out for simplicity. Stereochemistry (3D arrangement) can Each atom represented by its be illustrated by wedges. atomic symbol. All atoms drawn. Biol 1000 - Dr. M. Cardinal-Aucoin 12  Diversity of chemical functional groups constructed with carbon. Review Chapter 2 Biol 1000 - Dr. M. Cardinal-Aucoin 13  The Molecules of Life Provide source of energy and make up the cell wall in bacteria, plants and algae. 1. Carbohydrates Make up cell membranes, store energy, and act as signaling 2. Lipids molecules. 4. Nucleic Acids Encode and transmit genetic information. 3. Proteins Provide structural support and act as catalysts that facilitate chemical reactions. Biol 1000 - Dr. M. Cardinal-Aucoin 14  Polymers Most biological macromolecules are polymers made of many repeated units. – E.g. proteins made of many amino acid subunits. Biol 1000 - Dr. M. Cardinal-Aucoin 15  Polymers Polymers: complex molecules made up of repeated simpler units (monomers) connected by covalent bonds. Single unit = monomer (e.g. pearl) Chain or ring of of monomers = polymer (e.g. pearl necklace) Biol 1000 - Dr. M. Cardinal-Aucoin 16  Polymers Building polymers: Dehydration synthesis (or condensation reaction) (a) Dehydration reaction: synthesizing a polymer 1 2 3 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond. 1 2 3 4 Longer polymer Biol 1000 - Dr. M. Cardinal-Aucoin 17  Polymers Breaking down polymers: Hydrolysis reaction To cut with water (b) Hydrolysis: breaking down a polymer 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond. 1 2 3 Biol 1000 - Dr. M. Cardinal-Aucoin 18  Polymers Biological macromolecules are generally polymers made of monomer subunits: Polymer Monomer Carbohydrates Simple sugars Lipids Fatty acids bonded to Note: lipids are not true polymers but are grouped other organic together because they share hydrophobic properties. molecules. Proteins Amino acids Nucleic acids Nucleotides Biol 1000 - Dr. M. Cardinal-Aucoin 19  Carbohydrates Energy source Structure and support Biol 1000 - Dr. M. Cardinal-Aucoin 20  Carbohydrates Simple sugars CH2O – ratio of 1 : 2 : 1 Simple sugars are called “monosaccharides”. Simple sugars end in ‘-ose’ and are named based on the number of carbons. Many simple sugars used as fuel by many organisms. E.g. glucose, fructose, ribose, etc. Biol 1000 - Dr. M. Cardinal-Aucoin 21  Carbohydrates Aldoses (Aldehyde Sugars) Ketoses (Ketone Sugars) Simple sugars Trioses: 3-carbon sugars (C3H6O3) Monosaccharides are classified by: – The number of Cs in the skeleton. (e.g. 3C sugar = triose, 4C sugars = Glyceraldehyde Dihydroxyacetone tetroses, 5C sugar = pentose, and 6C Pentoses: 5-carbon sugars (C5H10O5) sugar = hexoses.) – The location of the C=O. aldehyde ketone Ribose Ribulose Hexoses: 6-carbon sugars (C6H12O6) Glucose Galactose Fructose Biol 1000 - Dr. M. Cardinal-Aucoin 22  Carbohydrates Glucose: chain to ring Though often drawn in linear form, in aqueous solution many sugars will form a ring. These two Aldehyde functional Functional groups groups can Alcohol react with each other. Biol 1000 - Dr. M. Cardinal-Aucoin 23  Carbohydrates Glucose: chain to ring Intermediate Remember: reactions are reversible and the forward and reverse reactions are in dynamic equilibrium. Biol 1000 - Dr. M. Cardinal-Aucoin 24  Carbohydrates Glucose: chain to ring A note about numbers: by convention the 6 C’s in the chain form are numbered from the HC=O end. This numbering is retained in the ring form. Fischer Projection Haworth Projection Biol 1000 - Dr. M. Cardinal-Aucoin 25  Carbohydrates Simple sugars In the ring form the H and OH groups become fixed (can no longer rotate freely around bond). Join these to form Isomers Join these to starch and glycogen. (anomers) form cellulose. Biol 1000 - Dr. M. Cardinal-Aucoin 26  Carbohydrates Glycosidic bonds Monosaccharides are linked to each other forming disaccharides and polysaccharides through glycosidic bonds. Formed between the carbon 1 of one monosaccharide and a hydroxyl group carried by an atom in a different monosaccharide. Biol 1000 - Dr. M. Cardinal-Aucoin 27  Carbohydrates Sugars Disaccharides are two monosaccharides linked together α-1,β-2-glycosidic linkage Transport sugar in plants. β-1,4-glycosidic linkage Transport sugar in milk. α-1,4-glycosidic linkage Found in brewing. Biol 1000 - Dr. M. Cardinal-Aucoin 28 Biol 1000 - Dr. M. Cardinal-Aucoin 29 Biol 1000 - Dr. M. Cardinal-Aucoin 30  Carbohydrates Polysaccharides Long chains of monosaccharides linked together. Energy storage: 1. Storage polysaccharides in plants are called starches, like amylose and amylopectin. 2. Storage polysaccharide in animals and fungi is called glycogen. Structural support: 1. Structural polysaccharide in plants is called cellulose. 2. Structural polysaccharide in fungi is called chitin. Biol 1000 - Dr. M. Cardinal-Aucoin 31  Carbohydrates Polysaccharides Plants store starch in chloroplasts and other Energy storage in plants: plastids. Starch: Amylose and Amylopectin (branched) α-1,4 glycosidic bond Sources: grains, corn, potatoes. Biol 1000 - Dr. M. Cardinal-Aucoin 32 Biol 1000 - Dr. M. Cardinal-Aucoin 33 Biol 1000 - Dr. M. Cardinal-Aucoin 34  Lipids Biol 1000 - Dr. M. Cardinal-Aucoin 35  Lipids Unlike proteins, nucleic acids, and carbohydrates, lipids are not made from repeating monomers. Instead of being defined by a structure, lipids are defined by a shared chemical property: they are hydrophobic. Structurally, lipids form a diverse group. Three major types of biologically important lipids: 1. Neutral fats Made from fatty acids. 2. Phospholipids 3. Steroids Biol 1000 - Dr. M. Cardinal-Aucoin 36  Lipids Neutral fats Function of neutral fats (e.g. triglycerides) in biological systems: 1. Energy storage 2. Insulation for cold 3. Protection of internal organs Biol 2230 - Dr. M. Cardinal-Aucoin 37  Lipids Phospholipids Function: Major constituents of cell membranes. Biol 2230 - Dr. M. Cardinal-Aucoin 38  Lipids Steroids Function: Constituents of cell membranes (e.g. cholesterol) Components of vitamins (e.g. Vitamin D) Components of hormones (e.g. growth hormones, sex hormones) c) Cortisone Biol 2230 - Dr. M. Cardinal-Aucoin 39 Biol 2230 - Dr. M. Cardinal-Aucoin 40  Nucleic Acids Store information Transmit information Biol 1000 - Dr. M. Cardinal-Aucoin 41  Nucleic Acids Polymer made of nucleotide subunits consisting of a nitrogenous base, a pentose sugar, and a phosphate group. Joined by phosphodiester bonds. Dehydration synthesis. Phosphodiester bond H2O nucleoside nucleotide Biol 1000 - Dr. M. Cardinal-Aucoin 42  DNA DNA in cells usually consist of two strands of nucleotides twisted around each other in the form of a double helix. RNA is usually single stranded. https://biologydictionary.net/dna-vs-rna/ Biol 1000 - Dr. M. Cardinal-Aucoin 43  Nucleic Acids The “Central Dogma” DNA provides the chemical blueprint of proteins!! Information storage. DNA codes for the primary structure of proteins. RNA is involved in the process of reading the instructions in DNA and making proteins. Biol 1000 - Dr. M. Cardinal-Aucoin 44  Proteins Biol 1000 - Dr. M. Cardinal-Aucoin 45  Proteins Proteins account for 50% of the organic matter in a typical animal body, and they play a critical role in almost all life processes. Enzymatic proteins Defensive proteins Storage proteins Transport proteins Biol 1000 - Dr. M. Cardinal-Aucoin 46  Proteins The diversity of functions is possible because of the many structures that are possible. Hormonal proteins Receptor proteins Contractile proteins Structural proteins Biol 1000 - Dr. M. Cardinal-Aucoin 47  Proteins Proteins are polypeptides (polymers) made of amino acid subunits. Cells only use the L isomer, not the D isomer. R group differs for each amino acid and determines its unique properties. – About 20 amino acids make up all natural proteins. Biol 1000 - Dr. M. Cardinal-Aucoin 48  Proteins Types of R-groups Amino acids (a.a’s) can be categorized according to their R group. Hydrophilic (polar) amino acids tend to be found on the outside of proteins (i.e. close to water). Note: each amino acid has a name, a three letter abbreviation, and a single letter code. Biol 1000 - Dr. M. Cardinal-Aucoin 49  Proteins Types of R-groups Hydrophobic (non-polar) amino acids tend to be found on the inside of proteins (i.e. away from water). Note: You need only recognize the general structure of an amino acid. You do not need to be able to identify each R group. Biol 1000 - Dr. M. Cardinal-Aucoin 50  Proteins Types of R-groups Some amino acids have special properties: – Glycine’s R group is very small (just H). – Proline puts a kink in a protein. – The SH in cysteine can bind to another SH in a nearby cysteine to covalently bind different parts of a protein together. Disulfide bond or bridge Biol 1000 - Dr. M. Cardinal-Aucoin 51  Proteins Some amino acids are considered essential because they cannot be made by the body and must be obtained from the diet. Biol 1000 - Dr. M. Cardinal-Aucoin 52  Proteins Proteins are chains of amino acids held together by peptide bonds. – Between C=O of one with NH of the next. – Dehydration synthesis. Peptide backbone: NCC-NCC-NCC Biol 1000 - Dr. M. Cardinal-Aucoin 53  Proteins Chains of amino acids have directionality (polarity). Amino (N) terminus Amino terminus Carboxyl (C) Carboxyl terminus terminus. Biol 1000 - Dr. M. Cardinal-Aucoin 54  Proteins Protein structure: Proteins have 4 levels of structural organization: Primary Secondary Tertiary Quaternary Primary structure: linked sequence of amino acids. each protein has a unique sequence of amino acids. Biol 1000 - Dr. M. Cardinal-Aucoin 55  Proteins Secondary structure: Interactions between stretches of aa’s result in certain specific configurations: α-helix and β-pleated sheet. 3D shape of parts of a protein. Formed by H-bonds between C=O of 1 aa and NH group of another. β-sheet H-bonds H-bonds Lysozyme (enzyme in saliva protects α-helix against bacterial infection) Biol 1000 - Dr. M. Cardinal-Aucoin 56  Proteins Tertiary structure: 3D confirmation of a single polypeptide chain, usually made of several secondary structural elements. Determined by: 1. distribution of hydrophilic and hydrophobic R-groups. ‒ Will fold hydrophilic on outside near water and hydrophobic near each other on inside. 2. different types of chemical bonds and interactions that form between various side chains. Lysozyme (enzyme in saliva protects against bacterial infection) Determines the protein’s function. Biol 1000 - Dr. M. Cardinal-Aucoin 57  Proteins Tertiary structure: 5 bonds that are important in protein folding and stability: 1. hydrogen bonds 2. disulfide bridges (between cysteines) 3. ionic bonds 4. Van der Waals forces 5. hydrophobic interactions Biol 1000 - Dr. M. Cardinal-Aucoin 58  Proteins Denaturation The tertiary structure of the protein determines its function. Most proteins can be unfolded, or denatured, by chemical treatment (e.g. pH, salt, etc.) or high temperature. Disrupts bonds. Denatured proteins lose their functional activity. Biol 1000 - Dr. M. Cardinal-Aucoin 59  Proteins Quaternary structure: Interaction of two or more polypeptide subunits to form a larger functional protein. E.g. hemoglobin (carries O2 in red blood cells) is made of 4 subunits, 2α and 2β. α-subunit β-subunit Biol 1000 - Dr. M. Cardinal-Aucoin 60  Proteins Form Function Biol 1000 - Dr. M. Cardinal-Aucoin 61  Proteins Amino acid substitution Biol 1000 - Dr. M. Cardinal-Aucoin 62  Proteins Pathogens: Prions Infectious agent composed of protein in a misfolded form. NO DNA or RNA!!! Prions are not considered living organisms… but are misfolded protein molecules which may propagate by transmitting a misfolded protein state! Induces existing, Prion enters properly folded proteins a healthy to convert into disease- organism causing misfolded prions. Biol 1000 - Dr. M. Cardinal-Aucoin 63  Proteins Pathogens: Prions Prions are stable proteins and accumulate in the infected tissues. Prion diseases: i. Bovine spongiform encephalopathy (BSE) (mad cow) ii. Scrapie (in sheep and goats) iii. Creutzfeldt-Jakob disease iv. Kuru Biol 1000 - Dr. M. Cardinal-Aucoin 64  Summary Chemistry of life – Polymers Carbohydrates – Mono- and di-saccharides – Polysaccharides – Structural and Energy storage Lipids – Neutral fats – Phospholipids (membranes) – Steroids (membranes and hormones) Biol 1000 - Dr. M. Cardinal-Aucoin 65  Summary Nucleic Acids – Nucleotide subunits – DNA vs RNA – Info storage Proteins – Amino acid subunits – Levels of protein structure – Functions within a cell Biol 1000 - Dr. M. Cardinal-Aucoin 66