Module 1 Basic Concepts of Life S23 Students PDF

Basic Concepts of Life Module 1 Module 1: Concepts Life 1) What constitutes life in general? at the molecular level? Life organizes… Molecules non living things become disorganized 2) What is a molecule? What are the molecules i...

Basic Concepts of Life Module 1 Module 1: Concepts Life 1) What constitutes life in general? at the molecular level? Life organizes… Molecules non living things become disorganized 2) What is a molecule? What are the molecules in biochemistry? Shared Molecular Characteristics of Life 3) three molecular characteristics that all forms of life share → obey the laws of thermodynamics → use ATP as energy currency → formed of both small and large biomolecules which show remarkable similarity between various forms of life Molecular Life When you break life forms down to their molecular constituents, seemingly distinct organisms actually share the same molecular characteristics… → all can use the molecule glucose for energy → all store their information as DNA → all convert food energy to ATP e.g. all living organisms have a gene coding for an enzyme that phosphorylates glucose question 1: What is LIFE? Typical conventional definition of “life” includes several main characteristics: VIDEO (https://www.youtube.com/watch?v=uM_CgOgJGG0) 7 Conventional Definitions of Life 1) Organization: Being composed of one or more cells, which are the basic units of life and are ‘organized’ into the whole organism. Whole Organism Homo sapiens (ex. _______________) liver Tissue (ex. ______) Cell hepatocyte (ex. ____________) ‘Biomolecules’ (carbs, fats, proteins, nucleic acids) even the cell itself is organized from the various biomolecules Conventional Definition of Life 2) Reproduction: Life has the ability to produce new organisms Strictly speaking, reproduction means the ability of one cell to form two new cells Conventional Definition of Life 3) Metabolism: Life undergoes the chemical processes that are necessary for the maintenance of life. Catabolism Anabolism substances are substances are broken down, synthesized, providing energy Metabolism using energy The concept of Metabolism is the central feature of the study of biochemistry and will be the focus of this course. Conventional Definition of Life 4) Growth: Life grows, it maintains a higher rate of building up than breaking down. → increase in size of the organism → progression from a simpler to more complex form Catabolism < Anabolism Metabolism Conventional Definition of Life 5) Homeostasis : Life regulates the internal environment to maintain a constant state → sweating to reduce body temperature → shivering to increase body temperature Some other examples of Homeostasis in biology are: → regulate levels of blood sugar with insulin/glucagon → regulate water and salt levels by producing urine → maintain neutral blood pH (by producing urine) → systems that eliminate toxins in body Conventional Definition of Life 5) Response to Stimuli : Life has the ability to respond, to react in the short term to a stimulus Some examples of responses to stimuli are: → microorganisms moving toward food, or away from poison → the leaves of a plant turning toward the sun → an animal chasing its prey Conventional Definition of Life 7) Adaptation: The ability to respond over a long period of time to one’s environment (another term would be: ‘evolution’) → determined by genes and environment Some examples of an organism adapting to its environment are: → melanin pigment in skin to protect against UV rays → adipose tissue insulates against cold → giraffes developing long necks to get to leaves in tall trees Conventional Definition of Life 7) Adaptation example: Toronto Star, May 4, 2010 Other Proposed Features of Life Carbon-containing → carbon is the chemical element that forms the basis of life on earth Reliance on water → water is a chemical substance needed for survival of all forms of life on earth Genetic information → uses DNA and RNA to store blueprint of of organism question 2: What is a molecule? Molecule: → the smallest particle of a substance that retains the properties of the substance → can be composed of one or more Atoms ex: water molecule (1 oxygen, 2 hydrogens) Atom: molecule the smallest particle of an element that retains the chemical properties of the element example: an oxygen atom Biological Molecules Biological molecules can contain a few, or up to many thousands of atoms nearly infinite possibilities Serine (an amino acid) Alcohol dehydrogenase enzyme C3H7NO3 (14 atoms) (protein composed of 374 amino acids) The atoms in a complex enzyme molecule are specifically oriented in space as well  Whole Organism Tissue What molecules do we see in biochemistry? Cell “Biological Molecules” 1. Proteins 4. Nucleic acids 2. Carbohydrates 3. Lipids functions? What elements (atoms) are in biomolecules (same # electrons in outer orbital) group (column) period (row) (same # electron orbitals) 117 chemical elements, 92 are found naturally on Earth, and the rest are synthetic elements Biomolecule elements form in nature 8O (O2) 1H (H2) 7N (N2) 15P 6C 16S when elements are combined in more complex molecules they take different forms question 3: What are the Shared Molecular Characteristics of Life Now that we know the 7 conventional characteristics of Life and what sorts of molecules Life forms contain, we can address the question: What are the shared molecular characteristics of Life forms? 1. Life obeys the laws of thermodynamics 2. ATP is the common energy currency of life 3. Life is composed of similar biological molecules both large and small → molecular characteristics of life are microscopic, you can’t see them with your eye The 3 Molecular Characteristics of Life 1. Life obeys the laws of thermodynamics → what are the laws of thermodynamics? 2. ATP is the common energy currency of life → what is ATP? 3. Life is composed of similar biological molecules both large and small: 4 classes… → proteins → lipids → carbohydrates → nucleic acids 1st Molecular Characteristic: Life Obeys the Laws of Thermodynamics Thermodynamics studies the movement of energy Typical physical thermodynamic system: heat (energy) moves from hot (boiler) to cold (condenser), and work is extracted, in this case by a series of pistons. boiler condenser In a biochemical thermodynamic system, energy comes from food and work is extracted by the body (ex. muscle contraction) 1st Law of Thermodynamics 1st Law: Energy can neither be created nor destroyed It can only change from one form to another *These processes Biochemical application: require oxygen (O2) energy from food is being transformed (changed) into → chemical energy (ATP) Carbon dioxide (CO2) and water (H2O) are produced as products of food breakdown. 2nd Law of Thermodynamics 2nd Law: All processes increase entropy (disorder) Biochemical application → Large food molecules (less entropy) are broken down into many smaller molecules ( more entropy) This is the process of CATA _____BOLISM Carbon dioxide (CO2) and water (H2O) are more numerous and much smaller in size than food molecules  one more point about the 2nd Law… In living organisms, the opposite process also is happening Anabolism → small molecules are also being organized into large molecules such as combining many small amino acids into large complex proteins (and therefore decreasing entropy) Doesn’t this contradict the 2nd law? yes, but…. we use a very large amount of energy (food) in order to cause a decrease in entropy and much of that energy is lost as heat… the release of waste heat produced by our metabolism increases the entropy of the universe and eventually all our complex molecules will break down, increasing entropy…. 2nd Molecular Characteristic: ATP is the common Energy Currency of Life In biochemistry, there are multiple sources of energy and multiple types of work performed energy (food) sources: types of work: ATP carbohydrate (CHO) muscle contraction (movement) lipids (fat) maintaining chemical gradients protein heat generation Does it make sense to have multiple sources of energy that are specialized for each type of work? no… convert all sources of energy to common energy currency (ATP) to do all work ATP – What is it? Common molecular ‘energy currency’ that transfers energy within cells in metabolism produced during photosynthesis (plants) and cellular respiration (animals), used for a multitude of cellular processes structure of ATP (Adenosine TriPhosphate) Triphosphate Adenosine → 3 phosphate → a “nucleoside” (PO42–) groups (discussed later) 3rd Molecular Characteristic: Life is composed of very similar small and large Biomolecules remember the Biomolecules: → carbohydrates → protein → lipids → nucleic acids Each of these can be divided into small and large categories for example, monosaccharides (glucose, fructose, and galactose would be considered ‘small’ carbohydrates while polymers glycogen and starch would be considered ‘large’ carbohydrates) the ‘nutrients’ in food are Biomolecules “small” Biomolecules In their simplest form, the biomolecules are found as: monomers Serine (amino acid) → a monomer is: a single unit, but can be attached together to form slightly larger molecules such as dimers, trimers, or ‘oligomers’ ‘small’ biomolecules fall within an arbitrary range: name # of units monomer 1 dimer 2 trimer 3 oligomer (“oligo” = a few) 4 → ~50 “large” Biomolecules In a more complex form, the biomolecules can exist as polymers (‘poly’ = many ) polymers are composed of repeating monomers joined by covalent bonds (more on chemical bonds later…) polymers contain: 100’s to 1000’s of monomers (more than 50: polymer) polymers can be: → long linear chains → branched → complex folded shapes Alcohol dehydrogenase (enzyme) What is a Nutrient? Any substance that is of nutritional value to an organism. nutrients can: provide energy, or provide the building blocks for the organism to maintain, grow, and repair itself. Some nutrients can be synthesized in the body, however some cannot → essential nutrient ex. Vitamin C: humans cannot make it but almost every ` other mammal can (only 4 out of 4000 mammals can’t) Micronutrients vs Macronutrients Nutrients Micronutrient Macronutrient Microminerals Vitamins Carbohydrates Proteins Lipids Macrominerals Micronutrient: a nutrient that is required in small amounts → all vitamins (A, B, C, D, E, K) → Microminerals, ex. Iron, Copper, Manganese, Zinc Macronutrient: a nutrient that is required in large amounts → carbohydrate, protein, lipid also, some minerals are required in larger amounts: Macrominerals Calcium, Potassium, Sodium, Magnesium, Phosphorous What do vitamins & minerals actually DO? Nutrients Micronutrient Macronutrient Microminerals Vitamins Carbohydrates Proteins Lipids Macrominerals Vitamins → act as ‘co-factors’ for enzymes, organic compounds that are only loosely bound to the enzyme during its reaction → but they are required for the enzyme to function properly obtained in food (or more recently in purified supplements) → vitamin deficiency results in reduced enzyme activity for example, thiamine (vit B1) essential for pyruvate dehydrogenase What do vitamins & minerals actually DO? Nutrients Micronutrient Macronutrient Microminerals Vitamins Carbohydrates Proteins Lipids Macrominerals Microminerals → Iron, Copper, Manganese, Zinc → Iron required for proper function of hemoglobin, a protein which carries oxygen through the blood also, some minerals are required in larger amounts: Calcium, Potassium, Sodium, Magnesium, Phosphorous → Sodium and Potassium are required for nerve signals Macronutrients: energy source Nutrients Micronutrient Macronutrient Microminerals Vitamins Carbohydrates Proteins Lipids Macrominerals Macronutrient: a nutrient that is required in large amounts → biomolecules: carbohydrate, protein, lipid → their role is primarily energy for the organism consuming them (though all three of these biomolecules have other roles as well) → (mostly structural) Biomolecules are nutrients so… biomolecules are nutrients specifically, they are: macronutrients needed by living organisms in large amounts the source of biomolecules is: food What about nucleic acids? What about Nucleic Acids? remember the definition of a nutrient: nutrients can: provide energy, or provide the building blocks for the organism to maintain, grow, and repair itself. dietary DNA and RNA provide us with nucleic acids necessary to: maintain, grow, and repair our own DNA and RNA Conclusion: nucleic acids: are nutrients but they aren’t usually considered in nutritional analysis because they don’t provide nutritional energy like CHO, protein and lipids so you won’t see nucleic acids listed on a food label (no calories) Nucleic Acid monomer: Nucleotide reminder: “bases” → ATP is a Nucleotide “phosphates” “sugar” RNA only Nucleic Acid polymer: DNA DNA contains the genetic instructions that are DNA backbone: the blueprint of all living organisms sugars connected by: DNA is organized into chromosomes phosphates A T Double-stranded and ‘base paired’ G C 2 DNA strands connected by: bases uses: Deoxyribose sugars (pairs with) (pairs with) When you consume a food (plant or animal) you consume their DNA, which is broken down paired bases during digestion into Deoxyribonucleotides connected by: hydrogen that can then be used to synthesize new DNA bonds → DNA stands for DeoxyriboNucleic Acid Nucleic Acid polymer: RNA RNA is the ‘messenger’ that carries the instructions from DNA from the nucleus of the cell into the cytoplasm where coded for protein is synthesized Complementary to DNA and is single-stranded Contains ribose sugars and uses uracil instead of thymine As with DNA, when you consume a food you consume their RNA, which is broken down during digestion into ribonucleotides that can then be used by the organism to make new RNA → RNA stands for RiboNucleic Acid  Textbook readings for the next module module 2: Chemical Foundations in Biochemistry textbook pages: chapter 1: p 5-13 secondary resources: general chemistry text → Nomenclature Hydrocarbons & Functional Groups → Chemical Bonds bond numbers, intramolecular & intermolecular → Electronegativity, Polarity, and Isomers Quiz #1 on the Concepts of Life module: Wed July 5 open at 8pm Wednesday until Thursday July 6, at 8pm (don’t miss it, remember it closes at 8pm Thursday…) report is available to view 9pm Thursday with correct answers along with your answers