Biophysics - Week Two - Building Blocks PDF

Biophysics Building Blocks of Life Objectives Discuss the different building blocks that comprise the cells and organisms Explain the structures observed within living organisms. Reminder of important vocabulary Macromolecule Polymer Carbohydrate Lipid Protein Amino Acid Nuclei...

Biophysics Building Blocks of Life Objectives Discuss the different building blocks that comprise the cells and organisms Explain the structures observed within living organisms. Reminder of important vocabulary Macromolecule Polymer Carbohydrate Lipid Protein Amino Acid Nucleic Acid Nucleotide Image from: https://cdn.pixabay.com/photo/2017/10/30/03/58/testosterone-2901425_1280.png  Important prefixes to learn (from Greek language) Poly (many) Mono (one) Di (two) Meros (part) Image from: https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcRzd- SQrwjTlHPnYY825ZJgWUCrsrXQ_QQrHQ&usqp=CAU  Importance of studying The study of carbon-based molecules is called organic carbon chemistry. Life on Earth is based on carbon-containing molecules For example, the cells are comprised of 72% water 25% carbon compounds Carbohydrates, Lipids, Proteins, Nucleic Acids 3% salts Sodium, Potassium, Chlorine Image from: https://upload.wikimedia.org/wikipedia/commons/a/af/Figure _02_03_02.jpg  What makes Carbon an important molecule for life? Carbon has four valence electrons It allows Carbon to form four covalent bonds This allows carbon to bond with as much as four atoms from Carbon or different elements. Image from: https://cdn.pixabay.com/photo/2019/08/23/16/50/carbon- 4426054_1280.png  Macromolecules of Life These are the carbon-containing molecules found in all living things and all living cells. They are formed by joining different organic molecules together. There are four macromolecules Carbohydrates Carbon, hydrogen, oxygen Proteins Carbon, hydrogen, oxygen, nitrogen, sulfur Lipids Carbon, hydrogen, oxygen Nucleic acids Carbon, hydrogen, oxygen, nitrogen, phosphorus Image from: https://cnx.org/resources/60a4a5093d359bf8057dc6bdaffc23ff9c5ae420/2322_F ig_23.22-a.jpg  Macromolecules Comprised of smaller subunits called monomers Once these smaller subunits combine, they form polymers. Image from: https://upload.wikimedia.org/wikipedia/commons/a/a7/1123ghjkghjk.jpg  Carbohydrates (CH2O)n or C1:H2:O1 ratio n = number of CH2O units in a chain There are different types of carbohydrates Monosaccharides Disaccharides Polysacchariades Image from: https://upload.wikimedia.org/wikipedia/commons/d/d0/217_Five_Important_Monosaccharides-01.jpg  Monosaccharides Included in the group of simple sugars Comprised of up to 7 repetitions of CH2O They function as sources of energy, storage of energy, components of other important macromolecules. Image from: https://upload.wikimedia.org/wikipedia/commons/d/d0/217_Five_Important_Monosaccharides-01.jpg Disaccharides Formed by two units of monosaccharides Image from: https://upload.wikimedia.org/wikipedia/commons/7/7a/Figure_34_03_01.jpg  Polysaccharides Formed by multiple monosaccharide molecules linked together. https://commons.wikimedia.org/wiki/File:219_Three_Important_Polysaccharides-01.jpg  Made up of carbon, hydrogen, and oxygen Typically functions as storage of energy and Lipids component of membranes. They can also serve as chemical messengers.  Different types of lipids Oils Fats Waxes Steroids https://upload.wikimedia.org/wikipedia/commons/2/20/Common_lipids_lmaps.pnghttps://upload.wikimedia.org/wikipedia/c ommons/9/96/222_Other_Important_Lipids-01.jpg  They are further categorized into oils and fats based on their state at room temperature Triglycerides Oils are liquid at room temperature Fats are solid at room temperature. They are comprised of three fatty acids and glycerol. https://upload.wikimedia.org/wikipedia/commons/2/22/220_Triglycerides-01.jpg Saturated vs Unsaturated Triglycerides Saturated means only single bonds present between all carbon atoms in the fatty acid tail. Unsaturated means that the fatty acid tails has at least one double bond. More than one double bond = polyunsaturated fat https://commons.wikimedia.org/wiki/File:221_Fatty_Acids_Sha pes-01.jpg  Difference between saturated and unsaturated fats https://microbenotes.com/saturated-vs-unsaturated-fatty-acids/ Phospholipids Comprised of the hydrophilic head and the hydrophobic tail Hydrophobic tail allow to create a barrier that serves to separate the watery environment within the cells. Important component of cell membranes https://commons.wikimedia.org/wiki/File:Phospholipid_TvanBr ussel.edit.jpg Other types of lipids Waxes Steroids Comprised of cholesterol Modified forms create hormones and secondary messengers. https://www.expii.com/t/steroids-and-waxes-definition- overview-10074 Proteins Comprised of amino acid monomers Amino acids are made of carbon, hydrogen, oxygen, nitrogen, and in some occasions sulfur Functions Enzyme, transport, and cell structure https://upload.wikimedia.org/wikipedia/commons/0/05/Protei n_structure.png 20 different amino acids https://upload.wikimedia.org/wikipedia/c ommons/4/4f/Amino_Acids-wide.svg Formation of proteins Proteins are formed through the peptide bond Bonds are formed between the amino group and the carboxyl group of proteins https://upload.wikimedia.org/wikipedia/commons/b/b5/Figure_03_04_03.jpg Levels of Protein Structure https://cdn.kastatic.org/ka- perseus- images/71225d815cafcc0910 2504abdf4e10927283be98.p ng Purpose of Proteins Structures of the body Muscles, skin, hair Cellular communication Enzymes Control cell growth Protection Storage Comprise a total of around 15% of the body mass. Nucleic acids It serves to store and transmit genetic information Comprised of monomers called nucleotides Which in turn is comprised of parts which include the ribose sugar, phosphate group, and the nitrogenous base. There are five different nucleotides that are combined together to form The sugars of these nucleotides form bonds with the phosphate group of the adjacent nucleotide. Nitrogenous bases interact to develop hydrogen bonds, resulting in double helix. https://upload.wikimedia.org/wikipedia/commons/5/51/Nucleotide_structure_within_a_polynucleotide_chain.png Two types of nucleic acids https://upload.wikimedia.org/wikipedia/commons/3/37/Differ ence_DNA_RNA-EN.svg  http://loretocollegebiology.weebly.com/uploads/1/4/8/5/14853288/1725518.jpg?838 Allows for temporary storage of energy after its release from the chemical bonds of macromolecules. Adenosine A special form of nucleotide triphosphate Adenosine plus three phosphate molecules Bonds between phosphate molecules contain the required energy. What is the relevance of these materials to Biophysics? Why? Understanding these materials should allow for the better understanding of the different processes that occur and the events that drive these processes. Understanding the biophysics of the materials allow for better understanding of the evolution of the biomolecules and biological systems. Physics topics on biological macromolecules. Intramolecular forces Fluctuations Transport and diffusion Movement and diffusion in cells Spatial organization of membrane components Thermodynamics in molecular interactions Polymer statistics and biological examples Chemistry kinetics and conformational transitions. Important techniques and instrumentation Spectroscopy Including concept of absorption, fluorescence, and phosphorescence Aside from light, may use X-Ray or NMR (Nuclear magnetic resonance or re-orientation of atomic nuclei) Light traps or laser tweezers Manipulate interactions of macromolecular systems Force measurements (directed and diffusion) Containment of particles and organelles in cells Scanning probe microscopy Atomic force microscopy for measurement and detection Unlike electron microscope, AFM can get a three-dimensional observation  Light microscopy Important Scanning confocal microscopy techniques and Single-molecule experiment instrumentation Fluorescence correlation microscopy – FCM Fluorescence recovery after photobleaching Fundamental aspects of Physics Systems with a large number of atoms Molecular crystals: Repetitive structures Importance of fluctuations Difference between forces in biomolecules and forces in solids and liquids Use of quantum physics (photosynthesis) Complexity and hierarchy of structures Order-disorder phenomena. Ising model Dissipative processes. Origin of life Information storage and transfer Production, storage and transfer of energy Biomolecular Physics Determination of the structure x-ray, NMR, EPR, hydrodynamics, ε, χ, computational methods Equilibrium properties Thermodynamics and statistical mechanics Cooperative phenomena Kinetic properties Relaxation, chemical kinetics Fluctuations Biomolecules & Biopolymers Constituents :H, C, N, O, P, S, Ca, Cu, Mg, Fe, Zn, Mn Biomolecules --Atoms --Quantum Physics SOLIDS: strong forces LIQUIDS: weak forces BIOMOLECULES: strong + weak forces Determination of structure Geometrical distribution of atoms within molecules, crystals and liquids Methods x-ray diffraction NMR Electron microscopy The scattering of electrons and x-rays depends on interatomic distances. Neutron diffraction is used for H-atoms. Tunneling microscopy Computational methods Microwave spectroscopy gives information on vibrational levels, moment of inertia - atomic distances Biomolecules → Life The interaction between biomolecules determines the development and evolution of living systems. Biomolecules contain a large number of atoms (102 to 1010) The hierarchy of living things Organism >1020 Cell 1010 Organelle 105–106 Biomolecule 103–104 Molecule 10 –100 Atom 1 Physics Information and Construction Proteins 20 building blocks, amino acids 100-200 amino acids per protein (range from 15 to 3000) L-amino acids only!!! Large number of possible sequences 20100 to 20200 (this is practically infinity) For each sequence large number of conformations 2200 about 1060 Instantaneous vs. average quantities Proteins Functions Enzymes Lysozyme, Ribonuclease, LADH, Carbonic anhydrase Storage Ferritin, Ovalbumen, Caseine Transport Hemoglobin, Myoglobin, Hemocyanine Protection Antibodies, Fibrinogen, TrombinHSP Hormones Insulin, Growth Factor Structure Collagen, alpha-keratin Light harvesting Rhodopsin, reaction centers Light production Luciferase