BIO 110 - 02 - Chemical Level PDF

Professor Lindboom-Broberg (LB) Chemical Level of Organization Atoms & Subatomic Particles Bonding & States of Matter Reactions & Enzymes Water & pH Biological Macromolecules Levels of Organization Remember these? Mat...

Professor Lindboom-Broberg (LB) Chemical Level of Organization Atoms & Subatomic Particles Bonding & States of Matter Reactions & Enzymes Water & pH Biological Macromolecules Levels of Organization Remember these? Matter Matter Anything that takes up space and has mass Mass The quantity of material in matter On Earth, mass is equivalent to weight (because gravity = 1) On a planet with 2 g’s, you’d weigh twice as much Atoms Atoms: Smallest stable units of matter Composed of subatomic particles Protons (p+) Have a positive electrical charge Mass = 1 amu Neutrons (n or n0) Are electrically neutral (uncharged) Mass = 1 amu Electrons (e–) Have a negative electrical charge Mass = 1/1836th of protons or neutrons Composed of two regions Nucleus Central area containing protons & neutrons Electron Shells (cloud) External rings containing electrons Atoms Periodic Table of Elements 118 known elements There are other hypothesized elements! Element 119. (n.d.) Encyclopedia Britannica. Retrived from, https://www.britannica.com/science/element-119 Atoms Atomic symbol One or two letter code for that element Atomic number Total number of protons in an atom A neutral atom will contain the same number of electrons Mass number Total number of protons and neutrons in a specific atom Atomic weight (atomic mass) Average mass number for all forms of that atom that exist Atoms Practice for yourself! 6p 6n 6e 1p 8p 0n 8n 1e 8e 50 82 p p 125 69 n n 82 e 50 e Atoms Alternative forms of atoms Isotopes: Atoms with a different number of neutrons More neutrons = heavier = greater atomic mass Each atom has isotopes present on Earth at specific percentages Used by science for labeling studies or radiometric dating Atoms Alternative forms of atoms Ions: Atoms with a different number of electrons Gained 1+ electron(s) = negative (anion) Lost 1+ electron(s) = positive (cation) +, +2, +3… –, –2, –3… Atoms Alternative forms of atoms Change the number of protons and you change the atom it is Ex: Carbon + 1 proton = Nitrogen cation Alchemy Medieval chemistry focused on two primary goals Transformation of various metals into gold (money) Creation of a universal elixir (fountain of youth) Never worked out We learned a lot and developed modern chemistry  Professor Lindboom-Broberg (LB) Bonding Atomic Interactions Types of atomic bonds Creating molecules & compounds Atoms – Bonds Electrons are located in the electron cloud The cloud is made up of various energy levels, or electron shells Every shell can hold 2n2 electrons 1st Shell = 2 electrons 2nd Shell = 8 electrons 3rd Shell = up to 18 electrons The valence shell is the outermost electron shell Dictates an atom’s chemical ability (ie. Bonding) Gold Hydrogen Carbon Atoms – Bonds Atoms are most stable when their valence (outer) shell is “full” Octet Rule: Most atoms bond to have 8 electrons in the valence shell (2 for 1st shell) Unfilled valence shells make an atom reactive Atoms will pull electrons off other atoms Atoms will give away their electrons Atoms will share electrons Filling valence shells is the basis for chemical bonding Atoms – Bonds Filling valence shells is the basis for chemical bonds There are three ways in which atoms can bond to one another 1. Ionic Bonds 2. Covalent Bonds 3. Hydrogen Bonds Atoms – Bonds Ionic bonds One atom steals an electron  negatively charged  anion One atom gives away an electron  positively charged  cation The opposing electrical charges now attract one another Example: sodium chloride Properties Charged Atoms easily separate (dissolve) in water (hydrophilic) Atoms – Bonds Covalent bonds Neither atom has the energy to steal or give away Instead, they fill their valence shells by sharing How MANY electrons do they share? Single bond shares one pair of electrons One electron contributed by each atom Double bond shares two pairs of electrons Two electrons contributed by each atom Triple bond shares three pairs of electrons Three electrons contributed by each atom Atoms – Bonds Covalent bonds Neither atom has the energy to steal or give away Instead, they share HOW are the electrons shared? Non-Polar covalent bonds share equally No partial charges Polar covalent bonds share unequally Atoms become partially charged δ δ δ Atoms – Bonds Polar covalent bonds have partially neg/pos ends Hydrogen bond Attraction of the small positive charges on hydrogen atoms (of a polar molecule) to negative charges on atoms (O or N) in other polar molecules Can change shape of molecules or pull molecules together Extremely weak individually Found in mass numbers Atoms – Bonds When bonds form, two things can be created 1. Molecules 2+ atoms held together by covalent bonds (molecular bonds) 2. Compounds 2+ atoms of two or more different elements in a fixed proportion, regardless of type of bond joining them. States of Matter The state of matter depends on the arrangement of atoms Solid Tightly packed atoms with regular arrangement Retains a fixed volume and shape Liquid Close with no regular arrangement Assumes the shape of its container Gas Well separated with no regular arrangement Assumes the volume and shape of its container  Professor Lindboom-Broberg (LB) Chemical Reactions How do atoms, molecules, and compounds interact with one another? Chemical Reactions The chemical reactions that take place in a cell are essential for many cellular functions… Providing energy Maintenance and repair Growth Cell division Secretion Contraction Chemical Reactions Chemical reactions diagrams Reactants: Participants at reaction start Usually on the left Products: Generated at end of reaction Usually on the right Reacta Produ nts cts Chemical Reactions To be living, a cell must take in and use energy Metabolism: Sum of a cell or organism’s total chemical reactions Anabolism: Sum of all synthesis reactions Catabolism: Sum of all decomposition reactions Reacta Produ Anabolic or nts cts Catabolic? Anabolic Catabolic Both Both Chemical Reactions Three categories of chemical reactions Decomposition / Catabolic: Breaking a molecule into smaller fragments Chemical bonds are broken Synthesis / Anabolic: Combining smaller fragments together Chemical bonds are formed Exchange: Reacting molecules are shuffled around May involve both decomposition and synthesis reactions Chemical Reactions Catabolic reactions Catabolism: Collective term for decomposition reactions in the body Breaking covalent bonds Release energy that can perform work Body can use energy for growth, movement, and reproduction Hydrolysis: A decomposition reaction that involves water. A water molecule is used to break the molecular bond One fragment gets H, the other gets OH Chemical Reactions Anabolic reactions Anabolism: Collective term for synthesis reactions in the body Refers to forming new chemical bonds Requires input energy Usually comes from other catabolic reactions Dehydration Synthesis (condensation): Formation of a molecular bond by removing a water molecule Opposite of hydrolysis Chemical Reactions Free Energy Diagram A graph of the energy along the timeline of a chemical reaction Chemical Reactions The direction of energy results in two reaction categories Exergonic: Net release of energy Common in the body and help to maintain body temperature Endergonic: Net intake of energy Include reactions to build molecules Chemical Reactions Activation energy: Minimum energy required to activate reactants in a reaction and allow reaction to proceed Outside the body – may be acquired by extremes in temperature, pressure, or lethal chemical factors Inside the body – cells use special proteins called enzymes Activation energy can restrict certain reactions from occurring Chemical Reactions Enzymes: Lower a reaction’s activation energy Allow reactions to proceed without any changes to itself Act as a catalysts: Accelerate chemical reaction without being permanently changed or consumed  Professor Lindboom-Broberg (LB) Water (H2O) The compound that made life possible. Water – Properties Water has polar covalent bonds Partial electrical charges Forms hydrogen bonds between molecules Water has very unique characteristics due its type and number of bonds Lubricant Cohesion & Adhesion Solvent Chemical Reactions Density Heat Capacity These properties allowed for life! Water – Dependence Salts dissolve in water (NaCl  Na+ + Cl–) Water can dissociate too H2O  Hydrogen ions (H+) and Hydroxide ions (OH–) Hydrogen ion (H+) Extremely reactive in solution Large numbers can break chemical bonds & disrupt cell/tissue function Concentration in body regulated precisely Hydroxide ion (OH–) Produced when water dissociates (along with H+) Reactive because it pulls H+s off of other molecules Water – Dependence Water – Dependence Buffers: Compounds that stabilize the pH of a solution by removing or replacing hydrogen ions Help to maintain normal pH of body fluids Buffer Systems: Help maintain pH within normal limits Example: Sodium bicarbonate (NaHCO3)  Professor Lindboom-Broberg (LB) Biological Macromolecules What molecules are responsible for the structure and function of biological life? Biological Macromolecules Organic: Carbon-based molecules Contain hydrogen and generally oxygen as well Groups Carbohydrates Lipids (fats) Protein Nucleic Acid Inorganic: Non-carbon-based molecules/compounds Biological Macromolecules Carbohydrates Lipids (fats) Proteins Nucleic Acids Biological Macromolecules Reactions in our bodies… Macromolecule: large molecule made up of monomer subunits Monomer: Individual subunits of macromolecules Dimer: Two subunits bonded together Polymer: Many monomers bonded together Thinking back… Repeating monomers join through dehydration synthesis to form polymers Hydrolysis reactions separate polymers to form monomers Biological Macromolecules (Carbs) Carbohydrates Sugars and starches (=saccharide) Monosaccharides Made of C, H, & O in ratio near 1:2:1 Two categories Simple Sugars Disaccharides Monosaccharide: Single carb subunit Glucose, Fructose, Galactose Complex Sugars Disaccharide: Two subunits combined Ex: Sucrose, Lactose, Maltose, etc. Polysaccharide Polysaccharide: Many subunits combined Glycogen: Storage form of carbs in animals Starch: Storage form of carbs in plants Roughly 1.5% of total body weight Most important function: Energy source Biological Macromolecules (Lipids) Lipids (fat) Examples: fats, oils, waxes Contain C, H, & O Carbon to hydrogen ratio is near 1:2 Much less oxygen than carbs May contain phosphorus (P), nitrogen (N), or sulfur (S) Most are insoluble in water (hydrophobic) Special transport mechanisms for them in the blood Four categories Fatty Acids – Slow burning energy source Glycerides – Storage form of lipids Steroids – Form hormones and cholesterol Phospholipids – Form cellular and organelle membranes Biological Macromolecules (Proteins) Proteins Contain C, H, O, & N (sometimes P & S) Most abundant organic molecule in the body Monomer = amino acid (AA) 20 different AAs in the body Polymer = Protein Three-dimensional shape determines functional properties Normally account for 20% of total body weight Biological Macromolecules (Proteins) Enzymes lower the activation energy of a reaction Facilitates many processes within the body Molecular Basis Substrates: Reactants in enzymatic reactions Active site: Specific region of an enzyme where substrates bind Site shape determined by tertiary or quaternary structure of enzyme Products: The final substance(s) that is (are) produced Biological Macromolecules (Proteins) Specificity Substrate and enzyme fit in a “lock and key” fashion Each enzyme binds only to substrate with particular shape and charge Each enzyme catalyzes only one type of reaction Biological Macromolecules (Proteins) Sensitivity Multiple enzymes in each cell Each enzyme is active under its own set of preferred conditions A change in conditions alters enzyme activity/function pH, temperature, pressure, concentrations, etc can denature enzymes Enzyme activation/inactivation is a form of short-term control over reaction rates and pathways Biological Macromolecules (Nucleic Acids) Nucleic acids Composed of C, H, O, N, & P Three classes 1. ​Deoxyribonucleic acid (DNA) 2. ​Ribonucleic acid (RNA) 3. High Energy Molecules (ie. ATP) Two primary functions Storage/transfer of information (DNA, RNA) Storage/transfer of energy (ATP) Nucleotides: Monomer subunit of nucleic acids Adenine, Cytosine Thymine, Guanine, Uracil Biological Macromolecules (Nucleic Acids) Adenosine triphosphate (ATP) allows energy transfer Formation of ATP from ADP is reversible ADP  ATP requires energy input for storage ATP  ADP releases energy These molecules are transportable Allows cells to store energy in one location and release it in another location Provides energy for many vital body functions Examples: Contraction of muscles or Synthesis of proteins, carbohydrates, and lipids