Chemistry of Life PDF

Basic Chemistry Matter and Energy ​ Matter: has mass and occupies space ○​ Made up of elements and compounds ○​ Affected by gravity ​ Energy: the ability to do work ○​ Moves matter ○​ Potential and kinetic ○​ Ex: sound, light, heat ​ Matter...

Basic Chemistry Matter and Energy ​ Matter: has mass and occupies space ○​ Made up of elements and compounds ○​ Affected by gravity ​ Energy: the ability to do work ○​ Moves matter ○​ Potential and kinetic ○​ Ex: sound, light, heat ​ Matter has a tendency to move to the lowest possible energy level ​ Element: pure substance made of only one kind of atom ○​ Cannot be broken down into other substances by chemical reactions ​ Compound: 2 or more different elements in a fixed ratio ○​ Characteristics may be different than those of its elements Atomic Structure ​ Atom: smallest unit of an element that retains the properties of that element ○​ Three subatomic particles: protons, neutrons, and electrons ​ Protons: AMU (aka Dalton) of 1, positive charge, found in the nucleus ​ Nucleus also has a positive charge ​ Neutrons: AMU of 1, no charge, found in the nucleus ​ Electrons: negligible AMU, negative charge, found in the electron cloud ​ Potential energy grows as electrons move further away from the nucleus ○​ When electrons absorb energy, they move further out and when they release energy, they move closer in ○​ Atomic Number: number of protons in an atom ○​ Mass Number: number of protons and neutrons in an atom ○​ Atomic Mass: total AMU of the nucleus (more specific than mass number) ​ Differs very slightly from mass number ​ Atoms are mostly empty space ​ Isotopes: atoms of the same element with different numbers of neutrons ○​ Unless said otherwise, an atom is neutral in electrical charge, meaning its protons must be balanced by an equal number of electrons ○​ Radioactive Isotopes: unstable due to high numbers of neutrons ​ Nucleus can spontaneously decay, giving off particles and energy ​ Can change one element to another ​ Can be used to trace atoms within the body since they are radioactive ​ Electrons exist at fixed levels of potential energy (electron shells)  ○​ Can’t exist in the space between shells ​ Valence Electrons: electrons on the outermost energy level ○​ Atoms with completed valence shells are unlikely to react (inert) ​ Valence: The bonding capacity of an atom corresponding to the number of covalent bonds that the atom can form ○​ Typically equals the number of unpaired electrons required to complete the atom’s valence shell ​ Orbital: The three-dimensional space or an electron is found 90% of the time Chemical Bonds ​ Strongest Bonds: ○​ Covalent: sharing electron pairs ​ Single Bond: the sharing of one pair of electrons ​ Double Bond: the sharing of two pairs of electrons ​ Triple Bond: the sharing of three pairs of electrons ​ Polar: covalent bonds between atoms that differ in electronegativity ​ Uneven electron distribution ​ Nonpolar: equal sharing of electrons ○​ Ionic: an electron is passed between two atoms, allowing for the newly formed ions (attracted to each other) to bond ​ Cation: positive charge ​ Anion: negative charge ​ Forms ionic compounds, or salts ​ Weaker Bonds: ○​ Hydrogen: Hydrogen of polar molecules bonds to the electronegative atom of other polar molecules ​ Electronegativity: the tendency of an atom to attract electrons ○​ Van der Waals Interactions: slight, fleeting attraction between atoms and molecules that are close together ​ Bonds are made and broken by chemical reactions ​ The structure of molecules affect their function ○​ Similar Shapes = similar functions ​ Structural Formula: shows arrangement of molecules ○​ Molecular Formula: only shows the numbers of each element ​ Dynamic Chemical Equilibrium: a state where a reversible reaction reaches a balance between the forward and reverse reactions ○​ Rate of forward and reverse reactions is roughly the same ​ Partially because of higher concentrations ○​ No net change in reactants/products  ​ Chemical Reactions: the making and breaking of chemical bonds, leading to changes in the composition of matter Properties of Water Water is a polar molecule ​ Unequal sharing of electrons in the covalent bonds between H+ and O2- ​ Hydrogen Bond: slightly negative O attracted to the slightly positive H ○​ Can make up to four bonds ​ 2 per oxygen ​ 1 per hydrogen ​ Oxygen needs 2 more electrons to complete the outermost shell ○​ Attracted to the single electron in Hydrogen ​ Electrons are pulled by the heavier mass of oxygen, making it more negative ○​ A surplus of 2 electrons in the oxygen allows it to form 2 bonds with 2 different hydrogens ○​ Each hydrogen atom bonds with one atom of oxygen Cohesive Behavior ​ Cohesion: hydrogen bonding between like molecules ○​ Surface Tension: a measure of how difficult it is to break or stretch the surface of liquid ​ Water is more strongly bonded to itself than to the air above, making it seem as if there is an invisible film on it ​ Adhesion: Bonding between unlike molecules ○​ Water on the edges of a graduated cylinder climb up (meniscus) ​ Capillary Action: movement of water up the roots of plants ○​ Adhesion: sticks to the side of the roots ○​ Cohesion: water is attracted to itself ​ Transpiration: when plants lose water from their surfaces and leaves Moderation of Temperature ​ Thermal Energy (Heat): total amount of kinetic energy in a system  ○​ Increases with volume ​ Temperature: a measure of the intensity of the heat ○​ Average of kinetic energy ​ Water has a high specific heat: The amount of heat that must be absorbed or lost for 1 G of a substance to change its temperature by 1℃ ○​ Water’s specific heat is defined as a calorie ○​ Takes a lot of energy to change the temperature of water ​ Water must absorb heat to break hydrogen bonds before it can start moving faster ○​ Large bodies of water absorb and store more heat ​ Why coastal areas are warmer ○​ Creates a stable marine/land environment ○​ Humans are about 65% water ​ Stable temperature that resists change (homeostasis) ​ Evaporative Cooling: the tendency of surfaces to cool down after liquid evaporates ○​ Water has a high heat of vaporization ​ Takes a lot of energy to go from liquid to gas ○​ Molecules with the greatest kinetic energy (heat) leave as gas ○​ This leads to stable temperatures in lakes and ponds ○​ Sweat, transpiration Expansion Upon Freezing ​ Insulation by Ice: less dense ice floats and insulates the liquid water below it ○​ Why fish survive winter ​ Between 0℃ and 4℃, water moves too slowly for hydrogen bonds to break ○​ As water freezes, molecules are forced apart from another, leading to ice’s lower density Water = Solvent of Life ​ Solution: liquid, homogenous mixture of 2+ substances ○​ Solute: what gets dissolved ○​ Solvent: dissolving agent (liquid) ​ Water is a versatile (universal) solvent ○​ Can dissolve a lot of different substances ○​ Water’s attraction to itself allows it to surround individual particles of different substances ​ Hydration Shell: The sphere of water molecules around each dissolved ion  ​ Hydrophilic Substances ○​ Affinity for water ○​ Polar or ionic ○​ Salt, phosphate, etc ​ Hydrophobic Substances ○​ Repeal water ○​ Non-polar ○​ Oils, lipids, cell membranes Acids and Bases ​ Water dissociates into H+ and OH- ○​ H+ joins with another water molecule, forming a hydronium ion ​ H+ does not exist on its own; rather, H+ is used as a substitute to represent H3O+ ​ Acids: increase H+ concentration (0-7) ​ Bases: reduces H+ concentration (7-14) ○​ Maybe by increasing OH- concentration or by absorbing H+ ​ The product of the H+ and OH- concentrations is 10-14 ○​ Ex: if a substance has an H+ concentration of 10-8, it must have an OH- concentration of 10-6 ​ pH: The negative logarithm of the hydrogen ion concentration ○​ pH = -log{H+] ​ Most biological substances are between pH of 6-8 ​ Each jump in pH is a 10-fold increase  ○​ 6 → 7: 10-fold increase ○​ 6 → 8: 100-fold increase ​ Buffers: minimize changes of H+ and OH- in a solution ○​ Weak acids and bases that can add/remove H+ when it is in depletion/excess ○​ Keep blood at pH 7.4 ​ Carbonic Acid (Bicarbonate System): important buffers in blood plasma ​ The rise of carbon dioxide levels has increased the carbonic acid concentration in oceans (ocean acidification) Carbon The Importance of Carbon ​ Organic Chemistry: branch of chemistry that specializes in the study of carbon compounds ​ Organic Compounds: contain Carbon and Hydrogen ​ Major elements of life: CHNOPS ○​ Calcium, phosphorus, potassium, sulfur, and a few other elements account for almost all of the remaining mass of organisms ○​ Trace elements: required by an organism in only minute quantities ​ Carbon enters life through producers changing it from CO2 to macromolecules ​ Complex organic molecules could arise spontaneously in early-Earth conditions Diversity of Carbon ​ Tetravalence: 4 valence electrons ○​ Form up to 4 covalent bonds ○​ Frequently bonds with H, O, N ​ Carbon can form single, double, or triple bonds ○​ -ane: single bond ○​ -ene: double bonds ○​ -yne: triple bonds ​ Organic molecules can be chains, ring-shaped, or branched ​ Typically, organic molecules are tetrahedral ​ Hydrocarbons: organic molecules containing only C and H  ​ Carbon can form isomers: molecules that have the same molecular formula but different atom arrangements (and therefore have different properties/functions) ○​ Structural: varies in covalent arrangement (shape) ○​ Cis-Trans: differ in spatial arrangement around a double bond (structural groups in different places) ​ Cis: functional groups on the same side ​ Trans: functional groups on opposite sides ​ Mainly in lipids ○​ Enantiomers: mirror images of molecules ​ Ex: thalidomide ​ Reduced morning sickness but caused birth defects ​ Converted inside the body from being helpful to harmful ​ Other examples: ibuprofen (S-ibuprofen > R-ibuprofen), albuterol (R-ibuprofen > S-ibuprofen) ​ Macromolecules: Carbohydrates, Proteins, Lipids, Nucleic Acids Functional Groups ​ Controls the behavior of organic molecules ○​ Ex: Testosterone and estradiol (male and female sex hormones respectively) differ only by 2 functional groups ​ Most common functional groups: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl ○​ All besides methyl can be chemically reactive ○​ All besides methyl and sulfhydryl are hydrophilic and increase the solubility of organic compounds in water ​ ATP: adenosine and three phosphate groups ​ Phosphate is hydrophilic and reacts readily with water, releasing energy and forming ADP Organic Compounds ​ Carbon is a versatile molecule ​ Functional groups attached to organic molecules give them specific properties ​ Monomers: singular units of organic molecules ○​ Polymers: multiple monomers linked together ​ Biological Macromolecules: large biological molecules ○​ Carbohydrates, proteins, nucleic acids, lipids ​ Dehydration Synthesis: the breaking down of bonds (releases H+ and OH-) that allows two carbon molecules to bond ○​ Creates water molecules ○​ Forms polymers ​ Hydrolysis: opposite of dehydration synthesis; the addition of H+ and OH- to break and create new bonds with molecules and break them down ○​ Forms glycosidic linkages ○​ Released monomers are absorbed into the bloodstream for distribution to all body cells ​ Cells can then form new polymers through dehydration synthesis  ​ Both dehydration synthesis and hydrolysis are facilitated by enzymes: specialized macromolecules that speed up chemical reactions Carbohydrates ​ Short-term energy ​ Made of carbon and water molecule (in a 1:1 ratio) ○​ 2:1 Ratio of hydrogen to oxygen ​ Monomers: monosaccharides ○​ Simple sugars ○​ Glucose, fructose, galactose ​ Two monomers together: disaccharides ○​ Glucose + glucose = maltose ○​ Glucose + fructose = sucrose (table sugar) ○​ Glucose + galactose = lactose (milk sugar) ​ Forms glycosidic linkages ​ Maltose, sucrose, and lactose are structural isomers ○​ all have the chemical formula C12H22O11 ​ Arranged differently ○​ Lost an H2O in hydrolysis ​ Polymers: polysaccharides ○​ Glycogen: stores energy in animals ○​ Starch: stores energy in plants ○​ Cellulose: structure in plants ○​ Chitin: structure of insect exoskeletons ​ Carbon Skeletons differentiate sugars ○​ Six-carbon sugars: hexoses ○​ Three-carbon sugars: trioses ○​ Five-carbon sugars: pentoses ​ Rings are the most stable form of many sugars under aqueous conditions ​ Storage polysaccharides in animals have lots of branches that can easily break off and provide energy ○​ Plant storage polysaccharides typically have fewer branches since they are used for long-term energy ​ Plant polysaccharides = starches (found in plastids such as chloroplasts) ​ Animal polysaccharides = glycogen (found in liver and muscle cells) ​ Structural polysaccharides: cellulose, chitin ○​ Cannot be broken down by enzymes that dissolve storage polysaccharides Lipids ​ All lipids are hydrohphobic unless bonded to a hydrophilic group ​ Monomers: glycerol and (up to) 3 fatty acids ○​ Fatty acids have a long carbon chain and a carboxyl group at the end ​ Polymers: fat, oil, cholesterol, phospholipids ○​ Ester linkages connect monomers ​ Saturated vs. Unsaturated Fats ○​ Saturated: every single carbon has a single bond to a hydrogen ​ No open bonds ​ Solids at room temperature ○​ Unsaturated: some carbons are double-bonded to other carbons ​ Double bonds are bendable ​ Liquid at room temperature ​ Trans Fats: artificially hydrogenated unsaturated fats ○​ Has trans double bonds ○​ Lowers HDL (good cholesterol) and raises LDL (bad cholesterol) ○​ Raises risk of cardiovascular diseases ​ Phospholipids contain phosphate groups ○​ The end with phosphate is polarized and can interact with water (hydrophilic) ○​ Key component of cells ○​ Micelle: ring of phospholipids ○​ Phospholipid Bilayer: 2 layers of phospholipids with their tails facing each other  ​ Steroids: carbon skeleton consisting of four fused carbon rings ○​ Ex: cholesterol Proteins ​ Types of proteins ○​ Enzymes: accelerate chemical reactions ​ Catalysts: chemical agents that selectively speed up chemical reactions without being consumed in the reaction ○​ Defensive: protect against disease ○​ Storage: store amino acids (typically for baby animals) ○​ Transport: transport substances ○​ Hormonal: coordinate an organism’s activities ​ Endocrine system ○​ Receptor: help cells read and respond to chemical stimuli ○​ Contractile + Motor: movement ○​ Structural: support ​ Monomers: amino acids (peptides) ○​ Have an amino group and a carboxyl group (one on each end) ○​ Also contain H ○​ Have a variable R-group (side chain) that differs based on what amino acid it is ○​ All revolve around an asymmetric alpha-carbon ​ Humans need 20 amino acids ○​ Nonpolar: ​ Glycine ​ Alanine ​ Valine ​ Leucine ​ Isoleucine ​ Methionine ​ Phenylalanine ​ Tryptophan ​ Proline ○​ Polar: ​ Serine ​ Threonine ​ Cysteine ​ Tyrosine ​ Asparagine ​ Glutamine ○​ Electrically Charged: ​ Aspartic acid ​ Glutamic acid ​ Lysine ​ Arginine ​ Histidine ​ Two Amino Acids: dipeptide ○​ Form peptide bonds through dehydration synthesis ​ 3+ Amino Acids: polypeptides ​ Polypeptide Backbone: connected chain of amino acids joined by amino and carboxyl groups ​ Protein Structure ○​ Primary: sequence of amino acids that make up a polypeptide ○​ Secondary: amino and carboxyl groups form hydrogen bonds ​ Folds into Beta-pleated sheets or alpha helices ○​ Tertiary: interactions between the R-groups of amino acids ​ Hydrophobic Interactions: The exclusion of nonpolar substances by water molecules ​ Disulfide Bridges: where two sulfurs from sulfhydryl groups bond together ○​ Quaternary: when a protein functions by being made of more than one polypeptide subunit  ​ Ex: collagen, hemoglobin ​ Sickle cell disease: hemoglobin binds together (not normal), limiting its capacity to carry oxygen ​ Renaturation: restoring a protein to its original structure ○​ Assisted by chaperonins, which create hydrophilic environments that fold proteins properly ​ Denaturation: breaking a protein's polypeptide chain ○​ Can be caused if the pH, salt concentration, temperature, or other environmental aspects are altered Nucleic Acids ​ James Watson and Francis Crick were the first to discover the double helix structure of DNA ○​ Build on the work of Rosalind Franklin ​ DNA (in eukaryotes) stays inside the nucleus ​ Regardless of the type of cell, DNA codes for mRNA, which then codes for the amino acids that make up proteins ​ Nucleotides: pentose (5-carbon sugar), nitrogenous base, phosphate group ○​ Pentoses: deoxyribose (lacks an oxygen) and ribose ○​ Nitrogenous Bases: A, T, C, G, U ​ Purines: double-ringed (A, G) ​ Pure as gold (Pur, A, G) ​ Pyrimidines: single-ringed (T, C, U) ​ Cut the py (CU, T, Py) ​ Sugar phosphate backbone is the outside of the “ladder” ○​ Nucleotides in the middle linked by H-bonds ​ Phosphodiester Bond: links 2 sugars together with a phosphate group (creates the backbone) ​ Semi-Conservative: in DNA replication, half of the old strand of DNA is conserved, while the other half is build by mRNA ​ **To count carbons, start with oxygen and go clockwise