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BIOL 130 Study Notes Unit II Cellular Chemistry

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University of Waterloo
BIOL 130
Richard Ennis

BIO 130 Study Notes Unit II Part A: Introduction to Cellular Chemistry Chemistry Dictates Biology: • Living organisms are complex chemical systems built from inanimate matter o Therefore, the chemistry used to sustain life must also obey the same physical principles as non-living matter Elements Present in the Human Body: • 99% of matter found in living organisms are made up of 4 elements: o “CHON” – Carbon, Hydrogen, Oxygen, and Nitrogen o They mostly combine in complex macromolecules present in simple forms (e.g. CO 2 H 2, etc.) Parts of an Atom: • Nucleus – dense core in the center, consisting of protons (positive charge) and neutrons (neutral charge) • Electrons – continually orbit the nucleus, associated with a negative charge • The number of protons defines the identity of the element o This is known as the atomic number • The number of protons + neutrons defines the mass of the element o This is known as the mass number • In any given element that has not undergone any reaction, an atom is “neutral” where the number of protons = the number of electrons o Electrons influence the reactivity of an atom • You may also alter the number of neutrons in an atom o This will not change its identity, but rather simply create a different species of that element (i.e. an isotope of that element) Electrons around the Atomic Nuclei: • Electrons travel in orbitals around the nucleus • These orbitals are grouped into layers or “shells”, based on how far the electrons in that shell travel from the nucleus  General formula to determine the max # per shell is 2n o In the first shell: max of 2 electrons o In the second shell: max of 8 electrons o In the third shell: technically its max is 18, but in this course it’s 8 as well • The innermost shells are the first to fill o Once the first is filled with a pair of electrons, the next shells will with 4 single electrons then subsequent electrons will form pairs with them • The outermost (i.e. valance) shell influences an atom’s reactivity; these electrons are called valance electrons o Unpaired valance electrons determine the number of bonds an atom can make  Example: Carbon  Has 6 electrons in total; the first 2 go into its first shell and the last 4 are orbiting its outermost shell.  Since carbon has 4 single electrons in its outermost shell, each of those 4 single electrons desires 4 other electrons to form pairs with them, which would otherwise complete the valance shell at 8 electrons  Therefore, carbon is capable of making up to 4 bonds. o A very easy way to deduce the number of bonds an element can make is to look at the periodic table and see how far away an element is from the noble gas aligned on the same row (this works for everything except for the transition metals) Unpaired Valance Electrons & Reactivity: • Completely filled valance shells = non-reactive (stable) • The elements that are close to filling valance shells are most reactive (e.g. Cl, F, O) • Atoms with the same # of valance electrons have similar chemical behaviour o However, with that being said, sodium (Na) and potassium (K) both have 1 valance electron, but K is more reactive o This is because K has more full shells of electrons between the nucleus and its outermost valance electron, meaning that the outermost electron is further away from the nucleus and is more easily stripped  Means K is more readily able to lose its outermost electron in a reaction in comparison to Na. • Elements abundant in organisms have at least one unpaired valance electron Unpaired Electrons & Biological Reactions: • Biological reactions are driven by the tendency of atoms o 1) fill their outer electron shells o 2) balance positive and negative charges • Atoms may achieve full valance shells by the following: o Sharing electrons by forming chemical bonds (i.e. COVALENT BONDING)  The # of bonds possible depends on how many electrons that atom needs to fill its outer shell completely o Transferring electrons to another atom (i.e. IONIC BONDING)  Atoms that do this are no longer electrically neutral and become “ions”  Elements that gain electrons become negatively charged “anions”  Elements that lose electrons become positively charged “cations” Types of Chemical Bonds: • Some definitions to consider first: o Molecule – a group of atoms held together by energy in a stable association o Compound – is a molecule composed of 2 or more different types of atoms • Covalent bonding: o 2 or more atoms share pairs of valance electrons (generally occurs with the bonding of 2 non-metals) o Covalent bonds are very strong in biological systems • Non-covalent bonds include: o Ionic bonding  The transfer of electrons to another element (generally occurs with the bonding between a metal and non-metal o Hydrogen bonding  A strong dipole-dipole attraction where a hydrogen atom is bound to a highly electronegative atom (e.g. N, O, or F)  H-bonding can occur within molecules (intramolecular) • Example: Water molecules o Partially positive H attracted to the partially negative O even though the molecule of H 2 is neutral overall  H-bonding can occur between molecules (intermolecular) • Example: Attraction between water molecules o The partially positive ends of H atoms of one water molecule are attracted to the partially negative O atoms in another molecule. o Hydrophobic interactions Types of Covalent Bonds: • There are 2 types of covalent bonds: non-polar and polar o Non-polar covalent bonds:  Electrons shared equally  Can be single bonds like (H2), double like 2O ) or even triple o Polar covalent bonds:  Electrons are NOT shared equally  Where one atom has a stronger pull on the electrons than the other, which makes one atom more electronegative than the other  Example: H 2 The Significance of the Water Molecule: • Water is the most abundant molecule in biological organisms o The human body as a testament to this is ~70% water • Water can act as a solvent to dissolve more types of molecules than any other solvent known o This is because of water’s polar nature • There is a polarization of water that causes a charge separation within the molecule o This allows multiple water molecules to be able to form hydrogen bonding driven by charge balance o The partially positive ends of hydrogen are attracted to the partially negative end of the oxygen • While H-bonds outside of biological systems are weak compared to ionic bonds, when applied to a biological context, they are among the stronger types of bonds • H-bonds are also easily broken, but can reform very quickly o This makes it an important type of bonding in many biological functions, as its ability to break and reform quickly is essential to the fast-nature of biological processes that sustain life • Water is a polar solvent that can dissolve polar compounds (i.e. most molecules formed through ionic bonding like NaCl) o Ionic bonds are therefore actually very weak within a biological context and are easily dissolved by the polar-nature of water Bond Lengths: • There is a correlation between bond length and bond strength o Typically the shorter the bond length, the stronger the bond actually is • Also in the process of forming a covalent bond, the distance between the electron being shared must be just right, otherwise the bonding won’t occur: o If the electrons are too close, then the nuclei repel one another o If the electrons are too far, then there is no attraction o But if the electrons align at a distance that is just right, the electron from either atom are attracted to each other’s’ nuclei Dissociation of Water: • Water is not a completely stable molecule; a small amount actually dissociates (ionizes) into 2 entities: + - o H2O  H + OH o But then, hydrogen ions don’t actually exist alone and end up usually joining with another water molecule, so the reaction really looks like this: Acid-Base Reactions: • Acid – a substance that donates (i.e. gives up) protons o Has a lower pH, and increases the [H ] in solution • Base – a substance that accepts (i.e. takes in) protons + o Has a higher pH, and decreases the [H ] in solution • Acid-base reactions o Are chemical reactions where protons are transferred • Most molecules act as either an acid or a base (water can be both) o Weak Acids: very few molecules dissociated (e.g. acetic acid, water) o Strong Acids: nearly all molecules dissociated and readily gives up protons (HCl) The pH Scale: • The pH scale ranged from 1 to 14 -pH o Uses the logarithmic scale: pH = -log[H+]  [H+] = 10 • There is a change by a factor of 10 per level on the pH scale (e.g. a substance with a pH of 3 is 10x more basic than a substance with a pH of 2) pK Values: a • pKa is the measure of proton binding affinity that allows us to distinguish between weak and strong acids o When pKa = pH the acid is 50% ionized o When pKa < pH the equilibrium lies to the right and the ionized form dominates  A low pKa indicates a strong acid since it readily gives up protons and most of the acid dissociates into the ionized form o When pKa > pH the equilibrium lies to the left and the non-ionized form dominates  A high pKa indicates a weak acid since it binds protons strongly and only a small amount of the acid dissociates into its ionized form. Carbon as a Building Block of Biology • Carbon is the most important atom in biology o Any molecule that contains carbon is considered “organic” o Carbon can for many combinations of single and double bonds o It may also be linked to form chains and ring structures • Carbon also gives biomolecules their shape • A chiral carbon is a carbon that is attached to 4 different atoms or 4 different groups of atoms and is therefore asymmetric • An alpha carbon is the first carbon that attaches to a functional group in the alpha position (below the plane) Functional Groups: • Are the components of organic molecules typically involved in reactions • These functional groups attach to carbons and determine the reactivity of biomolecules Part B: Macromolecules (Proteins, Nucleic Acids, Carbohydrates, and Lipids) Macromolecules: • Large and organized molecules created by polymerization • Biological macromolecules (biomolecules) provide the structure and carry out the activities of a cell • There are 4 groups of biomolecules: o Carbohydrates  Building blocks: sugars (monosaccharides) o Lipids  Building blocks: fatty acids + glycerol molecule o Nucleic Acids  Building blocks: nucleotides o Proteins  Building blocks: amino acids Generating Macromolecules: • Two types of reactions may occur with macromolecules – condensation or hydrolysis o Condensation Reactions:  Joins subunits (i.e. monomers) together via bonding to form larger molecules and the attachment of functional groups  One molecule of water is produced each time another subunit is attached, so therefore water is produced and expelled  Condensation of monosaccharides  disaccharides or polysaccharides  Condensation of amino acids  dipeptide (if there are 2) or polypeptide (if there are 3+)  Condensation of 3 fatty acids to glycerol  triglyceride (or lipids) o Hydrolysis Reactions:  Involves the addition of water molecules (consumes them) in order to break the bonds of larger biomolecules back into their smaller subunits  Essentially the reverse reaction of the condensation • Disaccharides & polysaccharides  monosaccharides • Dipeptide & polypeptides  amino acids • Triglyceride  fatty acids & glycerol Overview of Macromolecules: Macromolecule Subunit (Monomer) Function Example Proteins Amino acids Enzymes (Catalysts) Trypsin (functional, structural) Transport Hemoglobin Support Hair, silk Nucleic Acids Nucleotides Gene encoding Chromosomes (DNA, RNA) Gene expression mRNA Enzymes (catalysts) Ribozymes Carbohydrates Glucose or Energy storage Potatoes (Starch, glycogen, modified glucose Plant cell walls Celery cellulose, chitin support Crab shells Lipids Glycerol + Fatty Acids Energy store Butter, plant oil (Fats, phospholipids, or Cell membrane Lecithin other) Glycerol + Fatty Acids Cell communication Steroids + PO 4ing structures MACROMOLECULE #1: PROTEINS Function of Proteins: • More functions than any other macromolecule: “MEDTSS” o Movement – various structures that help cells move  Inside the cell: motor proteins  Outside the cell: flagella tail structure, contractile proteins o Enzymes – catalysis; accelerates chemical reactions o Defense – antibodies, complement proteins o Transport – moves/carries biological materials through cell membranes into circulation o Support – cytoskeletal fibers of cartilage, hair, or nails o Signalling/regulatory – hormones, membrane proteins, intracellular messengers Proteins are Polymers: • The subunit (monomer) of a protein are amino acids, which are connected in linear polymers in a specific sequence o 20 genetically encoded amino acid monomers able to be used • A string of amino acids is called a peptide; there is a suffix attached depending on how many amino acids are linked together (di-, tri-, tetra-…poly-) • A polypeptide that is folded and coiled into a specific conformation (i.e. shape) forms a protein o Though sometimes 2 or more peptide chains combine to form a functional protein as well Amino Acid Structure: • The general formula for a non-ionized amino acid: o Notice the amino group (-H 2) and the carboxyl group (-COOH) o The “R” stands for a “radical” which is simply side chain group that can also attach to the central alpha carbon • Amino acids can also be ionized under certain physiological conditions, and its general formula changes into the following: • When the amino acid ionizes, it becomes a zwitterion (i.e. a neutral molecule with both a positive and negative electrical charge) o Consider it as sort of like an intramolecular acid-base reaction within itself o The amino group (-H N2 acts like a base and accepts the proton and becomes the electrically positive (3H N) o The carboxyl group (-COOH) acts like an acid and donates the proton becomes the electrically negative (-COO) • Ionization of amino acids into zwitterions increases solubility, increases reactivity, and facilitates interactions with each other and other solutes. Amino Acids Side Chains (R-groups) • There are two classes of R-groups o Non-polar R-groups (hydrophobic)  No ions or electronegative atoms to form hydrogen bonds  Insoluble in water because the R-groups bury themselves in the peptide chain to avoid contact with water o Polar R-groups (hydrophilic)  UNCHARGED: but still have partial charges that can still form hydrogen bonds  CHARGED: have groups containing acids/bases, often containing ions or highly electronegative atoms, making them highly soluble in water. o See examples on next page… • Examples of non-polar (hydrophobic R-groups) o Mostly comprised of C and H and are not very reactive; also do not contain ions or electronegative atoms • Examples of polar (hydrophilic R-groups) o Polar (uncharged): have partial charges that can still form H-bonds and are water soluble; notice the O-atoms, or –OH molecules, and the S-atoms o Polar (charged): have ions or electronegative atoms that can form hydrogen bonds or ionic bonds, and therefore are highly soluble The Link between Amino Acids: Peptide Bonds • Amino acids are commonly joined together by a peptide bond o Long strands of amino acids joined by peptide bonding creates proteins • Peptide bonds are formed through condensation reactions, where water is produced as a by-product: • Notice that the –OH in the carboxyl group (-COOH) of one amino acid will detach and bind with the –H on the amino group (H 2) of the other amino acid to form water o Then the carbon of one amino acid (C-terminus) will bind to the nitrogen (N- terminus) of the other one (shown in grey) o They are always written with the N-terminus toward the left • Peptide bonds may also be broken through the reverse reaction of hydrolysis, where water is used up/consumed: The Peptide Chain: • Side chains extend from the peptide-bonded backbone in a long chain amino acids o The backbone is directional, starting from the N-terminus  C-terminus: • The peptide chain is flexible and can rotate at single bonds on either side o Can be 2000-3000 amino acids long • The first amino acid in the sequence with its N-terminus still has its free amino groups, and the last amino acid with its C-terminus still has its free carboxyl groups, but all other amino acids in between lose both theirs. Sickle Cell Anemia: • A disease in which red blood cells are abnormally shaped o As a result the hemoglobin is more hydrophobic, where its proteins stick together, causing the physical distortion in the blood cell to be sickle-shaped o These sickle-shaped blood cells have a decreased capacity to carry blood • Caused by a single mutation where one amino acid (glutamate) is substituted for valine instead, within one chain of hemoglobin protein. o Valine is very hydrophobic by contrast to the normal glutamate which is very hydrophilic o Therefore, when valine is substituted in, its non-polar nature makes the proteins in hemoglobin stick together and very hydrophobic as a result. Protein Structure: • The information for a protein (a polymer) to fold into a particular conformation/shape is given by the linear sequence of its monomer amino acid subunits that are present. • There are many different protein conformations/shapes that correspond with many different functions • However, they can all be broken down into 4 general levels of organization; o The first 3 levels are used to organize the folding within a single polypeptide, and the 4 level refers to the linking of 2 polypeptides together to form a functional protein • THE FOUR LEVELS: o Primary Structure:  Refers to the number and sequence of amino acids in the polypeptide  Determined by the DNA sequence in a gene  The sequence of amino acids in the primary structure will determine the protein’s ultimate shape in tertiary structure o Secondary Structure:  Consists of two major forms of regular repeating structures that are stabilized by hydrogen bonding  α-helices o Right-handed coiled or spiral formation in which every N-H group donates a hydrogen bond to a C=O group of the amino acids linked. o Different amino acids will have different frequencies in a helix structure, altering the nature (or faces) of the helix  β-pleated sheets o Structure is formed b/c of H-bonding between the amino (N-H) termini and carbonyl (C=O) termini laterally, forming a twisted pleated sheet.  Both are stabilized by hydrogen bonds betw
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