AP Bio Unit 1: Chemistry of Life

ATOMS, MOLECULES, IONS, AND BONDS

• Atom: consists of a nucleus of positively charged protons and neutrally charged neutrons; negatively charged electrons are arranged outside the nucleus

• Molecules: groups of two or more atoms help together by chemical bonds that form cause of the interaction of their electrons

• Electronegativity: the ability of an atom to attract electrons that determines the kind of bond that forms

  • Ionic bond: bonds between 2 atoms when one or more electrons are transferred from one atom to the other; occurs when the electronegativity of the atoms are very different and one atom has a much stronger pull on the electrons than the other atom in the bond

  • Covalent bond: bonds that form when electrons are shared, which means that neither atom completely retains possession of the electrons and occurs when electronegativities are similar

    • Non-polar covalent: form when electrons are shared equally; when two atoms sharing electrons are identical, the electronegativities are identical, and both atoms pull equally on the electrons

    • Polar covalent: form when electrons are shared unequally; atoms in this bond have different electronegativities and an unequal distribution of the electrons results

      • Pole: the electrons forming the bond are closer to the atom with the greater electronegativity and produce a negative charge near the atom

    • Single covalent, double covalent, and triple covalent: form when two, four, and six electrons are shared, respectively

  • Hydrogen bonds: weak bonds between molecules that form when a positively charged hydrogen atom in one covalently bonded molecule is attracted to a negatively charged area of another covalently bonded molecule

PROPERTIES OF WATER

1. Water is an excellent solvent

   • Solvent: a substance that dissolves other substances to form a solution

   • Hydrophilic: substances that dissolve in water because their polar covalent bonds are similarly soluble cause of the interaction of their poles with those of water

   • Hydrophobic: substances that don’t dissolve in water because they lack charged poles

   • Solute: a substance that dissolves in a solvent

   • Aqueous solution: water acts as the solvent and dissolves the solute

2. Water has a high specific heat capacity

   • Specific heat capacity: the degree to which a substance changes temperature in response to a gain or loss of heat; water has a high specific heat

   • Heat of fusion: the energy needed to change water from a solid to a liquid

   • Heat of vaporization: the energy needed to change water from a liquid to a gas

3. Ice floats cause water, unlike most substances that contract and become more dense when they freeze, expands as it freezes, becoming less dense than its liquid form. In the solid state of water, the weak hydrogen bonds between water molecules become rigid and form a crystal that keeps the molecules separated and less dense than in its liquid form

4. Water has strong cohesion and high surface tension

   • Cohesion: the attraction between like substances that occurs in water cause of the hydrogen bonds between water molecules

   • Surface tension: the cohesive force at the surface of a liquid that allows it to resist external forces caused by the strong cohesion between water molecules

5. Water has strong adhesion

   • Adhesion: the attraction of unlike substances resulting from the attraction of the poles of water molecules to other polar substances

   • Capillary action: the ability of a liquid to flow upward against gravity in narrow space due to cohesion and adhesion

ORGANIC MOLECULES: those that have carbon atoms

• Macromolecules: large organic molecules in living systems that can consist of thousands of atoms

  • Polymers: most macromolecules are polymers, molecules that consist of a single unit (monomer) repeated many times

• Functional groups: similar clusters of atoms; many organic molecules share similar properties cause they have similar clusters of atoms

  Functional Group	Examples	Characteristics
  hydroxyl	alcohols (ex: ethanol), glycerol, sugars	polar, hydrophilic
  carboxyl	acetic acids, amino acids, fatty acids, sugars	polar, hydrophilic, weak acid
  amino	amino acids	polar, hydrophilic, weak base
  phosphate	DNA, ATP, phospholipids	polar, hydrophilic, acid
  methyl	fatty acids, oils, waxes	non-polar, hydrophobic

• CARBOHYDRATES

  • They are classified into 3 groups according to the number of sugar molecules present

    1. A monosaccharide is the simplest kind of carbohydrate

       • Consists of a single sugar molecule

       • Sugar molecules have the formula (CH₂O)ₙ, where n is any number from 3-8

         • Glucose → n=6 (C₆H₁₂O₆)

           • Two forms of glucose: α-glucose and β-glucose

         • Fructose → n=6 (C₆H₁₂O₆)

    2. A disaccharide consists of two sugar molecules by a glycosidic linkage

       • Glycosidic linkage: a type of covalent bond that joins a carbohydrate (sugar) molecule to another group

       • Condensation reaction/dehydration reaction: a chemical reaction where a small molecule is lost

       • Hydrolysis: where one molecule is split to form two molecules by addition of water

       • Formation of common disaccharides:

         • glucose + fructose = H₂O + sucrose (common table sugar)

         • glucose + galactose = H₂O + lactose (sugar in milk)

         • glucose + glucose = H₂O + maltose (product of the breakdown of starch)

    3. A polysaccharide consists of a series of connected monosaccharides, and it thus classified as a polymer

       • Starch is a polymer of α-glucose molecules and is the principle energy storage molecule in plant cells

       • Glycogen is a polymer α-glucose that differs from starch by its pattern of polymer branching and is a major energy storage molecule in animal cells

       • Cellulose is a polymer of β-glucose molecules and serves as a structural molecule in the walls of plant cells and is the major component of wood

       • Chitin is a polymer similar to cellulose, but each β-glucose molecule has a nitrogen-containing group attached to the ring; it serves as a structural molecule in the walls of fungus cells and in the exoskeletons of insects, other than arthropods, and mollusks

  • The α-glucose in starch and the β-glucose in cellulose show the dramatic chemical changes that can arise from subtle molecular changes

    • The bonds in starch can easily be broken down (digested) by humans and other animals

    • Only specialized organisms can break the bond in cellulose

• LIPIDS

  •     Lipids are a class of substances that are nearly insoluble in water but are highly soluble in non-polar substances

    1. Triglycerides include fats and oils

       • Fatty acids: hydrocarbons (chains of covalently bonded carbons and hydrogens) with a carboxyl group at one end of the chain; they vary in structure by the number of carbons and by the placement of single and double covalent bonds between the carbons

       • Saturated fatty acid: has a single covalent bond between each pair of carbon atoms, and each carbon has two hydrogens bonded to it

       • Monounsaturated fatty acid: has one double covalent bond, and each of the two carbons in this bond has only one hydrogen atom bonded to it

       • Polyunsaturated fatty acid: similar to a monounsaturated fatty acid except that there are two or more double covalent bonds

    2. Phospholipid: looks like a triglyceride except that one of the fatty acid chains is replaced by a phosphate group; the 2 fatty acid “tails” of the phospholipid are non-polar and hydrophobic and the phosphate “head” is polar and hydrophilic

    3. Steroids are characterized by a backbone of four linked carbon rings

       • Ex: cholesterol (component of cell membranes) and certain hormones like testosterone and estrogen

• PROTEINS

  • Proteins can be grouped according to their function. The following are major categories:

    1. Structural proteins, such as keratin in the hair and horns or animals, collagen in connective tissues, and silk in spider webs

    2. Storage proteins, such as casein in milk, ovalbumin in egg whites, and zein in corn seeds

    3. Transport proteins, such as those in the membranes of cells that transport materials into and out of cells and as oxygen-carrying hemoglobin in red blood cells

    4. Defensive proteins, such as the antibodies that provide protection against foreign substances that enter the bodies of animals

    5. Enzymes that regulate the rate of chemical reactions

  • Amino acids: all proteins are polymers of amino acids meaning they consist of a chain of amino acids covalently bonded

  • Peptide bonds: covalent bonds between amino acids

  • Polypeptide: chain of peptide bonds

  • One protein differs from another by the number and arrangement of 20 different amino acids. Each amino acid consists of a central carbon bonded to an amino group, a carboxyl group, and a hydrogen atom

  • Levels of a structure of protein:

    • Primary structure: describes the order of amino acids; using three letters to represent each amino acid, the primary structure for the protein antidiuretic hormone (ADH) can be written as Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly

    • Secondary structure: three dimensional shape that results from hydrogen bonding between the amino and carboxyl groups of nearby amino acids; the bonding produces a spiral (alpha helix) or a folded plane (beta pleated sheet); proteins whose shapes are dominated by these two patterns often form fibrous proteins

    • Tertiary structure: includes additional three dimensional shaping and often dominates the structure of globular proteins; the following contribute to the structure

      • Hydrogen bonding between R groups of amino acids

      • Ionic bonding between R groups of amino acids

      • Hydrophobic effect occurs when the sulfur atom in the amino acid cysteine bonds to the sulfur atom in another cysteine, helping maintain the folds of the amino acid chain

    • Quaternary structure: describes a protein that is assembled from two or more separated peptide chains

• NUCLEIC ACIDS

  • The genetic information of a cell is stored in molecule of DNA that in turn passes its genetic instructions to RNA for directing various metabolic activities of the cell

  • A DNA nucleotide consists of a nitrogen base, a five carbon sugar (deoxyribose), and a phosphate group. The 4 DNA nucleotides are:

    • Adenine — a double ring base (purine)

    • Thymine — a single ring base (pyrimidine)

    • Cytosine — a single ring base (pyrimidine)

    • Guanine — a double ring base (purine)

    • Adenine always bonds with thymine and guanine always bonds with cytosine

  • DNA nucleotides form a single stranded DNA molecule when the phosphate group of one joins to the sugar of the adjacent nucleotide, becoming paired by weak hydrogen bonds between the bases and forming a double stranded DNA.

  • The two strands of a DNA helix are antiparallel, meaning they are oriented in the opposite direction.

    • One strand is arranged in the 5’ → 3’ direction: it begins with a phosphate group attached to the fifth carbon of the deoxyribose (5’ end) and ends where the phosphate of the next nucleotide would attach, at the third deoxyribose carbon (3’)

    • The adjacent one is oriented 3’ → 5’

  • RNA differs from DNA cause:

    1. The sugar in the nucleotides that make an RNA molecule is ribose, not deoxyribose like in DNA

    2. The thymine nucleotide doesn’t occur in RNA. It is replaced by uracil. When pairing of bases occurs in RNA, uracil pairs with adenine

    3. RNA is usually single stranded and doesn’t form a double helix like in DNA

CHEMICAL REACTIONS IN THE METABOLIC PROCESSES

• Activation energy: when reaction molecules collide and then have sufficient energy in order for chemical reactions to take place

• Catalyst: it accelerates the rate of the reaction because it lowers the activation energy required for the reaction to take place; it is any substance that accelerates a reaction but doesn’t undergo a chemical change itself and can be used over and over again

• Metabolism: chemical reactions that occur in biological systems

  • Catabolism: metabolisms includes the break down of substances

  • Synthesis or anabolism: formation of new products during metabolism

• Characteristics of metabolic processes:

  1. The net direction of metabolic reactions, that is, whether the overall reaction proceeds in the forward direction or in the reverse direction, is determine by the concentration of the reactants and end products

     • Chemical equilibrium: the condition where the rate of reaction in the forward direction equals the rate in the reverse direction, and, as a result, there is no net production of reactants or products

  2. Enzymes: globular proteins that act as catalysts for metabolic reactions; the following are characteristics of enzymes:

     • Substrate: the substance or substances upon which the enzyme acts

     • Enzymes are substrate specific (Ex: amylase catalyzes the reaction that breaks the α-glycosidic linkage in starch but can’t break the β-glycosidic linkage in cellulose)

     • An enzyme is unchanged as a result of a reaction and can perform its enzymatic function repeatedly

     • An enzyme catalyzes a reaction in both forward and reverse directions. The direction of net activity is determined by substrate concentrations and other factors. The net direction of an enzyme reaction can be driven in the forward direction by keeping the product concentration low

     • The efficiency of an enzyme is affected by temperature and pH (Ex: The human body is maintained at 98.6°F, near the optimal temperature for most human enzymes. Above 104°F, these enzymes begin to lose their ability to catalyze reactions as they become denatured. Most enzymes have an optimal pH of around 7.0

       • Denatured: enzymes lose their 3D shape as hydrogen bonds and peptide bonds begin to break down

     • The standard suffix for enzymes is “-ase” , so it is easy to identify enzymes that use this ending, although some don’t

     • Induced fit model: describes how enzymes work; Within the protein (enzyme) there is an active site with which the reactants readily interact because of the shape, polarity, or other characteristics of the active site. The interaction of the reactants (substrate) and the enzyme causes the enzyme to change shape. The new position places the substrate molecules into a position favorable to their reaction. Once the reaction takes place, the product is released

  3. Cofactors: nonprotein molecules that assist enzymes

     • Coenzymes: organic cofactors that usually function to donate or accept some component of a reaction, often electrons; some vitamins are coenzymes of components of them

     • Inorganic cofactors: often metal ions like Fe²⁺ and Mg²⁺

  4. ATP is a common source of activation energy for metabolic reactions. ATP is essentially an RNA adenine nucleotide with 2 additional phosphate groups. When ATP releases its energy, a hydrolysis reaction breaks the last phosphate bond of the ATP molecule to form ADP and an inorganic phosphate group. In reverse dehydration reaction, new ATP molecules are assembled by phosphorylation when ADP combines with a phosphate group using energy obtained from some energy-rich molecule

     • ATP + H₂O → ADP + Pᵢ + energy

• 5 common ways enzymes regulate reactions

  1. Enzymes have two kinds of binding sites — one an active site for the substrate and one or more possible allosteric sites for an allosteric effector. There are 2 kinds of allosteric effectors:

     • Allosteric activator: binds to the enzyme and induces the enzyme’s active form

     • Allosteric inhibitor: binds to the enzyme and induces the enzyme’s inactive form

     • Some inhibitors bind irreversibly, permanently changing the structure of the enzyme by modifying an amino acid. Other inhibitors are weakly bonded to the enzyme by ionic or hydrogen bonds and their effects are reversible

  2. Feedback inhibition: an end product of a series of reactions acts as an allosteric inhibitor, shutting down one of the enzymes catalyzing the reaction series

  3. Competitive inhibition: a substance that mimics the substrate inhibits an enzyme by occupying the active site. The mimic displaces the substrate and prevents the enzyme from catalyzing the substrate

  4. Noncompetitive inhibition: a substance inhibits the action of an enzyme by binding to the enzyme at a location other than the active site; the inhibitor changes the shape of the enzyme, which disables its enzymatic activity; many toxins and antibiotics are noncompetitive inhibitors

  5. Cooperativity: an enzyme becomes more receptive to additional substrate molecules after one substrate molecule attaches to an active site; this occurs in enzymes that consist of two or more subunits and each have their own active site