BIOL 112 Notes Jan 11th-Jan 13th

Chapter 2: Small Molecules Chemical bonds

There are many molecules that play major roles in biology. The most common ones consist of H, C, N, O, P and S (Highlighted in yellow)

The ones highlighted in red are found in tiny amounts for things such as co-factors or ions (e.g. K+ and Na+ are ions found in the functioning of transmitting signals in the nervous system) Atoms Every element has its own atom structure consisting of a nucleus with protons and neutrons, and electrons that orbit the nucleus.

The atomic number denotes the number of protons, this number is unique to each element (e.g. no 2 different elements have the same atomic number)
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The chemical symbol is the symbol for the element, in the format capital + lower case, or just one capital letter The electrons have a negative charge, protons have a positive charge and neutrons have no charge In the neutral state of the atom, the number of electrons = number of protons The proton and neutron both have a mass of about 1 atomic unit, or 1 Dalton (D) The atomic mass is the sum of the mass of the protons + the neutrons in the atom. However, atomic mass is not an exact number because it is measured from the weighted average of isotope abundance. Mass of electrons are neglected Isotopes

Isotopes of an element have different number of neutrons, Every isotope exists in a sample of the element in a set percentage (e.g. in a sample of carbon, there is 70% C-12 and 20% C-14 and 10% C-another mass, numbers are made up). This is known as isotope abundance Isotopes have identical chemical properties but are sometimes unstable, i.e. radioactive (Prone to decay) Radioactive isotopes can be used as tracers in medical imaging

Or they can be used for dating (E.g. Carbon-14 dating) to check the age of certain organisms/materials Chemical bonding

When elements participate in bonding, only the electrons are important. The valence electrons are the most important.
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1. Covalent bonding

A type of intramolecular force Electrons spend 90% of their time in the orbital (cloudly blue region) They wish to pair up with other orbitals so they form covalent bonds Covalent bond: sharing of electrons; happens when the electronegativity between two atoms is below 1.7. Elements with just 1 electron in an orbital is extremely unstable, never found in nature on its own, very reactive Very strong Each covalent bond has a predictable strength, length, and angle which makes it possible to predict the 3D structures of molecules (VSEPR) A double covalent bond occurs when atoms share two pairs of electrons H2C=CH2 Bonds between different molecules have different lengths E.g. H-H vs C-C or C-H Why does carbon form 4 bonds?

a. A covalent bond is made of 2 electrons b. These 2 electrons are shared, i.e. one electron comes from each atom
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c. Atoms can form bonds until their outermost shell is filled. Since noble gases already have filled outer shells, they are very unreactive. *In an H2O atom, since the O is very electronegative, it can take the electron from one of the hydrogens, kick out the proton and form an OH- ion. Electronegativity Electrons are not always shared equally between covalently bonded atoms The attractive force that an atom exerts on electrons is called electronegativity, which increases from left to right of the periodic table, and decreases from top to bottom Electronegativity differences result in dipoles in the molecules, giving them partial charges on different ends

Electrostatic attractions will exist between the molecules, resulting in intermolecular forces

2. Hydrogen bonding A special type of intermolecular force that results from dipoles created by hydrogen bonding with very electronegative elements N, O and F

BIOL 112 Notes Jan 11th-Jan 13th

*The molecular structure of ice, water and gas all have hydrogen bonding, but at different degrees. Due to hydrogen bonding in ice, the molecules are arranged in a crystalline structure where the molecules are more spread out than they are in water. This makes ice less dense, and hence floats on water.

Intermolecular bonds are responsible for growth of trees because they allow the water molecules to climb up the capillaries of the trees to reach the top and be used by the
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upper leaves, allowing them to grow. Water then evaporates through leaves, making room for more water molecules Evaporation explains why it is cooler when one walks into a forest because evaporation is an endothermic process

3. Ionic bonds

An intramolecular force Electrons are not shared at all. One takes the electron of another (Electronegativity must exceed 1.7) Stabilizes both atoms, the 2 ions have an electrostatic attraction Positively charged ions are called cations (t looks like +) Negatively charged ions are called anions Atoms that participate in ionic bonding form salts, which is a crystal lattice structure made up of cations and anions Dissolving of salts

When a salt is introduced into water, the partial charges of the water molecules can easily interfere with (replace) the ionic bonds The salts dissolve in water into ions, the water molecules have +ve and -ve charges and they dissociate the ionic bonds +ve sides attract anions, -ve sides attract cations Stronger ionic crystals like MgCl2 are harder to dissolve Polar molecules tend to be hydrophilic. Substances that are ionic or polar often dissolve in water due to hydrogen bonds Nonpolar molecules are called hydrophobic because they tend to aggregate with other nonpolar molecules in water (hydrophobic interactions) and not be attracted to polar water molecules

BIOL 112 Notes Jan 11th-Jan 13th

4. Hydrophobic interaction

A type of intermolecular interaction Water forces nonpolar molecules together, because doing so minimizes their disruptive effects on the hydrogen-bonded water network Hydrophobic molecules in water cluster together because when they are evenly distributed in water, they disrupt a lot of hydrogen bonds (energy consuming, just like energy needed to evaporate water). When clustered together, it is more energetically favorable. E.g. oil particles clump together when cooling down in soup Fairly weak but very important (e.g. Cell membranes form hydrophobic interactions and cluster together, resulting in a fluid lipid bilayer membrane that can pinch off and reform for endo/exocytosis) When heating up humans, they die very quickly because the high energy disrupts many of the hydrophobic interactions (around 45 degrees) 5. Van der Waals interaction
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Nonpolar molecules are also attracted to each other via relatively weak attractions, also called van der Waals forces (transient dipoles) Temporary dipoles that occur when electrons in the molecules move around This helps attract other temporary dipoles Very weak

Clicker question * Why is the ionic bond value so low? In my chemistry textbook they are much stronger.
5. Refers to individual ionic bonds. E.g. between NH3+ and COO- in the interior of proteins in the absence of water. Usually in biology, one discusses ionic bonds in terms of bonds within proteins with the absence of water. 1. salts cannot form anymore ionic bonds in water 2. Ionic bonds have a wide range of values depending on bond (NaCl vs MgCl2), doesn't answer question 3. NaCl bonds in crystal are stronger than hydrogen bonds, not reason why it dissolves 4. NaCl bonds in the crystal are strong, but in water, there are no ionic bonds between Na+ and Cl- in water

Chemical reactions Chemical reactions usually only involve covalent bonds

BIOL 112 Notes Jan 11th-Jan 13th

Chemical reactions can be written as equations, must be balanced to satisfy the law of conservation

Chemical reactions occur when atoms combine or change partners In a chemical reaction, reactants are converted into products Molarity A mole is the amount of substance in grams whose weight is equal to its molecular weight A 1 molar (1M) solution is one mole of a compound dissolved in water to make one liter Example: 1 mole of NaCl is the atomic weight of Na (23) plus one atomic weight of Cl (35.5), or 58.5 in grams. When 58.5g of NaCl are dissolved in water to make 1 liter, the solution is 1 molar. Acids and Bases

Acids: Acid releases/donate H+ ions in solution (or known as electron acceptors, Lewis acid) If the reaction (dissociation) is complete, it is a strong acid, such as HCl The carboxyl group (COOH) is common in biological compounds. It functions as a weak acid because it dissociates partially and reversibly o The dissociation can be explained by the electronegativity of the Oxygen, it can easily grab the electron from the H and release the proton H+ o COOH COO- + H+

Bases:

BIOL 112 Notes Jan 11th-Jan 13th

Bases accept H+ in solution (Release OH-) NaOH ionizes completely to Na+ and OH-. The OH- absorbs H+ to form water. It is a strong base The amino group ( NH2) is an important part of many biological compounds; it functions as a weak base by partially and reversibly accepting H o NH2 + H+ (NH3)+ pH

pH is the measure of hydrogen ion concentration It is defined as the negative logarithms of the hydrogen ion concentration in moles per litre (pH = -log [H+], or pH = -log [H3O+] when dissolved in water) A pH of 7 means the concentration of hydrogen ions is 1 x 10-7 mol/L of water Since it is a logarithmic scale, a pH decrease of 1 means a concentration of H+ by a factor of 10.

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