1.Subatomic particles and compounds. 2.Water and some important properties 3. pH scale 4. Carbon chemistry, alkanes

Essential elements of life. Subatomic particles of an atom. Compounds.

(a) Nitrogen deficiency (b) Iodine deficiency (Goiter)

Simplified models of an Atom 4 Nucleus (a) (b) In this even more simplified model, the electrons are shown as two small blue spheres on a circle around the nucleus. Cloud of negative charge (2 electrons) Electrons This model represents the electrons as a cloud of negative charge, as if we had taken many snapshots of the 2 electrons over time, with each dot representing an electron ‘ s position at one point in time.

H 2 O: H atoms partial (+) charge, O atoms partial (-) charge. Water is POLAR, and attracts other polar molecules. Polarity allows water to form weak H bonds with other polar substances…this is what makes H 2 0 a great solvent. This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. H2OH2O –– O H H ++ ++ Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

Van der Waals Interactions – Occur when transiently positive and negative regions of molecules attract each other 6

Hydrogen bond  – –  + +  + +  + +  + +  – –  – –  – – H H O

Liquid water: transient hydrogen bonds Ice: stable hydrogen bonds

Cohesion - tendency of molecules to stick together. Ex: H 2 0 evap. from a leaf. Adhesion - tendency to stick to other substances. Capillary Action High Specific Heat -Is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC

Water moderates air temperature Water moderates air temperature By absorbing heat from air that is warmer and releasing the stored heat to air that is cooler By absorbing heat from air that is warmer and releasing the stored heat to air that is cooler

Water has a high specific heat which allows it to minimize temperature fluctuations to within limits that permit life Water has a high specific heat which allows it to minimize temperature fluctuations to within limits that permit life – Heat is absorbed when hydrogen bonds break – Heat is released when hydrogen bonds form

Acids and Bases Dissociation of water molecules leads to acidic and basic conditions that affect living organisms Organisms must maintain homeostasis in the pH of their internal and external environments 15

Effects of Changes in pH Water can dissociate Into hydronium ions (H+ or H 3 O+) and hydroxide (OH-) ions Changes in the concentration of these ions Can have a great affect on pH in living organisms 16 H Hydronium ion (H 3 O + ) H Hydroxide ion (OH – ) H H H H H H + – +

1-14 Towards pH of 1= Acidic. Towards pH of 14 = Basic (alkaline) pH of 7 = neutral. Acids have a higher concentration of H+ ions, bases have a higher concentration of OH- ions. ( Hydroxide ) Difference of strength of 5 to 4, etc. (10x) ….ie: diff of 3 to 6 is?

Covalent: sharing of electrons; compounds held together by the sharing. Ionic: taking of electrons; compounds held together by oppositely charged ions.

Covalent Bonding A molecule –Consists of two or more atoms held together by covalent bonds A single bond –Is the sharing of one pair of valence electrons A double bond –Is the sharing of two pairs of valence electrons 22

Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects

(a) Structures of endorphin and morphine (b) Binding to endorphin receptors Natural endorphin Endorphin receptors Morphine Brain cell Morphine Natural endorphin Key Carbon Hydrogen Nitrogen Sulfur Oxygen

Six elements essential to life? Covalent vs. Ionic bond? Why is water a POLAR molecule? Cohesion vs. Adhesion? pH scaled Chemical vs. Structural formula Carbon chemistry

Carboxyl Group Amino Group Hydroxide Group Carbonyl Group Sulfhydryl Group Phosphate Group NH 2 OH COOH C=O S-H PO 4

Fig. 4-10c STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Carboxyl Acetic acid, which gives vinegar its sour taste Carboxylic acids, or organic acids Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). Acetic acidAcetate ion

Fig. 4-10d STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Amino Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Amines Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms). Ionized, with a charge of 1+, under cellular conditions. (ionized)(nonionized) Glycine

Fig. 4-10e STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Sulfhydryl (may be written HS—) Cysteine Cysteine is an important sulfur-containing amino acid. Thiols Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds.

Fig. 4-10f STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Phosphate In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. Glycerol phosphate Organic phosphates Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Has the potential to react with water, releasing energy.

Fig. 4-10g STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Methyl 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. 5-Methyl cytidine Methylated compounds Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function.

GENERAL TERMINOLOGY: Monomer(S) Polymer(S) Isomer(s)