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 simplifiedmodel, the electrons areshown as two small bluespheres on a circle around thenucleus.

Cloud of negativecharge (2 electrons)

Electrons

This model represents theelectrons as a cloud ofnegative charge, as if we hadtaken many snapshots of the 2electrons over time, with eachdot representing an electron‘sposition at one point in time.

• H2O: 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 H20 a great solvent.

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

–

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

Hydrogenbond

–

+

+ +

+

–

– –

H

HO

Liquid water:transient hydrogenbonds

Ice: stable hydrogen bonds

• Cohesion- tendency of molecules to stick together. Ex: H20 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 temperatureWater moderates air temperature• By absorbing heat from air that is warmer By absorbing heat from air that is warmer

and releasing the stored heat to air that is and releasing the stored heat to air that is coolercooler

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

breakbreak– Heat is released when hydrogen bonds Heat is released when hydrogen bonds

formform

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 H3O+) and hydroxide (OH-) ions• Changes in the concentration of these ions

Can have a great affect on pH in living organisms

16

H

Hydroniumion (H3O+)

H

Hydroxideion (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

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Morphine

Natural endorphin

KeyCarbonHydrogen

NitrogenSulfurOxygen

• 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

NH2

OH

COOH

C=O

S-H

PO4

Fig. 4-10c

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Carboxyl

Acetic acid, which gives vinegar its sour taste

Carboxylic acids, or organic acids

Has acidic propertiesbecause 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 acid Acetate ion

Fig. 4-10d

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Amino

Because it also has a carboxyl group, glycine is both an amine anda 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 OFCOMPOUND

FUNCTIONALPROPERTIES

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 ofcysteines in hairproteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breakingand re-forming thecross-linking bonds.

Fig. 4-10f

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

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 OFCOMPOUND

FUNCTIONALPROPERTIES

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 affectstheir shape and function.

GENERAL TERMINOLOGY:

•Monomer(S)•Polymer(S)•Isomer(s)