Unit 1: Biochemistry

I. Chemical Bonding

Compound—a substance consisting of two or more different elements combined in a fixed ratio

Sodium ChlorideChlorineSodium

+

Many of the compounds in living organisms contain carbon, hydrogen, oxygen, and nitrogen

– DNA, for example, contains all four of these elements

Different arrangements of elements provide unique properties for each compound

Only valence electrons (in the outermost energy level) are involved in chemical bonding

Atoms want to fill their outer energy levels by forming compounds.

Magnesium

Lithium

Hydrogen

Thirdshell

Firstshell

Secondshell

Sodium

Beryllium

Aluminum

Boron

Silicon

Carbon

Phosphorus

Nitrogen

Sulfur

Oxygen

Chlorine

Fluorine

Argon

Neon

Helium

A. Ionic Bond- formed when two ions with opposite charges attract each other

Due to transfer of valence electrons

cation (+) & anion (-) = ionic compound

metal & non-metal

stronger bonds, solids (at room temp), higher melting points

NaSodium atom

Transfer ofValence electron

ClChlorine atom

Na+

Sodium ionCl–

Chloride ion

Sodium chloride (NaCl)

+ –

Na+

Cl–

B. Covalent bond- formed when atoms share valence electrons

compound is called a molecule

2 or more non-metal elements

weaker than ionic bond, can be solid liquid or gas, low melting points

1. nonpolar covalent bonds – equal sharing of valence electrons

ex: H2, O2, CH4

2. polar covalent bonds – unequal sharing of valence electrons

one atom attracts electrons stronger than the other

ex: H2O

referred to as a polar molecule

(–) (–)

O

HH

(+) (+)

II. Water’s Life Supporting Properties

When hydrogen is part of a polar covalent bond it can form attractions with other atoms (ex: O, N, F)

This attraction is called a hydrogen bond (weaker than covalent bond; not really a bond)

The H of one water molecule is attracted to the O end of a nearby water molecule due to hydrogen bonding

Hydrogen bond

1. Cohesion - hydrogen bonding causes molecules of the same substance to stick together

stronger for water than other liquids

useful in plants that depend upon cohesion to help transport water and nutrients up the plant

related to surface tension - a measure of how difficult it is to break the surface of a liquid

2. Adhesion – attraction between 2 different substances

water forms hydrogen bonds with other substances like plant tissue and glass.

causes meniscus in graduated cylinder

capillary action- adhesion between water and glass causes water to rise in a narrow tube against the force of gravity.

Water-conductingcells

Adhesion

Cohesion

150 µm

Directionof watermovement

3. High Specific Heat- amount of energy required to raise 1 g of a substance 1°C.

due to hydrogen bonding, water has a greater ability to resist temperature change than other liquids

makes water a good insulator

4. Water’s Density

When water freezes, each molecule forms a stable hydrogen bond with four neighbors

• A three-dimensional crystal results

• There is space between the water molecules

Ice is less dense than water, so it floats

Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds

are stable

Hydrogen bond

5. Universal Solvent

Water is the greatest solvent on Earth.

Water's polarity gives it the ability to dissolve both ionic compounds and other polar molecules, such as sugar. (like dissolves like)

A solution is a uniform mixture of two or more substances

• dissolving agent =solvent

• substance dissolved= solute

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Ion insolution

Saltcrystal

The ions gradually become dispersed in the water, forming a solution.

III. pH Scale

some water molecules break apart into ions

hydrogen ions (H+)

hydroxide ions (OH–)

• Both are extremely reactive

• A balance between the two is critical for chemical processes to occur in a living organism

• Buffers minimize pH changes in humans by absorbing H+ or OH-

A. Acids - chemicals other than water that can contribute H+ to a solution

Ex: HCl (gastric acid) in your stomach that aids in digestion

An acidic solution has a higher concentration of H+ than OH–

B. Bases -chemicals that contribute OH- to a solution

Ex: sodium hydroxide (NaOH) provides OH–

Basic solutions have a higher concentration of OH– than H+

Acidic solution Neutral solution Basic solution

C. pH scale (pH = potential of H+) describes whether a solution is acidic or basic

ranges from 0 (most acidic) to 14 (most basic)

neutral (pH = 7)

pH<7 = acid

pH>7 = base

Acidic solution

pH scale

Battery acid

0

1

2

3

4

5

Lemon juice, gastric juice

Grapefruit juice, soft drink,vinegar, beer

Tomato juice

Rain water

Human urine

Saliva

Pure water

6

7

Human blood,tears

Seawater

8

9

10

11

12

13

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Neutral solution

Basic solution

NEUTRAL[H+]=OH–]

Incr

ea

sin

gly

AC

IDIC

(Hig

he

r c

on

cen

tra

tio

n o

f H

+)

14

Incr

ea

sin

gly

BA

SIC

(Lo

we

r c

on

cen

trat

ion

of

H+)

IV. Chemical Reactions

C6H12O6 + 6O2 6CO2 + 6H2O

reactants products

electron transferbetween atoms

creates

electron sharingbetween atoms

creates

ChemicalBonds

atomic number ofeach element

water

nonpolarcovalent bonds

(e)ions

(f) (g)

(h)

attraction betweenions creates

unequalsharing creates

can lead toexample is

equalsharing creates

has importantqualities due

to polarity and

have positivelycharged have neutral

have negativelycharged

number in outershell determines

formation of

number maydiffer in

number presentequals

(a)

Atoms

(b) (c)

(d)

atomic number ofeach element

have positivelycharged have neutral

have negativelycharged

number in outershell determines

formation of

number maydiffer in

number presentequals

(a)

Atoms

(b) (c)

(d)

electron transferbetween atoms

creates

electron sharingbetween atoms

creates

ChemicalBonds

water

nonpolarcovalent bonds

(e)ions

(f) (g)

(h)

attraction betweenions creates

unequalsharing creates

can lead toexample is

equalsharing creates

has importantqualities due

to polarity and