unit 1: biochemistry i. chemical bonding. compound—a substance consisting of two or more...
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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