Unit 2a Intro to Cellular Chemistry

objective of Unit 2:

To understand how the properties of a subset of atoms

give rise to simple molecules and larger more complex
macromolecules which in turn allow for the generation of
life.

2
 What are cells made of?

• four types of atoms make up 99% of all matter found in

living organisms
• carbon, hydrogen, oxygen, nitrogen (C, H, O, N)

• mostly combined in complex ‘macromolecules’

• also present in simple forms - CO2, H2O

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Elements Present in the Human Body

4
Figure 2-7
 Parts of an Atom
Isotopes
12C
13C
14C
Atomic number = 6

Figure 2-2

nucleus – dense core in centre, consists of protons and neutrons

electrons – continually orbit the nucleus

- # of protons – defining feature of an element = atomic number

- # protons + # neutrons = mass of an atom = mass number

- by default, an atom is ‘neutral’, with # protons = # electrons

- electrons influence reactivity of an atom ... 5
 Atomic Mass
• mass of a neutron or proton is approximated at one
‘atomic mass unit’ or dalton (Da)
• masses of electrons tiny  ignored
mass
number Isotopes
12C
1 4 12 23
H He C Na 13C
1 2 6 11
14C
atomic Atomic number = 6
number

practice opportunity:
How many protons does helium (He) have?
How many neutrons does hydrogen have? And helium?
Which is the ‘heaviest’ atom of these four?

6
Electrons travel around atomic nuclei in ‘orbitals’.

• orbitals are grouped into layers or shells, based on how far

the electrons in that shell travel from the nucleus

max 2 e- max 8 e- max 8 e-

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 Electrons, shells and valence
• innermost shells fill first

• once first shell filled with pair of electrons, next shells fill with
4 singles then subsequent electrons form pairs

• outermost ‘valence’ shell influences an atom’s reactivity

•electrons in outermost shell  valence electrons

• unpaired valence electrons determine the number of bonds an atom

can make

12 35 40
C Cl Ar
6 17 18

carbon: chlorine: argon:

4 unpaired electrons, 1 unpaired electron, no unpaired electrons,

8
 Unpaired Valence Electrons and Reactivity

Figure 2-5

- completely filled valence shells  non-reactive (stable) eg He, Ne, Ar

- closest to filling valence shell  most reactive eg Cl, Fl, O
- atoms with same # valence electrons have similar chemical behaviour
-Forms basis for ‘periodic’ table

- elements abundant in organisms have at least one unpaired valence electron 9

 Unpaired Electrons and Biological Reactions
• biological reactions are driven by tendency of atoms to
 fill outer shells
 balance positive and negative charges

How can atoms achieve full valence shells?

1. sharing electrons - forming chemical bonds
• number of bonds possible depends on how many electrons
that atom needs to fill its outer shell

2. transferring electrons from one atom to another

• atoms that are no longer electrically neutral  ions
35 -
• gain electron  negatively charged  anion Cl
• lose electron  positively charged  cation 17
23Na+
11 10
 Types of Chemical Bonds
covalent bonds - two or more atoms share pairs of
valence electrons
• strong bonds of biological systems

non-covalent bonds, including

• ionic bonds

• hydrogen bonds (H-bonds)

• hydrophobic interactions

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 Representations of Molecules
Methane Ammonia Water
Molecular CH4 NH3 H2O
formulas:

Structural
formulas:

Ball-and-stick
models:

Space-filling
models:
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 Covalent Bonds – sharing valence electrons
2 hydrogen atoms 2 oxygen atoms

+ +

+ +

one molecule hydrogen gas (H2) one molecule oxygen gas (O2)
H-H O=O
13
Both are examples of non-polar covalent bonds
 Types of Covalent Bonds
• electrons shared ‘equally’
• non-polar covalent bond

• can be single (like H2), double (O2) or even triple,

depending on number of electrons shared

• electrons not shared equally

• polar covalent bond
• one of the atoms has a stronger pull on the
electrons than the other
• pull on electrons = electronegativity

• example – H2O

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 Polar Covalent Bond: Water (H2O)
δ-

H H

δ+ δ+
water is a polar molecule - charge is unevenly distributed
 one part slightly negative, two parts slightly positive15
 Ionization and Ionic Bonds

+ -

If transfer of electron is between

Figure 2-12
Na and Cl, they form an ionic bond: 16
 Water – A Model for Hydrogen Bonds
• water is the most abundant molecule in biological
organisms
• human body is ~70% water

• water as a solvent can dissolve more types of molecules

than other molecule known – ‘Universal Solvent’

• the polarity of water is key to its role in biology

hydrogen bonding – electrical attraction between

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electronegative atom and partial positive of hydrogen
H-Bonding in Pure Water

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 Water as a Solvent
polar compound: eg NaCl non-polar: eg oil in water

hydrophilic – affinity for water hydrophobic – no affinity for water

“water loving” “water fearing”
All of water’s striking properties are a direct result of its ability to
form H-bonds.
Panels 2-2 & 2-7 19
 Bond Length vs Strength

Table 2-1, p. 48

The longer the bond, the weaker the bond

The shorter the bond, the stronger the bond

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Figure 2-8
 Dissociation of Water
• water is not a completely stable molecule
• small amount dissociates (ionize):

H2O  H+ + OH-
hydroxide ion
hydrogen ion

• hydrogen ions don’t actually exist alone, and will join

with other water molecules
• technically reaction looks like this:

Figure 2-15 21
 Acid-Base Reactions
substance that gives up (donates) protons  acid
(increases [H+] in solution)

substance that accepts protons  base

(decreases [H+] in solution)

chemical reaction that involves transfer of protons

 acid-base reaction

• most molecules act as either an acid or a base

• water can be both (both gives up and accepts protons)

weak acid: very few molecules dissociated (acetic acid, water)

strong acid: readily gives up protons (hydrochloric acid)

HCl  H+ + Cl- (HCl + H2O  H3O+ + Cl-)

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 Measuring acidity: the pH scale
• [H+] can vary by a factor of 100 trillion or more

• its concentration is expressed more conveniently via the pH

scale
– Range is 0 to 14
– compresses the range of concentrations by employing
logarithms

pH = - log [H+]

[H+] = 1 x 10-7 M = 0.0000001 M  pH = 7

[H+] = 1 x 10-6 M = 0.000001 M  pH = 6

[H+] = 1 x 10-2 M = 0.01 M  pH = 2

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24
 Why are acid-base reactions important in
biology?
• transfer of protons changes charge of proton donor
and acceptor
• change of charge changes their reactivity with
respect to H-bonding, other interactions

example:
• concentration of H+ in blood typically very low

arterial blood, [H+] = 0.0000000398 M = ~4 x 10-8 M

pH 7.4

If [H+] doubles = 0.0000000796 M = ~8x10-8 M;

pH = 7.1, you die in a few minutes …
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 Carbon as the Building Block of Biology
• carbon is most important atom in biology 12
• carbon-containing molecules  ‘organic’ C
6
• can form many combinations of single and double bonds
• can be linked to form chains, rings

organics

Table 2-2 Essential Cell

Biology (© Garland Science
2010)

p.52 26
Variations in Carbon Skeletons (Pure Hydrocarbons)

• carbon atoms give biomolecules their shape but other atoms

attached to carbons tend to determine their reactivity
• critical H, N, O, S, P containing attachments called functional
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groups
Variations in Carbon Skeletons (Pure Hydrocarbons)

• carbon atoms give biomolecules their shape but other atoms

attached to carbons tend to determine their reactivity
• critical H, N, O, S, P containing attachments called functional
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groups
 Functional Groups
• carbon atoms give
biomolecules their shape
but other atoms attached
to carbons determine
their reactivity
• critical N, O, P, and
S containing
attachments called
functional groups

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 Functional Groups
• are the components of organic molecules typically involved
in chemical reactions
• Seemingly minor changes in functional groups can have a
dramatic biological effect

estradiol (an estrogen) testosterone (an androgen)

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