Chapter 2: Chemical

Principles

Chemical Building Blocks & Chemical Bonds

• The smallest chemical unit of matter = atom

• Matter composed of one type of atom = element

– (e.g. Carbon [C], nitrogen [N], oxygen [O], sodium [Na])

• Two or more atoms combine to form: a molecule

– Either same type of

atom (e.g. N 2)

– Or different (e.g. CO 2)
– called a compound.

The structure of atoms

• Every atom has a centrally located nucleus
• Nucleus is made up of: Protons (+ charge)
and: Neutrons (neutral charge)
• Thus the nucleus bears a net positive charge
• Nucleus is stable and does NOT participate in chemical reactions.

1
Electrons (e-)
• Circle the nucleus and are negatively charged

• Stabilize the positive charge of the nucleus

• An equal number of electrons and protons will give a net charge

equal to neutral

• Unlike protons and neutrons,

which are densely packed in
the nucleus, the lighter
electrons orbit the nucleus in
“shells”

• Electron shells correspond

to different energy levels.

https://www.technologyuk.net/science/matter/electron-shells-and-orbitals.shtml

https://www.youtube.com/watch?v=ououF9nHUhk

Chemical Bonds
• Chemical bonds form between atoms through interactions of
electrons in their outer shells

• The goal of every atom is to become chemically stable, this is

achieved by filling its outermost shell with electrons
1st = 2 e-
2nd = 8 e-
3rd = 8 e-
• Atoms achieve a full
complement of
electrons by
combining together
to form molecules.

https://manoa.hawaii.edu/exploringourfluidearth/chemical/chemistry-and-seawater/ionic-compounds

Ions
• If an atom loses an electron it has an overall positive charge

• If an atom gains an electron it has an overall negative charge

• An atom (or group of atoms) that has a positive or negative charge

is called an ion

Cation – Loss of an electron Anion – Gained electron

Positive (ex. Sodium Na+) Negative (ex. Chloride Cl-).

https://www.gcsescience.com/a4-sodium-ion.htm

2
 3 kinds of chemical bonds found in living organisms:
– Ionic, covalent, hydrogen bonds

1. Ionic Bonds – result from attraction between ions of opposite

charges
• Anions and cations can
form ionic bonds to
neutralize their charges
• Attraction holds the ions
together to form a
compound, ex. NaCl.

2. Covalent Bonds
• Covalent bonds form when atoms share pairs of electrons

• Found in many compounds, especially those that contain carbon

• very strong bonds

• Carbon atoms can form

up to 4 covalent bonds

• ex. CH 4.

3. Hydrogen Bonds
• Occur between covalently bonded molecules that display polarity
• Ex. When hydrogens are bonded to oxygen, the larger oxygen atom
tends to pull the electrons closer to itself
• Creates a region with partial negative charge (O)
• And a region with partial positive charge (H)
• Ex. the water molecule H 2O
• These regions can now participate in hydrogen bonding.

3
Hydrogen Bonds
• Loose attraction between oppositely charged regions of different
molecules

• Weaker than ionic and covalent bonds

• Serve to bridge separate molecules together

• Ex. In water (H 2O) the H’s of one molecule are attracted to the O’s of
other molecules.

10

Water as the solvent of life

• Approx. 75% of cell weight is water

• Water has an unequal charge distribution

• Each water molecule can form up to four hydrogen bonds with other
water moleculesà GIVES WATER ITS UNIQUE PROPERTIES

• Imparts a high boiling

point (100°C)*

• Makes water resist rapid

changes in temperature.

* https://www.omnicalculator.com/chemistry/boiling-point-altitude
https://flexbooks.ck12.org/cbook/ck-12-chemistry-flexbook-2.0/section/15.2/primary/lesson/structure-of-ice-chem/

11

Water as the solvent of life

• Water is a polar solvent

• Unequal charge distribution allows it to dissolve many ionic compounds

• Positive region of water molecules surround negative ions

• Negative regions surround positive ions

• Holds the ions in solution

• Ex. NaCl easily dissolves into

Na+ and Cl- in water.

12

4
 Water as the solvent of life
• Water’s polarity facilitates the splitting
and joining of hydrogen ions (H +) and
hydroxide ions (OH -)

H 2O H + + OH -

• Makes these ions available for

chemical reactions

• pH scale describes the concentration

of H + ions in a solution

• Measure of acidity

• pH 7 = neutral (pure water)

• pH below 7 = acidic

• pH above 7 = basic or
alkaline.
https://www.youtube.com/watch?v=OQRoImeWtd0&t=101s

13

Organic Molecules
• Any molecule that contains both carbon and hydrogen

• Because each C atom can participate in 4 covalent bonds, carbon

can be used to build an enormous variety of compounds

• Four major classes of organic molecules make up the building

blocks of life:

1. Carbohydrates
• Large group of compounds including sugars and starches

• All contain the elements C, H and O often in the ratio C 1H 2O 1

• Ex. glucose = C 6H 12O 6

• Generally polar (so they dissolve in water)

• Ready source of energy for cells.

14

Types of Carbohydrates
1. Monosaccharides; mono = one
saccharide
• Simple sugars, ex. Glucose
2. Disaccharides; di = Two
• ex. Glucose + fructose =
Sucrose (table sugar)
3. Polysaccharides; poly = many

• Hundreds of monosaccharides
joined together
• Often not soluble in water

• ex. glycogen, starch.

15

5
 2. Lipids
• Includes fats, complex lipids (ex. phospholipids) and steroids

• Essential to the structure and function of membranes

• Used for energy storage
• Non-polar molecules:
Hydrophobic = water hating

Fats:
• Made from a glycerol backbone
+1 or more fatty acids:
• Monoacylglycerides: 1 fatty acid

• Diacylglycerides: 2 fatty acids

• Triacylglycerides: 3 fatty acids

Fatty acids can be:

• Saturated = no double bonds

• or unsaturated = double bonds.

16

Complex lipids such as

Phospholipids
• Contain glycerol, 2 fatty acids,
and a phosphate group
• The phosphate group is polar:

• Hydrophilic
• The fatty acid tails are non-polar:

• Hydrophobic
• Allows phospholipids to form
membranes in water
• Saturated fatty acids tend to form
membranes that are more solid
• Unsaturated fatty acids – more
fluid.

17

Biological membranes:
• Are made from a phospholipid bilayer

• Are semi-fluid (contain a mix of saturated and unsaturated fatty acids)

• Separate the watery inside of the cell from the watery environment.

18

6
 Steroids (or sterols)
• Structurally different from other lipids

• Built on a hydrophobic 4 ring structure

• Generally found in eukaryotes (not in prokaryotes)*

• Ex. Cholesterol, ergosterol and vitamin D.

• https://pubmed.ncbi.nlm.nih.gov/12519197/

19

3. Proteins
• Made up of building blocks: amino acids
• All contain: C, H, O, N (and some have S)
• required in all aspects of cell structure and function
• Some are structural
• But most act as enzymes – increase the rate at which chemical
reactions take place in living organisms

• Proteins typically contain: 20 different amino acids

• have at least one amino (-NH 2) and one carboxyl (-COOH) group
• side groups determine properties.
https://www.chegg.com/homework-help/questions-and-answers/amino-acid-gets-name-contain-amino-group-nh2-carboxyl-group-cooh-also-called-carboxylic-
ac-q39593512

20

Amino acids are joined to make proteins by covalent peptide bonds

• Protein = polypeptide = chain of amino acids

• shape and function of the protein is determined by the sequence of amino

acids.

https://i0.wp.com/www.compoundchem.com/wp-content/uploads/2014/09/20-Common-Amino-Acids-v3.png?ssl=1

21

7
Nucleic acids
• DNA = deoxyribonucleic acid

• RNA = ribonucleic acid

• Built of building blocks called

nucleotides

• Each nucleotide has 3 parts:

1. Nitrogenous Base:

• Purine ® 2 rings = Guanine (G) and Adenine (A)

• Pyrimidine ® 1 ring = Cytosine (C), Thymine (T) or Uracil (U)

2. Pentose sugar ® 5 carbon sugar

• Ribose or deoxyribose*

3. Phosphate.
* https://www.mun.ca/biology/scarr/Ribose_sugar.html

22

• Nucleotides are joined together by covalent

bonds to form a strand of nucleic acid
DNA
• Nitrogenous bases: A, G, T and C

• Sugar deoxyribose

• Double stranded

• Stores the genetic info of all

cellular organisms
RNA
• A, G, U and C

• Sugar ribose

• Single stranded

• Involved in communicating the instructions stored in DNA.

https://www.technologynetworks.com/genomics/lists/what-are-the-key-differences-between-dna-and-rna-296719
https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/

23

DNA structure
• Each strand is built from a
sugar phosphate backbone

• Two strands are held

together by hydrogen bonds
between nitrogenous bases

• Forms the double helix

Base pairing:

• A pairs with T

• G pairs with C

• Order of bases is specific and forms the genetic instructions for the
organism (ie. genes).

24