Basic Biochemistry
I. Chemistry – science dealing with the properties and transformation of all matter
A. Chemical reactions – transformations in which different forms of matter combine or
break
B. Element – matter that cannot be broken down into simpler substances via chemical
reaction
1. There are 92 naturally-occurring elements
2. Cannot be changed into a different element or destroyed via chemical reactions
3. About 25 elements are essential for life
A) 4 of these make up 96% of living matter
1) C, O, H & N
B) The remaining 4% primarily include P, S, Ca, K, Na, Cl, & Mg
C) trace elements are ones only required in small quantities
1) Fe, Cu & Zn are examples
C. Atom – smallest unit of an element that still has the properties of the element
D. Molecule – stable assembly of 2 or more atoms; O2 and H2O are examples
1. Its properties are independent of the elements that compose it
2. The subscript number indicates the number of atoms in the molecule
A) O2 has 2 oxygen atoms
B) H2O has 2 hydrogen atoms and 1 oxygen atom
E. Compound – assembly of 2 or more different elements; H2O & CO2
1. Its properties are independent of the elements that compose it
2. The subscript number once again indicates the number of atoms of each
element
F. Mixture – assembly of 2 or more compounds; doesn’t require a chemical reaction
II. Properties of an Atom
A. Atomic Structure
1. Mostly empty space; composed of subatomic particles
2. Has concentrated nucleus at its center
A) Contains protons
1) Positively charged
B) Also contains neutrons
1) No charge (neutral)
3. Electrons orbit the nucleus
A) Negatively charged
B) Balance out the (+) charge of the protons
4. Electrons orbit within specific energy levels
A) These energy levels make-up electron shells
1) Shells closest to the nucleus have the lowest energy; those farthest
from the nucleus have the highest energy
2) Each shell contains a set number of electrons
a) 1st shell – 2 electrons
b) 2nd shell – 8 electrons
, c) 3rd shell – 18 electrons
3) No matter how many shells or electrons are present, it is the outer
shell (valance shell) and its electrons that are involved in chemical
bonds
C. Chemical Bonds
1. Bond – a union of 2 or more atoms that involves the sharing or donating of
electrons
A) 2 types of bonds
1) Covalent bond – involves the sharing of one or more pairs of
electrons
a) 3 types of covalent bonds
i) Single covalent bond – one pair of electrons is shared
ii) Double covalent bond – two pairs of electrons are shared
iii) Triple covalent bond – three pairs of electrons are shared
2) Ionic bond – one atom donates an electron(s) to another atom
a) Results in 2 atoms attracted by opposing charges
b) Ionic compounds readily dissociate (come apart) in water
i) Ion – any charged particle
(a) Cation – positively charged
(i) Lost 1 or more electrons
(b) Anion – negatively charged
(i) Gained 1 or more electrons
2. Polar molecule – electrically neutral molecule that has an uneven distribution
of charges
A) Electrons are not shared evenly in covalent bonds
B) As a result, the electrons spend more time in orbit around the atom with
the higher electronegativity
1) Electronegativity – the tendency of an atom to gain electrons
C) This causes one side of the molecule to be slightly negative and one to be
slightly positive
D) Polar molecules mix well with water and are hydrophilic (“water loving”)
E) Polar molecules also interact well with other polar molecules but not
nonpolar molecules
F) Examples include water, carbohydrates, proteins, and nucleic acids
3. Nonpolar molecules – electrically neutral molecule with the electrons shared
evenly by the atoms
A) Result when both atoms of the bond have similar electronegativity values
1) Electrons orbit equally around both atoms
2) There are no charges on the molecule
B) Nonpolar molecules do not mix well with water and are hydrophobic
(“water fearing”)
C) Nonpolar molecules do not interact well with polar molecules and in
reality don’t “interact” with nonpolar molecules either
I. Chemistry – science dealing with the properties and transformation of all matter
A. Chemical reactions – transformations in which different forms of matter combine or
break
B. Element – matter that cannot be broken down into simpler substances via chemical
reaction
1. There are 92 naturally-occurring elements
2. Cannot be changed into a different element or destroyed via chemical reactions
3. About 25 elements are essential for life
A) 4 of these make up 96% of living matter
1) C, O, H & N
B) The remaining 4% primarily include P, S, Ca, K, Na, Cl, & Mg
C) trace elements are ones only required in small quantities
1) Fe, Cu & Zn are examples
C. Atom – smallest unit of an element that still has the properties of the element
D. Molecule – stable assembly of 2 or more atoms; O2 and H2O are examples
1. Its properties are independent of the elements that compose it
2. The subscript number indicates the number of atoms in the molecule
A) O2 has 2 oxygen atoms
B) H2O has 2 hydrogen atoms and 1 oxygen atom
E. Compound – assembly of 2 or more different elements; H2O & CO2
1. Its properties are independent of the elements that compose it
2. The subscript number once again indicates the number of atoms of each
element
F. Mixture – assembly of 2 or more compounds; doesn’t require a chemical reaction
II. Properties of an Atom
A. Atomic Structure
1. Mostly empty space; composed of subatomic particles
2. Has concentrated nucleus at its center
A) Contains protons
1) Positively charged
B) Also contains neutrons
1) No charge (neutral)
3. Electrons orbit the nucleus
A) Negatively charged
B) Balance out the (+) charge of the protons
4. Electrons orbit within specific energy levels
A) These energy levels make-up electron shells
1) Shells closest to the nucleus have the lowest energy; those farthest
from the nucleus have the highest energy
2) Each shell contains a set number of electrons
a) 1st shell – 2 electrons
b) 2nd shell – 8 electrons
, c) 3rd shell – 18 electrons
3) No matter how many shells or electrons are present, it is the outer
shell (valance shell) and its electrons that are involved in chemical
bonds
C. Chemical Bonds
1. Bond – a union of 2 or more atoms that involves the sharing or donating of
electrons
A) 2 types of bonds
1) Covalent bond – involves the sharing of one or more pairs of
electrons
a) 3 types of covalent bonds
i) Single covalent bond – one pair of electrons is shared
ii) Double covalent bond – two pairs of electrons are shared
iii) Triple covalent bond – three pairs of electrons are shared
2) Ionic bond – one atom donates an electron(s) to another atom
a) Results in 2 atoms attracted by opposing charges
b) Ionic compounds readily dissociate (come apart) in water
i) Ion – any charged particle
(a) Cation – positively charged
(i) Lost 1 or more electrons
(b) Anion – negatively charged
(i) Gained 1 or more electrons
2. Polar molecule – electrically neutral molecule that has an uneven distribution
of charges
A) Electrons are not shared evenly in covalent bonds
B) As a result, the electrons spend more time in orbit around the atom with
the higher electronegativity
1) Electronegativity – the tendency of an atom to gain electrons
C) This causes one side of the molecule to be slightly negative and one to be
slightly positive
D) Polar molecules mix well with water and are hydrophilic (“water loving”)
E) Polar molecules also interact well with other polar molecules but not
nonpolar molecules
F) Examples include water, carbohydrates, proteins, and nucleic acids
3. Nonpolar molecules – electrically neutral molecule with the electrons shared
evenly by the atoms
A) Result when both atoms of the bond have similar electronegativity values
1) Electrons orbit equally around both atoms
2) There are no charges on the molecule
B) Nonpolar molecules do not mix well with water and are hydrophobic
(“water fearing”)
C) Nonpolar molecules do not interact well with polar molecules and in
reality don’t “interact” with nonpolar molecules either
