Biochemistry Review

10/30/08
A. The Universe Notes
- Composed of energy (physics) and matter
(chemistry)

- Matter
- Everything in the universe is composed of
matter. This includes all living things, and the
atom is the fundamental unit of matter.

B. Atom
The smallest particle of an element that retains the
chemical properties of that element. Atoms of two or more
elements bonded together form a molecule.

Source: Life—The Science of Biology, 7th ed.

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Biochemistry Review

Energy levels - represent the orbital pathways of the

electrons, these levels may be compared to balls that fit
inside each other.

Electron - negatively charged particle which orbits the

nucleus. In normal, neutral atoms, the number of
electrons (e-) is equal to the number of protons.

- if the atom is not neutral/stable it will donate/accept

or share e- a stable compound

- to be stable the:
- inner most orbital needs 2e-
- and the outermost orbital needs 8e-
- (with the exception of Hydrogen and Helium,
which only need 2e-)
 the Octet Rule

Source: Life—The Science of Biology, 7th ed.

(diagram: CH4 - methane)

C has 4e- and therefore need 4e-

H has 1e- and therefore needs 1e- more

A little more than you wanted to know…

Fermions include:
(generally assoc. w/ matter)

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Biochemistry Review

Electrons
-
- common abbrv.= e
- are elementary particles
- with a negative charge,
- ions
- -
- anion – gains e , e.g., Cl
- +
- cation – loses e , e.g., Na

Protons
- 2 Up quarks + 1 down quark
- positive charge
- atomic number
- defines the type of element the atom forms

Neutron
- 1Up + 2 down quarks
- without a charge
- defines the isotope

Quark Source:
- elementary fermions http://en.wikipedia.org/wiki/Image:Standard_Mo
- form protons and neutrons del_of_Elementary_Particles.svg

Bosons include:
(generally assoc. w/ force carriers)

Photons - elementary particle responsible for electromagnetic

wavelengths.

Gluons - are elementary particles that cause quarks to interact,

and are indirectly responsible for the binding of protons and
neutrons together in atomic nuclei (nucleons).

Isotopes
- while the number of protons remains constant, the
number of neutrons may vary. Atoms of the same
element with a different number of neutrons are
called isotopes.

- most elements have one or two isotopes

i.e., Nuclides: Isotopes of Carbon include:

- include 8C thru 22C, e.g.,
- 11C – half life of 20.4 min
- 12C – most common isotope (stable)
- 13C – stable
- 14C – half life of 5,730±40years
- Collectively, all the isotopes of all the elements
form the set of nuclides.

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Biochemistry Review
Isotopes Have Different Numbers of Neutrons The isotopes of
hydrogen all have one proton in the nucleus, defining them as that
element. Their differing mass numbers are due to different numbers of
neutrons. Source: Life—The Science of Biology, 7th ed.
Radioisotopes
- some isotopes have unstable nuclei—their nuclei
tend to release particles, either neutrons (or
protons).
- all isotopes of the same element behave similarly
chemically
- therefore the radioisotope of the an element
normally found in an organism can be used to
“map” the pathway of the “tracer”
- e.g., Tomography……iodine-131 vs I-130 stable
(v.short half life…. not risky)
Ions
- An ion is an electrically charged particle, formed
when an atom loses or gains one or more electrons to
form a stable outer shell. All ions are cations or
anions.
e.g., HCl (g)  H+(aq) + Cl-(aq)
a. Cation. An ion with a positive charge, formed when an
atom loses electrons in a reaction (it now has more
protons than e-).
b. Anion. An ion with a negative charge, formed when an
atom gains electrons in a reaction (it now has more e-
than protons).
Cell Biology 4 Biochemistry Review
To discover how long an organism has
been dead (to determine how much C14
is left in the organism and therefore how
old it is), we count the number of beta
radiations given off per minute per gram
of material. Modern C14 emits about 15
beta radiations per minute per gram of
material, but C14 that is 5730 years old
will only emit half that amount, (the
half-life of C14) per minute. So if a
sample taken from an organism emits 7.5
radiations per minute in a gram of
material, then the organism must be
5730 years old.
Because the half-life of carbon-14 is
5,730 years, it is only reliable for dating
objects up to about 60,000 years old.
However, the principle of carbon-14
dating applies to other isotopes as well.
Potassium-40 is another radioactive
element naturally found in your body
and has a half-life of 1.3 billion years.
Other useful radioisotopes for
radioactive dating include Uranium -235
(half-life = 704 million years), Uranium
-238 (half-life = 4.5 billion years),
Thorium-232 (half-life = 14 billion
years) and Rubidium-87 (half-life = 49
billion years).
The use of various radioisotopes allows
the dating of biological and geological
samples with a high degree of accuracy.
However, radioisotope dating may not
work so well in the future. Anything that
dies after the 1940s, when Nuclear
bombs , nuclear reactors and open-air
nuclear tests started changing things, will
be harder to date precisely.
Biochemistry Review

More Vocab

Solvent - A substance, usually a liquid,

in which other substances are dissolved.
The most common solvent is water, and
is often referred to as a universal solvent

Solute - the substance which is dissolved

in a solvent. Dissolved solids, such as
the “salt” found in water, are solutes.

Solvate - The process by which solvent

molecules surround and interact with
solute ions or molecules. Ions in solution
are normally combined with at least one
molecule of solvent. This phenomenon is
termed solvation.

Dissociation - The process that may

Source: Life—The Science of Biology, 7th ed.
occur when a chemical compound is
dissolved in a solvent (e.g., water). The
molecules of the compound will break
up ("dissociate") into two or more ions
resulting in an ionically conducting
electrolyte solution. E.g., the common
table salt (sodium chloride) will
dissociate into a single charged sodium
cation and a single charged chloride
anion.

Emulsify - to break up into small pieces,

Sodium starts with: Chlorine starts with: e.g., soap, bile
- 11 protons - 17 Protons
- 11 electrons - 17 electrons Homogenized - To make uniform. To
break up particles into small, uniform-
sized pieces. Fat in whole milk may be
Gives up 1e-, Gains1e-, homogenized. Aside: 2% milk gets 35%
- 11 protons - 17 Protons of its calories from fat. The 2%
- 10 electrons - 18 electrons represents how much of the total weight
of milk is fat, which, to the consumer, is
almost meaningless. Skim = 4%, cal.
∴ Na+ ∴ Cl- from fat. 1% = 23% . Whole milk =
50%.-Skim and 1% fat milk all provide
Sodium has 1 e- in its outer Chlorine needs 1 e- to have slightly more nutrients than whole milk
and 2%fat milk,but they're much lower
orbital, by donating this 1 e-, 8 e- in its outermost orbital in fats (saturated fats).contains more fat
it would have 8 e- only in its shell, which it accepts from than reduced-fat (2%) milk, but it is low
outermost orbital shell (cf. the sodium in saturated fat and cholesterol-free, and
Octet Rule) contains fibre, and it's a good source of
protein.
∴ if Na+ donates its 1 e- and Cl- accepts, each can become
stable by forming an ionic compound, NaCl (“salt”).
Elements
www. chemical elements.com – basic info
www.webelements.com – detailed info

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Biochemistry Review

Elements are substances that cannot be broken down Humour:

chemically into simpler kinds of matter, i.e., an atom of
gold can not chemically be broken down to its component A neutron walks into a bar and says,
“How much for a beer (soy)milk?”
parts, electrons, protons and neutrons. And the bartender says, “For you, no
charge.”
- each atom of an element has the same number of
protons, its atomic number.
Two hydrogen atoms walk into a bar.
The first one says, “Oh, no, I’ve lost
- Common abbreviations an electron!” The other one says,
Hydrogen - H2 (gas), H+ (ion) “Are you sure?” The first one says,
Carbon - C (linch pin element of organic chemistry) “I’m positive!”
Nitrogen - N2
Oxygen - O2 (gas), O3 (ozone) Source: a Chemistry teacher
Sodium - Na+ (aka Natrium)
Magnesium - Mg2+
Phosphorus -P
Sulphur -S
Chlorine - Cl2, Cl-
Calcium - Ca2+
Potassium - K+ (aka Kalium)
Iron - Fe2+, Fe3+ (aka Ferrum)
Gold - Au (aka Aurum)
Silver - Ag (aka Argentum)
Mercury - Hg2+ (aka Hydragyrum)
Lead - Pb2+ (aka Plumbum)

C. Organic Chemistry
- Organic compounds always contain carbon and
hydrogen,
- and are often large and complex; they are the
principal building blocks of life

INORGANIC ORGANIC
- usually contain metals & nonmetals - contain C & H
- e.g., NaCl (salt), H20 - e.g., protein
- may contain metals
- assoc. w/ ionic bonding - e.g., Fe (hemoglobin)
- small # of atoms - always covalent
- non-living - large # of atoms
- small & simple - living
- large & complex

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