Transcript file - Athens Academy

Chapter 2 – the chemistry of life

Why is it important to have an
understanding of chemistry to study
anatomy?
– All biological functions can be explained
chemically

What are the components of life?
– Matter
– Energy
Nature of Matter: Atomic Structure
– Nucleus—very small size compared to the entire atom,
composed of
a) protons (p+): have a positive electrical charge,
have some mass, and
b) neutrons (n0): have no electrical charge, have the
same mass as a proton.
– Electrons (e-): these orbit the nucleus, they have a
negative electrical charge which is equal and opposite
the charge of a proton, they have a negligible mass.
– Atoms are usually electrically neutral—number of
electrons = number of protons.
Nature of Matter: Atomic Structure

How can we tell one atom from another? What is the
distinction?
– Atomic Number — the number of protons in an atom.
– Atomic Mass (weight) – mass of atom, which would include # of
protons + # of neutrons

Other Definitions
– Element – matter composed of atoms of only one kind.
» The number of protons in the nucleus of any given atom is always
the same AND each element has a different number of protons in its
nucleus
– Molecules: A combination of atoms where electrons in the
outermost orbital are either transferred or shared.
– Compound: A molecule that has two or more kinds of atoms.
– Chemical Formula: C6H12O6
http://wine1.sb.fsu.edu/chm1045/tables/period/PT_large.jpg
Earth’s crust
other
8%
Human body
other
7%
hydrogen
10%
oxygen
50%
oxygen
65%
silicon
26%
aluminum
8%
calcium
3%
iron 5%
carbon
18%
Table. 2.2
Nature of Matter: Key Components of the Atom
– Size - nucleus is much smaller than surrounding orbital and atoms
are really, really tiny.
– Identity – # of protons determines identity of atom. Neutrons only
provide additional mass.
– Charge - is determined by comparing the number of electrons to
number of protons. If they are equal, then atom is electrically
neutral. If they are not, then atom is existing in an ionic state.
– Reactivity – is determined by the valence electrons in the
outermost shell. The number of valence electrons really does make
a difference in the way an atom will behave around other atoms.
Some are stable; others are very reactive.
– Lowest Energy State – all matter (atoms being the smallest
particles of matter) always seek there lowest energy state, so they
prefer to be neutral and they prefer to have their outermost energy
shell full!
– Isotopes – Most atoms exist in various isotopic forms. How can
you tell? If number of neutrons is different from number of
protons, atom is in an isotopic state. # of neutrons = atomic mass
(weight) – atomic number.
Radioactive Isotopes
Medical Diagnosis
 Cancer Therapy
 Other Biological Uses

– Radiometric Dating
– Radioactive Labeling
Chemical Bonding


The goal of atoms is to find their lowest energy
state!
Types of bonds
– Ionic Bonding – one atom loses an electron and one
gains an electron.
– Covalent Bonding – two atoms share a pair of
electrons, sometimes equally/sometimes unequally.
» Single Covalent Bond (one pair of electrons)
» Double Covalent Bond (two pairs)
» Triple Covalent Bond (three pairs)
e-
e-
Hydrogen
e-
Helium
ee-
e-
e-
e-
e-
e-
ee-
e-
e-
Carbon
e-
e-
e-
Neon
e-
e-
eee-
e-
e-
ee-
e-
e-
ee-
e-
Sodium
unstable, very reactive
e-
e-
e-
ee-
e-
ee-
e-
e-
ee-
Argon e
e-
e-
ee-
stable, unreactive
Sodium atom (Na)
Chlorine atom (Cl)
e-
electron
transfer
e-
Chlorine ion (Cl-)
Ionic
Compound
(Na+ + Cl-)
Salt crystals
Polar vs. Non-polar Covalent Bonds

Nonpolar Covalent Bonds
– Neither nucleus exerts more attractive pull on shared
electrons (equal electronegativity and equal sharing,
like joint custody).

Polar Covalent Bonds
– H2O is most common example in the body
– Oxygen has a greater atomic number than hydrogen.
– Oxygen’s nucleus attracts the shared electrons with a
greater electronegativity than hydrogen in a water
molecule.
– Unequal sharing results in polar charges on different
parts of the molecule.
O
H
H
+
–
O
O
H
+
–
–
O
O
H
–
+
H
–
+
+ H
–
H
–
H
+
–
H
+
–
H
–
+
H
+
–
O
+
H
H
H
O
Hydrogen bond
H
O
H
Dissociation and Electrolytes
Functional Groups (Handout)

These are small groups of atoms that when attached to larger organic
molecules will give those molecules predictable properties such as
hydrophilic (polar) or hydrophobic (non-polar)/acid or base.
a)
Hydroxyl (R-OH): When attached to a hydrocarbon chain, it creates an
alcohol. This group is found all over sugars. Because it contains a polar
covalent bond, the Hydrogen atom is polar positive (+) and makes that part
of the molecule hydrophilic and capable of forming H-bonds.
b)
Carbonyl (>C=O): It contains a polar covalent bond and the oxygen is
therefore polar negative (-) which makes that part of the molecule
hydrophilic and capable of forming H-bonds. There are two types of
carbonyl:
1) Aldehyde: when the group is found at the end of a chain, and the
2) Ketone: when the group is found in the middle of a chain.
Functional Groups, Continued
c)
d)
e)
f)
Carboxyl (R-COOH): This group loses the H off of the hydroxyl group
which forms both a negative charged Oxygen (- ion) and a Hydrogen ion
(H+) is released into solution. This makes the molecule to which it is
attached an acid. The polar charges and the ionic charges cause this part
of a molecule to be highly hydrophilic.
Amino (>NH2): This group tends to pick up H+ ions from the solution
and causes the pH to rise. Therefore this group makes the molecule a
base. The group becomes ionically charged (+) and this makes this part
of the molecule highly hydrophilic.
Phosphate (R-PO4): This group releases H+ into solution making the
molecule to which it is attached both acidic and hydrophilic.
Methyl (R-CH3): The nonpolar covalent bonds in this group make the
part of the molecule to which it is attached hydrophobic.
ACIDIC
100
10-1
battery acid
1 hydrochloric acid
10-2
2
lemon juice, gastric
(stomach) juice
10-3
3 cola, beer, wine, vinegar
10-4
4 tomatoes
10-5
5 black coffee
10-6
6 urine
NEUTRAL 10-7
7 pure water
10-8
human blood
8 seawater
10-9
9 baking soda
10-10
10 Great Salt Lake
10-11
11
10-12
10-13
BASIC
0
10-14
12
13
household ammonia
household bleach
oven cleaner
14 lye
Chemical reactions

1.
2.
3.
Types of chemical reactions:
Synthesis reactions
Decomposition reactions
Exchange reactions – single or double
replacement
All metabolic pathways require energy at some
point! – ATP/ADP
Most biological reactions are reversible as well!
Fig. 2.20
Chemical reactions, cont’d

Reversible reactions - equilibrium
In the body, reactants and products tend to react with one
another back and forth until equilibrium is reached homeostasis

Reaction Rates – what affects rate of rxn?
– Concentration of reactants
– Temperature
– Enzymes (catalyst)
biochemistry
Inorganic Molecules – Molecules that do not
contain carbon
1.
Water – inorganic
a.
High Specific Heat, meaning water resists
temperature changes which helps in maintaining body
temperature.
b. High Heat of Vaporization – Evaporative Cooling
c. Effective lubricant – surface of the eye
d. Necessary reactant in chemical reactions – digestion
e. Universal Solvent – works for transport of nutrients
throughout body
Biochemistry, cont’d
Macromolecules of Life (organic) – Molecules
that contain carbon (Table 2.3 – page 31)

Carbohydrates – mono, di and polysaccharides

Lipids – fats, fatty acids, glycerol,
triaglycerols/triglycerides – saturated and
unsaturated fats

Proteins – amino acids
–

Enzymes – activation energy
Nucleic acids – DNA, RNA
Fig. 2.11
Fig. 2.12
Fig. 2.13
Fig. 2.14
OH
CH3
CH3
HC
CH3
O
CH3
CH2
CH2
testosterone
CH3
CH2
HC
OH
CH3
CH3
CH3
cholesterol
estrogen
HO
HO
Fig. 2.16a
Fig. 2.16b
Fig. 2.19b
The detailed structure of an animal cell’s plasma membrane, in cross section
Enzyme Action
Three-Dimensional Shape: Important in
Biology
– Compounds have very definite spatial
configurations.
– Shape determines how molecules can bind one
another, a critical step in many activities. This
is especially true where enzymes are concerned.
– Throughout biology we see a complementarity
of structure to function. This is easily seen
throughout all of biology.

Activation Energy & Enzymes