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botany notes: 005 Chapter 2

botany notes: 005 Chapter 2

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Chapter 2. The Chemistry of Living Matter
Matter is made up of 
elements
, substances that cannot be broken down by ordinary chemicalmeans into simpler particles. Each element is a collection of a particular kind of discrete particlematter called the atom. An
atom
is the smallest unit of an element that retains the chemical properties of that element.
Subatomic Particles.
Atoms are made up of even smaller, subatomic particles: the
proton
, the
neutron
, and the
electron
. Protons have positive charges, electrons are negatively charged, andneutrons are neutral.Each element has a different number of protons. The
atomic number
is a count of the number of protons in the elemental atom. Oxygen, for example, has 8 protons therefore its atomic number is8. Carbon has 6. Hydrogen has 1. Nitrogen has 7.Generally, atoms have approximately the same number of protons, neutrons, and electrons.Each proton or neutron has a mass of about 1.7x10
-24
gram. For convenience, this mass is defined as1 atomic mass or 1 Dalton. The mass of an electron is about 1/2000 that of a proton, so it is oftendisregarded when considering atomic mass. The protons and neutrons form the nucleus whileelectrons travel at the speed of light orbiting the nucleus. The
atomic mass
of an element is thenumber of protons plus neutrons in each nucleus.
Isotopes.
Atoms with the same number of protons but different number of neutrons are called
isotopes
. Two isotopes of ordinary hydrogen (1 proton, 0 neutrons) are
deuterium
(1 proton, 1neutron) and
tritium
(1 proton, 2 neutrons). Isotopes share the same atomic number but differ inatomic mass, the sum of the atom’s protons and neutrons. Thus, all hydrogen isotopes have theatomic number 1, but atomic masses of 1, 2, and 3, respectively. Isotopes with their extra neutronsare often unstable and undergo radioactive decay at typical and predictable rates, giving off subatomic nuclear particles until they reach stability. Tritium, with a half-life of 12.5 years, is veryuseful in biological research as a radioactive tag that allows hydrogen-containing compounds to betraced through metabolic pathways.
Ions.
Atoms with the same number of protons but different number of electrons form
ions
. NaCl (sodium chloride, table salt) when in water, dissolves and separates into its constituent ions, Na
+
and Cl
-
. The Na ion is positively charged because one of its electrons has been “kidnapped” bythe Cl ion. Na
+
then, has 11 protons, 11 neutrons, and only 10 electrons. Cl
-
on the other hand, has17 protons, 17 neutrons, but 18 electrons, making it negatively charged. Positively charged ions arecalled
cations
and negatively charged ions are called
anions
.
Chemical Bonds.
Following the octet rule, the innermost shell, or the lowest quantum level,for any atom never contains more than two electrons. Each shell external to this innermost shellmay contain up to eight electrons. The number of electrons in the outermost shell determines thecombining power (
valence
) of an atom. If the outermost shell contains eight electrons, (or in thecase of He, 2 electrons in the outermost shell) the atom will be unable to bond with any other atomand the element is said to be inert.Atoms with less than eight electrons in the outermost shell form bonds with other atoms tosaturate this shell. There are three major kinds of chemical bonds: covalent bonds, ionic bonds, andhydrogen bonds.
Covalent bonds
involve the sharing of electrons. Two atoms, each lacking anelectron in their outermost shells, will fill up the vacancies by sharing a pair of electrons.
Ionicbonds
involve the transfer of electrons from one atom to another so the atom either loses or gainselectrons.
Hydrogen bonds
form relatively weaker bonds between polar molecules or polarized
 
side groups of non-polar molecules. They are important in maintaining the shape of macromoleculesaiding in the performance of their biological functions.A
molecule
consists of two or more atoms joined by bonds. The atoms composing a moleculemay be the same (O
2
, H
2
) or different (H
2
O, CH
4
). A molecule composed of different atoms is calleda
compound
.
Acids, Bases, and Salts.
The hydrogen ion H
+
is one of the most important ions in livingorganisms. The hydrogen atom contains a single electron. When this electron is completelytransferred to another atom (not just shared with another as in covalent bonds), only the hydrogennucleus (essentially a single proton) remains. Any compound that releases H
+
ions (protons) whendissolved in solution is called an
acid
. An acid is classified as strong or weak depending on theextent to which the acid molecule is dissociated in solution. Examples of strong acids that dissociatecompletely in water are hydrochloric acid (HCl) and nitric acid (HNO
3
). Weak acids such ascarbonic acid (H
2
CO
3
) dissociate only slightly. A
base
, or 
alkali
, is a compound that releases OH
-
ions or accepts hydrogen ions in solution. Examples are caustic soda (NaOH) and ammonia water (NH
4
OH) which are common household chemicals. Acids and bases, when concentrated, are severeirritants and will burn the skin and the delicate covering of the eyes and mouth.A
salt
is a compound resulting from the chemical interaction of an acid and a base. For example, common salt, sodium chloride (NaCl), is formed by the interaction of hydrochloric acid(HCl) and sodium hydroxide (NaOH). In water, the HCl dissociates into H
+
and Cl
-
ions, thehydroxide reacts with H
+
to form water and Na
+
and Cl
-
remain as a dissolved form of salt. Thisreaction is shown in the following equation:
HCl+NaOH
 NaCl+H
2
O
8
Fig. 2.1.
Covalent bonds. Two atoms of chlorine form covalent bonds to produce chlorine gas.Cl Cl Cl
2
Na ClNaCl
Fig. 2.2.
Ionic bonds. Atoms of sodium and chlorine form ionic bonds to produce salt.
 
Fig. 2.3.
Hydrogen bonds. Four water molecules bonded by hydrogen bonds (dotted line)
 
acidbasesaltwate
Water.
Water is the predominant chemical component of living organisms. It makes up from 60 – 90% of the protoplasm. Its unique physical properties, which include the ability to solvate a widerange of organic and inorganic molecules, derive from water’s dipolar structure and exceptionalcapacity for forming hydrogen bonds. An excellent nucleophile, water is a reactant or product inmany metabolic reactions. Water has a slight propensity to dissociate into hydroxide ions and protons.A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its center. The twohydrogen atoms and the unshared electrons of the remaining orbitals occupy the corners of thetetrahedron. Water is a dipole, a molecule with electrical charge distributed asymmetrically about itsstructure. The strongly electronegative oxygen atom pulls electrons away from the hydrogen nuclei,leaving them with partial positive charge while its two unshared electron pairs constitute a region of local negative charge. This enables water to dissolve large quantities of charged compounds such assalts.
Organic Compounds
Of the 92 naturally occurring elements, 16 can be found in living things, and only 4 make up99% of living matter. These elements are carbon, hydrogen, oxygen, and nitrogen. In the study of  plants, we will mostly be concerned with organic compounds, that is, compounds that alwayscontain carbon and hydrogen. Five of the most important organic matters found in plants arecarbohydrates, proteins, lipids, nucleic acids, and secondary metabolites.
Carbohydrates.
Glucose and other simple sugars (
monosaccharides
), as well as thei polymers (
polysaccharides
), are called carbohydrates. Carbohydrates generally contain one oxygenand 2 hydrogen atoms for every carbon. For example, glucose and fructose consist of six carbonatoms, 12 hydrogen atoms, and 6 oxygen atoms, and have the formula
C
6
H
12
O
6
. Galactose,mannose, and many other monomers have this same formula, differing only in the arrangement of the elements. Common carbohydrates having different chemical formulas include ribose, xylose,arabinose, and ribose (C
5
H
10
O
5
); deoxyribose (C
5
H
10
O
4
); glucuronic acid and galacturonic acid(C
6
H
12
O
7
); and rhamnose (C
6
H
12
O
5
).Carbohydrates are synthesized from H
2
O and CO
2
by plantsthrough
photosynthesis
(a process on which all life depends because it is the starting point in the formation of food). They provide much of the immediate or ultimate food for animals andare much used by humans (food, fabrics, wood, paper, etc.). Themain role of carbohydrates in the protoplasm is to serve as asource of chemical energy.
Monosaccharides
rarely occur as free sugars in plants;rather they are usually bound to other kinds of molecules or linked together into larger carbohydrates. Two monosaccharides form a
disaccharide
. The mostcommon disaccharide in plants is
sucrose
, which is a glucose sugar and a fructose sugar linked9
Fig. 2.5.
The molecular structure of fructose (left) and glucose (right).
Fig. 2.4.
(a) Water as a polar molecule. (b) Water forming hydration shells around chloride and sodium ions.

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