Course: BIO 101: Introduction to Biology

Lecture 2
Part 1
Matter and elements
What is your body made of? You might zoom in a level and say that your body is made up of
many different types of cells. However, at the most basic level, your body—and, in fact, all of
life, as well as the nonliving world—is made up of atoms, often organized into larger structures
called molecules.
The term matter refers to anything that occupies space and has mass—in other words, the “stuff”
that the universe is made of. All matter is made up of substances called elements, which have
specific chemical and physical properties and cannot be broken down into other substances
through ordinary chemical reactions. Gold, for instance, is an element, and so is carbon. There
are 118 elements, but only 92 occur naturally. The remaining elements have only been made in
laboratories and are unstable.
Each element is designated by its chemical symbol, which is a single capital letter or a
combination of two letters. Such as C for carbon and Ca for calcium.
The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H),
and nitrogen (N), which together make up about 96% of the human body.
• The periodic table lists all the known elements, grouping together those with similar
properties.
• Most elements are metals, which are shiny and conduct electricity well. Metals include
gold, aluminium and iron which are all solid at room temperature. Mercury is the only
metal that is liquid at room temperature.
• Some elements are non-metals. Most non-metals are gases at room temperature and do
not conduct electricity. Non-metal elements with these properties include oxygen,
hydrogen and chlorine. A few non-metals, such as carbon and sulphur, are in a solid
state at room temperature.
The periodic table
By convention, elements are organized in the periodic table, a structure that captures important
patterns in their behavior. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869,
the table places elements into columns—groups—and rows—periods—that share certain
properties. These properties determine an element’s physical state at room temperature—gas,
solid, or liquid—as well as its chemical reactivity, the ability to form chemical bonds with other
atoms.
Atom
An atom is the smallest unit of matter that retains all of the chemical properties of an element.
For example, Gold atoms cannot be broken down into anything smaller while still retaining the
properties of gold. A gold atom gets its properties from the tiny subatomic particles it's made up
of.
An atom consists of two regions. The first is tiny nucleus, which is in the center of the atom and
contains positively charged particles called protons and neutral, uncharged, particles called
neutrons. The second, much larger, region of the atom is a “cloud” of electrons, negatively
charged particles that orbit around the nucleus. The attraction between the positively charged
protons and negatively charged electrons holds the atom together.
Most atoms contain all three of these types of subatomic particles—protons, electrons, and
neutrons. Hydrogen (H) is an exception because it typically has one proton and one electron, but
no neutrons.
Atomic number, mass number and isotope
Atoms of each element contain a characteristic number of protons. In fact, the number of protons
determines what atom we are looking at (e.g., all atoms with six protons are carbon atoms); the
number of protons in an atom is called the atomic number.
 All atoms of an element have the same atomic number
 Atomic number of hydrogen = 1
 Atomic number of carbon = 6
 Atomic number of sodium= 11
In contrast, the number of neutrons for a given element can vary. Atom that differ only in their
number of neutrons are called isotopes. Together, the number of protons and the number of
neutrons determine an element’s mass number: mass number = protons + neutrons. If you want
to calculate how many neutrons an atom has, you can simply subtract the number of protons, or
atomic number, from the mass number.

• Hydrogen 1 or Protium has 1 proton, 0 neutron

• Hydrogen 2 or Deuterium has 1 proton, 1 neutron
• Hydrogen 3 or Tritium has 1 proton, 2 neutrons

Electrons
• Carry a negative charge
• Repel one another
• Are attracted to protons in the nucleus
 • Move in orbitals
Electron shells and shell model
Atom has a central nucleus containing protons and neutrons, with the electrons in circular
electron shells at specific distances from the nucleus, similar to planets orbiting around the sun.
Each electron shell has a different energy level, with those shells closest to the nucleus being
lower in energy than those farther from the nucleus.
The electrons in an atom are arranged in shells that surround the nucleus, with each successive
shell being farther from the nucleus. Electron shells consist of one or more atomic orbitals.
Electrons in the same hell have the same energy, while electrons in different shells have different
energies.

• First shell
• Lowest energy
• Holds 1 orbital with up to 2 electrons
• Second shell
• 4 orbitals hold up to 8 electrons

The shell closest to the nucleus, 1n, can hold two electrons, while the next shell, 2n, can hold
eight, and the third shell, 3n, can hold up to eighteen.
Specifically, electrons don’t really circle the nucleus, but rather spend most of their time in
sometimes-complex-shaped regions of space around the nucleus, known as electron orbitals.
We can’t actually know where an electron is at any given moment in time, but we can
mathematically determine the volume of space in which it is most likely to be found—say, the
volume of space in which it will spend 90% of its time. This high-probability region makes up an
orbital, and each orbital can hold up to two electrons.

Part 2
Chemical Bonds, Molecules, & Compounds
Chemical bonds hold molecules together and create temporary connections that are essential to
life. Types of chemical bonds including covalent, ionic, and hydrogen bonds.
• Bond is union between electron structures of atoms
• Atoms bond to form molecules
• Molecules may contain atoms of only one element - O2
• Molecules of compounds contain more than one element - H2O
•
Why form chemical bonds? The basic answer is that atoms are trying to reach the most stable
(lowest-energy) state that they can. Many atoms become stable when their valence shell is filled
with electrons or when they satisfy the octet rule (by having eight valence electrons). If atoms
don’t have this arrangement, they’ll “want” to reach it by gaining, losing, or sharing electrons via
bonds.
Ionic bonds
Some atoms become more stable by gaining or losing an entire electron (or several electrons).
When they do so, atoms form ions, or charged particles. Electron gain or loss can give an atom a
filled outermost electron shell and make it energetically more stable.
Forming ions
Ions come in two types. Cations are positive ions formed by losing electrons. For instance, a
sodium atom loses an electron to become a sodium cation, Na+. Negative ions are formed by
electron gain and are called anions, for example, Cl-
When one atom loses an electron and another atom gains that electron, the process is called
electron transfer. Sodium and chlorine atoms provide a good example of electron transfer.
Sodium (Na) only has one electron in its outer electron shell, so it is easier (more energetically
favorable) for sodium to donate that one electron than to find seven more electrons to fill the
outer shell. Because of this, sodium tends to lose its one electron, forming Na+. Chlorine (Cl),
on the other hand, has seven electrons in its outer shell. In this case, it is easier for chlorine to
gain one electron than to lose seven, so it tends to take on an electron and become Cl -.
When sodium and chlorine are combined, sodium will donate its one electron to empty its shell,
and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and
have complete outermost shells. Because the number of electrons is no longer equal to the
number of protons, each atom is now an ion and ionic bonds are formed between these ions with
opposite charges.

Covalent bonds
Another way atoms can become more stable is by sharing electrons (rather than fully gaining or
losing them), thus forming covalent bonds. Covalent bonds are more common than ionic bonds
in the molecules of living organisms.
For instance, covalent bonds are key to the structure of carbon-based organic molecules like our
DNA and proteins. Covalent bonds are also found in smaller inorganic molecules, such as H 2O,
CO2. One, two, or three pairs of electrons may be shared between atoms, resulting in single,
double, or triple bonds, respectively. The more electrons that are shared between two atoms, the
stronger their bond will be.
As an example of covalent bonding, let’s look at water. Each hydrogen shares an electron with
oxygen, and oxygen shares one of its electrons with each hydrogen:
Polar covalent bonds
There are two basic types of covalent bonds: polar and nonpolar. In a polar covalent bond,
the electrons are unequally shared by the atoms and spend more time close to one atom than the
other. Because of the unequal distribution of electrons between the atoms of different elements,
slightly positive (δ+) and slightly negative (δ–) charges develop in different parts of the
molecule.
In a water molecule (above), the bond connecting the oxygen to each hydrogen is a polar bond.
Oxygen is a much more electronegative atom than hydrogen, meaning that it attracts shared
electrons more strongly, so the oxygen of water bears a partial negative charge (has high electron
density), while the hydrogens bear partial positive charges (have low electron density).

Nonpolar covalent bonds

Nonpolar covalent bonds form between two atoms of the same element, or between atoms of
different elements that share electrons more or less equally. For example, molecular oxygen O2 is
nonpolar because the electrons are equally shared between the two oxygen atoms.
Hydrogen bonds
In a polar covalent bond containing hydrogen (e.g., an O-H bond in a water molecule), the
hydrogen will have a slight positive charge because the bond electrons are pulled more strongly
toward the other element. Because of this slight positive charge, the hydrogen will be attracted to
any neighboring negative charges. This interaction is called a hydrogen bond.
Hydrogen bonds are common, and water molecules in particular form lots of them. Individual
hydrogen bonds are weak and easily broken, but many hydrogen bonds together can be very
strong.
Hydrophilic & Hydrophobic Substances
Nonpolar molecules that repel the water molecules are said to be hydrophobic; molecules
forming ionic or a hydrogen bond with the water molecule are said to be hydrophilic. This
property of water was important for the evolution of life. Hydrophobic interaction plays the most
critical roles in the formation of the lipid bilayer of the cell membrane and the folding of proteins
and nucleic acids; therefore, hydrophobic interaction is the foundation for the existence of life.
Why Ice Floats
Ice floats on water because it is less dense than water.
When water freezes into its solid form, its molecules are able to form more stable hydrogen
bonds locking them into positions. Because the molecules are not moving, they're not able to
form as many hydrogen bonds with other water molecules. This leads to ice water molecules not
being as close together as in the case of liquid water, thus reducing its density.
Most substances in their solid form are denser than their liquid forms. The opposite is true in
water. This property of water is somewhat unusual and rare.
Part 4
The pH and pH scale

 pH is calculated as the negative log of a solution’s hydrogen ion concentration:

An acidic solution has a high concentration of hydrogen ions (H+) greater than that of
pure water. A basic solution has a low H+ concentration, less than that of pure water.
The pH scale is used to rank solutions in terms of acidity or basicity (alkalinity). Since the scale
is based on pH values, it is logarithmic, meaning that a change of 1 pH unit corresponds to a ten-
fold change in H+ ion concentration. The pH scale is often said to range from 0 to 14, and most
solutions do fall within this range, although it’s possible to get a pH below 0 or above 14.
Anything below 7.0 is acidic, and anything above 7.0 is alkaline, or basic.
H+ concentration shifts away from neutral when an acid or base is added to an aqueous (water-
based) solution. For our purposes, an acid is a substance that increases the concentration of
hydrogen ions H+ in a solution, usually by donating one of its hydrogen atoms through
dissociation. A base, in contrast, raises pH by providing hydroxide OH-or another ion that scoops
up hydrogen ions and removes them from solution.
The stronger the acid, the more readily it dissociates to generate H +. For example, hydrochloric
acid (HCl) completely dissociates into hydrogen and chloride ions when it is placed in water, so
it is considered a strong acid. The acids in tomato juice or vinegar, on the other hand, do not
completely dissociate in water and are considered weak acids. Similarly, strong bases like
sodium hydroxide (NaOH) completely dissociate in water, releasing hydroxide ions (or other
types of basic ions) that can absorb H+.

Buffers
Most organisms, including humans, need to maintain pH within a fairly narrow range in order to
survive. For instance, human blood needs to keep its pH right around 7.4, and avoid shifting
significantly higher or lower – even if acidic or basic substances enter or leave the bloodstream.
Buffers, solutions that can resist changes in pH, are key to maintaining stable H + concentrations
in biological systems. When there are too many H+ ions, a buffer will absorb some of them,
bringing pH back up; and when there are too few, a buffer will donate some of its own H +ions to
reduce the pH. Buffers typically consist of an acid-base pair, with the acid and base differing by
the presence or absence of a proton (a conjugate acid-base pair).
Types of Buffer Solutions
• Acidic buffers are solutions that have a pH below 7 and contain a weak acid and one of
its salts. For example, a mixture of acetic acid and sodium acetate acts as a buffer
solution with a pH of about 4.75.
• Alkaline buffers, on the other hand, have a pH above 7 and contain a weak base and one
of its salts. For example, a mixture of ammonium chloride and ammonium hydroxide acts
as a buffer solution with a pH of about 9.25.