1.

1 Fundamental Chemistry of Life

-Element is a pure substance that cannot be broken down into simpler substances
using ordinary chemical or physical techniques.
-Smallest particle of an element is an atom.
-Elements differ in atomic structure
-Organic molecules are composed of Carbon, Hydrogen, and Oxygen. Often include
hydrogen
-Other elements are often found as ions or in inorganic compounds, makeup 4% of
all elements in the human body
-Rest if elements are less than 0.1%, and are called trace elements, ie. Fe and I
-Deficiency can lead to health issues.

Atomic Structure

-The number of protons in atoms defines its elemental identity. Has no net charge
because the number of protons = the number of electrons.
-The atomic number of atoms= the number of protons.
-Mass number= number of protons + neutrons

₁₆K³⁶
16=atomic number
36=mass number

Isotopes and Radioisotopes

Isotope- a form of an element that differs in its number of neutrons, behave the
same as isotopes of the same element given that they have the same charge
-Nuclei of some isotopes of an element are unstable and tend to break down; giving
off particles of matter that can be detected as radioactivity.
-Decay process transforms an unstable, radioactive isotope called a radioisotope into
an atom of another element.
-Radioisotope- a radioactive isotope of an element.
-Radioactive decay continues at a steady rate, with a constant proportion of
radioisotope atoms breaking down during a given time interval. The rate of decay is
independent of reactions or the environment.
-Used in medicine, biology.
-It’s easy to find in cells given their radioactivity and radioactive signals.
-Used in the new field of nuclear medicine to help with the diagnosis and treatment
of disorders.
 Electron Arrangements

-The arrangement of electrons determines the

chemical properties of atoms since they are
involved in chemical reactions.
-They move around the nucleus in something
called orbitals.
-Basically, remember this chart and Hund’s law.

Value of L 0 1 2 3

Letter Used s p d f

Name sharp principal diffuse fundamental

-Valence electrons- an electron in the outermost energy level or shell of an atom.

-Atoms with fewer electrons on valence shells are more reactive, remember noble
gas properties and their valence shells.
-Unfilled valence shell atoms have a stronger tendency to react with other atoms,
participate in reactions. All elements found in the human body have unfilled valence
shells.
-Underfilled atoms transfer electrons or share them and form molecules, ie. sodium
chloride. Sharing of electrons by C, H, O, and N (in other organic molecules) lies the
formation of countless chemical bonds that hold biological molecules together.

Chemical Bonds

-Ionic Bond- happens between a nonmetal and a metal ion, transfer of electrons.
-Cation is a positive ion, and the anion is a negatively charged ion.
-Covalent Bonds-happens between nonmetal ions, they share electrons.
-The strength of covalent bonds depends on the electronegativity of the atoms.
-There’s also VSEPR theory, lol I did a whole CPT about this, valence electron pairs will
repel each other, and move as far as possible from each other. If there are lone pairs
on the central atom, the molecule will be polar, if there isn’t any, and molecules have
no net dipole, the molecule will be nonpolar.
Polar Molecules

-The electronegativity difference determines whether or not a molecule is

polar-covalent or nonpolar-covalent.
-Polar covalent bond- a bond between two atoms, made up of unequally shared
electrons
-Polarity- partial positive or negative charge at the ends of a molecule.
-Polar molecules attract and align themselves to other polar molecules, and are
soluble in water, as water is also a polar molecule.
-Nonpolars like fats or oils (hexane), will not.

Intermolecular forces

-Intermolecular forces are the forces between molecules. Also known as van der
Waals forces.
-Hydrogen bond: the attractive force between a partially positively charged hydrogen
atom and a partially negatively charged atom in another molecule
-Occur between H atoms and highly electronegative atoms like N, O, and/or F
-Individual H-bonds are weak compared to ionic and covalent bonds but more
significant in large quantities.
-Lend stability to 3D structures of large molecules like proteins.
-Higher surface tension, capillary action
-Weaker attractive force makes them much easier to break than covalent or ionic
bonds, especially with an increase of temperature, which increases the movement of
the molecules.
-Break extensively at 45 degrees, rapidly overcome at 100

-Other intermolecular forces include dipole-dipole bonds and London dispersion

forces
-London dispersion can occur between any molecules, while dipole-dipole occur
between two nonmetal molecules, say CH4.
-Larger molecule= larger van der Waals forces
-Globular shaped molecules such as starches have fewer accessible atoms for van
der Waals forces and therefore tend to form less rigid solids

Chemical Reactions

-Thousands of chemical reactions occur inside cells, they have one thing in common;
they involve the breaking and formation of chemical bonds thereby changing the
arrangements of atoms and ions.
-Four major types: dehydration, hydrolysis, neutralization, and redox reactions.
-Dehydration reaction: a chemical reaction in which subunits of a larger molecule
are joined by the removal of water; also called a condensation reaction
-The most common method used by cells to join smaller molecules and assemble
extremely large macromolecules, such as complex carbohydrates and proteins

-Hydrolysis reaction: a chemical reaction in which water is used as a reactant to split

a large larger molecule into smaller subunits, basically, the addition of water to a
molecule to make two molecules from one

-Neutralization reaction: a reaction which an acid

and a base combine to create a salt and water

Acid + Base -> Water + Salt

-Redox reaction: an electron transfer reaction. 4th

type of reaction, where electrons are lost from one atom and gained by another
atom.
-Oxidation reaction is a reaction in which a molecule loses electrons while a
reduction reaction is a reaction where a molecule gains electrons.
1.2 Water: Life’s Solvent

-60% of human weight comes from water; 70% of the brain, 90% of lungs, 22% of
bone tissue comes from water
-All cellular processes occur in water since cellular components are dissolved,
suspended, and, surrounded by water.

Properties of Water

-Most abundant liquid on Earth and is known as “universal solvent”

-Water molecules are special because of their size, shape, polar structure, and ability
to associate with each other through hydrogen bonding
-Form readily in ice and liquid water, an average of 3.4 H-bonds with neighbouring
H2O molecules, forms a water lattice.
-Molecules the size of water are mostly gases, but the lattice that holds water
constantly breaks and reforms, which allows water molecules to slip past another to
reform lattice
-This is why water has fluid properties
-In ice, the lattice is a rigid crystalline structure, forms 4 H-bonds, has greater spacing
which makes it 10% less dense than liquid H2O.
-Because of its stabilizing H-bond lattice, water has a high specific heat capacity, the
amount of thermal energy to raise 1g of a substance by 1°.
As thermal energy flows into a sample of water, much of it is absorbed by the process
of breaking hydrogen bonds; so temp. of water increases relatively slowly as t.e. is
added.
-Specific heat: the amount of thermal energy required to raise the temperature of a
given quantity of a substance by 1°.
-Without H-bond lattice, water would boil at -81°, making it as a gas. Life wouldn’t
exist like this.
-Lattice lets H2O stay really close together- in something called cohesion; related to
surface tension.
-H2O molecules will form H-bonds on all sides except the side touching air, which
creates an imbalance in bonding, which produces a force that places the surface
water molecules under tension and makes them more resistant to separation than
the molecules below the surface
-Allows insects to walk on water
-H2O can also form H-bonds with other polar molecules, called adhesion.

-(see table 1 on page 20 for a summary of properties of water)

Aqueous Solutions

-H2O molecules are small and polar, which helps them readily surround polar and
charged molecules and ions of other substances.
-Surface coat of water is called a hydration shell; it reduces the attraction between
ions of another substance and promotes their separation. This separation allows the
substance to go into solution
-As molecules and ions dissociate, water molecules surround them forming the
hydration shell; tends to prevent ions from re-associating
-Result is an aqueous solution in which water is the solvent and the molecules or
ions of the other substance are the solute
-Polar molecules or charged ions that are strongly attracted to water are hydrophilic
molecules, whereas nonpolar molecules that are not strongly attracted to water are
called hydrophobic molecules.
-As the solvent inside the cells and in our blood, water dissolves thousands of solutes
that are necessary for life. Since they are dissolved, they can float and collide,
allowing chemical reactions to occur.

Ionization and pH

-Most critical property of water of H-bond properties is its ability to separate or

dissociate into ions.
-Pure water is more than just H20 molecules, at 25 degrees, water is a mix of H3O
and H+ ions.
-When two H2O molecules react one molecule transfers a hydrogen ion to the other,
therefore H+ and H3O form.
-This process is called the autoionization of water: the process in which a molecule
spontaneously dissociates into ions.

Acids and Bases

-When [H3O] is greater than [OH], the solution has the properties of an acid.
-Acidic solutions are sour, conduct electricity, and turn BLUE paper RED
-Acids increase [H3O] when dissolved in water, and in high enough concentrations,
will cause a chemical burn
- HCL + H2O -> H3O + Cl

-When [OH] is greater than [H3O], the solution has the properties of a base.
-They taste bitter, feel slippery, conduct electricity and change RED paper BLUE,
-Increase the [OH] in aqueous solutions, can happen in two ways
-Could dissociate when added to water
- NaOH -> Na + OH
-Or conjugate base and conjugate acid
- NH3 + H2O -> NH4 + OH
-pH means the power of hydrogen, ranges from 0 to 14 on increments of 10. (so if the
pH of 2 is compared to a pH of 1, pH 2 is 10 times greater)
-based on logarithms, pH = -log₁₀[H⁺]
-pH = 7<, solution is basic, pH = 7>, solution is acidic
-both pH within cells and external environment are important for the optimal
functioning of life.
-change of 0.1 or 0.01 in the pH level of a cell can highly affect biological reactions; a
small change in the pH of surrounding proteins causes structural changes that can
alter the functions of the proteins.
-Correct blood pH is crucial for maintaining good health, and pH in the stomach is
important for proper digestion and defense against micro-organisms.
-pH of water in the environment is also important for the survival of most organisms
on Earth, the changing pH of water on Earth kills coral reefs, one of the richest
ecosystems on the planet.

Strong and Weak Acids and Bases

-The strength of an acid or bases depends on the degree to which it ionizes when
dissolved in water.
-A strong acid, such as HCl, and a strong base, such as NaOH, are completely
dissociated in an aqueous solution. This means that all the molecules of HCl release
H⁺ ions that interact with water to form H3O, and all the OH ions are released from
NaOH and increase the [OH] of the water in which they are dissolved.
-Oppositely, weak acids and bases partially ionize in water.
-example: CH3COOH + H2O <-> CH3COO + H3O
-only 1.3% of the acetic acid CH3COOH, a weak acid, dissociates in water
-weak base or acid in water is a reversible reaction. When 1.3% of the acetic acid is
dissociated in water, equilibrium is reached
-The forward and backward reaction rates are the same, so the concentrations of all
the entities of the solution remain constant.
-Most acids and bases involved in biochemical reactions are weak

Neutralization Reactions and Buffers

-When acid and a base react with each other, they form a salt and water. This is
known as a neutralization reaction
-ie. NaOH + HCl -> H2O + NaCl
-Living organisms have some control over the internal pH of their cells by using
buffers.
-Buffer: a chemical that compensates for pH changes in a solution by accepting or
donating H⁺ ions.
-When a biological reaction releases excess H⁺ ions, buffers combine with the H⁺ ions
so they are no longer free in the solution.
-On the other hand, if the H⁺ ions in a solution decrease, buffers will release H⁺ ions.
-The buffering mechanism that helps to maintain a healthy blood pH from 7.35 to
7.45 is a good example of how buffers work in the body.
-In humans and mammals, buffers systems are based on a weak acid,
H2CO3(carbonic acid), which helps to main proper pH blood levels.
- H2CO3 -> HCO3 + H⁺
- H⁺ + HCO3 -> H2CO3
-Back and forth adjustments of too much or too little H⁺ ions of the buffer system
help to keep human blood within its normal pH range.
1.3 The Carbon Chemistry of Life

-Carbon makes up the base of every organic molecule, including the molecules
within cells. It is unparalleled in the biological world in its ability to form the
backbone of large diverse molecules
-This arises from carbon’s bonding properties- it can form rings and chains, as it has
four electrons on its valence shell- as a result carbon forms multi-ringed molecules,
diamonds, and nanotubes

Carbon Chains: The Backbone of Biochemistry

-As well as forming bonds with other atoms (like H, N, O, and S) carbon atoms bind to
each other to form long chains, rings or branched structures.
-Molecules consisting only of carbon atoms bonded to hydrogen atoms are called
hydrocarbons
-The chain of carbon atoms in a biochemical molecule is the carbon skeleton of the
molecule; they can be linear or branched or form a closed ring shape, ie. cyclohexane
-Many carbon contain rings can produce polymers, ie. the string of sugar molecules
that make up a complex sugar chain.
-Carbon can form double and triple bonds with itself on carbon chains (remember
alkenes and alkynes)
-No limit to the length of carbon chains, but rarely used by living organisms
-Other elements can add on to these chains, give different functional properties.
-Fall into four major groups; carbohydrates, lipids(fats), proteins, and nucleic acids.

Functional Groups

-Carbohydrates, lipids,
proteins, and nucleic acids
undergo synthesis and
degradation in living
organisms through
interactions between small
reactive groups of atoms
that are, themselves, part
of these large biochemical
molecules.
-The small reactive groups
are called functional
groups; either ionic or
strongly polar
-functional group: a group of atoms that affects the function of a molecule by
participating in chemical reactions

Characteristics of Functional Groups

-They are either ionic or strongly polar; makes them strongly attracted to polar
molecules, including water.
-Summarizing, the chemical or physical properties of a large biological molecule are
influenced by the polar and ionic characteristics of its functional groups.
-Forces of attraction created by ionic and polar groups are necessary in a chemical
reaction in order to form new bonds.
-Obviously, the nonpolar parts of a large biological molecule do not attract other
molecules.
-Polar groups often act as “handles”; they can influence the physical and chemical
properties of a molecule
-Ethane vs Ethanol = ethanol has a hydroxyl functional group so it is polar, dissolves
in water, is a liquid at room temp, and can be dissolved in the cell cytosol, where it
can be used as a fuel, whereas ethane cannot as it is a gas at room temp and won’t
dissolve in the cell cytosol
-The carboxyl group acts as an acid, releasing H+ ions to become negatively charged
-The amino group, (amino acids are proteins or something lol) acts as a base,
accepting H+ ions to become positively charged
-The phosphate group acts as an acid, releasing H+ ions to become negatively
charged

Dehydration and Hydrolysis Reactions

-Hydrolysis: larger molecules react with water and break down into smaller subunits.
-Dehydration: water is removed from subunits and they form one big molecule, or a
larger molecule if you want to be a nerd
1.4 Carbohydrates and Lipids

-Although both of these molecules can be quite large, they are relatively simple
molecules.
-They are mostly composed of carbon, hydrogen, and oxygen, arranged in many
different ways
-They perform many complex functions in cells; best known as energy sources in the
body, but they do more.
-Carbs play a role in structural support and cell-to-cell communication, they are the
raw material that is used to build other important molecules, such as amino acids,
lipids, and nucleic acids.
-Lipids play an important structural role in cells; all biological membranes are
composed of lipids, as well as hormones, some vitamins, and defence mechanisms
-Also provide insulation for nerve cells and have waterproofing qualities
-Functional groups on carbs and lipids influence their properties and functions

Carbohydrates

-They are biomolecules that consists of carbon, oxygen, and hydrogen

-Term comes from carbo- meaning carbon, and -hydrate meaning water.
-In photosynthesynthesizing plants and organisms, CO2 and water molecules are
used as raw materials to build carbohydrates
-Plants and algae produce millions of tonnes
-Used as energy sources in organisms, building materials, and used for cell
communication
-Found in fruits, vegetables, and grains

Monosaccharides

-The simplest type of a carbohydrate is a monosaccharide

-They consist of a single sugar unit; a building block for more complex carbohydrates
-Generally have a combination of 1 carbon: 2 hydrogens: 1 oxygen or CnH2nOn where
n represents the number of carbon atoms
-Glucose is most used monosaccharide; plants produce it during photosynthesis; it
provides energy for countless functions in plants and animals
-Monosaccharides that contain 3 carbons(triose), 5 carbons(pentose), or 6
carbons(hexose) are the most common in living organisms
-Though they can occur in linear form when formed in water, monosaccharides with
5 or more carbon atoms fold back and form a ring
-It occurs through a reaction of two functional groups in the same monosaccharide
-Once again, seen in glucose given that it has a carbonyl and a hydroxyl group.
-When it forms a ring, there are two outcomes possible at position 1?- these are
called isomers
-Means that molecules have the same chemical formula as other molecules, but it
differs as it has a different atom arrangement, automatically meaning it has different
properties(ie. Alpha-glucose is digestible in humans, beta-glucose isn’t)
-They also typically have polar functional groups; makes them polar, hydrophilic
molecules and means that small sugars are highly soluble in water.
-Monosaccharides are the sweetest, in taste lol you bozo
-As the size of the link of monosaccharides increases, sweetness increases

Disaccharides

-Disaccharides consists of two monosaccharides joined together by a dehydration

reaction
-Bonds of this type that link monosaccharides into larger carbohydrates are called
glycosidic bonds; these are bonds between two monosaccharides
-ie. A glycosidic bond forms between a-glucose and fructose monosaccharides,
resulting in the disaccharide sucrose.
-Linkages are designated as α or β, depending on the orientation of the -OH group
bonded to the 1-carbon
-Linkage in maltose is alpha, linkage in lactose is beta linkage
-They(disaccharides) contain the same functional groups as monosaccharides, which
makes them hydrophilic and polar; they are easily dissolved in water
-Sap is sucrose dissolved in water

Complex Carbohydrates: Polysaccharides

-Hundreds to thousands of monosaccharides can link together to form a complex

carbohydrate. They are molecules that are composed of hundreds to thousands of
monosaccharides linked together; an essential part of nutrition and a valuable
energy source
-Some complex carbohydrates are important for energy storage in cells, while others
are essential for structural support
-Starch and glycogen are examples of storage carbohydrates
-Cellulose and Chitin are examples of structural complex carbohydrates
-A polysaccharide molecule is a molecule that contains many linked
monosaccharides, with many subunits joined by glycosidic linkages
-It is a very large molecule assembled by the covalent linkage of smaller subunit
molecules.
-The dehydration synthesis reactions that assemble polysaccharides are examples of
polymerization
-Polymerization is the process in which small subunits are linked to form a large
molecule
-Those small subunits are called monomers, which link together to form polymers,
hence the term “polymerization”
-The linkage of non-identical units creates highly diverse and varied biological
molecules
-Many kinds of polymers are found in cells, not just polysaccharides. Ie. DNA is a type
of polymer
-The most common polysaccharides are plant starches, glycogen, and cellulose
-They assemble from hundreds or thousands of glucose units
-Cellulose is the main component of plant cell walls and it is the most abundant
organic molecule on Earth
-They have very large numbers of polar OH groups
-Since they are long, straight, and have very large numbers of polar OH groups, this
allows them to assemble side by side and form 100s and 1000s of H-bonds.
-These H-bonds is what gives cellulose fibers great strength
-Polysaccharides may be linear unbranched molecules, or they may contain
branches in which side chains of sugar units attach to the main chain
-They are very polar and hydrophilic
-Since they are such huge molecules, they attract water but cannot dissolve in it
-Think of paper towels which is why they clean up spills but can’t be dissolved in it, as
the paper towel is made up of cellulose fibers
-Table 1

Lipids

-The term lipid is a general term for a variety of non-polar biological molecules
-Mostly composed of hydrogen, carbon, and lesser amounts of oxygen
-Smaller than complex carbohydrates, so they are not considered to be
macromolecules
-They are not polymers of defined monomeric subunits
-They do not dissolve in water as they are generally nonpolar
-Insolubility in water contributes to their ability to form cell membranes.
-Some lipids are stored by cells, to be used as an energy source
-Other lipids serve as hormones that regulate cellular activities and as vitamins
-Fall into five categories:
-Fatty acids
-Fats
-Phospholipids
-Steroids
-Waxes

Fatty Acids

-The structural backbone of most lipids is derived from fatty acids

-They consist of molecules that consist of a carboxyl group and a hydrocarbon chain
-The carboxyl group gives the fatty acid its acidic properties
-Fatty acids in living organisms contain 4 or more carbons in their hydrocarbon chain
-Most common have even-numbered chains from
14 to 22 carbons
-As chain length increases, they become less
water-soluble
**-If the hydrocarbon chain of a fatty acid binds the
maximum possible number of H-atoms, and if all
the carbons are linked to each other with single
bonds, the fatty acid is saturated
-If there are double bonds in the fatty acid chain,
then it is unsaturated; meaning that the carbon
chain has more potential to form more bonds with
hydrogen
-One double bond=monounsaturated, more than one=polyunsaturated
-Presence of double bond causes it to bend, it has a “kink”

Fats

-A fat is a lipid that is made from two molecules: a fatty acid and a glycerol molecule
-1-3 fatty acid chains are joined to a single glycerol molecule
-through dehydration synthesis between -OH groups on glycerol and carboxyl group
on fatty acid
-Triglyecrides are the most popular fats: they have 3 fatty acid chains linked to 1
glyceorl molecule
-They can have either identical or different fatty acid chains linked to the glycerol in
fats
-Different organisms usually have distinctive combinations of fatty acids in their
tryglicerides
-Animals have lard and butter, only contain saturated fatty acids so they are called
saturated fats
-Plants have olive oil or canola oil, only contain unsaturated fatty acids so they are
called unsaturated fats
-Longer the chain, less fluid fats and fatty acids get
-Saturated longer than fatty acid so will be solid at room temp, fatty acid chains that
have kinks are bent and cannot be packed tightly, so they are more fluid and stay
liquids at room temp.
-Gram for gram, triglycerides yield than twice as much energy as carbohydrates;
excellent source of energy in the diet
-Unsaturated healthier than saturated; saturated gives an elevated risk of heart
attack

Phospholipids

-Cells could not exist without phospholipids

-They are lipids that are composed of saturated fatty acids with single bonds in their
hydrocarbon chain
-Primary lipids of cell membranes
-Triglycerides, glycerol forms backbone of the molecules
-A phospholipid has a polar end and a nonpolar end. The nonpolar end consists of
glycerol bonded to two fatty acids.
-Molecules that contain both polar and nonpolar ends are called amphipathic
molecules
-Head is polar and hydrophilic, the tail is nonpolar and hydrophobic
-Make up the lipid bilayer of cell membranes, an important structural feature of cells
-Hydrophilipc end faces outwards towards the water, the hydrophobic fatty acids
face inwards towards each other

Steroids

-Steroids are lipids that are composed of 4 carbon rings

-Small differences in side groups distinguish one steroid from another
-Most abundant steroids, sterols, have an -OH group at one end
-Even though they are completely hydrophobic, the single OH gives one end a very
slightly hydrophilic character
-Bc of that they have dual solubility properties
-Like phospholipids, tend to assume positions in cells that satisfy these properties
-Cholesterol is a steroid
-Beneficial as it converts into a number of compounds, incl. Vitamin D
-Too much is unhealthy
-Anabolic steroids are illegal in sports, help with athletes and bodybuilders
-Sex hormones are steroids, testosterone, estrogen, etc.

Waxes

-Large lipid molecules made up of long fatty acid chains linked to alcohols or carbon
rings
-Hydrophobic, extremely nonpolar, soft solids over a wide range of temps
-Ideal for waterproofing on plants and animals
-Cutin is a type of wax produced by plant cells to form waterproof coat that
conserves water and acts as a barrier to infections and diseases