Basic Chemistry & Biochemistry:

The Chemical Basis of Life

 Part I: Basic Chemistry:
Key Words and Concepts
• Element
• Atom
• Compounds
• Molecule
• Ions
• Acid and Base
• pH
• Diffusion and Osmosis
 Review: Basic Chemistry
• Matter
– anything that has a mass and takes up a space
– all matter is composed of elements

• Element
– is a substance that can not be broken down into simpler
substances. Example: oxygen (O), hydrogen (H), carbon
(C)

– Each element has a set of properties that distinguish it

from from other elements. Example: copper is a bronze
colored solid that conducts heat; oxygen is
odorless/colorless at room temperature.
 Review: Basic Chemistry
• Atom
– is the smallest particle of an element that retains the
characteristics of that element
• Example: all atoms of copper have the properties of
copper

– The center of each atom contains a nucleus composed of

2 different particles: protons (+ charge) and neutrons
(with no charge)
– Moving in regions outside the nucleus is a particle called
the electron (- charge)
Structure of an Atom
 Review: Basic Chemistry
• Atom
– Every atom in an element has an equal number
of protons and electrons, and is electrically
balanced, or neutral

– Every atom has energy, or the ability to do work

– This energy (called chemical energy), comes from

electrons in the atom
 Review: Basic Chemistry
• Compounds
– Substances made from elements are compounds. A
chemical formula shows the kinds and proportions of
atoms in a compound. Ex: NaCl stands for sodium chloride
(salt) from sodium (Na) and chlorine (Cl)

• Molecules
– Are the smallest units of a compound that still have the
properties of that compound. (in H2O, the ratio of H and O
is 2:1, so the formula is H2O)

• Ions
– Electrically charged (+/-) molecules are called IONS
 Review: Basic Chemistry
• Acids and Bases
– Two common groups of compounds that react
in water are ACIDS and BASES

– Acid is a substance that releases hydrogen

ions (protons) when mixed with water
(proton donor)
• Example: CH3COOH --–H20– H+ + CH3COO–

– Base is a substance that separates in water,

forming ions that react with hydrogen ions
(proton acceptor)
• Example: NaOH + CH3COOH --– H20 + CH3COONa
 Review: Basic Chemistry
• pH
– The strength of an acid or base is measured by the pH
scale (0-14, 7 being neutral: water)

– pH of acid solution: 0-7; of basic solution 7-14

– The pH scale is based on powers of 10. Thus Cola with a

pH of 3 is 10 times more acidic than Tomato juice with a
pH of 4

– Living cells are very sensitive to pH of their environment.

Our cells are in a pH of 7.2. If the pH changes by only
2/10th of a point, cells die
 Review: Basic Chemistry
• Diffusion & Osmosis

– Diffusion : movement of a
molecule/substance from a
higher to a lower
concentration

– Osmosis : movement of
water molecules through a
semi-permeable membrane
from a higher to a lower
water concentration
Biochemistry
 What is Biochemistry?
• Biochemistry is the study of the chemical
interactions of living things.

• Biochemists study the structures and

physical properties of biological molecules.
– Often are involved in the manufacture of new
drugs and medical treatments
Elements in Living Organisms

• The most common elements found in

living organisms include:
– Carbon (C)
– Oxygen (O)
– Nitrogen (N)
– Hydrogen (H)
– Phosphorus (P)
– Sulfur (S)
Periodic Table of the Elements (excerpt)
 Properties of Water
• Polar molecule
• Cohesion and adhesion
• High specific heat
• Density – greatest at 4oC
• Universal solvent of life

15
 Polarity of Water
• In a water molecule two hydrogen atoms form
single polar covalent bonds with an oxygen
atom. Gives water more structure than other
liquids
– Because oxygen is more electronegative, the region
around oxygen has a partial negative charge.
– The region near the two hydrogen atoms has a
partial positive charge.
• A water molecule is a polar molecule with
opposite ends of the molecule with opposite
charges.
16
• Water has a variety of unusual properties
because of attractions between these polar
molecules.
– The slightly negative regions of one molecule are
attracted to the slightly positive regions of nearby
molecules, forming a hydrogen bond.
– Each water molecule
can form hydrogen
bonds with up to
four neighbors.

17
Structure
Some Biologically Important H-bonds
 Importance of Hydrogen Bonds

• Source of unique properties of water

• Structure and function of proteins
• Structure and function of DNA
• Structure and function of polysaccharides
• Binding of substrates to enzymes
• Binding of hormones to receptors
• Matching of mRNA and tRNA
“ I believe that as the methods of structural chemistry are further applied to
physiological problems, it will be found that the significance of the hydrogen
bond for physiology is greater than that of any other single structural feature. ”
–Linus Pauling, The Nature of the Chemical Bond, 1939
 HYDROGEN BONDS
• Hold water molecules • Extraordinary Properties that
together are a result of hydrogen
• Each water molecule can bonds.
– Cohesive behavior
form a maximum of 4
– Resists changes in temperature
hydrogen bonds
– High heat of vaporization
• The hydrogen bonds
– Expands when it freezes
joining water molecules – Versatile solvent
are weak, about 1/20th as
strong as covalent bonds.
• They form, break, and
reform with great
frequency

21
 Water as a Solvent

• Water is a good solvent for charged and polar

substances
– amino acids and peptides
– small alcohols
– carbohydrates
• Water is a poor solvent for nonpolar substances
– nonpolar gases
– aromatic moieties
– aliphatic chains
Solvation and Hydration Spheres
Flickering Clusters and Clathrate Cages
 The Hydrophobic Effect
• Refers to the association or folding of
nonpolar molecules in the aqueous solution
• Is one of the main factors behind:
– protein folding
– protein-protein association
– formation of lipid micelles
– binding of steroid hormones to their receptors
• Does not arise because of some attractive
direct force between two nonpolar
molecules
Substrates Must Displace Water to
Bind Enzymes

➔
Approximate Bond Distance,
Strength, kJ/mole nm

12-30 0.3

20 0.25

<40 -

0.4 – 4.0 0.2

 Water Bound to Hemoglobin

Hb purified from water Hb with Water Removed

Osmotic Pressure
Cell Response to Osmotic Pressures
Plants Use Osmotic Pressure
Plants Use Osmotic Pressure

Protection Against Wind

 Moderates Temperatures on Earth
Water stabilizes air temperatures by absorbing heat from warmer air and
releasing heat to cooler air.
Water can absorb or release relatively large amounts of heat with only a slight
change in its own temperature.

Celsius Scale at Sea Level

• What is kinetic energy?
100oC Water boils • Heat?
• Temperature?
37oC Human body • Calorie?
temperature
• What is the difference in
23oC Room temperature
cal and Cal?
0oC Water freezes • What is specific heat?
36
 Specific Heat is the amount of heat that must be
absorbed or lost for one gram of a substance to change
its temperature by 1oC.

Three-fourths of the earth is covered by

water. The water serves as a large heat
sink responsible for:
1. Prevention of temperature fluctuations
that are outside the range suitable for
life.
2. Coastal areas having a mild climate
3. A stable marine environment

37
Evaporative Cooling
• The cooling of a
surface occurs when
the liquid evaporates
• This is responsible for:
– Moderating earth’s
climate
– Stabilizes
temperature in
aquatic ecosystems
– Preventing organisms
from overheating
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 Density of Water
• Most dense at 4oC
• Contracts until 4oC
• Expands from 4oC to
0oC

The density of water:

1. Prevents water from freezing from the bottom up.
2. Ice forms on the surface first—the freezing of the water
releases heat to the water below creating insulation.
3. Makes transition between season less abrupt.
39
– When water reaches 0oC, water becomes locked
into a crystalline lattice with each molecule bonded
to to the maximum of four partners.
– As ice starts to melt, some of the hydrogen bonds
break and some water molecules can slip closer
together than they can while in the ice state.
– Ice is about 10% less dense than water at 4 oC.

Fig. 3.5
 Solvent for Life
• Solution
– Solute
– solvent
• Aqueous solution
• Hydrophilic
– Ionic compounds
dissolve in water
– Polar molecules
(generally) are water
soluble
• Hydrophobic
– Nonpolar compounds
41
 Concentration of a Solution

• Molecular weight – sum of the

weights of all atoms in a molecule
(daltons)
• Mole – amount of a substance that
has a mass in grams numerically
equivalent to its molecular weight
in daltons.
• Avogadro’s number – 6.02 X 1023
– A mole of one substance has the
same number of molecules as a mole
of any other substance.

42
 Molarity
The concentration of a material in solution is called its molarity.

A one molar solution has one mole of a substance dissolved in one liter of
solvent, typically water.

Calculate a one molar solution of sucrose,

C12H22O11.
12 x12 = 144 For a 2M solution?
C = 12 daltons
1 x 22 = 22 For a .05 M solution?
H = 1 dalton
16 x 11 = 176 For a .2 M solution?
O = 16 daltons
342

43
 Dissociation of Water Molecules
• Occasionally, a hydrogen atom shared by two
water molecules shifts from one molecule to the
other.
– The hydrogen atom leaves its electron behind and is
transferred as a single proton - a hydrogen ion (H+).
– The water molecule that lost a proton is now a
hydroxide ion (OH-).
– The water
molecule with
the extra proton
is a hydronium
ion (H3O+).
• A simpler way to view this process is that a water
molecule dissociates into a hydrogen ion and a
hydroxide ion:
– H2O <=> H+ + OH-
• This reaction is reversible.
• At equilibrium the concentration of water
molecules greatly exceeds that of H+ and OH-.
• In pure water only one water molecule in every
554 million is dissociated.
– At equilibrium, the concentration of H+ or OH- is
10-7M (25°C) .
45
 Acids and Bases
• An acid is a substance that
increases the hydrogen ion
concentration in a solution.
• Any substance that reduces the
hydrogen ion concentration in a
solution is a base.
– Some bases reduce H+ directly by
accepting hydrogen ions.

• Strong acids and bases complete

dissociate in water.
• Weak acids and bases dissociate
only partially and reversibly.

46
 pH Scale
• The pH scale in any aqueous solution :
– [ H+ ] [OH-] = 10-14
• Measures the degree of acidity (0 – 14)
• Most biologic fluids are in the pH range
from 6 – 8
• Each pH unit represents a tenfold
difference (scale is logarithmic)
– A small change in pH actually indicates a
substantial change in H+ and OH-
concentrations.
47
 Problem
How much greater is the [ H+ ] in a solution
with pH 2 than in a solution with pH 6?

Answer:
pH of 2 = [ H+ ] of 1.0 x 10-2 = 1/100 M
pH of 6 = [ H+ ] of 1.0 x 10-6 = 1/1,000,000 M
10,000 times greater

48
 Buffers
• A substance that eliminates large sudden changes
in pH.
• Buffers help organisms maintain the pH of body
fluids within the narrow range necessary for life.
– Are combinations of H+ acceptors and donors
forms in a solution of weak acids or bases
– Work by accepting H+ from solutions when they
are in excess and by donating H+ when they
have been depleted.

49
 Acid Precipitation
• Rain, snow or fog with more strongly acidic than pH
of 5.6
• West Virginia has recorded 1.5
• East Tennessee reported 4.2 in 2000
• Occurs when sulfur oxides and nitrogen oxides react
with water in the atmosphere
– Lowers pH of soil which affects mineral solubility
– decline of forests
– Lower pH of lakes and ponds – In the Western
Adirondack Mountains, there are lakes with a pH
<5 that have no fish.

50
Water as a Reactant
 Biochemistry:
Where Chemistry & Biology Meet
• Living things require millions of
chemical reactions just to survive.
• Metabolism = all the chemical reactions
occurring in the body.
• Organic molecules:
– usually associated with living things.
– always contain CARBON.
– are “large” molecules, with many atoms
– always have covalent bonds (share electrons)
 What is Biochemistry
• Biochemistry is the application of chemistry to the
study of biological processes at the cellular and
molecular level.

• It emerged as a distinct discipline around the

beginning of the 20th century when scientists
combined chemistry, physiology and biology to
investigate the chemistry of living systems by:

A. Studying the structure and behavior of the complex

molecules found in biological material and

B. the ways these molecules interact to form cells, tissues and

whole organism
 Principles of Biochemistry
• Cells (basic structural units of living organisms) are highly
organized and constant source of energy is required to maintain
the ordered state.

• Living processes contains thousands of chemical rxns. Precise

regulation and integration of these rxns are required to
maintain life

• Certain important rxns E.g. Glycolysis is found in almost all

organisms.

• All organisms use the same type of molecules: CHO, proteins,

lipids & nucleic acids.

• Instructions for growth, reproduction and developments for

each organism is encoded in their DNA
 Cells
• Basic building blocks of life
• Smallest living unit of an organism
• Grow, reproduce, use energy, adapt, respond to their
environment
• Many cannot be seen with the naked eye
• A cell may be an entire organism or it may be one of billions of
cells that make up the organism

• Basis Types of Cells

 Cells May be Prokaryotic or
Eukaryotic

• Prokaryotes include bacteria & lack a nucleus or membrane-

bound structures called organelles

• Eukaryotes include most other cells & have a nucleus and

membrane-bound organelles (plants, fungi, & animals)
Nucleoid region contains the DNA Contain 3 basic cell structures:
•Cell membrane & cell wall • Nucleus
• Contain ribosomes (no membrane) • Cell Membrane
to make proteins in • Cytoplasm with organelles
their cytoplasm
Two Main Types of Eukaryotic Cells
Characteristic Bio-membranes and Organelles

Plasma Membrane
A lipid/protein/carbohydrate complex, providing a barrier and
containing transport and signaling systems.

Nucleus
Double membrane surrounding the chromosomes and the nucleolus.
Pores allow specific communication with the cytoplasm. The
nucleolus is a site for synthesis of RNA making up the ribosome

Mitochondrion
Surrounded by a double membrane with a series of folds
called cristae. Functions in energy production through metabolism.
Contains its own DNA, and is believed to have originated as a
captured bacterium.

Chloroplasts (plastids)
Surrounded by a double membrane, containing stacked thylakoid
membranes. Responsible for photosynthesis, the trapping of light
energy for the synthesis of sugars. Contains DNA, and like
mitochondria is believed to have originated as a captured
bacterium.
.

Rough endoplasmic reticulum (RER)

A network of interconnected membranes forming channels within the
cell. Covered with ribosomes (causing the "rough" appearance) which
are in the process of synthesizing proteins for secretion or
localization in membranes.
Ribosomes
Protein and RNA complex responsible for protein synthesis

Smooth endoplasmic reticulum (SER)

A network of interconnected membranes forming channels within the
cell. A site for synthesis and metabolism of lipids. Also contains
enzymes for detoxifying chemicals including drugs and pesticides.

Golgi apparatus
A series of stacked membranes. Vesicles (small membrane
surrounded bags) carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks while the proteins are
"processed" to a mature form. Vesicles then carry newly formed
membrane and secreted proteins to their final destinations including
secretion or membrane localization.
Lysosymes
A membrane bound organelle that is responsible for degrading
proteins and membranes in the cell, and also helps degrade materials
ingested by the cell.
 Vacuoles
Membrane surrounded "bags" that contain water and storage
materials in plants.

Peroxisomes or Microbodies
Produce and degrade hydrogen peroxide, a toxic
compound that can be produced during metabolism.

Cell wall
Plants have a rigid cell wall in addition to their cell membranes

Cytoplasm
enclosed by the plasma membrane, liquid portion called cytosol
and it houses the membranous organelles.

Cytoskeleton
Arrays of protein filaments in the cytosol. Gives the cell its
shape and provides basis for movement.
E.g. microtubules and microfilaments.

http://www.biology.arizona.edu copyright © 1997 - 2004..

 Bio-molecules
• Just like cells are building blocks of tissues likewise molecules are
building blocks of cells.
• Animal and plant cells contain approximately 10, 000 kinds of
molecules (bio-molecules)
• Water constitutes 50-95% of cells content by weight.

• Ions like Na+, K+ and Ca+ may account for another 1%

• Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

• Infinite variety of molecules contain C.

• Most bio-molecules considered to be derived from hydrocarbons.
• The chemical properties of organic bio-molecules are determined by
their functional groups. Most bio-molecules have more than one.
 Major Classes of small Bio-molecules

• Building blocks of proteins.

• 1. Amino • 20 commonly occurring.
acids: • Contains amino group and carboxyl group
function groups (behavioral properties)
• R Group (side chains) determines the
chemical properties of each amino acids.
• Also determines how the protein folds and
its biological function.
• Individual amino acids in protein connected
by peptide bond.

• Functions as transport proteins, structural

proteins, enzymes, antibodies, cell
receptors.
 Sugars
• Carbohydrates most abundant organic molecule
found in nature.
• Initially synthesized in plants from a complex series
of reactions involving photosynthesis.
• Basic unit is monosaccharides.
• Monosaccharides can form larger molecules e.g.
glycogen, plant starch or cellulose.

Functions
• Store energy in the form of starch (photosynthesis in
plants) or glycogen (in animals and humans).
• Provide energy through metabolism pathways and cycles.
• Supply carbon for synthesis of other compounds.
• Form structural components in cells and tissues.
• Intercellular communications
 Fatty acids

• Are monocarboxylic acid contains even number C atoms

• Two types: saturated (C-C sb) and unsaturated (C-C db)

• Fatty acids are components of several lipid molecules.
• E,g. of lipids are triacylglycerol, streiods (cholestrol, sex
hormones), fat soluble vitamins.

Functions
• Storage of energy in the form of fat
• Membrane structures
• Insulation (thermal blanket)
• Synthesis of hormones
 Biochemical Reactions
• Metabolism: total sum of the chemical reaction happening in a
living organism (highly coordinated and purposeful activity)
a. Anabolism- energy requiring biosynthetic pathways
b. Catabolism- degradation of fuel molecules and the production of
energy for cellular function

• All reactions are catalyzed by enzymes

• The primary functions of metabolism are:

a. acquisition & utilization of energy
b. Synthesis of molecules needed for cell structure and
functioning (i.e. proteins, nucleic acids, lipids, & CHO
c. Removal of waste products
Even though thousands of rxns sound very large
and complex in a tiny cell:

• The types of rxn are small

• Mechanisms o biochemical rxns are simple
• Reactions of central importance (for energy
production & synthesis and degradation of major cell
components) are relatively few in number
Frequent reaction encountered in biochemical
processes
1. Nucleophilic Substitution
• One atom of group substituted for another

2. Elimination Reactions
• Double bond is formed when atoms in a molecule is removed

3. Addition Reactions:
• Two molecules combine to form a single product.
• A. Hydration Reactions
• Water added to alkene > alcohol (common addition rxn)
4. Isomerization Reactions.
• Involve intramolecular shift of atoms or groups

5. Oxidation-Reduction (redox) Reactions

• Occur when there is a transfer of e- from a donor to
an electron acceptor

6. Hydrolysis reactions
• Cleavage of double bond by water.
 Energy for Cells

• Living cells are inherently unstable.

• Constant flow of energy prevents them from
becoming disorganized.
• Cells obtains energy mainly by the oxidation of bio-
molecules (e- transferred from 1 molecule to another
and in doing so they lose energy)
• This energy captured by cells & used to maintain
highly organized cellular structure and functions
How do complex structure of cells maintain high internal order?

1. Synthesis of bio-molecules

2. Transport Across Membranes

- Cell membranes regulate the passage of ions and molecules
from one compartment to another.

3. Cell Movement
- Organised movement- most obvious characteristics of living
cells. The intricate and coordinated activities required to
sustain life require the movement of cell components.
4. Waste Removal
- Animal cells convert food molecules into CO2, H20 & NH3. If
these not disposed properly can be toxic.
 Macromolecules of Cells
• Macro = large
• 4 types of macromolecules
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
 Macromolecule #1: Carbohydrates

• Sugars and groups of sugars

• Purposes: energy and structure
• Includes three types:
– Monosaccharide (1 sugar – quick energy)
– Disaccharide (2 sugars – short storage)
– Polysaccharide (many sugars – energy
long storage & form structures)
 Macromolecule #1: Carbohydrates

• Polysaccharide Examples:
–Glycogen— stored for future energy
needs. Found in liver, muscle & sperm.
–Cellulose— used to form fibers for plant
structures. Humans can’t digest (fiber).
Most abundant organic molecule.
–Chitin— exoskeletons of some crustaceans
& insects.
Polysaccharides
Polysaccharides
 Macromolecule #2: Lipids
• Insoluble in water (think oil & water)
4 types:
– 1-triglycerides (fats & oils)
• (long-term energy storage, insulation)
– 2-phospholipids (cell membranes)
– 3-steroids (cell signaling)
• cholesterol molecules modified to form sex hormones.
(e.g. testosterone, estrogen, etc.)
– 4-waxes (protection, prevents water loss)
• Used mainly by plants, but also bees, some furry
animals and humans.
Triglycerides
Phospholipids
 Macromolecule #3: Proteins
• Most complicated of all biological molecules.
• Serve the most varied purposes, including:
Support structural proteins (e.g., keratin, collagen)

Enzymes speed up chemical reactions

Transport cell membranes channels, transporters in blood

(e.g., Hemoglobin)
Defense antibodies of the immune system

Hormones cell signaling (e.g., insulin)

Motion contractile proteins (e.g., actin, myosin)

Collage
n
Antibodies
Cellular Transport
 Motion

actin & myosin

fibers in muscles
 Macromolecule #3: Proteins
• The building blocks of proteins are AMINO
ACIDS. There are only 20 types of Amino
Acids.
• There are millions of different proteins, and
they are all built from different
combinations of the 20 amino acids.
• Amino acids join together to form peptides,
polypeptides, and polypeptide chains.
 Macromolecule #4: Nucleic Acids

• Nucleotides: building blocks of nucleic acids.

– Each nucleotide contains
• (a) phosphate molecule,
• (b) nitrogenous base, and
• (c) 5-carbon sugar

• Several types of nucleic acids, including:

– DNA: deoxyribonucleic acid
• Genetic material, double stranded helix
– RNA: ribonucleic acid
• Genetic material, single stranded
– ATP: adenosine triphosphate
• High energy compound
DNA
Nucleotide Structure