CHAPTER 1: Introduction AGRICULTURE

•   Herbicides and Pesticides 

BIOCHEMISTRY •   Transgenic crops
 Study of chemical substances found
in living organisms and the chemical INDUSTRY
interactions of these substances with  Synthesis
each other   Detoxification
 Compounds, chemical reactions,
and molecular interactions involved Attributes of Life
in production maintenance and 1. Adaptation - body structures
reproduction of living organisms (physiology or morphology) that
 How cells manufacture the make living things fit to live in its
molecules needed for life and how habitat
the chemical reactions by which life 2. Growth and repair - ability to add
is maintained occur new tissue and repair or replace
 All living things make use of same damaged parts
type of biomolecules and use 3. Metabolism - biological and chemical
energy. Hence studied through activities that provide energy.
methods of chemistry and physics Catabolism vs Anabolism 
 Fundamental similarity of cells and 4. Reproduction - beget offsprings,
speculating on origin of life ensuring propagation and
 Cells and biomolecules arisen from continuance of species
very simple molecules such as H2O, 5. Complexity and organization -
CH4, NH3, N2 and H2 complexity refers to elaborate
 Field of biochemistry draws many structures needed to carry out
disciplines specific function while organization
 Answer questions on molecular is to put structures in order to
nature of life function efficiently.
6. Regulation - keep functions under
Biochemistry is a Research Discipline control (hormones, enzymes)
Applicable to Real World 7. Characteristic size and shape -
Most diseases have a biochemical basis unique morphology i.e., ant can
•   Diagnose and monitor diseases  never become as big as elephant
 Transaminase levels  8. Response to stimuli - respond
 Hemoglobin breakdown product - favorably or unfavorably to its
bilirubin  environment 
 Measure isoforms of Lactate 9. Locomotion - move on its initiative,
dehydrogenase to determine extent under its control
of myocardial infarctions 10. Variation and change - no two
•   Designer Drugs organisms are alike and no
 New and Improved Antibiotics organism remains unchanged
 New and Improved chemotherapy
agents
 Protein Diseases 
 Health maintenance (nutrition) -
intake of vitamins, amino acids, fatty
acids, various minerals and water
(BIOCHEMISTRY!!!)
 protein structure and function---
normal vs. sickle cell hemoglobin
 Alkaptunoria, albinism, pentosuria ---
inborn errors of metabolism
 Molecular mechanisms of
Oncogenes, and tumor suppressing
genes for normal cell growth
 How cholesterol contribute to heart
disease and why aspirin lower body
temperature

Chemical Foundations of Biochemistry

Biochemistry seeks to describe the
structure, organization, and function of living
organisms in molecular terms.
In order to understand
the life on the molecular
level, you must first
have a: 
 Knowledge of
the chemical
structures of the
biological molecules
 Understanding of the biological
function of the molecules
 Understanding of bioenergetics - the
study of energy flow in cells 

Organic Chemistry: study of

compounds of carbon 
 Cellular apparatus of
living organisms
made up of carbon 
 Biomolecules are
part of organic
chemistry 
 Reactions of
biomolecules can be
described by organic
chemistry methods
 Functional Groups: atom/group of
atoms that show characteristic
physical and chemical properties

Biomolecules: cells include large molecules

such as proteins, nucleic acids,
polysaccharides and lipids
 These biomolecules are polymers
(Greek: poly + meros, many + parts) 
 Derived from monomers (Greek:
mono + meros, single + parts)
Biological Micromolecules
 Amino Acid
 Sugars
 Nucleotides
 Lipids
Biological Macromolecules 
 Protein
 Carbohydrates
 Nucleic Acid
 Proteins and Nucleic Acids play a
role in life processes.
CHAPTER 1: The Cell
Cell are the Basis of Living Organisms
Classification of Living Cells
1. Prokaryotes - (Archaea & nucleus and mitochondria.
Eubacteria) lack of defined nucleus
or internal membrane structures
- with variable external env’t;
Usually unicellular but some may form
colonies
- Some live in extreme conditions
- Nucleoid region = DNA is a single
circular strand segregated in a
discrete mass in cell
- Cytosol has granular appearance
due to ribosomes
2. Eukaryotes - include unicellular
organisms (yeast), fungi and
multicellular plants and animals
- Typical
Eukaryotic
Cell – Animal
Organelles have very specific functions.
Some metabolic pathways are found in
single cellular component e.g. tricarboxylic
acid cycle (mitochondria), glycolysis
(cytosol), and DNA replication only in
Plasma Membrane is Limiting
Boundary of a Cell
 Outer surface in contact
inner surface with constant
env’t due to cytoplasm 
 Lipid nature of membrane
is semi-permeable
Cytoplasm/Cytosol
 Viscous aqueous environment (NOT
free flowing)
 Contains small molecules, nutrients,
salts, soluble proteins
 20-30% of cytosol is
protein – Very
concentrated
 Highly organized
environment **
 A major site of
cellular metabolism
(e.g. glycolysis)
 Contains cytoskeleton

- Class includes
Cytoskeleton
plants,  3-dimensional matrix made of
animals, fungi, protein fibers
protozoans,
 Functions
yeasts and
to give
some algaes.
cells
- Large cells (10-100 mm in diameter). shape,
10X bigger than prokaryotes. allows
cells to
- Surrounded by a membrane called move, guides internal organelle
plasma membrane movement.
- Composed of lipids and proteins Nucleus
- Serves as chemical barrier to the • Site of most DNA and RNA
outside environment synthesis
• Storage of genetic
- Contain INTERNAL membranes and information
compartments. (Unique feature) • Bound by a double
membrane
- Compartments = organelles • Largest organelle in
- Organelles contain organized eukaryotic cells
complexes of macromolecules that • DNA-protein complex -
perform a certain biological function. Chromatin, RNA processing for
ribosome synthesis occurs in
- Most enzymes are Nucleolus
compartmentalized
Endoplasmic Reticulum
- Compartmentalization results in • Network of interconnected, closed,
separation of biological function!!  membrane-bounded vesicles
- No cell wall in animal cells. • Attached to cell and
nuclear membrane
- Plants, fungi, algae generally have a • Used for
cell wall. manufacturing,
modification and
transport of cellular
Function of Subcellular Organelles in 
Eukaryote Cells materials
 • A cell can have
Two types: over 1000
 Smooth ER = site of lipid mitochondria!
synthesis Depends on need
 Rough ER = site of for energy---
protein synthesis via muscle cells have
ribosomes a lot of
• Ribosomes are made up of mitochondria.
RNA and proteins not bound by a • Enzymes needed
membrane for oxidation reactions, as well as
DNA (mtDNA) that differs from that
Lysosomes found in the nucleus, are found in
• Internal sacs the internal mitochondrial matrix
bound by a • Metabolic reactions for oxidation of
single membrane pyruvate by glycolysis, fatty acids,
• Responsible for AA are located in mitosol
degrading cell
components that Peroxisomes Have an Important Role in
have become Lipid Metabolism
obsolete for the cell or organism.
• Internal pH ~5 (very acidic) • contain enzymes involved in the
• Compartmentalization ESSENTIAL! metabolism of hydrogen peroxide  
Sequesters this biological activity hydrogen peroxide (H2O2) which is
from the rest of the cell. toxic to the cell 
• Enzymes in lysosomes degrade • Catalase converts H2O2   to water
polymers into their individual building
blocks.

Golgi Apparatus
• Flattened
vesicles of

lipid/protein/sugar
• Usually found near smooth ER and
nucleus
• Involved in protein and fat
processing and trafficking to other
organelles (e.g. lysosomes, plasma and oxygen and oxidation of various
membranes)  compounds by H2O2  
• Distribution and shipping department
for cell materials.

Mitochondria
• Have double
membrane (inner
and outer)
• Place where most
oxidative energy
production occurs
= “powerhouse” of
the cell
• Form ATP –
Convert oxygen and nutrients to
energy
• Small, typically the size of a
bacterium
• Contain a circular DNA molecule like
that of bacteria (own genome)
• Because of the double membrane,
size and presence of own genome,
mitochondria are believed to be
descendants of a bacteria that was
engulfed by a larger cell billions of
years ago = endosymbiotic
hypothesis.
CHAPTER 1: Water  Temporary dipoles from rapid
movement of e- from neutral atoms
Biomedical Importance/Clinical Correlations
• Predominant Multiple Forces Stabilize Biomolecules  
chemical component  DNA double helix structure
of living organisms WATER FORMS H-BOND
• Unique physical
properties; could
solvate
organic/inorganic molecules due to
dipolar structure & forming hydrogen
bonds
• Interaction with biomolecules
influence both biomolecule & water
structure
• Excellent nucleophile,
product/reactant for metabolic
reactions EXAMPLE OF BIOLOGICALLY
IMPORTANT H-BOND
Water is an ideal biological solvent
Water Molecules Form Dipoles, it is a polar
molecule
• Water molecule
is an irregular,
slightly skewed
tetrahedron with
oxygen at its
center  
• Strongly electronegative oxygen
atom in a water molecule attracts
electrons away from the hydrogen
nuclei  Water is an Excellent Nucleophile 
• Molecule with electrical charge • Metabolic reactions - attack by lone
distributed asymmetrically about its pairs of e-
structure is referred to as a dipole. residing on e-
rich molecules
termed
nucleophiles
upon e-poor
atoms called
electrophiles  
• Nucleophilic attack by water often
result to Hydrolysis of (e.g. amide or
ester bond). Conversely, water is
produced when joining monomers
• Enzymes accelerate hydrolysis;
Proteases for proteins    Amino acids
while Nucleases for phosphoester
bonds in DNA/RNA
Interactions with Water Influences Structure
of Biomolecules  Water Molecules Exhibit a Slight but
Covalent and Noncovalent Bonds Stabilize Important Tendency to Dissociate 
Biologic Molecules • act both as an acid and as a base
 covalent bond is the strongest force (ionization/proton transfer) 
that holds molecules together   • H2O + H2O ⇄ H3O + OH-
Biomolecules Fold to Position Polar & • At one instant it is an ion; an instant
Charged Groups on Their Surfaces later it is part of a water molecule
 amphipathic; possess charged • 1 (mol) of water weighs 18 g, 1 liter
groups & hydrophobic regions  (L) (1000 g) = 55.56 mol  
Hydrophobic Interactions   • Probability that H+ in pure water will
 nonpolar compounds self-associate exist as H+ = 1.8 × 10-9  
in an aqueous environment  • Kw - ion product for water; At
Electrostatic Interactions  
25°C Kw = 10-14 (mol/L)2 
 Between oppositely charged groups
- Salt bridges 
van der Waals Forces  
Biomedical Importance/Clinical
Correlations
Abnormal Medical Conditions as Reflected
in the pH of Blood
• Blood pH reflects changes in pH of
tissues => pathological condition
• Acidosis - if blood pH falls below
7.35 and above 7.45, as an Alkalosis
• Metabolic acidosis - excess
production of lactic acid or ketone
bodies occur in diabetes and
hypoxemia
 loss of HCO3- , changes pH
balance happens in diarrhea,
and chronic renal diseases
• Respiratory acidosis - restricted CO2
exhalation such as asthma, obesity
or breathing problems due to trauma
• Metabolic alkalosis - ingesting
bases, retention of HCO3-
• Respiratory alkalosis -
hyperventilation, fever

BUFFERS
A buffer solution is a solution of: 
1. A weak acid or a weak base and;
2. The salt of the weak acid or weak
base
         *Both must be present!
• A buffer solution has the ability to
resist changes in pH upon the
addition of small amounts of either
acid or base.

Consider an equimolar mixture of

CH3COOH and CH3COO-Na+

Add strong acid

H+ (aq) + CH3COO- (aq)  CH3COOH (aq)
Add strong base
OH- (aq) + CH3COOH (aq)      CH3COO-
(aq) + H2O (l)
CHAPTER 2: Protein pH neither basic or acidic. 6 amino
acids.
Characteristics of Proteins
 Most abundant substance in cell
next to water (15% of cell mass)
- More soluble in water, R group can
 Typical human cell (9,000) and H bond to H2O
human body (100,000) proteins
3.
 All proteins contain C, H, O, N most
have S
 Protein - unbranched polymer,
monomer unit = Amino Acid 
 Synthesis of enzymes, hormones,
tissue repair & energy 
 Presence of nitrogen (15.4 %) sets
them apart from lipids &
carbohydrates
 Casein - phosphorus (important for
infants); Hemoglobin - iron (O2 Polar acidic amino
transport) acid - one (-NH2)
& two (-COOH)
Amino Acids-Building Blocks of Proteins group 2nd (-
 Amino acid contains both Amino COOH) group part
group (-NH2) and Carboxyl Group (- of the side chain;
COOH) @physiological
 𝝰- amino acid = amino and carboxyl pH, side chain (-)
group attached to 𝝰-carbon charge & side
 R group - side chains (distinguishes chain (-COOH) group lost its acidic
𝝰- amino acids from each other) H atom.
4. Polar basic
 Vary in size, charge, functional
amino acid - two
group, hydrogen bonding & chemical
(-NH2) & one (-
reactivity
COOH) group;
@physiological
pH side chain (+)
charge; Nitrogen
atom has accepted a proton.
 Standard amino acid - one of 20 𝝰-
amino acid normally found in Essential Amino Acids
proteins Essential amino acids - standard amino
acids obtained from dietary resources; Body
Four Categories according to side chain cannot synthesize it in adequate amounts
polarity
1. Non polar amino acid - one (-NH2) & Complete dietary protein - contain all
(-COOH) group + nonpolar side essential amino acid in
chain  relative amount the body
 Hydrophobic when in protein; found needs, may or may not
interior of proteins (less contact w/ contain all non-essential
H2O) amino acid.
 Nine non polar amino acid;
Tryptophan (water could H bond with Incomplete dietary protein -
NH ring) do not contain adequate
amounts relative to body.

Limiting amino acid - essential amino acid

that is missing, or present in inadequate
amounts, in an incomplete dietary protein.

 Protein from animal sources is usually

 3 Types of polar amino acids,
varying degrees for water affinity.
 Hydrophilic within protein, often on
protein surface
2. Polar neutral amino acid - one (-
NH2) & (-COOH) group + polar but
neutral side chain; @physiological
complete dietary protein. Casein from
milk and proteins found in meat, fish, and
eggs except gelatin
 Protein from plant sources - incomplete
dietary protein except soy
 Complementary dietary proteins - two or
more incomplete dietary proteins that,
when combined, provide an adequate
 amount of all essential amino acids
relative to the body’s needs.
 Genetic modification increases plant
protein
Chirality of Amino Acids
 Four different groups attached to the
a-carbon atom in all of the standard
amino acids except glycine.
 Proteins and Amino Acids are L-
isomers by nature
 three species are actually in
equilibrium with each other, and the
equilibrium shifts with pH change 
Isoelectric Points pH at which an amino acid
exists primarily in its zwitterion form  
 15 amino acids w/ nonpolar or polar
neutral side chains @ pH4.8-6.3
 3 basic amino acids - higher
isoelectric points, & two acidic have
lower ones
Cysteine - Chemically Unique Amino Acid
 Contain sulfhydryl group (-SH group)
 Dimerizes with another with cysteine
to form cystine 
 Two cysteine residues linked by
disulfide bond

 Fischer Projection Rules

a. -COOH put at top; R group at bottom
b. -NH2 at horizontal; left = L; Right = D

Acid- Base Properties of Amino Acids

 Both an acidic group (-COOH) and a

basic group (-NH2) are present on

the same carbon in an a-amino

acid. 

 i n n e u t r a l
have a tendency to lose protons
(H+)

 in neutral solution, amino groups

have a tendency to accept protons
(H+)

 zwitterion
- molecule that
has a (+)
charge on one
atom & (-)
charge on
another atom,
but which has
no net charge