Chapters 1 - 7

Introduction to
BIOCHEMISTRY
The study of compounds, chemical
reactions, and molecular interactions that
are involved in the production,
maintenance and reproduction of living
organisms.
CH1: INTRODUCTION TO BIOCHEMISTRY

Characteristics of living things to ensure survival:

ADAPTATION
Presence of body structures that make living things
fit to live in its habitat.

GROWTH REPAIR
Ability to add new tissue Ability to replace damaged
parts

REPRODUCTION
Ability to beget offsprings, ensuring propagation &
continuance of species.

METABOLISM
Biological and
chemical
activities or
functions that
provide energy

COMPLEXITY ORGANIZATION
Elaborate structures Putting the different body
needed to carry out structures into order
laborious functions

REGULATION
Ability to keep the functions under control through
hormones & enzymes

CHARACTERISTICS RESPONSIVENESS
(Size & Shape) TO STIMULI

LOCOMOTION
Ability to move on its initiative, under its control

VARIATION & CHANGE

No two organisms are exactly the same
STEREOSPECIFICITY
Ability of certain molecules present in an organism
to interact with nature

ORGANIC INORGANIC
WATER
COMPOUNDS ELEMENTS

WATER

Nucleic Acids
ORGANIC
COMPOUNDS
Carbohydrates
Protein Fats & Lipids
INORGANIC Bulk elements

ELEMENTS
Trace elements
CH2: THE CELLULAR BASIS OF LIFE
Single-celled organisms 1 – 10 µm
Classified under MONERA & ARCHAEA
Normal beneficial inhabitants of our bodies
Others cause tooth decay, illnesses, even death

MESOSOME - Folded invaginations in the plasma membrane
CYTOPLASM - Contains multiple types of particles ( e.g.,

nucleoid, ribosomes)
- Small protrusions on the outside of the plasma
membrane
PILI
- Aids the prokaryote in attaching to surfaces
FLAGELLA - Long thin filaments which provides propulsion

ANIMAL
Has infinitely more genetic 10 - 100 µm

information than prokaryote
Contain multiple membrane bodies (organelles)

ANIMAL
NUCLEUS
Stores DNA
Involved in expression of genetic
information & ribosome assembly
Contains nucleolus

ANIMAL
MITOCHONDRION
•Oxidation of fuel
•Energy production
•Powerhouse of the cell
•(+) double membrane
•Separated by the
intermembrane space

ANIMAL
GOLGI APPARATUS
•(+) Cisternae
•Modification & transport of
proteins and lipids from the
endoplasmic reticulum
•Production of lysosomes

ANIMAL
ENDOPLASMIC RETICULUM
Participates in the processing,
synthesis, packaging, & transport
of proteins & lipids
ROUGH ER – (+) ribosomes
SMOOTH ER – (-) ribosomes;
produces some of the
cell’s lipids

ANIMAL
LYSOSOME
A membrane-enclosed bag of
hydrolytic, digestive enzymes
Responsible for:
•Intracellular digestion of materials brough
into cells
•Breakdown & recycling of
cellular components of
damaged parts of the
cell

PLANT
CELL WALL
For protection & support
PLASTIDS
Unique, double-
membrane
Used for photosynthesis
Assembly & storage of
starch

DIFFERENCE BETWEEN
(-) CYTOSKELETON (+)
Hundreds to
Less content DNA CONTENT
thousand times more
(-) ORGANELLES (+)
About 5-10
Smaller SIZE times larger

DIFFERENCE BETWEEN

DIFFERENCE BETWEEN

DIFFUSION
Movement of solute particles from a region of greater
concentration to one of lower concentration

OSMOSIS
Passage of solvent molecules from a region of lower
concentration to one of greater concentration through
a semi-permeable membrane
Solutions < Solute Solutions = Solute Solutions > Solute

DIALYSIS
Separation of colloidal particles from those of a true
solution by means of a semi-permeable membrane

ACTIVE TRANSPORT
Movement of materials against a concentration
gradient, requires enzymes and energy.

Result of unequal distribution of charges within a
molecule, causing the formation of centers which
are electron-rich, and others which are electron
poor.
CH3: MOLECULAR INTERACTIONS

Attractions between hydrogen atoms in polar
molecules.
Relatively weak compared to covalent bond, but is

much relatively stronger than most other non-
covalent interactions
Can exist within molecules or between molecules

Water has a higher melting point (0°) and higher
boiling point (100°) than other liquids of
approximately the same molecular weight
It has a maximum density at 4°C
It has high specific heat
It has high heats of vaporization &

fusion

ELECTROSTATIC INTERACTION
Attraction between oppositely-charged species.
O
ǁ
ION-ION CH3 ̶ CH2 ̶ CH2 ̶ N+ - - - O ̶ C ̶ CH2 ̶ CH2 ̶ CH2 ̶ CH3
H3

CH3
ION-DIPOLE CH3 ̶ CH2 ̶ CH2 ̶ N+ - - - δ- ̶ O = C
H3 CH3

CH3 CH3
DIPOLE-DIPOLE δ- O δ+ ̶ ̶ ̶ ̶ δ- O === C δ+
CH3 CH3

δ δ CH3
H-BOND δ- O ̶ ̶ ̶ ̶ H ̶ ̶ ̶ ̶ δ- O === C δ+
δ+ H CH3

O
ǁ
ION-ION CH3 +
̶ CH2 ̶ CH2 ̶ N - - - O ̶ C ̶ CH2 ̶ CH2 ̶ CH2 ̶ CH3
H3
CH3
ION-DIPOLE CH3 ̶ CH2 ̶ CH2 ̶ N+ - - - δ- ̶ O = C
H3 CH3
CH3 CH3
DIPOLE-DIPOLE δ- O δ+ ̶ ̶ ̶ ̶ δ- O === C δ+
CH3 CH3
δ δ CH3
H-BOND δ- O ̶ ̶ ̶ ̶ H ̶ ̶ ̶ ̶ δ- O === C δ+
δ+ H CH3

VAN DER WAALS FORCES
HYDROPHOBIC FORCES
Weak non-directional interactions responsible for the
clustering or packing
π - π COMPLEXATION
Form of induced dipole interaction in molecules that do not
have permanent dipole moments, but may become dipolar
in the presence of an electric field, or changed or dipolar
particles.
DISULFIDE LINKAGES
These are due to the presence of sulfahydryl groups, e.g.,
amino acids like cysteine that are capable of being oxidized
to form disulfide linkages CH3: MOLECULAR INTERACTIONS
THEORY ACIDS BASES
ARRHENIUS H+ RELEASES OH-
BRONSTED DONOR PROTON ACCEPTOR
ELECTRON
LEWIS ACCEPTOR DONOR
PAIR
CH4: ACID, BASE & BUFFERS

- Product formed when weak acid
CONJUGATE BASE
dissociates in water
MONOPROTIC - One ionizable hydrogen
DIPROTIC - Two ionizable hydrogen
MONOACIDIC - Yields one OH-
DIACIDIC - Yields 2 hydroxide radicals
POLYACIDIC - Yields many hydroxide ions

WEAK ACIDS AND BASES - Partially ionized
STRONG ACIDS AND BASES - Completely ionized
AMPHIPROTIC / - Substances that can function both

AMPHOTERIC as an acid or base

Acid - proton donor
Base – proton acceptor
PROTON – hydrated H+
H30+
Ionization of water:
H2O + H20 H30+ + OH-

CONJUGATE ACIDS & BASES
TO GET CONJUGATE BASE OF AND ACID:
Cancel one H atom from the acid formula
H3PO4

H3/ PO4

H2PO4-

H+ > OH-
OH- < H+
pH
pOH 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

STEPS IN CALCULATING [H+ ]
1. Enter pH value and affix a negative sign

2. Take the inverse log to get the [H+]
STEPS IN CALCULATING pH from [H+ ]

1. Enter [H+]
2. Take the log of [H+]
3. Reverse the sign

Plays a central role in the biological regulation of pH
COMPOSITION & MECHANISM OF BUFFER ACTION:

1. Weak acid and its salt
2. Weak base and its salt

Prepared using both acid & base conjugate
or
Start with the weak acid
Add a calculated amount of base

Study of carbon-containing compounds
Organic compounds are the primary

constituents of all living organisms.
CH5: ORGANIC CHEMISTRY

Saturated Compound – organic compounds in
which carbon atoms are bonded by SINGLE
bonds.
ex. Methane: CH4

H
H C H

Unsaturated Compound – compounds where
carbon atoms have double or triple bonds.
ex. ethene: C2H4

H H
H C C H

• Organic compounds can be classified into
with related structures and properties.
***As size of molecule increases the boiling
and freezing points increase.
Hydrocarbons are organic compounds that consist
of only Carbon and Hydrogen atoms.
H H H
H C H H C C H
H H H CH5: ORGANIC CHEMISTRY

Contain a BENZENE RING

WITHOUT CARBONYL CARBON
ORGANIC HALIDES
• R-X
where R = alkyl group
and X = halide (F, Cl, Br, I)
Cl
|
CH=C-CH2-CH3
|
Cl
1,2-dichloro-1-butene
bromoethane
WITHOUT CARBONYL CARBON

WITH CARBONYL CARBON

H O O
R ̶ C ̶ C
NH2 OH
⇌ R ̶ C ̶ C
NH3 O-
.. ..
1. Acidity: Amino acid > monocarboxylic acid

2. Basicity: Amino acid < primary amines
3. α hydrogen has a slightly acidic character
CH6: PROTEINS
• Major structural components of animal tissues
• Involved in maintenance of life processes:
Communication (nerves)
Defense (antibodies)
Metabolic regulation (hormones)
Biochemical catalysis (enzymes)
Oxygen transport (hemoglobin)
• Utilized in building of new tissues & maintaining
tissues
CH6: PROTEINS
Not stored to any appreciable extent
Giant polymers (MW range = several thousands to
millions)
Elementary composition:
55% carbon
7% hydrogen
23% oxygen
16% nitrogen
1% sulfur
<1% phosphorous
CH6: PROTEINS
.
CH6: PROTEINS
A. ACCORDING TO SHAPE
CH6: PROTEINS
A. ACCORDING TO FUNCTION
CH6: PROTEINS
CH6: PROTEINS
CH6: PROTEINS
CH6: PROTEINS
CH6: PROTEINS
CH6: PROTEINS
ACCORDING TO THE NATURE OF R:
1. Nonpolar or hydrophobic R
a. Alipathic R – ala, val, ile, leu
b. Aromatic R – phe, trp ACCORDING TO ACID-BASE
c. Imino acids – pro, hypro PROPERTIES
2. Polar but unchanged R
a. Aromatic – tyr, trp, phe Neutral – ala, val
b. With OH group – ser, thr Acidic – glu, asp
c. With a –S – group – cys, met Basic – arg, lys
d. With amide group – asn, gln
e. No R (i.e., R is an H) - gly
3. R is positively charged – lys, arg, his
4. R is negatively charged – asp, glu
CH6: PROTEINS
1. Generally soluble in water, insoluble in nonpolar
solvents
2. High MP (>200C) and low vapor pressure
3. Large dipole moments & high dielectric constants
4. Capable of optical isomerism
5. Aromatic amino acids absorb light in UV region
6. Naturally occurring amino acids have an L-
configuration
7. May be neutral, acidic, or basic.
CH6: PROTEINS
1. Amino acids with an alipathic R
CH6: PROTEINS
2. Amino acids with an aromatic R
CH6: PROTEINS
3. Amino acids with polar –OH group
CH6: PROTEINS
4. Amino acids containing sulfur
CH6: PROTEINS
5. Amino acids with amide group
CH6: PROTEINS
6. Imino acids
CH6: PROTEINS
7. Basic amino acids
CH6: PROTEINS
8. Acidic amino acids
CH6: PROTEINS
Acid-base properties
Amino acids are amphiprotic
Sources of H+:
a. The –COOH group

b. The protonated amine group
c. -SH group of cysteine
d. Guanidium moiety of arginine
e. Protonated nitrogen of the
heterocyclic ring of histidine
f. Phenolic OH of tyrosine
CH6: PROTEINS
Zwitterionic character of amino acids
Equilibrium forms (for acidic amino acids):
CH6: PROTEINS
-COOH group reactions
Esterification
Acylation
Decarboxylation reactions
histidine histamine
CO2
CH6: PROTEINS
-NH2 group reactions
Oxidized by strong OAs
Oxidized by mild OAs
CH6: PROTEINS
Reacts with 1-fluoro- 2,4, dinitrobenzene to yield yellow products
CH6: PROTEINS
Reacts with dansyl chloride to yield products
which fluoresces
CH6: PROTEINS
Reacts with isothiocyanates to yield corresponding
phenylthiocarbamyl amino acid derivatives
which cyclizes to form phenylthiohydantoin
CH6: PROTEINS
R group reactions
Ionization of the R groups
The –OH of serine may be phosphorylated in
biologically active proteins
………. NH ̶ CH ̶ CO ……….
|
CH2
|
OPO3H2
The –SH group of cysteine can be reversibly
oxidized with another molecule of cysteine to
form the disulfide linkage in cysteine
CH6: PROTEINS
Color reactions of amino acids
CH6: PROTEINS
Color reactions of amino acids
CH6: PROTEINS
1. N-terminal AA is named first
2. Add suffix –yl to the AA that donates C=0
group
When glu or asp is involved, the COOH group
involved must be identified
CH6: PROTEINS
Used to purify, characterize, & identify protein composition
CHROMATOGRAPHY
CH6: PROTEINS
CHROMATOGRAPHY
CH6: PROTEINS
Used to purify, characterize, & identify protein
composition
CH6: PROTEINS
ELECTROPHORESIS
Causes protein molecules with a net charge
(+/-) to move toward the electrodes when
placed in an electric field
The greater the net

charge, the faster
the molecule
migrates
CH6: PROTEINS
MICROBIOLOGIC METHODS
Used when certain microorganisms need amino
acids and their rate of growth is proportional to
amount of amino acid
ENZYMATIC
Glutamate + glu decarboxylase glutamine + CO2↑ (measured
volumetrically)
CH6: PROTEINS
OTHER METHODS:
a. Salt precipitation with (NH4)2SO4 and NA2SO4 followed by
centrifugation
b. Isoelectric precipitation
c. Precipitation with organic solvents
d. Use of molecular sieves
e. Crystallization (for albumins & globulins)
CH6: PROTEINS
Amino acid sequence determination
Total acid hydrolysis – to give amino acid residues

which may be separated & identified
Partial hydrolysis – by limiting the time, lowering

temperature, & using lower concentration of acid
Enzymatic hydrolysis
Trypsin
Chromotrypsin
Pepsin
CH6: PROTEINS
Amino acid sequence determination
Aminoterminal methods
Sanger method
Edman method
Use of aminopeptidases
Use of carboxypeptidases
CH6: PROTEINS
Biological catalysts
Soluble, colloidal catalysts produced by living cells
Responsible for carrying out complex reactions rapidly
Molecular weight = 12,000 to over a million
PROPERTIES OF ENZYMES:
1. Enormous catalytic power
2. High degree of specificity
3. Activity is subject to regulation
4. Does not modify the equilibrium constant nor the △G of a
reaction
5. Loses catalytic activity when subjected to heat, strong acids
& bases, organic solvents & other agents of denaturation
6. Names end in -ase
CH7: METABOLIC CONTROL: ENZYMES

TRIVIAL SYSTEM – based on the substrate of the
enzyme & the type of reaction catalyzed
INTERNATIONAL ENZYME COMMISSION (IEC SYSTEM)

Groups enzymes into 6 major classes, each with
subclasses & sub-subclasses, based on the type of
reaction catalyzed.

THEORIES
LOCK & KEY THEORY (Emil Fischer)

The lock is the enzyme and the key is the substrate.
Only the correctly sized key (substrate) fits into the
key hole (active site) of the lock (enzyme)
INDUCED FIT (Koshland)

It states that the shape of Active Sites are not
exactly Complementary, but are changed
according to the substrate molecules

Refers to the preference an enzyme displays toward certain
substrates due to uniqueness of the active sites of the
enzyme
Types of Specificity:
Absolute Specificity – enzymes catalyze a particular
reaction for a particular substrate only

enzyme
Group Specificity – enzymes act on structurally similar
molecules with the same functional group or structurally
related substrates

enzyme
Stereospecificity – enzymes act on one stereoisomeric
form of the substrate

enzyme
Linkage Specificity – enzymes act on a particular chemical
bond irrespective of structural features in the vicinity of
the linkage

Chapters 1 - 7

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Chapters 1 - 7

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Introduction to

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

VARIATION & CHANGE

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

CH1: INTRODUCTION TO BIOCHEMISTRY

Protein Fats & Lipids

INORGANIC Bulk elements

CH2: THE CELLULAR BASIS OF LIFE

CYTOPLASM - Contains multiple types of particles ( e.g.,

FLAGELLA - Long thin filaments which provides propulsion

CH2: THE CELLULAR BASIS OF LIFE

Has infinitely more genetic 10 - 100 µm

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

(-) CYTOSKELETON (+)

(-) ORGANELLES (+)

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

Solutions < Solute Solutions = Solute Solutions > Solute

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH2: THE CELLULAR BASIS OF LIFE

CH3: MOLECULAR INTERACTIONS

Relatively weak compared to covalent bond, but is

Can exist within molecules or between molecules

CH3: MOLECULAR INTERACTIONS

It has a maximum density at 4°C

It has high specific heat

It has high heats of vaporization &

CH3: MOLECULAR INTERACTIONS

CH3: MOLECULAR INTERACTIONS

CH3: MOLECULAR INTERACTIONS

CH3: MOLECULAR INTERACTIONS

CH3: MOLECULAR INTERACTIONS

CH3: MOLECULAR INTERACTIONS

ARRHENIUS H+ RELEASES OH-

BRONSTED DONOR PROTON ACCEPTOR

CH4: ACID, BASE & BUFFERS

DIPROTIC - Two ionizable hydrogen

MONOACIDIC - Yields one OH-

DIACIDIC - Yields 2 hydroxide radicals

POLYACIDIC - Yields many hydroxide ions

CH4: ACID, BASE & BUFFERS

STRONG ACIDS AND BASES - Completely ionized

AMPHIPROTIC / - Substances that can function both

CH4: ACID, BASE & BUFFERS

CH4: ACID, BASE & BUFFERS