BIOCHEMISTRY

COVERAGE: THE CHEMICALS OF LIFE

1. Lesson 1 | Introduction In 1. Water
Biochemistry ➢ Human cells are composed of about
2. Lesson 2 | The Cellular Basis Of Life 70% water, 80% in blood, and 60-70%
3. Lesson 3 | Numerical Language Of the body as a whole
Chemistry And Classifications And ➢ Water prevents dehydration and water
Properties Of Matter loss.
4. Lesson 4 | Atomic Structure And
Chemical Names And Formula
2. Organic Compounds
5. Lesson 5 | Quantitative Measurements
Of Elements And Compounds
➢ Nucleic acids (DNA and RNA),
6. Lesson 6 | Molecular Interaction
Proteins, Carbohydrates, and fats and
lipids

3. Inorganic Elements
LESSON 1 | INTRODUCTION IN ➢ Bulk elements [ N(nitrogen),
BIOCHEMISTRY Na(sodium), Mg(magnesium),
P(phosphorus), S(sulfur), Cl(chlorine),
➢ The Nature of Biochemistry K(potassium), and Ca(calcium) ] - we
➢ The Attributes of Life need relatively large amount to survive
➢ The Chemicals of Life ➢ Trace elements [Fe (iron), Zn (zinc), I
(Iodine)] - for survival this will be need
THE NATURE OF BIOCHEMISTRY
Biochemistry
LESSON 2 | THE CELLULAR BASIS OF
➢ A study of compounds, chemicals
reaction, and molecular interaction LIFE
➢ Combination of "Biology" and
"Chemistry" Morphology of Cells
1. Plasma Membrane - barrier; separate cells
➢ Some of diseases will discuss
from the environment
biochemistry 2. Cytoplasm - Is one of the main or the basic
part of the cell
3. Nucleic Acids
THE ATTRIBUTES OF LIFE 4. Ribosomes
(CHARACTERISTICS OF LIFE)

1. Adaptation - fit to live in habitat (penguins

egg; differ temperature. One species they
adjust depend on the habitat to adapt)
2. Growth and Repair
3. Reproduction
4. Metabolism
5. Complexity and Organization - about
structure and in order to function
6. Regulations
7. All living organisms possess a
characteristic size and shape Prokaryotes "Doesn't have nucleus & no
8. Responsiveness to stimuli or sensitivity membrane"
9. Locomotion or Motility • Bacteria (Monera) & Archaea
10. Variation and Change - Hybridations or
Eukaryotes "Has nucleus & membrane"
mutation/evolve
• Plants (Plantae), Animals (Animalia), & Fungi
11. Stereo specificity

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Living Things Three Major Divisions or
domains
• Bacteria ANIMAL EUKARYOTES
• Archaea
• Eukarya

PROKARYOTES

➢ Plasma Membrane - barrier (gate of

cell);
• Phospholipids molecules -
➢ Mesosome - plasma membrane may phosphate group, glycerol (making
fold into a multilayered structure integrity of plasma membrane), two
➢ Cytoplasm - contains multiple types fatty acid chains
particles ➢ Genetic Control of Organelles -
➢ Nucleoid - packaged form of DNA (it Nucleus, Nucleolus, and Nuclear
carries the genetic material; without Envelope
this prokaryotes cannot reproduce and ➢ Manufacturing, Storage,
cannot survive) Distribution, and Breakdown
➢ Ribosome - factories for assembly of Organelles - Endoplasmic reticulum
proteins (ER), Rough ER "ribosomes", Smooth
➢ Fimbria - small protrusions, which aid ER "lipids"
prokaryotes to attach to surfaces ➢ Golgi Apparatus - cisternae (one of
(attachment) the covering)
➢ Conjugation Pili - exchange of DNA; ➢ Vesicles - membrane-bound sacs
reproduce (pass DNA cell to cell) ➢ Lysosome - it is very important; it is
➢ Flagella - for locomotion (or to move) responsible for the intracellular
digestion; it can fight inside the cells
Prokaryotic cells include (Archaea and
Bacteria)
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➢ Peroxisomes - exist small vesicles;
function is containing to breakdown METHODS OF MATERIAL TRANSFER
toxic materials
➢ Mitochondria - supply energy to the 1. Diffusion - Movement of solute particles
cell (Power House of the Cell) has from region of greater concentration to lower
their own ribosome and DNA concentration
➢ Centrosome - responsible to organize 2. Osmosis (semi permeable membrane) -
during cell division passage of solvent molecules
➢ Centrioles - also organize • Tonicity - refers to the strength of a
microtubules solution in relation to osmosis
➢ Cilia and Flagella a. Isotonic Solutions (iso "equal" & tonic
➢ Cytoskeleton - microtubule, "solution or concentration") - same solute with
intermediate filament, and a concentration equal to the inside of cell
microfilaments b. Hypotonic Solutions - lower concentration
than that inside the cell
Parts of Plasma Membrane c. Hypertonic Solutions - greater
- Cholesterol concentration than that inside the cell
- Carbohydrates • Reverse osmosis - water
- Membrane Proteins purification method for domestic
- Phospholipid bilayer drinking water
3. Dialysis - the separation of colloidal
Components of Nucleus particles from those true solutions
- Nuclear envelope 4. Active Transport - the movement of the
- Nuclear pore materials against a concentration gradient.
- Nucleolus Uses ATP to transport

Rough ER - covered by ribosomes Melanocytes have a higher than usual number of

Smooth ER - production of lipids GOLGI APPARATUS

Lysosomes - contain powerful enzymes LESSON 3 | NUMERICAL LANGUAGE OF

known as lysozyme CHEMISTRY AND CLASSIFICATIONS
Peroxisomes - it carries oxidative enzymes AND PROPERTIES OF MATTER
that require oxygen
ACCURACY AND PRECISION
PLANT EUKARYOTES
➢ Accuracy - Indicates how close a
measurement is to the true or
accepted value
➢ Precision - refers to the closeness of
measurements within a set of data

➢ Cell Wall - protection and support ➢ High accuracy means it is close to the
➢ Plastids - (just like mitochondria)
true and accepted value. High
double membrane
precision is how the measurement
• Plastids used for photosynthesis
closes to each other.
are called chloroplast
3|MC2-BIOCHEM|BSN 1D|CHARLES MENDOZA
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DETERMINING SIGNIFICANT FIGURES
➢ Rule #1 - Every nonzero digit in a
reported measurements is significant
(ex. 553 has three S.F.)
➢ Rule #2 - Leftmost zeros before the
first nonzero digit are not significant,
they only act as placeholders to show
the position of the decimal point. (ex.
0.089 has two S.F)
➢ Rule #3 - Zeros in between nonzero
digits are significant. "Sandwich" (ex.
46073 has five S.F.)
➢ Rule #4 - Zeros to the right if a non
zero digit and to the right of the
decimal point are significant. (ex.
36.00 has four S.F.)
➢ Rule #5 - Zeros at the rightmost end of
a measurement that lie to the left of an
"understood decimal point" are not
significant if they serve as
placeholders. (ex. 80 000 has one For Multiplication or Division
S.F.) ➢ The answer should not have more
significant digits than the
SIGNIFICANT FIGURES IN measurements having the Fewest
MATHEMATICAL OPERATIONS Significant Digits

UNIST OF MEASUREMENTS

➢ Fundamentals SI Units
➢ 7 Fundamental Units - Length, Mass,
Time, Electric Current, Temperature,
Amount of Matter, & Luminous
For Addition or Subtraction Intensity
➢ Should not have more decimal places • 1000 m = 1 km
that the Least Accurate Measurement • 1.609 km = 1 mi
• 1kg = 2.2 lb.
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NATURE AND STATES OF MATTER CLASSIFICATION OF MATTER

States of Matter Matter

➢ Solid - rigid, fixed shape, fixed volume ➢ Mixture - Homogenous Mixture
(cannot be squashed) (solution) and Heterogenous Mixture
➢ Liquid - not rigid, no fixed shape, fixed (Colloids and Suspensions) "Hetero"
volume (cannot be squashed) two or more mixture; "Homo" one
➢ Gas - not rigid, no fixed shape, no phase
fixed volume (can be squashed) ➢ Pure Substance - Compound and
Element

Physical Methods of Separating Mixtures

➢ Magnets - normally used to remove
magnetic solids from the non magnetic
components of a mixture (ex. Nails
and Sand)
➢ Decantation - mixture of liquid and
heavy insoluble solids (ex. Sand and
Water)
➢ Evaporation - homogenous mixture
like saltwater may be separated into
their components (ex. Salt and Water)
➢ Sublimation - volatile solids may be
separated from nonvolatile substances
➢ Filtration - solid-liquid mixture is
allowed to pass through a filter,
Phase Changes trapping the solid in it.
➢ Absorbing Heat - Sublimation, ➢ Chromatography - the method used to
Evaporation, Melting separate components of different
degrees of solubility using a moving a
➢ Removal of Heat - Deposition, stationary fluid
Condensation, Freezing

5|MC2-BIOCHEM|BSN 1D|CHARLES MENDOZA

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LESSON 4 | ATOMIC STRUCTURE AND
CHEMICAL NAMES AND FORMULA

ATOMIC NUMBER AND MASS NUMBER

IONS AND MOLECULES

Ions and Molecules

• When a neutral atom gains or loses one or
more electrons, it becomes an electrically
Parts of an Atom charged particle ion
➢ Neutron - no charge part of the • Metals tend to lose electrons and become
nucleus positively charged 'cations'
➢ Proton - positively charged part of the • Non-Metals, on the other hand, gain
nucleus electrons and become negatively charged
➢ Electron - negatively charged surround 'anions'.
the nucleus

➢ An ion that consists of only one atom

is referred to as a "monatomic ion"
• Ex. Na+, Mg2+, Cl-

➢ Different atoms can also combine

"polyatomic ions"
• Ex. MnO4-, SCN-

Atomic Number - of an element represents

the number of protons in its nucleus
Mass Number - indicated the total number of
protons and neutrons; it is an estimate of the
element's atomic mass
➢ Lower script - represent atomic
number or (Z)
➢ Upper script - represent mass number
or (A)

Z = number of protons = number of electrons

A = number of protons + number of neutrons
number of neutrons = A –Z

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Group 1A: Alkali Metals (Li+) COMPOUNDS
Group 2A: Alkaline Earth Metals (Ba2+)
Group 1B to 8B: Transition Metals (Fe2+)
(Fe3+)
Group 7A (Halogens) and Group 6A (Oxygen
Family) (Br-) (S2-)
Nonmetals can also form polyatomic ions with
oxygen
NO2- nitrite (ite - low)
NO3- nitrate (ate - high)

Covalent Compounds
The halogens can form four different ➢ An 'ionic compound' results from an
polyatomic ions with oxygen attraction between a cation and an
➢ "hypo" = 1 atom (ex. Hypobromite) anion (Metal + Non-Metal)
➢ "ite"= 2 atom (ex. Bromite) ➢ In writing the chemical formula of ionic
➢ "ate" = 3 atom (ex. Bromate) compound by using a 'crisscross rule'
➢ "per" "ate" = 4 atom (Perbromate)

The oxygen in the polyatomic ion is

Some ionic compounds have water
substituted with a sulfur atom. In this case, a
molecules incorporated in their structure and
prefix "thio-"is added to the name of the anion
are called 'hydrated salts'
(cynate --> thiocynate)

'Acids' are compounds that can give off

hydrogen ions when dissolved in water
Ternary polyatomic ions may be formed by
(aqueous)
the addition of hydrogen atoms to binary
polyatomic atoms

A 'covalent compound' results when

nonmetals share electrons. Thus, covalent
compounds exist as molecules

When atoms of non-metals share electrons,

they form an electrically neutral aggregate
called molecule. "HAVE NO FEAR OF ICE
COLD BEER"

7|MC2-BIOCHEM|BSN 1D|CHARLES MENDOZA

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TYPES OF CHEMICAL FORMULAS

➢ Condensed Formula - is also text-

based; each carbon atom is listed
➢ Empirical Formula - an organic separately, with atoms attached to it
compound gives the simplest possible following. An exception is cyclic parts
whole number ratio of the different of molecules, eg. benzene, where the
types of atom within the compound carbons are grouped
(C2H4O) (CH3CH2CH2COOH)

ATOMIC MASS, AVOGADRO’S NUMBER

AND PERCENT COMPOSITION

Atomic Mass (amu - atomic mass unit)

➢ Mass of 1 atom of C-12 = 12.00 amu
Avogadro's Number and the Mole Concept
➢ 1 mole = 6.022 x 10^23 particles
(atoms, molecules)

➢ Molecular Formula - an organic

compound simply shows the number
of each type of atom present. It tells
you nothing about the bonding within
the compound (C4H8O2)

➢ Structural Formula - similar to

displayed formula; not all bonds are
shown, although all atoms are still Percent Composition from Chemical
indicated using subscript numbers. Formula
Carbon hydrogen bonds are often
simplified (H3C - CH2 - CH2)

8|MC2-BIOCHEM|BSN 1D|CHARLES MENDOZA

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LESSON 5 | QUANTITATIVE
MEASUREMENTS OF ELEMENTS AND
FORMULA

CHEMICAL COMPOUNDS

Reactants --> Products ➢ Decomposition (or Analysis) Reactions

➢ Reactants - the initial substance in AB -> A + B
chemical reactions
➢ Products - the output in chemical Activity Series of Metals
reactions

Catalyst - makes chemical reactions faster

Evidences of Chemical Reactions

➢ Change in color
➢ Evolution of gas (formation of bubbles)
➢ Evolution or absorption of heat
(warming, cooling, or flame)
➢ Formation of a precipitate (an insoluble
solid)

Basic Types of Chemical Reactions

(Always having Displacement)

➢ Single Replacement (or Substitution)

Reactions AB + X ' AX +B - depends
➢ Synthesis (or Combination) Reactions who's the most active in metal it will
A + B -> AB attached

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Law of Mass Conservation
➢ That the mass can neither be created
nor destroyed but is transformed from
one form to another.

John Dalton explains the mass law:

➢ Double Replacement (or Metathesis) Postulate 1: atoms cannot be created nor
Reactions AX + BY -> AY + BX destroyed
Postulate 2: atoms cannot be converted into
Activity Series of Metals atoms of another element
➢ The most active Metal is - Li or Lithium ➢ Atoms of original substances
➢ The least active Metal is - Au or Gold recombine to form different substances
in ac chemical reaction
Reactions in Aqueous Solutions
**Add Balancing Coefficients - never change
the subscripts of the substances

➢ Neutralization Reactions - involves and

acid and a base

➢ Precipitation Reactions - this type is

also a double replacement reaction,
where an insoluble solid called
precipitate is formed

BALANCING CHEMICAL EQUATIONS

BALANCING CHEMICAL EQUATIONS

➢ Chemical Reactions should always
follow Law of Mass Conservation

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STOICHIOMETRY LESSON 6 | MOLECULAR INTERACTION
Mass Relationship ELECTRONEGATIVITY AND POLARTIY
➢ These quantitative relationship in a
reaction are studied in stoichiometry Polarity
➢ The result of unequal distribution of
charges within a molecule, causing the
formation of centers which are electron
rich and others are electron poor.
➢ Polar (e.g. water)
**Mole ratio - the heart of stoichiometry ➢ Non-Polar (e.g. benzene)
***One amu is equal to 1.661x10^-24g ➢ Polarity molecule indicated positive
****One mole is equal to 6.022x10^23 and negative signs
(Avogadro's law) ➢ "Like associates with like"

The Structure of Water

Dipole Moment
➢ determine the electronegativity charge

Electro-Negativity
➢ Ionic Bond EN >= 1.7
➢ Polar Covalent Bond 1.7 > EN > 0.4
➢ Nonpolar Covalent Bond EN <= 0.4

Electro-Negativity Values of the Elements

Bond Polarity
➢ Results from the electron distribution
(electron density) between atoms as a
consequence of their electro
negativities
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UNIQUE PROPERTIES EXHIBITED BY
WATER

1. Water has higher melting point and higher

boiling point than other liquids of
approximately the same molecular weight
2. It has maximum density at 4 degrees
Celsius
3. It has high specific heat (you need to apply
and apply energy to increase heat)
4. It has high heat of vaporization and fusion
5. Water is a good solvent

OTHER NON-COVALENT
INTERACTIONS
Electrostatic Interaction

HYDROGEN BONDING

Hydrogen Bonds (H Bonds)

➢ Attractions between hydrogen atoms in
polar molecules
➢ A special type of dipole-dipole
interaction that exists only in ➢ Ion-ion (ion pairs, salt bridges, ionic
molecules that contain a hydrogen bond)
atom bonded to a small highly
electronegative atom such as N, O, or
F
➢ Most H-bonds have a bond energy of
2-49 kj/mol in contrast to the bond
energy of single covalent bonds with
bond energies between 250-500 kj/mol
➢ Can exists within molecules
(intramolecular) or (intermolecular)

➢ b. Ion-dipole force - acts between an

ion (either positive or negative), and a
polar molecule. Cations (positively
charged ion) & Anions (negatively
charged ions)

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➢ 5. Disulfide linkages – are due to the

presence of sulfhydryl groups, e.g.,
➢ c. Dipole-dipole force - exist between amino acids like cysteine that are
polar molecules capable of being oxidized to form
disulfide linkages.
➢ d. H-bond – is a special type of dipole-
dipole interaction that exists only in
molecules that contain a hydrogen
atom bonded to a small, highly
electronegative atom such as N,O, or
F

Matthew 19:26
“With Men This Is Impossible; But With
God All Things Are Possible”

Good luck Future RN’s ^_^

➢ e. London Dispersion Forces - are
intermolecular forces of attraction that
exist between all atoms and
molecules. Moreover, these are the
only forces acting in nonpolar
molecules

➢ 2. Van der Waals Forces - are

relatively weak interaction (usually less
than 2kJ/mol) that tend to bind
nonpolar groups to their neighbors Legends:
➢ 3.Hydrophobic Forces - are weak non- Sky Blue Highlight – Terms
directional interactions responsible for
the clustering or packing together of Yellow – Definitions
non-polar groups in an aqueous Green – Important Details
environment

➢ 4. Pi-pi Complications - is a form of

induced dipole interactions in
molecules that do not have permanent
dipole moments, but may become
dipolar in the presence of an electric
field, or neighboring charged or dipolar
particles (e.g. aromatic rings of
benzene).

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