1ST Semester Prelim

BIOCHEMISTRY FOR MED LAB SCIENCE LECTURE

CHEM 103 M

WHAT IS BIOCHEMISTRY? Study of interactions of organic and inorganic

chemicals found in the living human body.
During the time of the pandemic, everybody is
holed up in their homes due to quarantine. Most • A field that focuses on how the chemical
people have gained weight due to inactivity and reactions in the body occur.
indulgence in food, and some realized that maybe • Biochemical substance: a chemical
it's time for them to change their routine and start substance found within a living
to do weight loss exercises, an hour per day. organism. e.g. plasma
• Divided into 2 groups:
• Gain weight – fats deposit in bellies, BIOINORGANIC SUBSTANCES and
thighs. BIOORGANIC SUBSTANCES.
• The building up of lipids due to
inactivity – slows down the breakdown
of macromolecules.
• No energy/fuel-halt in the cascade of
cycles

Getting plump and slimming down is just a result

of biochemical processes in the body.

• Can you define what a biochemical

process is?
• When you hear the term biochemical
process, what 5 words can you think of? Bioorganic Substances: makeup only about 1/4
of total body mass.

BIOCHEMISTRY Bioinorganic Substances: water makes up about

2/3 of total body mass (4-5% of body mass comes
Biochemistry is the study of chemical from Inorganic salts).
substances found in living organisms and the
chemical interactions of these substances with
each other. OVERVIEW

A field in which discoveries are made about how • Many biochemical compounds, ranging
cells manufacture the molecules needed for life. from small molecules to large polymers
are capable of releasing or accepting
Macromolecules: protons (H+) at physiologic pH, as a
1. Carbohydrates -CHO consequence, may carry a charge.
2. Lipids - CHO • Most biochemical reactions occur in
3. Proteins – CHON(S) aqueous solutions.
4. Nucleic Acids – CHONP • The pH of a solution is the negative
log10 of its hydrogen ion concentration
BIO – Biology (Life and Study) [H+]
CHEMISTRY – a branch of science dealing with pH = -log [H+]
chemicals

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• ACIDS-> PROTON DONORS (Donate

H+) • The pH of a solution is the negative log10
• BASES-> PROTON ACCEPTORS of its hydrogen ion concentration [H+]:
(Accept H+)
pH= -log10[H+]

Henderson-Hasselbalch For pure water

[H+] = [OH-] = 1x10-7
• The equation describes the relationship pH= -log10[1x10-7] or pH= -log[1x10-7]
between pH, Pk (the negative log of the pH= 7
dissociation constant), and the
concentrations of an acid and its Therefore, the pH of pure water is 7.
conjugate base.
Acids and Bases
𝑝𝐻 = 𝑝𝐾𝑎 + log [𝑐𝑜𝑛𝑗𝑢𝑔𝑎𝑡𝑒 𝑏𝑎𝑠𝑒]
𝑤𝑒𝑎𝑘 𝑎𝑐𝑖𝑑 • Bronsted–Lowry scheme:

𝑝𝑂𝐻 = 𝑝𝐾𝑏 + log [𝑐𝑜𝑛𝑗𝑢𝑔𝑎𝑡𝑒 𝑎𝑐𝑖𝑑] An acid is a proton (H+) donor

𝑤𝑒𝑎𝑘 𝑏𝑎𝑠𝑒 A base is a proton (H+) acceptor

• BUFFERS consist of solutions of acid- • PROTON: a hydrogen atom that has

base conjugate pairs that resist changes lost its electron and is designated H+
in pH when H+ or OH- are added. • Thus, acids are chemical compounds
• Acids that are ingested or produced by that tend to give up H+ ions when
the body are buffered by bicarbonate placed in water
and by proteins, particularly
hemoglobin. These buffers help to • Example: when hydrochloric acid (HCl)
maintain the pH in the body within the is placed in water, the reaction that
range compatible with life. occurs is:
• Enzymes are sensitive to pH changes.
Hydronium Ion
• WATER is the solvent of life. It HCl + H2O= H3O+ + Cl–
dissociates in the following manner: Donate H+ Accept H+

H2O =H+ + OH- • Example: when ammonia (NH3) is

placed in water:
• with an Equilibrium Constant of
NH3 + H2O= NH4+ + OH–
𝐾 = [H+][OH−] Accept H+ Donate H+
[H2O]

• Because the extent of dissociation is not CONCLUSION

appreciable, H2O remains constant at
55.5 M, and the ion product of H2O is ACID + WATER
PROTON DONOR: ACID
Kw= [H+ ][OH-]= 1x10-14 PROTON ACCEPTOR: WATER (BASE)
>The acid will have a (-) charge
[H+][OH-] = 1x10-14
[1x10-7] [1x10-7] = 1X10-14

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BASE + WATER Acids and their Conjugate Bases
PROTON DONOR: WATER
PROTON ACCEPTOR: BASE • Conjugate Acid – originally a base that
> The base will have a (+) charge accepted an H+
Base + Proton
• Acidic solutions have [H3O+] greater
than 10–7 M (what follows from the Kw • Conjugate Base – originally an acid
expression is that [OH–] is less than 10–7 that donated an H+
M). Acid – Proton
• Hence, their pH would fall below 7.
• Acid-Base Conjugate Pair
• Basic solutions have a [H3O+] less than - Acid + Conjugate Base
10–7 M (what follows from the Kw - Base + Conjugate Acid
expression is that [OH–] is greater than
10–7 M).
• Hence, their pH would fall above 7

• pH is short for the power of hydrogen

Acetic acid
• The relationship of pH to the Water
concentration of H+ ions is given.

pH = – log[H+]
Conjugate Acid: Base + Proton (H+)
• The pH scale ranges from 0 to 14, Conjugate Base: Acid – Proton (H+)
reflecting [H+] from 1 M (pH = 0) to 10–
14 M (pH = 14).

Basic: >7
Neutral: 7 Hydronium Ion
Acidic: <7 Acetic Ion

Acid-Base Conjugate Pair

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Buffers

• BUFFER: A solution that contains a

weak acid and its conjugate base and
has the special property of being able to
resist changing its pH when either a
base or an acid is added to it.

WHY THE TERM “BUFFER”?

• Because the solution is protected, or
buffered, from pH changes even when
H3O+ or OH– ions are added to the
solution
>H3O+ Produced once acid is added to
the sol’n
> OH- Produced once a base is added
to the sol’n

• Buffers help biochemists study

biomolecular reactions in the laboratory
by stabilizing the pH of solutions used
for experiments.
• Example of a buffer:

The Henderson-Hasselbalch Equation

• pH is a direct measure of the H+

concentration
• pKa represents a particular acid’s ability
to ionize (dissociate into ions, including
H+).
pH= pKa + log [𝐛𝐚𝐬𝐞]
[𝐚𝐜𝐢𝐝]
• Base-> Conjugate base
• Acid-> Conjugate acid
• Henderson-Hasselbalch equation is
handy for dealing with pH calculations
involving weak acids and their conjugate
High H3O+ = low pH (more acidic)
bases. Because H3O+ is an acid
• This equation is very important to
biochemists, who are always concerned High OH- = High pH (more basic)
with keeping proteins and other Because OH- is a base
biological molecules in the lab at their
proper pH.

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BEAKER WITH ACETATE IONS → Important Buffers in the Body
ADDED WITH HCI:
1. HCl reacts with water which is also present in A. Carbonic Acid Bicarbonate Buffer
the beaker. B. Phosphate Buffer System
HCl + H2O = H3O+ + Cl – C. Protein Buffer System
2. The newly added H3O+ causes a disturbance in
the system (since there are more H3O+ than
before. A. Carbonic Acid Bicarbonate Buffer
3. The feedback should be to reduce the Cellular respiration produces carbon dioxide as a
concentration of H3O+. waste product. This is immediately converted to
4. This is when the acetate ions in the beaker will a bicarbonate ion in the blood. On reaching the
try to react with H3O+. lungs it is again converted to and released as
5. The H3O+ will naturally give up H+. carbon dioxide.
6. Acetate ions will accept the free H+, producing
acetic acid (plus H2O).

More
presence of
H+ increases
pH in Blood
B. Phosphate Buffer System
The phosphate buffer system operates in the
internal fluids of all cells. It consists of
dihydrogen phosphate ions as the
(mono)hydrogen ion donor (acid) and hydrogen
phosphate ion as the ion acceptor (base).

C. Protein Buffer System

Hemoglobin makes an excellent buffer by

binding to small amounts of acids in the blood
before they can alter the pH of the blood.
• What if a strong base is added to the
solution?
Other proteins containing amino acid histidine
are also good at buffering.

NOTE:
Buffers will protect the pH of the solution to
some extent, but if they are flooded by large
amounts of H3O+ or OH– ions, all the available
conjugate acid or base molecules will have been
used up and pH changes will rapidly occur.

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HYPOVENTILATION 1828 FRIEDRICH WÖHLER disproved
* High concentration of CO2; low concentration of this belief of vitalism by synthesizing
oxygen in the blood. urea, an organic molecule, and a
waste product of animal metabolism,
from ammonium cyanate, an
inorganic molecule obtained from
mineral (i.e., nonliving) sources
>CO2 + >H2O → >carbonic acid → >Bicarbonate →
>H+ ions → <pH in body (>acidity) called as acidosis Many science historians believe
this in vitro synthesis of urea by
HYPERVENTILATION Wöhler is the starting point of
* High concentration/ saturation of oxygen in the
blood; low concentration of CO2 in the blood.
Biochemistry.
1836 THEODORE SCHWANN
<CO2 + <H2O → <carbonic acid → <Bicarbonate → proposed that the process of
<H+ ions → >pH in body (>basicity) called as fermentation is solely limited to
alkalosis
living yeast cells.
1850s- Carbohydrates, lipids, and nucleic
HISTORY OF BIOCHEMISTRY 1890s acids were recognized.
1856 LOUIS PASTEUR’S experiment
18Th Century showed that fermentation depends
“The 18th century marked the onset of highly on the physiological functions
physiological chemistry, a sub-field of chemistry that occur in bacteria and living yeast
that dealt more with extracellular chemistry, such cells
as the chemistry of digestion and body fluids." 1869 FRIEDRICH MIESCHER first
identified what he called “nuclein”
1775 ANTOINE LAVOISIER first inside the nuclei of human white
proposed a mechanism for blood cells.
photosynthesis. 1893 EDUARD BUCHNER'S first
1780s ANTOINE LAVOISIER proposed demonstration of alcoholic
that the combustion of a candle is fermentation in cell-free yeast
similar to the respiration of animals, extracts was considered by many as
as both need O2. For the first time, a the starting point for the birth of
physiological process was explained biochemistry.
regarding a nonliving mechanism
20th Century
19th Century 1900s EDUARD BUCHNER proposed the
Early “Vitalism” was a common belief. concept of the enzyme. He prepared
1800s The compounds found in living a cell-free extract of yeast which he
organisms (i.e., organic molecules) called the zymase. It fermented
can only be produced by living glucose and produced carbon dioxide
organisms and could not be produced and ethanol.
in the laboratory. 1904 CARL NEUBER coined the term
“Biochemistry”.
Vitalists argued that it was the 1919 PHOEBUS LEVEN (Russian
presence of a “vital force” (life force physician and chemist) first
or spirit) that distinguished the discovered the order of the three
living organic world from the major components of a single
inanimate inorganic world. nucleotide (phosphate, pentose
1810s- A major substance from animals and sugar, and nitrogenous base).
1830s plants was identified, composed of C,
H, O, and N. The term “Protein”, He is also the first to discover the
meaning the most important thing, carbohydrate component of RNA
was first used in 1838.
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(ribose), and the carbohydrate the additive effect of
component of DNA (deoxyribose). many noncovalent
1937 HANS KREBS discovered the bonds can stabilize a
process known as the Citric Acid molecule;
Cycle (also known as Krebs cycle) very important in the chemical links
which is a series of chemical structure of proteins; between two atoms or
reactions that occur during cellular and ions in which the
respiration. electron pairs are
1950 ERWIN CHARGAFF noted that shared;
the nucleotide composition of DNA weak interactions also termed as
differs among species and does not among ions, molecular bonds; and
repeat in the same order. molecules, and parts
of molecules.
“Chargaff’s Rule”: The amount of •also found in other
cytosine (C) is equal to the amount chemical species,
of guanine (G), and the amount of such as radicals and
thymine (T) is equal to the amount of macromolecules
adenine (A).
1953 JAMES WATSON and FRANCIS Almost all of the Bonding pairs or
CRICK introduced three- complexities in the shared pairs are the
dimensional and double-helical body are accounted electron pairs that
models of the DNA. for by a myriad of participate in a
1958 Insulin was the first protein identified noncovalent covalent bonding
by FREDERICK SANGER. interactions within
1961 The genetic code is made up of and between
specific triplets of DNA bases that macromolecules.
encode for particular amino acids Their very weakness Sharing bonding
1977 FREDERICK SANGER makes noncovalent pairs allows each
successfully sequenced the DNA of bonds so essential, for atom to achieve a
the human mitochondrial genome it allows them to be stable outer electron
which consisted of more than 16 000 continually broken shell, similar to that
nucleotides and re-formed in the seen in noble gas
dynamic molecular atoms.
interplay that is life.
CHEMICAL BONDS AND BONDING Stabilize bonds bet.
SPECIFICS Enzyme-substrate macromolecules
interactions
1. Covalent Bonds: 2 Types of Covalent
• Nonpolar and Polar Covalent bonds: Nonpolar
2. Noncovalent Bonds: (pure) covalent &
• Hydrogen bonds Polar covalent
• Charge-charge interactions
• Dipole-dipole interactions Stabilize bonds bet.
• Van der Waals macromolecules
• Hydrophobic bonds
3. Ionic Bond NON-COVALENT COVALENT BOND
BOND TYPES: TYPES:
Noncovalent vs Covalent 1. Hydrogen Bonds A. NONPOLAR
NON-COVALENT COVALENT 2. Charge-Charge (PURE)
BONDS BONDS Interactions COVALENT
• not as strong as •very strong; 3. Dipole-Dipole * Occurs when atoms
covalent bonds, but Interactions equally share electron
4. Van der Waals pairs.
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5. Hydrophobic *Only identical atom (e.g. O, N, S) is shared with another
Bonds atoms (having the electronegative atom.
same
electronegativity) * Hydrogen bonds are constantly being made and
truly engage in equal remade.
sharing
*Examples: H2, N2, * The half-life of a hydrogen bond is about 10
and CH4 seconds.
B. POLAR
COVALENT * A hydrogen bond has an energy of 21 kJ/mol.
*A bond between 2 >Structure and properties of biological
nonmetal atoms that molecules.
have different A very important interaction is responsible for the
electronegativities structure and properties of water, as well as the
and therefore have structure and properties of biological
unequal sharing of the macromolecules.
bonding electron pair.
*Example: HCI, Example: The hydrogen bonds formed in water.
PbCl2

Covalent Bonds

Biological Significance of Covalent Bond

* Covalent bonds are strong enough to held
macromolecule chains together to preserve the
sequence of subunits for a long time.

* One kind of non-polar covalent bond that is Figure 1-2. Water molecules bonded by
very significant in macromolecules is called a hydrogen bonds.
peptide bond.
2. Charge- Charge Interactions
* A peptide bond joins together chains of amino * Electrostatic interactions between two charged
acids, which involves in the construction of particles (positive and negative charge)
protein.
* These interactions are potentially the
* Glycosidic bond (glycosidic link) is the type of strongest noncovalent forces and can extend over
chemical linkage between the monosaccharide greater distances than other noncovalent
units of disaccharides, oligosaccharides, and interactions.
polysaccharides, which is formed by the removal
of a molecule of water. EXAMPLE: The stabilization of sodium
chloride or table salt (NaCl) crystals by
* A phosphodiester bond joins one DNA interionic attraction (however water weakens
nucleotide to another. these interactions).
* An ester bond joins one fatty acid to glycerol * Consequently, the stability of biological
which could produce TAG (triacylglycerol). polymers (more than 1 basic unit attached) in
an aqueous environment is not strongly
Noncovalent Bonds dependent on charge-charge interactions, but
such interactions do play a role in the recognition
1. Hydrogen Bonds of one molecule by another.
* Hydrogen bonds result when a hydrogen atom
that is covalently bound to an electronegative
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EXAMPLE: Most enzymes have either anionic
or cationic sites that bind oppositely charged * An electric monopole is a single charge, while
reactants. a dipole is two opposite charges closely spaced to
each other. Molecules that contain dipoles are
called polar molecules and are very abundant in
nature.

* For example, a water molecule (H2O) has a

large permanent electric dipole moment.

Figure 1-3 Charge-charge interaction between

the enzyme and reactant (substrate).

3. Salt Bridges
* Attractions between oppositely charged
functional groups of proteins.

* A salt bridge buried in the hydrophobic

interior of a protein is stronger than one on the
surface because it can’t be disrupted by water
molecules. The most accurate term for such
interactions is ion-pairing.
Figure 1-5 Attractive and Repulsive Dipole-
* Charge-charge interactions are also
Dipole Interactions. © 2020, Bedford, R.
responsible for the mutual repulsion of similarly
charged ionic groups.
These dipole-dipole attractions give water many
of its properties, including its high surface
* Charge repulsions influence the structures of
tension.
individual biomolecules as they interact with
other, like-charged molecules (similar to the
5. Van der Waals
hydrophobic effect).
* Van der Waals forces are the weakest
intermolecular force and consist of dipole-
dipole forces and dispersion forces.

*Occur when adjacent atoms come close enough

that their outer electron clouds just barely
touch. This action induces charge fluctuations
Figure 1-4 Salt bridge Interaction between that result in a nonspecific, nondirectional
charged amino acids attraction.

4. Dipole-Dipole Interactions 6. Hydrophobic Interactions

* Dipole-dipole interactions occur when the * This interaction is an effective interaction
partial charges formed within one molecule are between two nonpolar molecules that tend to
attracted to an opposite partial charge in a avoid water and, as a result, prefer to cluster
nearby molecule. around each other.

* Dipole-dipole interactions are electrostatic * Nonpolar molecules are not good acceptors of
interactions between the permanent dipoles of the hydrogen bond. When a nonpolar molecule is
different molecules. These interactions align the placed in water, the hydrogen bonding network of
molecules to increase the attraction. water is disrupted.
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* The water molecules reorganize around the

solute and make a sort of cage (clathrate), similar
to the structure of water in ice, to gain back the
broken hydrogen bonds.

Figure 1-8 Positively charged Ca2+ bonding

with negatively charged F- to form an ionic
compound CaF2

THE NATURE OF WATER

Objectives
Figure 1-7 Hydrophobic interactions between * You should be able to know the properties of
three amino acids water as well as the use of water in the body of a
living organism. Especially the human body.
This reorganization results in a considerable loss Water
in the configurational entropy of water and
therefore an increase in the free energy G.

Ionic Bonds
* Ionic bonding is a type of chemical bond in
which valence electrons are lost from one atom
and gained by another.

* This exchange results in a more stable, noble

gas electronic configuration for both atoms
involved.

*An ionic bond is based on attractive electrostatic

forces between two ions of opposite charge. * Water molecules are attached by hydrogen
bonds
* Example: Sodium fluoride, NaF, from a
sodium atom and a fluorine atom. 1. Water as a good solvent able to dissolve a
specific solute
* In this reaction, the sodium atom loses its single * Water is thus an excellent solvent for charged
valence electron to the fluorine atom, which has compounds
just enough space to accept it. • Charged compounds→ are the
substances that when exposed/
* The ions produced are oppositely charged suspended to water, they are able to
(cations + and anions -) and are attracted to one somewhat have charges in their
another due to electrostatic forces. molecules.
• E.g., Sodium Chloride, the ions of the
sodium chloride are able to dissociate to
sodium and chloride.
NaCl + HCl =
Na+ attracted to (–) side of water
Cl- attracted to (+) side of water

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* When you put Sodium Chloride in water, it H+ attached to →Cl-
quickly dissociates because sodium chloride is a O- attached to →Na+
charged compound, that is it carries a charge Attached via hydrogen bonding
especially when it is suspended in water Opposite attracts

• The positive-charged side of water 2. Oil doesn’t mix with water because oil is a
surrounds negatively charged molecules, type of lipid
and the negatively charged side of water
surrounds positively charged molecules. * Lipids are non-polar
• Positive side of water is attracted to * Non- polar molecules cannot interact with
negatively charged particles, vice versa. water, have low solubility in water and are
Opposite attracts hydrophobic (water hating; no charge on the
surface→ meaning no attraction with water).
* The charges associated with these molecules * Water is a poor solvent for hydrophobic
form hydrogen bonds with water, surrounding molecules such as lipids.
the particle with water molecules. This is * Nonpolar molecules experience hydrophobic
referred to as a sphere of hydration, or a hydration interactions in water: the water changes its
shell, and serves to keep the particles separated or hydrogen bonding patterns around the
dispersed/ suspended in the water. hydrophobic molecules to produce a cage-like
structure called a clathrate

* Water molecules have positive and negative

side
* Charged molecules have positive and negative
side

* Water is therefore referred to as a solvent: a

substance capable of dissolving other polar
molecules and ionic compounds.
• Ionic compounds are the charged
compounds because they carry charges in
their molecular structure
• Polar molecules are substances that have
a high solubility in water
• Water can form hydrogen bond with
charged particles

Water molecule H2O 3. Two properties of water

A. Water is a polar molecule

* One side is slightly positive
+1 * The other side is slightly negative
-1 Charge
Charge Cation B. water is highly cohesive
Anion * Form bonds or attraction for molecules of the
same kind
* H2O—bond with another—H2O
Charged Particles/ Molecules (Cl-)(Na+)
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4. Water as a vital nutrient in the human cell membranes would lack structure, and
body without proper membrane structure, cells would
be unable to keep important molecules inside
A. Water as a building block the cell and harmful molecules outside the cell.
• Building block→ substance / compound
that is a special ingredient in building or * Without the proper shape of the cell, the cell
synthesizing bigger molecules or could lose its selective permeability function. No
compounds more control on the substances that go in or go
• Important reactant in the synthesis of out of the cell.
bigger molecules such as carbohydrates,
nucleic acids, lipids and proteins

A.1 Shape of the Cell

* Visually, water fills cells to help maintain
shape and structure. The water inside many cells
(including those that make up the human body)
creates pressure that opposes external forces,
similar to putting air in a balloon. As shape is
critical for biochemical processes, this is also
one of water’s most important roles.

* Cells are spherical shape and the substance

that keeps the shape is water. Water can provide
outward force that pushes the membrane of the A.2 DNA and Protein
cell. * Water drives the folding of amino acid chains
as different types of amino acids seek and avoid
* Plasma is also composed of water. Force interacting with water.
exhibited by the water both inside and outside the • Amino acid→ building block of
cell should be equal to maintain the shape of the proteins; 1 protein molecule contains a
cell. lot of amino acids (amino acid chain);
very long amino acid chain (protein)
* Shape is critical in biochemical processes. It tends to fold
usually depends on the shape of the compound. • There are non-polar and polar amino
Especially the proteins, specifically the enzymes. acids. Non-polar amino acids in an
Irregularly shaped enzymes can jeopardize the amino acid chain do not like water so the
biochemical process making it difficult to non-amino acid molecule in the chain
produce the end product. tend to move away from the water
making it amino acid chain “fold”

* Water molecules surround DNA in an ordered

fashion to support its characteristic double-helix
conformation.
* Water also contributes to the formation of • Water gives structure to the double helix
membranes surrounding cells. Without water, structure of the DNA
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5. Chemical Reactions of Water and spinal cord, and is particularly important for
the fetus, who is protected by a water cushion.
*Water is directly involved in many chemical * Lessens friction on the surface of the tissue
reactions to build and break down important
components of the cell. PROTEINS
* Molecules like DNA and proteins are made of
repetitive units of smaller molecules. Putting Introduction to Proteins
these small molecules together occurs through a * Amino acids (molecular formula/ structure)
reaction that produces water. * Classifications of amino acids
* Water is required for the reverse reaction that * Peptide Bonds
breaks down these molecules, allowing cells to
obtain nutrients or repurpose pieces of big REVIEW ON THE TERMINOLOGIES
molecules.
• Synthesis→ products are bigger
compound + H2O
• Hydrolysis reactants (bigger compounds
+ H2O + Enzymes) → products are
smaller compounds

A. Water as a Buffer
* Prevents drastic changes in the pH of the
solution when an acid or base is added.
* Proteins require a specific structure to function
properly, so it’s important to protect them from
acids and bases. Water does this by acting as both
an acid and a base. 1. non-superimposable mirror images
2. Enantiomers
3. Chiral Centers
4. Chiral molecules

5. L- FORM VS. D-FORM

* L→ Levorotatory
* D→ Dextrorotatory

Protein
B. Water as a carrier
* Water is essential for cellular homeostasis * Is a naturally-occurring, unbranched polymer
because it transports nutrients to cells and in which the monomer units are amino acids.
removes wastes from cells. • Monomer units→ basic units
* It is the medium in which all transport systems
function, allowing exchanges between cells, * A Protein can have CHONS in its molecular
interstitial fluid and capillaries structure
• Carbon
C. Water as a lubricant and shock absorber • Hydrogen
* Water, in combination with viscous molecules, • Oxygen
forms lubricating fluids for joints; for saliva, • Nitrogen
gastric and intestinal mucus secretion in the • Sulfur
digestive tract; for mucus in airways secretion in
the respiratory system and for mucus secretion in
the genito-urinary tract.
* By maintaining the cellular shape, water also
acts as a shock absorber during walking or
running. This function is important for the brain
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Amino Acids and Peptide Bonds REVIEW ON THE FUNCTIONAL
GROUPS
Amino acid contains Carboxyl Group
(-COOH) 1. Carboxyl Group
* The carboxyl group is an organic functional
O group consisting of a carbon atom double bonded
-C to an oxygen atom and single bonded to a
hydroxyl group.
OH * The carboxyl group is commonly written as
-C(=O) OH or -COOH.
* An amino acid usually contains a carboxyl
group, an amino group and a side chain (denoted 2. Amino Group
by “R”; any functional group), all bonded to the * A functional group that consists of a nitrogen
alpha carbon atom. atom attached by single bonds to hydrogen
• Amino Group (-NH2) atoms, alkyl groups, aryl groups, or a
• Amino Group in expanded form combination of these three.
* An organic compound that contains an amino
group is called an amine.
* Written as –NH2
• Called “Amino” in amino acid→
• all amino acids will vary on their side because it contains amino group in its
chain; “R” is the distinguishing structure
characteristic among all amino acids • Called “Acid” in amino acid→ because
it contains carboxyl group in its structure;
* Amino acids are usually on the L- can be known as the carboxylic acid
conformation.
* At physiologic pH, amino acids carry a 3. Alpha Carbon Atom
positive charge (NH3+) on their amino groups * The alpha carbon in organic chemistry refers to
and a negative charge (COO-)on their carboxyl the first carbon that attaches to a functional group
groups. (the carbon is attached at the first, or alpha,
position). By extension, the second carbon is the
beta carbon.

Figure 1. Amino acid in physiologic pH

• Physiologic pH→ it could mean the

normal blood pH which could range from
7.35-7.45

* The side chains (R) of the amino acids contain * In nature, the vast majority of amino acids take
different chemical groups (alkane, alkene, the L configuration as opposed to the D
alkynes, benzene, etc.). Some side chains carry configuration.
a charge. → the charge of the side chain is used * The L and D configurations are enantiomers of
to distinguish if an amino acid is polar or non- each other, in other words, they have the same
polar, acidic or basic chemical structure and order to their
* Peptide bonds or Amide bonds link adjacent molecules, but they are mirror images of each
amino acid residues in a protein chain. other.
* Molecules with enantiomers polarize light that
is shown through it, and assigned an L or D
based on which way the light bends when shown
through a solution.

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* Most amino acids naturally only occur in the * Other amino acids exist for which there is no
L conformation, which make them genetic code.
enantiomerically pure. * As of now, there are only 20 amino acids known
* Interestingly enough, most medications are only to have genetic codes which can be decoded
active in one of the two conformations, and the during the translation process
enantiomer actually causes the side effects
associated with that drug. Structure of Amino Acids

1. Most amino acids contain carboxyl (+), an

amino group (-), and a side chain (R group), all
attached to the alpha carbon atom.

(NH2) (COOH)

-
H +

Figure 2. Original Structure/ Molecular

structure before the exposure to physiologic pH:

*Carboxyl group is (+)

*Amino group is (-)

* However, it isn't cost effective to isolate the

active enantiomer and the side effects generally
aren't bad enough to warrant a need for it
(thalidomide is an example that comes to mind; (NH3+) (COO-)
the enantiomer of the safe drug is what caused the
birth defects).
• Thalidomide→ alleviate nausea and +
vomiting in pregnant women -

*However, amino acids are naturally isolated in

their conformation so they are sold as L-amino
acid.
Figure 3. When exposed at physiologic pH
AMINO ACIDS (7.35- 7.45):
* About 20 Amino acids (standard amino *Carboxyl group is (-)
acids) are used for the synthesis of proteins by the *Amino group is (+)
mRNA-directed process that occurs in ribosomes. Process:
• mRNA- directed process→ known as 1. COOH will let go of H → becomes COO-;
translation- codes of mRNA being negative because it lost a proton (H+)
translated to amino acids to form 2. H+ is now floating
proteins (about 20 amino acids to form 1 3. NH2 accepts floating H+→ becomes NH3+;
protein) positive because it gained a proton (H+)

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A. Acid- Base Properties of Amino Acids * Basic/ alkaline solution- carboxyl group
carries a negative charge
*In pure form= appear as white, crystalline solids * Physiologic pH- carboxyl group carries a
with relatively high decomposition points. negative charge
* Not very soluble in water. * Acidic solution- carboxyl group no charge
* Amino acids are charged species because of
their amino group and their carboxyl group in * Carboxyl group can either accept or donate
their molecular structure. They will always carry protons which is a similar behavior to buffers. In
a charge in their molecular structure depending this sense, amino acids can also act as buffers.
on the pH that they are exposed to. Amino acids are the natural buffers of the body.

B. Amino Acid Structure F. Amino Group when exposed in acidic and

alkaline solution

* Acidic environment or exposed to pH

- presence of many floating H+ in a specific
environment so the normal response of the body
is to get rid/ lesson the presence of the H+

* Amino group (NH2) of the amino acid will be

able to react with the protons (H+) forming now
Figure 4. Original Molecular Structure of Amino the (NH3+)
Acid Before the Exposure to the Physiologic pH
* Basic/ alkaline solution- amino group no
charge
C. In Neutral Solution (In Physiologic pH) * Physiologic pH- amino group carries a positive
charge
* Carboxyl Group loses proton *Acidic solution- amino group carries a positive
charge
* Amino group accepts proton Acidic solution Attracts the proton

* Refer to Figure 3. When exposed at physiologic

pH (7.35- 7.45) for explanation

D. Zwitterion Alkaline solution Let go of proton

* O molecule that has a positive charge on one
atom and a negative charge on another atom, but * Amino group can either accept or donate
which has no net charge. protons which is a similar behavior to buffers. In
* In solution and solid states, amino acids exist this sense, amino acids can also act as buffers
as zwitterion because amino acids carry both due to the presence of carboxyl group and
positive (amino group) and negative (carboxyl amino group of amino acid. Amino acids are the
group) charges natural buffers of the body.
No charge
E. Carboxyl Group when exposed in acidic and No charge

alkaline solution
Alkaline solution Let go of proton

Acidic solution Attracts the proton

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2. All of the 20 amino acids except glycine are *Hydrophobic amino acids: Leucine,
of the L-configuration. Because glycine does isoleucine, valine, glycine and alanine
not contain an asymmetric carbon atom, it is
not optically active and thus, it is neither D nor A.1 ALIPHATIC and AROMATIC (rings/
L. benzene rings) AMINO ACIDS (with few
exceptions)
Exceptions:
1. Glycine does not have a side chain. Its alpha A.1.1 Aliphatic Amino Acids (Alkanes,
carbon contains two hydrogens. Alkenes, Alkynes)
2. In proline, the nitrogen is part of the ring
Symmetric
• nonpolar (no polar interactions with
- The alpha carbon has 2 polar molecules) and hydrophobic
hydrogens attached to it. If you (water hating; no interaction with
H cut the atom in half, both sides
are similar. Therefore, no L or water).
D conformation of glycine. • Hydrophobicity increases with
cut increasing number of C atoms in the
hydrocarbon chain.
• Increase in C atoms= also increases in
hydrophobicity= becomes less soluble in
water= it becomes more non-polar
• Prefer to remain inside protein
Figure 5. Molecular structure of Glycine molecules with the exception of alanine
and glycine (both are hydrophobic
supposedly) BUT they are (ambivalent
amino acids; found inside/ outside the
Carboxyl→ protein)→ ambivalent meaning they are
 Hydrogen
not considered as hydrophobic
amino→
molecules; ambivalent means that the
Side chain also molecules have the capability to
attached to amino
group interact with water because their side
chain is very small; its hydrophobicity
is very low; no effect on the interaction
Figure 6. Molecular structure of Proline of water and the protein

3. The classification of amino acids is based on

their side chains.

* Side chain (R) classifications:

• Polar
• Non-polar
• Neutral
• Acidic
• Basic

A. Hydrophobic Amino Acids (non- polar) a) Glycine and Alanine can be inside or
outside the protein molecule.
* Hydrophobic amino acids (water hating) have b) Glycine has such a small side chain that
side chains that contain aliphatic groups/ hydro it does not have much effect on the
carbon chain (alkenes, alkanes, alkynes) that can hydrophobic interactions.
form hydrophobic interactions.

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Figure 8. Amino acids under the Aromatic R

Group

B. Hydroxyl, Sulfhydryl, and Disulfide

Figure 7. Examples of Nonpolar, aliphatic R
groups/ hydrophobic R groups B.1 Hydroxyl Groups (OH-)
* Hydroxyl groups found on serine, tyrosine,
A.1.2 Aromatic Amino Acids (have benzene and threonine can form hydrogen bonds.
ring in their side chains) * If a specific amino acid contains hydroxyl
groups in its specific side chain, that side chain
• nonpolar (no interaction with water) can basically interact with water
and hydrophobic * (OH-) Oxygen here is in covalent bonding with
• To different degrees, all aromatic amino hydrogen)
acids absorb ultraviolet light.
• Aromatic amino acid examples:
Tyrosine, Tryptophan, Phenylalanine
• Tyrosine and tryptophan absorb more
than do phenylalanine
• Exception: Tryptophan is a borderline
member of the nonpolar group
(supposedly, aromatic amino acids have
no interaction with water BUT) because
it can weakly interact with water
molecules through hydrogen bonding
with the NH ring location on
Tryptophan’s side chain ring structure B.2 Sulfhydryl Groups
• Tryptophan is responsible for most of * Sulfur is found mainly in proteins in the form
the absorbance of ultraviolet light (ca. of sulfhydryl groups (symbolized as –SH) or
280 nm) by proteins. disulfide group (symbolized as -S-S-).
• Tyrosine is the only one of the aromatic * Sulfur is present in cysteine (-SH) and
amino acids with an ionizable side chain methionine (- S-S)
(accept or release protons). * The sulfhydryl groups of two cysteines can
form a disulfide, producing cystine.
• Tyrosine is one of three hydroxyl
containing amino acids.
Cysteines + Cysteines → Produces Cystine
(New Amino Acid Formed)

Cysteines VS Cystine:
* Cysteine has a specific sulfide groups (-SH) in
its side chain
* Cystine has disulfide group (-S-S) in its side
chain

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* Remember: We know that in physiologic pH,
the normal behavior of your amino group is to
New bond
accept protons that’s why the amino group of
Cysteine formed Cystine lysine, arginine and histidine are positive

Cysteine 1
Cysteine 2
Released

Cysteines + Cysteines → Produces Cystine

(New Amino Acid Formed)

Process:  carboxyl group

1. Hydrogens (H) from cysteine 1 and cysteine 2
will be released
2. Sulfur (S) from cysteine 1 and 2 will form a new
bond resulting to a new amino acid called
Figure. Negatively charged R groups
Cystine
* Aspartate or also called as aspartic acid and
C. Ionizable Group
glutamate or glutamic acid.
* Remember: In physiologic pH, the carboxyl
* Ionizable groups are present on the side chains group is negative because they tend to let go of
of five amino acids. the protons (H+) that is why the carboxyl group
* Five amino acids: Aspartate, Glutamate, of the aspartate and glutamate are negative.
Histidine, Lysine, and Arginine.
* Ionizable groups can carry a charge,
D. Amides (-CONH2)
depending on the environment they are exposed * Amides are present on the side chains of
to or depending on the pH (basic, acidic or
asparagines and glutamines.
neutral).
* Amides are derived from carboxylic acids. A
* When charged, these ionizable groups of the
carboxylic acid contains the -COOH group, and
amino acids can form electrostatic interactions.
in an amide the -OH part of that group is replaced
* (Adding or removing one or more electrons by an -NH2 group.
gives a net electric charge to an atom.) *So . . . amides contain the -CONH2 group.

amino acid + amino acid → forming Amides

-COOH (from Amino acid 1) + NH2 (from

Amino acid 2)→ forming the Amide

 Aliphatic

 Amino
group

Figure. Positively charged R groups

* Lysine, Arginine and Histidine are positively * The side chain of proline forms a ring with the
charged because in their side chain they have this nitrogen and is attached to the alpha carbon.
specific amino group attached to a specific * It is not an essential amino acid, which means
aliphatic group that the human body can synthesize/ produce it.

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* Essential amino acid is a specific amino acid * Presence of amino group (NH2) in the side
that is not produced by the body; the body does chain makes Proline polar
not have the capability to produce that specific
amino acid. BUT the body needs that specific * Presence of amide group (-CONH2) in the side
amino acid hence, we get that specific amino acid chain makes the Asparagine and Glutamine
from food sources. polar
 alkyl group
20 Standard Amino Acids
 Side chain/
Amino grp/ amine→ alkyl group
nitrogen

* The side chain of proline is also attached to the

amino group, forming a ring structure.
* The only amino acid that has this structure due
to the involvement of side chain and the amino
group

* It is unique among the 20 protein- forming

amino acids in that the amine nitrogen is bound to
not one but two alkyl groups, thus making it a
secondary amine.

Figure. Polar, Uncharged R Groups

* Proline, Asparagine and Glutamine forms

polar interactions with other polar molecules
such as water

* Presence of Hydroxyl group (-OH) makes

Serine and Threonine polar molecules; they can
form hydrophilic interactions with water.

* Presence of Sulfhydryl group (SH) makes

Cysteine polar

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2. Polar/ Hydrophilic Amino Acids

* Opposite of the Nonpolar Hydrophobic amino

acids
* Can form polar interactions with water or other
polar molecules
* Contains one amino group, one carboxyl group,
and a polar side chain.
* Neutral hydrophilic amino acid, acidic
hydrophilic amino acid, or basic hydrophilic
amino acid (alkaline)

3. Polar, NEUTRAL (polar, uncharged)

Amino Acids

* Does not carry charges in their side chain

* Contains one amino group, one carboxyl group,
Classification of Amino Acids Based in
and a polar but neutral side chain.
Polarity and Charges (Acidity and Basicity)
* Neither acid nor base at physiologic pH.
* Side chain can form hydrogen bond with water.
1. Nonpolar/ Hydrophobic Amino Acids

* Contains one amino group, one carboxyl group,

and a nonpolar side chain.

* Non polar side chain of the amino side chain

could be aliphatic or aromatic.

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5. Polar, BASIC (polar, positively charged)
Amino Acids

* Contains one amino group, one carboxyl group,

and a second amino group as the side chain.
* Basic at physiologic pH.
* Remember: Amino group accepts protons in
physiologic pH
* Side chain –NH2 bears a positive charge,
making it –NH3 +

4. Polar, ACIDIC (Polar, negatively charged)

Amino Acids

* They are acidic because they contain another

carboxyl group in their side chain. Carboxyl
groups tend to carry negative charge in their
structure.

* Since carboxyl groups can release H +start

superscript, plus, end superscript into solution,
they are considered acidic.

* Contains one amino group, one carboxyl group,

and a second carboxyl group as the side chain.
* Acidic at physiologic pH, meaning they carry
negative charge
* Side chain -C(=O) OH bears a negative charge,
* Whatever is the behavior of first amino group
making it C(=O) O-
will be the same behavior for the second amino
group in an amino acid (e.g., amino acid Lysine).
E.g., 1st amino group is positive, the second
amino group is also positive.

Essential Amino Acids

* They are called essential amino acids because

the body cannot produce these amino acids, you
need to eat food to get these essential amino
acids.
* Standard amino acids that need to be obtained
from the diet because the human body cannot
synthesize it in adequate amounts from another
substances (lipids or carbohydrates).

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Figure. These are the list of essential amino acids

that we need to get from food.

PEPTIDES AND PROTEIN STRUCTURE

AND ITS CLASSIFICATIONS

Peptide Bond/ Amide Bond

* Peptide bond is bond that attaches one amino
acid to another amino acid
* Is a covalent chemical bond formed between
two molecules when the carboxyl group of one
molecule reacts with the amino group of the
other molecule, causing the release of a molecule
of water (H2O).
* Dehydration Synthesis reaction (also known
as a condensation reaction), usually occurs Amide or peptide group/ bond/ link or
between amino acids.

* Amino acid + amino acid→ products are water CHARACTERISTICS OF A PEPTIDE

(by-product) + peptide (major product) BOND
* Peptide is a molecule consisting of two or more
amino acids 1. The atoms involved in the peptide bond form
* It is a dehydration reaction because it has a a rigid, planar unit.
by-product of a water molecule 2. Because of its partial double-bond character,
the peptide bond has no freedom of rotation.
* The resulting C(O)NH (is an amide group) 3. However, the bonds involving the alpha carbon
bond is called a peptide bond, and the resulting can rotate freely.
molecule is an amide.
* The four-atom functional group -C(=O)NH- is * Peptide bond has a rigid structure due to the
called a peptide link. Polypeptides and proteins double bond character from the -C(=O)NH
are chains of amino acids held together by molecular structure
peptide bonds, as is the backbone of Proteins. * Rigid structure- no rotation, no movement
* Peptide bonds covalently join the alpha
carboxyl group of each amino acid to the alpha * Peptide bonds are extremely stable, strong, and
amino group of the next amino acid in the protein needs high amount of energy for the bond to
chain. break. Cleavage generally involves the action of
the proteolytic enzymes
* Peptide= amino acid #1 + amino acid #2 + …
* But we need to constantly breakdown proteins
(break down those peptide bonds that link
proteins), we need a process where in we can
easily breakdown/ cleave proteins. It would be a
waste of energy if our body uses high amount
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energy to break down peptide bonds that link
proteins. So, we resort to using proteolytic
enzymes.
* Proteolytic enzymes→ this enzyme specifically
targets the peptide bonds to break it in order to
release amino acids. In this sense, the proteins
are gradually degraded/ broken down into amino
acids (amino acids are the building blocks of * N- terminal amino acid (N- Terminus)→ it is
proteins) called as N-terminal because it is the only amino
acid that has the complete NH2 group (amino
Peptides group) in its structure.

* Amino acids bond together (through peptide B. All other amino acid residues have names
bonds) to form an unbranched amino acid that end in -yl. The -yl suffix replaces the -ine
(peptide). or -ic acid ending of the amino acid name,
except for tryptophan (tryptophyl), cysteine
1. Dipeptide (cysteinyl), glutamine (glutaminyl), and
* Two amino acid residues (meaning, only 2 asparagine (asparaginyl).
amino acids that are linked together)
* e.g., 1
2. Oligopeptide • Serine→ Seryl
* Peptides with 10-20 amino acid residues • C-terminal→ methionine
• Final name: Serylmethionine
3. Polypeptide * e.g., 2
* Long unbranched chain of amino acids • Glutamine→ Glutaminyl
• C- terminal→ alanine
Writing of Structural Formula and • Final name: Glutaminylalanine
Abbreviated Formula
C. The amino acid naming sequence begins at
the N-terminal amino acid residue

2. Example:
* Assign IUPAC names to:
1. Glu-Ser-Ala (Tripeptide)
• Glutamic acid→ Glutamyl
• Serine→ Seryl
• C-terminal→ Alanine
• Final name: Glutamylserylalanine or L-
Peptide Nomenclature glutamyl-L-serylalanine
1. Rules:
A. The C-terminal amino acid residue keeps its * Do not put space in between the final name
full amino acid name. * Why the L? → remember that most amino acids
are usually in L- form; since most amino acids
* C- terminal amino acid (C-Terminus)→ are in L- form, you do not really need to put the
locate the amino acid that still has an attached “L” in the final name
carboxyl group in its structure; the only amino
acid that still has its carboxyl group (COOH) 2. Gly-Tyr-Leu-Val (Tetrapeptide)
attached is the last amino acid in the far right • Glycine→ Glycyl
of the amino acid chain. • Tyrosine→ Tyrosyl
• Leucine→ Leucyl
* e.g., the last amino acid in the far right is the
• C- terminal→ Valine
methionine, expect that methionine is included
• Final name: Glycyltyrosylleucylvaline

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ENZYMES * After the substrate binds, the enzyme portion
The Catalysts of Biological Systems changes shape.

* Whatever the reaction, the enzyme’s

conformation changes to help the reaction to go
into completion.
* The final process in the reaction is the release
of the product.

The Basics of Enzymes Enzyme Nomenclature

* Proteins that catalyze specific reactions without * The Enzyme Commission of IUB first divided
being consumed all known enzymes into six categories, based on
* Remarkable molecular devices that determine the type of the reaction they carried out.
the patterns of chemical transformations.
* Mediate the transformation of one form of
energy into another
* Catalytic power and specificity are the most
striking characteristic of enzymes.

1. The generic enzyme reaction

In this equation:
• E is for Enzyme
• S is for substrate
• ES is for Enzyme-Substrate Complex 1. Oxidoreductase
• P is for the product of the reaction * Oxidoreductases catalyze oxidation reduction
reactions. At least one substrate becomes
2. The role of enzyme- substrate complex oxidized and at least one substrate becomes
* In any reactions requiring a catalyst, one of the reduced.
most important steps is the attachment of the
catalyst to the starting reactant (substrate)
* These attachment to the catalyst must occur 2. Transferase
before the substrate can have a group added, a * Transferases catalyze group transfer reactions-
bond broken, or a structural rearrangement. the transfer of a functional group from one
* There is no covalent bond formed when this molecule to another.
complex is generated.
* Formation of the enzyme-substrate complex is 3. Hydrolase
reversible; the complex can either proceed * In hydrolysis reactions, C-O, C-N, and C-S
onward to product formation or can dissociate bonds are cleaved by addition of H2O in the form
back to separate enzyme and substrate molecules. of OH- and H+ to the atoms forming the bond.
* The ES complex involves a more complicated
reaction strategy. 4. Lyase
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* Lyases cleave C-C, C-O, C-N, and C-S bonds
by means other than hydrolysis or oxidation.

5. Isomerase
* Isomerases just rearrange the existing atoms of
a molecule, that is, create isomers of the starting
material.
* Other hydrolases function as digestive
6. Ligase enzymes, for example, by breaking the peptide
* Ligases synthesize C-C, C-S, C-O, and C-N bonds in proteins.
bonds in reactions coupled to the cleavage of high
energy phosphate bonds in ATP or some other For the Formation or Removal of a Double
nucleotide Bond with Group Transfer
For Oxidation and Reduction Processes * The functional groups transferred by these
lyase enzymes include amino groups, water, and
* Enzymes that carry out these reactions are ammonia.
called oxidoreductases. For example, alcohol Examples:
dehydrogenase converts primary alcohols to 1. Decarboxylases-remove CO2 from alpha- or
aldehydes. beta- keto acids
2. Dehydratases-remove water, as in fumarase
(fumarate hydratase):

* In this reaction, ethanol is converted to

acetaldehyde, and the cofactor, NAD (+), is
converted to NADH. In other words, ethanol is
oxidized, and NAD (+) is reduced.
* Remember that in redox reactions, one substrate
is oxidized and one is reduced.

For Group Transfer Reactions 3. Deaminases-remove ammonia, for example, in

the removal of amino groups from amino acids:
* These enzymes, called transferases, move
functional groups from one molecule to another.
For example, alanine aminotransferase shuffles
the alpha-amino group between alanine and
aspartate:

For Isomerization of Functional Groups

* Other transferases move phosphate groups * In many biochemical reactions, the position of
between ATP and other compounds, sugar a functional group is changed within a molecule,
residues to form disaccharides, and so on. but the molecule itself contains the same number
and kind of atoms that it did in the beginning.
For Hydrolysis

* These enzymes, termed hydrolases, break

single bonds by adding the elements of water. For
example, phosphatases break the oxygen-
phosphorus bond of phosphate esters:
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* Prosthetic group: A cofactor covalently

formed to the enzyme (non-enzyme entity)

* Apoenzyme: The protein component of the

enzyme

* Holoenzyme: The apoenzyme + Cofactor(s)

* In other words, the substrate and product of the (entire Enzyme)
reaction are isomers.
* The isomerases (for example, triose phosphate COFACTORS CLASSIFICATIONS:
isomerase, shown following), carry out these 1. Activator ions which are loosely bound
rearrangements. 2. Metal ions of Metalo-enzymes which are
tightly bound.
Single Bond Formation by Eliminating the
Elements of Water COENZYMES CLASSIFICAITONS:
1. Co-substrates which are loosely bound
1. Hydrolases 2. Prosthetic group which is tightly bound.
* Break bonds by adding the elements of water.
COFACTORS COME FROM A VARIETY
2. Ligases OF SOURCES:
* Carry out the converse reaction, removing the * foods
elements of water from two functional groups to * vitamins
form a single bond. * sunlight
* synthesis from common metabolites
3. Synthetases
* Are a subclass of ligases that use the hydrolysis Enzymatic Requirements of Enzymatic
of ATP to drive this formation. Reactions

Example: 1. non-enzymatic reaction

* Aminoacyl-transfer RNA synthetases join * Formation of a “high energy state” where lots
amino acids to their respective transfer RNAs in of energy is required.
preparation for protein synthesis; the action of
glycyl-tRNA synthetase is illustrated in this 2. Enzymatic reaction
figure: * Lower activation energy- The reaction occurs
via the E-S complex with low energy
requirement.

Cofactors of Enzymes

* Cofactor: Chemical required for the enzyme to

function (like the ions K+, Mg++, Ca++ and
Fe++)
Enzyme Kinetics
* Coenzyme: Organic compound required for
enzymatic function (ATP is the most common)
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Where:
K1: The rate constant for the formation of the ES • E= the enzyme
complex • S= the substrate
K2: Rate constant for the formation of the
• ES= the enzyme-substrate complex
product(P)
• P= product
*Rate limiting step: Formation of the E-S • K1 and K2= rate constants
complex
*(Requires the collision of a E+S)
Therefore, K1<<K2

Reaction Rate/ Velocity

* Expressed as mg of substrate converted

/minute
* Usually measured shortly after combining the E
and S
* Initial velocity= Vo

1. Maximum Velocity (Vmax)

* When Vo is measured over time, there is a
linear increase. But at some point, there is * From the concept, the Michaelis-Menten
“saturation “(more substrate than the enzyme in equation was derived:
the reaction)

* This is described as saturation kinetics.

* Every molecule of the enzyme is bound to a * Where:
substrate at any instant. Km=K2/K1 and Vmax is the maximum
* This is the limit to the maximum velocity of velocity.
the enzymatic reaction.
* The rate of formation of products (the
2. Reaction rate depends on: velocity of the reaction) is related to the
B.1 The probability of collisions between concentration of the enzyme-substrate complex:
components (i.e. concentrations) V=K2[ES]
B.2 The affinity of the E+S
* Km is the substrate concentration at which
The Michaelis- Menten Equation V=1/2 of vmax
* During a reaction, an enzyme-substrate
complex is formed that * When [S] = Km, substitution of Km for [S] in
1. Dissociates (to reform the free enzyme and the Michaelis-Menten equation yields
the substrate) or V=1/2 Vmax
2. Reacts (to release the product and regenerate
the free enzyme).
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* When the velocity is plotted versus [S], a
hyperbolic curve is produced.

Enzyme Specificity

* This is the EXTENT to which an enzyme is

restricted to a specific substrate, a specific group
substrate, a specific type of chemical bond, or a
specific type of chemical reaction.
* Active site: determines the degree of enzyme
specificity. 2. Power of Hydrogen (pH)
* Optimum pH → the pH at which an enzyme
exhibits its maximum activity.
* The charge on the acidic and basic amino acids
located at the active site depends on the pH.
* Most enzymes exhibit maximum activity over a
narrow pH range.
* Pepsin = 2.0
* Trypsin = 8.0

FACTORS THAT AFFECT ENZYME

ACTIVITY 3. Substrate Concentration

* This is the measure of the rate at which an

enzyme converts substrate to products in a
biochemical reaction.
* Factors that affect the enzyme activity:

1. Temperature
2. pH
3. Substrate concentration
4. Enzyme concentration * The rate at which an enzyme accepts substrate
molecules and releases product molecules at
1. Temperature substrate saturation is given by its TURNOVER
* Optimum temperature→ the temperature at NUMBER.
which an enzyme exhibits maximum activity. * Turnover number→ the number of substrate
* Humans = 37C molecules transformed per minutes by one
* >40C is life threatening → denatures enzyme molecule of enzyme under optimum conditions of
* Temperature is a measure of the kinetic energy pH, temperature, and saturation.
of molecules. * Example: Carbonic anhydrase → 36,000,000
* Increase temperature = increase reaction rate
(velocity) 4. Enzyme Concentration
* Temperature> optimum temperature →
denaturation occurs.

Biochemistry for Med Lab Science Lecture CHEM 103 M 63

1ST Semester Prelim

Biochemistry for Med Lab Science Lecture CHEM 103 M 64

1ST Semester Prelim
BIOCHEMISTRY FOR MED LAB SCIENCE LABORATORY
CHEM 103 M

LAB SAFETY AND SPILL TREATMENT (burners, matches) must not be in use.
The above liquids must not be stored near
Laboratory Safety Rules radiating heat sources, such as the
laboratory oven.
1. Do not work alone in the laboratory. 11. Before using electrical appliances, make
2. Unauthorized experiments are not sure they are grounded.
allowed. 12. Flasks with flat bottoms or thin walls
3. Eating, drinking, and smoking in the should not be desiccated
laboratory are strictly prohibited. 13. Before leaving the laboratory, electrical
4. Become familiar with the location and equipment should be turned off, and gas
the use of standard safety features in the burners extinguished. No tap water
laboratory. The laboratory is equipped should be left running.
with fire extinguishers, eyewashes,
safety showers, fume hoods, and first-aid Accidents and Injuries
kits. Any question regarding the use of
these facilities should be addressed to 1. Chemical splatters into the eye. First, the
your instructor. eyelid should be opened by using the
5. Special care for eye protection is thumb and the pointing finger. Then, by
required. Safety glasses must be used using the eyewash kit, the eye should be
when certain procedures are being rinsed with large amounts of water.
carried out. The instructor will call the When an acid or alkaline solution gets
students' attention to those procedures. into the eye, the eye should be rinsed with
The use of contact lenses is not 1 % NaHCO3 or 1 % boric acid,
recommended since they reduce the rate respectively. The victim should be taken
of self-cleansing of the eye. to the doctor as soon as possible.
6. While heating a solution one should 2. Burning. The burned spot on the skin
make sure not to overheat it; therefore, should not be treated with water; rather,
vigorous mixing of the solution by a special bandage should be used. See a
shaking or stirring is required. The mouth doctor if necessary.
of the glassware containing the solution 3. Poisoning. Prompt medical treatment
to be heated should never be pointed should be obtained. All injuries and
toward anyone. accidents must be reported to the
7. Handling of strong acids and bases instructor.
requires special attention. When diluting
concentrated acids, the acid should be
poured into the water and never the Spill Treatment
opposite.
8. The pipets should never be filled with You should not clean up a spill if:
solutions of toxic substances, biological
fluids, strong acids, and bases by mouth 1. You don’t know what the spilled
suction. Use either automatic pipets or material is
pipet pumps. 2. You lack the necessary protection or
9. Volatile liquids and solids that are toxic equipment to do the job safely
or irritating should be handled under 3. The spill is too large to contain
fume hoods. 4. The spilled material is highly toxic
10. While handling flammable liquids such 5. You feel any symptoms of exposure.
as ether, alcohols, benzene, naked flame

Biochemistry for Med Lab Science Laboratory CHEM 103 M 65

1ST Semester Prelim
Spill Response Scheme neutralization or absorption kit.

Evaluate and notify • Medium Spill: 300 cc’s to 5

1. Assess the toxicity, flammability, or liters; respond with absorption
other properties of the material (see label using an absorption spill kit.
& MSDS)
2. For flammables, remove or turn off • Large Spill: More than 5 liters;
ignition sources such as motors, pumps, call UMW PD and OEMS
fridges. immediately.
3. Determine if there is an immediate health
threat to you or your neighbors. If so, 6. The absorption technique should be to
alert neighbors, isolate the area, and call distribute loose spill control materials
for help using the phone numbers above. over the entire spill area, working from
4. If the spill is minor, begin cleanup the outside, circling to the inside. This
following the steps below reduces the chance of splash or escape of
the spilled chemical beyond the present
Basic Spill Control Procedures boundary perimeter.

1. Immediately alert the area supervisor and • NOTE – Bulk absorbents and
other occupants of the area of potential many spill pillows do not work
risk. with hydrofluoric acid.
2. Use Personal Protective Equipment, POWERABSORB (by 3M)
following specific procedures for use of products or their commercial
Personal Protective Equipment. equivalent will handle
hydrofluoric acid. Acid
• Example: Never enter a neutralizers typically have a
contaminated space color change indicator which
(atmosphere) without protection, shows when acids have been
i.e., the use of a respirator. The neutralized.
use of a respirator or self-
contained breathing apparatus 7. When spilled materials have been
requires specialized training. If absorbed, use a brush and scoop to place
respiratory protection is materials in an appropriate container.
necessary and no trained Polyethylene bags may be used for small
employees are available, contact spills. 5-gallon buckets or 20-gallon
UMW PD immediately. drums with polyethylene liners may be
appropriate for larger quantities of
3. If the situation is potentially saturated absorbent materials.
volatile/flammable, evacuate the area of 8. Once all the material and spill residue has
potential risk immediately, ventilate the been placed in an appropriate container a
space, and attempt to suppress or control hazardous waste sticker or label must be
the potential ignition source. completed identifying the material as
4. Protect floor drains or other potential “Spill Debris” involving the specific
avenues of environmental release as chemical and affixed to the container.
much as possible. Spill socks and 9. Decontaminate the surface where the
absorbent materials may be placed spill occurred using mild detergent and
around drains as needed. water, when appropriate.
5. Determine the extent of the spill and 10. Report any hazardous chemical spill to
clean up as follows: OEMS for follow-up and review.

• Small Spill: Up to 300 cc’s;

respond with chemical treatment
or absorption with a
Biochemistry for Med Lab Science Laboratory CHEM 103 M 66
1ST Semester Prelim
PH AND BUFFERS Colorless
Hydrogen Bubbles
Test Acids Neutral Bases
Litmus Red Blue Blue Conclusion: Acid
Paper
(Blue) 6.) Vinegar
Litmus Red Red Blue Red→ Red
Paper Blue→ Red
(Red) Colorless
Phenolph Colorless Colorless Pink Hydrogen Bubbles
thalein
Conclusion: Acid
Metal Hydroge No No
n Change Change Concentration pH Conductivity
Bubbles Strong High Low High
Acid
Examples: Strong High High High
Base
1.) Baking Soda Weak High Low Medium
Red→ Blue Acid
Blue→ Blue Weak High High Medium
Pink Base
No Change * Or vice versa

Conclusion: Base
BIOCHEMICAL PROCESSES
2.) Sugar Solution Laboratory Activity #2
Red→ Red
Blue→ Blue Learning Outcomes
Colorless
No Change 1. By the end of this activity, the students
will be able to:
Conclusion: Neutral 2. explain the principle of in the movement
of gases across a membrane;
3.) Liquid Hand Soap 3. describe the process of osmosis;
Red→ Red 4. explain the movement of water through
Blue→ Blue cell membranes;
Colorless 5. compare and contrast three osmotic
No Change states: hypotonic, isotonic, and
hypertonic; and
Conclusion: Neutral 6. explain the process of emulsification.

4.) Ammonia Biochemical Processes

Red→ Blue
Blue→ Blue * Biochemical processes mediate the interaction
Pink of cells with their environment and are
No Change responsible for most of the information
processing inside the cell. Networks of
Conclusion: Base interacting proteins underlie many of these
processes.
5.) Lemon Juice
Red→ Red
Blue→ Red
Biochemistry for Med Lab Science Laboratory CHEM 103 M 67
1ST Semester Prelim
THREE MAJOR TYPES OF
BIOCHEMICAL PROCESSES ARE
DISTINGUISHED

1. Metabolic Pathways
* Are sequences of chemical reactions, each
catalyzed by enzymes, where certain product
molecules are formed from other small substrates.
Metabolites are usually small molecules while
enzymes are proteins.

2. Signal Transaction Networks

* Are pathways of molecular interactions that
provide communication between the cell
membrane and intracellular end-points, leading to 1. DIFFUSION
some change in the cell. Signals are transduced
by modification of one protein’s activity or * Diffusion is the movement of molecules from a
location by another protein. region of higher concentration to a region of
lower concentration down the concentration
gradient.

A. Dialysis
* It is the diffusion of solutes across a selectively
permeable membrane. A selectively permeable
membrane is the one that allows only specific
ions and molecules to pass through, while
obstructs the movement of others.
A. Reception
* a cell detects a signaling molecule from the
outside of the cell. A signal is detected when the
chemical signal (also known as a ligand) binds to
a receptor protein on the surface of the cell or
inside the cell.

B Transduction
* When the signaling molecule binds the receptor
it changes the receptor protein in some way. This
change initiates the process of transduction.
Signal transduction is usually a pathway of
several steps. Each relay molecule in the signal
transduction pathway changes the next molecule
in the pathway. 2. OSMOSIS
C. Response It is the movement of solvent molecules from the
* Finally, the signal triggers a specific cellular region of lower concentration of solute to the
response. region of higher concentration of solute through a
semipermeable membrane. Since water is
3. Gene Regulation Circuits solvent in every living being, biologists
* Determine whether or not a particular gene is define osmosis as the diffusion of water across a
expressed at any particular time. Transcription selectively permeable membrane. For example,
factors, proteins that promote or repress plants take water and minerals from roots with the
transcription, either directly or indirectly bind help of osmosis.
regulatory DNA elements.
Biochemistry for Med Lab Science Laboratory CHEM 103 M 68
1ST Semester Prelim
PROPERTIES OF PROTIENS

*The solubility of proteins in aqueous buffers

depends on the distribution of hydrophilic and
hydrophobic amino acid residues on the protein’s
surface. Hydrophobic residues predominantly
occur in the globular protein core, but some exist
in patches on the surface. Proteins that have high
hydrophobic amino acid content on the surface
have low solubility in an aqueous solvent.

* Hydrolysis of the protein is what happens when

the peptide bonds are broken. This process needs
water and an enzyme (proteolytic enzyme). The
result of hydrolysis is smaller amino acid chains
(peptides), and free amino acids. The solution
containing the protein pieced (small peptide
chains and free amino acids) is called a
hydrolysate solution

QUALITATIVE ANALYSIS OF PROTEINS

* Proteins, also known as polypeptides, are

3. EMULSIFICATION organic compounds made up of amino acids.
They are arranged in a linear chain and folded
* Emulsification, or to emulsify something, is into a globular form. Proteins are essential parts
defined as the mixing of two liquids that usually of organisms and they participate in virtually
are immiscible to form an emulsion. Two liquids every process within cells. Many proteins are
can form different types of emulsions depending enzymes that catalyze biochemical reactions and
on which liquid was dispersed in which, with one are vital to metabolism. The size of a protein is an
liquid being the dispersed phase and the other important physical characteristic and scientists
being the external phase, which is added into the often use particle size analyzers in their studies
dispersed phase. Our ability to emulsify also to discuss protein size or molecular weight.
plays a vital role in the human digestion process
and occurs in the small intestine to aid the The Structure of Proteins
breakdown of fats.
Most proteins fold into unique three-dimensional
structures. The shape that a protein folds into
naturally is known as its native conformation.
While most proteins can fold unassisted through
the chemical properties of their amino acids,
others require the aid of molecular chaperones.

There are four distinct aspects of a protein’s

structure:

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1ST Semester Prelim
Qualitative Analysis of Proteins *On adding alkali to these nitro derivative salts,
the color change from yellow to orange.
1. Biuret Test:
* This is one of the most general tests for proteins.
When a protein reacts with copper (II) sulphate, a
positive test is the formation of a copper complex
that has a violet color/ deep/ blue/ purple color.

*The test works for any protein or compound that

contains two or more of the following groups:

• -C(=O)NH
• -C(=O)NH2,
• -CH2NH
• -C(=NH)NH2
• -C(=S)NH2

2. Ninhydrin (triketohydrindene hydrate)

Test:
* Amino acids with a free –NH2 group and
• All proteins + biuret
proteins containing free amino groups react with
• Free amino acids – biuret
ninhydrin to give a purple-blue complex.
• All proteins and amino acids + ninhydrin,
EXCEPT PROLINE amino acid
• Only proline – ninhydrin
• Egg albumin and casein contain tyrosine
(phenolic group) + Millon’s
• Amino acids aside from tyrosine –
3. Millon’s Test: Millon’s
* This test is specific for the detection of phenolic
groups.

4. Xanthoproteic test:
* This s used to detect amino acids containing an
aromatic nucleus (tyrosine, tryptophan and
phenylalanine) in a protein solution which gives
yellow color nitro derivatives on heating with
conc. HNO3.

* The aromatic benzene ring undergoes nitration

to give yellow colored product. Phenylalanine
gives negative or weakly positive reaction though
this amino acid contains aromatic nucleus
because it is difficult to nitrate under normal
condition.
Biochemistry for Med Lab Science Laboratory CHEM 103 M 70