M1: Introduction to Biochemistry (Review of Prerequisite Concepts)
 Hydroxyl group- polar, hydrogen bond donor
Functional Groups
 A specific arrangement and group of atoms in
molecules that determine chemical properties
and reactions.
 Molecules may have the same molecular
formula but have different molecular structure
(arrangement of atoms)
 Functional group’s properties can be influenced
by their location in the molecule, presence of
proximal atoms/functional groups.
Functional groups of Alkenes
 Double-bonds- high electron density
 Cis-trans isomerism influences molecular and
bulk property
 Cis-configuration leads to “kinks” in a molecule
 Trans-configuration promotes structural
similarity to alkanes
 Reactions of pi bonds: electrophilic addition
 Markovnikov’s Rule- guide for determining
attachment site of substituents
Functional groups of Alcohols
and acceptor; plays a role in H-bonding with
water molecules
 Reactions of hydroxyl groups: oxidation (into
aldehyde, ketone), dehydration (into ether or
alkene), esterification (with carboxylic acids)
 Reacts with aldehyde to form hemiacetal,
reacts with ketone to form hemiketal
Functional groups of Ethers
 Comparable to alkanes in terms of polarity; has
a net dipole moment but has weak polarity
 Reactions of ether group: cleavage
 Reactions of aromatic ether: similar to aromatic
reactions; ether group is e-donating
 Aromatic alcohol acidity > alkyl alcohol acidity
Functional group of Aromatic molecule
 Aromaticity criteria:
-Total pi e-= 4n+2 (Huckle’s rule)
-all atoms are sp2 hybridized
-continuos conjugation
 Types: benzoid, nonbenzoid, heterocyclic
 Participates in pi to pi interactions or VDW int
 UV-absorbers
 Reaction: electrophilic aromatic substitution
(Depends on either o-, p- or m- director)
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M1: Introduction to Biochemistry (Review of Prerequisite Concepts)

Functional group of Aldehyde

Functional group of Carboxylic acid

 Aldehyde= terminal group; H-bond acceptor

with H2O, but not with itself; polar
 Carbon and oxygen atoms are sp2-hybridized
 Reaction: nucleophilic addition, oxidation,
reduction, halogenation, including hemiacetal
formation

Functional group of Ketone

 Carboxyl group: polar functional group;
exhibits resonance stability; acidity is
attributed to resonance stability
 Carbon, carbonyl oxygen and hydroxyl oxygen
are sp2-hybridized
 Reaction: salt formation, nucelophilic acyl
substitution, reduction, oxidation
(decarboxylation)

Functional group of Esters

 Ketone: non-terminal group; H-bond acceptor

with H2O but not with itself
 Carbon and oxygen atoms are sp2-hybridized
 Reaction: nucleophilic addition, reduction;
ketones are resistant to oxidation

Keto-enol tautomerism

 Ester: non-terminal group; H-bond acceptor

with H2O, but not with itself

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M1: Introduction to Biochemistry (Review of Prerequisite Concepts)
 Lactones are cyclic esters (has pharmacological
applications)
 Reaction: hydrolysis, saponification

Amines and Amides

Molecular Composition of biological

membranes

 Amine- nitrogen bonded to alkyl group

 Amide- nitrogen bonded to carbonyl carbon
 Amines are basic functional groups (proton
acceptors), found in amino acids
 Amides are not basic
 Chemical reactions of amines: acylation (to
form amides), alkylation
 Chemical reactions of amides: hydrolysis,
reduction, dehydration
Prokaryotic and Eukaryotic Cell:
Basic Concepts to Remember:
 Biomolecules contain a lot of functional groups,
making the structures complex and interesting
 Each functional group predicts its chemical
reactivity UNLESS there are steric hindrances,
intra molecular interactions or kinetic or
electronic barriers
 Intramolecular interactions influence bulk
properties of complex biomolecules
 Thermodynamics and kinetics play a role in
reactivity
 In vivo chemical environments are different
from in vitro chemical environments

Cells and their Molecular Composition

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M1: Introduction to Biochemistry (Review of Prerequisite Concepts)
Cells rough or smooth, depending on the presence of
 As much as we are unique individuals, we are
still similar with each other because of the cells
that make up or bodies.
 We are made up of a cell that is why we refer
to cells as the foundation unit of life.
 Cells are composed of organelles, water and
inorganic ions. These organelles are composed
of organized assemblies of macromolecules and
simple molecules. The basis of organelle
functions depends on their molecular
compositions. So it is important to know how
molecules are organized in these structures.
But what are the macromolecules and simple
molecules that can be found in the cell?
 Hermann Staudinger, a Nobel laureate, first
came up with the term “macromolecule”. His
first proposal states that smaller biological
molecules would covalently link together
forming large biological carbohydrates, proteins
and nucleic acid. These substances are called
biomolecules. The simple molecules, on the
other hand, would be your fatty acids,
phospholipids, monosaccharides, amino acids,
and nucleotides.
 The performance of a cell depends on the
interactions that happen from within- how
molecules react with one another.
Macromolecules with a net positive charge
interact molecules on the opposite charge.
Structural Composition of
Eukaryotic Cells
 Nucleus: this is a distinguishing feature of
eukaryotic cells that makes it different from
prokaryotes. The nucleus is the “brain” of the
cell since it controls and regulates cellular
activities. It also contains the genomic DNA and
histone proteins, important components for
the continuation of the organism’s generation.
Past the nuclear envelope that separates
chromatin from the cytoplasm, we will
encounter----
 Endoplasmic reticulum: it is a flat, single-
membrane that can be classified into either
ribosomes.
a. Rough ER: collective site for protein
synthesis.
b. Smooth ER: site for lipid synthesis and
metabolism of drugs.
 Ribosomes: these organelles are composed of
RNA and proteins and are known as the
machinery for protein synthesis.
 Golgi apparatus: composed of lipids, proteins,
and polysaccharides. It is referred to as the
factory site of the cell because its function is all
about processing, packaging, and exporting
proteins to the other organelles.
 Mitochondria: these are made up of double
membranes with proteins and lipids with the
inner matrix containing soluble and insoluble
enzymes, RNA and DNA. These generate energy
that the cell needs for its activities. They serve
as the so-called powerhouse or energy storage
of the cell.
 Peroxisomes and lysosomes: found uniquely in
animal cells. The presence of peroxides and
intracellular debris are taken care of by these
two cellular components.
a. Peroxisomes contain catalase and other
oxidative enzymes
b. Lysosomes contain enzymes for
hydrolysis
 Chloroplasts: uniquely found in plants. They
harness energy from sunlight to generate ATP.
These are double-membrane organelles
containing protein, lipids, RNA, DNA,
ribosomes, and chlorophyll.
 Cytoplasm: it contains the fluid matrix that
holds and assists all organelle movement. It is
composed of a cytoskeleton that is made of
soluble proteins, enzymes, nutrients, and salts
in an aqueous solution.
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M1: Introduction to Biochemistry (Review of Prerequisite Concepts)
 Cell membrane: encloses the cell in bilayer and double bonds in fatty acids components
proteins. It is Also composed of lipids and some
carbohydrates.
 Let us focus our attention the outer layer of the
cell which is the cell membrane. It is comprised
of the following major components:
phospholipids, cholesterol, and membrane
proteins.
 This membrane encloses the cell, making a
protective barrier against the environment.
 It is also through the cell membrane that cell to
cell communication is possible.
 A notable characteristic of the cell membrane
is its impermeability to water soluble
substances- which barricades the cell into two
aqueous compartments- the internal and
external environment.
PHOSPHOLIPIDS:
 The double layers are made up of specific types
of phospholipids that are distributed in each
layer. These include phosphatidylcholine (PC),
phosphatidylethanolamine (PE),
phosphatidylserine (PS), phosphatidylinositol
(PI), and sphingomyelin that are asymmetrically
distributed between the inner and outer
leaflets of the membrane bilayer.
 To understand the connection between the
membrane bilayer and how phospholipids
contribute to such structural arrangement, we
must first determine the chemical structure and
component of a phospholipid.
 Component of phospholipid: It is one of the
types of lipids that contains C, H, O, N and P. C,
H, O is usually observed at the tail while N and
phosphorus are found at the head. The head
containing the phosphate group is polar.
Meaning, it readily interacts with water. This is
the complete opposite of the tail portion. It is
hydro-phobic being nonpolar due to the
presence of the fatty acid chain that repels
water. Considering that both the internal and
external environment of the cell is aqueous in
nature, the polar heads are exposed while the
nonpolar tails are sandwiched in the middle.
 Cell Membrane Fluidity: as cell membrane
contains phospholipids, the presence of single
affect the orientation of these fatty acids,
making them appear as kinks. So if we are to
assemble them altogether, they will contribute
to the fluidity in the interior of the cell.
 Specific phospholipids found in each layer:
a. PC and sphingomyelin comprise the
majority of the outer layer. This is often
observed in the nervous system as they
facilitate nervous transmission.
b. For the inner layer, phosphatidyleserine and
phophatidylethanolamine. PE is associated
with receptor molecules of the cell while PS
is likely to contribute to the cellular
regulation- apoptosis.
c. Found in the inner part of the cell
membrane is the phosphatidylinositol. PI is
converted into phosphatides that regulate
membrane remodeling during exocytosis,
endocytosis, and vesicular trafficking by
recruiting and/or activating proteins that
sense the curvature of the lipid bilayer,
form scaffolds on the membrane and
regulate actin assembly.
 Aside from phospholipids, another component
that is abundant in the cell membrane is
cholesterol which inserts itself in between the
phospholipids.
 Continuation of Cell Membrane Fluidity:
CHOLESTEROL:
 Everytime the hydrocarbons are subjected to
changes of temperature from high to low, the
cholesterol acts in between impeding the
motion of phospholipids which aids in
maintaining the integrity of the cell membrane
by keeping it intact.
 Thus, continuous flow to the membrane is
possible.
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M1: Introduction to Biochemistry (Review of Prerequisite Concepts)
MEMBRANE PROTEIN:
 It helps in the movement of important
substances in and out of the cell.
 Membrane proteins are classified into two:
a. Integral Proteins: attached to the
membrane surface
b. Peripheral Proteins: freely moving and can
separated themselves from the structure
 Role of membrane protein is connected to the
characteristic movement that happens across
the cell membrane.
 Osmosis: this involves the movement of a
solvent that needs to pass through a semi-
permeable membrane to an area of higher
concentration of solute. In this case, water is
the solvent, and the cell membrane acts as the
semi-permeable structure. To regulate this, we
have aquaporins. Aquaporins transport water
via this process. There are 9 isoforms of
aquaporins distributed all over the body in each
organ. But why regulate water concentration in
the first place? Because water is a powerful
solvent that can disrupt the functioning of the
cell whenever it is deficient or in excess.
 Active Transport: another cellular process
observed across the cell but which requires
energy. It also needs a carrier to be able to
move a particular molecule across the cell
membrane from a low concentration to a high
concentration. One good example is the
Sodium-Potassium pump that utilizes ATPase as
the active transport protein.
 Passive Transport: this is somewhat similar to
active transport in such a way that it needs a
carrier to move across the cell membrane but
the only difference is that, no energy is needed
to perform its function. An example of a passive
transport protein is Glucose transporter (GLUT).
 Moving on, we also have the ligand-gated ion
channels. The net charge of the molecule
influences the interaction for transportation.
Usually this type of movement across said
channels are observed in Acetylcholine
receptors (AchR) which are found in neurons
and neuromuscular junctions.
 These major components of cell membrane are
essential for the cell, but what about surface
protection? Is there a component responsible
for it? Yes, there is, it is the glycocalyx.
Remember our riddle? It mentions about “a
synergy”, cell to cell interaction is made
possible because of the glycocalyx. It is because
it serves as a unique marker for recognition and
interaction. Such interaction would of course
need adhesion at the surface for specific
identification. All of these are attributed to its
component, the oligosaccharide which is a
carbohydrate. So not only lipids and proteins
are involved, carbohydrates through minor in
composition, still provide a functional use for
the cell membrane.
Toulmin Argumentation Pattern
 A method use to exercise our capacity to
rationalize the things that we are curious of and
to determine how we can relate one concept to
another.
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M1: Introduction to Biochemistry (Review of Prerequisite Concepts)
 There are six elements in TAP:
1. Claim: the conclusion to which the person is
tying to convince the audience to believe
2. Data: the factual evidence that led the
person to said conclusion
3. Warrant: provides the logical reasoning
that connects the data to the claim
4. Backing: provides additional information
5. Qualifier: can address that the claim is not
absolute. It specifies any limitation that the
data or claim has.
6. Rebuttal: is the counterargument which can
be directed to the data and the warrant
that points out the possible flaw in the
argument. This is provided by the other
person that is against the claim.
 Example of TAP:
Garlic has antibacterial property. Antiobitics
stops infection caused by bacteria. Is it safe to
infer that Garlic can replace antibiotics for
treatment?