a.

Anabolism: building up of polymers

PRPM113: PHARMACEUTICAL BIOCHEMISTRY b. Catabolism : breaking down of polymers
1st Semester 2023-2024 BSP2F 3. Molecular Genetics: storage and transmission of
Prof. JR LAPIG biological processes.

Biochemistry and Pharmacology

MIDTERMS COVERAGE Pharmacology – study of drugs.

➢ MODULE 1: Biochemistry: Scope and Application in

How is Biochemistry related to Pharmacology, or drugs?
Pharmacy
1. Biochemistry provides a whole understanding of all chemical
➢ MODULE 2: Lipids and Related Substances
processes occurring and related to living cells at the molecular
➢ Learning Term 1: Long Quiz (M1 and M2)
level that's associated with drug action.
➢ MODULE 3: Amino Acids and Proteins
➢ MODULE 4: Enzymes
2. Biochemistry helps to acquire data on the adverse effects,
➢
molecular targets, & characterization of medicine or different
M1: Biochemistry: Scope and Application in chemical substances within the living cells & organisms.
Pharmacy
Book: Chapter 1 & 40

GUIDE QUESTIONS
● What are the CHEMICAL STRUCTURES of components
of biomolecules?
- Proteins, nucleic acids, lipids and
carbohydrates.
● How do the interactions of these components give rise
to organized supra-molecular structures, cells , Major Causes of Diseases:
multicellular tissues, and organisms? ● Physical agent: extreme temp
- Atom > molecules> organelles> organisms ● Chemical agent: drugs
● How does living matter extract energy from its ● Biological Agents: microorganisms
surrounding in order to remain alive? ● Lack of O2 in hemoglobin
- metabolism ● Genetic disorders: molecular, congenital
● How does organism store and transmit the info it needs ● Immunologic rxn: autoimmune disease, anaphylaxis
to grow and to reproduce itself accurately? ● Nutritional imbalances: hypo/ hyper
Central dogma (replication, translation and ● Endocrine imbalances: hypo/ hyper
transcription)
● What chemical changes accompany the reproduction, Three examples of metabolic analogs designed by biochemists
aging, and death of calls and organisms? and used as important drugs.
-
● How are chemical reactions controlled inside living
cells?
Normal biological Analog used as Application
molecule drug

M1L1: INTRODUCTION TO BIOCHEMISTRY

DEFINITION
Biochemistry: science of the Hypoxanthine, a Leukemia: Incorporation of
precursor of purine 6-mercaptopurine
chemical basis of life.
bases in DNA and 6-mercaptopurine, a derivative blocks
- study of the chemical constituents RNA further DNA
hypoxanthine analog
of living cells and the reactions and that blocks nucleic synthesis.
processes they undergo. acid synthesis
Bios: life Chemistry: matter
Absence of physics and chemistry = nonliving things.

Aims of Biochemistry Thymidine, a normal AIDS: AZT derivative’s

constituent of DNA inhibit enzyme
1. To understand life in molecular terms ; and responsible for DNA
3-azido-2’,3
2. To describe the structure, organization, and functions of Living dideoxythymidine synthesis
Matter in molecular terms . (AZT), An inhibitor of
Areas: Antiretroviral: To the RNA-directed
manage/suppress the DNA synthesis of the
1. Structural Chemistry: components of living org, AIDS virus
replicating viruses
relationship of biological function to chemical structure.
2. Metabolism: totality of chemical reaction occurring in
living matter
 ➔ Organic molecules: produced abiotically early on the
earth.
Epinephrine, an Asthma: Binding of
adrenal hormone that isoproterenol mimics •All biological molecules in all organisms are made from
controls many Isoprolerenol, by hormone binding to the same set of subunits.
cellular functions binding to certain target cell. thereby • Such subunits have been successfully produced in the
membrane receptors blocking stimulation
laboratory by simulating the conditions of the early
for epinephrine, it
mimics the action of times of the earth.
this hormone

BIOMOLECULES IN A CELL

M1L2: BIOMOLECULES

BIOMOLECULES:

➔ consists mainly of C, H, N, O, S, P
➔ occur naturally in living orgs
➔ very large molecules of atom (covalent bond)
◆ Proteins
◆ Carbohydrates
◆ Lipids
Cell wall: polysaccharide (cellulose: most abundant organic
◆ Nucleic Acids
substance)
Forms:
Vacuole: small molecules (water)
● Monomers: simple subunits/ building blocks of
Chloroplast: liquid, protein, carbohydrates
polymers (amino acid, nucleotide, saccharides)
● Polymers: made by joining monomers
Fluid Mosaic Model
• Peptide, Oligopeptide, Polypeptide, Protein
• Nucleic acid, i.e. DNA, RNA
Proteins:
• Oligosaccharide, Polysaccharide
● Integral protein: direct association with the lipid bilayer
-long chain of monomers (peptides, nucleic acids,
● Peripheral proteins: embedded on the surface of the
protein, polysaccharide). Ex. large complex molecules
membrane
(macromolecules)
● Monomers: small
Plasma membrane:
molecules which are chemically
• Forms closed
joined to form the larger, more
compartments on the
complex biological molecules
cytoplasm to define cell
called polymers.
boundaries.
● Polymers: long chains
• Has selective
of monomers joined chemically.
permeabilities and acts
Large, complex molecules
as a protective barrier to
(macromolecules) are polymers.
the uncontrolled flow of
water and other composition between the inside and outside of
the cell
• The selective permeabilities for ions and
How are Biomolecules Synthesized?
substrates are provided by:
Small organic molecules are used as sub-
▫ transporters and
units that combine to synthesize longer
▫ ion channels
molecules.
• Exchanges material with the extracellular environment by
Biomolecules are joined together or broken
exocytosis, and endocytosis.
apart by removing or adding water.
• Gap junctions: specialized membrane structure which adjacent
cells exchange materials
SYNTHESIS OF BIOMOLECULES:
• Plays key role in cell-to-cell interaction and transmembrane
1. Dehydration synthesis: removal of H2O
signaling.
2. Hydrolysis: adding H2O; splitting of biomolecules back
Alteration in membrane components can affect water balance, ion
to its original subunits
in flux and may also lead to:
- Familial hypercholesterolemia: mutation in the gene
ANABOLISM VS. CATABOLISM
encoding LDL receptor
a. Anabolism: building up of polymers
- Cystic fibrosis: mutation in the gene encoding the CFTR
(Condensation)
protein, a Cl- transporter
b. Catabolism : breaking down of polymers
- Wilson disease: • mutation in the gene encoding a
(Hydrolysis/Addition rxn)
copper-dependent ATPase
- • Membranes has an asymmetric structures
 Cholesterol
Intracellular and Extracellular Fluid - CPPP: steroidal nucleus,
cyclopentanoperhydrophenanthrene
- Resides mainly in the plasma membrane but also found
in lesser quantities in mitochondria, Golgi complex, and
nuclear membrane.
- Acts as stabilizer that limits the movement of
phospholipids layers, which slide back and forth in the
membrane.

Tiny gaps/ gap junctions

- Special areas of membrane structures through which
adjacent cells exchange material;
- Enable small molecules such as oxygen to diffuse readily
Lipid into and out of the cell
Components of the Plasma Membrane - The steady stream of oxygen into the cell enables it to
carry out aerobic respiration (provides the energy
needed to carry out cell functions)

Transporters
- Specific proteins involved in facilitated diffusion and
active transport.

Lipids:
Phospholipids
- phosphate, glycerol
- head: hydrophilic, polar
- tail: hydrophobic, non polar
(fatty acids)
- straight tail: saturated
“PING-PONG” MECHANISM OF FACILITATED DIFFUSION
fatty acid
- In this model, the carrier protein exist in two principal
- kink tail: unsaturated
conformation
• “PING” STATE
- carrier is exposed to high concentrations of solute, and
➔ Between lipid/ non lipid soluble substance which
molecules of solute bind to specific sites.
penetrates readily? LIPIDS. thicker and non-polar
- binding induces conformational change.
• “PONG” STATE
Liposome: can trap non-lipids
- the conformational change exposes the carrier to lower
Micelle: can trap lipids
concentration of solute.

Hydrophobic interactions: driving force to

Active Transport vs. Facilitated Diffusion
form bilayer

PROTEINS IN THE PLASMA MEMBRANE

Types of Transporters:
UNIPORT SYSTEM
▫ Moves one type of molecule
bidirectionally
Glycoproteins
- Important integral membrane proteins, where they play
a role in cell-cell interactions: • SYMPORT SYSTEM
- Enabling the immune system to detect foreign cells, ▫ Moves two solutes in the
such as invading bacteria, which carry different same direction
glycoproteins. • ANTIPORT SYSTEM
▫ Moves two molecules in opposite directions (Na+ in, Ca ++ out)
Anomerism:
Ion Channels ● alpha: downward
- Ion channels are large transmembrane proteins that
● beta: upward
serve to provide a pathway for ions to diffuse at a high
rate across the cell membrane according to their
electrochemical potential Glucosidic bonds (binds disaccharides)
Types: ● Sucrose: Glucose+ Fructose
- Ligand-Gated: molecule bind to a receptor, opens the ● Lactose: Glucose+Galactose
channel ● Maltose: Glucose+ Glucose
- Voltage-Gated:open/close accdg to change in
membrane potential Polysaccharides:
- Mechanically-Gated: respond to mechanical stimuli
Starch
(pressure, touch)
● amylose (linear)
● amylopectin (branched)
● cellulose
M2 : BIOMOLECULES (continuation)
❖ LIPIDS

ANABOLISM CATABOLISM ● fatty acids

● non-polar, insoluble in water
-building up -breaking down
● long-chain monocarboxylic acids
-dehydration synthesis -hydrolysis ● even number of C atoms
(condensation reaction) (addition reaction) ● CH3(CH2)nCOOH
● phospholipid, steroid, wax, triglyceride
- H2O in the product side - H2O in the reactant side ● Lipid bilayer - made by phospholipid

TRI/GLYCERIDES
BIOMOLECULES
- lipids possessing a glycerol with one or more fatty
1. Proteins: amino acid
acyl groups
2. Carbohydrates: saccharides
- Glycerol (propane-1,2,3-triol)
3. Nucleic Acid: nucleotides
- trihydric: have three potential attachment sides
4. Lipids: heterogenous group (no common subunit)
for fatty acids
- insoluble in water; soluble in organic
- alcohol + carboxylic acids= esters
chemicals

❖ NUCLEIC ACIDS
❖ CARBOHYDRATES

● DNA (deoxyribonucleic acid): double-strand;

● General Formula for monosaccharides: (CH2O)n
ATCG
● “hydrate of carbon”
● RNA (ribonucleic acid): single-strand; AUCG
● 1 Carbon and 2 Hydrogen
● macromoecules: increasing dimensional
● examples:
complexity: primary, secondary, tertiary, and
○ monosaccharide (glucose, galactose,
fructose) quaternary
○ disaccharide (sucrose, maltose, lactose)
○ oligosaccharide (rhamnose) Nucleotides consist of:
○ polysaccharides (starch, glycogen, ● 5-carbon sugar (pentose)
cellulose) ● nitrogenous base
● an ion phosphoric acid
*E.coli: most studied prokaryote because it is easy to
isolate; used in recombinant DNA technology
Purine (2 fused rings) Pyrimidine
Isomers: same molecular
PuGA: Guanine, Adenine PyCUT: Cytosine, Uracil
formula but different (RNA), Thymine (DNA)
structures
-Cyclic-Fischer Projection
-Haworth projection
❖ PROTEINS

● most abundant biomolecule

 ● chains of amino acids (20 combinations) Chemical Elements of Cells:
● polypeptides (polymer of amino acid) ● Hydrogen: 60%
● eg. keratin, hemoglobin ● Oxygen: 25%
● Carbon: 12%
● Nitrogen: 5%
Water-soluble: B, C
● Others: P,S, Ca, Mg, Na,Cl
Vitamin Deficiency ● Trace amounts: Fe, Cu, Mn, etc.

B1: thiamine Beriberi Major Absorbed Nutients:

● Glucose: major body fuel molecule (oxidized ADP> ATP)
B2: riboflavin Cheilosis, angular stomatitis, ● Glycerol and fatty acids and other fat molecules: major
dermatitis fuel for skeletal muscles
● Amino Acids: structural and contractile protein,
B3: niacin enzymes, hormones, respiratory molecules
● Vitamins : coenzymes act with enzymes
B4: biotin rash about the eyebrow, muscle
pain, fatigue (rare)

B5: panthotenic HTN

acid

B6: pyridoxine Depression, confusion,

convulsion

B9: folic acid anemia, neural-tube defects in

development

B12: anemia, pernicious anemia,

cyanocobalamin methylmalonic-acidosis

C: ascorbic acid scurvy

Lipid-soluble: A,D, E, K

Vit Fxn Deficiency

A vision, growth night blindness,

(Retinol) reproduction cornea amage,
respiratory and GI
tract damage

D regulation of rickets, skeletal

(cholecalcif calcium and deformities,
erol) phosphate impaired growth
metabolism osteomalacia,
soft-bending bones

E Antioxidant inhibition of sperm

(b-alpha prodction, lesion in
tocopherol) muscles and nerves
(rare)

K Blood subdermal
(phytomena coagulation hemorrhaging
dione)

Functional Groups:
● Hydroxyl: alcohol
● Carbonyl: aldehydes/ketones
● Carboxyl: carboxylic acids
● Amino Groups: amines
GLOSSARY OF TERMS (pg 28-29)