PHARMACEUTICAL BIOCHEMISTRY (PBIO 2 1 1 )

PHARMACEUTICAL BIOCHEMISTRY (PBIO 2 1

1)

COLLEGE OF PHARMACY
 Introduction

Cell Structure a n d
Fu n ction
 Know what biochemistry is and its principle.
 Know the components of a cell and its major
types of bio-molecules.
 Understand how the role of cell organisation and
different types of chemical reactions involved in
maintaining high degree of internal order.

Biochemistry is the application of chemistry to
the study of biological processes at the cellular
(anabolism (maliit - malaki) and molecular
level (malaki to maliit)
 → STUDY OF THE CHEMISTRY OF LIFE
- It emerged as a distinct discipline around the
beginning of the 20th century when scientists
combined chemistry, physiology and biology to
investigate the chemistry of living systems by:
A. Studying the structure and behavior of the complex
molecules found in biological material and (lipids,
steroids)
B. the ways these molecules interact to form cells, tissues
and whole organism
 Cells (basic structural units of all living organisms) are highly
organized and constant source of energy is required to
maintain the ordered state.
 Living processes contains thousands of chemical
reations. Precise regulation and integration of these
rxns are required to maintain life
→ oxidation, kreb’s cycle, glucorinization, etc.


Certain important reactions E.g. Glycolysis (breakdown

 of molecular level into Glycogen) is found in almost all
organisms.
 All organisms use the sa m e type of molecules: CHO,
proteins, lipids (fatty acids) & nucleic acids (DNA,
RNA)
Instructions for growth, reproduction and developments for
each organism is encoded in their DNA
 Basic building blocks of life
 Smallest living unit of an organism
 Grow, reproduce, use energy, adapt, respond to their
environment
 Many cannot be seen with the naked eye
 A cell may be an entire organism or it may be one of billions
of cells that make up the organism
Prokaryotes include bacteria & lack a nucleus or membrane-
bound structures called organelles (bacteria and archaea)
→ Any unicellullar organism that does not contain a membrane-
bound nucleus or organelles
→ replicates entire genomes at once
→ Chromosomes – 1 long single loop of DNA

Eukaryotes include most other cells & have a nucleus and

membrane-bound organelles (plants, fungi, & animals, protists
cell)
→ Any cell that contains a clearly define nucleus and membrane -
bound organelle
→ Highly regulated with selected genetic sequence
→ Multicellular
→ More than 1 chromosome
→ Ability to store hereditary information
 CHARACTERISTICS PROKARYOTIC CELL EUKARYOTIC CELL
Size of the cell <1–5 micrometer in 10-100 micrometer in
diameter diameter
Example Bacteria and Archaea Animals and Plants
Nucleus Absent Present
Present; e.g lysosomes,
Membrane-enclosed Absent golgi complex,
organelles endoplasmic reticulum,
mitochondria,
chloroplast
Flagella Consist of two protein Complex; consist of
building blocks multiple microtubule
Cell wall Usually present; Only in plant cell and
chemically complex fungi (chemically
simpler cell wall)
 CHARACTERISTICS PROKARYOTIC EUKARYOTIC
Plasma membrane Usuall no Yes
with steriod
Cytoplasm No cytoskeleton or Cytoskeleton;
cytoplasmic cytoplasmic
streaming streaming
Ribosomes Smaller Larger
Cell division Binary fission Mitosis

Prokaryotic cells, as well as eukaryotic cells, are covered

with the plasma membrane, which is located on top of
the cell membrane or mucous capsule. Despite of its
relative simplicity, prokaryotes are typically
independent cells.
Nucleoid region contains the DNA
• Cell membrane & cell wall
•Contain ribosomes (no membrane)
to make proteins in
their cytoplasm
Contain 3 basic cell structures:
• Nucleus
• Cell Membrane
• Cytoplasm with organelles
Characteristic B io- me mbra ne s a n d O rg a ne lle s
Plasma Membrane- TRANSPORTER/GATE KEEPER
A l i p i d /p rotei n /carb ohyd rate co m p l ex, p rov i d i n g a
barrier a n d c o n t a i n i n g tr an sp o r t a n d s i g n a l i n g
systems.
→ Embedded at the top of the plasma membrane

Nucleus – found In the center of cell

Double m em b r an e s u r ro u n d i n g t h e ch ro m o so m es a n d t h e
n u c l e o l u s ( s i t e o f s y n t h e s i s o f R N A ) . Po res al l ow sp eci fi c
co m mu n i cati on wi th t h e c y t o p l a s m . The n u c l e o l u s i s a
s i t e for s y n t h e s i s o f RNA m a k i n g u p t h e r i b o so m e
Mitochondrion – powerhouse of the cell (energy)
Su rro u n d ed b y a d o u b l e m e m b r a n e wi th a s e r i e s o f fo l d s
cal l ed cr i stae . Fu n cti o n s i n e n e r g y p ro d uction t h ro u g h
m etab o l i sm . C o n tai n s i ts ow n DNA, a n d i s b e l i eve d to h av e
o r i gi n ated a s a c ap t u re d b acter i u m .

Chloroplasts (plastids) - photosynthesis

Su rro u n d ed b y a d o u b l e m em b r an e , c o n t a i n i n g s t a c ke d
t hy l a ko i d m e m b r a n e s . R e s p o n s i b l e for p h o t o s y n t h e s i s , t h e
t r ap p i n g o f l i gh t e n e r g y for t h e s y n t h e s i s o f s u g a r s .
C o n tai n s DNA, a n d l i ke m i to c h ondr ia i s b e l i eve d to h av e
o r i gi n ated a s a c ap t u re d b acter i u m .
 Rough endoplasmic reticulum (RER)
A n etwo r k o f i n terco n n ected m e m b r a n e s fo r m i n g c h a n n e l s
wi th i n t h e cell. Covered wi th r i b o so m es ( c a u s i n g t h e
"rough" ap p e a r a n c e ) w h i c h are i n t h e p ro c e s s o f
s y n t h e s i z i n g p ro tei n s for secreti o n or localization i n
m em b r an es
Ri b o so m e → Protein a n d RNA c o m p l ex re s p o n s i b l e for p ro tei n
synthesis
Smooth endoplasmic reticulum (SER)
A n etwo r k o f i n terco n n ected m e m b r a n e s fo r m i n g c h a n n e l s
wi th i n t h e cell. A s i t e for s y n t h e s i s a n d m etab o l i sm o f l i p i d s.
Also c o n t a i n s e n z y m e s for d e t ox i f y i n g c h e m i c a l s i n c l u d i n g
d r u g s a n d p esti ci d es .
Golgi apparatus
A s e r i e s o f s t a c ke d m e m b r a n e s . Ve s i c l e s ( sm al l m em b r an e
s u r ro u n d e d b a g s ) carr y m ater i al s from t h e RER to t h e Golgi
a p p a r a t u s . Ve s i c l e s m ove b e t we e n t h e s t a c k s w h i l e t h e
p ro tei n s are "p ro cessed " to a m atu re form. Ve s i c l e s t h e n
carr y n e w l y fo r m ed m em b r an e a n d s e c re t e d p ro tei n s to
their fi n al d e s t i n a t i o n s i n c l u d i n g secreti o n or m e m b r a n e
localization
Lysosomes
A m e m b r a n e b o u n d o r g a n e l l e th at i s re s p o n s i b l e for
d e g r a d i n g p ro tei n s a n d m e m b r a n e s i n t h e cell, a n d a l s o
h e l p s d e g r a d e m ater i al s i n g e s t e d b y t h e cell.
 Vacuoles
M e m b r a n e s u r ro u n d e d " b ag s " th at co n tai n water a n d
s t o r age m ater i al s i n p l an ts .

Peroxisomes or Microbodies
Pro d u ce a n d d e g r a d e hy d ro ge n p eroxi d e
( H 2O2) , a toxic c o m p o u n d th at c a n b e
p ro d u c e d d u r i n g metabolism.

Cell wall
P l a n t s h av e a r i gi d cell w a l l i n add i ti o n to their cell m e m b r a n e s

Cytoplasm
e n c l o s e d b y t h e p l a s m a m em b r an e , l i q u i d por tion cal l ed cy to so l
a n d it h o u s e s t h e m e m b r a n o u s o r g a n e l l e s .

Cytoskeleton
Arrays o f protein fi l am en ts i n t h e cy to so l . Gi ves t h e
cell i ts s h a p e a n d p rov i d e s b a s i s for m ovem en t.
E . g . m i cro tu b ul es a n d m i crofi lamen ts.
 ELEMENTS
 SIMPLE ORGANIC COMPOUNDS (MONOMER)
 MACROMOLECULES (POLYMER)
 SUPRAMOLECULAR STRUCTURES
 ORGANELLES
 CELLS
 TISSUES
 ORGAN SYSTEM
 ORGANISMS
 Just like cells are building blocks of tissues likewise molecules are
building blocks of cells.
 Animal and plant cells contain approximately 10, 000 kinds of
molecules (bio-molecules)
 Water constitutes 50-95% of cells content by weight.
 Ions like Na+, K+ and C a + m a y account for another 1%
 Almost all other kinds of bio-molecules are organic (C, H, N, O, P,
S)
 Infinite variety of molecules contain C.

Most bio-molecules considered to be derived from hydrocarbons.
 The chemical properties of organic bio-molecules are determined
by their functional groups. Most bio-molecules have more than
one.
 • Building blocks of proteins.
 1. Amino • Contains amino group and carboxyl group
function groups (behavioral properties)
acids: • R Group (side chains) determines the chemical
properties of each amino acids.
• Carboxyl group, amino group, the hydrogen,
alpha carbon (alpha – carbon is connected to 4
functional group/ different group), r group / r
side chain (important: determines the chemical
properties of each amino acids)
• Also determines how the protein folds and its
biological function.
• Individual amino acids in protein connected
by peptide bond/ peptide link.
• Functions as transport proteins, structural
proteins, enzymes, antibodies, cell
receptors.
• Naka highlight- R side chain
• Polar and charged amino acids – water soluble
• Naka highlight- R side chain
• Nonpolar amino acids – water insoluble and lipid soluble
 Polar and charge amino acids
• Serine (Ser) • Tyrosine (Tyr)
• Threonine (Thr) • Asparagine (Asn)
• Cysteine (Cys) • Glutamine (Gln)
Acidic Basic
• Aspartic acid (Asp) • Lysine (Lys)
• Glutamic acid (Glu) • Arginine (Arg)
• Histidine (His)
Nonpolar amino acids
• Glycine (Gly) • Methionine (Met)
• Alanine (Ala) • Phenylalanine (Phe)
• Valine (Val) • Tryptophan (Trp)
• Leucine (Leu) • Proline (Pro)
• Isoleucine (Ile)
EXAMPLES OF PROTEINS

• Keratin (Peacock feather)

• Silk (Spider’s web)
• Keratin (Human Hair)
2. MONOSACCHARIDES
• Carbohydrates most abundant organic molecule found in
nature. 1 st in line for energy
• Initially synthesized in plants from a complex series of
reactions involving photosynthesis.
• Basic unit is monosaccharides.
• Monosaccharides can form larger molecules e.g.
glycogen, plant starch or cellulose.
• Building block or monomer of polysaccharide
Functions
• Store energy/ Storage polysaccharide in the form of starch
(photosynthesis in plants) or glycogen (in animals and
humans).
• Provide energy through metabolism pathways and cycles.
• Supply carbon for synthesis of other compounds.
• Form structural components in cells and tissues.
• Intercellular communications
• Polymerization – combination of two monosaccharide
• Building up – from monomer to polymer
• Known as dehydration synthesis. – removes water nagdidikit sila
therefore nagkakaroon tayo ng malaking molecule
• Breaking down – from polymer to monomer
• Known as Hydrolysis – addition of water
• Chitin – structural polysaccharide for animals
• Cellulose – structural polysaccharide for plants
Storage polysaccharides
Starch – for plants
Glycogen - for animals
- Building blocks of lipids
- Are monocarboxylic acid contains even number C atoms
- Functional Group: Carboxylic acid, they contain even number
of carbon atoms
- Two types: saturated (C-C sb) (SSB – saturated single bond)
and unsaturated (C-C db) (UDB- Unsaturated double bond)
- Fatty acids are components of several lipid molecules.
- E,g. of lipids are triacylglycerol, steroids (cholesterol, sex
hormones), fat soluble vitamins (Vit A, D, E, K).

Functions:
- Storage of energy in the form of fat (fats - second line of
energy)
- Membrane structures
- Insulation (thermal blanket)
- Synthesis of hormones
Triacylglycerol
• DNA - Deoxyribonucleic Acid
• RNA - Ribonucleic acid
• CARRIES GENETIC MATERIAL
• STORES HEREDITARY INFORMATION
• HELPS TO MAKE PROTEIN MOLECULES
Metabolism: total sum of the chemical reaction happening in
a living organism (highly coordinated and purposeful
activity)
a. Anabolism- energy requiring biosynthetic pathways
a. Building up – monomer to polymer
b. Catabolism- degradation of fuel molecules and the
production of energy for cellular function
a. Breaking down – polymer to monomer
• All reactions are catalyzed by enzymes
• Amylase to digest starch
• Protease to digest protein
• Lipases to digest lipids
The primary functions of metabolism are:
a. acquisition & utilization of energy
b. Synthesis of molecules needed for cell structure and
functioning (i.e. proteins, nucleic acids, lipids, & CHO)
c. Removal of waste products
1. Nucleophilic Substitution
 One atom of group substituted for another

2. Elimination Reactions
 Double bond is formed when atoms in a molecule is

removed

3. Addition Reactions:
 Two molecules combine to form a single product.
 A. Hydration Reactions
 Water added to alkene > alcohol (common addition rxn)
4. Isomerization Reactions.
 Involve intramolecular shift of atoms or groups

5. Oxidation-Reduction (redox) Reactions

 Occur when there is a transfer of e- from a donor

to an electron acceptor

6. Hydrolysis reactions
 Cleavage of double bond by water.
 Fall 07 CHEM 3750 Organic Chemistry I Prof. Schoffers, WMU

Classes of Organic Compounds 1. Hydrocarbons – only contain C, H

2. Compounds containing oxygen (O)
Are defined by functional groups (FGs) 3. Compounds containing nitrogen (N)

Class FG, Description Examples

Abbrev
iation
1. Hydrocarbons
1.1. Alkanes R-H Contain only carbon methane (CH4), ethane (CH3-CH3),
and hydrogen, only propane (CH3-CH2-CH3), butane,
single bonds pentane, hexane, cyclopentane,
cyclohexane
Alkyl group R- Alkyl group, R group, methyl (-CH3), ethyl (-CH2CH3)
R = abbreviation for
any alkyl group
1.2. Alkenes Contain C=C double ethene (ethylene, CH2=CH2), propene
bond (propylene, CH3CH=CH2)
cis / trans isomers 2-butene
possible
1.3. Alkynes Contain C≡C triple ethyne (H-C≡C-H, acetylene), propyne
bond (H-C≡C-CH3)
H H
1.4. Aromatic Hydrocarbons Ar 3 C=C in a 6- C C
(=Arenes) membered ring, H C C H
separated by C-C ≡ C C
benzene H H
bonds
Ar- Aryl group
phenyl group
2. Organic Compounds
Containing Oxygen
2.1. Alcohols R-OH Contain hydroxyl methanol (CH3OH), ethanol (CH3-CH2-
group (OH) OH)
2.2. Ethers R-O-R Contain ether (C-O-C) dimethyl ether (CH3-O-CH3)
R-O-R’ bond
O CH3
cyclohexyl methyl ether
2.3. Aldehydes & Ketones Both contain carbonyl O
group (C=O) C
formaldehyde H H
Aldehyde O O
C C
R H ethanal (acetaldehyde) H3C H
Ketone O methyl ethyl ketone (2-butanone)
C O
R R'
C
H3C CH 2 CH 3
 Fall 07 CHEM 3750 Organic Chemistry I Prof. Schoffers, WMU

Class FG, Description Examples

Abbrev
iation
2.4. Carboxylic Acids RCOOH Carbonyl (C=O) + O
RCO2H hydroxyl (OH) group C
O ethanoic acid (acetic acid) H 3C OH

C CH3COOH, CH3CO2H
R OH
butyric acid (butanoic acid)
CH3CH2CH2COOH
smell of rancid butter
2.5. Carboxylic Acid
Derivatives
2.5.1. Acid chlorides O O
C C
R Cl acetyl chloride H3C Cl
2.5.2. Esters O O
C C
R OR' methyl acetate H3C OCH3
2.5.3. Amides O O
C C
R NH 2 acetamide H3C NH 2

3. Organic Compounds
Containing Nitrogen
3.1. Amines R-NH2 All amines are basic methylamine H3C NH2
R-NH-R’
R N R'
R''
3.2. Amides O Amino group next to O
C carbonyl group C
R NH 2 N-methylacetamide H3C NHCH 3
O
C
R NHR'
O
C
R NR'R''

3.3. Nitriles R-C≡N, Contains a C≡N triple acetonitrile H3C C N

R-CN bond
C N
benzonitrile