THE CELL

Redario C. Laygo, M.D.

Department Of Biochemistry, Molecular
Biology & Nutrition
 Reasons Why Study Biochemistry

• Biochemical studies lead us to a

fundamental understanding of life

• Biochemistry has a profound impact on

our understanding of medicine, health,
nutrition, and the environment

• Biotechnology will also advance from

biochemical studies
 Importance Of Biochemistry In
Medicine
• Human nutrition

• Diagnosis of diseases

• Treament of disease states

• Creation of “designer” drugs

 Biochemistry Defined
• Science which describes:
- structure
- organization
- function
of living matter in molecular terms

• “the study of life at the molecular level”

 The Three Primary
Areas(Subdivisions) of Biochemistry

Structure/ Information
Function

Bioenergetics
 Objective of Biochemistry
• is the complete understanding at the
molecular level of all of the chemical
processes associated with living cells

• Biochemistry and Molecular biology:

– draw on techniques from:
• Biology
• Chemistry
• Physics
– provide a key interface between these fields
 Objective of Biochemistry
• Biochemists and Molecular biologists investigate
all forms of life, such as:
– Viruses
– Bacteria
– Yeast
– Fungi
– Plants
– Animals

• Much of this research examines life at the

cellular and subcellular level.
WATER AND ITS PROPERTIES
WATER AND ITS PROPERTIES
 NONCOVALENT BONDING
FORMED BY WATER

Hydrogen Bonds
Electrostatic Interactions
Van der Waals Forces
Hydrophobic Interactions
 Types of Van der Waals Forces

Dipole-dipole interactions
Dipole-induced dipole interactions
Induced dipole-induced dipole
interactions
 Types of Van der Waals Forces

Dipole-dipole interactions
- Keesom interactions
 Types of Van der Waals Forces

Dipole-induced dipole interactions

- Debye interactions
 Types of Van der Waals Forces
Induced dipole-induced dipole
Interactions
-

– London dispersion forces

 NONCOVALENT BONDING
FORMED BY WATER

Hydrophobic Interactions
 THERMAL PROPERTIES OF
WATER
- hydrogen bonding is responsible for this
property
- each water molecule can form hydrogen
bonds with four other water molecules
- hydrogen bonding is maximum in the solid
form of water
 THERMAL PROPERTIES OF
WATER
- at melting point, 15% of hydrogen bonds

break
- hydrogen bonds continuously break and
form at liquid state of water
- at boiling point, water molecules break
free from one another and water vaporizes
 THERMAL PROPERTIES OF
WATER
- Heatof Vaporization – energy required to
vaporize one mole of liquid at a pressure of one
atmosphere
- Heat Capacity – energy that must be added or
removed to change the temperature by one
degree Celsius
- water has very high heat of vaporization and
heat capacity
 SOLVENT PROPERTIES OF
WATER
- water is a remarkable solvent because of

its dipolar structure & its capacity to form

H bonds
- organic molecules with ionizable groups
and neutral molecules dissolve in water
 SOLVENT PROPERTIES OF
WATER
- nonpolar compounds are not soluble in

water
- amphipathic molecules, those that contain
both polar & nonpolar groups form
micelles when mixed with water
 How Life Started

THE BIG BANG

THEORY
 The Big Bang
Primeval EXPLOSION

Condensation of matter

1st generation of stars

(Hydrogen & helium)

Thermonuclear reactions

Heavier elements:
carbon, nitrogen, oxygen, etc.(periodic table members)
The Big Bang
Maturation

Instability

EXPLOSION

Novas & Super Novas

Condensation

2nd Generation of Stars

(Complete with planetary systems)
 Elements Found In Organisms
• First tier elements:
carbon, hydrogen, nitrogen, oxygen
• Second tier elements:
calcium, chlorine, magnesium, phosphorus, potassium,
sodium, sulfur
• Third tier elements:
cobalt, copper, iron, manganese, zinc
• Fourth tier elements:
aluminum, arsenic, boron, bromine, chromium,
fluorine, gallium, iodine, molybdenum, nickel, selenium,
silicon, tungsten, vanadium
 Approximate Elementary
Composition of the Human Body
Element % Element %
Carbon 50 Potassium 1
Oxygen 20 Sulfur 0.8
Hydrogen 10 Sodium 0.4
Nitrogen 8.5 Chloride 0.4
Calcium 4 Magnesium 0.1
Phosphorus 2.5 Iron 0.01
Manganese 0.001
Iodine 0.00005
 Attributes Of Living Things
• Capacity to extract energy from molecules
called nutrients

• Power to actively respond to changes in

their environment

• Display the attributes of growth,

differentiation, and reproduction
Hierarchical Organization Of
Organisms
 5. Cellular level
6. Macromolecular level

7. Micromolecuar level 4. Tissue level

Glucose, Galactose
Amino Acids
Nitogenous bases
Fatty Acids

1. Organization level

3. Organ level

2. System level
 Macromolecules
Proteins 20 species of amino
acids
Nucleic acids 8 types of nucleotides

Polysaccharides 8 common sugars

Lipids fatty acids

FIVE MAJOR COMPLEX
BIOMOLECULES
Eukaryotic and Prokaryotic Cells
Eukaryotic and Prokaryotic Cells
Eukaryotic and Prokaryotic Cells

synthesized in nucleolus
Eukaryotic and Prokaryotic Cells
 SUBCELLULAR
FRACTIONATION
Biochemical research often requires the isolation
of a particular subcellular organelle either:
- to study the organelle intact
- more commonly to isolate and to study a
specific substance from that organelle
 SUBCELLULAR
FRACTIONATION
• usual process by which an organelle is isolated
for study
• method involves:
• essentially the homogenization or destruction of cell
boundaries by different mechanical or chemical
procedures
• then separation of the subcellular fractions according
to mass, surface, & specific gravity
• generally entails three phases:
• Extraction
• Homogenization
• Centrifugation
 SUBCELLULAR
FRACTIONATION
 Extraction / Cell Disruption

objective:
- maximum disruption of whole cell with
minimum damage to subcellular
compartments particularly the organelles to
be studied
- must be done using mild conditions to
prevent loss of biologic activities of the cell
 Methods Available to Lyse Cells
Blending
- shearing of cellular tissue by rotating blades

Grinding
- cells are merely rubbed against an abrasive, hence
against each other
- makes use of mortar and pestle, ground- glass
beads, sand & aluminum or glass homogenizers

Sonication
- most popular method because:
(a) subcellular organelles can be recovered in a reasonably
intact, undamaged state
(b) the severity of the treatment can be finely controlled
 Methods Available to Lyse Cells
Osmotic Shock
- mildest technique
- cells are suspended in a solution of high solute
concentration causing migration of water out of the cell,
then transferred to pure water, whereupon the water
rushes into the cell and it bursts open

High-pressure Extrusion
- forcing a concentrated suspension through a small
opening under several thousand pounds of pressure
- efficient method for small cells such as bacteria
 Methods Available to Lyse Cells
Treatment with Lysozyme
- most delicate procedure confined to bacterial cell
- uses lysozyme which is an enzyme that breaks up the
rigid cell wall structure of bacteria yielding a protoplast:
cell protected only by its membrane
- the protoplast is then subjected to osmotic shock
 Methods Available to Lyse Cells
Homogenization
- once cells have been disrupted, their constituents
will be liberated into the sucrose solution
- the resulting suspension is a cell-free system
containing many intact organelles:
- is known as the homogenate
 Methods Available to Lyse Cells
Centrifugation
- process of separation of the soluble cell fluid from
the particulate matter as well as the further
fractionation of the latter in the homogenate
 Methods Used in Centrifugation
Differential-velocity or Rate-zonal Centrifugation
principle:
• homogenates have a different mass-to-volume ratio
(density) i.e., heavier bodies will sediment under low
speeds and low gravitational forces while lighter
substances will require higher speeds and higher
gravitational forces.

• efficient fractionation can be achieved by starting on

the low side and performing series of separate and
successive centrifugation toward the high side
 Methods Used in Cetrifugation
Equilibrium Density-gradient Centrifugation
- organelles are separated by their density but
not by their size
- the impure organelles fraction is layered on top
of a solution that contains a gradient of a dense
nonionic substance (e.g. sucrose or glycerol)
then the tube is centrifuged at a high peed for
several hours to allow each particle to migrate
to equilibrium point
 Methods Used in Centrifugation
Purity of organelle preparation is assessed by the
following:
1. morphology - electron microscopy
2. content of marker molecules (enzymes & chemicals)
e.g. cytochrome c – mitochondria
catalase – peroxisomes
acid phosphatase – lysosomes
ribosomes – RER/cytoso
3. Immunological Techniques
uses antibodies specific for the organelle-
membrane proteins
e.g. clathrin
 Cell
• Universal unit of life

• Classification:
prokaryotes
eukaryotes
Prokaryotic Cell
Comparison – Prokaryotes and Eukaryotes
Property Prokaryotic Cells Eukaryotic Cells

Size Small(0.2-5um) Large(10-50um)

Membrane-bounded nucleus No nucleoid Yes – nucleus, nucleolus,

chromosomes
Organelles No Yes – membrane systems
ER & Golgi Complex
Microtubules No Yes

Microfilaments No Yes organelles w/o

Intermediate filaments No Yes membranes

Exocytosis & endocytosis No Yes

Mode of cell division Cell fission Mitosis & Meiosis

Genetic Information DNA molecules complex with DNA complex with proteins
relatively few proteins notably histones to form
chromosomes
Processing of RNA Little Much

Ribosomes Small(70S) 3RNA molecules & 35 Large(80S) 4RNA molecules &

proteins 75 proteins
Eukaryotic Cell
Nucleus
 Nucleus
• Found in all cells except RBC & platelets
• Largest subcellular organelle
• Three constituents:
- nuclear membrane
- nucleolus - “pacemaker” of the cell
- site of ribosomal RNA synthesis
- chromatin – fine fibers made up of nucleo-
somes containing nuclear proteins
called histones
• Function – storage of genetic information
Mitochondrion
 Mitochondrion
• Oval, sausage or kidney shaped
• Parts:
outer membrane
inner membrane
intermembranous space
cristae
matrix
Inner Membrane(mitochondrion)
• With infoldings
• “elementary bodies” with headpiece, stalk and basepiece
- headpiece - contains F1 subunit w/c contains ATP synthetase
- stalk - attach F1 subunit to basepiece
- contains “oligomycin sensitivity conferring protein”
(OSCP)
- basepiece - contains Fo subunit w/c contains enzymes of
respiratory chain in association w/ enzymes of
oxidative phosphorylation
• Highly selective permeability
- has transport systems for specific substances: ATP ADP,
pyruvate, succiniate, α-ketoglutarate, malate, aspartate
Inner Membrane(mitochondrion)
• EXCEPTION to highly selective permeability
- freely permeable to uncharged small molecules: O2,
H2O, CO2, NH3 & monocarboxylic acids such as 3-
OH butyric acid, acetoacetic acid, acetic acid
• Inner leaflet of mitochodrial membrane
- contains: succinate dehydrogenase
3 hydroxy butyrate dehydrogenase
• Outer leaflet of mitochondrial membrane
- contains: glycerol 3 PO4 dehydrogenase
 Intermembranous Space
• “sucrose space”
• Contains: creatine kinase
adenylate kinase
NAD+
CoA pool
 Mitochondrial Matrix
• Contains: DNA
ribosomes
enzymes of Krebs Cycle
enzymes of β-oxidation of fatty
acids
enzymes of ketogenesis
calcium PO4 granules
 Mtochondrion
• Function:
- responsible for aerobic biochemical
processes such as:
Krebs Cycle
oxidative phosphorylation
β-oxidation of fatty acids
initial steps of urea cycle
 Mitochondrial Oxidation
• Involves:
- oxidation of pyruvate or other metabolites to CO2
coupled to reduction of electron carriers: NAD+, FAD

• Electron transfer from NADH and FADH2 to O2

• Utilization of energy stored in the transmembrane proton

concentration gradient for ATP synthetase thru F1F0
ATP complex in inner mitochondrial membrane
 Mitochondrion (sperm cell)
Tissues with a especially heavy demand of
ATP as an energy source usually contain cells
rich in mitochondria. For example, the single
coiled mitochondrion of a sperm cell located
at axoneme where ATP is needed to propel
the cell.
 Endoplasmic Reticulum
Cisternae: tubular membranes or
flattened sacs
Lumen: internal space enclosed
by ER membrane
ER is continuous with the outer
membrane of the nuclear
envelope and therefore, the
space between the two nuclear
membrane is part of the same
compartment of the lumen of the
ER. RoughER - studded with ribosomes for protein synthesis
Smooth ER - synthesis of lipids and steroids like
cholesterol and the steroid hormones. Also for
detoxification and inactivation of drugs and other harmful
compounds.
Rough Endoplasmic Reticulum
Ribosomes
 Prokaryotic Ribosomes
• Contains 65% RNA and 35% proteins
making up 70S
• Has 2 subunits: 50S 34 CHONs
2 RNA(23S, 5S)
30S 21 CHONs
1 RNA(16S)
 Eukaryotic Ribososmes
• Has two subunits making up 80S:
- 60S 45 CHONs
3 RNA(28S, 5.8S, 5S)
- 40S 30 CHONs
1 RNA(18S)
Smooth Endoplasmic Reticulum
• No ribosomes
• Synthesize steroids, phospholipids, TAGs
• Synthesize carbohydrates to conjugate w/
proteins to form glycoproteins
• Participate in glycogenolysis
• Detoxification of xenobiotics (cyt P450)
• In muscle cells: sarcoplamic reticulum
involved in active accumulation & release of
Ca++ ions for muscle contraction
 Microsomes
• Endoplasmic reticulum fragmented into
small closed vesicles
• Types: rough microsomes
smooth microsomes
 Golgi Complex
Stack flattened vesicles
Function:
Processing and packaging secretory proteins
Synthesis of complex polysaccharides
 Golgi Complex
• Usually located near the cell nucleus
• In animal cells it’s close to centrosome or
cell center
• Collection of flattened-membrane bound
cisternae resembling stacks of plates
• Golgi vesicles w/c are asstd. w/ golgi stacks
transport proteins, lipids to & from golgi &
between golgi cisternae
 Golgi Complex
• Two types:
- non clathrin-coated vesicles for
unselected (constitutive) transport
- clathrin-coated vesicles for signal-
mediated (inducible) transport
 Golgi Complex
• Two faces of golgi stacks:
- cis-face or entry face – closely related
to the transitional elements of the ER
- trans-face or exit face – distended into
a tubular reticulum called trans golgi
network (TGN)
 Golgi Complex
• Process N-linked oligosaccharide chains
1. Two broad classes:
- complex oligosaccharides
- high mannose oligosaccharides
2. Provide resistance to protease
digestion
• Assemble proteoglycans
1. O-linked glycosylation of O-linked
oligosaccharides
2. catalyzed by glycosyl transferases
Lysosomes
 Lysosomes
• Membrane-bounded vesicles involved in intracellular
digestion carried out by hydrolytic enzymes active under
acidic pH
• Lumen’s acidi pH(5) maintained by H+pump in the
membrane using energy from ATP hydrolysis to pump
H+s into the vesicle
• Membrane contains: transport proteins and H+pumps
• Membrane proteins are highly glycosylated
 Lysosomes
• Heterogenous organelles reflecting a wide
variety of digestive functions mediated by
acid hydrolases
• Digestive functions: digestion of
1. intra & extracellular debris
2. phagocytosed microorganisms
3. even cell nutrition-principal site of
cholesterol assimilation from LDL
 Lysosomes
• Three pathways for obtaining materials for
digestion:
1. endocytosis
2. autophagy
3. phagocytosis
 Lysosomes

ACID HYDROLASES
NUCLEASES
PROTEASES
GLYCOSIDASES
LIPASES
pH 5 PHOSPHATASES
SULFATASES
PHOSPHOLIPASES

pH 7.2
H+

ATP ADP + Pi
Peroxisomes
 Peroxisomes
• Microbodies
• Surrounded by only a single membrane
• Do not contain DNA nor ribosomes
• Source of 3 hepatic oxidative enzymes:
= D-amino acid oxidase
= urate oxidase
= catalase – constitute up to 40% of
total peroxisomal protein
• Found in all cells
 Peroxisomes
• Important site of O2 utilization
RH2 + O2 R + H 2O 2

H2O2 + R’H2 catalase R’ + 2H2O(liver,renal cells)

2H2O2 catalase 2H2O + O2

 Peroxisomes
• Usually diverse organelles
• Can adapt remarkably to changing
conditions
• Import all their components from cytosol
• New peroxisomes are formed by organelle
growth and fission
Cell Membrane
 Cell Membrane
• Thickness about 75 – 95 A
• Composed of lipids, proteins, carbohydrates
• A lipid bilayer
- amphipathic
- two dimensional
• Fluidity depends on its composition
- phase transition
- Tm
- amount of cholesterol molecules
 Cell Membrane
• Solvent for membrane proteins
• Asymmetrical
• Glycolipids are present
GM1
• Functions: involve the specific membrane
proteins – receptors
* cell signaling * diffusion barrier
* tissue organization * sites of some
* transport enzymes
Cell Membrane
 Cytoplasm
The cytoplasm of eukaryotic cells contains
the cytosol and cytoskeleton
Cytoskeleton Cytosol
A three-dimensional array Semifluid subtance inside
of interconnected the cytoplasm excluding the
filaments and tubules nucleus
Maintain cell shape and Space for many biological
high level internal activities, such as protein
organization synthesis, fat synthesis, and
A framework for the initial steps in the
positioning and actively release of energy from
moving organelles sugars.
 Cytoskeletal Elements
• Maintain cellular morphology
intracellular transport mitosis
cell motility meiosis
• Filamentous structures
microfilaments – actin (β and γ)
microtubules – tubulins (α and β)
* kinesin – move vesicles toward (+) end of
microtubular formation
* cytosolic dynein – move vesicles toward (-) end of
microtubular formation
* axonemal dynein – power cilliary & flagellar
movements
* dynamin - endocytosis
Microfilaments
Examples: muscle contractile cells,
link with plasma membrane, forming
cleavage furrows (divide cytoplasm
during animal cell separation)
Structure: monomer - G actin proteins
form double helical strands of F-actin
Polarity: subunits face the same
direction
Cytoskeleton: contents
 Cytoskeletal Elements
• Intermediate filaments
* keratins
* vimentin-like - vimentin
- desmin
- glial fibrillary acid protein
- peripherin
* neurofilaments - L,M,N
* lamins - A, B, C
Intermediate filaments (IFs)
Most stable and least soluble among the three, regarded as the scaffold for the
entire cytoskeletal framework; Variable in different cell types (6 of them).
Structure: Rodlike segments - dimer - tetramer (protofilament) - join in an
overlapping manner.
 Major Intracellular Markers
Organelles
Nucleus DNA

Mitochondrion Glutamate dehydrogenase

Ribosome High content of RNA

Endoplasmic reticulum Glucose 6 phosphatase

Lysosome Acid phosphatase

Plasma membrane Na+K+ ATPase

5’ nucleotidase
Golgi complex Galactosyl transferase

Peroxisome Catalase , uric acid oxidase

Cytosol Lactate dehydrogenase

Cytoskeleton No specific marker