Biochemistry
enzymes on a simple reaction, the hydrolysis of
- study of the molecular basis of life.
- study of biomolecules and the different processes
they undergo inside the human body as they
affect the life, health and nutrition status of the
individual
- Biochemistry is concerned with the
physicochemical processes underlying digestion,
absorption, circulation, respiration, metabolism,
growth and reproduction
- biochemistry has an impact to different processes
inside the body due to the fact that once
biomolecules enter the body, they will already be
process by some organs and enzymes. Once
processed, these biomolecules will be converted
to nutrients and substances necessary to support
body processes such as those mentioned earlier.
A good knowledge in Biochemistry will
help you understand the structure and
behavior of biological molecules or
biomolecules. This in turn would allow
appreciation of the processes undergone
by food once ingested.
History of Biochemistry
1. Friedrich Wohler (1828)
- His experiment laid the foundation for
modern biochemistry
- He heated ammonium cyanate (inorganic
compound) to form urea (organic compound
found in urine and blood)
- Demonstrated that organic compounds
need not necessarily be formed in living
organisms
2. Two Major breakthroughs in the
history of Biochemistry
a. Discovery of enzymes and its
roles
Enzymes – catalysts of biological reactions
➢ Starch amylase glucose
➢ Amylase from the example is the enzyme
necessary to degrade starch into its simplest
form which is monosaccharide. This shows
how significant enzyme is in any biological
reactions. With its discovery, better
understanding of metabolic processes was
achieved.
Berzelius – formulated the general principles
of catalysts
➢ Lead to the recognition that ptyalin in
saliva, pepsin of gastric juice and amylase
of sprouted malt were biological catalysts
Emil Fischer – studied the catalytic effect of yeast
sucrose
➢ Substrate + enzyme = intermediate
compound
❖ Proposed the lock-and-key theory of
enzyme action (enzyme – lock;
substrate – key). This includes the idea
that a particular substrate is acted
upon by a specific enzyme.
❖ Almost all reactions that occur in living
cells are catalyzed by enzymes and
thus proceed at very high rates
Carl Neuberg – introduced the term Biochemistry
in 1903 and thus was named as the father of
biochemistry. His notable contribution to science
includes the discovery of the enzyme carboxylase.
This is necessary in the decarboxylation of pyruvic
acid. His experience and contribution to the field of
biochemistry paved way to a better understanding of
metabolic pathways which was investigated by later
researchers.
b. Identification of Nucleic Acid as
information molecules
• Oswald Avery, Colin Macleod and
Maclyn McCarty (1944)
➢ They extracted DNA from a toxic strain of
Streptococcus pneumonia and mixed the DNA
with a non-toxic strain
• James D. Watson and Francis H.C. Crick
(1953)
➢ They deduced the 3D structure of DNA
➢They discovered DNA replication process,
which then transmits biological information to
succeeding generation.
• The central Dogma
➢ States that the information encoded in DNA is
transcribed to RNA and then translated to protein
➢ DNA Transcription RNA translation CHON
➢This is significant in understanding protein
synthesis and interrelated to cell function.
Branches of Biochemistry
1. Molecular Anatomy
- Molecular Anatomy talks about the different
structures and properties of the different
biomolecules. Biomolecules are any organic or
inorganic matter which when introduced into the
body (eaten, injected or inhaled) will either
positively or negatively affect vital life processes.
 - E.g. food, medicine, chemicals, poisons. They DNA (deoxyribonucleic acid) and RNA
also pertain to carbon-containing compounds (ribonucleic acid).
that make up the various parts of the living cell
and carry out the chemical reactions that enable
it to grow, maintain and reproduce itself, and use 2. Molecular Physiology
and store and energy. In this case, biomolecules
are also known as biopolymers. They are
- Molecular Physiology is concerned about the functions of
the different biological molecules.
macromolecules created by joining many
smaller organic molecules, or monomers via Work within cells
condensation.
1. Mechanical work – a change of location or
• Carbohydrates are organic compounds posture of an organism, cell or cellular structure
containing carbon, hydrogen and oxygen,
with a hydrogen-oxygen ratio of 2:1. These
include simple sugars (monosaccharides)
and their polymers (polysaccharides) and
contain several hydroxyl groups
(polyalcohols). Sugar structures can be
represented in several ways which include:

1. Fischer Projection – linear

representation - Open chain form i.e.
ribose

2. Osmotic or electrical work – compounds or

ions are often moved against a concentration gradient

2. Haworth Projection- - Ring form

(biochemical form

Proteins are biomolecules that contain an

amino group and a carboxylate group as well as a
side chain. These are made up of different amino
acids joined by an amide bond or a peptide bond
and its shape is determined by the sequence of its
amino acid residues which is encoded by a gene.
The protein function depends on its 3D structure
or conformation.
Lipids are generally, water-insoluble organic
compounds that form the biological membrane.
The simplest lipids are the fatty acids, long chain
hydrocarbons with a carbohydrate group at one
end.
Nucleic acids are polymers composed of
monomers called nucleotides. Nucleotides contain
a 5-carbon sugar, a heterocyclic nitrogenous base
and at least one phosphate group. There are two
nucleotides, the ribonucleotides and
deoxyribonucleotides. In ribonucleotides, the
sugar is ribose while in deoxyribonucleotides, the
sugar is deoxyribose. The two nucleic acids are
3. Synthetic work – a change in chemical bonds
required to generate complex molecules from simple
precursors
• The energy required to carry out this work can only
come from chemical bond energy. This is achieved by
coupling energetically favorable reactions to those
that require a net energy input
Metabolic pathways are referred to as organized
sequence of chemical reactions that are needed to extract
the chemical bond energy from energy supplying
compounds and to synthesize different biological molecules.
Enzymes – controls the metabolic pathways by
catalyzing each of the steps in a pathway
Hormones – intercellular messengers that helps
regulate the amount of substrate and enzymes
 Importance of metabolic pathways
- It permits control of the rate and direction of
the cellular activity
- It prevents very large chemical bond energy
releases which would be damaging to cells
- It permits branch points
- Allows pathways to be directed (under
different circumstances) to different end
products
2 types of metabolic pathways
1. Linear metabolic pathway – series of
reactions generates a final product
➢A B C D ➢ the reducing power is provided by the
➢ Each reaction is catalyzed by an
enzyme
2. Cyclic – series of reactions regenerates
the first reactant
A B
D C
METABOLISM
- The sum total of the physical and chemical
processes and reaction taking place among
the ions, atoms and molecules of the living
body. These processes are concerned with the
role of the cells of an organism to transform
energy, maintain their identity and reproduce.
2 PHASES OF METABOLISM
ANABOLISM – is the constructive phase of
metabolism. It is the process of synthesis required for
the growth of new cells and the maintenance of all
tissues.
➢ combine small molecules to form complex
molecules
➢ accomplished by breaking down ATP to
ADP
➢ anabolic reactions often involve chemical
reductions
electron donor NADPH
➢ anabolism is a divergent process in which a
few biosynthetic precursors from a wide variety
of polymeric or complex
CATABOLISM – is the destructive phase of
metabolism. It is a continuous process concerned with
the production of the energy required for all external
and internal physical activity
➢ It involves the maintenance of body
temperature and the degradation of complex
chemical units into simpler substances that
can be removed as waste products from the
body through the kidneys, intestines, lungs
and skin
➢ Functions
i. Serve to capture chemical energy
from the degradation of energy-rich
fuel molecules
ii. Allows molecules in the diet to be
converted into building blocks
3 stages of Catabolism
1. Hydrolysis of complex molecules into
component building blocks
• Proteins to amino acids
• Polysaccharides to
monosaccharides
• Triglycerides to free fatty acid
2. Conversion of building blocks to
simple intermediates
• Sugars usually enter the glycolysis
pathway in the form of glucose or
fructose which are eventually
converted to acetyl CoA
• Amino groups are removed from amino
acids and the remaining carbon
skeletons enter the catabolic
processes at many steps of glycolysis
and the citric acid cycle
• Fatty acids are converted to Acetyl
CoA
 3. Oxidation of acetyl CoA and the
production of ATP
NB. Anabolic and catabolic processes should
be proportionately done in order to maintain the
biological equilibrium or homeostasis in the
living body
Catabolic pathway
- AKA degradative pathway
- Breaks down complex biomolecules to a
few simple molecules
Anabolic pathways
- AKA synthetic pathway
- Form complex end products from simple
precursors
Oxidation Reduction Reactions
- Involve electron transfer between
molecules
- Dehydrogenase is the enzyme for redox
reactions.
- Makes use of cofactors (accepts or
donates electrons)
Oxidation
- Involves loss of electrons from a molecule
- Often accompanied by a loss of one or more
hydrogen atoms from the molecule
Reduction
- Involves gain of electrons by a molecule
- Often accompanied by a gain of one or more
hydrogen atoms by the molecule
FAD – from double to single bond - Example:
succinate to fumarate
NAD – from secondary alcohol to ketone - Example:
pyruvate to lactate
Biomolecules are substances such as foods, drugs
or nutrients that are ingested by the body. These
include proteins, lipids, and carbohydrates. These
different substances will undergo different processes
once introduced to the body.
PROCESSESS UNDERGONE BY
BIOMOLECULES
A. DIGESTION
- it refers to the breakdown of large foodstuffs into
smaller particles
- 2 forms:
➢ Physical digestion – the mechanical
conversion of big food into smaller observable
particles
➢ Chemical Digestion – the conversion of big
food particles into smaller absorbable forms with
the participation of enzymes, hormones and
digestive juices
B. ABSORPTION
- it refers to the diffusion or movement or nutrients and
other ingested materials from the small intestines
(jejunum) into the blood stream
- the process is facilitated by microvilli which are
mobile, fingerlike projections that increases the
absorptive area of the GIT
C. ASSIMILATION
- it refers to the selective uptake of specific nutrients
by an organ in the body
- in other words, the absorbed nutrients are not
uniformly distributed in the body
- For example:
➢ Bones and teeth would take up more of the
calcium and phosphorus
➢ Thyroid gland would take up most of iodine
➢ Hair would take up zinc
➢ Bone marrow take most of the iron and
copper to make RBC
➢ Adipose tissues would take up most of the
fat
➢ Liver would take up most of the sugars
D. UTILIZATION
- the process by which the absorbed
nutrients are used by the different cells for
a specific purpose or function
- e.g. ATP (adenosine triphosphate) –
energy used by all cells in the body
E. INTEGRATION INTO TISSUES
- the process by which the absorbed
nutrients are included or incorporated into
the structural framework of the body like in
the bones, muscles, teeth, hair, skin,
joints, and ligaments
F. BIOTRANSFORMATION AND Absorption
METABOLIC DEGRADATION
- the process by which the cell absorbs form their
- the process by which all harmful and potentially environment - examples are water, minerals and other
toxic materials introduced into the body (like food, materials essential for life
preservatives, food coloring, and chemicals like
Biosynthesis
formalin) are inactivated or detoxified by the liver
into something non-toxic or even less toxic thus, no - cells organize complex chemicals from building units or
significant harm is done on the body substances
-2 forms Excretion

➢ Metabolic degradation – breakdown of
complex substances into simpler ones that act as
active metabolites or end products for energy
production
➢ Biosynthesis – combination of simpler
substances to build complex substances for cell
repair, growth and reproduction
G. EXCRETION
- process by which metabolic wastes are finally
expelled or removed from the body
- these wastes when allowed to accumulate
inside will destroy cells and tissues so these
must be dispensed off fast
- Organs of excretion:
➢ Kidneys – urine
➢ Lungs – volatile acids in the form of
CO2
➢ Skin – sweat (hypotonic NaCl)
➢ GIT – stool or feces or undigested
residue of food (excreted through
defecation
CELL
- basic unit of life
- is an independent, simplest structural
unit of life
- It is the fundamental unit biological
activity and is capable of reproduction
- Before a system is even formed, there
is a need for cells since cells form
tissues, tissues to organs, and organs
to systems.
- adult has nearly 100 trillion cells and
there are about 200 different types of
cells
- products of cell activities which are not needed for further
cell functioning of the body.
Egestion
- soluble, non-digested particles are eliminated by the cell
Secretion
- substances that are synthesized by the cells are expelled
from the membrane
- the elimination influences extracellular activities and
helps in the functioning of the body
- examples are hormones
Movement
- includes locomotion of cells by means of special
structures like cilia and flagella
Irritability
- Cells react to external factors or conditions around them
- Cells may also alter their functions in response to this
external factor
Respiration
- breaking down food molecules into chemical energy
Reproduction
- the cell copies or replicates it DNA and increase its
number by cell division
- cells give rise to new cells
TYPES OF CELLS
PROKARYOTIC CELLS
- primitive types with not distinct nucleus and cytoplasm
EUKARYOTIC CELLS
- more developed cells because they have definite
nuclear and cytoplasmic structures. e.g. human cells
(about 75 trillion

ORGANELLES OF LIVING CELLS

The cell performs several functions 1. NUCLEUS
which include the following: - master control of the cell
Nutrition - it directs, orders and regulates all the metabolic
activities of the cell
- process by which cell obtain food molecules to - an oval, round or elliptical structure usually centrally
support their other activities located inside the cell
- it has a double layered membrane
Digestion

- the process by which food particles are broken General Rule:

down into smaller, soluble units suitable for cell - there is 1 nucleus in one cell except in erythrocytes
use (RBC’s) and Thrombocytes (platelets) which are non-
nucleated
- on the other hand, muscle cells are multinucleated

Abnormalities in the nucleus
- abnormalities in the nucleus which may suggest
cancer or malignant degeneration
➢ a very big nucleus, out of proportion to the cytoplasm
➢ multiple nuclei
STRUCTURES FOUND IN THE NUCLEUS
a. NUCLEOLUS
- small, discrete, round, densely staining structure -
made up of RNA
- the more nucleoli, the faster in multiplying and dividing
➢ intensely staining concentration of RNA
➢ it is known to produce most of the RNA
especially rRNA which gives rise to
ribosomes
b. CHROMOSOME
- linear strands of chromatin material which contain the
genes which represent all the traits of an individual
- the genes are composed of segmented DNA
c. Nuclear Envelope
- consists of 2 membranes
- outer membrane is porous – serves as passageway of
information
- outer envelope is continuous with the endoplasmic
reticulum - The outer envelope also performs some
secretory and transport processes
- The inner membrane maintains stable relationships with
the genetic material
Pores – considered as gateways of exchange of
information from the nucleus to the cytoplasm
- The nuclear envelop encloses the karyoplasm
which in turn is suspended with DNA and RNA
DNA – copy information form genetic
material (Transcription)
RNA – Genetic information is used in
protein synthesis (translation)
- The nuclear envelop governs
nucleocytoplasmic interactions
TYPES OF TRAITS
D. MITOCHONDRIA
1. DOMINANT TRAIT
- it is one which is present or evident or manifested
in majority of the offspring or children in every
generation
- e.g. black hair is dominant over blond hair
2. RECESSIVE TRAIT
- is one which may be seen only in a minority of
offspring’s
- the trait may even disappear in one generation but
will re-appear in succeeding generations
TYPES OF EXPRESSION OF
HEREDITARY TRAITS
1. PHENOTYPES
- the physical observable aspects of heredity
as handed down from parents to offspring’s
- e.g. color of eyes, bridge of the nose, dimples
2. GENOTYPE
- the non-observable, non-physical aspects of
heredity
- e.g. IQ, talent, allergy (asthma), diabetes,
epilepsy, hemophilia, insanity, color blindness
2. CYTOPLASMIC ORGANELLES
- living structures which actively participate in
the metabolism in cells
-these are “little organs” that serve a
specialized function
A. RIBOSOMES
- “Factory sites” for the manufacture of
cell protein - Structures which contain
RNA
- These are the sites where amino acids
are joined together by peptide bonds to
form a polypeptide chain forming a
new protein
B. GOLGI APPARATUS
- a specialized portion of ER
- the primary site for packaging cellular
secretion
- Site of synthesis of large
carbohydrates
- Serve as temporary storage depots
for cellular secretions
C. LYSOSOMES
- known as the “suicide bag of the cell”
- encapsulated granules which contain
a very strong proteolytic enzyme (e.g.,
hyaluronidase, acid hydrolase)
Note: when microbes or toxins enter
the cell, these enzymes are released in
order to destroy or inactivate the
invading microbes. Therefore,
lysosomes are for intracellular defense
mechanism
- known as the “powerhouse of the cell”
- an ovoid or elliptical structure having 2 layers:
the outer layer is continuous while the inner
layer has infoldings or invaginations called
cristae matrix
- the only organelle capable of generating
energy in the form of ATP
- the only organelles which contains DNA
(deoxyribonucleic acid) used for self-
replication or the capacity to reproduce copies
of its own
 E. ENDOPLASMIC RETICULUM
--composed of network of tubes, tubules, and
microtubules connecting the nuclear membrane
and cell membrane
- this system of tubules acts as excretory,
respiratory and circulatory passageway of
substances in and out of the cell such as O2,
CO2 and cellular waste products
Types of Endoplasmic Reticulum
A. Rough Endoplasmic reticulum – contain
ribosomes
- the ribosomes are connected to the
membrane by a ribosome-binding
protein celled ribophorins - believed as
passageway of proteins manufactured
by the ribosome
- used as a means of communication
- they channel products from the outside
and other parts of the cell
- thought as the cell’s membrane factory
- found abundantly in the pancreas
B. Smooth Endoplasmic reticulum – do not
contain ribosomes
- metabolizes small proteins
- contains cellular detoxification
mechanisms
- seems important in synthesizing and
secreting steroid hormones, enzymes of
protein metabolism and enzymes of lipid
synthesis
- functions in cholesterol synthesis and
breakdown, fat metabolism and
detoxification of drugs
3. CYTOPLASMIC INCLUSIONS
- these are inert bodies which have no effect on cellular
activities
A. VACUOLES
- spaces within the cytoplasm which serve as:
✓ temporary dumping site of cellular garbage
✓ storage of glycogen
✓ storage of fat
B. PIGMENTS
2 types according to origin
1. Exogenous origin
- picked-up from the outside of the body
- e.g. Dust in the lung, Minerals in bones,
lipochromes and carotenoids form food
2. Endogenous in origin
Hemoglobin- gives the red pigmentation of
blood as has several metabolites that could give
rise to endogenous pigments seen in cells
Hemosiderin – metabolite of hemoglobin -
golden brown pigment seen in phagosomes in
the liver and the spleen
Bilirubin – metabolite of hemoglobin -
a yellowish pigment that is non-iron
containing found in the liver cells
Melanin – a brown-black pigment
found in the skin and eye
Lipofuchsin – a brownish pigment
seen in the heart, liver, CNS as the
animal ages - may be found in the
nucleus and the cytoplasm - the origin
and function of lipofuchsin is unknown
C. FAT DROPLETS
- found as small globules within many
cells
- most prominent in adipose tissues
- they are stored as triglycerides (liquid
at body temperature
D. CRYSTALS
- usually found along steroid-secreting
cells
- found in the nucleus and cytoplasm -
origin and function is also unknown
E. GLYCOGEN
- found in the liver and skeletal
muscles
- found in small clusters called rosettes
- an individual glycogen measures 15-
30 nm in diameter
- it is associated with the smooth
endoplasmic reticulum within
lysosomal particles
4. CELL MEMBRANE
- also known as plasmalemma or plasma
membrane
- it is the analogue of cell wall in plants
Layers of Cell Membrane
A. Mucopolysaccharide or carbohydrate
layer
– strongest layer of the cell membrane
B. Outer protein layer Peripheral protein
- attached to the inner or outer surface of
the membrane, do not extend through it
C. Double layered lipid coat or lipid bilayer
- made up of phospholipids, cholesterol and glycolipids.
This is the most important layer for selective
permeability.
- The lipid bilayer is permeable to oxygen, carbon
dioxide, water and steroids, but impermeable to
glucose
D. Inner protein layer
- extend into or through the lipid bilayer
Transmembrane proteins
- span the entire lipid bilayer. These act as channels
and transporters to assist the entrance of certain
substances, for example, glucose and ions
Functions of the Cell Membrane
A. Protection - protects inside of the cell from
external forces (microbes, toxins and chemicals)
 B. Limits - it limits territorial boundaries of the cell
C. Morphology - give size and shape to the cell
D. Selective permeability - does not allow some
substances to pass thru and allows the passage of
only specific substance
Factors Affecting Passage of Substances
1. Degree of ionization (non-ionized form, more
diffusible)
2. Lipid solubility
3. Water solubility
4. Size of the substance
Classification of fluids in the body
Intracellular fluid
- Nucleoplasm + cytosol
- A solution containing small amounts of gases (O2
and CO2), nutrients and salts
Interstitial Fluid
- The fluid that continuously bathes the exterior of the
cells
- Contains nutrients (amino acids, sugars, fatty acids,
vitamins), regulatory substances (hormones,
neurotransmitters) salts and waste products
Selective permeability
- A barrier allows some substances to pass through
it while excluding others
- The plasma membrane is said to be selectively
permeable to substances
2 types of movements in the cell membrane
1. Passive (transport) processes
- substances move across cell membranes without
the input of any energy; use the kinetic energy of
individual molecules or ions
- No need for carrier CHONS (proteins) as well as
energy or ATP
- Osmosis
Facultative or Facilitated Transport
- Does not require energy
- Needs specific carrier proteins
- Cannot move substances against
concentration gradient
2. Active (transport) processes
- cell uses energy, primarily from the breakdown
of ATP, to move a substance across the
membrane
- Requires specific carrier CHONS
- Even against a concentration gradient
Active Transport
- cell uses energy
- Requires specific carrier CHONS
- Even against a concentration gradient
the main difference between the two is the need for
carrier protein and energy of active process
whereas, passive requires neither. However, that the
transport mechanism that requires just the carrier
protein is known as facilitated or facultative
transport. Active transport requires both energy in
the form of ATP and carrier protein.
Two types of passive transport processes
1. Diffusion
- The process by which molecules (and ions) tend
to scatter themselves throughout the available
space
- Molecules move down their concentration
gradient
Factors affecting the speed of diffusion
o Size of molecules
o Temperature o Presence of other molecules
o Distance/size of container
Molecules will move passively through the
plasma membrane if:
- They are small enough to pass through its pores
- They can dissolve in the fatty portion of the
membrane
Simple diffusion
- Unassisted diffusion of solutes through the
plasma membrane
o Lipid soluble: fats, fat-soluble vitamins,
oxygen, carbon dioxide
o small molecules: ions such as chloride
Facilitated diffusion
- A protein “carrier” is needed as a transport
vehicle
- It provides a means for certain substances
(glucose), that are both lipid-insoluble and too
large to pass through the membrane pores
- No expenditure of energy because they follow the
concentration gradient
Importance of diffusion
- It saves the cell a great deal of energy
- Glucose and oxygen continuously move into the
cell (where they are in lower concentration)
- Carbon dioxide continually moves out of the cell
into the blood (where it is in lower concentration)
 2. Osmosis Tonicity and its effect to RBCs
- Diffusion of water through a selectively
Filtration
permeable membrane
- The process by which water and solutes are forced
o Because water is highly polar, it is repelled through a membrane (or capillary wall) by fluid, or
by the lipid core of the plasma membrane hydrostatic pressure
- Pressure gradient – gradient involved in filtration
Osmotic pressure o It pushes solute-containing fluid (filtrate)
- The tendency of a solution to hold from the higher-pressure area to the lower-
water or pull water into it pressure area
- The higher the solute concentration, - Occurs in the kidneys
the greater the osmotic pressure
Sodium-potassium pump
Tonicity
- Simultaneously carries sodium ions out of and
- the ability of a solution to change the potassium into the cell
size and shape of cells by altering the - Needed for normal transmission of nerve impulses -
amount of water they contain Na+ - extracellular cation
- K+ - intracellular cation
Type of solutions - “No pump-no transport”
Isotonic
- Solutions that have the same solute and water Bulk transport Two types
concentration as cells do Exocytosis
- Cause no visible changes in cells - Moves substances out of the cells
- When infused into the bloodstream, the red - A means by which cell actively secrete hormones,
blood cells retain their normal size and disklike mucus and other cell products or eject certain cellular
shape wastes
- Examples: Ringer’s lactate, 5% dextrose, 0.9% - The product to be secreted is packaged first in the
saline solution golgi body

Endocytosis
Hypertonic solution - An ATP-requiring processes that take-up, or engulf,
- A solution that contains more solutes, or extracellular substances by enclosing them in a small
dissolved substances, than there are inside the membranous vesicle
cells - Types
- Water is in greater concentration inside the cell
o Phagocytosis – cell eating
than outside and thus it follows its concentration
▪ Happens when cell form pseudopods
gradient and leaves the cell
(flowing cytoplasmic extension)
- Crenation – cell shrinking
- It is given to patients with edema o Bulk-phase endocytosis
(Pinocytosis) – cell drinking
Hypotonic solution ▪ Happens when the plasma membrane
- A solution that contains fewer solutes than the invaginates to form pits and then its edges
cell does - Water rushes into the cell as it follows fuse around the droplet
its concentration gradient ▪ Routine function (cells in the lining of SI
- The cell will swell and then bursts and kidney tubule cells)
- Cytolysis – cell bursting
- Examples: distilled water, tea, cola, apple juice
and sports drinks
- Given intravenously to extremely dehydrated
patients (but with care)
 PH AND THE CHEMISTRY OF
- Does not contradict the Arrhenius definition of acid and base;
RESPIRATION an Arrhenius acid is a Bronsted-Lowry acid that has
dissociated in water by transferring its proton to the solvent
When we exercise, our heart rate, systolic blood
pressure, and cardiac output (the amount of
blood pumped per heart beat) all increase. Blood
flow to the heart, the muscles, and the skin
increase. The body's metabolism becomes more
active, producing CO2 and H+ in the muscles.
We breathe faster and deeper to supply the
oxygen required by this increased metabolism.

Properties of Acids and Bases

Acids Bases
Turns blue litmus paper Turns red litmus paper
to red to blue
Has a sour Has a bitter, biting taste
taste
- An Arrhenius base (OH-) is also a Bronsted-Lowry base
Neutralizes base Neutralizes acids
because it accepts a proton in neutralization.
Reacts with active Has s slippery, soapy
metals to produce feeling (due to dissolving - The difference is that it is no longer the only base that can
hydrogen gas a thin layer of skin) exist in water. Any species, molecular or ionic, as long as it
can accept a proton, whether in solution or in gas phase
Theories: reaction, is considered a base.
Arrhenius Concept of Acids and Bases
- Proposed by Svante August Arrhenius (1959 –
1927), a Swedish physicist and chemist
- Defined an acid as a substance that yields
hydrogen ions (H+ or H3O+) when dissolved in
water and a base as a substance that yields
hydroxide ions (OH-) when dissolved in water
- Arrhenius suggested that acids are compounds
that contain hydrogen and can dissolve in water to
release hydrogen ions into solution
- Arrhenius defined bases as substances that
dissolve in water to release hydroxide ions (OH-) - When acid donates a proton to water, it becomes a potential
into solution proton acceptor and therefore a base. When water accepts a
proton, it acts as a base and becomes a potential acid
- Conjugate acid-base pair – an acid and a base that are
related by a transfer of proton

Bronsted-Lowry Definition of Acids and

Bases
- Proposed in 1923 by Johannes Bronsted and
Thomas Lowry, working independently
- More general that Arrhenius theory since it is
not limited to water solutions
- Defined an acid as any substance that donate
a proton (H+) and a base is any substance that
accepts proton (H+)
- any substance that can donate a hydrogen ion
is an acid (under the Brønsted definition, acids
are often referred to as proton donors because
an H+ ion, hydrogen minus its electron, is simply
a proton).
- The Brønsted base is defined as any
substance that can accept a hydrogen ion LEWIS DEFINITION OF ACIDS AND BASES
- the Brønsted-Lowry definition also explains - Proposed by G.N. Lewis in 1923
why substances that do not contain OH- can act - Most general definition and includes all substances that are
like bases. acids and bases according to Arrhenius and Bronsted –Lowry
concept
- Defines an acid as any species that can accept a pair of
electrons, and a base is any species that can donate a pair of
electrons

- In 1923 G. N. Lewis suggested another way of looking
at the reaction between H+ and OH- ions. In the
Bronsted model, the OH- ion is the active species in
this reaction it accepts an H+ ion to form a covalent
bond. In the Lewis model, the H+ ion is the active
species it accepts a pair of electrons from the OH- ion
to form a covalent bond.
Henderson-Hasselbalch equation
- The Henderson-Hasselbalch equation is useful for
estimating the pH of a buffer solution and finding the
equilibrium pH in an acid-base reaction.
- The equation can be used to determine the amount of
acid and conjugate base needed to make a buffer
solution of a certain pH.
- The Henderson–Hasselbalch equation mathematically
connects the measurable pH of a solution with the pKa
(which is equal to -log Ka) of the acid. The equation is
also useful for estimating the pH of a buffer solution and
finding the equilibrium pH in an acid-base reaction. The
equation can be derived from the formula of pKa for a
weak acid or buffer
A modified version of the Henderson-Hasselbalch
equation can be used to relate the pH of blood to
constituents of the bicarbonate buffering system:
Where:
pKaH2CO3 = acid dissociation constant of carbonic
acid which is equal to 6.1
[HCO3-] = the concentration of bicarbonate in the blood
[H2CO3] = the concentration of carbonic acid in the
blood
The chemistry of respiration
- Respiration – exchange of gases between the
outside air and the body
- Tissues must be adequately supplied with oxygen.
Why?
- At rest: 250 mL of oxygen is used and 200 mL of
carbon dioxide is eliminated
The body takes up 5% oxygen and give up 4% CO2
because some oxygen are utilized for biological
oxidation and formation of water Nitrogen remains the
same because nitrogen is supplied by nitrogenous
organic compounds (proteins, amino acids etc.)
Types of respiration
- External Respiration – the exchange occurring
between the outside air and the venous blood through
the lungs
- Internal respiration – the exchange occurring
between the blood and the tissues
Physical theory of respiration
Diffusion
- the law that governs the exchange of gases between
the outside air, the blood and the different tissues of
the body
- gas flows from a higher to a lower tension
Tension
- the pressure exerted by gas in solution
- Denoted by the symbol p
- e.g., pCO2 – pressure of the dry gas of CO2 in
mmHg with which dissolved carbonic acid in the blood
is in equilibrium
pO2 – pressure of the gas with which
dissolved oxygen in the blood is in equilibrium
- The tension exerted by an individual gas in a
mixture of gases is obtained by multiplying the total
pressure (760 mmHg at sea level) by the percentage
of gas in question.
To compute for the oxygen tension (pO2):
pO2 = 260 mmHg x 20.96 = 159 mmHg
Oxygen tension in different parts of the body in mmHg
Inspired air = 159 – 160
Alveolar air = 108
Venous blood = 40 – 50
Arterial blood = 100
Tissues = 20 – 50
Note that the alveolar pressure is 108 mmHg and the
venous blood pressure is 40 mmHg. The difference in
pressure serves to drive the oxygen from the lungs to
the blood. Also note that the partial pressure of
oxygen in arterial blood is 100 mmHg. This blood is
carried into the tissues with a partial pressure of only
20 – 50 mmHg
Conditions that affect the diffusion of oxygen
from alveolar to venous blood
• Size of the epithelial wall – the combined
thickness of the capillary wall and the
respiratory epithelium is not more than 0.004
mm
• The speed of the flow of blood – brings all
RBCs in contact with alveolar air
• The affinity of oxygen to hemoglobin

pCO2 in the various parts of the body in mmHg
• Tissues = 50 – 70
• Arterial blood = 40
• Venous blood = 46 - Alveolar air = 36
• Expired air = 20
• Atmospheric air = 0.3
The difference of 10mmHg between
venous blood and alveolar air is enough to
drive the CO2 from the blood to the lungs
due to the rapidity of diffusion of CO2
which is 30 times that of O2
THE CHEMICAL CONTROL OF RESPIRATION
- Exerted by the respiratory centers in the medulla
and upon the chemical receptors located at the
bifurcation of the common carotid arteries and at the
arch of the aorta.
Rate and depth of respiration
Carbon dioxide
• Main factor that regulate the rate and depth
of respiration
• Increase CO2 in blood = increase rate and
depth of respiration leading to increased
pulmonary ventilation
• Leads to immediate elimination of CO2
• Decrease CO2 in blood = slow and shallow
respiration leading to decreased pulmonary
ventilation
• Leads to decreased elimination of CO2
EFFECT OF pH CO2 is low; pH is
high = normal rate and depth of
respiration CO2 is low: pH is low
= decreased ventilatory rate
• Low oxygen pressure in arterial
blood = depression of the respiratory
center, but stimulation of the carotid
and aortic chemoreceptors
• The stimulation of the carotid and
aortic chemoreceptors causes the
stimulation of respiration and
increased ventilation
• Important in the physiological
adjustment to low atmospheric
oxygen tension during an ascent to
high altitudes
Oxygen transport
• 0.2 – 0.3% - amount taken by the blood plasma
when exposed to alveoli air
• Whole blood will take up around 70 – 80 times
the amount that the plasma will take
• The oxygen carrying capacity of blood is a
function of hemoglobin concentration -
Hemoglobin forms a reversibly stable complex
in which the iron remains in the ferrous state
• 96% - oxygen saturation of the RBC’s leaving the lungs
- 64%
• oxygen saturation of venous hemoglobin
• 32% - oxygen that is delivered in the tissues
Since there are around 15 g of hemoglobin per 100
mL of blood and each gram can combine with 1.34
mL of oxygen (Hufner factor), then 6.4 mL of O2 has
been supplied to the tissues for every 100 mL of
blood passing through the capillaries
• 1.34 X 15 X 0.32 = 6.4 mL of O2
DISSOCIATION OF OXYHEMOGLOBIN
Factors Affecting the Dissociation of
Oxyhemoglobin
1. Low oxygen pressure - low pO2 will increase
dissociation of oxyhemoglobin to hemoglobin and
oxygen
2. High CO2 pressure – increase pCO2 will decrease
the affinity of hemoglobin for oxygen (Bohr’s effect)
- The effect of CO2 reflects the acidity of carbonic acid
solutions
- Increased pCO2 decreases the amount of
oxyhemoglobin within the RBC’s
- Increased pCO2 is actually the effect of carbonic acid
formation with consequent lowering of pH
- The equilibrium of the hgb-O2 system is altered
causing the dissociation curve to shift to the right (acid
side of isoelectric point of hgb side of dissociation
curve)
3. low pH – acids other than carbonic acid (e.g. lactic
acid) increases the dissociation of oxyhemoglobin
- More marked when there is a relatively low pO2
4. Rise of temperature – increase in temperature will
increase the dissociation of oxyHgb - In warm-blooded
animals, Hgb gives up O2 more readily when passing
from high to low tension than in cold-blooded animals -
Patients with high fever cause the Hgb to release O2 to
tissues
5. Presence of electrolytes – at low pO2, Hgb gives
up O2 more readily in the presence of electrolytes that
it does in pure solution
Carbon dioxide transport
- 50 volumes % - CO2 content of arterial blood
- 55 – 60 volumes % - CO2 content of venous blood
• Each 100 mL of blood transports 5 – 10 mL of
CO2 from tissues to lungs
- Three forms of CO2 that is carried in the blood
1. As dissolved H2CO3 (5%)
2. As carbamino bound CO2 (20%)
3. As bicarbonate combined with cations, Na and K (75%)
As H2CO3
- This form is important because any change in its
concentration will caused marked alteration in the
blood pH
- Occurs in very small amounts
 As carbamino compound
- This is formed with the proteins especially hemoglobin
- The free amino group of the protein reacts with CO2
- This is an important factor in the physiological
efficiency of the respiratory cycle due to its high
rate of reversibility
- The difference of the CO2 between arterial and
venous blood is due to the difference in the
carbamino bound form of CO2
- Arterial blood – more oxyHgb favors the
release of CO2
- Venous blood – less acid reduced Hgb favors
the Hgb – CO2 combination
➢ Venous blood carries more CO2 in the
form of carbamino compound than
arterial blood
As HCO3-
- As CO2 enters the RBC, the CO2 is hydrated to
carbonic acid using carbonic anhydrase (CA). This
enzyme also causes its reverse dehydration
-At normal pH, most of the H2CO3 is present in the
form of HCO3-
Carbonic anhydrase
Catalyzes the synthesis of H2CO3 from CO2 and
H2O and the degradation of H2CO3 into H+ and
HCO3-
Henrique (1928) discovered in the enzyme in
RBC’s. It is also found in the muscles, parietal cells
of the stomach participating in HCl production and
in the kidney, tubules catalyzing hydrogen excretion
Effect of CO2 on blood
- H2CO3 is carried in the blood in the form of
bicarbonate
At pH 7.4, a ratio of 20:1 must exist between
--
bicarbonate and H2CO3
- As long as this ratio is maintained, the
pH of the blood will be normal
- Any alteration n the ratio will disturb
the acid-base balance of the blood
- Venous blood carries more CO2 than arterial
blood
- The pH of venous blood is more acid by only 0.01
to 0.03 units (pH 7.4 vs pH 7.43)
Blood buffers
1. Plasma proteins – they release sufficient cations to
account for the carriage of about 10% of the total CO2
2. Phosphates – within red blood cells – responsible for
about 25% of the total CO2 carried
3. Hgb and oxyhemoglobin – accounts for 60% of the
CO2 carrying capacity of blood - Hemoglobin is able to
react with protons or dissociate to yield protons
THE CHEMICAL THEORY OF RESPIRATION
1. The wall of the RBC is permeable to water, CO2,
H2CO3, Cl- and H+ but not the Hgb and plasma
proteins and only slightly to Na+ and K+
2. Most of the Na ions are in the plasma, while those of
potassium are in the cells
3. In the RBC, most of the proteins (Hgb) are combined
with K, the amount varying in the different stages of
the cycle
4. the carbonic anhydrase in the RBC hastens the
transformation of CO2 and water into carbonic acid
and vice versa
Gaseous exchange in the tissues
A. Carbon dioxide exchange
➢ CO2 is continually produced as a result of
metabolic processes
➢ 5% is taken up by the blood
➢ In the RBC, 20% of the CO2 combines with Hgb
forming carbamino compounds
➢ 75% is synthesized into H2CO3
➢ Increased CO2 = increased H2CO3
➢ H2CO3 will then ionize into hydrogen and
carbonic acid ion
➢ HCO3- accumulates in the RBC, the concentration
of which will become higher than the plasma
➢ What will happen?
o First chloride shift (Hamburger’s
phenomenon)
▪ To maintain electrolytic equilibrium, the Cl-
ions of the plasma will diffuse into the red
blood cells
B. Oxygen exchange
- oxyHgb (in the form of K oxyhemoglobinate)
gives up O2 to tissues to become reduced Hgb
- Reduced Hgb is a weaker acid and will require
less K
- Some K will be available for combination
 Two opposing phenomena in the oxygen exchange:
1. H2CO3 tends to lower the pH within the RBC
2. The transformation of oxyHgb to reduced Hgb involves a
change of pK from 6.2 to 7.7 which tend to rise the pH in the
cell
The net result of these processes is to maintain the
pH essentially unchanged Isohydric effect – the shift
that takes place at a constant pH
- The combined result of the isohydric effect and the chloride
shifts is to increase the effective osmotic pressure within the
cells
- Water is then redistributed between the cells and the
plasma
- Hematocrit (the relative volume occupied by RBC’s) is
higher in arterial blood compared to venous blood
o 45 – 49 volumes %
GASEOUS EXCHANGE IN THE LUNGS
A. Carbon Dioxide Exchange
- CO2 found in plasma and RBC diffuses into the alveoli
to the outside air
- Carbamino compounds dissociates to release CO2
- Carbonic anhydrase splits H2CO3 to CO2 and H2O
H2CO carbonic anhydrase H2O + CO2
B. Oxygen Exchange
- Oxygen combines with reduced Hgb to produce oxyHgb
- oxyHgb is more acidic thus it takes up K to buffer it
- K is liberated from Cl and HCO3- = this hastens the
release of CO2
- HCO3- is rapidly lost in RBC’s, HCO3- from the plasma
diffuses into the RBC’s
o What will happen?
▪ Second Chloride shift – Cl- goes out from the
RBCs to maintain electrolytic balance
Hemoglobin H
- Abnormal Hgb consisting of 4 B-chains
- Has oxygen affinity 10x normal Hgb
- Does not exhibit Bohr’s effect
- The conformation of the entire Hgb molecule
contribute to the affinity of Hgb for oxygen
Fetal Hemoglobin (HgBF)
- As compared to HgBA (adult), in addition to 2
alpha chains, it has 2 gamma chains instead of the
2 beta chains
- The ϒ-chain contains isoleucine and a single
sulfhydryl group
- This structure shows high affinity for oxygen
- Compared to maternal blood which is 33%
saturated, fetal blood has 58% saturation at 30
mm of O2, 37C and pH 6.8
- HgBF normally disappears after 4 – 6 months
except in anemic conditions
-
Myoglobin
- A hemoprotein capable of reversibly binding oxygen
found in muscles
- Exhibits Bohr’s effect
- MgB can accept O2 from HgB and store it in the
muscle and release it to cytochrome oxidase when O2
supply becomes inadequate
- O2 remain fixed to Mgb when the muscle is at rest
- When pO2 falls, O2 dissociates and becomes
available for oxidation
- Mgb is abundant in the cardiac muscle, muscle of
diving mammals and flight muscle of birds
Acid – base balance - Depends on the 1:20 ratio of
carbonic acid to bicarbonate - Acids produced during
metabolic activities: carbonic acid, sulfuric, phosphoric
and organic acids
Acid – base balance
- Depends on the 1:20 ratio of carbonic acid to
bicarbonate
- Acids produced during metabolic activities:
carbonic acid, sulfuric, phosphoric and organic
acids
- H2CO3 – principal acid produced during tissue
oxidation
- Phosphoric and sulfuric acid – comes from sulfur
and phosphorus containing proteins
- Fruits and vegetables (rich in + radicals like Na, K,
Ca), can release potentially basic substances
Factors that maintain normal pH in the body
1. Buffer systems in the blood
2. CO2 elimination through the lungs
3. Renal excretion of acids and bases
4. Renal formation of ammonia – base conservation
 Buffer system of the blood
A. Buffer action of hemoglobin
- The buffering effect is due to the imidazole group of histidine
- Exerts is buffering effect on H2CO3
- H+ is buffered by Hgb and HCO3- diffuses out in the plasma
in exchange for chloride.
B. Buffer action of bicarbonate
- Bicarbonate is the major buffer of the extracellular fluid
- Exerts buffering effects on fixed acids
- There is more bicarbonate found in the extracellular fluid
than other buffer component
- There is limitless supply of CO2
- There are physiological mechanisms which maintain the
extracellular pH function by controlling the bicarbonate or
CO2 concentration
- The HCO3-/H2CO3 buffer operates in conjunction with
Hgb
- As long as adequate amount of bicarbonate is present, it
can dispose of the fixed acids efficiently
o Alkali reserve – the amount of bicarbonate that
serves as a measure of the alkali available for
neutralization of fixed acids
- True plasma
o as pCO2 is increased there is an appreciable
increase HCO3- so that the pH does not fall so
rapidly
o as the pCO2 decreases, the HCO3- also
decreases thus preventing the expected rise in Ph
Carbon dioxide elimination through the lungs
Factors:
1. The sensitivity of the respiratory center to slight
changes of CO2 pressure and the H+ concentration
- If CO2 in increased by 1-5 mmHg it will increase
pulmonary ventilation eliminating the excess CO2; same
for H+
- Low pCO2 and H+ leads to hypoventilation, CO2 is
retained until it comes back to normal.
2. The diffusibility of CO2 from the blood thru the
pulmonary epithelium into the alveoli air
Renal excretion of acids and bases
- If the fixed acids that have been temporarily neutralized
by the HCO3-, are not eliminated, it will be taken care of
by the kidneys.
- Urinary pH is about 6.0 and the pH of blood is 7.45 –
the difference in pH represents the amount of acid the
kidneys remove from the blood
- Urinary pH may vary from 4.5 – 8.2 – our kidneys can
excrete excess acids and bases making it the most
important regulator of acid base balance
- Uses HPO4/H2PO4
Renal formation of ammonia
- Urinary ammonia is formed in the distal portion of
the uriniferous tubules: the site of acidification of
urine
- Ammonia is derived from the amide grp of
glutamine (60%) and from amino acids (40%)
- Factors that stimulate the formation of ammonia
o Increased hydrogen ion concentration
o Diminished bicarbonate of the blood and
glomerular filtrate NH3 + H NH4+
- This prevents the accumulation of H+ and allows
continued exchange of H+ with Na+
- The amount of Na+ reabsorbed in the distal tubule
reflects the amount of both H+ and NH4+ ions in the
urine
- Thus the fixed alkali (Na+) of the blood is
conserved.
- Renal secretion of ammonia is more significant
than acidification
- Failure of formation of NH3 may be the cause of
acidosis and dehydration in the lower nephron
nephrosis
- Alterations of the carbonic acid factor calls for
compensation by the kidneys
- Alterations of the bicarbonate factor calls for
compensation by the lungs
Abnormalities of acid-base balance
Metabolic acidosis - Produced whenever the
available base/alkali reserve (Na or K) is decreased
although the total base may remain unchanged.
- Conditions that may cause metabolic acidosis:
diabetic acidosis, fasting, starvation, severe
diarrhea, kidney failure or uremia (the retention of
anions PO4 and SO4 also decreases the available
base)
- Compensation: increased respiration (acidotic
breathing) to eliminate more CO2
o As the hyperpnea resulting from the acidosis
becomes less, as acidosis improves, so the
stimulus for correction disappears before
complete compensation = the pH remains low,
the CO2 combining power is less.
Respiratory acidosis (Hypoventilation) NUCLEOPROTEINS

- Occurs whenever there is interference with the exchange of - Conjugated proteins

gases within the lungs so that CO2 is not adequately blown off - Proteins + nucleic acids
- If CO2 is retained, the carbonic acid concentration increases - Sources
in the blood serum
o Tissues with closely packed cells and big nuclei
- The ratio of H2CO3: HCO3- favors the carbonic acid =
elevated H concentration and acidosis ▪ Thymus, liver, spleen, kidney and
- Conditions that may lead to respiratory acidosis: narcosis from pancreas
drugs, CNS depression, emphysema, bronchiectatis,
poliomyelitis (during paralysis of respiration) o Found in bacteria, bacteriophage, chromosome
- Compensation: kidneys will attempt to readjust by excreting and simple filterable viruses
more ammonia and chloride, this conserves Na+ o Na+
becomes available for combination with HCO3- to increase the - Protein component: simple proteins, albumins,
alkali reserve histones or protamines
- Constitute a large part of the nuclear material of
o Compensation is usually incomplete the cell
o The ratio remains in favor of the carbonic acid - Also found in the cytoplasm, particularly
o Result: low pH with high CO2 combining power in the ribosome (concerned with protein
synthesis)
Management:

o Requires more efficient removal of CO2

o Cautious administration of HCO3- and increased excretion of PROPERTIES OF NUCLEOPROTEINS
ficed anions
- Acidic
- Soluble in alkalies with which they form salts
Respiratory alkalosis (hyperventilation) - Precipitated from solutions by acetic acid but are re-
dissolved by dilute HCl
- Produced in nay condition causing hyperventilation, when - Not coagulated by heat
this is not the result of interference with the gaseous - Exhibit similar precipitation and color reactions with
exchange in the lungs proteins
- Increased ventilation blows off large amounts of CO2
- Plasma carbonic acid concentration is decreased
- The ration between HCO3/H2CO3 is decreased, H+ conc is
lowered, pH remains high,
- CO2 combining power is normal or lower
- Conditions that may lead to respiratory alkalosis: among
nervous patients who are breathing deeply and rapidly due to
some frightening symptom or situation, high fevers, CNS
lesions and anoxia of the cardiac type due to high altitudes
- Compensation:
o Kidneys excrete more bicarbonate
o This improves the ratio of HCO3: H2CO3 but not completely
(remains in favor of the bicarbonate
IMPORTANCE OF NUCLEOPROTEINS
- They are closely associated with chromosomes
TYPES OF TRAITS
1. DOMINANT TRAIT VIRUSES AS NUCLEOPROTEINS
- it is one which is present or evident or manifested in • 1935 – W.M. Stanley isolated the virus that causes tobacco
majority of the offspring or children in every generation mosaic disease
- e.g. black hair is dominant over blond hair • 1986 – Bawden and Pirie – the virus that causes tobacco
mosaic disease is a ribonucleoprotein
2. RECESSIVE TRAIT
- is one which may be seen only in a minority of VIRUSES
offspring’s - Can reproduce inside living cells but are incapable of
- the trait may even disappear in one generation but will doing so independently
re-appear in succeeding generations - Nucleoproteins have the ability to reproduce but should
be within a host cell
TYPES OF EXPRESSION OF HEREDIATRY TRAITS - The RNA alone possesses biological activity, the protein
1. PHENOTYPES the physical observable aspects of serve as coat
heredity as handed down from parents to offspring’s
e.g. color of eyes, bridge of the nose, dimples BACTERIOPHAGES
- Viruses of bacteria
2. GENOTYPE the non-observable, non-physical - The protein helps in the penetration of the bacterial cell
aspects of heredity e.g. IQ, talent, allergy (asthma), - Only the nucleic acid enters the cell
diabetes, epilepsy, hemophilia, insanity, color blindness
ANIMAL VIRUSES
- They are classified by containing either DNA or RNA
 - Alloxan – 2,4,5,6 – tetraoxypyrimidine
o Produces experimental diabetes - 2 –thiouracil o Used for
thyroid treatment
- 5 – fluorouracil
o Used for a variety of cancers (breast and digestive)

2. PURINE
Includes pyrimidine and imidazole ring
Include:
NUCLEIC ACIDS
o Adenine – 6 – aminopurie
- Macromolecules
o Guanine – 2-amino-6-oxypurine
- first discovered in the nuclei of cells - contain all
the information to direct the activities of a cell and
its reproduction
- essential in understanding genetics
- to understand the many aspects of diseases like
their
o Pathophysiology
o genetic basis of the disease

Functions of Nucleoproteins and Nucleic acids

OTHER BIOMOLECULES WITH THE PURINE
A. To reproduce their own kind (duplication)
BASE STRUCTURE:
B. To store, express and transmit genetic information
C. The undergo mutation Hypoxanthine – 6-oxypurine
o metabolic by-product
Components Xanthine - 2,6-dioxypurine
- Elementary components: 15 - 16% N; 9 – 10% P o Metabolic by-product

Properties of Nucleic acids Uric acid – 2,6, 8 –trioxypurine

- Insoluble in alcohol
- Slightly soluble in cold water
- Readily dissolves in hot water and dilute alkalies
forming alkali salts
- Precipitated by HCl and excess acetic acid
Molecular anatomy of nucleic acids
- Hydrolysis yields nitrogen base, sugar and
phosphoric acid
o Metabolic by-product
Caffeine – 1,3,7 – trimethylxanthine
o Plant source: coffee
Theobromine – 3,7 – dimethylxanthine
o Plant source: tea and cocoa
6-mercaptopurine
o Used for the treatment of leukemia

I. NITROGENOUS BASE II. SUGARS

- Ribose
1. PYRIMIDINE - Deoxyribose
• 6-membered ring structure
• Include:
o A. cytosine – 2 – oxy-4-aminopyridine
o B. uracil – 2,4 – dioxypyrimidine
oC. Thymine – 5 – methyl – 2,4 -
dioxypyrimidine
III. PHOSPHORIC ACID
- H3PO4
- H2O3POH

OTHER BIOMOLECULES THAT CONTAIN THE

PYRIMIDINE STRUCTURE:

- 5-hydroxymethylcytosine
o found in bacteriophage
- 5-hydroxymethyluracil
o found in B. subtilis in place of thymine in DNA
- Vitamin B1 – thiamine
o Important in metabolic processes
 CLASSIFICATION OF NUCLEOSIDES

NUCLEOSIDE –
SUGAR + BASE = NUCLEOSIDE
Uses:
- glycosidic linkage
- For purine nucleosides
o C1 of sugar to N9 of purine
- For pyrimidine nucleosides
o C1 of sugar to N1 of pyrimidine

NITROGENOUS BASE + SUGAR + PHOSPHATE =

NUCLEOTIDE

NUCLEOTIDE
- Basic structural unit of nucleic acids
- It is the monomer for nucleic acids

Chemically:
o Phosphoric acid ester of nucleoside
o Strongly acidic
Includes:
o Adenylic acid
o Guanylic acid
o Thymidic acid
o Cytidylic acid
o Uridylic acid

Formation of bonds:
- For deoxyribose
o Phosphorylation at C3 and C5
o C1 and C4 – involved in furanose
o C2 – no –OH group
- For ribose
o Phosphorylation at C2, C3 and C5
o C1 and C4 – involved in furanose ring
formation
Names of Nucleosides and Nucleotides in
DNA and RNA Comparison of the DNA and RNA

Base Nucleosides RNA

Nucleotides
Adenine (A) Adenosine Adenosine
(A) monophosphate
(AMP)
Guanine (G) Guanosine Guanosine
(G) monophosphate
(GMP)
Cytosine (C) Cytidine (C) Cytidine
monophosphate
(CMP)
Uracil (U) Uridine (U) Uridine
monophosphate
(UMP)

DNA
Adenine (A) Deoxyadeno Deoxyadenosine
sine (A) monophosphate
(dAMP)
Guanine (G) Deoxyguano Deoxyguanosine
sine (G monophosphate
(dGMP)
Cystosine (C) Deoxycytidin Deoxycytidine
e (C) monophosphate
(dCMP)
Thymine (T) Deoxythymi Deoxythymidine THE DNA
dine (T) monophosphate - A polymeric substance made up of the four nucleotides
(dTMP) (dAMP, dGMP, dCMP, dTMP)
- Size varies with the complexity of the organisms (E. coli = 8
million nucleotides; human = 500 million nucleotides)
- The chemical basis of heredity
Functions of Nucleoproteins and Nucleic - Genome – the sum total of all hereditary material contained
acids in a cell
o Within the genome are chromosomes
- To reproduce their own kind (duplication)
o Within chromosomes are genes – fundamental
- To store, express and transmit genetic
units of heredity
information
o Gene – segment of the DNA chain that controls
- They undergo mutation
the formation of a molecule of RNA A Self-regulated
Learning Module 83 Structure of the DN
2 Types of Nucleic Acids
Structure of the DNA
1. Deoxyribonucleic acid (DNA)
Internucleotide linkages
- Main carrier of genetic information
- Link that join nucleotides together
- The basic information pathway
- It is of the diester type
- The chemical basis of heredity - Yields D-2’-
- Between C3 and C5 of the sugar molecule (3,5-
deoxyribose, phosphoric acid and four
phosphodiester bridges)
nitrogenous bases of which are adenine (A),
- Double Helical Structure
guanine (G), cytosine (C) and thymine (T)
- The early 1950’s, James Watson and Francis Crick
determined that DNA had a doublehelical structure with
2. Ribonucleic acid (RNA)
two nucleotide strands winding about each other like a spiral
- Aids in expressing genetic characteristics
staircase
- A copy form a portion of the DNA which
becomes a template for synthesizing an
intended protein
- Yield ribose, phosphoric acid and four
nitrogenous bases namely adenine (A), guanine
(G), cytosine (C) and uracil (U) upon hydrolysis
 NB THE DNA STRUCTURE SHOWING HYDROGEN
BONDS:
- Held by hydrogen bonds

- Amino is joined to a keto group

A-T: 2 HYDROGEN BONDS

T- A: 2 HYDROGEN BONDS

G – C: 3 HYDROGEN BONDS

C – G: 3 HYDROGEN BONDS

- Sugar- phosphate outside, bases inside

CHARGAFF’S RULES OF THE DNA

- The base composition of the DNA of an organism
is constant in all
- The amount of adenine is always equal to the
amount of thymine
- The amount of guanine is always equal to the
amount of cytosine
- The is a 1:1 purine - pyrimidine ratio

Replication of DNA molecules

DNA Replication is the biochemical process by
which DNA molecules produce exact duplicates of
themselves.
Each time the cell divides, an exact copy of
the DNA of the parent cell is needed for the
new daughter cell

Enzymes involved
1. DNA helicase
- causes the DNA helix to unwind
2. DNA ligase
- Joins Okazaki fragments together
o Okazaki fragments – short segments of the
DNA molecule
- Forms the other strand of the DNA (3’ to 5’)
- Nicks – gaps in the daughter strand
3. DNA polymerase
- catalyzes the formation of a new phosphodiester linkage
between the nucleotide and the growing strand
- Can operate only in the 5’ to 3’ direction
- Only one strand can grow continuously in the 5’ to 3’
direction
THE BASIC DNA STRUCTURE
STEPS IN DNA REPLICATION
Step 1 - The enzyme DNA helicase causes the two
strands to unwind, producing two separate strands
Step 2 - Free nucleotides pair with their complementary
base on the template strands by means of hydrogen
bonds
Step 3 - DNA polymerase joins the newly attached
nucleotides to create one continuous strand in the 5’ to
3’ direction
 Step 4 - The other strand is formed in short
segments (Okazaki fragments) in the 3’ to 5’
direction. The segments are joined together by DNA
ligase
CHROMOSOMES
- Histone – DNA complexes
- Structural units that provide the most stable
arrangement for the long DNA molecule
- An individual DNA molecule bound to a group of
proteins - 15% by mass DNA and 85% by mass
protein
- Different organisms have different number of
chromosomes
o Humans 46; mosquito 6; frog 26; dog 78;
turkey 82
FOUR (4) major differences between RNA
and DNA
1. Ribose is the sugar unit in RNA - Thymine is
replaced by uracil in RNA. Uracil pairs with
adenine
2. RNA is single stranded, thus it does not contain
equal amounts of specific bases
3. The RNA is much smaller than the DNA (from 75
nucleotides to a few thousand nucleotides)
THE BASIC RNA STRUCTURE
5 major types of RNA
1. Heterogeneous nuclear RNA (hnRNA)
2. Messenger RNA (mRNA)
3. Small nuclear RNA (snRNA)
4. Ribosomal RNA (rRNA)
5. Transfer RNA (tRNA)
Heterogeneous Nuclear RNA
- RNA formed directly by DNA transcription.
Post - - transcription processing converts the
heterogeneous nuclear RNA to messenger RNA
Small nuclear RNA
- RNA that facilitates the conversion of
heterogeneous nuclear RNA to messenger RNA
- It contains from 100 to 200 nucleotides
Messenger RNA (mRNA)
- Carries genetic information from the DNA in the
nucleus to the ribosomes for protein synthesis
- Each gene in a DNA produces separate mRNA
when certain protein is required by the cell
- A template made from DNA
- It carries the code that directs the synthesis of
proteins
- The size of the mRNA depends of the number of
nucleotides in that particular gene - mRNA + hnRNA
= 5 – 10% of total RNA material
Transfer RNA (tRNA)
- The smallest RNA molecule
- Functions
o Interprets the genetic code
o Brings specific amino acids to the ribosome
for protein synthesis
o Link the genetic code to the amino acids in
the proteins
- There are different tRNA’s for all the amino acids
- Each tRNA consists of a single chain of about 70-90
nucleotides
- Makes up 10 – 15% of cellular RNA
Cloverleaf model of the tRNA
- Anticodon loop – Hydrogen bonds between one of the
complementary nitrogen bases in the chain produce loops
that give an overall cloverleaf structure. At the center loop,
there are three bases known as anticodon that are
complementary to three bases on an mRNA codon
o Composed of 7 unpaired nucleotides
o 3 of which make up an anticodon
- Other loops enable the tRNA to bind to the ribosome and
other specific enzymes during protein synthesis
• An ester bond is form between the tRNA and its
specific amino acid to form aminoacyl tRNA during
protein synthesis.
• The 3 base sequence called the anticodon helps in
recognizing the codon for its specific amino acid on
the mRNA during protein synthesis.
Ribosomal RNA (rRNA)
- The most abundant RNA
- Makes up of 60% of the structural material of
ribosomes
- Ribosomes o the site of protein synthesis
o small, complex structures in the cytoplasm
composed of rRNA and protein
- RNA that combines with specific proteins to form
ribosomes , the physical sites for protein synthesis
- The rRNA present in ribosomes has no
informational function
Synthesis of RNA: Transcription
- The transfer of genetic information from DNA by the
formation of mRNA
- In this process, which occurs in the nucleus, the
nucleotides on one strand of DNA are copied or
transcribed in their complementary bases in a
messenger RNA molecule
- However, the entire DNA cell is not necessarily
transcribed, only individual genes or group of genes
are copied
- The process is aided by the enzyme RNA
polymerase which is able to recognize the initiating
signal and the terminating sequence for a particular
gene that needs to be copied
- Example
Bases on a DNA template strand
- Oncogenes – present in cancerous or malignant
cells and code for proteins that control cell growth
o Cancerous cells lose control of oncogene
transcription
o Control is lost when DNA is altered
o Oncogenes are transcribed too often, cell
growth is uncontrolled – cancer develops -
Tumor suppressor genes (p53)
o Genes code for proteins that allow cell growth
only if the cells are correctly functioning
– Apoptosis
o Self-destruction of potential cancer cells
o Due to active tumor-suppressor gene
Translation
- The overall function of the rRNA’s in the cell is to
facilitate the lack of synthesizing protein
- After the genetic information encoded in DNA is
transcribed into mRNA, it moves out of the nucleus to
the ribosomes in the cytoplasm
- At the ribosome, translation by the tRNA’s converts
the genetic information in the mRNA’s into a
sequence of amino acids in proteins
The Central Dogma (by Francis Crick in 1957)
- Explains the flow of genetic information within a cell
- Also known as “one gene-one protein hypothesis”
- The genetic information contained in one gene of a DNa
molecule is used to make one molecule of mRNA by a
process known as transcription
- The genetic information in that mRNA molecule is then used
to make one protein by a process known as translation
Protein Synthesis
I. Transcription - The process by which a segment
of the DNA is cut off or nicked from the molecule
by the enzyme - RNA polymerase - The detached
portion together with its accompanying
nitrogenous base will serve as a template for the
formation of a complementary strand finally
resulting to the formation of a mRNA (occurs in the
nucleus) - To reconstruct the DNA molecule:
OKAZAKI fragments are put together by ligase -
mRNA leaves the nucleus and goes to the
ribosomes, it carries with it the codon
II. Translation - the process by which tRNA accepts
the codon carried by the mRNA, reacts, translates
and decodes the message - pertains to the
production of the 20 amino acids
III. Formation of polypeptide Chain - amino acids in
the cytoplasm are activated by combining with
ATP. The tRNA will transport individual amino
acids to the ribosomes based on the arrangement
which follows strictly the dictates of the codon
The Genetic Code
- Genetic information from DNA in encoded in the mRNA
as a sequence of nucleotides
- The genetic code is the sequence of three bases (or
triplet), called a codon, that specifies the amino acid
order for the synthesis of proteins
Codon – a sequence of three bases in mRNA that
specified a certain amino acid to be placed in a protein.
A few codons signal the start or stop of transcription
Anticodon – the triplet of bases in the center loop of
tRNA that is complementary to a codon on mRNA
 Genetic code for Messenger RNA (Introduction to
General, Organic and Biochemistry by Hein 8TH
edition)
2. Elongation – after the initiator tRNA attaches to the
mRNA codon, the elongation of the polypeptide chain
starts
a. The formation of the peptide chain which
assembles one amino acid at a time
b. Translocation – the shift of a ribosome along
mRNA from one codon (three bases) to the
next codon during translation
c. The process of elongation continues as the
ribosome moves along (translocates) the
mRNA, one codon at a time

3. Termination
a. Protein synthesis stops when a ribosome encounters
the codon UGA, UAA or UAG

PROTEIN SYNTHESIS

TC

- Termination codon or nonsense codon

- They do not encode any amino acids
- Act as signals to indicate where the synthesis of a
protein molecule is to end

Example:
Codon Message (A.A.)
AAA Phenylalanine
AAT Leucine
TAC Methionine
ATA Tyrosine
GTG Histidine
ACC Tryptophan

*64 three-lettered codons (there is more than 1 codon

for most amino acids)
Genetic Mutations - A mutation is a change in the DNA
base sequence that alters the structure and function of
the protein in the cell
Characteristics of the codon
Kinds of Mutation:
o Universal
A. Beneficial
▪ All plants, animals and bacterial cell have the same
B. Harmful
codon to specify each amino acid
a. Lethal
o Degenerate C. Silent
▪ More than one triplet can code for a particular amino
acid Types of Mutation
o Continuous
▪ Non-overlapping A. Substitution – a mutation that replaces one base in a
▪ Adjacent codons do not overlap DNA with a different base. The change in the codon may
cause a different amino acid to be inserted at that point in
the polypeptide
Three Processes involved in the Biosynthesis of
Proteins

1. Initiation
a. The codon AUG or GUG (AUG is more
common)signals the start of protein synthesis
b. Once the correct starting point has been
identified, a special initiator tRNA binds to the
ribosome
 B. Frame Shift Mutation – a mutation that inserts or
deletes a base in a DNA sequence
Factors that Cause Mutation:
- Viruses
- Chemicals (industrial chemicals, pesticides, food
additives, hair dyes and cosmetics)
- Ultraviolet light (overexposure to sum)
- X-rays
Mutagen
- The agents that causes mutation which include
chemical agents or various types of radiation
- Ames test – developed by Bruce Ames, is the
standard test for mutagenicity
The following shows the effect of mutation:
Some Genetic Diseases
A. Down’s syndrome – is the leading cause of mental
retardation, occurring in about 1 of every 800 live births.
Mental and physical problem including heart and eye
defects are the result of the formation of three
chromosomes, usually chromosome 21, instead of a pair
B. Sickle-cell anemia – a defective hemoglobin from a
mutation in a gene on chromosome 11 decreases the
oxygen-carrying capacity of red blood cells that take on a
sickle-shape, causing anemia and plugged capillaries
from red blood cell aggregation
C. Galactosemia – absence of the transferase enzyme
required for the metabolism of galactose-1- phosphate,
leading to cataracts and mental retardation.
D. Cystic fibrosis – the most common inherited disease,
thick mucus secretions make breathing difficult and block
pancreatic functions
E. Familial hypercholesterolenemia – a mutation of
a gene on chromosome 19 characterized by high
cholesterol levels leading to early coronary heart
disease in 30-40 year-old persons
F. Muscular Dystrophy (Duchenne) – one of 10 forms
of MD caused by a mutation in the X chromosome
occurring in about 1 of 10,000 males due to the low or
abnormal production of dystrophin by the x gene, a
muscle-destroying disease beginning at about age 5
with death by age 20
G. Hemophilia – one or more defective blood clotting
factors leading to poor coagulation, excessive bleeding
and internal hemorrhages
H. Tay-Sach’s disease – a defective hexosaminidase
A, causing an accumulation of gangliosides resulting in
mental retardation, loss of motor control and early
death
I. Huntington’s disease – a genetic disease appearing
in middle age affecting the nervous system that leads
to total physical impairment, result of a mutation in a
gene on chromosome 4, which can now be mapped to
test people in families with HD
4 Means of Manipulating Genes
A. Genetic Engineering
B. Recombinant DNA technology
C. Genetic manipulation (GM)
D. Gene splicing
• Over the past 25 years, geneticists have been
cutting, splicing, and rejoining DNA from different
genes to form a new synthetic DNA called
recombinant DNA
Genetic Engineering
- Uses the techniques of molecular cloning and
transformation to alter the structure and characteristics of
genes directly
- Most of this experimentation has been done with E. coli,
which contains a single chromosome and several small
cyclic DNA particles called plasmids
Some Successful Applications of Genetic
Engineering
- Improving crop technology
- Manufacture of synthetic human insulin thru the
use of modified bacteria (E. coli plasmids)
- Manufacture of erythropoietin in hamster’s ovary
cells
- Production of new types of experimental mice
such as the oncomouse (cancer mouse) for
research
- Created the human growth hormone as a
replacement for a drug that was previously
extracted from human cadavers
- In 1987, the FDA approved the first genetically
engineered vaccine for humans for hepatitis B
- The protein interferon, which helps fight viral
infections and possibly cancer, has been
produced by recombinant DNA
- Creation of genetically modified organisms
(GMO’s)such as foods and vegetables that resist
pest and bacterial infection and have longer
freshness than otherwise
- Human genetic engineering can be used to treat genetic
diseases
- Human genetic engineering is already being used on a
small scale to allow infertile women with genetic defects in
their mitochondria to have children, healthy human eggs
from a second mother are used - Genetic engineering has
the potential to change human beings, appearance,
adaptability, intelligence, character and behavior.

How is this accomplished?

A. Isolation of the genes of interest
B. Insertion of the genes into a transfer vector, such as a
plasmid, viral vector or liposomes
C. Transfer of the vector to the organism to be modified
D. Transformation of the cells of the organism
E. Selection of the GMO from those that have not been
successfully modified