Elton John D.

Delos Santos, RN, MAEd, MAN

Instructor, UB-SN

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 Welcome to Introduction to
Biochemistry, where you will begin to
learn how life works at the molecular
level. Biochemistry is at the nexus of
the physical, natural and medical
sciences, yet has developed its own
language and culture that are distinct
from those disciplines.
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 The knowledge and tools of biochemistry
(along with the closely related discipline
of molecular biology) will continue to be
at the forefront of discoveries in medicine
and biotechnology, driving advances in
such areas as molecular and
personalized medicine, nanotechnology,
agriculture, environmental remediation
and evolution.
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 The concepts and skills obtained
in this course will prepare you for
more advanced training in
biochemistry & molecular biology
for careers in biotechnology and
biomedical research, as well as
in medicine and other health
professions. 4
UNIT I: FOUNDATIONS
 Definition of terms
 Aims
 Biochemistry and medicine
UNIT II: WATER and pH
 Water
 pH

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UNIT II: THE CELL
1. Plant versus animal
2. Parts & functions
3. DNA & RNA
4. enzymes

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 UNIT III: BIOCHEMISTRY OF DIGESTION
1. Definition
2. Factors affecting digestion
3. Phases – salivary, gastric and
intestinal digestion; pancreatic, intestinal
juices; bile
4. Chemical changes in the large
intestines and feces- overview,
fermentation, putrefaction, deamination,
decarboxylation; detoxification; chemical
composition of feces
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 UNIT IV: CARBOHYDRATES
1. Definition and general structure; Location and
Physiologic Significance/ Importance and functions
4. Classifications- monosaccharides, disaccharides and
polysaccharides
5. Digestion and absorption and metabolism
6. Gylcogen-glucogenesis, glycogenolysis & metabolism
7. The Main powerhouse: location, Krebs cycle, electron
transport, oxidative phosphorylation, alcohol
metabolsim
8. lactose, fructose & galactose metabolisms
9. Glucoronate
10. Test for carbohydrates; Clinical significance of CHO
metabolism/clinical disorders-DM, GSDs
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 UNIT V: PROTEINS
1. Pproteins- location & important
functions, classifications, categories of
structure
2. Amino acids- definition & general
structure, location, properties & important
functions, classifications, metabolism,
3. Lipids- lipolysis, Knoops’s Beta, lipid
storage, tests for lipids, clinical
significance of lipid metabolism/disorders
like obesity, lipid storage diseases
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 Additional topics: own reading
1. The combo cycle- location,
lipoprotein, glycolipid, glycoprotein
2. Blood and guts
3. Vitamins, hormones, minerals
4. Clinical disorders that involve
biochemistry: vitamins,
hormones and minerals
5. Biochemistry and aging
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 Lecture-discussion
 Oral questioning
 Group or individual reporting
 Activities and experiments for the
laboratory
 Library works/discovery
 others

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1 stgrading examination-
Sept. 4-8, 2018
 Midterm examinations-
October 16-20, 2018
 Final examinations- Nov.
28-29; December 3-
4,2018
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1 stgrading: Cumulative
 Midterms:
[(Tentative Midterm grade x 2) + 1st
grading grade]/ 3
 Finals
[(Tentative final grade x 2) + midterm
grade]/ 3
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 Chary, TM. & Sharma, H. (2004). Practical
Biochemistry for Medical & Dental Students,
1st ed. Noida: Gopsons Papers Ltd., Sector
60.
 Goldberg, S. (2004). Clinical Biochemistry
made ridiculously simple, 2nd ed. Florida:
Medmaster, Inc
 Murray, R., Bender, D., Botham, K.,
Kennelly, P., & Weil, P. (2012). Harper’s
Illustrated Biochemistry, 29th ed. Mcgraw-
Hill Companies.

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 Harvey, R., Champe, P., &
Ferrier, D. (2005). Lippincott’s
Illustrated Reviews:
Biochemistry, 3rd ed.
Lippincott Williams & Wilkins
 Stoker, H. (2017).
Biochemistry , 3rd ed. C & E
Publishing, Inc.
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 1. Use your knowledge of fundamental principles of chemistry
and physics (e.g. molecular bonding, thermodynamics,
kinetics) to explain important concepts in biochemistry.
 2. Describe and interrelate the hierarchical levels of protein
structure (1˚ to 4˚) and provide examples of how this structure
relates to the function (or dysfunction) of various classes of
proteins.
 3. Explain how enzymes can increase the rates of biochemical
reactions at the molecular level, and how enzymes may be
inhibited and regulated. 16
 4. Outline the major pathways by which
precursor biomolecules (carbohydrates, lipids,
amino acids) are synthesized and degraded, and
the key points at which these pathways are
regulated.
 5. Describe how organisms obtain, store, and
utilize energy through metabolic interconversion
of biomolecules.
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 6. Understand how metabolic pathways are
controlled to maintain homeostasis of organisms
under normal physiological conditions, and how
this may be disrupted by certain pathological
states.
 7. Place biochemical events within a genomic
and cellular context.

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 Living matter consists of small number of elements
 Elemental composition of human body (98%)
 C- 61.7% N-11%,O- 9.3% ,P- 3.3% ,S- 1%,H- 5.7%-
most abundant, essential elements for all
organisms
 Na- 0.7%,Mg- 0.3%, K- 1.3%, Ca- 5%, Cl-0.7% =
less abundant, essential elements for all organisms
 Fe, Mn, Co, Cu, Zn, = trace levels, essential
elements for all organisms
 V, Cr, Mo, B, Al, Ga, Sn, Si, As, Sc, I = trace
elements essential for some organisms
 Most organisms are ca 70% water

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 The Physical Laws of Life

•Philosophers thought life contained a “vital force” or VITALISM but

this has been rejected by modern science.

•Haldane – simple organic compounds from H2O, N2

and CO2
•Urey – chemical synthesis of urea

•Living organisms operate within the same physical laws that apply to
physics and chemistry:

•Conservation of Mass, Energy

•Laws of Thermodynamics
•Laws of Chemical Kinetics
•Principles of Chemical Reactions
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 Molecular Logic of Life
These physical laws describe several axioms that make up
the Molecular Logic of Life. These axioms define:

•Energy converted to work

•Catalytic chemical transformations
•Assembly of molecules with great complexity from
simple subunits.
•Complex molecules combine to form supra molecular
components, organelles and finally assemble into a cell.
•Store and pass on instructions for the assembly of all
future generations from simple non-living precursors
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 Life is in constant flux
Enzyme catalyzed reactions- Substrates  Products 10-3 sec -
milli sec
Unwinding of DNA 10-6 sec - micro sec

10-15 s 10-12 s 10-9 s 10-8 s 10-6 s 10-3 s 10 s

103s
femto pico nano micro milli sec

•femto fs excitation of chlorophyll

•pico ps charge separation in photosynthesis
•nano ns hinge protein action
•10-8 10 ns fluorescence lifetime
•micro ms DNA unwind
•milli ms enzymatic reactions
•103 generation of bacteria
•2.3 x 109 sec average human life span 24
 What distinguishes living organisms?

1) Structurally complicated and highly organized

a. intricate internal structures
b. many kinds of complicated molecules

proteins, DNA, RNA, starches, and lipids etc. (inanimate objects

sand clay are mixtures of simple compounds)

2) Living organisms:
a. extract
b. transform ENERGY
c. store
d. use
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a. Living things can extract energy from the
environment
Chemical: Chemoautotrophs or lithoautotrophs

H2S  2H+ +S +2e-

2NH3 + 4O2  2HNO3 + 2H2O
4FeCO3 + O2 + 6H2O  4Fe(OH)3 + 4CO2
or
Sunlight: Photoautotrophs
nCO2 + nH2O + hu (CH2O) + nO2

b. Energy is needed to build and maintain structures

a) mechanical energy - muscles
b) chemical energy - electric eel
c) osmotic energy - plant turger
d) light energy -bioluminescence
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3) Most characteristic attribute of living things is self-
replication and self assembly
it is the quintessence of the living state

1 single bacteria  109 in 24 hr

With near-perfect fidelity during replication!

A crystal at equilibrium grows but life at equilibrium is death!

Life is a set of relationships characterizing the nature, function and

interaction of biomolecules.

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 Mid 1700- Karl Schelle- Swedish founder of
biochemistry; studied chemical composition of
matter
 1840- Schleiden & Schwann formulated the CELL
theory
 1875- Walter Flemming discovered CHROMOSOMES
 Carl Newberg- German Scientist; coined the word
BIOCHEMISTRY
 1897- Edward & Hans Buchner found that yeasts
extracts could bring about fermentation of sugar
into ethanol
 1925- Embden & Mayerhoff described the
GLYCOLYTIC pathway
 1937- Hans Kreb proposed the KREB cycle
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 1953- James Watson & Francis Crick
described the double helical structure of DNA
 1997- Paul Boyer & J.Walker discovered the
“ROTARY engine” that generated ATP
 Danish J. Skou studied the “pump” that drives
sodium and potassium across membrane
 Stanley Frusiner- discovered the organism
that caused “MAD COW DISEASE”
 Ruska, et. al – discovered the electron
microscope & provided a whole new level of
insight into cellular structure

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Section 1.7
Discovery and Abundance of the Elements
Abundance of Elements (in Atom Percent) in the
Universe

Return to TOC

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Section 1.7
Discovery and Abundance of the Elements
Abundance of Elements (in Atom Percent) in the
Earth’s Crust

Return to TOC

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 SERUM ELECTROLYTE CONVENTIONAL SI

Na+ 135-145mEq/L 135-145

mmol/L
Cl- 98-106 mEq/L 98-
106mmol/L
HCO3 22-26mEq/L 22-26
mmol/L
Ca++ 8.5-10mg/dL 2.1-2.6
mmol/L
PO4 1.7-2.6 mEq/L 0.8-1.5
inorganic absorption (2.5-4.5 mg/dL) mmol/L
Mg++ 1.6-2.6mEq/dL 0.8-1.3
mmol/L
K+ 3.5-5.1mEq/dL 3.5-5.0
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Biochemistry: Life at the Molecular Level

Biochemistry is the
study of biological
processes
at a chemical level

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2. To understand how life began

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 Most and perhaps all of the
disease has a biochemical
basis
 The major cause of disease
is by influencing the various
biochemical mechanisms in
all parts of the body
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 Biochemistry is the science concerned
with studying the various molecules
that occur in living cells and organisms
and with their chemical reactions
 It has become the basic language of all
biologic science. It is concerned with
the entire spectrum of life forms, from
relatively simple viruses and bacteria
to complex human beings
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 Biochemistry is the science concerned
with studying the various molecules
that occur in living cells and organisms
and with their chemical reactions
 It has become the basic language of all
biologic science. It is concerned with
the entire spectrum of life forms, from
relatively simple viruses and bacteria
to complex human beings
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 An advanced biochemical knowledge has
illuminated many areas of medicine and
nursing. Conversely, the study of
diseases have often related previously
unsuspected aspects of biochemistry.
The determination of the sequence of the
human genome, nearly completes, will
have a great impact on all areas of
biology, including biochemistry,
bioinformatics, and biotechnology
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 Biochemical approaches are often fundamental
in illuminating the causes of disease in
designing appropriate therapies

 The judicious use of various biochemical

laboratory test is an integral component of
diagnosis and monitoring of treatment

 A sound knowledge of biochemistry and of

other related discipline is essential for the
national, nursing and related health science
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1. Prevent diseases:
It helps for prevention,
treatment of diseases
and also increases the
production or yield.
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2. Enhance growth:
Biochemistry gives an
idea of how the use
of fertilizers can increase
plant growth, their yield,
quality of food etc.
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3. Enhance Yield:
Some hormones promote
growth, while other promote
flowering fruit formation etc. In
fisheries, use of substances to
promote fish growth, their
reproduction, etc can be
understood.
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4. Adulteration: Even the
composition of food material
produced, their alteration or
adulteration for example in honey
can be found by biochemical
tests. Biochemistry tests help
prevent contamination.
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5. Biochemical tests for
the pesticide residues or other
toxic waste in plant, food grain
and soil can be evaluated. Hence
during import and export of food
grains a biochemical check of the
toxic residues is done to fix the
quality. 85
6. In animal husbandry, the
quality of milk can be
checked
by biochemical tests. It also
helps diagnose any disease
condition in animals
and birds 86
7. Biochemical tests for
the pesticide residues or other
toxic waste in plant, food grain
and soil can be evaluated. Hence
during import and export of food
grains a biochemical check of the
toxic residues is done to fix the
quality.
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8. In fisheries, the water quality is
regularly monitored by biochemical tests.
Any drastic change in water chemistry &
composition of fishery ponds can lead to
the vast death of fishes and prawns, hence
the tests are done on regular basis to see
salt content (calcium content), pH,
accumulation of waste due to not
changing water for long etc.
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1. Photosynthesis: This describes
how carbohydrates are synthesized
by use of sunlight, CO2, and water in
the green leaves of plants. It goes on
to explain about different complex
enzymes involved in the process to
combine the energy of sun within the
molecules H2O+ CO2 in the form of
carbohydrates.
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2. Respiration: By use of
above photosynthesis
pathway, plants leave out
Oxygen while taking up
Carbon dioxide from
the air.
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3. Different sugars: Biochemistry
defines different types of carbohydrates
formed in plants like trioses (3 carbon
sugars i.e. glyceraldehyde), tetroses (4),
pentoses (5), hexoses (6= glucose),
heptuloses (7) etc. Heptuloses are the
carbohydrates which go on to form the
nucleic acids i.e deoxyribonucliec acid
(DNA), ribonucleic acid (RNA).

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4. Plants secondary
metabolites: Biochemistry also
describes how the plant
products like gums, tannins,
alkaloids, resins, enzymes,
phytohormones are formed
inside the plants.
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5. Other functions: It also describes
how plants fruits get ripened, how
plant seed germinates, the
respiration process inside the plant
cell, how proteins and amino
acids are formed on rough
endoplasmic reticulum and fats are
formed on smooth ER.
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1. Food chemistry gives an
idea of what we eat, i.e. it’ s
components like
carbohydrates, proteins, fats,
etc. and also the possible
physiological alteration due to
their deficiency.
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2. The role of nutrients: Due to
biochemistry the importance of
vitamins, minerals, essential fatty
acids, their contribution to health were
known. Hence there is a frequent
recommendation for inclusion of
essential amino-acids, cod liver oil,
salmon fish oil etc. by physicians and
other health and fitness experts.
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1. Drug Constitution: Biochemistry gives an
idea of the constitution of the drug, its chances
of degradation with varying temperature etc.
How modification in the medicinal
chemistry helps improve efficiency, minimize
side effects etc.
 The half-life: This is a test done on
biochemical drugs to know how long a drug
is stable when kept at so and so temperature
 Biochemical tests: These tests helps fix the
specific half-life or date of expiry of drugs.
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2. Drug storage: The storage
condition required can be estimated
by the biochemical test. For example
many enzymes, hormones are stored
for dispensing. These get
deteriorated over time due to
temperature or oxidation,
contamination and also due to
improper storage. 97
3. Drug metabolism: It also gives an
idea of how drug molecules
are metabolized by many biochemical
reactions in presence of enzymes.
This helps to avoid drugs which have
a poor metabolism or those with
excessive side effects from being
prescribed or dispensed to the
patient. 98
1. Physiology: Biochemistry
helps one understand the
biochemical changes and related
physiological alteration in the
body. Pathology of any disease is
studied through biochemical
changes.
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2. Pathology: Based on the symptoms
described by the patient, the physician
can get a clue on the biochemical change
and the associated disorder. For
example, if a patient complains about
stiffness in small joints, then the
physician may predict it to be gout and
get confirmed by evaluating uric acid
levels in the blood. As uric acid
accumulation in blood results in gout. 10
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3. Nutrition deficiency: In the
present scenario, many people rely
on taking multivitamin & minerals
for better health.
The function and role of
the vitamin in the body are
described only by biochemistry.
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4. Hormonal deficiency: There are
many disorders due
to hormonal imbalance in especially
women and children. The formation,
role of hormones in the normal body
function is taught in biochemistry by
which the physician can understand
the concerned problem during
treatment. 10
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 In nursing, importance of clinical
biochemistry is invaluable. When a patient is
in the hospital nurses need to keep a watch
on how his condition is progressing through
clinical biochemistry. That is the treatment
helping him recover from said condition etc.
Almost all the diseases or disorders have
some biochemical involvement. So the
diagnosis of any clinical condition is easily
possible by biochemical estimations
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1. Kidney function test: For
example in kidney disorders,
other chemotherapy treatment
etc urine test help understand
the extent of excretion of drugs
or other metabolites, the change
in pH, the color of urine etc.
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2. Serum cholesterol
test: Evaluation of blood
cholesterol level and other
lipoproteins helps
understand the proneness of
the patient to cardiovascular
diseases. 10
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3. Blood test:
In diabetes, biochemical analytical
test for blood glucose level (above
150mg/ deciliter helps one understand
the severity of diabetes disorder.
-Another biochemical test for ketones
bodies in urine also indicates the stage of
diabetes. The appearance of ketone
bodies or ketone urea is mostly the last
stage of diabetes. 10
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4. Liver function
tests help understand
the type of disease or
damage to the liver, the
effect of any medication
on liver etc. 10
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