Module 1: Introduction to Biochemistry 1.

Metabolic degradation
CHEMISTRY conversion of a substance into an active
 study of the composition and properties of metabolite
matter 2. Biotransformation
 study of compounds, chemical changes and conversion of a substance to another for
reactions occurring in living system biosynthesis
GENERAL AND INORGANIC CHEMISTRY Excretion
 study of elements in the periodic table and an pH and BUFFERS
overview of chemistry in general Dissociation or lonization
ORGANIC CHEMISTRY  a process by which a polar compound (contains
 study of carbon containing compounds (+) and (-) ions) is broken apart into its
BIOCHEMISTRY - or BIOLOGICAL CHEMISTRY individual lonic components when placed in an
 from "BIO" - which means life aqueous solution
MOLECULAR BIOCHEMISTRY  occurs in the presence of water.
 study of macromolecules and their metabolic Example:
activities in the body. a. POLAR
 It includes the entrance in the human body,  NaCl -> Na+ CI
digestion, absorption, assimilation, utilization, b. NON-POLAR
integration into the tissues, metabolic  C12H22O11
degradation and eventually, excretion from the ELECTROLYTES
body.  substances whose water solutions conduct
2 ASPECTS OF BIOCHEMISTRY: electricity
MOLECULAR ANATOMY STRONG ELECTROLYTES
 different biomolecules which comprise the cell  completely ionized in H2O solutions
MOLECULAR PHYSIOLOGY E.g.
 dynamic part of biochemistry which includes  strong acids - HCI, HNO3, H2SO4
the functions and metabolic activities of  strong bases - NaOH, KOH, Ca(OH)2
biomolecules in the cell.  salt solutions - any salt dissolved in water such
Digestion as NaClsol'n&CaFsol'n
 Physical - mechanical breakdown WEAK ELECTROLYTES
 Chemical - further breakdown with the aid of  incompletely or partially lonized in H2O solution
enzymes  a large percent remains unionized
Absorption E.g.
 passage of end products of digestion from the  weak acids - acetic acid
small intestine into the blood  weak bases - aniline, ammonia
Assimilation NON-ELECTROLYTES
 selective absorption  substances whose water solution do not
Utilization conduct electricity
 cell is the important unit of life. Hence a large E.g.
number of chemical reactions in the cell utilize  dry solids
the nutrients absorbed to produce materials  Organic compounds
needed for our existence
Integration
 refers to the overlap of many functions of the
systems of the human body, as well as its
accompanied form.
Module 2: pH and Buffers 2. The pOH of the solution is 5.7. Calculate the pH of the
solution?
WATER EQUILIBRIUM / IONIZATION OF WATER
Solution:
Water
14 = pH + pOH
 considered as a weak electrolyte. It is
pH = 14 - 5.7
amphoteric and amphiprotic in nature.
pH = 8.3
Amphoteric
 can react both as an acid and as a base
3. If the pOH is 4.3. What is the [OH-] concentration?
Amphiprotic
Solution:
 a substance that can both accept and donate a
[OH-] = antilog - pOH
proton or H
[OH-] antilog - 4.3
IONIZATION CONSTANT OF WATER OR KW
[OH-] = 5.01 x 10-5
Kw=[H₂O+] [OH-]
Where:
4. What is the pOH of the solution if the [H3O+]
 [ ] = Represents concentration either in F concentration is 5.2x10^-3?
(Formality) or in M (Molarity) Solution:
Note: pH = -log (H^3O+)
 Use F as a unit if the solute is an element, ion or pH = -log (5.2x10^-3)
compound pH = 2.28
 Use M as unit if the solute is a compound only
 F = gram/ Formula weight 14 = pH + pOH
 M= gram/ Molecular weighted pOH = 14 - 2.28
pH EXPRESSION pOH = 11.72
 introduced by a Danish biochemist by the name
of Sorensen 5. If the Ka of an acid is 1.7 x 10^-5, calculate the pka
Formulas: and pkb values of the acid?
Solution:
pKa= -log Ka
pKa= -log 1.7 x 10^-5
pKa = 4.77

14 = pKa + pKb
pKb = 14 - pKa
pkb = 14 - 4.77
pKb = 9.23
BUFFER
 a mixture of a weak electrolyte with its salt
Function:
Sample Problems:
1. What is the pH of the solution if the [H3O+]  Resist drastic / great / marked change in pH of a
concentration is 5.5x10-4 M? system even upon the addition of either a
Solution: Strong Acid (SA) or Strong Base (SB)
pH = -log (H^3O+) 2 TYPES:
pH = -log (5.5x10^-4) ACID BUFFER - mixture of weak acid + salt of weak acid
pH = 3.26  E.g. HAC +NaAc, (KAc, MgAc^-)

BASE BUFFER - mixture of WB + salt of WB

 Eg. WEAK ACIDS OR BASES BUFFER CELLS AND TISSUES
 NH^4OH + NH^4C AGAINST PH CHANGES
 NH^4OH+NH^4NO3  In cells and tissues, phosphate and bicarbonate
buffer systems maintain intracellular and
NEUTRALIZATION extracellular fluids at their optimum
 E.g. base + acid -> salt + water (physiological) pH, which is usually close to pH
 NaOH + HCI NaCl + HOH 7.
HOW BUFFERS WORK:  Enzymes generally work optimally at this pH.
 Buffers work by neutralizing any added acid (H+  The intracellular and extracellular fluids of
ions) or base (OH- ions) to maintain the multicellular organisms have a characteristic
moderate pH, making them a weaker acid or and nearly constant pH.
base.  The organism's first line of defense against
ACIDS & BASES: changes in internal pH is provided by buffer
THEORIES systems.
Arrhenius/Ionic theory  The cytoplasm of most cells contains high
 Acid: Yield H+ in water solution concentrations of proteins, and these proteins
 Base: Yield OH- in water solution contain many amino acids with functional
Lewis theory groups that are weak acids or weak bases.
 Acid: Electron pair acceptor Sample problems:
 Base: Electron pair donor 1. What is the pH of a mixture of 0.042 M NaH2PO4 and
Bronsted-lowry theory or conjugate acid-base pair 0.058 M Na2HPO4? pKa: 6.86
theory Solution:
 Acid: Proton donor Though both NaH2PO4 and Na2HPO4 has acidic
 Base: Proton acceptor hydrogen but first one has two and second one has one
acidic hydrogen respectively. NaH2PO4 is much more.
Conjugate Base - anion produced from the dissociation acidic than Na2HPO4, hence NaH2PO4 acts as an acid
of acid; removal of hydrogen while Na2HPO4 acts as a salt of NaH2PO4 with a strong
Conjugate Acid - proton hydrogen donor; formed when base NaOH.
it combines with hydrogen pH = pKa + log (conjugate base / acid)
pH = 6.86 + log (0.058 / 0.042)
Ans: 7.0

2. What would be the pH of a 100mL solution

containing 0.24M formic acid (HCHO2; Ka= 1.8x10^-4)
and 0.24M sodium formate (NaCHO2)
Solution:
"Convert Ka to pKa using the formula, pKa= -log Ka
pKa= -log Ka
HENDERSON-HASSELBACH EQUATION pKa= -log 1.8x10^-4
 The pH of a solution of a weak acid (or base) pKa = 3.74
and its salt is given by the Henderson- pH = pKa + log (conjugate base / acid)
Hasselbalch equation: pH 3.74 + log (0.24/0.24)
Ans: 3.74
3. What would be the pH of a 100mL solution TYPES OF ACIDOSIS:
containing 0.15M formic acid (HCHO2; Ka= 1.8x10^-4) Metabolic Acidosis
and 0.15M sodium formate (NaCHO2)?  occurs when there is excessive loss of bases,
Solution: such as bicarbonate (HCOs) or sodium
Convert Ka to pKa using the formula, pKa= -log Ka  due to a decrease in blood HCO
pKa= -log Ka CAUSES:
pKa= -log 1.8x10^-4  severe ketosis & Diabetes Mellitus (DKA)
pKa = 3.74  Eclampsia
pH = pKa + log (conjugate base / acid)  High lipid diet
pH 3.74+ log (0.15/0.15)  Urinuria
Ans: 3.74 TREATMENT:

 Administration of sodium bicarbonate along

Module 3: Acidosis and Alkalosis with fluids and other electrolytes
 Metabolic acidosis can be compensated
Normal blood pH: 7.35-7.45
through intravenous
Factors Affecting Blood pH:
Respiratory Acidosis (hypoventilation)
Nature of diet
 associated with an increased level of CO2 in the
a. Proteins, fats, ketogenic substances
blood, occurring when there is interference
 Tend to acidify blood pH
with respiratory gas exchange
 Presence of SO4^=, PO4, H+ (acids)
 carbon dioxide combines with water to form
b. Fruits and vegetables
carbonic acid (H2CO3)
 Tend to alkalinize blood pH
 carbonic acid can dissociate into hydrogen ions,
 Na, K, Mg, Ca, OH (bases)
which will lower the pH of the blood (acidosis)
Vigorous Exercise
CAUSES:
 Tend to acidify blood pH
 depression to respiration
 Conversion of ATP to lactic acid leading to
 obstruction to respiration
muscular cramps.
TREATMENT:
ACIDOSIS and ALKALOSIS
 Respiratory Acidosis can be compensated
 metabolic disturbances in the acid-base balance
through suction of H2CO3 or through oxygen
of the body.
tanks
ACIDOSIS
Acidosis can be compensated through:
 condition in which the acidity of body fluids &
 Increase production of ammonia in the kidney
tissues is abnormally high
 Increase excretion of acids by the kidneys.
 due to a decrease in normal blood pH
 Increase excretion of H2CO3 through the lungs
 major physiological effect in general:
ALKALOSIS
depression of the CNS through depression of
 condition in which the alkalinity of body fluids
synaptic transmission
and tissues is abnormally high.
 Gaseous acidosis - more than the normal
 This arises because of a failure of the
amount of CO2 is retained in the body. E.g.
mechanisms that usually maintain a balance
drowning
between alkalis and acids in the arterial blood.
 Renal acidosis - kidney failure results in
 associated with loss of acid through vomiting or
excessive loss of bicarbonate or retention of
excessive sodium bicarbonate intake
phosphoric and sulfuric acids
 due to an increase in blood pH
 Patients with diabetes mellitus have a form of
acidosis in which sodium, potassium and ketone
bodies are lost in the urine
  major physiological effects: over excitability of
the CNS through facilitation of synaptic
transmission
TYPES OF ALKALOSIS
Metabolic Alkalosis
 is usually associated with excessive loss of
potassium and chloride
 due to an increase in blood HCO3
CAUSES:
 overdosage of alkaline drugs
 excessive loss of gastric HCI due to persistent
vomiting or severe vomiting (Cl^- loss) or the
use of diuretics except acetazolamides.
 diarrhea (K^+)
Respiratory Alkalosis
 produced by hyperventilation (salicylate
poisoning or artificial respirator) which lowers
the CO₂ level of the blood
 due to a decrease in blood H2COs due to
hyperventilation
 breathing that is abnormally deep in relation to
the amount of physical exercise may lead
alkalosis which may produce symptoms of
muscular weakness or cramps
Alkalosis can be compensated through:
 Decrease production of ammonia by the
kidneys.
 Decrease excretion of acids by the kidney
 Decrease excretion of H2CO3 through the lungs
In interpreting the ABG results, remember ROME -
Respiratory - Opposite / Metabolic - Equal
Collection of an arterial blood gas specimen
1. Obtain vital signs.
2. Determine whether the client has an arterial
line in place (allows for arterial blood sampling
without further puncture to the client).
3. Perform the Allen's test to determine the
presence of collateral circulation"
 The Allen's test is performed before obtaining
an arterial blood specimen from the radial
artery to determine the "presence of collateral
circulation and the adequacy of the ulnar
artery.
 Failure to determine the presence of adequate
collateral circulation could result in severe
ischemic injury to the hand if damage to the
radial artery occurs with arterial puncture.
 The nurse first would explain the procedure to
the client.
 To perform the test, the nurse applies direct
pressure over the client's ulnar and radial
arteries simultaneously.
 While applying pressure, the nurse asks the
client to open and close the hand repeatedly;
the hand should blanch.
 The nurse then releases pressure from the ulnar
artery while compressing the radial artery and
assesses the color of the extremity distal to the
pressure point.
 If pinkness fails to return within 6 to 7 seconds,
the ulnar artery is insufficient, indicating that
the radial artery should not be used for
obtaining a blood specimen.
 Finally, the nurse documents the findings. Other
sites can be used if the radial artery is not
deemed adequate, such as the brachial or
femoral artery.
Respiratory acid-base Imbalance
 Remember that the respiratory function
indicator is the Pco2.
 In a respiratory imbalance, you will find an
opposite relationship between the pH and the
Pco2; in other words, the pH will be elevated
with a decreased Pco2 (alkalosis) or the pH will
be decreased with an elevated Pco2 (acidosis).
 Look at the pH and the Pco2 to determine
whether the condition is a respiratory problem.
Respiratory acidosis: The pH is decreased; the Pco2 is
elevated.
Respiratory alkalosis: The pH is elevated; the Pco2 is
decreased.
Metabolic acid-base imbalance
 Remember, the metabolic function indicator is
the bicarbonate ion. In a metabolic imbalance,
there is a corresponding relationship between
the pH and the HCO3; in other words, the pH
will be elevated and the will be elevated
 (alkalosis), or the pH will be decreased and
there will be decreased (acidosis).
 Look at the pH and the to determine whether
the condition is a metabolic problem.
Metabolic acidosis: The pH is decreased; the HCO3 is
decreased.
Metabolic alkalosis: The pH is elevated; the HCO3 is
elevated.
 In a respiratory imbalance, the arterial blood
gas (ABG) result indicates an opposite
relationship between the pH and the Pco2. In a
metabolic imbalance, the ABG result indicates a
corresponding relationship between the pH and
the bicarbonate.
Compensation
 refers to the body processes that occur to
counterbalance the acid-base disturbance
(Zoom In to see clearly)
 pH - identifies the presence of acidemia or
alkatemia.
 Po2 - pressure exerted by oxygen dissolved in
the plasma.
 Pco2 - pressure of dissolved CO2, gas in the
blood.
 HCO – bicarbonate.
 O2 saturation - percentage of oxygen that
hemoglobin is carrying related to the total
amount the hemoglobin could carry.
 Base excess - primarily reflects the
concentration of bicarbonate and is affected
only by metabolic processes; positive values
reflect matabolic alkalosis and negative values
reflect metabolic acidosis.
Module 4: Cell: The Basic Unit of Life
CELL - the functional and structural units of life
Robert Hooke
 He used a microscope to examine cork (plant)
"Cytology: Study of cell
Robert Brown
 Discovered the nucleus in1883
Matthias Schleiden
 All plants are composed of cells
Theodor Schwann
 Discovered that animals are made up of cells
Rudolf Virchow
 He observed under a microscope that cells are
dividing. He concluded That cells come only
from other cells preexisting cells. His theory
now debunked the spontaneous generation
theory
Prokaryotic Cell VS. Eukaryotic Cell
PROKARYOTES
 Greek "prenucleus"
 DNA not enclosed within a membrane
 DNA is usually a singular circularly chromosome
 DNA not associated with histones
 Lack membrane bound organelles
 Cell walls contain polysaccharide peptidoglycan
 Divide by binary fission
EUKARYOTES
 DNA is found in a nucleus and enclosed in
nuclear membrane
 DNA found in multiple chromosomes
 Histones with DNA
 Membrane bound organelles
 Cell walls chemically simple
 Mitosis
Differences of Prokaryotic and Eukaryotic:
Prokaryotic
 Nucleoid
 Circular DNA that floats freely around cell
 Simpler DNA
  No membrane bound organelles
 Typically much smaller  Chromosomes - linear strands of chromatin
 Divide by binary fission material that contains the genes
 Typically unicellular  Genes carriers of hereditary traits
 Anaerobic and aerobic  Traits physical or non-physical characteristics
Eukaryotic handed down from parent to offspring from
 Nucleus generation to generation
 Linear DNA that is held in the nucleus  Dominant trait - is when trait is manifested or is
 Complex DNA present in every generation
 Membrane bound organelles  Recessive trait - when trait may skip a
 Typically much larger generation and only to reappear in future
 Divide by mitosis and meiosis generation
 Typically multicellular PARTS OF THE CELL:
 Aerobic  Nucleus
Similarities of Prokaryotic and Eukaryotic:  Cytoplasm
 Chromosomes NUCLEUS
 DNA as genetic material  ovoid, oval or circular
 Ribosomes  "master control of the cell"
 Cytoplasm  it is centrally located, one nucleus is present for
 Plasma Membrane every cell
 Sometimes have cell walls  it regulates, controls and modifies all the
 Vacuoles metabolic activities of the cell-shoul
Plant Cell VS Animal Cell CYTOPLASM
PLANT CELL  All of the parts of the protoplasm excluding
 Plant cells are larger than animal cells. nucleus. It includes:
 The plasma membrane of a plant cell is  Cytoplasmic organelles - living structure found
surrounded by a rigid cell of cellulose. within the cytoplasm which are directly
 Plastids are present. involved in the metabolic activities of the cell
 Most mature plant cells have a large central sap  Inclusion bodies-inert, non-living structures
vacuole. ORGANELLES:
 Plant cells have many simpler units of and Cell membrane
prominent Golgi apparatus. Functions:
 Plant cells lack centrosomes and centrioles.  Protection
ANIMAL CELL  Limits the territorial boundaries of the cell
 Animal cells are generally small in size.  Gives the cell a definite shape and size
 Cell wall is absent.  Serves as a semi-permeable membrane which
 Except the protozoan Euglena no animal cell selectively allows diffusion of substances in and
possesses plastids. out of the cell
 Vacuoles in animal cells are many and small. Mitochondria
 Animal cells have a single highly complex Golgi.  "powerhouse of the cell"
 Animal cells have centrosome and centrioles.  Generates ATP from substances coming from
2 TYPES OF CELLS: CHO, CHON and fats
Autosomes or Somatic cells - body cells Endoplasmic reticulum
Eg. Liver cells, brain cells  A network of tubes, tubules, microtubules
Germ cells or Sex cells which act as circulatory and excretory systems
Eg. Sperm cells, egg cells of the cell
  It is where substances pass through  Storage form of carbohydrate is glycogen which
a. Smooth or agranular - transport cell products undergo glycogenolysis to give glucose from
other than proteins which ATP is subsequently produced
b. Rough or granular - transport proteins coming FATS
from ribosomes.  Second source of energy
Golgi apparatus  Stored in the form of triglycerides in adipose
 Act as temporary storage "depot" of cellular tissues
products  Provides elasticity to the cell
Ribosomes. PROTEINS (CHON)
 Masses made up of RNA  Give strength to cell membrane; NOT stored in
 Attached to the ER the same manner as CHOand fats; provides
 Template of protein synthesis. tensile strength and elasticity to the cell
 It is where amino acids are joined by bonds to ELECTROLYTES
form a protein  Charged particles, either cation (+) or anion (-)
Lysosomes  Main intracellular (+) is K+
 Contain very potent or hydrolytic enzymes  Main extracellular (+) is Na+
which are responsible for digesting food in the  Main intracellular (-) is PO4^-3
cell  Main extracellular (-) is Cl-
Vacuoles
 Space occupied by water or fluid CELL ORGANELLES - subunits of the cell
Functions: CELL ORGANELLE
 Temporary dumping site for cellular garbage or Nucleus
debris  Nucleic acids, proteins, lipids
 Storage of food - CHO, fats  Manufacture of nucleic acids
Centrosome Nucleoli
 Small, rounded chromatin bodies attached to  RNA, proteins
the nuclear membrane  Manufacture of RNA and proteins
 Regulates reproduction or division of cells Ribosomes
COMPONENTS OF THE CYTOPLASM:  RNA, proteins
WATER  Manufacture of proteins
 Most abundant compound of cytoplasm Lysosome
 Fluid medium to which all chemical reactions of  Proteins Eg. enzyme
the cell take place  Defense
 Aqueous solution or medium of excretion of Membranes
waste matter  Lipids, proteins, carbohydrates
 Water content the cytoplasm determines the  Regulatory
size and shape of the cell Golgi apparatus
 Isotonic solutions -0.9% NaCl, no effect on the  Proteins, carbohydrates, lipids
cell  Packing, transport, CHO synthesis
 Hypotonic solutions <0.9% NaCl, swell of cells Mitochondria
(hemolysis)  Proteins, carbohydrates, lipids, nucleic acids,
 Hypertonic solutions >0.9% NaCl, shrinkage of coenzyme
cells (crenation)  Oxidation reaction, electron transport
CARBOHYDRATES (CHO)
 Main source of fuel or energy for the metabolic
activities of the cell
Module 5: Amino Acids
AMINO ACIDS
 Building blocks/stones of proteins
 Fundamental sub-units of proteins
Carboxyl group - acidic properties
Amino group - basic properties
Chiral C - asymmetric carbon
PROPERTIES:
Physical:
 White crystalline substances
 Soluble in cold water, except cysteine and
tyrosine which are more soluble in hot water
 Insoluble in alcohol and ether except proline
and hydroxyproline
 All amino acids except proline are precipitated
off from their solutions by alcohol, but not by
(NH4)2SO4 or NaCl
 Most of them are sweet like glycine, alanine,
serine and proline, others like leucine are
tasteless; while some are bitter like arginine
CHEMICAL:
1. Amino acids are amphoteric due to the
presence of both carboxyl and amino groups as
mentioned above. As such they form crystalline
salts with metallic bases and with mineral acids
2. Form esters with alcohol - by fractional
distillation
3. Amino acids can be acetylated, benzylated or
methylated in the presence of acetic acid,
benzoic acid or methyl group, respectively.
 These reactions occur in the body during
detoxication processes
4. All amino acids except proline and
hydroxyproline react with nitrous acid with the
liberation of nitrogen gas.
 This is the principle involved in Van Slyke
method for determining amino groups in
proteins, blood and other biological
substances
5. FORMALDEHYDE REACTION: When an excess of
neutral formaldehyde is added to neutral amino
acid solution, a distinctly acid mixture is
produced
 The hydrogens of the amine group are
replaced by a methylene group thus
destroying the basic property and allowing
the carboxyl to assert itself freely
 Subsequent titration with standard alkali
measures the amount of the free carboxyl
groups.
 Basis of Sorensen test
6. Amino acids form acyl halides
 The amino group is previously protected by
acetylation.
 The protecting (-CO-CHs) group may
subsequently be removed by using HCI
7. By heating with barium hydroxide, primary
amines are formed due to the breaking off the
carboxyl group with formation of CO2
8. When amino acids are dehydrated, they unite
with each other forming a ring,
diketopiperazine
 On boiling with HCI, diketopiperazine yields
dipeptide
 Fischer utilized this process in synthesizing
polypeptides from amino acids
CHARACTERISTICS:
1. Optically active
 All amino acids are optically active except
glycine ( its side chain is a hydrogen atom)
 Due to the presence of chiral/asymmetric
carbon
 Ability to rotate the plane p,arized light in a
polarimeter
a. dextrorotatory (+) - plane polarized light shifted
to the right
b. levorotatory (+) - plane polarized light shifted to
the left
2. Amphoteric / ampholyte
 Can act as an acid (proton donor) & as a base
(proton acceptor)
 COOH-proton donor (acid)
 NH2-proton acceptor (base)
3. Zwitterion / dipolar ion
 Possesses both a positive or negative ion
 Acidity is due to TT electron delocalization. The
OH bond in COOH weakens so it is readily/easily
given off or lost as a proton and is accepted by
the lone pair in NH
4. Isoelectric Point (pl)
 The pH value at which zwitterion state exists at E. AROMATIC AMINO ACIDS (NON-POLAR)
a maximum  Phenylalanine (phe)
 Amino acids & proteins assume a zero net  Tyrosine (tyr)
charge  Tryptophan (trp)
 Amino acids & proteins are least soluble
 No integration in an electric field F. SULFUR-CONTAINING AMINO ACIDS
Above pl: favors anionic state  Methionine (meth)
Below pl: favors cationic state  Cysteine (Cys or cys1)
Eg. Isoelectric Point (pl):  Cystine (Cys or Cys2)
 Asp - 2.8
 Glu - 3.2 G. HYDROXY-CONTAINING AMINO ACIDS
 Ser - 5.7  Serine
 Val - 6  Threonine
 ala - 6.1
 lys - 9.7 H. IMINO ACIDS - not an amino acid because of the
 arg - 10.8 absence of NH2 but only NH
IMPORTANCE OF pl:  Proline (pro)
 Used in buffer systems  Hydroxyproline (hpr)
 For separation & identification purposes - since
each amino acid has its distinct pl I. ALIPHATIC R-GROUP (NON-POLAR)
 Show structural changes in globular CHON- the  Glycine
explanation of structures of biological reactions  Alanine
5. ACID-BASE PROPERTY  Proline
 ACIDIC  Valine
 BASIC  Leucine
CLASSIFICATION OF AMINO ACIDS:  Isoleucine
ACCORDING TO R-GROUP  Methionine
A. NEUTRAL OR STRAIGHT CHAIN AMINO ACIDS:
(POLAR) A. ESSENTIAL / INDISPENSABLE AMINO ACIDS
 Glycine (gly)  Those which cannot be synthesized in the body
 Alanine (ala)  Must be provided in the diet
 Primarily concerned with growth and
B. BRANCHED CHAIN AMINO ACIDS: maintenance of life
 Valine (val) These are:
 Leucine (leu)  Phenylalanine
 lsoleucine (ile)  Valine
 Threonine
C. ACIDIC AMINO ACIDS: (POLAR)  Tryptophan
 Aspartic acid (asp)  Histidine
 Glutamic acid (glu)  Isoleucine
 Methionine
D. BASIC AMINO ACIDS (POLAR)  Arginine
 Lysine (lys)  Leucine
 Histidine (his)  Lysine
 Arginine (arg)
B. NON-ESSENTIAL/DISPENSABLE AMINO ACIDS  During metabolism, part of the carbon skeleton
 Those which can be produced in the body of these amino acids will enter the ketogenic
These are: pathway and the other part to glucogenic
 Glycine pathway
 Norleucine These are:
 Glutamic acid  Isoleucine
 Citruline  Phenylalanine
 Alanine  Threonine
 Tyrosine  Tyrosine
 Hydroxyglutamic acid  Tryptophan
 Proline
 Serine C. Purely glucogenic
 Cysteine  are purely glucogenic as they enter only into the
 Aspartic acid glucogenic pathway which provides a substrate
 Hydroxyroline for gluconeogenesis.
These are:
C. CONDITIONALLY ESSENTIAL AMINO ACIDS  All the remaining 14 amino acids
 When a person is suffering from a moderate to
severe chronic illness, person may lose the OTHER USES:
ability to manufacture enough non-essential  Arginine - essential in spermatogenesis
amino acids and thus require supplementation.  Glutamic acid - has been widely studied for its
 Problems with digestion will also necessitate effect in raising the general intelligence level of
supplementation of "non-essential" amino subnormal patients
acids.  Used for the treatment of psychomotor and
 These amino acids are normally non-essential, petit mal attacks
but become essential during times of  Glycine: Simplest amino acid and has is sweet in
physiological stress. Then these amino acids taste.
have to be taken in food or through  Inhibitory amino acid neurotransmitters (IAA):
supplements GABA, glycine, B-alanine, Taurine
These are:  Excitatory amino acid neurotransmitters: L-
 Arginine glutamate, L-Aspartate, L-cysteine, and L-
 Glycine Homocysteine
 Cysteine
 Tyrosine
 Proline
 Glutamine
 Taurine

A. Purely Ketogenic
 because it is converted to ketone bodies
These are:
 Leucine
 Lysine

B. Ketogenic and Glucogenic

 are partially ketogenic and partially glucogenic.
Module 6: Proteins C. GLUTELINS
PROTEINS  Soluble in dilute acids and alkalies but insoluble
 Came from the Greek word "PROTEIOS" in neutral solvents
meaning "pre-eminence" or of first importance Examples:
 Most important macromolecule  c.1. glutenin - wheat
 Organic compounds of high molecular weight  c.2. oryzenin - rice
(macromolecular) made up of many amino
acids joined together by means of peptide D. PROLAMINES
linkages.  Insoluble in ordinary solvent but soluble in 70%
 Peptide bond is a covalent bond and can be alcohol at about neutral point
dipeptide, tripeptide, tetrapeptide, and  Not coagulable by heat
oligopeptide. T Present in plants such as:
 Made up of C, H, O, N; usually S and traces of d.1. gliadin-wheat
Fe, Cu, I, Mn, Zn etc. d.2. zein corn
 Litmus paper: red - blue d.3. hordein- barley
CLASSIFICATION OF PROTEINS:
According to hydrolysis products: E. HISTONES
SIMPLE PROTEINS  Soluble in water, dilute acids and alkalies but
 These are true proteins found abundantly in not in dilute ammonia
both plants and animals plucort  Not readily coagulated by heat
 On hydrolysis with enzymes they yield a-amino  Strongly basic and occur in the tissues in the
acids and their derivatives form of salt combinations with acid substances
EXAMPLES: like the heme of the hemoglobin
A. ALBUMINS Examples;
 Soluble in water and dilute neutral salt solutions e.1. globin-hemoglobin
 They are conjugated by heat and precipitated e.2. thymus histone
by full saturation with (NH4)2SO4 but not with e.3. scobrone-mackerel
NaCl except in the presence of acid
Members of this group are: F. PROTAMINES
a.1. serum albumin-blood  Contain small number of amino acids
a.2. lactalbumin-milk  Soluble in water and dilute acids and alkalies
a.3. ovalbumin- egg white  Not coagulated by heat
 Strongly basic and form soluble salts with
B. GLOBULINS strong mineral acids
 Soluble in neutral dilute salt solutions but not in Example:
water  1.1. salmin-salmon sperm
 Coagulated by heat and can be precipitated
from their solutions by half saturation with G. SCLEROPROTEINS (Albuminoids)
(NH4)2SO4 and complete saturation with NaCI  Soluble in water and neutral solvents
Members of this group are: Example
b.1. ovoglobulin- egg white g.1. keratin - epidermal tissues
b.2. edestin-hempseed 9.2. elastin - ligaments
b.3. legumin peas 9.3. collagen - hides, bones and cartilages
b.4. myosinogen-muscles CONJUGATED PROTEINS
b.5. serum globulin – blood  Made up of protein molecules combined with
non-protein groups
EXAMPLES:
A. NUCLEOPROTEINS TWO DIVISIONS OF DERIVED PROTEINS:
 Combination of histones and protamines with PRIMARY PROTEIN DERIVATIVES
nucleic acids  Have undergone slight intramolecular
 Soluble in dilute solutions of NaCl and can be rearrangement through the hydrolytic action of
extracted from the tissues by the use of this certain physical and chemical agents
solvent  Synonymous with denatured proteins
 Precipitated by acidification EXAMPLES:
Typical of this group are: A. PROTEANS
a.1. chromatins- obtained from grandular  Are insoluble substances resulting from the
tissues and germ of grains preliminary action of water, dilute acids or
enzymes
B. GLYCOPROTEINS Examples:
 Compounds of proteins with a carbohydrate a.1. myosann- myosin
component a.2. edestan-edestin
 Utilized for lubricating purposes in view if their
slimy nature B. METAPROTEANS
 Not digested by the enzymes of the GIT  Are products of further hydrolysis
 Help in protecting the membranes of the tract  Soluble in weak acids and alkalies but insoluble
against digestion in neutral salt solution
Examples: Examples:
b.1. mucin-saliva b.1. acid metaproteans- acid albuminate
b.2. tendomucoid-tendons b.2. alkali metaproteans - alkali albuminate
b.3. osseomucoid-bones
C. COAGULATED PROTEINS
C. PHOSPHOPROTEINS  Insoluble products resulting from either the
 Have the prosthetic group (H3PO4) joined to action of heat, alcohol, ultraviolet rays or even
the protein molecule simple mechanical shaking
Examples:  Examples: cooked egg albumin, cooked meat
c.1. casein-milk
c.2. vitelin - egg yolk SECONDARY PROTEIN DERIVATIVES
 Products of more extensive hydrolysis
D. CHROMOPROTEINS  Mixtures of fragments of original protein
 Protein compounds with hematin or similar varying in composition and size
pigments in their molecules  Soluble in water and non-coagulability by heat
Examples are: hemoglobin, cytochromes and EXAMPLES:
rhodopsin A. PRIMARY PROTEOSES
 Soluble in water
E. LIPOPROTEINS  Precipitated by conc. HNO, and by half
 Have fatty substances combined with their saturation with (NH4)2SO4 of ZnSO4
molecules like lecithin, cephalin etc.  Not coagulated by heat
 Present in the blood serum, brain tissues, cell
nuclei, egg yolk and milk B. SECONDARY PROTEOSES
DERIVED  Precipitated only by complete saturation with
 Include substances formed from simple and ammonium sulfate but not with nitric acid or
conjugated proteins picric acid
  for mechanical strength of bones
C. PEPTONES KERATIN
 Soluble in water  hair
 Not coagulated by heat and not precipitated by
saturation with ammonium sulfate but by 5. PROTECTION PROTEINS
certain alkaloidal reagents such as  "natural defense proteins
phosphotungstic and tannic acids EXAMPLE:
 Antibodies
D. PEPTIDES
 Are combinations of two or more amino acids, 6. CATALYTIC PROTEINS
the carboxyl group of one being united with the  used to catalyze blochemical reactions
amino group of the other EXAMPLE:
 Examples are: di, tri, tetra, penta and poly  Enzymes
peptides
7. CHEMICAL MESSENGERS
II. ACCORDING TO BIOLOGICAL SIGNIFICANCE  hormonal action
1. TRANSPORT PROTEINS EXAMPLE:
 carry/circulate small molecules and ions  Hormone - internally secreted compounds that
EXAMPLES: affect the functions of organs and tissues when
A. HEMOGLOBIN transported by the body fluids
 carries 02 from lungs to other tissues.  Almost all of the compounds in the body are
B. SERUM ALBUMIN protein in nature
 distribute fatty acids between fat tissues and
other organs ACCORDING TO CONFORMATION/SHAPE:

2. STORAGE PROTEINS A. FIBROUS

 store small molecules and ions  Polypeptide chains are arranged tightly parallel
EXAMPLES: fibers and sheets
A. OVALBUMIN  Forms the structural framework of the body
 used to store amino acids used as nutrients by  Insoluble in H2O
chicken embryos found in eggs EXAMPLES:
B. FERRETIN a. Collagen-most important protein in human
 "liver protein" connective tissue
 Store Fe in humans and other animals.  Insoluble in H20 but maybe boiled to form a
 Source: liver digestive, coagulate protein called "GELATIN"
b. Elastin-similar to collagen but cannot be converted
3. CONTRACTILE PROTEIN to gelatin
 conduction of nerve impulses  Formed in arteries, ligaments, tendons and
 Muscular motion and coordination of motion dermis of skin
EXAMPLE: c. Keratin insoluble, indigestible, fibrous protein
A. myosin + muscle protein for contraction  Major component of hair, nails and feathers

4. STRUCTURAL PROTEIN B. GLOBULAR

 provide mechanical support and structure  Polypeptides are arranged in compact spherical
EXAMPLES: forms
COLLAGEN  Soluble in water
EXAMPLES:  Valine - valyl
 Antibodies, Enzymes  Histidine - histidyl
 Cysteine - cysteyl
C. MIXED  Leucine - leucyl
 Resembles fibrous protein in terms of strength  Arginine - arginyl
 Cystine - cystyl
 Isoleucine - isoleucyl
Module 7: Peptides, Protein Structures and  Serine - seryl
Denaturation  Phenylalanine - phenylalanyl
 Aspartic acid - aspartyl
PEPTIDE BONDS
 Tyrosine - Tyrosyl
 Are chains of amino acid.
 Threonine - threonyl
 Two amino acid molecules can be covalently
joined through a substituted amide linkage,
CHARACTERISTICS OF PEPTIDE BOND
termed a peptide bond to yield a dipeptide.
 The peptide bond is a partial double bond.
Such a linkage is formed by removal of the
 The C-N bond is 'trans' in nature and there is no
elements of water (dehydration) from the alpha
freedom of rotation because of the partial
carboxyl group of one amino acid and the
double bond character.
alpha-amino group of another
 The distance is 1.32A which is midway between
 Peptide bond formation is an example of a
single bond (1.49A) and double bond (1.27A).
condensation reaction, a common of reactions
 The side chains are free to rotate on either side
in living cells.
of the peptide bond.
 Three amino acids can be joined by two peptide
 The angles of rotation, known as Ramachandran
bonds to form a tripeptide; similarly, four amino
angles, therefore determine the spatial
acids can be linked to form a tetrapeptide, five
orientation of the peptide chain. (Dr GN
to form a pentapeptide, and so forth.
Ramachandran did pioneering work on the
 When a few amino acids are joined in this
structural aspects of proteins during 1950s and
fashion, the structure is called an oligopeptide.
1960s).
When many amino acids are joined, the product
is called a polypeptide.
PROPERTIES OF PROTEINS:
 Although the terms "protein" and "polypeptide"
I. PHYSICAL
are sometimes used interchangeably, molecules
 Generally, CHON are colorless, odorless and
referred to as polypeptides generally have
tasteless except protein hydrolyzates
molecular weights below 10,000, and those
 Varied solubility in solvents such as acids, bases
called proteins have higher molecular weights.
and salt solutions
 Form colloidal dispersion, thus do not pass
NAMING A PEPTIDE:
through membranes
 Change the ending of the 1st succeeding amino
 Molecular weights of some of the proteins are:
acids into -yl but retain the name of the last
Insulin (5,700); Hemoglobin (68,000); Albumin
amino acid
(69,000); Immunoglobulins (1,50,000);
These are:
 Those of low molecular weight are soluble in
 Glycine - glycyl
H₂O
 Glutamic acid - glutamyl
 Those of high MW are macromolecular are
 Tryptophan - tryptophyl
totally insoluble in water
 Alanine - alanyl
 Shape of the proteins also vary. Thus, Insulin is
 Lysine - lysyl
globular, Albumin is oval in shape, while
 Methionine - methionine
 Fibrinogen molecule is elongated. Bigger and
elongated molecules will increase the viscosity
of the solution.
I. CHEMICAL PROPERTIES
 Observed when there are changes in chemical
composition
A. Amphoteric / ampholyte
 Possess both a positive and negative ion
 Due to the presence of -COOH (proton donor)
 Due to the presence of -NH2 (proton acceptor)
 Are generally good buffers
B . Proteins are precipitated by:
a. Organic acids
Eg. Trichloroaceticacid, Phosphomolybdic acid,
b. Inorganic acids
c. Salts of heavy metals
Eg. CuSO4, Pb(Ac)2, HgCl2,
Salts of Copper, Zinc, Lead, Cadmium and
Mercury are toxic, because they tend to
precipitate normal proteins of the
gastrointestinal wall. Based on this principle,
raw egg is sometimes used as an antidote for
mercury poisoning.
d. Alkaloidal reagents
reagents of plant origin
Eg. Tannic acid, Picric acid, Sulfosalicylic acid,
Tungstic acid, Phosphotungstic acid,
e. High concentration of a neutral salt solution or
"salting out"
Process which leads to the destruction of the
destruction of the 4 levels of organization of
CHON
As a general rule, higher the molecular weight
of a protein, the salt required for precipitation
is lesser.
f. Alcohol (powerful protein precipitating agent)
LEVELS OF ORGANIZATION OF CHON:
1. PRIMARY STRUCTURE (1°)
 Linear arrangement of amino acid in a
polypeptide chain joined together by means of
peptide linkages nap
 Denotes the number and sequence of amino
acids in the protein.
 The higher level of organizations are decided by
the primary structure.
 Insulin is an example of protein with primary
level of organization. It has two polypeptide
chain. The Chain A (Glycine Chain) has 21 amino
acids, and Chain B (Phenylalanine) chain has 30
amino acids.
2 CHARACTERISTICS OF A PEPTIDE LINKAGE:
1. A strong bond - due to the electron
delocalization towards the carbonyl group
2. Exhibit geometric isomerism
 Cis isomer - both above or both below; both left
or both right
 Trans isomer - 1 above and 1 below; 1 left and 1
right
 Due to the restricted rotation in the double
bond, groups attached to C and N may be
projected side
1. SECONDARY STRUCTURE (2°)
 Involves folding of polypeptide chains due to it -
boding of peptide bonds
 refers to particularly stable arrangements of
amino acid residues giving rise to recurring
structural patterns.
 the steric relationship of amino acids, close to
each other.
2 TYPES OF SECONDARY STRUCTURE:
A. ALPHA HELIX
 formed due to intramolecular H bonding
 the helix is held by hydrogen bonds between
the oxygen atom in a carbonyl group of one
amino acid and the hydrogen atom of the
amino group that is just four amino acid units
farther along the chain.
 Proline and glycine disrupt the regularity of the
alpha helical backbone conformation.
 It is the most common and stable conformation
for a polypeptide chain.
 It is a spiral structure.
 It is generally right-handed. Left handed alpha
helix is rare, because amino acids found in
proteins are of L-variety, which exclude left
handedness. Proline and hydroxyproline will not
allow the formation of alpha helix.
INTRAMOLECULAR
 within the molecules / peptides
B. BETA- PLEATED SHEAT
 due to intermolecular H bonding
 the pleats are formed by similar hydrogen
bonds between continuous sequences of
carbonyl and amino groups that are further
separated on the backbone of the polypeptide
chain
 Represented by dotted lines
INTERMOLECULAR
 between different peptide
H-BOND
 a weak bond due to the weak attraction
between a a+H and lone pairs of an atom
2 FORMS OF H-BOND:
INTRAMOLECULAR H-BOND
 within the molecule
INTERMOLECULAR H-BOND
 different compounds are involved either similar
or non-identical
2. TERTIARY STRUCTURE
 Furthermore unfolding of polypeptide chains
due to formation of bonds like H-bond, peptide
bond, covalent bond, disulfide bond, ionic bond,
and hydrophobic interactions.
 denotes the overall arrangement and inter-
relationship of the various regions, or domains
of a single polypeptide chain.
 denotes three dimensional structure of the
whole protein.
 defines the steric relationship of amino acids
which are far apart from each other in the
linear sequence, but are close in the three-
dimensional aspect.
 The process by which a polypeptide chain
assumes a large-scale, three-dimensional shape
is called protein folding.
 Domain is the term used to denote a compact
globular functional unit of a protein
 The arrangements of the tertiary structure
elements in a protein form a "fold". A typical
example is calmodulin, the calcium binding
regulatory protein which regulates intracellular
calcium level.
3. QUATERNARY STRUCTURE
 Most complex aspect of protein strand
 Involves polypeptide chains tightly woven with
each other
 results when the proteins consist of two or
more polypeptide chains held together by
noncovalent forces
 It is stabilized by relatively weak interactions.
 Hemoglobin is an example of protein with
quaternary structure.
DENATURATION OF PROTEINS
 Destruction of the secondary, tertiary and
quaternary structures of CHON leading to
changes in its physical, chemical and biological
characteristics
 Involves transformation of a well-defined folded
structure of a protein formed under
physiological conditions, to an unfolded state
under non-physiological condition.
2 TYPES OF DENATURATING AGENTS:
1. PHYSICAL
 Includes heat, UV rays, high pressure
 Many human proteins denature at temperature
above about 45°C, which is one reason that
humans cannot withstand high fever or
exposure to high temperature for a long time.
 Heat can be used to disrupt hydrogen bonds
and non-polar hydrophobic interactions. This
occurs because heat increases the kinetic
energy and causes the molecules to vibrate so
rapidly and violently that the bonds are
disrupted.
 Medical supplies and Instruments are sterilized
by heating to denature proteins in bacteria and
thus destroy the bacteria.
2. CHEMICAL
 Acids, bases, organic solvents, heavy metals,
detergents
 Changes:
a. Physical- increased viscosity
 b. Chemical-decreased solubility
c. Biological- increased digestibility by enzymes A. Hydrolysis
(loss of hormonal and antigenic action)  By acids, bases and protein - splitting enzyme
(proteinase/protease)
 Strong acids and bases change the pH of the  Opposite of peptide formation
solution containing proteins and therefore
change the ionization of acidic and basic side Example:
chains, leading to disruption of ionic bonds.  Protein
 Heavy metals, because they are charged, also  Proteoses
bind to charged side chains, disrupting salt  Peptones
bridges (ionic bonds).  Polypeptides
 A 70% alcohol solution is used as a disinfectant  Dipeptides
on the skin. This concentration of alcohol is able  Amino acids
to penetrate the bacterial cell wall and
denature the proteins and enzymes inside of Advantages of Protein Denaturation
the cell.  The study of denaturation of protein helps in
 Alcohol denatures proteins by disrupting the the field of proteomics.
side chain intramolecular hydrogen bonding.  To determine the concentration of protein in
 Heavy metal salts act to denature proteins in any given food samples.
much the same manner as acids and bases. Denatured proteins are easily digested in the stomach
 Heavy metal salts usually contain Hg2, Pb2, Ag" as compared to undenatured proteins.
TI, Cd2 and other metals with high atomic
weights.
 This reaction is used for its disinfectant
properties in external applications. For
example, AgNO3 is used to prevent gonorrhea
infections in the eyes of new born infants.
 Silver nitrate is also used in the treatment of
nose and throat infections, as well as to
cauterize wounds. This same reaction is used in
reverse in cases of acute heavy metal poisoning.
In such a situation, a person may have
swallowed a significant quantity of a heavy
metal salt.
 As an antidote, a protein such as milk or egg
whites may be administered to precipitate the
poisonous salt. Then an emetic is given to
induce vomiting so that the precipitated metal
protein is discharged from the body.
 Detergents are amphipatic in nature and
proteins have hydrophobic and hydrophilic
sides, the detergent is attracted to these and
forces the protein apart and denatures the
proteins.
 An alkylating agent cannot denature protein
such as iodoacetic acid.