BIOCHEMISTRY

Session 1 – 7 (A Comprehensive Review)

Sir. KJ Rabaya
 02
INTRODUCTION TO
BIOCHEMISTRY
 DEFINITION OF TERMS

01 CHEMISTRY
deals with the study of the
03 INORGANIC CHEMISTRY
chemistry of non-carbon compounds
composition and properties of (except for carbonates, bicarbonates,
matter cyanide, carbon dioxide)

02 ORGANIC CHEMISTRY 04 BIOCHEMISTRY

study of the structure, properties, the study of compounds, chemical
composition, reactions, and changes and reactions occurring in
preparation of carbon-containing
living systems
compounds
 Two Aspects of Biochemistry TAKE
NOTE OF
THIS
• MOLECULAR ANATOMY
• MOLECULAR PHYSIOLOGY
• dynamic part of biochemistry which includes the functions and metabolic activities of biomolecules in the cell.
a. Digestion
Physical – mechanical breakdown
Chemical – further breakdown with the aid of enzymes
b. Absorption – passage of end products of digestion from the small intestine into the blood
c. Assimilation – selective absorption
d. Utilization -cell is the important unit of life. Hence a large number of chemical reactions in the
cell utilize the nutrients absorbed to produce materials needed for our existence
e. Integration - refers to the overlap of many functions of the systems of the human body, as
well as its accompanied form.
f. Metabolic degradation – conversion of a substance into an active metabolite
g. Biotransformation – conversion of a substance to another for biosynthesis
h. Excretion
 02
pH and BUFFER
 DEFINITION OF TERMS
TAKE
NOTE OF
pH measure of the acidity or basicity of aqueous or other liquids solutions THIS

“potential of HYDROGEN ion”

Normal pH of extracellular fluids (e.g. blood plasma) is pH 7.35 to 7.45

Normal pH of gastric juices is pH 1-3.

Ka - Acid Dissociation Constant (Strong Acids)

Kb - Base dissociation constant (Strong Base)
Kw - ion-product constant of liquid water
pKa – [negative log of] Acid Dissociation Constant (Weak Acids)
pKb - [negative log of] Base dissociation constant (Weak Base)
 ACID BASES
TAKE
NOTE OF
• Low pH values correspond to • High pH values correspond to low THIS
high concentrations of H+ concentrations of H+

EXAMPLES EXAMPLES
• Strong acids • Strong bases
* Hydrochloric Acid (HCl) * Sodium Hydroxide (NaOH)
* Nitric Acid (HNO3) * Calcium Hydroxide (Ca(OH)2)
* Sulfuric Acid (H2SO4) * Potassium Hydroxide (KOH)

• Weak acids • Weak bases

* Ammonia (NH3)
* Acetic acid (CH3COOH)
* Aniline
WATER
TAKE
NOTE OF
THIS
AMPHOTERIC SUBSTANCES
are those that has potential to act either as an acid or a base

RATIONALE:

On dissociation, it ionizes into H+ and OH− (hydroxide) ion. The presence of

H+ indicates an acid and the presence of OH− ion indicates a base.

AMPHIPROTIC SUBSTANCES
are those that has to both accept and donate a proton (Hydrogen)
** PROTic = PROTon
 TAKE
NOTE OF
THIS

ONOR

EPTOR
 CONJUGATE ACID-BASE PAIR
TAKE
NOTE OF
THIS
REACTANT PRODUCT

CONJUGATE ACID
formed when a proton (Hydrogen) is added to a base
** nadagdagan ng H pag-dating sa Product side ng reaction

CONJUGATE BASE
formed when a proton (Hydrogen) is removed from an acid
** nabawasan ng H pag-dating sa Product side ng reaction, usually negatively charged
molecule/ atom
CONJUGATE ACID-BASE PAIR
TAKE
NOTE OF
THIS
** may Hydrogen sa chemical formula ** almost lahat ay negatively charged (anion)

CONJUGATE ACID CONJUGATE BASE

HCl (hydrochloric acid) Cl- (chloride anion)
H3O+ (hydronium) H2O (water)
HAc (acetic acid) Ac- (acetate)
HNO2 (nitrous acid) NO2- (nitrite)
H2O (water) OH- (hydroxide)
HCO3- (bicarbonate) CO3- (carbonbarte)
H2CO3 (carbonic acid) HCO3- (bicarbonate)
 Buffer / Buffer Solution

• a mixture of a weak electrolyte and salt.

• Its pH changes very little when a small amount of strong acid or base is
added to it.
• Can resists drastic/ extreme changes in pH.

EXAMPLE of BUFFERS:
• Hac and Ac- (Acetic acid + Acetate)
• NaH2PO4 and Na2HPO4 (Sodium dihydrogen Phosphate and Disodium
Hydrogen Phosphate)
• NH4OH and NH4NO3 (Ammonium Hydroxide and Ammonium Nitrate)
 Henderson-Hasselbalch Equation
• relates the pH of a solution containing a mixture of the two components to
the acid dissociation constant, Ka, and the concentrations of the species in
solution.
• simple buffer solution consists of a solution of an acid and a salt of
the conjugate base of the acid.
Other formulas:
pH = -log [H+]
pOH = -log [OH-]
pH + pOH = 14
[H3O+] = antilog - pH
[OH-] = antilog - pOH
pKa = -log [Ka]
pKb = -log [Kb]
pKb + pKa = 14
 03
ACIDOSIS and
ALKALOSIS
 ACIDOSIS
• Condition in which the acidity of bodily fluids and tissue is abnormally high
• Decrease in normal blood pH
• Major physiological effect in general: depression of CNS through synaptic
transmission

GASEOUS ACIDOSIS
- More than the normal amount of CO2 is retained in the body
- Example: Drowning

RENAL ACIDOSIS
- Kidney failure results in excessive loss of bicarbonate or retention of
phosphoric and sulfuric acid
 ACIDOSIS
Acidosis can be compensated through:

• Increase production of ammonia (NH3) in the kidney

• Increase excretion of acids by the kidneys
• Increase excretion of carbon dioxide (CO2) through the lungs
 TYPES OF ACIDOSIS

CAUSES: TREATMENT:
METABOLIC
ACIDOSIS - Severe ketosis such in
cases of Diabetic
- Administration of Sodium
Bicarbonate along with
Ketoacidosis (DKA) fluids and other
- Occurs when excessive - Eclampsia electrolytes.
loss/ decrease of bases - High Lipid Diet - Can be compensated
such as bicarbonates - Anuria through intravenous
(HCO3-) in the blood
 TYPES OF ACIDOSIS

RESPIRATORY CAUSES: TREATMENT:

ACIDOSIS - Depression to respiration - Can be compensated
- Hypoventilation - Obstruction to respiration through suction of
- Associated with an carbonic acid (H2CO3)
increase level of CO2 - Oxygen tanks
in the blood
- Occurs when lungs or
breathing disorder
affects the body’s
ability to breathe out
CO2, leading too much
acid in the body
 ALKALOSIS
• Condition in which the alkalinity of bodily fluids and tissues are abnormally
high
• Caused by losing too much acid from the body, or by having too much
bicarbonate in the blood
• Due to an increase in the blood pH
• Major physiological effects: over excitability of the CNS through facilitation
of synaptic transmission

Alkalosis can be compensated through:

• decrease production of ammonia (NH3) in the kidney

• decrease excretion of acids by the kidneys
• decrease excretion of carbon dioxide (CO2) through the lungs
 TYPES OF ALKALOSIS

METABOLIC CAUSES:
ALKALOSIS - Overdosage of alkaline
drugs
• Caused by losing too - Excessive loss of gastric
much acid from the HCl due to persistent
body, or by having too vomiting
much bicarbonate in - Severe vomiting (Cl- loss)
the blood - Use of diuretics except for
• Excessive loss of acetazolamide
potassium and - Diarrhea (K+ loss)
chloride
 TYPES OF ALKALOSIS

RESPIRATORY CAUSES:
ALKALOSIS - Decrease CO2 levels
- Decrease in blood
• Caused by carbonic acid due to
hyperventilation hyperventilation
(Salicylate poisoning or
artificial respirator)
which lowers the CO2
level in the blood.
LUNGS
- Regulates the CO2 levels via exhalation

KIDNEYS
- Responsible for maintaining normal pH balance increasing or decreasing
bicarbonate levels
NORMAL VALUES
NORMAL VALUES
04
THE CELL
Cell is the basic structural and functional
unit of living organisms.
 CELL THEORIES
ANTONIE VAN LEEUWENHOEK
- “Father of Microscopy”
- First to observed bacteria and protozoa – “animalcules – small animals”

ROBERT HOOKE
- Wrote and published “Micrographia”
- coined the word “cell.” Cell means little rooms in Latin

MATTHIAS SCHLEIDEN
- “All plants are composed of cells”

THEODOR SCHWAN
- Discovered that animals are made up of cells.

RUDOLF VIRCHOW
- He is known as the “Father of Pathology.”
- Discovered that all living cells come only from other living cells.
 PROKARYOTES EUKARYOTES
TAKE
Greek “prenucleus” DNA is found in a nucleus and NOTE OF
THIS
enclosed in nuclear membrane
DNA not enclosed within a membrane DNA found in multiple chromosomes

DNA is usually a singular circularly DNA is double helical in shape

chromosome
DNA not associated with histones DNA with histones

Lack of membrane bound organelles Membrane bound organelles

Cell walls contains polysaccharide Cell walls chemically simples

peptidoglycan
Divided by binary fission Mitosis

Both aerobic and anaerobic Mostly aerobic except for Trichomonads

 STRUCTURE OF CELL

01 PLASMA MEMBRANE
Made up of two layers of lipid
03 NUCLEUS
Present in all the cells except red
molecules in which protein blood cells and sieve tube cells
molecules are floating well developed in plant and animal cells,
undeveloped in bacteria

02 CELL WALL 04 CYTOPLASM

Non-living and outermost covering of Contains a clear liquid portion called
a cell (plants & bacteria) cytosol and various particles
Present in both eukaryotes and
prokaryotes
 components of CYTOPLASM
TAKE
NOTE OF
THIS

1. WATER
Most abundant compound of cytoplasm
2. CARBOHYDRATES (CHO)
Main source of fuel or energy for the metabolic activities of
the cell.
3. FATS
Second source of energy
Stored in the form of triglycerides in adipose tissues
Provides elasticity to the cell
4. PROTEINS (CHON)- Give strength to cell membrane;
provides tensile strength and elasticity to the cell.
5. ELECTROLYTES
 STRUCTURE OF CELL

05 ROUGH ENDOPLASMIC
RETICULUM
07 GOLGI BODIES
Acts as a temporary storage or depot of
Transport proteins coming from cellular products
ribosomes

06 SMOOTH ENDOPLASMIC
08 LYSOSOMES
RETICULUM Filled with hydrolytic enzymes that
helps in digesting of large molecules
synthesize lipids phospholipids as
in plasma membranes, and
steroids
 STRUCTURE OF CELL

09 VACUOLES
store various substances
10 CENTROSOME
Form spindle fibers which help in the
including waste products movement of chromosomes during cell
division

11 MITOCHONDRIA 12 PLASTIDS
Synthesize energy-rich compound ATP They are responsible for
“powerhouse of the cell” activities related to making and
storing food.
 STRUCTURE OF CELL

13 CHROMOPLASTS
They are responsible for
14 CHLOROPLASTS
Convert light energy into chemical
different colours found in leaves, energy in the form of food
fruits, flowers and vegetables.

15 LEUCOPLASTS 16 CYTOSKELETON
Leucoplasts are colourless plastids Formed by microtubules and
that store foods. microfilaments
Give structural strength to the cell
05
AMINO ACID
- building blocks of protein
 GENERAL STRUCTURE TAKE
NOTE OF
THIS
CHIRAL/ ASSYMETRICAL
ZWITTER ION / CARBON (except for Glycine)
DIPOLAR ION
- Possesses
both
positive and
negative
charge
- Net charge
is equals to
ZERO BASIC ACIDIC
PART PART
IDENTIFICATION TESTS FOR AMINO ACIDS
TAKE
NOTE OF
NINHYDRIN TEST THIS

- (+) Violet solution will indicate the presence of amino acid

XANTHOPROTEIC TEST (SUN-thoproteic, sun = yellow)

- (+) Yellow solution will detect aromatic amino acids (WaYF)

SORENSEN TEST
- The basis of this test is formaldehyde reaction
VAN SLYKE
- Method for determining amino group in proteins, blood, and
other biological substance.
CHEMICAL REACTIONS
** When an amino acid is dehydrated,
they unite with each other forming a
diketopiperazine ring

DIKETOPIPERAZINE RING + Hydrochloric Acid à DIPEPTIDE

** Diketopiperazine ring, on boiling with Hydrochloric acid yields DIPEPTIDE

** Fischer utilized diketopiperazine synthesizing polypeptides from amino acid
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

A. STRAIGHT CHAIN / NEUTRAL AMINO ACID

(MNEMONICS: Straight si Ariana Grande)

• Alanine Ala A
• Glycine Gly G
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

B. BRANCHED CHAIN AMINO ACID

(MNEMONICS: may iba’t ibang store BRANCH where you can VILe)

• Valine Val V
• Isoleucine Ile I
• Leucine Leu L
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

C. ACIDIC AMINO ACID

(MNEMONICS: aciDEc)

Aspart(d)ic Acid Glu(e)tamic Acid

Asp Glu
D E
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

D. BASIC AMINO ACID

(MNEMONICS: It’s ur baby Zebby, Zeinab HaRaKe)

• Histidine His H
• A(r)gnine Arg R
• Ly(k)sine Lys K
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

E. AROMATIC AMINO ACID

(MNEMONICS: Aromatic ring = wedding ring, wedding ring = wife

[WaYF])

• T(w)ryptophan Trp W
• T(y)rosin Tyr Y
• (f)Phenyalanine Phe F
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

F. SULFUR-CONTAINING AMINO ACID

(MNEMONICS: kilala mo ba si MC and Lassy? If yes si MC tandaan mo HAHA)

• Methionine Met M
• Cysteine Cys C
** Cys + Cys à CYSTINE
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

G. HYDROXY-CONTAINING AMINO ACID

(MNEMONICS: gOH-ST, gOH-ST, gOH, gOH, gOH, gOH-ST!!!)

• Serine Ser S
• Threonine Thr T

H
 CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

H. IMINO ACID (-C, -NH, -COOH)

(MNEMONICS: Imino PO)

I I •
•
Proline
Hydr(o)xyproline
Pro
Hyp
P
O
CLASSIFICATION OF AMINO ACID ACCDG TO R-GROUP

I. ALIPHATIC AMINO ACID

(MNEMONICS: LIVAG MP )

Leucine Leu L
Isoleucine Ile I
Valine Val V
Alanine Ala A
Glycine Gly G

[pasintabi Methionine Met M

po sa mga Proline Pro P
kumakain]
CLASSIFICATION OF AMINO ACID ACCDG TO IMPORTANCE

I. ESSENTIAL / INDESPENSABLE AMINO ACID

- Cannot be synthesized in the body
- Should be included in the diet
- Primarily concerned with growth and maintenance of life

MNEMONICS: Phenylalanine Phe F

For The Win Threonine Thr T
Let Me Know Tryptophan Trp W
V I R
Leucine Leu L
Methionine Met M
Lysine Let K

Valine Val V
Isoleucine Ile I
Arginine Arg R
CLASSIFICATION OF AMINO ACID ACCDG TO IMPORTANCE

I. NON-ESSENTIAL / DESPENSABLE AMINO ACID

- Can be synthesized in the body

- Amino acids such as: [MNEMONICS: DACS TeleGram)
- Aspartic Acid Asp D
- Alanine Ala A
- Cysteine Cys C
- Serine Ser S
- Threonine Thr T
- Glycine Gly G
- Other Amino acids (outside the 20 amino acids):
- Citruline
- Hydroxyglutamic Acid
- Hydroxyproline
- Norleucine
CLASSIFICATION OF AMINO ACID ACCDG TO IMPORTANCE

I. CONDITIONALLY ESSENTIAL / INDESPENSABLE AMINO ACID

MNEMONICS:
P Q R Proline Pro P
C G Y Glutamine Gln Q
[boom] Taurine Arginine Arg R
Cysteine Cys C
Glycine Gly G
Tyrosine Tyr Y

Boom! Taurine
OTHER USES: TAKE
NOTE OF
❖ Arginine – essential in spermatogenesis THIS

❖ Glutamic acid
• has been widely studied for its effect in raising the general
intelligence level of subnormal patients
• Used for the treatment of psychomotor and petit mal attacks
❖ Glycine: Simplest amino acid, has is sweet in taste and is the
only not optically active amino acid.
❖ Inhibitory amino acid neurotransmitters (IAA): GABA, glycine,
B-alanine, Taurine
❖ Excitatory amino acid neurotransmitters: L-glutamate, L-
Aspartate, L-cysteine, and L-Homocysteine
06
PROTEINS
CLASSIFICATION OF PROTEINS ACCDG TO HYDROLYSIS PRODUCTS

I. SIMPLE PROTEINS
- These are true proteins found abundantly in both plants and animals
- On hydrolysis with enyzmes they yiekd amino acids and derivatives

EXAMPLES:
A. ALBUMINS B. GLOBULINS
- ovoglobulin (egg)
- serum albumin (blood)
- lactalbumin (milk) - edestin (hempseed)
- ovalbumin (egg white) - Legumin (peas)
- Myosinogen (muscles)
- Serum globulin (blood)
CLASSIFICATION OF PROTEINS ACCDG TO HYDROLYSIS PRODUCTS

I. SIMPLE PROTEINS
EXAMPLES: E. HISTONES
- Globin (hemoglobin)
- Thymus histone
C. GLUTELINS - Scobrone (mackerel)
- Glutenin (wheat)
- Oryzenin (rice)
F. PROTAMINES
D. PROLAMINES - Salmin (Salmon sperm)
- Gliadin (wheat)
- Zein (corn) G. SCLEROPROTEINS
- Hordein (barley) - Keratin (epidermal tissues – hair, nails)
- Collagen (bones, cartilages, hides)
- Elastin (ligaments)
CLASSIFICATION OF PROTEINS ACCDG TO HYDROLYSIS PRODUCTS

II. CONJUGATED PROTEINS

- Made with protein molecule combined with non-protein molecule

EXAMPLES:
A. NUCLEOPROTEIN
- Combination of histones, protamines with nucleic acid
EXAMPLES:
• Chromatins

B. GLYCOPROTEIN
- Compounds of protein with carbohydrates
EXAMPLES:
• Mucin (saliva)
• Tendomucoid (tendons)
• Osseomucoid (bones)
CLASSIFICATION OF PROTEINS ACCDG TO HYDROLYSIS PRODUCTS

II. CONJUGATED PROTEINS

EXAMPLES:
C. PHOSPHOPROTEINS
- Have prosthetic group phosphoric acid (H3PO4)
EXAMPLES:
• Casein (Milk)
• Vitelin (eggyolk)

D. CHROMOPROTEINS
- Compounds of protein with hematin or similar pigments
EXAMPLES:
• Hemoglobin
• Cytochrome
• Rhodopsin
CLASSIFICATION OF PROTEINS ACCDG TO HYDROLYSIS PRODUCTS

II. CONJUGATED PROTEINS

EXAMPLES:

E. LIPOPROTEINS
- Have fatty substances like lechitin, cephalin, etc.
- Present in the blood serum, brain tissue, cell nuclei, egg yolk, milk.

III. DERIVED PROTEINS

- Include substances formed from simple and conjugated proteins
CLASSIFICATION OF PROTEINS ACCDG TO BIOLOGICAL SIGNIFICANCE

A. TRANSPORT PROTEINS
- Carries/ circulates small molecules and ions
EXAMPLES:
• Hemoglobin – carries oxygen
• Serum Albumin – distribute fatty acids between fat tissue and other
organs

B. STORAGE PROTEINS
- Store small molecules and ions
EXAMPLES:
• Ovalbumin – used to store amino acids used as nutrients by chicken
embryo
• Ferretin – “liver protein”, store Fe in human and other animals
CLASSIFICATION OF PROTEINS ACCDG TO BIOLOGICAL SIGNIFICANCE

C. CONTRACTILE PROTEIN
- Muscular motion and coordination of motion
EXAMPLES:
• Myosin + muscle protein for contraction

D. STRUCTURAL PROTEIN
- Provide mechanical support and structure
EXAMPLES:
• Collagen – for mechanical strength of bones
• Keratin – hair and nails

E. PROTECTION PROTEIN
- “Natural defense proteins”
EXAMPLES:
• Antibodies
CLASSIFICATION OF PROTEINS ACCDG TO BIOLOGICAL SIGNIFICANCE

F. CATALYTIC PROTEIN
- Used to catalyzed biochemical reactions
EXAMPLES:
• Enzymes

G. CHEMICAL MESSENGER
- Hormonal action
EXAMPLES:
• Hormones
CLASSIFICATION OF PROTEINS ACCDG TO CONFORMATION/ SHAPE

A. FIBROUS PROTEIN
- Arranged tightly parallel fibers and sheets
EXAMPLES:
• Collagen
- Most important protein in human connective tissue
• Elastin
- Similar to collagen but cannot be converted to gelatin
• Keratin
- Major component of hair, nails and feather

B. GLOBULAR
- Polypeptides are arranged in compact spherical forms
EXAMPLES:
• Antibodies
• Enyzmes
07
PROTEIN STRUCTURE
LEVEL OF ORGANIZATION OF PROTEINS

PRIMARY STRUCTURE
• Linear arrangement of amino acid in a polypeptide chain joined together
by means of peptide linkages
• Denotes the number and sequence of amino acids in the protein.
• EXAMPLE: Insulin
LEVEL OF ORGANIZATION OF PROTEINS

SECONDARY STRUCTURE
• 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

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. (helix breakers)
LEVEL OF ORGANIZATION OF PROTEINS

SECONDARY STRUCTURE
2 TYPES OF SECONDARY STRUCTURE

BETA-PLEATED SHEET
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

2 FORMS OF HYDROGEN BONS:

A. INTRAMOLECULAR H- BOND
– within the molecule
B. INTERMOLECULAR H-BOND
– different compounds are involved either similar or
non-identical
LEVEL OF ORGANIZATION OF PROTEINS

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.
• 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
LEVEL OF ORGANIZATION OF PROTEINS

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.
Good luck with your exam! Wishing all
the best in your academic and
professional life! Padayon, future nurses!

Sir Kyle, now signing off :)