Biochemistry Reviewer
➢ Protein Diseases
Study of chemical substances found in
living organisms and the chemical
interactions of these substances with
each other
❏ Compounds, chemical reactions, and
molecular interactions involved in
production maintenance and reproduction
of living organisms
❏ How cells manufacture the molecules
needed for life and how the chemical
reactions by which life is maintained occur
❏ All living things make use of same type of
biomolecules and use energy. Hence
studied through methods of chemistry and
physics
❏ Fundamental similarity of cells and
speculating on origin of life
❏ Cells and biomolecules arisen from very
simple molecules such as H2O, CH4 , NH3 ,
N2 and H2
❏ Field of biochemistry draws many
disciplines
❏ Answer questions on molecular nature of
life
Biochemistry is a Research Discipline
Applicable to Real World
Most diseases have a biochemical basis
• Diagnose and monitor diseases
➢ Transaminase levels
➢ Hemoglobin breakdown product - bilirubin
➢ Measure isoforms of Lactate dehydrogenase to
determine extent of myocardial infarctions
• Designer Drugs
➢ New and Improved Antibiotics
➢ New and Improved chemotherapy agents
Most diseases have a biochemical basis
➢ Health maintenance (nutrition) - intake of
vitamins , amino acids, fatty acids, various minerals
and water (BIOCHEMISTRY!!!)
➢ protein structure and function--- normal vs.
sickle cell hemoglobin
➢ Alkaptunoria, albinism, pentosuria --- inborn
errors of metabolism
➢ Molecular mechanisms of Oncogenes, and
tumor suppressing genes for normal cell growth
➢ How cholesterol contribute to heart disease and
why aspirin lower body temperature
Biochemistry is a Research Discipline Applicable to Real
World
Agriculture Industry
• Herbicides and Pesticides • Synthesis
• Transgenic crops • Detoxification
Attributes of Life - Quick Recap
1. Adaptation - body structures (physiology or
morphology) that make living things fit to live in its
habitat.
2. Growth and repair - ability to add new tissue and
repair or replace damaged parts.
3. Metabolism - biological and chemical activities that
provide energy. Catabolism vs Anabolism.
4. Reproduction - beget offsprings, ensuring
propagation and continuance of species.
5. Complexity and organization - complexity refers to
elaborate structures needed to carry out specific
function while organization is to put structures in order
to function efficiently
6. Regulation - keep functions under control (hormones,
enzymes).
7. Characteristic size and shape - unique morphology
i.e., ant can never become as big as elephant.
8. Response to stimuli- respond favorably or
unfavorably to its environment.
9. Locomotion - move on its initiative, under its control
10. Variation and change - no two organisms are alike
and no organism remains unchanged
molecules
● Understanding of bioenergetics - the study of
energy flow in cells
Chemical Foundations of Biochemistry
Organic Chemistry : study of compounds of carbon
● Cellular apparatus of living organisms made up of
carbon
● Biomolecules are part of organic chemistry
● Reactions of biomolecules can be described by
organic chemistry methods
● Functional Groups: atom/group of atoms that
show characteristic physical and chemical

Chemical Foundations of Biochemistry

Biochemistry seeks to describe the structure,
organization, and function of living organisms in
molecular terms
In order to understand the life on the molecular
level, you must first have a:
● Knowledge of the chemical structures of the
biological molecules

● Understanding of the biological function of the properties

 of DNA
- Extensive membrane system and intracellular
organelles

Chemical Foundations of Biochemistry

Biomolecules: cells include large molecules such as
proteins, nucleic acids, polysaccharides and lipids
● These biomolecules are polymers (Greek: poly +
meros, many + parts)
● Derived from monomers (Greek: mono + meros,
single + parts)

Function of Subcellular Organelles in Eukaryote

CELL TO WATER
Cell are the Basis of Living Organisms
Classification of Living Cells:
1. Prokaryotes - (Archaea & Eubacteria) lack of
defined nucleus or internal membrane structures
- Usually unicellular but some may form colonies
- Some live in extreme conditions
- Cytosol has granular appearance due to
ribosomes
2. Eukaryotes - include unicellular organisms
(yeast), fungi and multicellular plants and animals
- Cell volume 1000 to 10,000 times larger
- Defined nucleus with membrane that contain bulk
Cells
Organelles have very specific functions. Some
metabolic pathways are found in single cellular
component e.g. tricarboxylic acid cycle
(mitochondria), glycolysis (cytosol), and DNA
replication only in nucleus and mitochondria.
Plasma Membrane is Limiting Boundary of a Cell
● Outer surface in contact with variable external env’t;
inner surface with constant env’t due to cytoplasm
● Lipid nature of membrane is semi-permeable
Nucleus is Site of DNA and RNA synthesis
● DNA-protein complex - Chromatin, RNA
processing for ribosome synthesis occur in
Nucleolus
Endoplasmic Reticulum Has a Role in Protein
Synthesis and Many Synthetic Pathways
● Rough appearance due to Ribosomes -
biosynthesis of proteins for membranes and
organelles
● Involved in protein folding, Smooth ER
involved in lipid synthesis
Golgi Apparatus- is Involved in Secretion of
Proteins
● Major site of new membrane synthesis
● Enzymes in golgi catalyze transfer of carbohydrate
units to proteins and form glycoproteins
Mitochondria Supply Most of the Cellular Need for
ATP
● Synthesis of over 90% of required ATP; double
membrane
● enzymes needed for oxidation reactions, as well
as DNA (mtDNA) that differs from that found in the
nucleus, are found in the internal mitochondrial
matrix ● Metabolic reactions for oxidation of
pyruvate by glycolysis, fatty acids, AA are located in
mitosol

Peroxisomes Have an Important Role in Lipid

Metabolism
● contain enzymes involved in the metabolism of

structure & forming hydrogen bonds

hydrogen peroxide hydrogen peroxide (H2O2 )
which is toxic to the cell
● Catalase converts H2O2 to water and oxygen and
oxidation of various compounds by H2O2
WATER
Biomedical Importance/Clinical Correlations
❖ Predominant chemical component of living
organisms
❖ Unique physical properties; could solvate
organic/inorganic molecules due to dipolar
❖ Interaction with biomolecules influence both
biomolecule & water structure
❖ Excellent nucleophile, product/reactant for
metabolic reactions
WATER IS AN IDEAL BIOLOGIC SOLVENT
Water Molecules Form Dipoles, it is a polar
molecule
❏ water molecule is an irregular, slightly skewed
tetrahedron with oxygen at its center
❏ strongly electronegative oxygen atom in a water
molecule attracts electrons away from the
hydrogen nuclei
❏ molecule with electrical charge distributed
asymmetrically about its structure is referred to as
a dipole
INTERACTIONS WITH WATER INFLUENCES
STRUCTURE OF BIOMOLECULES

❖ Covalent and Noncovalent Bonds Stabilize EXAMPLE OF BIOLOGICALLY IMPORTANT H-BOND

Biologic Molecules
➢ covalent bond is the strongest force that holds
molecules together
❖ Biomolecules Fold to Position Polar & Charged
Groups on Their Surfaces
➢ amphipathic; possess charged groups &
hydrophobic regions
❖ Hydrophobic Interactions
➢ nonpolar compounds self-associate in an
aqueous environment
❖ Electrostatic Interactions
➢ Between oppositely charged groups - Salt WATER IS AN EXCELLENT NUCLEOPHILE
bridges ❖ van der Waals Forces
❏ Metabolic reactions - attack by lone pairs of e-
➢ Temporary dipoles from rapid movement of e- residing on e- -rich molecules termed nucleophiles
from neutral atoms upon e- -poor atoms called electrophiles
❖ Multiple Forces Stabilize Biomolecules ❏ Nucleophilic attack by water often result to
➢ DNA double helix structure Hydrolysis of (e.g. amide or ester bond).
WATER FORMS H-BOND Conversely, water is produced when joining
monomers
❏ Enzymes accelerate hydrolysis; Proteases for
proteins Amino acids while Nucleases for
phosphoester bonds in DNA/RNA
WATER MOLECULES EXHIBIT A SLIGHT BUT
IMPORTANT TENDENCY TO DISSOCIATE

❏ act both as an acid and as a base

(ionization/proton transfer) H2O + H2O ⇄ H3O +
OH-
❏ At one instant it is an ion; an instant later it is
part of a water molecule
❏ 1 (mol) of water weighs 18 g, 1 liter (L) (1000 g)
= 55.56 mol
❏ Probability that H+ in pure water will exist as H+
= 1.8 × 10-9 ❏ K w - ion product for water ; At 25°C
Kw = 10-14 (mol/L)2
Biomedical Importance/Clinical Correlations
Abnormal Medical Conditions as Reflected in the
pH of Blood
● Blood pH reflects changes in pH of tissues =>
pathological condition
● Acidosis - if blood pH falls below 7.35 and above
7.45, as an Alkalosis
● Metabolic acidosis - excess production of lactic
acid or ketone bodies occur in diabetes and
hypoxemia ○ loss of HCO3 - , changes pH balance
happens in diarrhea, and chronic renal diseases
● Respiratory acidosis - restricted CO2 exhalation
such as asthma, obesity or breathing problems due
to trauma ● Metabolic alkalosis - ingesting bases,
retention of HCO3 -
● Respiratory alkalosis - hyperventilation, fever

BUFFERS A buffer solution is a solution of:

1. A weak acid or a weak base and;
2. The salt of the weak acid or weak base Both
must be present!
A buffer solution has the ability to resist changes
in pH upon the addition of small amounts of
either acid or base.
 PROTEINS
Characteristics of Proteins

❖ Most abundant substance in cell next to water

(15% of cell mass)
❖ Typical human cell (9,000) and human body
(100,000) proteins
❖ All proteins contain C, H, O, N most have S
❖ Protein - unbranched polymer, monomer unit =
Amino Acid
❖ Synthesis of enzymes, hormones, tissue repair
& energy
❖ Presence of nitrogen (15.4 %) sets them apart
➔ 3 Types of polar amino acids, varying degrees
from lipids & carbohydrates
for water affinity.
❖ Casein - phosphorus (important for infants);
➔ Hydrophilic within protein, often on protein
Hemoglobin - iron (O2 transport)
surface
Amino Acids-Building Blocks of Proteins
2. Polar neutral amino acid - one (-NH2) & (-
● Amino acid contain both Amino group (-NH2) COOH) group + polar but neutral side chain;
and Carboxyl Group (-COOH) @physiological pH neither basic or acidic. 6 amino
● 𝝰- amino acid = amino and carboxyl group acids. - More soluble in water, R group can H bond
attached to 𝝰-carbon to H2O
● R group - side chains (distinguishes 𝝰- amino
acids from each other)
● Vary in size, charge, functional group, hydrogen
bonding & chemical reactivity

Amino Acids-Building Blocks of Proteins

➔ Standard amino acid - one of 20 𝝰- amino acid

normally found in proteins
Four Categories according to side chain polarity
1. Non polar amino acid - one (-NH2) & (-COOH)
group + nonpolar side chain - Hydrophobic when in
protein; found interior of proteins (less contact w/
H2O) - Nine non polar amino acid; Tryptophan
(water could H bond with NH ring )
3. Polar acidic amino acid - one (-NH2) & two (-
COOH) group 2nd (-COOH) group part of the side
chain; @physiological pH, side chain (-) charge &
side chain (-COOH) group lost its acidic H atom

meat, fish, and eggs except gelatin

4. Polar basic amino acid - two (-NH2) & one (-
COOH) group; @physiological pH side chain (+)
● Protein from plant sources - incomplete dietary
protein except soy Essential Amino Acids
● Complementary dietary proteins - two or more
incomplete dietary proteins that, when combined,
provide an adequate amount of all essential amino acids
relative to the body’s needs.
● Genetic modification increase plant protein

Chirality of Amino Acids

● Four different groups attached to the a-carbon atom
in all of the standard amino acids except glycine.
● Proteins and Amino Acids are L-isomers by nature
● Fischer Projection Rules a. -COOH put at top; R group

charge; Nitrogen atom has accepted a proton

Essential Amino Acids
● Essential amino acids - standard amino acids
obtained from dietary resources; Body cannot
synthesize it in adequate amounts Essential Amino
Acids
● Complete dietary protein contain all essential
amino acid in relative amount the body needs, may
or may not contain all non essential amino acid
● Incomplete dietary protein do not contain
adequate amounts relative to body
● limiting amino acid - essential amino acid that is
missing, or present in inadequate amounts, in an
incomplete dietary protein. at bottom b. -NH2 at horizontal; left = L; Right = D
Essential Amino Acids
● Protein from animal sources is usually complete
dietary protein. Casein from milk and proteins found in
Peptides
Peptide nomenclature:
Rule 1: C-terminal amino acid residue keep its full
name Rule
2 : All other amino acid residue end in -yl except
(tryptophyl, cysteinyl, glutaminyl and asparaginyl)
Rule 3: Amino acid naming sequence begins at N-
terminal end
A. Glu-Ser-Ala = Glutamylserylalanine
B. Gly-Tyr-Leu-Val = Glycyltyrosylleucylvaline
Biochemically Important Small Peptides
A. Small Peptide Hormones - nonapeptide; 6
residues held in form of loop by disulfide bond
from cysteine residues
● Oxytocin - regulates uterine contractions and

lactations
● Vasopressin (ADH - Antidiuretic Hormone) -
function in kidneys, decrease urine output, to
decrease H2O eliminated during dehydration
 B. Small peptide neurotransmitters
● Enkephalins - pentapeptide neurotransmitters,
bind at receptor sites of brain to reduce pain
Met-enkephalin and Leu-enkephalin = only differ at
amino acid at C-terminal end -painkillers morphine
based on binding at receptor sites as Enkephalins
C. Small peptide Antioxidants
● Glutathione- tripeptide, regulator of redox
reaction, protect cells from peroxides and
superoxides (ROS)
Unusual feature; bonded to Cys through side chain
carbonyl group rather than 𝝰-carboxyl group.

General Structure of Proteins

● Protein- peptide with at least 40 amino acid

residues; protein and polypeptide used
interchangeably
● 10,000 amino acid on most proteins, 400-500
amino acid residues on some proteins, 40-100 on
small proteins.
According to peptide chain
I. Monomeric protein - one peptide chain
II. Multimeric Protein - more than 1 peptide chain -
Peptide chains present = Protein sub units
According to chemical composition
I. Simple Protein - only Amino Acid is present, may
have sub unit as long as amino acid is present
II. Conjugated Protein - more than one peptide
chain and contain non amino acid entities
Prosthetic group - non amino acid group present in
conjugated protein
● Conjugated proteins may be further classified
according to the nature of the prosthetic group(s)
present.
Lipoproteins - lipid prosthetic groups,
glycoproteins - carbohydrate groups,
metalloproteins - specific metal, and so on
 Tertiary Structure of Proteins
-3D shape from interaction of R groups
Interactions Responsible for Tertiary Structure
1. Disulfide Bonds - strongest bond for tertiary
structure,-SH of two cysteine to
form covalent bond ; intramolecular or
intermolecular disulfide bond
2. Electrostatic Interaction (Salt Bridges) - acidic R
group and basic R group: at different pH carry
charges -COO- and NH3+, cation and anion
3. Hydrogen Bonds - occur in amino acids with
polar R groups; weak, disrupted by pH changes
 Protein Classification Based on Shape

Fibrous protein - molecules w/ elongated shape &

one dimension much longer - Linear and form
aggregate to form macromolecular structure
Globular protein - peptide chains folded into
spherical or globule shapes - Hydrophilic side
chains on outside; hydrophobic in interior
1. Fibrous = water-insoluble, whereas globular =
dissolve in water.
2. Fibrous = single type of secondary structure,
whereas globular often contain several types of
secondary structure.
3. Fibrous = structural functions that provide
support & external protection, whereas globular
proteins are involved in metabolism

Protein Denaturation

● partial or complete disorganization of 3d

structure, disruption of secondary, tertiary and
quaternary structural interactions
● cannot affect the primary structure
● biochemical function of protein depends on 3D
structure, loss of biochemical function =
denaturation
● some refold 3D structure = renaturation; 4. More globular types, but in human body more
extensive denaturation is irreversible fibrous present
● loss of water solubility = consequence of
denaturation ; coagulation = precipitation out of
solution of denatured protein
Protein Classification Based on Function
1. Catalytic proteins. Role of biochemical catalysts
= enzymes
2. Defense proteins. immunoglobulins or
antibodies fxn in immune system
3. Transport proteins. Bind to small biomolecules
and transport e.g. hemoglobin
4. Messenger proteins. transmit signals to
coordinate biochemical processes between
different cells, tissues, and organ ex. Hormones
12. Fluid-balance proteins. Maintain fluid balance
between blood & tissue; e.g. albumin and globulin
in capillary beds
Lipoproteins
Lipoproteins - conjugated proteins that are
composed of both lipids and amino acids.
Lipoproteins are classified on the basis of their
density
- plasma lipoprotein - involved in the transport
system for lipids in the bloodstream

5. Contractile proteins. Necessary for movement.

Filament like proteins in muscles, flagella of sperm
6. Structural proteins. Stiffness and rigidity ex.
Collagen & keratin

7. Transmembrane proteins. @ cell membrane and

control movement
8. Storage proteins. Bind & store molecules for
future use ex ferritin
9. Nutrient proteins. Important in early stages of
life e.g. Casein in milk
10. Regulatory proteins. Site of binding for
messenger proteins & enact function
11. Contractile proteins. Necessary for movement.
Filament like proteins in muscles, flagella of sperm
1. Chylomicrons. transport dietary triacylglycerols
from the intestine to the liver and to adipose
tissue.
2. Very-low-density lipoproteins (VLDL). Transport
triacylglycerols synthesized in the liver to adipose
tissue.
3. Low-density lipoproteins (LDL). transport
cholesterol synthesized in the liver to cells
throughout the body.
4. High-density lipoproteins (HDL). collect excess
cholesterol from body tissues and transport it back
to the liver for degradation to bile acids.