BIOCHEM LECTURE

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1B COMPOSITION OF PROTEIN
PROTEIN AND AMINO ACIDS

●​ Protein molecules are primarily made of the

following elements that are all present in all
LECTURE COVERAGE
amino acid
1 Protein Pg. 1 ○​ Carbon (C)
a.​ Definition of Protein ○​ Hydrogen (H)
b.​ Composition of Protein
○​ Oxygen (O)
c.​ Structure of Protein
○​ Nitrogen (N)
2 Amino Acid Pg. 2 ●​ In addition, proteins may also contain:
a.​ Structure of Amino Acid ○​ Sulfur (S) – found in amino acids like
b.​ Properties of Amino Acids
c.​ Classifications of Amino Acids cysteine and methionine
d.​ Functions of Amino Acids ○​ Phosphorus (P) – especially in
phosphoproteins
○​ Trace elements are often essential for
protein functions such as enzyme
PROTEIN
activity or hormone production. These
are:
1A DEFINITION OF PROTEIN ■​ Iron (Fe)
■​ Copper (Cu)
■​ Iodine (I)
●​ Protein are the most abundant ■​ Manganese (Mn)
macromolecules found within the living cells ■​ Zinc (Zn)
○​ They play crucial roles in virtually every ●​ The exact complete structure of large protein
biological process and are essential for molecules is still highly complex and not always
the structure, function, and regulation of fully determined,
the body's tissues and organs. ○​ because of their enormous size and
○​ Proteins are the main building blocks diversity.
of protoplasm, the living part of the ○​ However, we do know that proteins vary
cell, and are therefore indispensable to greatly in molecular weight, ranging
life. from about 5,000 to 8,000,000
●​ These are large, complex molecules are organic daltons, depending on their length and
compounds of high molecular weight, complexity.
composed of alpha (α) amino acids linked ●​ Due to their large molecular size, proteins
together by peptide bonds. exhibit colloidal properties in solution.
●​ The term "protein" was first introduced by the ○​ A colloid is a type of mixture where the
Dutch chemist Gerrit Jan Mulder in 1839. molecules are large enough to scatter
○​ He derived the word from the Greek light but not settle out of solution.
"proteios," meaning “of prime ■​ This property helps proteins
importance” or “preeminence,” to reflect maintain their structure and
the essential nature of proteins in remain suspended in fluids like
biological systems. blood plasma and cytoplasm.

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BIOCHEM LECTURE
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1C STRUCTURE OF PROTEIN 2A STRUCTURE OF AMINO ACID

●​ Proteins are made up of hundreds to thousands

of α-amino acids connected by peptide bonds.
○​ Each peptide bond forms when the
carboxyl group (-COOH) of one amino
acid reacts with the amine group (-NH₂)
of another, releasing a molecule of water
(H₂O).
■​ This reaction is called a
condensation reaction or
dehydration synthesis (two
molecules combine to form a
larger molecule, releasing water
as a byproduct) ●​ The central carbon atom in an amino acid is a
●​ Proteins can be broken down (hydrolyzed) into chiral carbon because it’s attached to four
smaller units: different groups:
■​ Proteoses ○​ A carboxylic acid functional group
■​ Peptones (-COOH)
■​ Polypeptides ○​ An amino group (𝑁𝐻2)
■​ α-Amino acids ○​ A Hydrogen atom
○​ This breakdown can occur through: ○​ An R group (side chain)
■​ Enzymatic hydrolysis (e.g., by ■​ The R group determines the
digestive enzymes like pepsin or specific type and properties of
trypsin) each amino acid
■​ Chemical hydrolysis using
strong acids or bases with heat

●​ This step-by-step breakdown helps our bodies

digest dietary proteins into usable amino acids,
which are then used to synthesize new proteins
as needed for growth, repair, and metabolism.

AMINO ACID

●​ Amino acids are the monomers or the

fundamental building blocks of proteins
●​ Their polarity plays a pivotal role in protein
structure, function, and interactions.

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BIOCHEM LECTURE
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2B PROPERTIES OF AMINO ACID Chemical Properties

Chemical Property Description Examples / Notes

Physical Properties

Property Description Examples / Notes Amphoteric Amino acids can They donate protons
Nature act as both acids in basic solutions and
and bases due to accept protons in
Solubility Soluble in water; Depends on the presence of acidic solutions.
slightly soluble in R-group and pH –COOH and –NH₂
alcohol; insoluble in groups.

organic solvents
Peptide Bond Amino acids form Foundation for
Formation peptide bonds via building
Melting Very high (>200°C); Due to strong ionic
condensation polypeptides and
Point decomposes on interactions
reactions proteins.
heating (zwitterions) between –COOH
and –NH₂.
Optical Most are optically Glycine is the only
Activity active (rotate non-chiral amino Hydrophobicity / Determined by Nonpolar R-groups =
polarized light) acid Hydrophilicity the R-group (side hydrophobic; Polar
chain) of the R-groups =
Crystalline Typically white, Appears as amino acid. hydrophilic.
Nature colorless, salt-like solids
Reaction with The –COOH Important in
crystalline solids
Alcohols group can react modification and

Zwitterions Exist as molecules NH₃⁺ and COO⁻ (Esterification) with alcohols to derivatization in lab
form esters. chemistry.
with both + and – groups present
charges at Acylation / The –NH₂ group Used to form N-acyl
physiological pH Carbonyl reacts with acyl derivatives in
Reactions and carbonyl analytical chemistry.
Taste Varies: sweet, Glycine: sweet; compounds.
bitter, or tasteless Arginine: bitter
Charge and The net charge of Important in protein
UV Absorb UV light Tryptophan, Isoelectric Point an amino acid purification (e.g.,
Absorption (especially aromatic Tyrosine, (pI) changes with pH; electrophoresis,
amino acids) Phenylalanine at a specific pH, isoelectric focusing).

absorb at ~280 nm net charge = 0.

Reactivity of Side Some R-groups e.g., Cysteine forms

Chains have functional disulfide bonds;
groups that can Serine undergoes
undergo chemical phosphorylation.
reactions.

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BIOCHEM LECTURE
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Non-Polar Aliphatic Amino Acid
2B CLASSIFICATION OF AMINO ACID
●​ A class of amino acids characterized by having
hydrocarbon chains (non-aromatic rings) in
Feature Polar Amino Nonpolar
Acids Amino Acids their side groups (R groups)
●​ These amino acids have hydrophobic side
Side Chain Contains Mostly chains that do not interact favorably with water
Composition electronegative hydrocarbons
atoms (e.g., O, (C and H
N, S) atoms)

Water Hydrophilic Hydrophobic

Interaction (water-loving) (water-fearing)

Location in Often on Often in protein

Proteins protein surface interior (avoid
(interact with water)
water)

Hydrogen Can form Cannot form

Bonding hydrogen and hydrogen bonds
ionic bonds

Common Serine, Alanine, Valine,

Examples Threonine, Leucine,
Asparagine, Isoleucine, Non-Polar Aromatic Amino Acid
Glutamine, Phenylalanine,
Cysteine, Methionine,
●​ Characterized by having a side chain that
Histidine Tryptophan
contains an aromatic ring and does not
Role in Enzymes Often involved Often interact strongly with water.
in contribute to ●​ These amino acids are hydrophobic, meaning
active/catalytic structural they tend to cluster together in the interior of
sites stability proteins, away from the aqueous environment
●​ Tyrosine also has an OH group, making it
Peptide Design Used in Used in
Usage hydrophilic/ hydrophobic partially polar
soluble peptides membrane
interacting
peptide

Interaction Hydrogen Van der Waals

Forces bonding, ionic interactions
interactions

Examples of –OH, –NH₂, –SH, Methyl,

Functional amide groups isopropyl,
Groups benzyl,
thioether

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Polar Neutral Amino Acid

●​ Those with polar, uncharged side chains.

●​ These amino acids have R-groups that can
participate in hydrogen bonding with water,
making them hydrophilic
●​ R groups contain electronegative atoms (like O,
N, or S)

Negatively Charged (Acidic) Amino Acid

●​ R groups contain carboxylic acid groups

(-COOH) that are deprotonated at physiological
pH
●​ Net negative charge
●​ Acidic behavior (donate protons)
●​ They participate in ionic interactions and are
often involved in enzyme active sites and ion
channels.

Sulfur-Containing Amino Acid

Amino Sulfur Group Special Role

Acid Group Classificati
on

Cysteine –SH (thiol) Polar, Disulfide bond

uncharged formation

Essential in the
presence of
Methionine
Positively Charged (Basic) Amino Acid
Methionine –S–CH₃ Nonpolar, Start of protein
(thioether) aliphatic synthesis ●​ R groups have extra amino groups (𝑁𝐻2) that

Essential are protonated at physiological pH

Amino Acid ●​ Net positive charge
●​ Basic behavior (accept protons)

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BIOCHEM LECTURE
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●​ They can form ionic bonds with negatively 3.​ Glutamine
charged molecules, critical in protein structure ➔​ The most abundant amino acid in
and function. muscles.
➔​ Helps build and preserve muscle tissue.
➔​ Maintains the body's acid-alkaline
balance.
➔​ Acts as "brain fuel" by enhancing mental
function and activity.
➔​ Promotes a healthy brain function
➔​ Necessary for the synthesis of nucleic
acids – DNA and RNA.

4.​ Asparagine
➔​ Essential for proper functioning of the
nervous system.
➔​ Helps maintain balanced cellular
function in the brain and nervous
system.
2C FUNCTIONS OF AMINO ACID ➔​ Aids in detoxifying ammonia from the
body.
Non-Essential Amino Acid - can easily synthesize a ➔​ mainly involved in the transportation of
few on its own nitrogen into our body cells, formations
1.​ Alanine of purines and pyrimidine for the
➔​ Known as the "mother of all amino synthesis of DNA, the development of
acids." the nervous system and improving our
➔​ Plays a key role in the transfer of body stamina.
nitrogen from peripheral tissues to the
liver. 5.​ Glutamic acid
➔​ Remove toxins from our body and in the ➔​ An excitatory neurotransmitter in the
production of glucose and other amino central nervous system (brain and spinal
acids. cord).
➔​ Facilitates potassium transport into
2.​ Cysteine spinal fluid.
➔​ Functions as a powerful antioxidant that ➔​ Helps correct personality disorders and
helps detoxify harmful substances. is used to treat epilepsy, intellectual
➔​ Used in the treatment of rheumatoid disability, muscular dystrophy, and
arthritis and atherosclerosis. ulcers.
➔​ Promotes recovery from severe burns ➔​ Mainly involved in the development and
and surgeries. functioning of the human brain.
➔​ Slows the aging process.
◆​ Skin and hair (especially curly 6.​ Tyrosine
hair) contain 10–14% cystine. ➔​ Serves as a precursor to adrenaline,
◆​ Important for making collagen norepinephrine, and dopamine.
◆​ It affects the texture and ➔​ Helps regulate mood, metabolism, and
elasticity of the skin nervous system activity.

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➔​ Plays a vital role in the production of the ➔​ plays a major role in metabolism and in
thyroid hormones -T3 and T4, in promoting the synthesis of other amino
synthesizing a class of neurotransmitters acids.
and melanin, which are natural pigments
MNEMONIC
found in our eyes, hair, and skin. Nonessential Amino Acids (10 Total)
7.​ Proline "A Cool Giant Always Gets The Perfect Strong Grit
➔​ Technically an imino acid, not a true Attire
amino acid. A – Alanine P – Proline
➔​ Known as an “α-helix breaker” for C – Cysteine S – Serine
disrupting α-helical protein structures. G – Glutamine G – Glycine
➔​ Improves skin texture by supporting A – Asparagine A – Aspartate
collagen production and slowing G – Glutamic Acid
collagen loss with age. T – Tyrosine
➔​ mainly involved in the repairing of the
tissues in the formation of collagen,
preventing the thickening and hardening
Essential Amino Acid - cannot be synthesized by our
of the walls of the arteries
body
(arteriosclerosis) and in the regeneration
of new skin.
1.​ Phenylalanine
➔​ Important for the utilization of vitamin C
8.​ Serine
and production of thyroxine (thyroid
➔​ A component of phosphoproteins
hormone).
(contains a phosphate group).
➔​ Some individuals lack the enzyme to
➔​ Contributes to the formation of myelin
convert phenylalanine (Phe) to tyrosine
sheaths around nerves.
(Tyr).
➔​ Aids in producing immunoglobulins and
➔​ In such cases, Phe is diverted to form
antibodies.
phenylpyruvic acid, leading to
➔​ helps in promoting muscle growth and in
Phenylketonuria (PKU).
the synthesis of immune system
◆​ PKU causes intellectual disability
proteins.
in infants if untreated and is
managed by limiting dietary Phe
9.​ Glycine
(e.g., avoiding high-protein
➔​ ..
foods).
➔​ helps in maintaining a healthy nervous
10.​Aspartic acid
system and in boosting memory power.
➔​ Acts as a major excitatory
neurotransmitter.
2.​ Valine
➔​ Increases stamina; beneficial for chronic
➔​ Important for nervous system function.
fatigue and depression.
➔​ Assists in muscle and tissue repair.
➔​ Protects the liver by aiding in ammonia
➔​ Maintains proper nitrogen balance in the
removal.
body.
➔​ Combines with other amino acids to
➔​ acts as an important component in
create molecules that neutralize and
promoting muscle growth.
eliminate toxins from the bloodstream.
➔​ Threonine helps in promoting the
functions of the immune system.

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BIOCHEM LECTURE
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3.​ Threonine ➔​ Maintains myelin sheaths protecting
➔​ Important in tissue building and nutrient nerve cells.
utilization. ➔​ Decarboxylates to form histamine, a
➔​ Helps maintain proper protein balance in powerful vasodilator involved in allergic
the body. responses and fever symptoms.
➔​ Antihistamines work by blocking
4.​ Methionine histamine's effects.
➔​ Initiates protein synthesis. ➔​ Involved in many enzymatic processes
➔​ Acts as a powerful antioxidant and and in the synthesizing of both red blood
sulfur source, helping prevent disorders cells (erythrocytes) and white blood cells
of the hair, skin, and nails. (leukocytes)
➔​ Reduces histamine levels, which can ➔​ Required in the diet in childhood during
affect brain signal transmission. periods of rapid growth

8.​ Isoleucine
5.​ Arginine ➔​ Necessary for hemoglobin formation.
➔​ Enhances the size and activity of the ➔​ Stabilizes and regulates blood sugar and
thymus gland, which produces T cells energy levels.
(vital for immune function). ➔​ stimulating the pancreas to synthesize
➔​ Used in treating male infertility by insulin, and transporting oxygen from
increasing sperm count and improving the lungs to the various parts.
blood flow to the penis. 9.​ Leucine
➔​ A major component of collagen, ➔​ Involved in digestive enzyme production.
beneficial for arthritis and connective ➔​ Works with isoleucine and valine to
tissue disorders. promote healing of muscle tissue, skin,
➔​ Stimulates the pancreas to release and bones.
insulin. ➔​ Involved in promoting protein synthesis
➔​ Required in the diet in childhood during and growth hormones.
periods of rapid growth
10.​Lysine
➔​ Found abundantly in collagen.
6.​ Tryptophan ➔​ Aids in the absorption of other amino
➔​ Found in charred meat/fish (associated acids.
with carcinogens). ➔​ Essential in forming collagen, which
➔​ Ivolved in the production of vitamin B3 makes up cartilage and connective
and serotonin hormones. tissues.
◆​ This serotonin hormone plays a ➔​ necessary for promoting the formation
vital role in maintaining our of antibodies, hormones, and enzymes
appetite, regulating sleep and and in the development and fixation of
boosting our moods. calcium in bones.
7.​ Histidine
➔​ Exhibits buffering capacity at
physiological pH, unique among amino
acids.
➔​ Abundant in hemoglobin. Essential for
tissue growth and repair.

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BIOCHEM LECTURE
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MNEMONIC
Essential Amino Acids (10 Total)
PVT - MATHILL
P - Phenylalanine
V - Valine
T - Threonine

M - Methionine
A - Arginine
T - Tryptophan
H - Histidine
I - Isoleucine
L - Leucine
L - Lysine

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