BIOCHEMISTRY LECTURE

Marvin Catacutan | 2nd Semester | BS Nursing

A.Y. 2024 – 2025

I. ENZYMES ●​ Role of Cofactors

○​ Provide chemically reactive functional
-​ Proteins that act as catalysts for biochemical groups that apoenzymes lack.
reactions. ○​ Can be small organic molecules or
-​ Speed up cellular reactions millions of times faster inorganic ions.
than uncatalyzed reactions. ○​ Coenzyme – A small organic molecule
-​ Not consumed in reactions; only help them occur that serves as a cofactor.
more rapidly. ○​ Typical Inorganic Cofactors – Zn²⁺, Mg²⁺,
-​ Thousands of different enzymes per cell; each Mn²⁺, Fe²⁺, Cl⁻.
reaction requires a specific enzyme. ○​ Dietary minerals are important sources of
●​ Origin & Early Use inorganic ion cofactors.
○​ From Greek: en ("in") + zyme ("yeast"). ●​ Catalytic Efficiency
○​ Used in bread and alcohol production ○​ Enzymes – Increase reaction rates by up
before chemical properties were to 10²⁰ times over uncatalyzed reactions.
understood. ○​ Nonenzymatic Catalysts – Typically
●​ Types of Enzymes enhance rates by 10² to 10⁴ times.
○​ Globular Proteins – Most enzymes.
○​ Simple Proteins – Only amino acid NOMENCLATURE AND CLASSIFICATION
chains. OF ENZYMES
○​ Conjugated Proteins – Contain additional
chemical components. -​ Named based on function rather than structure.
○​ RNA-based Enzymes – Some enzymes ●​ Substrate – The reactant in an enzyme-catalyzed
made of ribonucleic acid (RNA). reaction.
●​ Factors Affecting Enzyme Activity ●​ Three Key Aspects of Enzyme Naming
○​ pH & Temperature – Small changes 1.​ Suffix "-ase" identifies enzymes (e.g., urease,
significantly impact activity. sucrase, lipase). Some older enzymes retain the
○​ Heat Sensitivity – High fever (>106°F) suffix "-in" many of which are digestive enzymes.
can denature enzymes. (e.g., trypsin, chymotrypsin, pepsin).
○​ Handling Sensitivity – Vigorous shaking 2.​ Prefix indicates reaction type:
can destroy enzyme activity. ○​ Oxidase → Oxidation reaction
●​ Comparison with Non Biochemical Catalysts ○​ Hydrolase → Hydrolysis reaction
○​ Much larger than laboratory catalysts. 3.​ Substrate name is often included:
○​ Controlled by cellular substances. ○​ Glucose oxidase → Acts on glucose.
○​ If a chemical is needed, enzymes are ○​ Pyruvate carboxylase → Acts on pyruvate.
activated. ○​ Succinate dehydrogenase → Acts on
○​ Once enough is produced, enzymes are succinate.
deactivated. ○​ Urease, lactase → Do not specify reaction
○​ Cells increase or decrease enzyme levels type but catalyze hydrolysis (e.g., urease
as needed. hydrolyzes urea, lactase hydrolyzes
○​ Can speed up specific reactions without lactose).
affecting overall cellular chemistry. SIX MAJOR CLASSES OF ENZYMES
ENZYME STRUCTURE (BASED ON REACTION TYPE)
●​ Two Structural Classes of Enzymes 1.​ Oxidoreductase – Catalyzes oxidation-reduction
○​ Simple Enzymes – Composed only of reactions.
protein (amino acid chains). ○​ Requires a coenzyme that is
○​ Conjugated Enzymes – Contain a non oxidized/reduced.
protein part in addition to the protein part. ○​ Example: Lactate dehydrogenase removes
●​ Components of Conjugated Enzymes hydrogen atoms from a molecule.
○​ Apoenzyme – The protein part of a ○​ Oxidases – Oxidation of a substrate.
conjugated enzyme. ○​ Reductases – Reduction of a substrate.
○​ Cofactor – The non protein part of a ○​ Dehydrogenases – Introduction of a
conjugated enzyme. double bond by removing two H atoms,
○​ Holoenzyme – The biologically active which are accepted by a coenzyme.
enzyme formed from the apoenzyme + 2.​ Transferase – Transfers a functional group from
cofactor. one molecule to another.

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○​ Transaminase – Transfers an amino ○​ More favorable reaction conditions inside
group. the complex lead to faster product
○​ Kinase – Transfers a phosphate group formation.
from ATP → ADP. ●​ Lock-and-Key Model
3.​ Hydrolase – Catalyzes hydrolysis reactions (bond
breaking using water).
○​ Lipases – Hydrolysis of ester linkages in
lipids.
○​ Proteases – Hydrolysis of amide linkages
in proteins. ○​ Rigid, fixed active site shape.
○​ Nucleases – Hydrolysis of ○​ Only specific substrates with a
sugar–phosphate ester bonds in nucleic complementary shape can bind.
acids. ○​ Analogy – A lock accepts only a specific
○​ Carbohydrases – Hydrolysis of glycosidic key.
bonds in carbohydrates. ●​ Induced-Fit Model
○​ Phosphatases – Hydrolysis of
phosphate–ester bonds.
4.​ Lyase – Adds/removes groups to/from double
bonds (without hydrolysis or oxidation).
○​ Dehydratases – Remove H₂O from a
substrate. ○​ Active site is flexible, adapting to fit the
○​ Decarboxylases – Remove CO₂ from a substrate.
substrate. ○​ Analogy – A glove changes shape when a
○​ Deaminases – Remove NH₃ from a hand is inserted.
substrate. ○​ Combines specificity of the lock-and-key
○​ Hydratases – Add H₂O to a substrate model with enzyme flexibility.
5.​ Isomerase – Catalyzes isomerization reactions ●​ Forces Involved in Substrate Binding
(rearranges atoms). ○​ Electrostatic interactions (e.g., positive
○​ One reactant → One product (isomeric amino groups attracted to negatively
form). charged residues).
○​ Racemases – Convert D-isomer to ○​ Hydrogen bonds.
L-isomer, or vice versa. ○​ Hydrophobic interactions.
○​ Mutases – Transfer a functional group ○​ Cofactors (metal ions) assist in binding
within the same molecule. substrate molecules.
6.​ Ligase – Bonds two molecules together using ATP ENZYME SPECIFICITY
energy.
○​ ATP hydrolysis → ADP provides required -​ The degree to which an enzyme’s activity is
energy. restricted to:
○​ Synthetases – Form a new bond between ○​ A specific substrate
two substrates, with ATP participation. ○​ A specific group of substrates
○​ Carboxylases – Form a new bond ○​ A specific type of chemical bond
between a substrate and CO₂, with ATP ○​ A specific type of chemical reaction
participation. -​ Determined by the active site
○​ Some active sites accommodate only one
MODELS OF ENZYME ACTION compound.
●​ Enzyme Active Site ○​ Others can bind a family of closely related
○​ Small region of the compounds.
enzyme involved in ●​ Types of Enzyme Specificity
catalysis. ○​ Absolute Specificity – Catalyzes only
○​ Three-dimensional one reaction.
structure formed by ■​ Example: Catalase converts H₂O₂
folding and bending of → O₂ + H₂O and accepts only
the protein. hydrogen peroxide.
○​ Usually a crevice-like location. ○​ Group Specificity – Acts on molecules
●​ Enzyme–Substrate Complex with a specific functional group (e.g.,
○​ Intermediate species formed when the hydroxyl, amino, phosphate).
substrate binds to the active site. ■​ Example: Carboxypeptidase
○​ Provides an alternative reaction pathway cleaves amino acids from the
with lower activation energy. carboxyl end of a peptide chain.

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○​ Linkage Specificity – Acts on a particular ●​ Substrate Concentration
type of chemical bond, regardless of the ○​ Reaction rate increases with
molecular structure. substrate concentration until
■​ Example: Phosphatases full saturation occurs; then
hydrolyze phosphate-ester bonds the rate levels off.
in all phosphate esters. ○​ Increasing substrate
■​ Most general type of specificity. concentration → Increases enzyme activity
○​ Stereochemical Specificity – Acts only until saturation is reached.
on a specific stereoisomer. ○​ Saturation Curve – At maximum enzyme
■​ Example: L-amino acid oxidase capacity, additional substrate won't
catalyzes oxidation of L-amino increase reaction rate.
acids but not D-amino acids. ○​ Turnover Number – The number of
substrate molecules transformed per
FACTORS THAT AFFECT ENZYME ACTIVITY
minute by one enzyme molecule under
●​ Temperature optimal conditions.
○​ Higher temperature → ●​ Enzyme Concentration
Faster molecular ○​ Reaction rate increases
movement → More with increasing enzyme
collisions between concentration, assuming
substrate and enzyme. enzyme concentration is
○​ Reaction rate increases much lower than that of
with temperature until the substrate.
point at which the protein is denatured and ○​ More enzyme molecules → More substrate
activity drops sharply. processed → Higher reaction rate.
○​ Too high temperature → Denaturation of ○​ Cells maintain low enzyme levels to save
enzyme (disrupts tertiary structure). energy (substrate is usually in higher
○​ Optimum temperature for human enzymes concentration than enzyme).
≈ 37°C (normal body temp.). ○​ Increasing enzyme concentration (with
○​ Above 40°C → Risk of denaturation, constant substrate) increases the reaction
especially in critical enzymes (e.g., CNS rate proportionally.
enzymes).
EXTREMOZYMES
○​ Sterilization uses high heat to denature
bacterial enzymes (e.g., autoclaves in ●​ Extremozymes - Microbial enzymes active in
hospitals). extreme conditions that would inactivate human
●​ pH enzymes.
○​ Maximum enzymatic activity ●​ Extremophiles - Microorganisms thriving in
is possible only within a extreme environments (e.g., hydrothermal vents,
narrow pH range; outside high-pressure zones).
this pH range, the protein is ●​ Acidophiles - Grow at pH ≤ 3.0
denatured and activity drops ●​ Alkaliphiles - Grow at pH ≥ 9.0
sharply. ●​ Halophiles - Require high salt
○​ Enzyme activity depends on concentration (>0.2 M NaCl)
properly charged amino acids at the active ●​ Hyperthermophiles - Thrive at 80–122°C
site. ●​ Piezophiles - Grow under high hydrostatic
○​ Small pH changes (<1 unit) can cause pressure
denaturation. ●​ Cryophiles - Thrive at ≤15°C
○​ Optimum pH varies by enzyme:
ENZYME INHIBITION
○​ Most enzymes function at pH 7.0–7.5.
○​ Pepsin (stomach enzyme) → Optimum pH -​ A process where substances (inhibitors) decrease
= 2.0. or stop enzyme activity by binding to the enzyme.
○​ Trypsin (small intestine enzyme) → ●​ Reversible Competitive
Optimum pH = 8.0. Inhibition
○​ pH variations can also alter substrate ○​ Inhibitor resembles the
charge, reducing enzyme efficiency. substrate in shape and
○​ Acidic conditions inhibit enzyme activity in charge.
microorganisms (e.g., pickling prevents ○​ Competes with the
spoilage). substrate for the active
site.
○​ No reaction occurs when the inhibitor
binds, but it prevents substrate binding.

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○​ Reversible – Weak interactions (e.g., ●​ Proteolytic Enzymes & Zymogens
hydrogen bonds) hold the inhibitor in ○​ Proteolytic enzyme - enzymes that
place. catalyzes the breaking of peptide bonds
○​ Increasing substrate concentration can that maintain the primary structure of a
reduce inhibition. protein
○​ Example: Antihistamines compete with ■​ Generated in an inactive form and
histidine for histamine production. then later, when they are needed,
○​ Example: Ethanol is used to treat methanol are converted to their active form
poisoning by competing for alcohol ■​ Most digestives and blood clotting
dehydrogenase. enzymes
●​ Reversible Noncompetitive Inhibition ○​ Zymogens (proenzymes) are inactive
precursors of a proteolytic enzyme.
■​ Activated by removing part of the
structure (e.g., pepsinogen →
pepsin).
●​ Covalent Modification

○​ Inhibitor binds to a site other than the

active site.
○​ Substrate still binds, but enzyme shape
changes, preventing catalysis.
○​ Increasing substrate concentration does
not fully reverse inhibition.
○​ Enzyme activity altered by
○​ Lowering inhibitor concentration can
adding/removing chemical groups.
restore enzyme activity. ○​ Phosphorylation (kinases) → Can activate
○​ Example: Heavy metal ions (Pb²⁺, Ag⁺,
or deactivate.
Hg²⁺) bind to sulfhydryl (-SH) groups,
■​ Protein kinases
disrupting enzyme structure.
■​ Addition of the phosphate group
●​ Irreversible Inhibition
from the enzyme
○​ Inhibitor forms a strong covalent bond with ■​ Glycogen phosphorylase group
the active site.
from the enzyme
○​ Permanently inactivates the enzyme.
■​ Glycogen phosphorylase
○​ Excess substrate cannot reverse inhibition. (glycogen to glucose)
○​ Examples: Nerve gases, organophosphate
■​ Phosphorylation deactivates
insecticides, and chemical warfare agents.
glucose synthase (synthesis of
REGULATION OF ENZYME ACTIVITY glycogen
○​ Dephosphorylation (phosphatases) →
-​ Prevents energy waste and controls metabolism. Opposite effect.
●​ Allosteric Enzymes ■​ Phosphatases
○​ Have quaternary ■​ Removal of the phosphate group
structure with substrate from the enzyme
& regulator binding ○​ Example: Glycogen metabolism enzymes
sites. regulated by phosphorylation.
○​ Positive regulators →
Increase activity. PRESCRIPTION DRUGS THAT INHIBIT ENZYME
○​ Negative regulators → ACTIVITY
Decrease activity.
●​ Feedback Control ●​ ACE Inhibitors
○​ Block angiotensin-converting enzyme
(ACE) → Lowers blood pressure.
○​ Prevents conversion of angiotensinogen to
angiotensin (vasoconstrictor).
○​ Product inhibits the first enzyme in a ○​ Example: Lisinopril (from Brazilian pit viper
pathway (negative feedback). venom).
○​ High product levels → Enzyme activity ●​ Sulfa Drugs
decreases. ○​ First antibiotics discovered (sulfanilamide).
○​ Low product levels → Enzyme activity ○​ Act as competitive inhibitors against PABA
increases. (Para-aminobenzoic acid) (needed for
bacterial folic acid synthesis).

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○​ Do not affect humans (we get folic acid II. VITAMINS & MINERALS
from diet).
●​ Penicillins NUTRITION
○​ Inhibit transpeptidase, preventing bacterial ●​ Focuses on the study of food, water, and other
cell wall formation. nutrients and the ways in which they are used by
○​ Cause bacterial lysis by weakening cell living organisms
walls. ●​ Necessary for the body to function and remain
○​ Act as irreversible inhibitors by binding healthy
covalently to enzyme active sites. ○​ Macronutrients (Major Elements)
○​ Some bacteria produce penicillinase, ■​ Carbohydrates, Proteins, Fats
which inactivates penicillin. ■​ Required in large quantities
○​ Methicillin & amoxicillin are ■​ Present in excessive
penicillinase-resistant. concentration in plant
●​ Food-Enzyme Interactions ■​ Majority are minerals, some are
○​ Cytochrome P450s enzymes metabolize non-minerals (C, H, and O)
drugs in the liver. ■​ Usually not toxic to the cell if they
○​ Some foods/herbs inhibit these enzymes, are present in relatively higher
slowing drug breakdown. concentration than the normal
○​ "Grapefruit effect" increases drug levels in level
the bloodstream, potentially dangerous. ■​ Examples: C, H, O, N, P, K, Ca,
S, and Mg
MEDICAL USES OF ENZYMES
○​ Micronutrients (Trace Elements)
■​ Vitamins, Minerals
■​ Frequent in small quantities
■​ Present in low concentration in
plant
■​ Are minerals
■​ Can be toxic for the plant; can be
toxic to the cell if more than the
required quantity
■​ Examples: Fe, Mn, CU, ZN, Mo,
●​ Diagnosis of Diseases
B, Cl, and Ni
○​ Some enzymes are not normally in the
●​ In addition to nutrients, body also requires water
blood but are found in specific organs and
and fiber
tissues.
○​ 45-75% of human body mass is water
○​ If these enzymes appear in the
○​ Fiber is an indigestible plant material made
bloodstream, it indicates organ or tissue
mostly of
damage.
cellulose
○​ Assays of abnormal enzyme activity help
●​ The Daily Value (DV) are
diagnose diseases like liver damage, heart
a set of nutritional
attack, pancreatitis, and bone disorders.
guidelines established by
●​ Treatment of Diseases
the FDA use on food
○​ Tissue plasminogen activator (TPA)
labels
activates plasminogen, which dissolves
blood clots in heart attack patients. MACRONUTRIENTS
○​ Enzyme therapy is used for digestive
●​ Carbohydrates - Provide energy for body functions
disorders, blood clotting issues, and
and useful materials for the synthesis of cell and
genetic enzyme deficiencies.
tissue components
●​ Clinical Laboratory Analysis
○​ Simple carbohydrates
○​ Many blood tests rely on enzymes to
○​ Complex carbohydrates
detect specific substances.
●​ Lipids - Concentrated source of energy. Lipids
○​ The Blood Urea Nitrogen (BUN) test uses
contain some fat-soluble vitamins and help carry
urease to break down urea into ammonia,
them throughout the body
which is then measured to assess kidney
○​ About 95% of the lipids in foods and in our
function.
bodies is in the form of triglycerides. The
○​ Enzymes are also used in tests for glucose
fatty acids in the triglycerides can be either
levels, cholesterol, and liver function.
saturated or unsaturated.
■​ Triglycerides containing a high
concentration of unsaturated fatty

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acids are liquids at room
temperature (oils).
■​ Triglycerides containing a high
concentration of saturated fatty
acids are solids at room
temperature (fats).
○​ Lipids: 9 cal/g
○​ Proteins and carbohydrates: 4 cal/g
○​ Improve the texture of foods, absorb and
retain flavors, and are digested more
slowly than other foods, prolong the feeling WATER SOLUBLE VITAMINS
of satiety (satisfaction and fullness after a
meal). VITAMIN C
■​ Linoleic and linolenic acids are ●​ Forms and Synthesis
essential fatty acids because they ○​ Exists in oxidized (dehydroascorbic acid)
cannot be synthesized in the and reduced (ascorbic acid) forms.
body and must be obtained from ○​ Humans, monkeys, apes, and guinea pigs
the diet. cannot synthesize vitamin C and must
●​ Proteins - Necessary to produce new tissue, obtain it from diet.
maintenance and repair of cells, production of ○​ Other species synthesize it from L-gulonic
enzymes, hormones and other important acid, converted by lactonase and oxidase
nitrogen-containing compounds enzymes.
VITAMINS ●​ Functions
○​ Collagen synthesis – Helps form
-​ Essential nutrients, hydroxyproline and hydroxylysine,
required in small amounts, essential for skin, ligaments, tendons,
obtained from diet bones, and teeth.
-​ Function as cofactors in ○​ Iron absorption and function – Maintains
many enzymes iron in a functional state as a cofactor in
-​ Needed in microgram to enzymatic reactions.
milligram amounts daily ○​ Antioxidant role – Protects cells,
●​ Example: Vitamin regenerates vitamin E and folate, and is
B12 RDA = 2.0 often added as a food preservative.
micrograms/day ○​ Amino acid metabolism – Involved in the
-​ Well-balanced diet usually meets vitamin needs production of norepinephrine and
-​ Supplements may be needed for pregnancy, illness, thyroxine.
or deficiency ○​ Highest concentration in the adrenal
-​ Synthetic and natural vitamins are chemically glands.
identical and equally effective ●​ Daily Requirement and Sources
●​ Water-Soluble (9) ○​ RDA varies: 30 mg/day (Great Britain), 60
○​ Vitamin C, Thiamin, Riboflavin, mg/day (U.S. and Canada), 75 mg/day
Niacin, Panthothenic acid, (Germany).
Vitamin B6, Biotin, Folate, Vitamin ○​ 100 mg/day saturates tissues, excess is
B12 excreted.
○​ Excreted in urine, require ○​ Rich sources: Peppers, citrus fruits,
frequent intake strawberries, cabbage, and spinach.
○​ Low risk of toxicity
○​ Function mainly as coenzymes THE B VITAMINS
●​ Fat-Soluble (4) ●​ There are nine water-soluble vitamins; vitamin C is
○​ Vitamin A, Vitamin D, Vitamin E, separate, while the other eight are grouped as B
Vitamin K vitamins.
○​ Stored in fat tissues, needed ●​ All B vitamins function as enzyme cofactor
periodically precursors, except vitamin C.
○​ Higher risk of toxicity ●​ Nomenclature and Naming History
○​ Rarely function as coenzymes, ○​ Initially, vitamins were classified as either
involved in other physiological fat-soluble (A) or water-soluble (B).
roles ○​ As more water-soluble vitamins were
discovered, they were named B1, B2, B3,
etc.

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○​ Later, a common name system replaced ●​ Pantothenic Acid (B5)
numbered B vitamins.
●​ List of B Vitamins and Alternative Names
○​ B1 – Thiamin
○​ B2 – Riboflavin (formerly vitamin G)
○​ B3 – Niacin (Nicotinic acid, Nicotinamide)
○​ B5 – Pantothenic acid ○​ Found in almost all plant and animal
○​ B6 – Pyridoxine, Pyridoxal, Pyridoxamine tissues.
○​ B7 – Biotin (formerly vitamin H) ○​ Component of Coenzyme A (CoA), crucial
○​ B9 – Folate (Folic acid) for metabolism of carbohydrates, lipids,
○​ B12 – Cobalamin and proteins.
●​ Discontinued Vitamin Labels ○​ Another pantothenic acid-containing
○​ B4 (Adenine) and B8 (Adenylic acid) were coenzyme is Acyl carrier protein (ACP),
later identified as DNA metabolites, not which may be regarded as a “giant
true vitamins. coenzyme A molecule.”
STRUCTURAL CHARACTERISTICS OF THE B VITAMINS ■​ Important in the biosynthesis of
fatty acids
-​ B vitamins exist in food in a form different from their ●​ Vitamin B6 (Pyridoxine, Pyridoxal,
active enzyme cofactor form. Pyridoxamine)
-​ Once ingested, they undergo modifications to
become active in the body.
●​ Thiamin (B1)

○​ Exists in plant (pyridoxine) and animal

○​ Structure includes a six-membered (pyridoxal, pyridoxamine) sources.
heterocyclic amine and a five-membered ○​ Active form pyridoxal phosphate (PLP) is
thiazole ring. involved in amino acid metabolism.
○​ Coenzyme form: thiamin pyrophosphate ●​ Biotin (B7)
(TPP) is essential for decarboxylation of
α-keto acids.
●​ Riboflavin (B2)
○​ Contains fused
ring structures
with ribose sugar.
○​ Forms two
○​ Fused two-ring system with one ring
coenzymes:
containing sulfur and the other ring
flavin adenine
containing nitrogen. Attached to the sulfur
dinucleotide
containing ring is a pentanoic acid residue.
(FAD) and flavin mononucleotide (FMN),
○​ Obtained from diet and produced by gut
both involved in redox reactions.
bacteria.
●​ Niacin (B3)
○​ Functions as a CO₂ carrier in enzymatic
○​ Found as
reactions.
nicotinic acid
and
nicotinamide.
○​ Converted into
coenzymes Nicotinamide adenine
dinucleotide (NAD+) and Nicotinamide
adenine dinucleotide phosphate ○​ Free biotin is biologically active.
(NADP+), essential for redox reactions. ○​ The coenzyme form is formed by biotin’s
○​ Originally named from its connection to pentanoic acid attaching to lysine at the
nicotine but renamed to avoid confusion. enzyme’s active site.
○​ Biotin acts as a carrier for CO₂, attaching
at a specific nitrogen site.

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●​ Folate (B9) FAT-SOLUBLE VITAMINS
-​ Include Vitamins A, D, E, and K
-​ Mostly nonpolar, making them soluble in cell
membranes
-​ Involved in membrane-related processes
●​ Vitamin A

○​ Found in various forms, including

polyglutamates in food.
○​ Active form tetrahydrofolate (THF) is
essential for methylation reactions and
DNA synthesis. ○​ Preformed vitamin A forms are called
○​ Found in dark leafy greens; required in retinoids.
enriched grain products to prevent birth ■​ The retinoids include retinal,
defects. retinol, and retinoic acid.
●​ Vitamin B12 (Cobalamin) ○​ Found in two forms: retinoids (preformed)
and carotenoids (provitamin)
○​ Beta-carotene is the main plant-based
precursor
○​ Functions:
■​ Vision: Forms rhodopsin for light
detection in the eyes
■​ Cell Differentiation: Regulates
○​ Contains cobalt, making it the only vitamin specialized cell development
with a metal atom. ■​ Epithelial Health: Maintains skin
○​ Active form methylcobalamin is crucial for and internal linings
alkyl group and hydrogen transfer. ■​ Reproduction & Growth:
○​ Produced only by microorganisms; Supports sperm production and
humans must obtain it from animal-based fetal development
foods or fortified cereals. ●​ Vitamin D

○​ Two forms: D3 (cholecalciferol) from

animals and D2 (ergocalciferol) from
plants
○​ Synthesized in skin from cholesterol with
sunlight exposure
○​ Activated in liver and kidneys through
hydroxylation
○​ Found in fatty fish, egg yolks, and fortified
foods
○​ Functions:
■​ Maintains calcium and phosphate
levels
■​ Enhances absorption in intestines
■​ Stimulates calcium retention in
kidneys
■​ Aids in bone formation
●​ Vitamin E

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○​ Exists in four forms: alpha-, beta-, delta-,
and gamma-tocopherol (main form of
vitamin E)
○​ Alpha-tocopherol is the most active form
and has the greatest biochemical activity
○​ Found in plant oils, green vegetables, and
whole grains
○​ Functions:
■​ Antioxidant: Prevents oxidation of
polyunsaturated fats
■​ Protects vitamin A and cell
membranes
■​ Supports lung cell protection
against oxygen exposure
■​ Given to premature infants to
prevent oxidative damage
●​ Vitamin K
MINERALS
●​ Inorganic substances which is needed in small
amounts that must be obtained from food
●​ Divided into 2 groups:
○​ Major Minerals
○​ Minor Minerals
○​ Two forms: K1 (phylloquinone) from
plants and K2 (menaquinone) from MAJOR MINERALS
animals and bacteria ●​ Calcium
○​ Synthesized by intestinal bacteria and ○​ Functions: Teeth and bones, blood clotting,
obtained from leafy greens nerve and muscle contraction, heart
○​ Functions: regulation
■​ Essential for blood clotting by ○​ Sources: Dairy products, fortified white
producing prothrombin bread, green vegetables, nuts and seeds
■​ Involved in protein biosynthesis ○​ Deficiency: Stunted growth can cause
for bone and kidney function rickets and osteoporosis
■​ Given to pre-surgical patients to ●​ Phosphorus
prevent excessive bleeding ○​ Functions: Bones and teeth accompanied
by calcium, muscle contraction
○​ Sources: Dairy products, nuts, meat, fish,
oats, cocoa
○​ Deficiency: Rarely deficient but could
cause tiredness and depression
●​ Potassium
○​ Functions: Muscle contraction and in
maintaining body fluid. It is necessary for
the building of muscle and for normal body
growth.
○​ Sources: Banana, celery, meat, fruits, milk,
grains, legumes, raisins, dates, figs
○​ Deficiency: Dry skin, acne, muscle spasms
or weakness
●​ Magnesium
○​ Functions: Muscle contraction, DNA
synthesis, controls blood sugar and blood
pressure, cofactor of enzymes
○​ Sources: Cheeses, cocoa, chocolate, nuts,
beans
○​ Deficiency: Hypocalcemia

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MIDTERMS | CHEM113 2ND SEMESTER
●​ Sodium ○​ Functions: Antioxidant, supports thyroid
○​ Functions: Maintains water balance in the function, helps prevent cell damage
body and controls body temperature, helps ○​ Sources: Brazil nuts, fish, eggs, whole
you sweat when body temperature rises grains
○​ Sources: Cheese, smoked meats, fish, ○​ Deficiency: Weakened immune system,
table salt muscle weakness
○​ Deficiency: Deficiency is highly unlikely ●​ Chromium
●​ Chloride ○​ Functions: Helps regulate blood sugar,
○​ Functions: Maintains fluid balance, aids enhances insulin action
digestion as part of stomach acid (HCl) ○​ Sources: Whole grains, broccoli, potatoes,
○​ Sources: Table salt, seaweed, rye, nuts
tomatoes, celery ○​ Deficiency: Impaired glucose metabolism
○​ Deficiency: Rare, but may cause ●​ Manganese
dehydration and muscle weakness ○​ Functions: Bone formation, metabolism,
●​ Sulfur enzyme cofactor
○​ Functions: Component of amino acids and ○​ Sources: Nuts, whole grains, tea, legumes
vitamins, supports protein structure, ○​ Deficiency: Weak bones, impaired growth
detoxification ●​ Molybdenum
○​ Sources: Meat, fish, eggs, garlic, onions, ○​ Functions: Supports enzyme activity, helps
cruciferous vegetables break down toxins
○​ Deficiency: Rare, usually occurs with ○​ Sources: Legumes, whole grains, nuts
protein deficiency ○​ Deficiency: Rare, but may cause metabolic
disturbances
MINOR MINERALS
●​ Iron III. LIPIDS
○​ Functions: Production of hemoglobin in red STRUCTURE AND CLASSIFICATION
blood cells to carry oxygen in the blood
○​ Sources: Red meat, liver, eggs, bread, -​ Lipids do not have a common structural feature but
green vegetables are classified based on solubility.
○​ Deficiency: Anemia -​ Lipids are organic compounds that are insoluble in
●​ Zinc water but soluble in nonpolar organic solvents.
○​ Functions: Aids the immune system, ●​ Structural Diversity includes esters, amides,
cofactor in enzymes, needed for the alcohols and can be acyclic, cyclic, or polycyclic,
senses of smell and taste but all are insoluble in water.
○​ Sources: Meat (especially lamb), oats, ●​ Classification based on biochemical function:
eggs, nuts ○​ Energy-storage lipids - Triacylglycerols.
○​ Deficiency: Retarded growth ○​ Membrane lipids - Phospholipids,
○​ Excess: Enlarged liver sphingoglycolipids, cholesterol.
●​ Iodine ○​ Emulsification lipids - Bile acids.
○​ Functions: Essential for thyroid hormone ○​ Messenger lipids - Steroid hormones,
production, regulates metabolism eicosanoids.
○​ Sources: Iodized salt, seafood, dairy ○​ Protective-coating lipids - Biological
products (e.g., milk & yogurt), eggs waxes.
○​ Deficiency: Goiter, hypothyroidism ●​ Classification based on hydrolysis
●​ Fluoride (saponification reaction):
○​ Functions: Strengthens tooth enamel, ○​ Saponifiable lipids (can be hydrolyzed in
prevents dental cavities basic solution) - Triacylglycerols,
○​ Sources: Fluoridated water, tea, fish, phospholipids, sphingoglycolipids,
toothpaste biological waxes.
○​ Deficiency: Increased risk of tooth decay ■​ Saponifiable lipids break down
○​ Excess: Fluorosis (white spots on teeth) into smaller molecules in basic
●​ Copper aqueous solution.
○​ Functions: Helps form red blood cells, aids ○​ Nonsaponifiable lipids (cannot be
in iron absorption, supports immune hydrolyzed) - Cholesterol, steroid
function hormones, bile acids, eicosanoids.
○​ Sources: Shellfish, nuts, seeds, whole ■​ Nonsaponifiable lipids do not
grains, chocolate react with water and remain
○​ Deficiency: Anemia, weakened immune intact.
system
●​ Selenium

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MIDTERMS | CHEM113 2ND SEMESTER

TYPES OF FATTY ACIDS

●​ Fatty acids are naturally occurring monocarboxylic
acids, usually with an even number of carbon atoms
and an unbranched chain. PHYSICAL PROPERTIES OF FATTY ACIDS
●​ Rarely found free in nature, usually part of complex
lipids. ●​ Physical properties of fatty acids & lipids depend on
●​ Classified by chain length: carbon chain length & degree of unsaturation.
○​ Long-chain: C12–C26 ●​ Water solubility:
○​ Medium-chain: C8–C10 ○​ A direct function of carbon length -
○​ Short-chain: C4–C6 ↓ Solubility = ↑ Carbon chain length.
●​ Saturated & Unsaturated Fatty Acids: ○​ Short-chain fatty acids - Some solubility
○​ Saturated (SFA) - Only single bonds in the due to the polar carboxyl group.
carbon chain. ○​ Long-chain fatty acids - Insoluble as the
○​ Monounsaturated (MUFA) - One double nonpolar hydrocarbon chain dominates.
bond, usually in cis configuration. ○​ Short-chain fatty acids are sparingly
○​ Polyunsaturated (PUFA) - Two or more soluble because of the carboxylic acid
double bonds (up to six). polar group.
●​ Fatty acids are commonly named using IUPAC & ●​ Melting points:
common names: ○​ Determined by carbon chain length &
○​ Example: Linoleic acid (IUPAC: degree of unsaturation.
cis,cis-9,12-octadecadienoic acid). ○​ ↑ Carbon chain length = ↑ Melting point.
●​ Shorthand Notation for Fatty Acids: ○​ ↓ Melting point = ↑ Degree of unsaturation.
○​ Two numbers (carbon atoms:double ○​ Saturated fatty acids - Higher melting
bonds). points than unsaturated with the same
○​ Example: 18:0 (C18, no double bonds), carbon count.
18:2 (C18, two double bonds). ○​ More double bonds = Lower melting point.
○​ Delta (Δ) notation specifies double-bond ○​ Long-chain saturated fatty acids - Solids
positions: 18:3(Δ9,12,15). at room temperature.
●​ Omega Notation: ○​ Long-chain unsaturated fatty acids -
○​ Omega (ω) system counts from the methyl Liquids at room temperature.
(non-carboxyl) end. ●​ Lower melting points in unsaturated fatty acids:
○​ Omega-3 - Double bond 3 carbons from ○​ Cis double bonds create bends in the
methyl end. carbon chain.
○​ Omega-6 - Double bond 6 carbons from ○​ Prevents tight packing of molecules.
methyl end. ○​ More double bonds = Weaker
●​ Omega-6 Fatty Acids share a common methyl-end intermolecular forces = Lower melting
structural feature. point.
●​ Fatty acids serve as key building blocks in
ENERGY-STORAGE LIPIDS: TRIACYLGLYCEROLS
biochemically important lipid structures.
●​ Carbohydrate glycogen - most widespread
energy-storage material within cells
●​ Triacylglycerols store energy in specialized cells
called adipocytes, mainly found under the skin, in
the abdominal cavity, mammary glands, and around
organs.

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MIDTERMS | CHEM113 2ND SEMESTER
●​ Triacylglycerols store energy more efficiently than
glycogen because they can be packed into a small
volume.
●​ Triacylglycerols are triesters, consisting of glycerol
(a three-carbon alcohol) and three fatty acids.
●​ Esterification reaction: One glycerol + Three fatty
acids → Triacylglycerol + Three water molecules.
●​ Structural representation:
○​ Block diagram - Shows four subunits
(glycerol + three fatty acids).
○​ General structural formula - Highlights
three ester linkages.
●​ Acyl group: The portion of a carboxylic acid
remaining after the -OH group is removed. DIETARY CONSIDERATIONS AND
●​ Triacylglycerols contain three acyl groups attached TRIACYLGLYCEROLS
to glycerol and are also known as triglycerides.
●​ Simple triacylglycerol - Formed when all three ●​ High dietary fat intake is linked to obesity, diabetes,
fatty acids are identical (rare in nature). cancer, hypertension, & heart disease.
●​ Mixed triacylglycerol - Contains different fatty ●​ Nations with high-fat diets generally have higher
acids (most biochemically important heart disease rates, but exceptions exist (e.g.,
triacylglycerols). Mediterranean countries, Inuit people).
●​ Common in biological systems: One fatty acid is ●​ "Good Fats" vs. "Bad Fats":
saturated, one monounsaturated, and one ○​ Saturated fats (SFAs) - "Bad fats",
polyunsaturated. increase heart disease risk.
○​ Monounsaturated fats (MUFAs) - "Good
FATS AND OILS fats", reduce heart disease & breast
●​ Fats and oils are naturally occurring mixtures of cancer risk.
triacylglycerols with various fatty acids. ○​ Polyunsaturated fats (PUFAs) - Can be
○​ Fats - Solid or semi-solid at room good or bad, depending on omega
temperature (25°C), primarily from animal classification.
sources. ●​ Recommended fat intake:
○​ Oils - Liquid at room temperature (25°C), ○​ Total fat ≤ 30% of total calories.
primarily from plant sources (except fish ○​ MUFAs ≤ 15%, PUFAs ≤ 10%, SFAs <
oils). 10%.
●​ Composition varies based on dietary and climatic ○​ Sources of MUFAs: Olive, avocado, canola
factors (e.g., corn-fed vs. peanut-fed hogs, warm oils, tree nuts, peanuts.
vs. cold climate flaxseed). ●​ Omega-3 & Omega-6 Fatty
●​ Fats contain mostly saturated fatty acids: Acids:
○​ Linear structure allows tight packing, ○​ Inuit people consume
leading to higher melting points. more omega-3 (from fish),
○​ Animal fats remain semi-liquid at body Americans consume more
temperature for movement. omega-6 (from plant oils).
●​ Oils contain more mono- & polyunsaturated ○​ Cold-water fatty fish (salmon, mackerel,
fatty acids: tuna) are high in omega-3.
○​ Cis double bonds create bends, preventing ○​ Lean warm-water fish (cod, halibut,
tight packing and resulting in lower melting snapper) contain less omega-3.
points. ○​ Overfishing has led to research on
○​ Fish oils stay liquid even in cold water, omega-3 production from algae via genetic
preventing solidification. engineering.
●​ Pure fats & oils are colorless, odorless, and
tasteless
○​ Flavors in plant oils come from trace
compounds present during processing.
●​ Higher fatty acid unsaturation = more likely to be an
oil.
○​ Exception: Coconut oil - Highly saturated
but remains liquid due to short-chain fatty
acids (e.g., lauric acid, 12:0).

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MIDTERMS | CHEM113 2ND SEMESTER
●​ Essential Fatty Acids ■​ Micelle - spherical cluster of
○​ Linoleic acid (18:2, omega-6) & Linolenic molecules in which the polar
acid (18:3, omega-3) must be obtained portions of the molecules are on
from diet. the surface, and the nonpolar
○​ Needed for membrane structure & portions are located in the interior.
biosynthesis of longer-chain omega-3 & ●​ Hydrogenation
omega-6 acids.
○​ Deficiency leads to skin irritation,
infections, dehydration, & liver
○​ Hydrogen is added to carbon-carbon
abnormalities.
double bonds, increasing saturation and
○​ Infants need essential fatty acids for
melting point.
growth; human breast milk has higher
○​ Partial hydrogenation converts liquid
content than cow’s milk.
(usually plant oils) oils into semi-solid fats
(e.g., margarine, shortening, peanut
butter).
●​ Linoleic acid → Arachidonic acid → Eicosanoids ○​ Some cis double bonds convert to trans,
(regulate blood pressure, clotting, etc.). forming trans fats, which pose health risks.
●​ Oxidation

●​ Linolenic acid → EPA & DHA (important for brain &

eye development).
●​ Fat Substitutes (Artificial Fats) ○​ Carbon-carbon double bonds present in
○​ Developed to create low-fat, low-calorie the fatty acids residues of a triacyl-glycerol
foods. are subject to oxidation with molecular
○​ Mimic fat texture & taste but are not true oxygen (from air) as the oxidizing agent.
lipids. ○​ Oxygen reacts with double bonds,
CHEMICAL REACTION OF TRIACYLGLYCEROLS breaking them and forming aldehydes and
carboxylic acids, leading to rancidity and
●​ Hydrolysis bad odor.
○​ Reverse of esterification, requires acid, ○​ Commercially prepared foods use
base, or enzymes. antioxidants (Vitamin C, E, BHA, BHT) to
○​ Acidic hydrolysis → Glycerol + Free fatty prevent oxidation.
acids. ○​ Sweat oxidation by skin bacteria
○​ Basic hydrolysis → Glycerol + Fatty acid contributes to body odor.
salts.
○​ In digestion, enzymes stepwise remove MEMBRANE LIPIDS: PHOSPHOLIPIDS
fatty acids, forming monoacylglycerol or
free glycerol (complete hydrolysis).
●​ Saponification
○​ A reaction carried out in an alkaline (Basic)
solution.
○​ In the first step, triacylglycerol undergoes ●​ Cell membranes contain 80% lipids, mainly
hydrolysis, breaking its ester bonds and phospholipids, sphingoglycolipids, and cholesterol.
forming glycerol and three fatty acids ●​ Phospholipids, the most abundant membrane
lipids, consist of fatty acids, a phosphate group, a
.
platform (glycerol or sphingosine), and an alcohol.
○​ In the second step, the fatty acids react
●​ Glycerophospholipids have two fatty acids, a
with a strong base (NaOH or KOH),
phosphate, and an alcohol attached to glycerol.
producing fatty acid salts (soap) and water.
●​ Sphingophospholipids have one fatty acid, a
phosphate, and an alcohol attached to sphingosine.
○​ Soap-making was historically done using ●​ Phospholipids vs. Triacylglycerols:
wood ash (KOH) and lard, but modern Phospholipids are polar (membrane lipids),
production occurs under high pressure and triacylglycerols are nonpolar (energy storage).
temperature using sodium carbonate ●​ Glycerophospholipids
(Na₂CO₃).
○​ Soap cleans by forming micelles, where
nonpolar dirt gets trapped in the
hydrophobic interior.

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MIDTERMS | CHEM113 2ND SEMESTER
○​ Phosphoric acid is the parent source for ○​ Undergo hydrolysis & saponification, with
the minus one charged phosphate group amide linkages behaving like ester
used in the formation of linkages.
glycerophospholipid. ○​ Sphingomyelins (choline-attached
○​ Contain four ester linkages, undergo sphingophospholipids) are important in
hydrolysis and saponification, yielding five myelin sheath (nerve protection &
reaction products. insulation).
○​ Phosphate group comes from phosphoric
MEMBRANE LIPIDS: SPHINGOGLYCOLIPIDS
acid.
○​ Attached alcohol can be choline, ●​ Sphingoglycolipids are membrane
ethanolamine, or serine, forming lipids containing a fatty acid and a
phosphatidylcholines, carbohydrate attached to
phosphatidylethanolamines, or sphingosine.
phosphatidylserines. ●​ Fatty acid is linked via an amide
○​ Phosphatidyl group – fatty acid, glycerol, bond, while a monosaccharide or
and phosphate portions of a oligosaccharide is attached via a
glycerophospholipid. glycosidic bond.
●​ Structure & Function ●​ Structure: "Head and two tails"
○​ Head = Polar (phosphate + alcohol) like glycerophospholipids and
○​ Tails = Nonpolar (fatty acids) → dual sphingophospholipids, but the head contains a
polarity. sugar instead of phosphate-alcohol.
●​ Undergo hydrolysis & saponification, breaking
amide and glycosidic linkages.
●​ Types of Sphingoglycolipids
○​ Cerebrosides - Contain a single sugar
○​ Phosphatidylcholines (lecithins) - Cell
(glucose or galactose); simplest
membranes, emulsifiers (mayonnaise, ice
sphingoglycolipids.
cream, custards); found in egg yolks and
■​ Found in the brain (7% of dry
soybeans
mass) & myelin sheath.
○​ Phosphatidylethanolamines &
○​ Gangliosides - More complex, with a
phosphatidylserines (cephalins) - Blood
branched chain of up to seven
clotting, found in heart, liver, brain.
monosaccharides residue
■​ Present in gray matter & myelin
sheath.
○​ All membrane lipids contain at least one
fatty acid residue.

MEMBRANE LIPIDS: CHOLESTEROL

●​ Sparingly soluble in water blood; thus, protein
carrier system is needed for cholesterol distributions
(lipoproteins)
●​ Sphingophospholipids ●​ Specific compound rather than a family of
compounds
●​ There are no fatty acid residues present and neither
glycerol nor sphingosine is present as the platform
molecule.
●​ Cholesterol is a steroid membrane lipid, unlike
phospholipids and sphingoglycolipids, which are
families of compounds.

○​ Based on sphingosine (18-carbon amino

dialcohol).
○​ Fatty acid attached via amide linkage,
phosphate via ester linkage, and alcohol to
○​ Steroid - lipid whose structure is based on
phosphate.
a fused-ring system that involves three

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MIDTERMS | CHEM113 2ND SEMESTER
6-membered rings and one 5-membered CELL MEMBRANES
ring
■​ Most steroids have an oxygen
functional group (=O or -OH) at
carbon 3 and some kind of side
chain at carbon 17.

●​ Lipid-based structure that separates the cell interior

from the external environment.
●​ Functions: Controls substance movement,
maintains cell integrity.
●​ Structure: C27 steroid with a fused-ring system ●​ Composition: Up to 80% lipids (phospholipids,
(three 6-membered + one 5-membered ring), an glycolipids, cholesterol), plus proteins and
-OH group at C3, a double bond between C5 and carbohydrates.
C6, and a branched side chain at C17. ●​ Lipid Bilayer
●​ No fatty acids, glycerol, or sphingosine. ○​ Formed by phospholipids and
●​ Function & Distribution sphingoglycolipids.
○​ Found in cell membranes (up to 25% by ○​ Hydrophilic heads face water; hydrophobic
mass), nerve tissue, and brain (10% of dry tails face inward.
mass). ○​ Held by intermolecular forces (not covalent
○​ Limited water solubility due to small polar bonds), allowing fluidity.
head (-OH) and nonpolar steroid nucleus. ○​ Unsaturated fatty acids prevent tight
○​ Most cholesterol is synthesized in the liver packing, keeping the membrane flexible.
(800–1000 mg/day), while some comes ○​ Cholesterol regulates rigidity, fitting
from diet. between fatty acid chains.
○​ Excess dietary intake raises total body ●​ Membrane Proteins
cholesterol. ○​ Integral proteins - Penetrate the bilayer,
●​ Transport & Health Impact some fully spanning it.
○​ Cholesterol is transported by lipoproteins: ○​ Peripheral proteins - Located on
■​ LDL (Low-Density Lipoprotein) membrane surface, interacting via weak
→ carries cholesterol from liver to forces.
tissues ("bad cholesterol" – ○​ Functions: Transport molecules, act as
increases blood cholesterol). receptors.
■​ HDL (High-Density Lipoprotein) ●​ Membrane Carbohydrates
→ carries excess cholesterol from ○​ Found on outer membrane, attached to
tissues to liver ("good cholesterol" proteins (glycoproteins) or lipids
– lowers blood cholesterol). (glycolipids).
○​ ↑ LDLs + ↓ HDLs = ↑ Blood cholesterol ○​ Function as cell markers, aiding in cell
levels recognition.
■​ High LDL levels contribute to ●​ Transport Across Membranes
atherosclerosis, where plaque
buildup in arteries can lead to
heart attacks.
○​ To lower cholesterol, reduce animal
products (meat, dairy) and eat more fruits
and vegetables.

○​ Passive Transport – Diffusion from high

to low concentration, no energy required
(O₂, H₂O, urea).
○​ Facilitated Transport – Uses carrier
proteins, no energy required (glucose,
chloride ions).
○​ Active Transport – Moves against
gradient, requires ATP energy, uses
"pumps" (sodium, potassium ions).

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MIDTERMS | CHEM113 2ND SEMESTER

EMULSIFICATION LIPIDS: BILE ACIDS ○​ Estrogens (female sex hormones) -

Synthesized in ovaries and adrenal cortex
■​ Regulate menstrual cycle and
secondary sex characteristics.
■​ Stimulate mammary gland
development during pregnancy.
○​ Androgens (male sex hormones) -
Synthesized in testes and adrenal cortex
●​ Bile acids are cholesterol derivatives that function ■​ Promote male secondary sex
as lipid emulsifiers in digestion. characteristics and muscle
●​ Produced in the liver, stored in the gallbladder, and growth.
released into the small intestine. ○​ Progestins (pregnancy hormones) -
●​ Emulsifier - substance that can disperse and Synthesized in ovaries and placenta
stabilize water-insoluble substances as colloidal ■​ Prepare uterus for implantation
particles in an aqueous solution. and suppress ovulation.
●​ Bile acids - cholesterol derivatives that functions as ●​ Synthetic Steroids
a lipid-emulsifying agent in the aqueous ○​ Oral contraceptives - Combine synthetic
environment of the digestive tract. estrogen and progestin to prevent
●​ Bile - medium through which bile acids are supplied ovulation.
to the small intestine. ○​ Morning-after pill (RU-486) - Blocks
○​ A fluid containing emulsifying agents that progesterone, terminating pregnancy.
is secreted by the liver, stored in the ○​ Anabolic steroids - Synthetic androgens
gallbladder, and released into the small that enhance muscle growth, but have
intestine during digestion serious side effects.
○​ Contains bile pigments (from hemoglobin ●​ Adrenocorticoid Hormones
breakdown), cholesterol, electrolytes ○​ Produced by the adrenal glands (above
(bicarbonate ions) the kidneys), these regulate ion balance
●​ Structure & Function and glucose metabolism.
○​ Modified cholesterol with: ■​ Mineralocorticoids - Regulate
■​ Tri- or dihydroxy groups. Na+ and K+ balance (e.g.,
■​ Oxidized carboxyl group at C17. aldosterone).
■​ Amide linkage with glycine or ■​ Glucocorticoids - Regulate
taurine, increasing polarity and glucose metabolism and reduce
solubility. inflammation (e.g., cortisol and
○​ Examples: Cholic acid, 7-deoxycholic acid, cortisone).
12-deoxycholic acid. ●​ Cortisone &
○​ Key bile acids: Glycocholic acid (glycine), Prednisolone: Used to
Taurocholic acid (taurine). treat inflammatory
●​ Role in Digestion diseases like rheumatoid
○​ Breaks down dietary lipids into smaller arthritis.
droplets for enzyme action.
MESSENGER LIPIDS: EICOSANOIDS
○​ Increases cholesterol solubility in bile to
prevent crystallization. ●​ Eicosanoids are oxygenated C20 fatty acid
○​ Bile contains bile acids, bile pigments derivatives that act as local messenger lipids. They
(hemoglobin breakdown), cholesterol, and are not true hormones since they act only in the
electrolytes. tissues where they are synthesized and have a
●​ Gallstones short lifespan. The main precursor is arachidonic
○​ Form when cholesterol crystallizes due to acid (20:4).
bile imbalance. ●​ Physiological Effects
○​ 80% of gallstones in Western countries are ○​ Inflammation response
mostly cholesterol. ○​ Pain and fever production
○​ Blood pressure regulation
MESSENGER LIPIDS: STEROID HORMONES ○​ Blood clotting induction
●​ Steroid hormones are cholesterol derivatives that ○​ Reproductive function (e.g., labor
function as chemical messengers in the body. They induction)
are divided into sex hormones and adrenocorticoid ○​ Sleep/wake cycle regulation
hormones. ●​ Types of Eicosanoids
●​ Sex Hormones ○​ Prostaglandins - C20-fatty-acid derivative
that contains a cyclopentane ring and
oxygen-containing function groups

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MIDTERMS | CHEM113 2ND SEMESTER
■​ Eighth and twelfth carbon atoms ○​ Highly nonpolar, making waxes
of fatty acid become connected to water-insoluble and water-repellent.
form a five-membered ring = ●​ Functions
prostaglandin ○​ Humans & animals - Secreted by skin
■​ Regulate body temperature, glands to protect hair and skin, keeping
inhibit gastric juice secretion, them pliable and lubricated.
increase secretion of mucus ○​ Fur & feathers - Provide water repellency,
protection in stomach, smooth especially for aquatic birds, helping them
muscle activity, electrolyte retain body heat in cold water.
balance, pain, and inflammation. ○​ Plants - A thin wax layer on leaves
■​ Aspirin inhibits prostaglandin prevents excessive water loss and protects
synthesis, reducing inflammation against parasites (important for plants in
and fever. arid regions).
○​ Thromboxanes - A messenger lipid that is ○​ Insects - The wax coating helps reduce
C20-fatty-acid derivative that contains a water loss due to their high
cyclic ether ring and oxygen-containing surface-area-to-volume ratio.
functional group ●​ Uses
■​ Bound between carbons 8 & 12 ○​ Carnauba wax - Extracted from Brazilian
■​ Promote blood clot formation and palm trees, known for its hardness and
platelet aggregation. high-gloss finish. Used in car wax, floor
■​ Produced by blood platelets. polish, shoe polish, and cosmetics.
○​ Leukotrienes - Contain three conjugated ○​ Lanolin - A mixture of waxes from sheep
double bonds wool, commonly used in skin creams and
■​ Found in white blood cells ointments to retain moisture and soften the
(leukocytes). skin.
■​ Linked to inflammation and ○​ Beeswax - Secreted by bees, used in
allergy responses. candles, cosmetics, and polishes.
■​ Drugs that inhibit leukotriene ●​ Synthetic Alternatives
synthesis are used to treat ○​ Carbowax - A polyether-based synthetic
asthma and allergic reactions. wax, now used in place of biological waxes
in cosmetics and ointments.
PROTECTIVE-COATING LIPIDS: BIOLOGICAL WAXES
●​ Other Waxes
○​ Mineral waxes (also called paraffin
waxes) - Derived from petroleum
●​ Biological waxes are lipids composed of a processing, consisting of long-chain
monoester of a long-chain fatty acid and a alkanes.
long-chain alcohol. ■​ Uses: Found in candles,
●​ Unlike fats and oils, which are triesters, waxes waterproof coatings for milk
contain only one ester functional group. cartons, waxed paper, and
●​ They are highly nonpolar, making them polishes.
water-insoluble and hydrophobic. ○​ Blended waxes: Some products combine
●​ Found in plants, animals, and humans, providing biological and mineral waxes, such as
protective and water-repellent properties. beeswax candles.
●​ They are resistant to degradation, making them
useful in natural and industrial applications.
●​ Used in pharmaceuticals, cosmetics, polishes,
waterproof coatings, and lubricants.
●​ Structure

○​ Fatty acids - Usually saturated, containing

14–36 carbon atoms.
○​ Alcohols - Saturated or unsaturated,
containing 16–30 carbon atoms.
○​ Ester linkage - Connects the fatty acid
and alcohol.

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MIDTERMS | CHEM113 2ND SEMESTER

SAPONIFIABLE AND NON SAPONIFIABLE LIPIDS ○​ Include:

■​ Cholesterol
●​ Saponification is a hydrolysis reaction in a basic ■​ Bile Acids
solution that breaks down certain lipids into smaller ■​ Steroid Hormones
molecules. ■​ Eicosanoids
●​ Lipids are classified based on their ability to ○​ Cholesterol, bile acids, and steroid
undergo saponification: hormones share a four-ring steroid
○​ Saponifiable lipids - Undergo hydrolysis nucleus.
in a basic solution. ○​ Eicosanoids are derived from fatty acids
○​ Nonsaponifiable lipids - Do not hydrolyze but remain a single molecule.
in basic solution.
IV. NUCLEIC ACID
TYPES OF NUCLEIC ACIDS
●​ Two types of nucleic acids are found in higher
organisms: Deoxyribonucleic acid (DNA) &
Ribonucleic acid (RNA).
●​ Deoxyribonucleic acid (DNA)
○​ Found mainly in the nucleus.
○​ Stores & transfers genetic information.
○​ Controls cell functions indirectly.
○​ Passed from existing cells to new cells
during cell division.
●​ Ribonucleic acid (RNA)
○​ Occurs in all parts of a cell.
○​ Functions in protein synthesis, which is
essential for cellular functions.
●​ All nucleic acids are unbranched polymers.
●​ A nucleic acid is an unbranched polymer made up
of nucleotides.

NUCLEOTIDE BUILDING BLOCKS

●​ A nucleotide is a three-subunit
●​ Saponifiable Lipids molecule in which a pentose sugar is
○​ Contain ester, amide, or glycosidic bonded to both a phosphate group
linkages that can be broken by hydrolysis. and a nitrogen-containing
○​ Include: heterocyclic base.
■​ Triacylglycerols – three ester ●​ More complex than monosaccharides & amino
linkages. acids.
■​ Glycerophospholipids – four ●​ A nucleotide consists of three subunits:
ester linkages. ○​ Pentose sugar.
■​ Sphingophospholipids – one ○​ Phosphate group.
amide and two ester linkages. ○​ Nitrogen-containing heterocyclic base.
■​ Sphingoglycolipids – one
Pentose Sugars
amide, one ester, and one
●​ The sugar unit in a
glycosidic linkage.
nucleotide is either ribose
■​ Biological Waxes – one ester
or 2'-deoxyribose.
linkage.
●​ Difference between the
○​ Hydrolysis breaks these linkages,
two sugars:
releasing their building blocks (fatty acids,
○​ Ribose (RNA): Has a –OH group on
alcohols, phosphate groups, sugars).
carbon 2'.
○​ Fatty acids released in saponification
○​ 2'-deoxyribose (DNA): Has a –H atom
become fatty acid salts due to the basic
instead of –OH at carbon 2' (deoxy- means
environment.
“without oxygen”).
●​ Nonsaponifiable Lipids
●​ RNA contains ribose, while DNA contains
○​ Do not contain ester, amide, or glycosidic
2'-deoxyribose.
linkages, so they cannot be broken down
by hydrolysis.
○​ Contain only one building block and do not
require linkages for assembly.

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MIDTERMS | CHEM113 2ND SEMESTER
Nitrogen-Containing Heterocyclic Bases ■​ Purine bases attach through N-9,
●​ Five nitrogen-containing while pyrimidine bases attach
heterocyclic bases are through N-1.
nucleotide components. ■​ The bond connecting the sugar
●​ Three bases are derivatives and base is a β-N-glycosidic
of pyrimidine (a monocyclic linkage.
base with a six-membered 2.​ A molecule of water is formed as the two
ring): molecules bond together; a condensation
○​ Thymine (T) - 5-methyl-2,4-dioxo reaction occurs.
derivative. ●​ Eight nucleosides exist in nucleic acids:
○​ Cytosine (C) - 4-amino-2-oxo derivative.
○​ Uracil (U) - 2,4-dioxo derivative.
●​ Two bases are derivatives of purine (a bicyclic
base with fused five- & six-membered rings):
○​ Adenine (A) - 6-amino derivative of
purine. ●​ Nucleosides are named based on the base they
○​ Guanine (G) - 2-amino-6-oxo purine contain:
derivative. ○​ Pyrimidine bases (-idine suffix): Cytidine,
●​ Both heterocyclic compounds are bases because thymidine, uridine.
they contain amine functional groups (secondary or ○​ Purine bases (-osine suffix): Adenosine,
tertiary) & amine functional groups exhibit basic guanosine.
behavior (proton acceptors; Section 17.6). ○​ Prefix "deoxy-" is used if deoxyribose is
●​ Adenine (A), Guanine (G), & Cytosine (C) are present; no prefix if ribose is present.
found in both DNA & RNA. ●​ Examples:
●​ Uracil (U) is found only in RNA, while Thymine (T) ○​ Ribose + adenine → adenosine.
usually occurs only in DNA. ○​ Deoxyribose + thymine → deoxythymidine.
NUCLEOTIDE FORMATION
●​ Addition of a phosphate group to a nucleoside
produces a nucleotide.
●​ Important characteristics of nucleotide
Phosphate formation:
●​ Phosphate, the third 1.​ The phosphate group is attached to the
component of a sugar at the C-5' position through a
nucleotide, is derived phosphate-ester linkage.
from phosphoric acid 2.​ As with nucleoside formation, a molecule
(H₃PO₄). of water is produced in nucleotide
●​ Under cellular pH conditions, the phosphoric acid formation.
loses two of its hydrogen atoms, forming a ■​ Overall, two molecules of water
hydrogen phosphate ion (HPO₄²⁻). are produced when combining a
NUCLEOTIDE FORMATION sugar, base, and phosphate into a
nucleotide.
●​ The formation of a nucleotide from a sugar, base, ●​ Nucleotides are named by appending
and phosphate occurs in two steps: "5'-monophosphate" to the nucleoside name.
1.​ The pentose sugar and nitrogen-containing ○​ Example: Adenosine + phosphate →
base react to form a nucleoside (not a Adenosine 5'-monophosphate (AMP).
nucleotide, s versus t). ●​ Abbreviations for nucleotides:
2.​ The nucleoside reacts with a phosphate ○​ Use one-letter base symbols (A, C, G, T,
group to form a nucleotide. U) + MP for monophosphate.
●​ Nucleotides are the building blocks of nucleic acids. ○​ A lowercase "d" is added when
NUCLEOSIDE FORMATION deoxyribose is present.
○​ Examples:
●​ A nucleoside is a two-subunit molecule where a ■​ AMP = Adenosine
pentose sugar is bonded to a nitrogen-containing 5'-monophosphate.
heterocyclic base. ■​ dAMP = Deoxyadenosine
●​ Important characteristics of nucleoside formation: 5'-monophosphate.
1.​ The base is always attached to C-1' of the
sugar (the anomeric carbon atom), which
is always in a β-configuration.

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MIDTERMS | CHEM113 2ND SEMESTER
sugar molecules through a 3',5'-phosphodiester
linkage:
○​ One phosphoester bond at the 5' carbon of
one sugar.
○​ One phosphoester bond at the 3' carbon of
the other sugar.
2.​ Nucleotide chains have directionality:
○​ The 5' end carries a free phosphate group
PRIMARY NUCLEIC ACID STRUCTURE attached to the 5' carbon atom.
○​ The 3' end carries a free hydroxyl group
attached to the 3' carbon atom.
○​ By convention, nucleotide sequences are
read from the 5' end to the 3' end.
3.​ Acidic nature of nucleic acids:
○​ Each nonterminal phosphate group in the
●​ Nucleic acids are polymers where the repeating
backbone carries a -2 charge.
units (monomers) are nucleotides.
○​ The original phosphoric acid molecule had
●​ Nucleotide units are linked through
three –OH groups; two are used in
sugar–phosphate bonds.
3',5'-phosphodiester linkages, while the
●​ The structure consists of a chain of alternating
remaining –OH exhibits acidic behavior.
sugar and phosphate groups, with base groups
○​ This acidic property is why nucleic acids
protruding at regular intervals.
are called acids.
●​ Two general types of nucleic acids:
○​ Ribonucleic acid (RNA): A nucleotide
polymer where each monomer contains
ribose, a phosphate group, and one of the
bases (adenine, cytosine, guanine, or
uracil).
○​ Deoxyribonucleic acid (DNA): A
nucleotide polymer where each monomer
contains deoxyribose, a phosphate group,
and one of the bases (adenine, guanine,
cytosine, or thymine).
●​ The sugar–phosphate
chain is called the nucleic
Specifying the Primary Structure
acid backbone.
●​ The sequence of nucleotide bases is written using
○​ DNA backbone:
one-letter abbreviations, starting with the 5' end of
Alternating
the strand.
phosphate &
●​ Example: 5'-T–G–C–A-3'.
deoxyribose units.
○​ RNA backbone: Parallels Between Nucleic Acid & Protein Structure
Alternating phosphate & ribose units. 1.​ DNA, RNA, and proteins all have backbones that do
not vary in structure.
BASE SEQUENCE IN NUCLEIC ACID 2.​ The sequence of attachments to backbones (bases
●​ The sequence of bases attached to the sugar units in nucleic acids, R groups in proteins) distinguishes
distinguishes different DNA & RNA molecules. different DNA, RNA, and protein molecules.
●​ Only four bases are found in any given nucleic 3.​ Both nucleic acid polymer chains & protein polymer
acid: chains have directionality:
○​ Adenine (A), Guanine (G), Cytosine (C) in ○​ Nucleic acids: 5' end & 3' end.
both DNA & RNA. ○​ Proteins: N-terminal end & C-terminal
○​ Thymine (T) in DNA, Uracil (U) in RNA. end.
●​ The primary structure of nucleic acids refers to the
sequence in which nucleotides are linked together.
●​ The sugar–phosphate backbone remains constant,
meaning the primary structure depends only on the
base sequence.
Key Features of Nucleic Acid Structure
1.​ Each nonterminal phosphate group of the
sugar–phosphate backbone is bonded to two

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MIDTERMS | CHEM113 2ND SEMESTER
○​ Wherever T is in one strand, A is in the
other.

●​ Knowing one strand’s sequence allows

determination of the complementary strand.
●​ Example:
○​ 5'-A–A–G–C–T–A–G–C–T–T–A–C–T-3'.
○​ Complementary strand:
3'-T–T–C–G–A–T–C–G–A–A–T–G–A-5'.
●​ Hydrogen Bonding in DNA
○​ Hydrogen bonds stabilize the double helix,
despite being weak individually.
○​ Base stacking interactions further stabilize
THE DNA DOUBLE HELIX
DNA.
●​ Nucleic acids have secondary (3D) structures, ●​ Base Stacking Interactions
which differ for DNA & RNA. ○​ Bases stack like coins, keeping their rings
●​ Base composition data showed a pattern: parallel.
○​ %A = %T and %C = %G. ○​ Hydrophobic interactions & London forces
○​ Example: Human DNA contains 30% A, between stacked bases stabilize DNA.
30% T, 20% G, 20% C. ○​ These interactions contribute as much, if
●​ Watson & Crick's 1953 model explained this pattern not more, to stability than hydrogen bonds.
using a double-helix structure. ●​ The Term "DNA Molecule"
Structure of the DNA Double Helix ○​ Technically a misnomer for two reasons:
1.​ DNA carries negative charges due to
phosphate groups, making it an ionic
species rather than a neutral molecule.
2.​ The two DNA strands are held together by
noncovalent hydrogen bonds, not covalent
bonds.
○​ Despite this, the term "DNA molecule" is
widely accepted and commonly used.
REPLICATION OF DNA MOLECULES

●​ Two polynucleotide strands are coiled around each ●​ DNA carries genetic information & must be copied
other like a spiral staircase. exactly before cell division.
●​ Sugar–phosphate backbones are the outer ●​ DNA replication is the process where DNA
"banisters", while bases extend inward. molecules produce exact copies of themselves.
●​ Strands are connected by hydrogen bonds between ●​ Base pairing in the DNA double helix is key to
complementary bases. understanding this process.
●​ Strands are antiparallel: DNA Replication Overview
○​ One runs 5' → 3', the other 3' → 5'. ●​ The two strands of DNA
Base Pairing separate, acting as
●​ Only purine-pyrimidine pairs fit inside the helix due templates for new strands.
to size constraints. ●​ Each original strand pairs
●​ A–T & G–C are the only stable pairings. with free nucleotides to
●​ Complementary base pairing explains equal form two identical daughter DNA molecules.
amounts of A = T & G = C. ●​ Steps of replication:
●​ DNA strands are complementary, not identical: 1.​ DNA helicase unwinds the double helix, breaking
○​ Wherever G is in one strand, C is in the hydrogen bonds (like a zipper).
other. ○​ The unwinding site is called the replication
fork.

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MIDTERMS | CHEM113 2ND SEMESTER
2.​ Free nucleotides in the nucleus pair with OVERVIEW OF PROTEIN SYNTHESIS
complementary bases of the template strand.
○​ A pairs with T, C pairs with G. ●​ DNA controls protein synthesis, determining
3.​ DNA polymerase: hereditary traits.
○​ Ensures ​correct base pairing. ●​ Two phases of protein synthesis:
○​ Catalyzes phosphodiester bond formation
between nucleotides.
○​ Moves along the template strand, ○​ Transcription (DNA → RNA).
repeating the process. ○​ Translation (RNA → Protein).
4.​ Two daughter DNA molecules form, each RIBONUCLEIC ACIDS
containing:
○​ One original (parent) strand. ●​ Although RNA is single-stranded, it can fold into
○​ One newly synthesized strand double-helical regions if complementary bases align
(semi-conservative replication). (hairpin loop structure).
●​ (RNA) vs. DNA
The Replication Process in Detail
○​ Sugar: RNA has ribose, DNA has
deoxyribose.
○​ Base: RNA has uracil (U) instead of
thymine (T).
○​ Structure: RNA is single-stranded, DNA is
double-stranded.
○​ Size: RNA is smaller (75 to a few thousand
1.​ DNA polymerase can only synthesize DNA in the 5'
nucleotides).
→ 3' direction.
●​ Types of RNA
○​ The leading strand is synthesized
○​ hnRNA (Heterogeneous Nuclear RNA) -
continuously in the 5' → 3' direction.
Formed directly from DNA transcription,
○​ The lagging strand is synthesized in short
later processed into mRNA.
fragments (Okazaki fragments) as DNA
○​ mRNA (Messenger RNA) - Carries
unwinds.
genetic instructions for protein synthesis.
○​ DNA ligase joins Okazaki fragments,
○​ snRNA (Small Nuclear RNA) - Assists in
closing the gaps (nicks) in the lagging
converting hnRNA → mRNA.
strand.
○​ rRNA (Ribosomal RNA) - Combines with
2.​ DNA replication can start at multiple points.
proteins to form ribosomes, where protein
○​ Replication bubbles form at several interior
synthesis occurs.
sites of the DNA molecule.
○​ tRNA (Transfer RNA) - Delivers amino
○​ Replication proceeds bidirectionally,
acids to ribosomes for protein assembly.
allowing faster duplication of large DNA
molecules. TRANSCRIPTION: RNA SYNTHESIS
●​ DNA directs hnRNA/mRNA synthesis, which carries
genetic instructions.
●​ A gene is a DNA segment coding for a specific
hnRNA/mRNA molecule.
●​ Human genes contain 1,000–3,500 nucleotides.
Steps in Transcription
●​ Anticancer Drugs & DNA Replication 1.​ RNA polymerase unwinds DNA, exposing a gene.
○​ Some anticancer drugs inhibit DNA 2.​ Free ribonucleotides align along the template
replication, preventing cancer cell division. strand, forming base pairs:
●​ Chromosomes ○​ A–U, G–C (U replaces T in RNA).
○​ An individual DNA molecule bound to a 3.​ RNA polymerase links nucleotides, forming hnRNA.
group of proteins 4.​ Transcription stops at a termination signal, and:
○​ After replication, DNA interacts with ○​ hnRNA & RNA polymerase detach.
proteins called histones, forming ○​ DNA rewinds into its original double-helix
chromosomes. form.
○​ Chromosomes = DNA + histone proteins. ●​ Template vs. Informational Strand
○​ Composition: 15% DNA, 85% protein. ○​ Template strand: The DNA strand used
for hnRNA/mRNA synthesis (copied 3' →
5').
○​ Informational strand: The non-template
DNA strand, which gives the same

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MIDTERMS | CHEM113 2ND SEMESTER
sequence as the RNA produced (except U Features of the Genetic Code
replaces T). 1.​ Degenerate: Many amino acids have more than
●​ Post-Transcription Processing: Formation of one codon (e.g., Arg, Leu, Ser have 6 codons
mRNA each).
○​ hnRNA is converted to mRNA by: 2.​ Synonymous codons differ only in the third
■​ Removing introns (non-coding base, allowing flexibility in mutations.
regions). 3.​ Nearly universal: The same codons specify the
■​ Joining exons (coding regions) same amino acids in almost all organisms.
together. 4.​ Start codon: AUG (Methionine) initiates protein
○​ Splicing is facilitated by snRNA & synthesis.
spliceosomes, which remove introns and 5.​ Stop codons: UAG, UAA, UGA signal the end of
join exons. translation.
●​ Alternative Splicing
ANTICODONS AND tRNA MOLECULES
○​ A single gene can produce multiple
proteins through alternative splicing. ●​ tRNA molecules act as
○​ Different exons are combined in various intermediaries, delivering amino
ways, increasing protein diversity. acids to mRNA during protein
○​ Explains how 20,000–25,000 genes can synthesis.
generate 150,000–200,000 proteins. ●​ Each tRNA carries one specific
●​ Human Transcriptome amino acid and has a cloverleaf
○​ Transcriptome - All mRNA molecules that structure.
can be generated from a genome. ●​ Two key tRNA features:
○​ mRNA diversity is more important than 1.​ 3' end binds to an amino
gene count in determining cell behavior. acid via an ester bond,
○​ Different cells process DNA differently, catalyzed by
producing different mRNAs & proteins. aminoacyl-tRNA synthetase.
○​ A single gene can be spliced in up to 8 2.​ Anticodon: A three-nucleotide sequence
different ways, dramatically increasing the that is complementary to an mRNA codon,
number of possible proteins. ensuring correct amino acid placement.
●​ Base pairing between the anticodon (tRNA) &
THE GENETIC CODE
codon (mRNA) ensures proper translation of the
●​ mRNA base sequence determines the amino acid genetic code into a protein.
sequence in a protein.
TRANSLATION: PROTEIN SYNTHESIS
●​ Codon: A three-nucleotide sequence in mRNA that
codes for a specific amino acid. ●​ Translation is the process by which mRNA codons
●​ Since there are only 4 bases (A, C, G, U), a are deciphered and a particular protein molecule is
three-base codon system allows 64 possible synthesized.
combinations, more than enough to code for 20 ●​ The substances needed for translation: mRNA,
amino acids. tRNA, amino acids, ribosomes, & enzymes.
●​ 61 codons specify amino acids, while 3 are stop ●​ Ribosome - an rRNA–protein complex that serves
codons that signal the end of protein synthesis. as the site of translation.
●​ Marshall Nirenberg & Har Gobind Khorana won the ●​ The number of ribosomes in a higher organism’s
1968 Nobel Prize for deciphering the genetic code. cell varies from hundreds of thousands to millions.

Ribosome Structure
1.​ Contains four rRNA molecules & about 80 proteins
packed into two subunits (one small, one large).
2.​ Each subunit is 65% rRNA & 35% protein by mass.
3.​ Active site (for protein synthesis) is in the large
subunit.
4.​ The active site is mainly rRNA, making the
ribosome a ribozyme.
5.​ mRNA binds to the small subunit during translation.
Steps in Translation
1.​ tRNA Activation
○​ Amino acid interacts with
ATP, forming a
high-energy complex.

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MIDTERMS | CHEM113 2ND SEMESTER
○​ The complex reacts with tRNA, attaching Efficiency of mRNA Utilization
the amino acid at the 3' end via ester ●​ Multiple ribosomes attach to one mRNA, forming
linkage. polyribosomes (polysomes).
2.​ Initiation ●​ This allows multiple proteins to be synthesized at
once, reducing cell energy usage.

○​ mRNA binds to the ribosome (small

subunit).
○​ First codon (AUG) aligns at the P site.
○​ tRNA with methionine (anticodon UAC) MUTATIONS
binds to AUG.
●​ Mutation - An error in base sequence in a gene
○​ Large ribosomal subunit attaches, forming
that persists during DNA replication.
the initiation complex.
●​ Can cause altered genetic information, affecting
3.​ Elongation
amino acid sequence during protein synthesis.
●​ Mutagens - Substances or agents that cause
genetic changes
○​ Radiation - Ultraviolet light, X-rays,
radioactivity, cosmic rays.
■​ UV light from the sun can cause
skin cancer by altering DNA in
skin cells.
○​ Chemical Agents - Nitrous acid (HNO₂)
○​ New tRNA enters the A site, carrying the
causes deamination of nitrogen bases.
next amino acid.
■​ Example: Cytosine → Uracil,
○​ Peptide bond forms between amino acids
altering codons (e.g., CGG →
at the P & A sites.
UGG).
○​ tRNA at P site leaves, and ribosome shifts
■​ Nitrites, nitrates, & nitrosamines
(translocation).
in food can form nitrous acid in
○​ The process repeats, forming a growing
the body, leading to DNA
polypeptide chain.
damage.
4.​ Termination
○​ Stop codon (UAA, UAG, UGA) appears. DNA Repair Mechanism
○​ No tRNA matches the stop codon. ●​ Repair enzymes recognize & replace altered bases.
○​ Polypeptide is cleaved & released from the ●​ Most altered DNA is repaired, but some mutations
ribosome. persist.
5.​ Post-Translation Processing Point Mutation
○​ Methionine is removed from most proteins. ●​ One nucleotide is substituted for another.
○​ Covalent modifications occur (e.g., ●​ Effects vary:
disulfide bridges form). ●​ No effect.
○​ Folding completes, forming the final ●​ Changes protein primary structure.
protein shape. ●​ Stops protein synthesis.

NUCLEIC ACIDS AND VIRUSES

●​ Viruses - Small disease-causing agents, not truly
alive, needing host cells to reproduce.
●​ Structure - Contains DNA or RNA, surrounded by a
protein coat.
●​ Replication - Attaches to host cell, injects genetic
material, and hijacks the cell’s machinery to
reproduce.
●​ Viral Diseases - Includes cold, flu, mumps,
measles, rabies, smallpox, hepatitis, AIDS.
●​ Retroviruses
○​ Contain RNA instead of DNA.
○​ Use reverse transcriptase to create viral
DNA inside the host.

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MIDTERMS | CHEM113 2ND SEMESTER
○​ Example: HIV (AIDS virus) - Attacks ○​ Tnr
helper T cells, weakening the immune ○​ Recombinant DNA is inserted into
system. bacteria.
●​ Vaccines ○​ Bacteria replicate, creating identical
○​ Contain weakened/inactive virus to clones.
stimulate antibody production. ○​ Artificial DNA synthesis allows scientists to
○​ Used against polio, mumps, smallpox, design custom genes.
yellow fever.
THE POLYMERASE CHAIN REACTION
●​ Genetic Engineering
○​ Intentional modification of an ●​ PCR is a method for rapidly producing multiple
organism’s DNA to alter traits. copies of a DNA nucleotide sequence.
○​ First genetically modified organisms ●​ Billions of copies of a specific DNA sequence
(GMOs): (gene) can be produced in a few hours.
■​ Bacteria (1973), mice (1974), ●​ Requires only a few chemicals, a container, and a
insulin-producing bacteria (1982). source of heat (now fully automated).
■​ Genetically modified crops (since ●​ DNA in small quantities can be amplified to
1994) - Herbicide tolerance, amounts large enough for analysis.
insect resistance. Applications of PCR
●​ Used for diagnosing diseases and detecting
pathogens in the body.
●​ Helps in prenatal diagnosis of genetic disorders like
muscular dystrophy and cystic fibrosis.
●​ Definitive method for detecting the AIDS virus.
●​ Applications of Genetic Engineering ●​ Valuable tool in forensic investigations (DNA
○​ Crops - Herbicide-resistant corn, fingerprinting).
insect-resistant cotton, enzyme-modified ●​ A single drop of blood, semen, or hair strand from a
corn for ethanol production. crime scene can be amplified and compared with
○​ Medical - Insulin, human growth hormone, suspects' DNA.
therapeutic proteins. Key Components of PCR
○​ Genetic modifications - Extending ●​ DNA polymerase - an enzyme present in all living
tomato shelf life, pest-resistant mustard organisms that helps replicate DNA.
plants. ●​ Primer - a short starter nucleotide chain that binds
●​ Recombinant DNA (rDNA) to a complementary DNA strand.
●​ Deoxyribonucleotides - building blocks added by
DNA polymerase to replicate DNA.
Basic Steps in PCR
●​ Denaturation - Original DNA is heated to separate
its strands.
●​ Annealing - Primers bind to complementary
strands of the DNA template.
○​ Combines DNA from different organisms. ●​ Extension - DNA polymerase adds nucleotides to
○​ Uses plasmids from bacteria (E. coli). build new DNA strands.
○​ Steps of rDNA production: ●​ Repeat - Process is repeated multiple times,
1.​ Dissolve bacterial cell membrane creating millions of copies of the original DNA.
to release DNA.
2.​ Isolate plasmids.
3.​ Use restriction enzymes to cut
plasmid DNA.
4.​ Extract gene from another
organism.
5.​ Splice gene into plasmid using
DNA ligase.
6.​ Insert recombinant plasmid into
bacteria (transformation).
●​ Restriction Enzymes
○​ Cut DNA at specific sequences.
○​ Creates “sticky ends” that help combine
foreign DNA with plasmids.
●​ Transformation & Cloning

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