Biochemistry of Biomolecules

Part I. Carbohydrates

1.1 Definition and general characteristics

Carbohydrates are organic compounds containing carbon, hydrogen, and oxygen. They include simple sugars and complex carbohydrate polymers and serve as energy sources, energy reserves, structural components, and participants in cellular recognition.

Many carbohydrates have the approximate empirical formula (CH2O)n, although this formula does not apply to every carbohydrate.

Examples: Glucose, fructose, lactose, sucrose, starch, glycogen, and cellulose.

Importance of carbohydrates in the human body

• Provide energy for cellular activities.
• Maintain blood glucose availability, particularly for the brain and red blood cells.
• Store energy as glycogen in the liver and skeletal muscles.
• Form parts of DNA, RNA, ATP, and other biologically important molecules.
• Contribute to cell-surface recognition through glycoproteins and glycolipids.
• Participate in the structure of the extracellular matrix.

1.2 Classification of carbohydrates

Carbohydrates are classified mainly according to the number of monosaccharide units and their chemical structure.

A. Monosaccharides

Monosaccharides are the simplest carbohydrates and cannot be hydrolyzed into smaller carbohydrate units.

They generally contain a single carbonyl group and multiple hydroxyl groups.

Classification by carbonyl group

• Aldoses: contain an aldehyde group in their open-chain form. Examples: glucose and galactose.
• Ketoses: contain a ketone group in their open-chain form. Example: fructose.

Classification by number of carbon atoms

Class	Number of carbon atoms	Example
Triose	3	Glyceraldehyde
Tetrose	4	Erythrose
Pentose	5	Ribose
Hexose	6	Glucose
Heptose	7	Sedoheptulose

Glucose is an aldohexose, while fructose is a ketohexose.

B. Oligosaccharides and disaccharides

Oligosaccharides contain a small number of monosaccharide units. Disaccharides contain exactly two monosaccharide units joined by a glycosidic bond.

Disaccharide	Components	Important source or role
Sucrose	Glucose + fructose	Table sugar
Lactose	Glucose + galactose	Milk sugar
Maltose	Glucose + glucose	Produced during starch digestion
Trehalose	Glucose + glucose	Found in fungi and some other organisms

C. Polysaccharides

Polysaccharides are large carbohydrate polymers containing many monosaccharide units.

They are classified into:

• Homopolysaccharides: contain one type of monosaccharide unit.
• Heteropolysaccharides: contain two or more different types of monosaccharide-derived units.

Important examples include the following.

1. Glycogen

• Major carbohydrate storage polymer in humans.
• Stored primarily in the liver and skeletal muscles.
• Contains α(1→4) glycosidic linkages in its chains and α(1→6) linkages at branch points.
• Its branching allows rapid mobilization of glucose units.

2. Starch

• Principal carbohydrate storage form in plants.
• Consists of amylose and amylopectin.
• Amylose is predominantly linear, with α(1→4) linkages.
• Amylopectin is branched, with α(1→4) chains and α(1→6) branch points.

3. Cellulose

• Structural polysaccharide of plant cell walls.
• Contains β(1→4) glycosidic linkages.
• Humans lack cellulase, the enzyme required to digest cellulose.
• Functions as dietary fiber in humans.

1.3 Chemical structure of carbohydrates

A. Open-chain and cyclic structures

Monosaccharides can exist in open-chain and cyclic forms. In aqueous solution, glucose predominantly exists in cyclic forms produced by an intramolecular reaction between its carbonyl group and a hydroxyl group.

The cyclic structure may form:

• Pyranose: a six-membered ring.
• Furanose: a five-membered ring.

Glucose commonly occurs as glucopyranose, whereas fructose can occur in both furanose and pyranose forms.

B. Alpha and beta anomers

When a monosaccharide cyclizes, the former carbonyl carbon becomes the anomeric carbon. Two configurations can form at this carbon, called alpha and beta anomers.

In D-glucose's Haworth representation:

• α-D-glucose has its anomeric hydroxyl group opposite the direction of the C5 substituent.
• β-D-glucose has its anomeric hydroxyl group on the same side as the C5 substituent.

The two forms can interconvert in solution through the open-chain form, a process called mutarotation.

C. Glycosidic bond formation

A glycosidic bond connects the anomeric carbon of a sugar to an appropriate atom in another molecule, commonly oxygen.

The linkage determines important properties, including whether an enzyme can digest the carbohydrate.

For example, human digestive enzymes can hydrolyze the α-linkages in starch, but humans cannot digest the β(1→4) linkages of cellulose.

1.4 Biological functions of carbohydrates

1. Energy production: Glucose is oxidized through metabolic pathways to produce ATP.

2. Energy storage: Glycogen provides a rapidly mobilizable glucose reserve.

3. Structural function: Carbohydrate chains in glycosaminoglycans contribute to extracellular matrix structure and hydration.

4. Cell recognition: Carbohydrate chains on glycoproteins and glycolipids contribute to cell adhesion, immune recognition, and blood-group antigens.

5. Nucleotide formation: Ribose and deoxyribose are components of RNA and DNA.

6. Protein-sparing effect: Adequate carbohydrate availability can reduce the need to use amino acids for glucose production.

1.5 Clinical and laboratory significance

• Diabetes mellitus: Characterized by chronic hyperglycemia resulting from impaired insulin secretion, insulin action, or both.
• Hypoglycemia: Low blood glucose that may cause sweating, confusion, seizures, or loss of consciousness.
• Lactose intolerance: Reduced lactase activity leads to bloating, abdominal discomfort, and diarrhea after lactose consumption.
• Glycogen storage diseases: Inherited enzyme defects disrupt glycogen synthesis or breakdown.
• Abnormal carbohydrate metabolism: Can contribute to metabolic disorders and altered blood glucose regulation.

Laboratory applications: Blood glucose measurement, oral glucose tolerance testing, and HbA1c measurement are used in diabetes evaluation. HbA1c estimates average glycemia over approximately the preceding 2–3 months.

Part II. Proteins

2.1 Definition and general characteristics

Proteins are nitrogen-containing biological macromolecules composed of amino acids linked through peptide bonds. They are essential for cellular structure, enzymatic catalysis, transport, immunity, movement, and physiological regulation.

Most proteins contain carbon, hydrogen, oxygen, and nitrogen; some also contain sulfur, phosphorus, or other elements.

Examples include hemoglobin, albumin, collagen, insulin, immunoglobulins, and enzymes.

2.2 Amino acids: the building blocks of proteins

An amino acid generally contains four groups attached to a central alpha carbon:

1. Amino group.
2. Carboxyl group.
3. Hydrogen atom.
4. Variable side chain (R group).

At physiological pH, amino acids generally exist as zwitterions, carrying both a positively charged amino group and a negatively charged carboxyl group.

The R group determines the amino acid's polarity, charge, size, and chemical behavior.

Classification of amino acids

A. According to side-chain properties

Category	Examples	Properties
Nonpolar	Glycine, alanine, valine, leucine	Often occur in hydrophobic protein regions
Polar, uncharged	Serine, threonine, glutamine	Participate in hydrogen bonding
Acidic	Aspartate, glutamate	Usually negatively charged at physiological pH
Basic	Lysine, arginine, histidine	Can accept protons or carry positive charge

B. According to nutritional requirements

• Essential amino acids: Must be obtained through the diet in adequate amounts. Examples include leucine, lysine, valine, and tryptophan.
• Nonessential amino acids: Can normally be synthesized by the body. Examples include alanine and aspartate.
• Conditionally essential amino acids: May require increased dietary supply during growth, illness, or specific metabolic conditions. Examples include arginine and glutamine in certain circumstances.
• As many as 300 amino acids are found in nature but only 20 amino acids are standard as they are coded by genes (genetic codes).
• Other non-standard amino acids are modified amino acids and called non-protein amino acids.
• Amino acids are colorless, crystalline solid which are usually soluble in water but insoluble in organic solvent.

2.3 Peptide bond formation

A peptide bond is a covalent amide bond formed between the carboxyl group of one amino acid and the amino group of another.

Two amino acids form a dipeptide. Additional amino acids produce oligopeptides and polypeptides.

A polypeptide has two ends:

• N-terminus: The end with a free amino group.
• C-terminus: The end with a free carboxyl group.

During protein synthesis, ribosomes join amino acids in a specific sequence according to the genetic information carried by messenger RNA.

2.4 Four levels of protein structure

1. Primary structure

The linear sequence of amino acids in a polypeptide chain. Amino acids are joined by peptide bonds.

Clinical example: A single amino acid substitution in beta-globin produces the abnormal hemoglobin associated with sickle cell disease.

2. Secondary structure

Local folding patterns of the polypeptide backbone, principally alpha helices and beta-pleated sheets. Hydrogen bonds between backbone groups stabilize these structures.

3. Tertiary structure

The overall three-dimensional conformation of a single polypeptide chain. It is stabilized by hydrophobic interactions, hydrogen bonds, ionic interactions, van der Waals forces, and sometimes disulfide bonds.

4. Quaternary structure

The arrangement of multiple polypeptide subunits into a functional protein complex.

Example: Adult hemoglobin (HbA) contains two alpha and two beta subunits.

Not every protein possesses quaternary structure; this level occurs only when multiple polypeptide subunits associate.

2.5 Classification of proteins

Proteins can be classified according to their shape and chemical composition.

A. According to shape

Type	Characteristics	Examples
Fibrous	Elongated, often structural, generally less soluble	Collagen, keratin
Globular	Compact, folded, often soluble	Albumin, hemoglobin, many enzymes
Membrane proteins	Embedded in or associated with biological membranes	Receptors, ion channels

B. According to composition

Simple proteins: Yield amino acids as their principal products upon hydrolysis. Examples include albumins and globulins.

Conjugated proteins: Contain a protein component combined with a non-protein component called a prosthetic group or associated non-protein moiety.

Examples include:

• Glycoproteins: proteins associated with carbohydrate groups.
• Lipoproteins: complexes of proteins and lipids.
• Hemoproteins: proteins containing heme, such as hemoglobin.
• Metalloproteins: proteins containing metal ions.

2.6 Denaturation of proteins

Denaturation is the disruption of a protein's native three-dimensional conformation without necessarily breaking its peptide backbone.

Causes

• Excessive heat.
• Extreme pH.
• Organic solvents.
• Detergents.
• Certain heavy metal ions.

Consequences

• Loss of biological activity.
• Changes in solubility.
• Altered physical properties.
• Aggregation or precipitation in some conditions.

For example, heating egg white causes its proteins to unfold and aggregate. In laboratory assays, denaturation can be deliberately used to precipitate proteins or prepare specimens for analysis.

2.7 Functional roles of proteins

Function	Example	Biological role
Catalysis	Amylase	Accelerates biochemical reactions
Oxygen transport	Hemoglobin	Transports oxygen in blood
Plasma transport	Albumin	Transports substances and maintains oncotic pressure
Structural support	Collagen	Provides tensile strength to connective tissue
Hormonal regulation	Insulin	Regulates glucose metabolism
Immunity	Immunoglobulins	Participate in immune defense
Contraction	Actin and myosin	Enable muscle contraction
Storage	Ferritin	Stores iron
Coagulation	Fibrinogen	Precursor of fibrin in clot formation

2.8 Clinical and laboratory significance of proteins

• Albumin: Evaluated in liver disease, renal protein loss, inflammation, and nutritional assessment.
• Hemoglobin: Measured in the investigation of anemia and other hematological disorders.
• C-reactive protein (CRP): Increases in many inflammatory conditions.
• Immunoglobulins: Investigated in immune disorders and selected infectious and hematological diseases.
• Urinary proteins: Persistent proteinuria may indicate renal disease.
• Serum protein electrophoresis: Separates serum proteins into characteristic fractions and helps investigate monoclonal gammopathies and other disorders.

Common laboratory investigations include total serum protein, albumin, calculated globulin, albumin-to-globulin ratio, urine protein, and serum protein electrophoresis.

Part III. Lipids

3.1 Definition and general characteristics

Lipids are a diverse group of organic molecules that are generally poorly soluble in water but soluble in nonpolar organic solvents.
They include triglycerides, phospholipids, glycolipids, cholesterol, and steroid hormones.
Unlike proteins and nucleic acids, lipids do not form one uniform class of polymers with a common repeating monomer.

3.2 Classification of lipids

A. Simple lipids

Simple lipids are esters of fatty acids with alcohols.

• Triacylglycerols (triglycerides): Consist of glycerol and three fatty acids.
• Waxes: Contain long-chain fatty acids esterified with long-chain alcohols.

B. Complex lipids

Complex lipids contain fatty acids and additional chemical groups.

• Phospholipids: Major components of biological membranes.
• Glycolipids: Contain carbohydrate groups and contribute to membrane organization and cell recognition.
• Lipoproteins: Complexes of lipids and proteins that transport lipids in blood.

C. Derived lipids

Derived lipids are substances obtained through the hydrolysis or breakdown of simple and compound lipids. This broad category includes fatty acids, glycerol, sterols, and lipid-derived signaling molecules.

Examples include cholesterol, steroid hormones, and eicosanoids.

3.3 Fatty acids

Fatty acids consist of a hydrocarbon chain with a terminal carboxyl group.

Classification by saturation

Type	Structural feature	Example
Saturated	No carbon–carbon double bonds	Palmitic acid
Monounsaturated	One carbon–carbon double bond	Oleic acid
Polyunsaturated	Two or more double bonds	Linoleic acid

Cis double bonds introduce bends in many unsaturated fatty acid chains and can influence membrane fluidity.

Essential fatty acids

Humans cannot synthesize certain fatty acids in sufficient amounts because they lack the enzymes needed to introduce double bonds at specific positions.

The two essential fatty acids are:

• Linoleic acid (omega-6).
• Alpha-linolenic acid (omega-3).

They are required for normal membrane function and serve as precursors for other biologically important lipids.

3.4 Triglycerides

Triglycerides, also called triacylglycerols, consist of one glycerol molecule esterified with three fatty acids.

Biological functions

1. Long-term energy storage in adipose tissue.
2. Thermal insulation.
3. Cushioning and protection of internal organs.
4. Supply of fatty acids for energy metabolism.

Triglycerides provide approximately 9 kcal per gram, making them a concentrated energy source.

3.5 Phospholipids and biological membranes

Phospholipids are amphipathic molecules with both hydrophilic and hydrophobic regions.
Many phospholipids contain a glycerol backbone, two fatty acid chains, and a phosphate-containing polar head group.

In an aqueous environment, phospholipids can spontaneously organize into bilayers. The hydrophilic heads face the aqueous surroundings, while the hydrophobic tails face inward.

The resulting membrane:

• Separates intracellular and extracellular environments.
• Regulates movement of substances.
• Provides a platform for membrane proteins.
• Participates in signaling and cell recognition.

Important distinction: Phospholipids are structural components of membranes, whereas triglycerides primarily serve as energy-storage molecules.

3.6 Cholesterol and steroids

Cholesterol is a sterol characterized by four fused hydrocarbon rings, a hydroxyl group, and a hydrocarbon side chain.

Functions of cholesterol

• Maintains cell membrane organization and influences membrane fluidity.
• Acts as a precursor for steroid hormones.
• Provides the precursor for bile acid synthesis.
• Is converted through a multistep pathway into vitamin D precursors.

Steroid hormones derived from cholesterol include cortisol, aldosterone, estrogen, progesterone, and testosterone.

Lipoprotein transport

Because triglycerides and cholesterol are poorly soluble in aqueous plasma, they are transported in lipoprotein particles.

Lipoprotein	Principal function
Chylomicrons	Transport dietary triglycerides from the intestine
VLDL	Transport triglycerides produced by the liver
LDL	Delivers cholesterol to peripheral tissues
HDL	Participates in cholesterol transport back toward the liver and other pathways

LDL and HDL are not simply “bad” and “good” cholesterol; they are distinct particles with different compositions and functions. Elevated LDL cholesterol is an established risk factor for atherosclerotic cardiovascular disease.

3.7 Biological functions of lipids

Energy storage: Triglycerides store energy efficiently in adipose tissue.
Membrane structure: Phospholipids, cholesterol, and glycolipids contribute to membrane organization.
Insulation and protection: Adipose tissue reduces heat loss and cushions organs.
Hormonal activity: Steroid hormones regulate metabolism, reproduction, and electrolyte balance.
Vitamin absorption: Dietary lipids support the absorption of vitamins A, D, E, and K.
Cell signaling: Eicosanoids and other lipid mediators participate in inflammation, vascular regulation, and other cellular responses.

3.8 Clinical and laboratory significance of lipids

• Hypertriglyceridemia: Very high triglyceride concentrations increase the risk of acute pancreatitis.
• Elevated LDL cholesterol: Contributes to atherosclerotic cardiovascular disease.
• Fat malabsorption: May result in deficiencies of fat-soluble vitamins.
• Fatty liver disease: Excess accumulation of triglycerides in hepatocytes may occur in metabolic dysfunction and other conditions.

The lipid profile commonly includes total cholesterol, triglycerides, HDL cholesterol, and LDL cholesterol. Results should be interpreted with other clinical risk factors.

Part IV. Nucleic Acids

4.1 Definition

Nucleic acids are biological macromolecules responsible for storing, transmitting, and expressing genetic information.

The two major types are:

• DNA: Deoxyribonucleic acid.
• RNA: Ribonucleic acid.

Both are polymers of nucleotides connected through phosphodiester bonds.

4.2 Components of nucleic acids

A nucleotide contains three components:

1. A pentose sugar.
2. A nitrogenous base.
3. One or more phosphate groups.

A nucleoside contains a sugar and a nitrogenous base but no phosphate group.

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Nitrogenous bases

Nitrogenous bases are classified into two groups.

Purines

• Adenine (A).
• Guanine (G).

Pyrimidines

• Cytosine (C).
• Thymine (T).
• Uracil (U).

DNA contains adenine, thymine, guanine, and cytosine. RNA generally contains adenine, uracil, guanine, and cytosine.

4.3 DNA structure

DNA usually consists of two polynucleotide strands arranged in a double helix.

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Main structural characteristics

• The sugar is deoxyribose.
• The two strands run in opposite directions and are therefore antiparallel.
• Nucleotides within each strand are linked by 3′–5′ phosphodiester bonds.
• Adenine pairs with thymine through two hydrogen bonds.
• Guanine pairs with cytosine through three hydrogen bonds.
• The sugar-phosphate backbone lies on the outside of the double helix, while the bases are oriented inward.

Functions of DNA

1. Stores hereditary information.
2. Replicates before cell division.
3. Serves as a template for RNA synthesis.
4. Contains genes that encode proteins and functional RNA molecules.
5. Transmits genetic information to daughter cells.

4.4 RNA structure and types

RNA generally contains ribose and is usually single-stranded, although it can fold into complex secondary and tertiary structures.

Its bases are adenine, uracil, guanine, and cytosine.

Major types of RNA

RNA type	Full name	Main function
mRNA	Messenger RNA	Carries genetic information for protein synthesis
tRNA	Transfer RNA	Delivers amino acids to the ribosome
rRNA	Ribosomal RNA	Forms the structural and catalytic core of ribosomes
miRNA	MicroRNA	Regulates gene expression
siRNA	Small interfering RNA	Participates in sequence-specific gene silencing

Messenger RNA

mRNA carries information copied from DNA to the ribosome, where its codons help determine the amino acid sequence of a protein.

Transfer RNA

tRNA carries specific amino acids and uses its anticodon to recognize complementary codons in mRNA during translation.

Ribosomal RNA

rRNA combines with ribosomal proteins to form ribosomes and plays a direct catalytic role in peptide-bond formation.

4.5 Comparison of DNA and RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Typical structure	Double-stranded	Usually single-stranded
Main role	Genetic information storage	Gene expression and regulation
Chemical stability	Generally more stable	Generally less stable
Location in human cells	Mainly nucleus; also mitochondria	Nucleus, cytoplasm, ribosomes, and other compartments

4.6 Central dogma of molecular biology

The central dogma describes the usual flow of genetic information.

DNA

Replication

RNA

Transcription

Protein

Translation

Replication: DNA is copied to produce DNA.

Transcription: RNA is synthesized using DNA as a template.

Translation: Ribosomes use mRNA information to synthesize a polypeptide.

Some viruses use reverse transcription, in which RNA serves as a template for DNA synthesis.

4.7 Biological significance of nucleic acids

• DNA stores genetic information.
• RNA enables the expression and regulation of genetic information.
• Nucleotides also participate in energy transfer, signaling, and metabolic reactions.
• ATP provides energy for many cellular processes.
• Cyclic AMP acts as an intracellular signaling molecule.
• Nucleotides are components of important coenzymes, including NAD⁺ and FAD.

4.8 Clinical and laboratory significance

Nucleic acids are fundamental to molecular diagnostics.

• PCR: Amplifies selected DNA sequences.
• Reverse-transcription PCR: Converts RNA into complementary DNA before amplification.
• Real-time PCR: Monitors nucleic acid amplification during the reaction.
• DNA sequencing: Identifies nucleotide sequences and genetic variants.
• Molecular pathogen detection: Detects genetic material from infectious agents.
• Genetic testing: Investigates inherited disorders and selected cancer-associated variants.

These methods are widely used in infectious disease diagnosis, hematological malignancy investigation, inherited disease testing, and biomedical research.