Biochemistry: Module 1 – Introduction to Biochemistry (Notes)

Objectives

  • Define & differentiate Biochemistry from other branches of chemistry

  • Know the components of the cell and its major biomolecules

  • Describe a virus in terms of structure, features, and existence

What is Biochemistry?

  • Biochemistry is the branch of science concerned with chemical and physiological processes and substances that occur within living organisms.

Emergence and core definition

  • Emerged as a distinct discipline around the beginning of the 20th century.

  • It integrated chemistry, physiology, and biology to investigate the chemistry of living systems by:

    • A) Studying the structure and behavior of the complex molecules found in biological material;

    • B) Understanding how these molecules interact to form cells, tissues, and whole organisms.

Biochemistry in daily life and applications

  • Medicine and Healthcare

  • Nutrition

  • Diagnostic Tests

  • Genetic Engineering

  • Biotechnology

  • Forensic Science

  • Agriculture

Fields linked to biochemistry

  • Genetics

  • Biological sciences

  • Chemistry

  • Structural Biology

  • Microbiology & Immunology

  • Developmental Biology

  • Molecular & Cellular Physiology

  • Molecular Pharmacology

  • Neurobiology

  • Pathology

Principal areas of biochemistry

  1. Structural chemistry of the components of living matter and the relationships of biological function.

  2. Metabolism: the totality of chemical reactions that occur in living matter.

  3. Molecular genetics: chemistry of processes and substances that store and transmit biological information to understand heredity and the expression of genetic information at the molecular level.

Advances in biochemistry

  • Modern refinement of biochemical techniques and development of more sophisticated, sensitive instrumentation.

  • Enabled exploration of chemical mechanisms in development and differentiation of cells.

  • Enabled study of physiology and intracellular mechanisms.

Key advances include

  • Elucidation of DNA and RNA structures and the transmission of genetic information.

  • Understanding metabolic mechanisms in cells and how nutrients are transformed.

  • Studying the transformation by which glucose, amino acids, and lipids from foods are converted into body components (anabolism) or used for energy (catabolism) via metabolic pathways.

  • Visualization of molecular changes via X-ray diffraction techniques.

  • Use of isotopic tracers in metabolic pathways.

  • Chromatographic procedures to isolate intermediates in metabolic reactions.

  • Radioimmunoassay techniques to quantify biomolecules such as insulin and hormones.

Uses of biochemistry (illustrated through application areas)

  • Nutrition: relates dietary requirements to metabolic utilization and fates of nutrients (e.g., why vitamins are essential).

  • Clinical chemistry: biochemical measurements aid diagnosis and monitoring treatment; e.g., detecting certain enzymes in blood serum indicates tissue damage.

  • Pharmacology and toxicology: studies how external chemicals affect metabolism; drugs and poisons interfere with specific metabolic pathways.

  • Environmental science: understanding herbicides/pesticides; improving selectivity and understanding resistance mechanisms.

Why biochemistry is important for science students

  • Highlights the relevance of biochemistry to future work across medicine, research, industry, and public health.

The biomolecules of life (cellular building blocks)

  • The cell is organized into levels:

    • Level 1: Monomeric units (nucleotides, amino acids, sugars).

    • Level 2: Macromolecules (proteins, nucleic acids, polysaccharides, lipids).

    • Level 3: Supramolecular complexes (e.g., chromatin, plasma membrane).

    • Level 4: The cell and its organelles.

  • Key framework: approximately $10{,}000$ kinds of biomolecules in animal and plant cells.

  • Water makes up about $50 ext{-}95 ext{\%}$ of cellular content by weight.

  • Ions such as Na$^+$, K$^+$, Ca$^{2+}$ may account for about $1 ext{\%}$.

  • Most biomolecules are organic (C, H, N, O, P, S) and are derived from hydrocarbons; their chemical properties are determined by their functional groups, often with more than one functional group.

Major biomolecules and their monomers, bonds, examples, elements, and functions

  • Carbohydrates

    • Monomers: Glucose (monosaccharides)

    • Bond: glycosidic bond

    • Examples: Starch, Cellulose

    • Elements: $C, H, O$

    • Functions: Energy source, structural component, storage (reserve) food

  • Proteins

    • Monomers: Amino acids

    • Bond: peptide bond

    • Examples: Insulin, Collagen

    • Elements: $C, H, O, N, S$

    • Functions: Enzymes, structure, movement, defense, hormones

  • Nucleic Acids

    • Monomers: Nucleotides

    • Bond: phosphodiester bond

    • Examples: DNA, RNA

    • Elements: $C, H, O, N, P$

    • Functions: Stores genetic information

  • Lipids

    • Monomers: Fatty acids and glycerol

    • Bond: ester bond

    • Examples: Fats, Oils, Waxes

    • Elements: $C, H, O$

    • Functions: Energy source, insulation, membrane components, hormones

Cells and biomolecules

  • Cells are the smallest living unit of an organism; they grow, reproduce, use energy, adapt, and respond to their environment.

  • Some cells are microscopic; a cell may be the entire organism or one of many in a multicellular organism.

  • Major cell types are Prokaryotic and Eukaryotic.

    • Prokaryotes: lack a nucleus and membrane-bound organelles (e.g., bacteria).

    • Eukaryotes: possess a membrane-bound nucleus and organelles; organisms may be multicellular or single-celled; all animals are eukaryotes; other eukaryotes include plants, fungi, protists.

Phylogeny: three domains and LUCA

  • Phylogenetic tree shows three domains of life: Eubacteria, Archaea, and Eukaryota.

  • All share a Last Universal Common Ancestor (LUCA).

  • Within Eukaryota, four kingdoms: protists, animals, fungi, and plants.

Cell structures and organelles (overview)

  • Cell Membrane (plasma membrane)

    • Separates cell from surroundings; provides shape; encloses and protects cell.

    • Selectively permeable; composed of a phospholipid bilayer with embedded proteins; components include:

    • Glycolipids, phospholipids, cholesterol, alpha-helix membrane proteins, globular proteins, and oligosaccharide side chains.

  • Cell Wall (in plants and some fungi, bacteria)

    • Surrounds plasma membrane; provides protection and support; contains pectin (gel-forming during cooking).

    • Primary cell wall and secondary cell wall with middle lamella (pectin) between walls.

  • Protoplasm

    • The jelly-like living substance of the cell; contains water, minerals, salts, and organic compounds; includes:

    • Cytoplasm: surrounds nucleus

    • Nucleoplasm/Karyoplasm: material inside the nucleus

  • Nucleus

    • Control center; governs cellular reproduction and differentiation; directs metabolic activities.

    • Parts: Nuclear membrane, Nucleolus, Chromatin, Chromosomes.

  • Endoplasmic Reticulum (ER)

    • System of double membranes forming channels; attached to cell and nuclear membranes; provides surfaces for reactions.

    • Rough ER: ribosome-studded; Smooth ER: ribosome-free.

  • Ribosomes

    • Protein factories; synthesize proteins using mRNA templates; composed of RNA and proteins; can be free or associated with ER.

  • Mitochondria

    • Powerhouse of the cell; ATP production; inner/outer membranes, matrix, inner membrane folds (cristae), ATP synthase particles.

  • Golgi Complex

    • Protein packaging factory; receives, modifies, sorts, and ships proteins; cis face and trans face; vesicle transport.

  • Centrosome

    • Contains centrioles; organizes spindle during cell division; centrioles composed of nine triplets of microtubules.

  • Lysosomes

    • Digestive compartments with hydrolytic enzymes; breakdown of food and damaged organelles; involved in autophagy.

  • Peroxisomes

    • Microbodies involved in oxidation of nutrients; detoxify hydrogen peroxide to water and oxygen.

  • Plastids (plants)

    • Large organelles; types include chromoplasts (pigments), leucoplasts (starch/oil/protein storage); chloroplasts contain chlorophyll for photosynthesis; structure includes stroma, thylakoids, and granum.

  • Vacuoles

    • Membrane-bound cavities; store fluids or granular material; types include food vacuoles and contractile vacuoles.

  • Cytoskeleton

    • Interconnected network of fibers that support internal organization, cell shape, movement, and enzyme stability.

    • Types: microfilaments, microtubules, intermediate filaments.

  • Cilia, Flagella, Microvilli

    • Cilia: short, numerous; move substances over surfaces.

    • Flagella: long, fewer; enable cell movement.

    • Microvilli: small projections increasing surface area for osmosis and absorption.

Plant vs. Animal cells (diagrams and comparisons)

  • Plant cells typically have cell walls, chloroplasts, large central vacuoles, and plasmodesmata.

  • Animal cells lack cell walls and chloroplasts but have centrioles and lysosomes; various organelles appear in both with differing abundances.

Virus: Structure, life cycle and classification

  • Viruses are infectious agents with a simple, acellular organization; they lie at the interface of living and non-living because they have properties of both.

  • They are active only inside living cells; outside, they behave as inert particles; viruses are obligate intracellular parasites.

  • The study of viruses is Virology.

Virus structure components

  • Envelope (may be present or absent): outer covering composed of proteins, lipids, and host-derived carbohydrates; spikes may be present that bind to host receptors.

  • Capsid: protein shell made of capsomeres protecting the genetic material.

  • Nucleic acid genome: DNA or RNA (can be dsDNA, ssDNA, dsRNA, or ssRNA).

  • Classification by genome type and structure: Helical, Polyhedral, Spherical, Complex.

  • Bacteriophages: viruses that infect bacteria; typically have a head (capsid) with genetic material and a tail that binds host cells; components include capsid head, collar, sheath, baseplate, and tail fibers.

Genome types (summary)

  • DNA viruses: dsDNA and ssDNA

  • RNA viruses: dsRNA and ssRNA

  • Examples include coronaviruses as +ssRNA viruses with crown-like spikes on the envelope.

Corona virus example

  • Coronaviruses are positive-sense single-stranded RNA (+ssRNA) viruses with a crown-like appearance under EM due to spike glycoproteins on the envelope.

Viral infection lifecycle (typical for an RNA virus archetype)

  • Attachment: virus binds to a host cell receptor.

  • Entry: virus or its genome enters the cell.

  • Genome replication and gene expression: genome is copied and viral proteins are expressed.

  • Assembly: new viral particles are assembled from genome copies and proteins.

  • Release: completed viral particles exit the cell to infect others.

Note

  • The lifecycle described here is representative of a ssRNA virus model; other virus types may differ in replication strategies (e.g., reverse transcription in retroviruses like HIV).

Closing

  • Recap: Biochemistry connects chemistry with biology at cellular and molecular levels; it explains structure, interactions, metabolism, and genetic information flow; it underpins our understanding of health, disease, and biotechnology.