Biomolecules, Cell Structure, Membrane Function, and Metabolism: Study Notes for Biology College Students

The Structure and Function of Large Biological Molecules

Biomolecules: Classes and Organization

Biomolecules are organic molecules essential to living organisms, classified into four primary groups: carbohydrates, proteins, nucleic acids, and lipids. These molecules are often organized as monomers (single units) and polymers (chains of monomers), except for lipids, which do not form true polymers.

• Monomers: Individual building blocks (e.g., glucose, amino acids, nucleotides).

• Polymers: Long chains of monomers linked by covalent bonds (e.g., starch, proteins, DNA).

Building and Breaking Down Polymers

• Dehydration Synthesis: Forms covalent bonds between monomers, building polymers by removing water.

• Hydrolysis: Breaks covalent bonds in polymers by adding water, releasing energy.

Carbohydrates

Carbohydrates are carbon-based molecules with many hydroxyl groups, also known as saccharides. They are classified by size:

• Monosaccharides: Single carbohydrate units (e.g., glucose).

• Oligosaccharides: 2–20 covalently linked monosaccharides.

• Polysaccharides: More than 20 monosaccharides (e.g., starch, cellulose).

Glycosidic bonds link monosaccharides in polysaccharides. Functions:

• Structural support: Cellulose in plant cell walls, chitin in exoskeletons.

• Energy storage: Starch in plants, glycogen in animals.

Proteins

Proteins are functional molecules made of one or more polypeptides, each folded into a specific three-dimensional structure.

• Amino acids: Monomers of proteins, each with a central carbon, hydrogen, amino group, carboxyl group, and unique R-group.

• Peptide bonds: Covalent bonds linking adjacent amino acids.

• Directionality: Proteins have N-terminal and C-terminal ends.

Classification of Amino Acid Chains

Term	Length of Amino Acid Chain
Amino acid	Single protein unit or monomer
Oligopeptide	2–20 covalently linked amino acids
Peptide	Less than 50 covalently linked amino acids
Polypeptide	Greater than 50 covalently linked amino acids
Protein	One or multiple polypeptide chains in their folded functional forms

Denatured Proteins & Chaperones

• Denatured proteins: Lose their shape and function due to environmental changes (pH, temperature, salt concentration).

• Chaperone proteins: Assist in refolding denatured proteins.

• Protein misfolding: Implicated in diseases like cystic fibrosis, Alzheimer's, Parkinson's, and mad cow disease.

Nucleic Acids

Nucleic acids (DNA and RNA) are polymers that store and encode genetic information.

• Nucleotides: Monomers consisting of a phosphate group, pentose sugar, and nitrogenous base.

• Phosphodiester bonds: Covalent bonds linking nucleotides.

• Directionality: 5' phosphate end and 3' hydroxyl end.

Nitrogenous bases:

• Pyrimidines: Single-ringed (cytosine, thymine, uracil).

• Purines: Double-ringed (adenine, guanine).

DNA: Double helix, stores hereditary information, uses deoxyribose sugar, bases: A, T, C, G. RNA: Single-stranded, uses ribose sugar, bases: A, U, C, G.

Lipids

Lipids are hydrophobic biomolecules, highly diverse in structure and function.

• Fatty acids: Hydrocarbon chains with a carboxyl group; can be saturated (solid, only single bonds), unsaturated (liquid, double bonds), or trans fats (artificial, unhealthy).

• Triglycerides: Three fatty acids linked to glycerol; main fat storage in animals.

• Phospholipids: Major component of cell membranes; amphipathic with hydrophilic head and hydrophobic tails.

• Steroids: Four fused carbon rings; cholesterol is a key membrane component.

• Waxes: Fatty acids bound to long-chain alcohols; protection and water loss prevention.

A Tour of the Cell

Microscopy

• Light microscopes: Use light to magnify small objects.

• Electron microscopes: Use electrons for higher magnification; SEM for external surfaces, TEM for internal structures.

Prokaryotic vs. Eukaryotic Cells

Domains of Life	Cell Type	Nucleus	Organelles	Cell Size	Cellularity
Bacteria	Prokaryotic	Absent	Absent	Small (1 μm)	Unicellular
Archaea	Prokaryotic	Absent	Absent	Small (1 μm)	Unicellular
Eukarya	Eukaryotic	Present	Present	Large (100 μm)	Unicellular or Multicellular

Cellular Organelles

• Nucleus: Stores DNA, surrounded by nuclear envelope, contains nucleolus.

• Endoplasmic Reticulum (ER): Rough ER (ribosome-coated, protein synthesis), Smooth ER (lipid synthesis).

• Golgi Apparatus: Modifies, sorts, and packages proteins.

• Lysosomes: Digestive enzymes, found in animal cells.

• Peroxisomes: Break down toxic compounds, found in all eukaryotes.

• Central Vacuole: Storage and turgor pressure in plant cells.

Energy-Related Organelles

Mitochondria

Mitochondria are the site of cellular respiration, producing ATP from food sources.

• Two membranes: outer and folded inner (cristae).

• Matrix: contains enzymes, ribosomes, and mitochondrial DNA.

• Intermembrane space: region between membranes.

Chloroplasts

Chloroplasts are the site of photosynthesis in plant cells, converting sunlight into sugars.

• Two membranes: inner and outer.

• Stroma: matrix with DNA, ribosomes, enzymes.

• Thylakoids: sacs containing chlorophyll.

• Granum: stacks of thylakoids.

• Stomata: pores for gas exchange.

Cytoskeleton

The cytoskeleton is a network of proteins providing cell shape, structure, movement, and transport.

• Microfilaments (Actin): Smallest, cellular movement/division.

• Intermediate Filaments: Variable proteins, structural support.

• Microtubules: Largest, transport vesicles.

Cell Junctions

Cell junctions allow direct interaction between neighboring cells.

Junction Type	Description
Tight	Membrane protein links cells, creating a leak-proof barrier (animal cells).
Anchoring (Desmosomes)	Intermediate filaments anchor neighboring cells (animal cells).
Gap	Protein channels connect cytoplasms of two animal cells.
Plasmodesmata	Gaps in cell walls connect cytoplasms of two plant cells.

Membrane Structure and Function

Biological Membranes

Biological membranes are phospholipid bilayers with embedded proteins and cholesterol, forming a fluid mosaic.

• Phospholipids: Amphipathic, major component.

• Integral membrane proteins: Span the bilayer.

• Peripheral membrane proteins: Located on the membrane's perimeter.

Membrane Protein Functions

Membrane proteins perform diverse functions:

• Recognition: Cell identification.

• Anchorage: Cytoskeleton and ECM anchoring.

• Transduction: Signal molecule receptors.

• Transport: Molecular transport across membrane.

• Linkage: Connects cells via protein linkage.

• Enzymes: Catalyze enzymatic processes.

Membrane Fluidity

Factors affecting membrane fluidity:

• Temperature

• Saturation of fatty acids

• Cholesterol content (fluidity buffer)

Concentration Gradients and Diffusion

• Concentration gradient: Difference in substance concentration between two areas.

• Diffusion: Movement from high to low concentration (down gradient).

Membrane Transport

Biological membranes are selectively permeable.

• Passive transport: No energy required; includes simple and facilitated diffusion.

• Active transport: Requires energy (ATP); moves molecules against gradient.

• Transport proteins: Uniporters (one molecule, one direction), symporters (multiple molecules, same direction), antiporters (multiple molecules, opposite directions).

Osmosis

Passive diffusion of water across membranes; direction depends on tonicity (hypotonic, isotonic, hypertonic).

• Water moves from hypotonic to hypertonic solutions.

• Osmoregulation maintains solute and water balance.

Bulk Transport

• Exocytosis: Movement out of the cell via vesicle fusion.

• Endocytosis: Movement into the cell via vesicle formation; includes phagocytosis (solid), pinocytosis (liquid), receptor-mediated endocytosis (specific).

An Introduction to Metabolism

Metabolism and Metabolic Pathways

Metabolism is the sum of all chemical reactions in an organism, organized into metabolic pathways.

• Catabolic pathways: Release energy by breaking down complex molecules (e.g., cellular respiration).

• Anabolic pathways: Use energy to build complex molecules (e.g., photosynthesis, protein synthesis).

Energy and Thermodynamics

• Potential energy: Stored energy (e.g., chemical bonds).

• Kinetic energy: Energy of motion.

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Energy conversions increase entropy (disorder).

Chemical Reactions

• Endergonic reactions: Require energy input (nonspontaneous).

• Exergonic reactions: Release energy (spontaneous).

Free energy (G): Portion of a system's energy available to do work.

• Change in free energy ($\Delta G$) determines spontaneity: $\Delta G = \Delta H - T\Delta S$

• $\Delta G = G_{final} - G_{initial}$

ATP: Cellular Energy Currency

ATP (adenosine triphosphate) powers cellular activity.

• Three components: chain of three phosphate groups, pentose sugar, adenine base.

• ATP hydrolysis releases energy, forming ADP and inorganic phosphate.

• Energy coupling: Exergonic reactions drive endergonic reactions via ATP hydrolysis.

• Phosphorylation: Transfer of phosphate group to another molecule, activating it.

Enzymes

Enzymes are biological catalysts that speed up reactions without being consumed.

• Substrates: Reactants catalyzed by enzymes.

• Activation energy ($E_a$): Minimum energy required to start a reaction; enzymes lower $E_a$.

• Enzyme-substrate complex: Substrate binds at active site.

• Cofactors: Non-protein substances required for catalysis (e.g., metal ions, coenzymes).

Enzyme Inhibition

• Competitive inhibitors: Compete for active site, block substrate binding.

• Noncompetitive inhibitors: Bind at allosteric site, alter enzyme function.

Metabolic Pathways and Feedback

• Catabolic pathways: Break down molecules, release energy.

• Anabolic pathways: Build up molecules, require energy.

• Negative feedback: Final product inhibits earlier step, decreases production.

• Positive feedback: Final product stimulates earlier step, increases production.

Additional info: Genomics and proteomics are fields studying the structure, function, and mapping of genomes and proteomes, respectively.