Source: APK2105 Textbook, University of Florida
Difficulty: Introductory to Intermediate Prerequisites: Chapter 1 notes (body organisation, fluid compartments, basic cell types).
Chapter 2 zooms in from whole-body organisation to the molecular and cellular level. It covers the four major biomolecules (carbohydrates, lipids, proteins, nucleotides), the detailed structure of the cell and its organelles, how cells join together, and how proteins are synthesised from DNA. This is the chemistry-meets-biology chapter. If you are comfortable with these molecules and structures, the metabolism chapter (Ch. 3) will feel much more manageable. If you skipped general chemistry, expect to spend extra time on the biomolecules section.
The body's chemistry runs on four biomolecule classes: carbohydrates, lipids, proteins, and nucleotides. Cells are bounded by a fluid phospholipid bilayer studded with proteins, and contain specialised organelles for energy production, protein processing, waste disposal, and structural support. Protein synthesis follows DNA → mRNA (transcription) → protein (translation), with post-translational modifications before the protein reaches its final destination.
Biomolecules
Molecules synthesised by living organisms that contain carbon atoms. The four main types are carbohydrates, lipids, proteins, and nucleotides.
Monosaccharide
The simplest carbohydrate unit. Common examples: glucose, fructose, galactose. Think of these as the individual sugar building blocks.
Disaccharide
Two monosaccharides covalently bonded together. Examples: sucrose, lactose, galactose.
Polysaccharide
Many monosaccharides bonded in long chains. Used for energy storage (glycogen, starch) or structural purposes (cellulose).
Condensation (Dehydration Synthesis)
A reaction that joins two molecules by removing water. This is how di- and polysaccharides are built.
Hydrolysis
A reaction that breaks a bond by adding water. One fragment receives a hydrogen, the other receives a hydroxyl group. The reverse of condensation.
Amphipathic
A molecule that contains both polar (hydrophilic) and non-polar (hydrophobic) regions. Phospholipids are the classic example.
Triglyceride
One glycerol molecule bonded to three fatty acids. Glycerol is a three-carbon alcohol; each fatty acid is a long carbon chain with a carboxyl group (-COOH) on one end.
Phospholipid
A lipid containing two fatty acids and a phosphate group. The phosphate end is the hydrophilic head; the fatty acid tails are hydrophobic. These form the basis of cell membranes.
Steroid
A lipid built from three six-carbon rings and one five-carbon ring. Cholesterol is the most common example.
Amino Acid
The monomer of proteins. Contains a central carbon, an amino group (-NH2), a carboxyl group (-COOH), a hydrogen, and a variable R group that determines the amino acid's identity.
Polypeptide
A chain of amino acids joined by peptide bonds through condensation reactions. Proteins are made of one or more polypeptides.
Plasma Membrane
The phospholipid bilayer that encloses every cell, separating its contents from the external environment. Contains embedded proteins, cholesterol, and carbohydrates.
Integral Membrane Proteins
Proteins embedded in the phospholipid bilayer. They are amphipathic: polar regions face outward, non-polar regions sit within the bilayer. Transmembrane proteins span the entire membrane.
Peripheral Membrane Proteins
Proteins loosely attached to the inner surface of the membrane. They can detach without damaging the membrane and primarily give structural support to the cell.
Glycocalyx
A carbohydrate-rich protective layer on the outer surface of the cell membrane. Involved in cell recognition and cell adhesion.
Aquaporins
Membrane proteins that form water channels, allowing water to pass through the membrane.
Endoplasmic Reticulum (ER)
A network of membranes surrounding an inner lumen. Rough ER has ribosomes (protein synthesis); smooth ER does not (lipid synthesis, detoxification).
Golgi Apparatus
Stacked, flattened discs (cisternae) that receive, modify, and sort proteins. The cis face receives from the ER; the trans face ships outward.
Mitochondria
Double-membraned organelles where ATP production occurs, specifically in the mitochondrial matrix (the innermost compartment). Often called the powerhouse of the cell.
Lysosomes
Single-membrane vesicles containing digestive enzymes that break down waste and debris within the cell. Defective lysosomes cause diseases such as Tay-Sachs.
Peroxisomes
Small organelles that break down toxic substances through oxidation. Contain catalase, which converts toxic hydrogen peroxide into water and oxygen. House up to 50 types of enzymes.
Ribosomes
Dense packages of rRNA responsible for protein synthesis. Composed of a small (30S) and large (50S) subunit. Can float freely in the cytosol or attach to rough ER.
Cytoskeleton
A non-rigid internal framework of filaments that provides structural support, transports materials, suspends organelles, and enables cell movement.
Microfilaments (smallest): e.g. actin, microvilli
Intermediate filaments (medium): e.g. keratin, myosin
Microtubules (largest): hollow tubes, e.g. cilia and flagella
Tight Junctions
Nearly impermeable junctions between epithelial cells, linked by integral proteins called occludins. They prevent substances from leaking between cells.
Desmosomes
Strong cell junctions found in tissues under mechanical stress. Connected by glycoprotein plaques and filaments called cadherins.
Gap Junctions
Junctions that allow direct communication between adjacent cells via membrane protein channels called connexons. Common in smooth muscle and cardiac tissue.
Genetic Code
The correspondence between DNA base sequences and specific amino acids. Governs the expression of all genetic information.
Gene
A section of DNA that codes for a specific protein (or proteins).
Genome
The complete collection of all genes in a given species.
Transcription
The process of synthesising mRNA from a DNA template. Occurs in the nucleus. RNA polymerase binds to the promoter sequence, DNA uncoils, and a complementary mRNA strand is built.
Translation
The process of building a polypeptide from an mRNA template. Occurs at ribosomes in the cytoplasm. tRNA molecules deliver amino acids matching each codon on the mRNA.
Codon
A three-base sequence on mRNA that corresponds to one amino acid. AUG is the initiator codon (codes for methionine, always the first amino acid).
Introns
Non-coding sequences within a gene that are removed during post-transcriptional processing before the mRNA leaves the nucleus.
Leader Sequence
The first functional sequence of amino acids on a new polypeptide. Determines where the protein will be synthesised (cytosol or rough ER) and where it will ultimately go.
Glycosylation
The addition of carbohydrate groups to a protein during post-translational processing, occurring in the ER and Golgi apparatus.
Four classes: carbohydrates, lipids, proteins, nucleotides
Common functional groups to know:
Hydroxyl (-OH)
Sulfhydryl (-SH)
Phosphate (-HPO4)
Carboxyl (-COOH)
Amino (-NH2)
General formula: CH2O (carbon, hydrogen, oxygen in a 1:2:1 ratio)
Polar molecules (attract water); non-polar molecules are hydrophobic (attracted to lipids)
Covalent bonds form when atoms share electrons
Monosaccharides: glucose, fructose, galactose
Disaccharides: sucrose, lactose, galactose (two monosaccharides joined)
Polysaccharides: glycogen and starch (energy storage), cellulose (dietary fibre)
Synthesis = condensation (water is produced)
Breakdown = hydrolysis (water is consumed to split the bond)
Triglycerides: 1 glycerol + 3 fatty acids
Phospholipids: 2 fatty acids + 1 phosphate group; the phosphate end is the hydrophilic head
Steroids: ring structures (3 six-carbon rings + 1 five-carbon ring); cholesterol is the most common
Amphipathic molecules have both polar and non-polar regions
Amino acids: central carbon + amino group + carboxyl group + hydrogen + R group
Polypeptides form through condensation (peptide bond formation)
Proteins are polymers of amino acids
Every cell has a plasma membrane enclosing a nucleus and cytoplasm
Cytoplasm = organelles + cytosol
Phospholipid bilayer: hydrophobic tails face inward, hydrophilic heads face outward
Components scattered within the membrane:
Integral proteins (embedded), peripheral proteins (surface-attached)
Cholesterol (prevents crystallisation of hydrophobic tails, maintains fluidity)
Carbohydrates bonded to lipids and proteins (glycolipids, glycoproteins)
The membrane is considered "fluid" because its components can move freely within the layer
Integral membrane proteins are amphipathic; polar heads face the aqueous environment, non-polar portions sit within the bilayer
Transmembrane proteins span the entire membrane and serve as channels for ions/proteins or catalyse reactions
Peripheral membrane proteins can detach without damaging the membrane; they provide structural support
Aquaporins are specialised pore-forming proteins for water transport
Covalently bonded to membrane lipids
Form the glycocalyx (protective layer, cell adhesion)
Involved in cell recognition (e.g. red blood cell identification)
Enclosed by a nuclear envelope (double membrane with nuclear pores)
Contains DNA as thin strands called chromatin
The nucleolus is the primary site for rRNA production
Functions: transmission and expression of genetic information
Contains inclusions (stored energy as triglycerides and glycogen)
Houses enzymes for glycolysis and other metabolic processes
Contains secretory vesicles for exporting materials from the cell
Endoplasmic reticulum: rough ER (ribosomes attached, protein synthesis) and smooth ER (no ribosomes, lipid synthesis)
Golgi apparatus: cisternae stacked in layers; cis face receives from ER, trans face dispatches to the membrane or outside the cell
Mitochondria: double-membraned; ATP production occurs in the mitochondrial matrix
Lysosomes: single-membrane vesicles that digest waste. Defective lysosomes cause Tay-Sachs disease (lipid accumulation, ultimately fatal)
Peroxisomes: break down toxic substances via oxidation; contain catalase; house up to 50 enzyme types
Ribosomes: small (30S) and large (50S) subunits; synthesise proteins; float freely or attach to rough ER
Non-rigid framework of filaments providing support, transport, and movement
Three sizes to remember:
Microfilaments (smallest): actin, microvilli
Intermediate filaments (medium): keratin, myosin
Microtubules (largest): hollow tubes; form cilia and flagella. Flagella are found only in sperm cells
Tight junctions: nearly impermeable, found in epithelial tissues, linked by occludins
Desmosomes: found in tissues under stress, connected by glycoprotein plaques and cadherins
Gap junctions: found in smooth muscle and cardiac tissue, connected by connexons, allow cells to communicate directly
Metabolism: all chemical reactions in the body
Anabolism: building larger molecules from smaller ones
Catabolism: breaking larger molecules into smaller ones
Membrane transport: movement of molecules across the cell membrane
Intercellular communication: chemical messages sent to target cells with specific receptors (e.g. ADH triggering the kidney to retain water)
Genetic code: the correspondence between DNA sequences and amino acids
Gene: a section of DNA coding for a specific protein
Genome: the full collection of genes in a species
mRNA carries the code from the nucleus through the cytoplasm
RNA polymerase binds to the promoter sequence
DNA is uncoiled
Complementary mRNA strand is assembled (elongation)
Introns are removed during post-transcriptional processing
Initiation factors bind to the 5' cap of mRNA
tRNA delivers the correct amino acid (anticodon matches the mRNA codon)
Ribosome has two sites: P site (holds the growing chain) and A site (receives the next tRNA)
Peptidyl transferase catalyses peptide bond formation between amino acids
Methionine is always the first amino acid (AUG is the initiator codon)
The leader sequence determines where synthesis occurs (cytosol or rough ER) and where the finished protein goes (cytosol, mitochondrion, peroxisome, nucleus)
For ER-bound proteins: leader sequence binds signal recognition proteins on the ER → polypeptide enters the rough ER lumen → passes to smooth ER → Golgi apparatus
Unnecessary amino acids (including the leader sequence) are removed
Lipids or carbohydrates may be added (glycosylation occurs in the ER and Golgi)
Smooth ER packages the polypeptide into a vesicle for transfer to the Golgi
Protein moves from the cis to trans face of the Golgi and is dispatched to its final location
Carbohydrate general formula: CH2O (1:2:1 ratio of C:H:O)
Condensation: A + B → AB + H2O (synthesis, releases water)
Hydrolysis: AB + H2O → A + B (breakdown, consumes water)
Amino acid structure: central C bonded to NH2, COOH, H, and R group
Phospholipid bilayer behaviour is the reason that oil and water do not mix, and why cell membranes can self-assemble. This principle is exploited in drug delivery systems (liposomes).
Tay-Sachs disease is a direct consequence of lysosome malfunction. Understanding organelle roles helps explain how single-gene defects lead to systemic disease.
Students often think the cell membrane is a rigid wall. It is not. It is a fluid structure whose components drift laterally, which is why it is called the "fluid mosaic model."
Condensation and hydrolysis are frequently mixed up. Remember: condensation builds (and produces water), hydrolysis breaks (and uses water).
Students sometimes assume transcription and translation both happen in the nucleus. Transcription occurs in the nucleus; translation occurs at ribosomes in the cytoplasm.
The initiator codon AUG codes for methionine. Students sometimes forget that every newly synthesised protein begins with methionine, even if it is later removed.
⚠️ Know the four biomolecule classes and be able to identify each from a description or structure.
⚠️ Be able to describe the phospholipid bilayer and explain why it is "fluid." Know the roles of integral vs. peripheral proteins.
⚠️ The steps of transcription and translation are heavily tested. Be able to walk through the sequence from DNA → mRNA → protein.
⚠️ Know what happens at the P site vs. the A site of a ribosome.
⚠️ Understand the role of the leader sequence in determining protein destination.
⚠️ Cell junction types (tight, desmosome, gap) and where each is found are common exam material.
True or False: Hydrolysis produces water as a byproduct.
Fill in the blank: The three cytoskeletal filament types, from smallest to largest, are __________, __________, and __________.
True or False: Peripheral membrane proteins span the entire phospholipid bilayer.
Fill in the blank: The initiator codon is __________ and it codes for the amino acid __________.
True or False: Gap junctions are mainly found in epithelial tissue.
Answers: 1. False (hydrolysis consumes water; condensation produces it). 2. Microfilaments, intermediate filaments, microtubules. 3. False (transmembrane proteins do; peripheral proteins sit on the surface). 4. AUG; methionine. 5. False (they are mainly found in smooth muscle and cardiac tissue).
Q: Compare and contrast the three types of cell junctions. Where in the body would you find each?
A: Tight junctions are nearly impermeable and are found in epithelial tissues, linked by occludins. Desmosomes are found in tissues under mechanical stress and are joined by glycoprotein plaques with cadherin filaments. Gap junctions are found in smooth muscle and cardiac tissue, connected by connexon channels that allow direct cell-to-cell communication.
Q: Describe the structure of the plasma membrane and explain the roles of its main components.
A: The plasma membrane is a phospholipid bilayer with hydrophobic tails facing inward and hydrophilic heads facing outward. Integral proteins are embedded within the bilayer (some span it entirely as transmembrane proteins, acting as channels or catalysts). Peripheral proteins attach to the inner surface for structural support. Cholesterol maintains membrane fluidity by preventing tail crystallisation. Carbohydrates on the outer surface form the glycocalyx for cell recognition and adhesion.
Q: Outline the steps of protein synthesis from DNA to a finished, delivered protein.
A: Transcription occurs in the nucleus: RNA polymerase binds the promoter, DNA uncoils, and a complementary mRNA strand is built. Introns are spliced out. The mature mRNA moves to the cytoplasm. Translation occurs at ribosomes: tRNA delivers amino acids matching mRNA codons, peptidyl transferase forms peptide bonds, and the polypeptide chain grows from the P site to the A site. The leader sequence directs the protein to its synthesis location (cytosol or rough ER) and its final destination. Post-translational modifications (removal of unneeded amino acids, glycosylation) occur in the ER and Golgi before the protein is dispatched.
Q: What is the difference between rough and smooth endoplasmic reticulum?
A: Rough ER has ribosomes attached to its surface and is the site of protein synthesis. Smooth ER lacks ribosomes and is involved in lipid synthesis and other functions. Both are networks of membranes surrounding an inner lumen.
Q: A patient has Tay-Sachs disease. Which organelle is malfunctioning and what is the consequence?
A: Lysosomes are less effective than needed. Because they cannot adequately break down lipids, lipids accumulate within cells, eventually causing cell death and, in severe cases, death of the individual.
The biomolecule chemistry here (especially carbohydrates and lipids) connects directly to Chapter 3's material on metabolism, glycolysis, and the Krebs cycle.
Membrane transport (briefly introduced in Section 2.4) will be expanded significantly in later chapters covering osmosis, diffusion, and active transport.
Protein synthesis connects to gene expression topics later in the course and is foundational for understanding how hormones and enzymes are produced.
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