Source: APK2105C Final Exam Review, University of Florida
Tags: carbohydrates, lipids, proteins, amino acids, nucleotides, DNA, RNA, cell membrane, organelles, cell junctions, APK2105C
Difficulty: Introductory to Intermediate Prerequisites: Part 1 of these notes (Cell Fundamentals, Body Organisation and Basic Chemistry). You should be comfortable with covalent bonds, polarity and functional groups before working through this section.
Once you understand atoms and bonds, the next step is learning the four families of biomolecules the body is built from: carbohydrates, lipids, proteins and nucleic acids. Each has a distinct structure that dictates its function. Those molecules are then organised inside a cell whose membrane, organelles and junctions you need to know in detail. This section bridges chemistry and cell biology, and almost every exam question about organelles, DNA or membrane structure draws from it.
The body's four major biomolecule classes are carbohydrates (energy), lipids (membranes, energy storage, signalling), proteins (structure and function) and nucleic acids (genetic information and energy transfer). Cells are bounded by a phospholipid bilayer studded with proteins, and contain specialised organelles (nucleus, ER, Golgi, mitochondria, lysosomes, etc.) that divide labour. Cell junctions (tight, gap, desmosomes) control how adjacent cells communicate and hold together.
Carbohydrates
Composed of carbon, hydrogen and oxygen in a 1:2:1 ratio. Carbons bond to hydroxyl groups and hydrogen. The presence of hydroxyl groups makes carbohydrates polar.
Monosaccharides
Simple sugars composed of a single unit. Glucose is the most common and is the only simple sugar the body can convert into a useful energy form. Fructose and galactose are two other common forms.
Ribose and deoxyribose
Two monosaccharides that are important components of nucleotides and genetic material.
Disaccharides
Formed by covalent bonds between two monosaccharides. Sucrose (table sugar), lactose (milk sugar) and maltose (malt sugar) are common examples.
Polysaccharides
The covalent bonding of several monosaccharides into a chain.
Glycogen
A polymer of glucose subunits and the source of energy most often used for exercise. Think of it as the body's short-term glucose warehouse, stored mainly in liver and muscle.
Starch
A polysaccharide found in plants (potatoes, grains). Digestion breaks it into glucose subunits.
Cellulose
A fibrous plant polysaccharide humans cannot digest. Known as dietary fibre; it provides bulk in the gastrointestinal tract and aids digestion.
Lipids
Fats that serve three primary functions: structural components of cell membranes, energy storehouses and signalling molecules.
Amphipathic
A lipid molecule containing both a polar region (dissolves in water) and a nonpolar region (repels water).
Saturated fatty acids
Carbons linked only by single bonds, fully occupied by hydrogen atoms. Straight-chain shape.
Unsaturated fatty acids
Some double bonds between carbons cause bends or "kinks." Oils are unsaturated fats.
Trans fats
Produced by hydrogenation, which converts the bent "cis" form to a straightened "trans" form.
Triglycerides
The storage form of fats. A glycerol molecule with three hydroxyl groups combines with the carboxyl groups of three fatty acids.
Phospholipids
Lipids where glycerol combines with two fatty acids (one unsaturated) and a phosphate group. The phosphate group forms the polar head; the fatty acid tails form the nonpolar region. They are the molecules that form the bilayer of cell membranes and micelles.
Phospholipid bilayer
The core structure of cell membranes. Hydrophobic tails face inward; hydrophilic heads face outward toward the aqueous environment.
Micelle
A spherical arrangement of phospholipids. Heads face outward (toward water); tails face inward, forming a hydrophobic interior.
Steroids
Lipids characterised by four fused carbon rings (three 6-sided, one 5-sided). Functions range from growth to sexual development.
Eicosanoids
Signalling molecules that exert complex control over many bodily systems, mainly in inflammation, immunity and CNS messaging. Made by breaking down parts of individual cells.
Peptide bond
The covalent bond that holds amino acids together.
R-group (side chain)
The part of the amino acid that differs between the 20 amino acids. All chemical diversity of amino acids arises from this group.
Condensation reaction
A reaction that releases water. Peptide bonds form by condensation: the amine group of one amino acid joins the carboxyl group of another, releasing H₂O.
Peptides
Short chains of amino acids, usually fewer than 50.
Proteins
Chains generally longer than 50 amino acids, folded and shaped to determine a specific function.
Conformation
The three-dimensional structure of a protein, on which its function is highly dependent.
Primary structure
The sequence of amino acids in the polypeptide chain.
Secondary structure
Coiling or folding of the polypeptide chain into twists and corrugations (alpha helices, beta sheets).
Tertiary structure
Further folding and looping into a three-dimensional shape, created by interactions between R-groups of different amino acids.
Quaternary structure
Two or more polypeptide chains bound together. Haemoglobin (four subunits, carries oxygen) is the classic example.
Nucleotides
Molecules composed of one or more phosphate groups, a 5-carbon sugar and a nitrogenous base. They function in energy transfer (ATP), signalling and forming genetic material.
Pyrimidines
Single-ring nitrogenous bases: cytosine (and thymine in DNA, uracil in RNA).
Purines
Double-ring nitrogenous bases: adenine and guanine.
DNA (deoxyribonucleic acid)
Two strands of nucleotides coiled into a double helix. Bases: adenine (A), guanine (G), cytosine (C), thymine (T). Strand ends are labelled 3' (carbohydrate end) and 5' (phosphate end).
Law of complementary base pairing
G always pairs with C; A always pairs with T (in DNA) or U (in RNA). This means that in any strand of DNA, A + G = C + T.
Uracil
In RNA, thymine is replaced by uracil. Thymine is NOT a base in RNA.
Nucleotide monophosphate / diphosphate / triphosphate
A nucleotide with one, two or three phosphate groups, respectively. ATP is adenosine triphosphate.
The membrane separating the cytoplasm from the surrounding environment is the cell (plasma) membrane. It is made of phospholipids, proteins and carbohydrates.
Cholesterol sits among the phospholipid tails and acts against hydrophobic interactions, causing crystallisation of the bilayer and decreased fluidity.
Transmembrane proteins span the entire membrane. A carrier protein is one example; it transports molecules from one side to the other.
Peripheral membrane proteins are loosely bound to the membrane surface and often function as part of the cytoskeleton.
Integral proteins are interwoven throughout the membrane.
Nucleus: enclosed by a nuclear envelope with nuclear pores for selective molecule movement. DNA exists inside as thin threads called chromatin (it condenses only during cell division). The nucleolus within the nucleus is the site of ribosomal RNA (rRNA) synthesis.
Endoplasmic reticulum (ER): an elaborate membrane network enclosing an interior compartment (lumen).
Rough ER: studded with ribosomes; involved in protein synthesis. Has a flat-sac appearance and is continuous with the outer nuclear membrane.
Smooth ER: lacks ribosomes; stores calcium and synthesises lipids. In the liver, it contains enzymes that break down toxic substances.
Golgi apparatus: membrane-bound flattened sacs (cisternae). The distribution and shipping organelle for the cell's chemical products.
Mitochondria: the "powerhouse" of the cell. Bounded by two membranes:
Outer membrane separates the mitochondrion from the cytosol.
Inner membrane divides each mitochondrion into two compartments: the intermembrane space and the mitochondrial matrix (innermost compartment).
The inner membrane houses the electron transport chain and is folded into cristae to increase surface area.
The mitochondrial matrix is a gel-like solution of roughly 50% protein, containing enzymes for the oxidation of pyruvate, amino acids, fatty acids and the Krebs cycle.
Lysosomes: spherical organelles surrounded by a single membrane containing very acidic enzymes. They degrade nonfunctioning organelles, cellular waste and bacteria. Think of them as floating garbage disposals.
Peroxisomes: slightly smaller than lysosomes, also single-membrane. They degrade amino acids, fatty acids and toxic foreign matter. The process produces the toxic by-product hydrogen peroxide.
Ribosomes: dense granules of rRNA and proteins that carry out protein synthesis. They are NOT located in the Golgi apparatus. Found on rough ER or free in the cytosol.
Cytoskeleton: a flexible lattice of microfilaments and microtubules providing structural support. Microtubules are long hollow tubes that also form cilia (short, hair-like) and flagella (long, tail-like) for motility.
Centrioles: barrel-shaped structures of nine microtubules in a circular arrangement. Important for microtubule orientation and serve as the body of cilia and flagella.
Vaults: barrel-shaped, approximately three times larger than ribosomes. Their function is not fully understood but may include intracellular transport and resistance to chemotherapy in cancer treatment.
Tight junctions: integral membrane proteins called occludins fuse adjacent cells to form a nearly impermeable barrier. Found in epithelial tissue; they restrict or regulate molecular movement between lumen and blood.
Gap junctions: connexons (each made of six connexin proteins) connect adjacent cells, forming channels for ions and small molecules. They provide direct electrical and metabolic coupling between cells.
Desmosomes: found in tissues under mechanical stress (heart, uterus, skin). Glycoprotein plaques anchor intracellular filaments, and cadherins cross the plasma membrane into the extracellular space. They prevent cells from being torn apart.
Complementary base pairing: A pairs with T (DNA) or U (RNA); G pairs with C. In any DNA strand: A + G = C + T.
Condensation reaction (peptide bond formation): amino acid₁ (−NH₂) + amino acid₂ (−COOH) → peptide bond + H₂O.
Protein structure hierarchy: primary → secondary → tertiary → quaternary.
The phospholipid bilayer is the reason oil and water do not mix in your kitchen: the same hydrophobic/hydrophilic principles that keep cooking oil in droplets govern how your cell membranes form and maintain their barrier. Tight junctions in the intestinal lining are why stomach acid does not leak into surrounding tissue, and why drug delivery across the gut wall is a major pharmaceutical challenge.
Students often confuse saturated and unsaturated fats. Saturated = all single bonds, straight chains, solid at room temperature. Unsaturated = at least one double bond, kinked chains, liquid (oils) at room temperature.
Ribosomes are sometimes placed in the Golgi apparatus on exams. They are not found there. They sit on the rough ER or float freely in the cytosol.
Thymine and uracil are frequently mixed up. Remember: thymine is in DNA only; uracil replaces it in RNA.
The quaternary structure of a protein requires more than one polypeptide chain. A single folded chain has tertiary structure, not quaternary.
⚠️ Know the hierarchy of protein structure (primary through quaternary) and what determines each level.
⚠️ Distinguish the three types of cell junctions by structure and function (tight, gap, desmosome).
⚠️ Be able to identify each organelle by a brief description of its structure and role.
⚠️ Understand cholesterol's effect on membrane fluidity (it decreases fluidity by causing crystallisation).
⚠️ The law of complementary base pairing and A + G = C + T are commonly tested.
True or false: Glycogen is a monosaccharide. (False, it is a polysaccharide.)
Fill in the blank: The inner mitochondrial membrane is folded into structures called _______. (Cristae.)
True or false: Occludins are the protein subunits of gap junctions. (False, occludins form tight junctions. Connexins form gap junctions.)
Fill in the blank: The _______ structure of a protein is determined by the sequence of amino acids. (Primary.)
True or false: Phospholipids are amphipathic. (True.)
Q: What are the three primary biological functions of lipids?
A: They serve as structural components of cell membranes, function as energy storehouses (triglycerides) and act as important signalling molecules (eicosanoids, steroids).
Q: Describe the structure of a phospholipid and explain how phospholipids arrange themselves in a cell membrane.
A: A phospholipid has a polar (hydrophilic) head containing a phosphate group and two nonpolar (hydrophobic) fatty acid tails. In a cell membrane, they form a bilayer: hydrophobic tails face inward toward each other, and hydrophilic heads face outward toward the aqueous environment on both sides.
Q: Name the organelle responsible for each function: (a) protein synthesis, (b) lipid synthesis, (c) packaging and shipping of cell products, (d) degradation of waste and bacteria.
A: (a) Rough ER (with ribosomes), (b) Smooth ER, (c) Golgi apparatus, (d) Lysosomes.
Q: According to the law of complementary base pairing, what base pairs with adenine in DNA? In RNA?
A: In DNA, adenine pairs with thymine. In RNA, adenine pairs with uracil.
Q: Distinguish between tight junctions, gap junctions and desmosomes.
A: Tight junctions (occludins) seal adjacent cells into a nearly impermeable barrier. Gap junctions (connexins/connexons) form channels allowing ions and small molecules to pass between cells. Desmosomes (cadherins) anchor cells together against mechanical stress.
The phospholipid bilayer introduced here is the barrier that all of Part 4 (Membrane Transport) deals with. Protein structure connects directly to enzyme function in Part 3, because an enzyme's conformation determines its active site shape and catalytic activity. Nucleotides (especially ATP) reappear centrally in Part 3's coverage of metabolism and energy production.
carbohydrates, monosaccharides, glucose, fructose, galactose, disaccharides, sucrose, lactose, maltose, polysaccharides, glycogen, starch, cellulose, lipids, saturated fat, unsaturated fat, trans fat, triglycerides, phospholipids, phospholipid bilayer, micelle, steroids, eicosanoids, amphipathic, peptide bond, amino acids, R-group, condensation reaction, protein structure, primary, secondary, tertiary, quaternary, conformation, nucleotides, DNA, RNA, purines, pyrimidines, base pairing, uracil, thymine, cell membrane, cholesterol, transmembrane protein, integral protein, peripheral protein, nucleus, chromatin, nucleolus, rough ER, smooth ER, Golgi apparatus, mitochondria, cristae, lysosomes, peroxisomes, ribosomes, cytoskeleton, microtubules, cilia, flagella, centrioles, vaults, tight junctions, gap junctions, desmosomes, occludins, connexins, cadherins, APK2105C