bio: Ch 3
3.1 Organic Molecules
An organic molecule must contain carbon and hydrogen in order to be considered organic.
The chemistry of carbon contributes to the diversity of organic molecules (carbon is tetravalent, allowing many bonding patterns).
Functional groups determine the chemical reactivity of organic molecules. Some functional groups are nonpolar (hydrophobic) and others are polar (hydrophilic).
The organic molecules in cells are called biological molecules.
Isomers are molecules that have the same chemical formula (composition) but different structures.
3.2 Carbohydrates and Lipids
Biological molecules are synthesized by dehydration synthesis reactions and degraded by hydrolysis reactions.
Living organisms are composed of four types of biological molecules: carbohydrates, lipids, proteins, and nucleic acids.
Polysaccharides, proteins, and nucleic acids are polymers formed when their monomers join to create long chains.
Lipids are a varied group and do not have a single, universal monomer.
The characteristics of these molecules are summarized in Table 3.1.
Table 3.1 summary (Biological Molecules)
Class of Organic Molecule: Carbohydrates | Lipids | Proteins | Nucleic acids
Examples: Monosaccharides, disaccharides, polysaccharides | Fats, oils, phospholipids, steroids | Proteins | DNA, RNA
Monomer: Monosaccharides | Glycerol + fatty acids (triglycerides) | Amino acids | Nucleotides
Functions: Immediate energy and stored energy; structural molecules | Long-term energy storage; membrane components | Structural, enzymatic, carrier, hormonal, contractile; support, metabolism, transport, regulation, motion | Storage of genetic information; processing that information to form proteins
Carbohydrates
Carbohydrates are primarily used as energy molecules, though some have structural roles.
Glucose is a monosaccharide that serves as blood sugar and as a monomer of starch, glycogen, and cellulose.
Its isomers are fructose and galactose.
Ribose and deoxyribose are monosaccharides found in nucleic acids.
Sucrose is a disaccharide (glucose + fructose), known as table sugar.
Other disaccharides include maltose and lactose.
Polysaccharides (all polymers of glucose) include:
Starch: stores energy in plants
Glycogen: stores energy in animals
Cellulose: makes up the structure of plant cell walls
Cellulose is a key structural component in plants; cellulose forms plant cell walls.
Chitin is a polysaccharide that contains amino groups.
Lipids
Lipids are hydrophobic molecules that often serve as long-term energy storage molecules.
Fats and oils are triglycerides (glycerol + three fatty acids).
Triglycerides with saturated fatty acids (no double bonds) are solids and are called fats.
Triglycerides with unsaturated fatty acids (one or more double bonds) are liquids and are called oils.
Trans fats are unsaturated fats with a unique form of chemical bond in the fatty acid chain.
Phospholipids have the same structure as triglycerides, except that a group containing phosphate replaces one fatty acid.
Phospholipids make up the plasma membrane and other cellular membranes.
Steroids are lipids with a four-ring hydrocarbon structure.
Cholesterol is a steroid and a component of the plasma membrane.
The sex hormones testosterone and estrogen are steroids.
3.3 Proteins and Nucleic Acids
Proteins
Proteins are polymers of amino acids.
A peptide is composed of two amino acids linked by a peptide bond.
Polypeptides contain many amino acids.
Proteins perform a wide range of functions, including acting as enzymes to accelerate chemical reactions.
A protein has several levels of structure:
Primary structure: the primary sequence of amino acids.
Secondary structure: a helix or pleated sheet.
Tertiary structure: folding and twisting of the secondary structure.
Quaternary structure: more than one polypeptide chain interacting.
If a protein loses its structure, it is said to be denatured.
Nucleic Acids
Nucleic acids are polymers of nucleotides; they are responsible for storing and transmitting genetic information.
DNA (deoxyribonucleic acid) contains the sugar deoxyribose; it is double-stranded and forms a double helix.
DNA strands are joined by complementary base pairing: A\;\text{pairs with}\; T, \quad G\;\text{pairs with}\; C.
The information in DNA is contained in sequences of nucleotides called genes.
RNA (ribonucleic acid) serves as a helper to DNA during protein synthesis; its sugar is ribose and it contains the base uracil in place of thymine.
RNA is single-stranded and does not form a double helix.
ATP (adenosine triphosphate) is a modified nucleic acid used as a main energy carrier for most cells.
Table 3.2: DNA vs RNA Structures
DNA: Sugar = Deoxyribose | Bases = A, G, T, C | Strands = Double-stranded | Helix = Yes
RNA: Sugar = Ribose | Bases = A, G, U, C | Strands = Single-stranded | Helix = No
Thinking Critically About Biology
Why do physicians refer to forms of cholesterol as
Organic vs Inorganic Molecules
Organic chemistry studies organic molecules; inorganic chemistry covers substances without a direct carbon-hydrogen relationship.
An organic molecule contains atoms of carbon and hydrogen.
Organic molecules make up portions of cells, tissues, and organs (biomolecules).
An inorganic molecule does not contain a combination of carbon and hydrogen.
Examples of inorganic molecules: Water (H₂O) and table salt (NaCl).
This chapter focuses on the diversity and functions of organic molecules in cells (biomolecules).
Recognizing the Importance of Functional Groups
Functional groups are specific combinations of bonded atoms that always have the same chemical properties and react in the same way, regardless of the carbon skeleton.
The reactivity of an organic molecule is largely determined by its attached functional groups.
In illustrations, the letter R represents the remainder of the molecule, indicating where the functional group attaches to the hydrocarbon chain.
Functional groups help determine whether a molecule will be polar/hydrophilic or nonpolar/hydrophobic, and influence solubility in water.
The Carbon Atom and Bonding Basis for Diversity
Carbon has a total of 6 electrons, with 4 electrons in its outer shell.
To complete its outer shell, carbon almost always shares electrons, typically with hydrogen, nitrogen, and oxygen—the elements that dominate living organisms.
Because carbon is small and needs four electrons to complete its outer shell, it can form up to 4 bonds with other atoms.
Carbon atoms most often bond with other carbon atoms, creating stable C–C bonds that enable long carbon chains.
Hydrocarbons are chains of carbon atoms bonded only to hydrogen atoms.
A carbon atom in a hydrocarbon can start a branched chain, and hydrocarbons can form ring structures (cycloalkanes).
Carbon atoms can also form double bonds with other atoms, including another carbon atom: ext{C=C}.
Isomerism and Structural Diversity
The versatile nature of carbon allows the same chemical formula to produce molecules with different structures (isomers).
Isomers differ in how atoms are arranged but have the same number and types of atoms.
This structural diversity leads to a wide range of functions for organic molecules.
Figure 3.2 illustrates how hydrocarbons are highly versatile, varying by:
Number of carbon atoms
Placement of double bonds C=C
Possible branching
Ring formations
The Carbon Skeleton (Backbone) and Functional Groups
The carbon skeleton (backbone) defines the overall shape of the molecule.
The reactivity and properties of an organic molecule are greatly influenced by its functional groups attached to the skeleton.
A functional group is a specific arrangement of atoms that imparts characteristic chemical behavior to the molecule.
The symbol R represents the remainder of the molecule (the hydrocarbon chain) to which a functional group attaches.
Molecules with the same carbon skeleton can differ in their properties due to different functional groups attached.
Functional Groups: Chemical Properties and Examples
Functional groups influence whether a molecule is polar/hydrophilic or nonpolar/hydrophobic.
Carboxyl groups (—COOH) render molecules polar (hydrophilic) and weakly acidic.
Phosphate groups contribute to the structure and function of nucleic acids (e.g., DNA).
Nitrogen-containing amino groups are present in proteins and amino acids.
Since cells are mostly water, water solubility is important for molecular activity; hydrocarbons are largely hydrophobic (water-insoluble), but adding functional groups can increase water solubility.
The functional groups also identify the types of reactions the molecule will undergo.
Functional Groups in Biochemistry: Formation of Fats and Proteins
Fats are formed by the interaction of molecules containing alcohol groups and carboxyl groups.
Proteins are formed when the amino and carboxyl functional groups of nearby amino acids link together.
Example interactions: amino group (-NH₂) and carboxyl group (-COOH) participate in peptide bond formation.
Organic Molecules in Everyday Life and Agriculture
Organic molecules contain carbon and hydrogen, which is why vegetables and fruits are considered organic.
The term “organic” in farming has a different meaning: production standards aim to minimize or avoid pesticides and harsh chemicals, growing crops as naturally as possible.
This illustrates two contexts in which the term “organic” is used:
In biology/chemistry: organic molecules with C–H bonds.
In agriculture: farming practices labeled as organic due to standards and methods.
The Roles of Biomolecules (Figure 3.1)
Carbohydrates: form fiber that provides structural support in plants.
Proteins: help form structural features such as the long flagella of Salmonella bacteria.
Lipids: store energy (e.g., the oil within corn plants).
Nucleic acids: store genetic information (DNA).
Connecting the Concepts
Carbon and hydrogen are the basis of organic molecules found in living organisms.
Functional groups determine chemical properties, reactivity, and solubility.
Structure dictates function: isomerism and skeleton shape lead to diverse roles in biology.
Real-world relevance includes biomolecule function, solubility in water, and agricultural practices.
Check Your Progress 3.1 (Key prompts)
1. Explain the difference between an organic and inorganic molecule.
2. List the attributes of a carbon atom that allow it to form a variety of molecules.
3. Explain the importance of functional groups.
Building Blocks of Biological Polymers
Biological polymers are built from monomers (building blocks) and form polymers when monomers link together.
A dehydration synthesis (condensation) reaction builds polymers by removing a water molecule, allowing monomers to bond. The process removes an —OH group from one monomer and an H atom from another, effectively removing a molecule of water. Example: for glucose polymerization, two glucose units form maltose with the release of one H₂O molecule. In general, n monomers yield a polymer plus (n−1) H₂O molecules:
ext{Monomer}1 + ext{Monomer}2 + \cdots + ext{Monomer}n \rightarrow ext{Polymer} + (n-1) \mathrm{H2O}.A hydrolysis reaction breaks bonds by adding water, opposite of dehydration synthesis. Water attaches to monomer units to separate them. Example: a polymer can be cleaved into its constituent monomers by hydrolysis.
A common example of polymer synthesis in lipids: glycerol + 3 fatty acids form a triglyceride with the release of 3 H₂O molecules.
ext{Glycerol} (\mathrm{C3H8O3}) + 3\, \text{Fatty Acids} (\mathrm{R-COOH}) \rightarrow \text{Triglyceride} + 3\, \mathrm{H2O}.These reactions appear in figures referenced in the text (Fig. 3.4a for synthesis, Fig. 3.4b for hydrolysis).
Carbohydrates
In living organisms, carbohydrates serve as an immediate energy source and, in plants and fungi, structural components as well.
Carbohydrates may exist as saccharide monomers or as polymers of saccharides.
Glucose is a common monosaccharide and a central energy source in cells; photosynthetic organisms produce glucose using solar energy.
The term carbohydrate can refer to a monosaccharide, disaccharide, or polysaccharide.
Monosaccharides (energy molecules) often have multiple polar hydroxyl groups and are water-soluble; in cells, they commonly form ring structures.
Monosaccharide examples and formulas:
Glucose: ext{C6H{12}O_6} (central energy source)
Fructose and galactose are isomers of glucose.
Ribose: ext{C5H{10}O5}; Deoxyribose: ext{C5H{10}O4}; important components of RNA and DNA.
Disaccharides: formed by dehydration synthesis linking two monosaccharides. Common disaccharides:
Maltose (two glucose units): ext{C{12}H{22}O_{11}}; involved in beer production via fermentation to ethanol.
Sucrose (glucose + fructose): ext{C{12}H{22}O_{11}}; digested to glucose and fructose; fructose ultimately converted to glucose for energy.
Lactose (glucose + galactose): ext{C{12}H{22}O_{11}}; found in milk; lactose intolerance occurs when lactose cannot be digested.
Polysaccharides (polymer of monosaccharides) include:
Energy storage:
Starch (plants): exists in nonbranched and branched forms; serves as short-term energy storage in plant cells (e.g., potato starch).
Glycogen (animals): highly branched; stored mainly in liver and muscle; branching increases susceptibility to enzymatic attack for rapid glucose release; insulin regulates glucose storage and release.
Structural roles:
Cellulose (plants): long, unbranched chains of glucose with bonds different from those in starch/glycogen; forms strong microfibrils in plant cell walls; humans cannot digest cellulose, but it provides dietary fiber.
Chitin: polymer of glucose with an amino group attached; found in insect exoskeletons and fungal cell walls; not digestible by humans but used in wound dressings and cosmetics.
Fiber in the diet:
Soluble fiber dissolves in water and can bind cholesterol; sources include fruits and oats.
Insoluble fiber adds bulk to feces and aids digestion; sources include bran, nuts, seeds, and whole grains.
High-fructose corn syrup (HFCS) and diet:
HFCS is made by converting glucose to fructose in corn syrup; high intake of refined sugars and white starches is associated with health concerns; nutritionists favor minimally processed carbohydrates with fiber and nutrients.
Structural and energy roles emphasize that carbohydrates are used for immediate energy and, in some organisms, for structural materials (cell walls, fibers).
The energy and storage aspects are coordinated by hormones (e.g., insulin) that regulate glucose storage and release.
Lipids
Lipids are diverse but share a common trait: they are hydrophobic and insoluble in water due to long nonpolar hydrocarbon chains and a relative lack of hydrophilic functional groups.
Major lipid categories include fats and oils (triglycerides), phospholipids, steroids, waxes, and more.
Lipids play roles in long-term energy storage, insulation, cell membrane structure, and signaling (steroids and hormones).
Fats and Oils: Long-Term Energy Storage
Subunits: glycerol and fatty acids.
Glycerol: ext{C3H8O_3}; contains three —OH groups and is water-soluble.
Fatty acids: long hydrocarbon chains with a carboxyl group at one end; typical carbon length is 16 or 18 carbons (e.g., palmitic acid C₁₆H₃₂O₂, stearic acid C₁₈H₃₈O₂).
A fat or oil forms when the carboxyl ends of three fatty acids react with the three —OH groups of glycerol, releasing three H₂O molecules (a dehydration synthesis). Such a fat/oil is a triglyceride.
General equation: ext{Glycerol} (\mathrm{C3H8O3}) + 3\, ext{Fatty Acids} (\mathrm{R-COOH}) \rightarrow \text{Triglyceride} + 3\, \mathrm{H2O}.
Lipids store a large amount of energy per molecule due to the hydrocarbon chains.
Hydrolysis breaks triglycerides into glycerol and fatty acids, releasing energy when metabolized.
Fatty Acids: Saturated, Unsaturated, and Trans Fats
Fatty acids can be saturated or unsaturated:
Saturated fatty acids have no C=C double bonds in their carbon chain; chains are straight and can pack tightly, making fats solid at room temperature (e.g., butter).
Unsaturated fatty acids contain one or more C=C double bonds; these introduce kinks (cis configuration) that prevent tight packing, making oils liquid at room temperature (e.g., olive oil).
Monounsaturated fats have one double bond; polyunsaturated fats have many.
Trans fats: if a fatty acid has a double bond with the hydrogen atoms on opposite sides (trans configuration), it is a trans fat. Trans fats are often formed during partial hydrogenation of liquids to make them more solid. They can contribute to the buildup of plaque in blood vessels (atherosclerosis).
Health implications:
Saturated fats and trans fats tend to stick together in the bloodstream, promoting atherosclerosis and related cardiovascular risks.
Unsaturated fats, particularly monounsaturated and polyunsaturated fats, are associated with reduced risk of atherosclerosis and are common in olive oil, canola oil, and certain fish.
Omega-3 Fatty Acids
A special class of unsaturated fats essential for health: omega-3 fatty acids (n-3).
Important omega-3s: linolenic acid (ALA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA).
Benefits: brain health, cardiovascular protection; DHA may reduce risk of Alzheimer's disease; EPA/DHA can be synthesized in small amounts from ALA in the body.
Common sources: cold-water fish (e.g., salmon, sardines) and plant-based sources like flax oil (linseed oil).
Phospholipids: Membrane Components
Phospholipids are lipids that contain a phosphate group; structurally similar to triglycerides but with one fatty acid replaced by a charged phosphate-containing group.
Polar head: hydrophilic, water-soluble.
Nonpolar tails: hydrophobic, water-insoluble.
In aqueous environments, phospholipids arrange into a bilayer with polar heads facing outward and nonpolar tails inward, forming the basic structure of cell membranes.
The phospholipid bilayer provides selective permeability and a fluid matrix for membrane proteins and lipids.
Steroids: Four Fused Rings
Steroids have a characteristic four fused carbon ring skeleton and are insoluble in water.
Cholesterol: a key component of animal cell membranes and a precursor to steroid hormones.
Hormones: testosterone and estrogen are steroids derived from cholesterol; their effects differ due to attached functional groups on the same carbon skeleton.
Anabolic steroids: synthetic testosterone-like compounds used to increase muscle mass but can disrupt hormonal balance and cause health problems; banned in professional sports.
Connections: Carbohydrates and Lipids in Biology
Carbohydrates and lipids both serve energy and structural roles, often complementing each other in energy storage, membrane structure, and signaling.
The body regulates carbohydrate storage and lipid metabolism through hormones (e.g., insulin) and signaling pathways; dietary choices influence health outcomes (energy balance, cholesterol levels, cardiovascular risk).
Check Your Progress 3.2
1) Describe the different classes of carbohydrates, and give an example of a structural and an energy carbohydrate.
2) List the classes of lipids and provide a function for each.
Notable Formulas and Terms
Glucose: ext{C6H{12}O_6}
Disaccharides (example formulas): ext{C{12}H{22}O_{11}} (for maltose, sucrose, lactose)
Glycerol: ext{C3H8O_3}
Triglyceride formation (dehydration synthesis):
ext{Glycerol} (\mathrm{C3H8O3}) + 3\, \text{Fatty Acids} (\mathrm{R-COOH}) \rightarrow \text{Triglyceride} + 3\, \mathrm{H2O}Dehydration synthesis general form: ext{Monomer}1 + \text{Monomer}2 + \cdots + \text{Monomer}n \rightarrow \text{Polymer} + (n-1) \mathrm{H2O}
Ribose: \text{C5H{10}O5}; Deoxyribose: \text{C5H{10}O4}
Omega-3 fatty acids: ALA, DHA, EPA; sources include fish and flax oil.
Phospholipid bilayer structure: polar head (hydrophilic) and nonpolar tails (hydrophobic) arrange to form cellular membranes.
Cholesterol and steroid hormones have four fused rings; functional groups attached determine specific effects (e.g., testosterone vs estrogen).
// End of notes
Proteins
Proteins are of primary importance in the structure and function of cells. The section highlights multiple roles and examples to show how essential proteins are to life.
Major functions of proteins:
Support: structural proteins such as keratin (hair, fingernails), collagen (skin, ligaments, tendons), and the protein in spider webs. They contribute to the framework and integrity of tissues.
Metabolism: many proteins are enzymes that act as catalysts, bringing reactants together and speeding up chemical reactions. Enzymes are specific for particular reactions and participate in nearly all metabolic processes.
Transport: channel and carrier proteins in the plasma membrane regulate substance movement into and out of cells. In blood, proteins such as hemoglobin transport molecules (e.g., oxygen).
Defense: antibodies are proteins that target pathogens to prevent infection.
Regulation: hormones act as intercellular messengers that influence cellular metabolism (e.g., insulin regulates blood glucose; human growth hormone (hGH) influences height).
Motion: contractile proteins (actin and myosin) enable muscle contraction and cellular movements; muscle activity also helps regulate body temperature.
Examples and context from figures:
Fig. 3.15a: keratin and collagen illustrate structural roles.
Fig. 3.15b: hemoglobin demonstrates transport function (oxygen transport in red blood cells).
Fig. 3.15c: actin and myosin illustrate muscle movement and contraction.
Dietary and metabolic emphasis:
Proteins support body structure and function, but they are not the cell’s preferred energy source (see Section 7.5).
Some dietary proteins may be high in fat (e.g., beef), while others (e.g., fish) include beneficial oils that can influence cardiovascular health (Fig. 3.16).
Structural diversity and organization:
The structures of cells differ by the proteins they contain (e.g., muscle cells with actin/myosin, red blood cells with hemoglobin, support cells with collagen).
Dietary sources of proteins are shown in Fig. 3.16; small servings can provide all essential amino acids if varied.
Amino Acids
Proteins are polymers whose monomers are amino acids.
Amino acids have a common core structure: a central carbon (alpha carbon) bonded to
a hydrogen atom,
an amino group (–NH₂),
a carboxyl group (–COOH),
a variable side chain, or R group.
There are 20 different amino acids, differing by their R groups, which range from a single hydrogen atom to complex ring structures.
Properties of R groups determine amino acid behavior: some are polar, some are charged, and some are nonpolar/hydrophobic.
The order and composition of amino acids in a polypeptide determine its final three-dimensional shape and function.
Size examples:
Ribonuclease (a small protein) contains barely more than ext{approximately } 100 amino acids.
Titin (a very large protein) contains over 3.3 imes 10^{4} amino acids, and is a key part of muscle structure.
The concept of sequence variety:
A protein’s amino acid sequence is unique for each polypeptide, and most proteins contain one or more polypeptide chains.
Even a small change in the amino acid sequence can produce a different fold and loss of function.
Peptides and Peptide Bonds
A peptide forms when two amino acids are joined by a dehydration synthesis reaction between the carboxyl group of one amino acid and the amino group of another:
\text{AminoAcid}1-COOH + \text{AminoAcid}2-NH2 \rightarrow \text{AminoAcid}1-CO-NH-AminoAcid}2 + H2O.The covalent bond formed is a peptide bond; the atoms involved share electrons unevenly because oxygen is more electronegative than nitrogen, making the bond polar.
A chain of many amino acids linked by peptide bonds is a polypeptide; a protein is one or more polypeptide chains folded into a functional 3D shape.
Some proteins are small; others are extremely large (e.g., Titin cited above).
The primary structure is the linear sequence of amino acids; this sequence determines higher levels of structure and ultimately function.
Examples: different proteins with diverse functions arise from different amino acid sequences.
Levels of Protein Structure
All proteins have multiple levels of structure: primary, secondary, tertiary, and quaternary.
Primary structure: the sequence of amino acids in the polypeptide chain.
Secondary structure: local folding patterns stabilized mainly by hydrogen bonding between nearby peptide bonds.
Alpha helix (helical regions).
Beta pleated sheet (pleated, accordion-like regions).
Tertiary structure: the overall three-dimensional shape of a single polypeptide, determined by interactions among the R groups (side chains) within the chain. Types of interactions include
Ionic bonds,
Hydrogen bonds,
Covalent bonds (disulfide bridges),
Hydrophobic interactions leading to tight packing of nonpolar R groups.
The tertiary structure is sensitive to environmental conditions (pH, temperature); changes can disrupt interactions and alter the shape.
Quaternary structure: the arrangement and interaction of multiple polypeptide chains in a protein that has more than one chain.
Example: hemoglobin has four polypeptide chains; each chain has its own primary, secondary, and tertiary structure.
Quaternary structure can affect function; disruptions can impair activity, such as oxygen transport by hemoglobin if its quaternary structure is altered.
Fibrous vs globular proteins:
Fibrous proteins have rodlike shapes and often provide structural support (e.g., keratin, collagen).
Globular proteins have rounded 3D shapes and include many enzymes and hemoglobin.
Protein Denaturation and Function
Protein function depends on correctly folded structure; environmental changes can denature proteins.
Denaturation occurs when the tertiary (and sometimes quaternary) structure is disrupted, often by changes in pH or temperature.
Example: frying an egg denatures albumin in the egg, causing it to solidify and change color.
Denaturation can render proteins nonfunctional, though their amino acid sequence remains the same.
Nucleic Acids: DNA and RNA
Nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
They are polymers made of monomers called nucleotides.
Each nucleotide has three parts:
A phosphate group,
A five-carbon sugar (deoxyribose in DNA; ribose in RNA),
A nitrogen-containing base.
The sugar differences give DNA the name deoxyribose (one less oxygen) and RNA the name ribose.
DNA bases: A,\ G,\ C,\ T (adenine, guanine, cytosine, thymine).
RNA bases: A,\ G,\ C,\ U (uracil replaces thymine).
DNA structure:
DNA acts as the storage location for genetic information inside the cell.
Information is stored in sequences of nucleotides called genes, which specify the amino acid sequence in proteins.
DNA is a double helix: two strands spiral around; the backbone is phosphates bound to sugars; bases project inward.
Complementary base pairing holds the two strands together: A\text{-}T with two hydrogen bonds, G\text{-}C with three hydrogen bonds.
Complementary base pairing is crucial for replication (copying DNA).
RNA structure and role:
RNA processes the genetic information contained in DNA to produce proteins.
RNA is usually single-stranded.
RNA structure and interactions with DNA are explored in later sections (e.g., Section 11.1–11.2).
DNA for humans:
The Human Genome Project revealed a complete sequence of about 3\times 10^9 bases and just under 2.0\times 10^4 genes.
ATP as an energy molecule (a nucleotide derivative):
In addition to forming parts of nucleic acids, the nucleotide adenine is a component of ATP, which acts as an energy carrier in cells (to be discussed in Section 5.2).
RNA structure figure (concept): RNA is single-stranded and contains uracil (U) instead of thymine (T).
Connecting the Concepts: Proteins and Nucleic Acids
The R group of an amino acid determines its behavior and the interactions within the polypeptide.
The order of amino acids in a polypeptide determines its shape, and the shape determines function.
DNA contains the information for the sequence of amino acids in polypeptides; genetic differences lead to differences in proteins across organisms.
Small genetic changes can cause large changes in protein function and can lead to disease.
Example: sickle-cell disease arises from a single amino acid substitution in hemoglobin:
One of the hemoglobin chains is 146 amino acids long.
In sickle-cell disease, valine (Val) replaces glutamate (Glu) at the sixth amino acid position: at position 6 the codon change leads to the substitution ext{Glu}
ightarrow ext{Val}.This single substitution alters the red blood cell shape from normally round and flexible to sickled and rigid, causing blockages in small vessels, pain, organ damage, anemia, and can be fatal if untreated.
Root cause: inherited faulty DNA code for a single amino acid in the beta chain of hemoglobin.
Overall: proteins and nucleic acids are interdependent in biology: nucleic acids encode protein structure, and proteins execute cellular functions that enable life.
Real-World and Educational Relevance
Proteins perform diverse roles from structural support to catalysis and signaling; understanding their structure helps explain function and disease.
Nucleic acids store and transmit genetic information, guide protein synthesis, and underlie inheritance and variation across populations.
The distinction between DNA (double-stranded, deoxyribose, thymine) and RNA (single-stranded, ribose, uracil) is foundational for understanding gene expression and regulation.
The Human Genome Project highlighted the scale of genetic information and its link to human biology, evolution, and medicine.
The sickle-cell example demonstrates how genotype influences phenotype and disease risk, reinforcing the link between molecular biology and clinical outcomes.
Quick Review Prompts (Check Your Progress 3.3)
1. Summarize the roles of proteins in the body.
2. Describe the levels of protein structure (primary, secondary, tertiary, quaternary).
3. Explain how nucleic acids differ in structure from other biological molecules (DNA vs RNA; bases, sugar, backbone; replication and transcription concepts).
Key Equations and Notation Used in This Section
Peptide bond formation (dehydration synthesis):
\text{AminoAcid}1-COOH + \text{AminoAcid}2-NH2 \rightarrow \text{AminoAcid}1-CO-NH-AminoAcid}2 + H2O.Base pairing in DNA:
A \leftrightarrow T \quad (two\;H-bonds), \quad G \leftrightarrow C \quad (three\;H-bonds).Protein structure levels (conceptual):
Primary: sequence of amino acids (Aa1, Aa2, \dots, Aa_n)
Secondary: local folding (alpha helix, beta pleated sheet) stabilized by hydrogen bonds
Tertiary: overall 3D shape determined by interactions among R groups
Quaternary: interactions between multiple polypeptide chains
Genome scale references:
Human genome bases: \approx 3 \times 10^9
Human gene count: \approx 2.0 \times 10^4
Protein example sizes:
Titin amino acid length: \approx 3.3\times 10^{4}
Hemoglobin polypeptide chain length: \approx 146 amino acids
Proteins
Proteins are of primary importance in the structure and function of cells. The section highlights multiple roles and examples to show how essential proteins are to life.
Major functions of proteins:
Support: structural proteins such as keratin (hair, fingernails), collagen (skin, ligaments, tendons), and the protein in spider webs. They contribute to the framework and integrity of tissues.
Metabolism: many proteins are enzymes that act as catalysts, bringing reactants together and speeding up chemical reactions. Enzymes are specific for particular reactions and participate in nearly all metabolic processes.
Transport: channel and carrier proteins in the plasma membrane regulate substance movement into and out of cells. In blood, proteins such as hemoglobin transport molecules (e.g., oxygen).
Defense: antibodies are proteins that target pathogens to prevent infection.
Regulation: hormones act as intercellular messengers that influence cellular metabolism (e.g., insulin regulates blood glucose; human growth hormone (hGH) influences height).
Motion: contractile proteins (actin and myosin) enable muscle contraction and cellular movements; muscle activity also helps regulate body temperature.
Examples and context from figures:
Fig. 3.15a: keratin and collagen illustrate structural roles.
Fig. 3.15b: hemoglobin demonstrates transport function (oxygen transport in red blood cells).
Fig. 3.15c: actin and myosin illustrate muscle movement and contraction.
Dietary and metabolic emphasis:
Proteins support body structure and function, but they are not the cell’s preferred energy source (see Section 7.5).
Some dietary proteins may be high in fat (e.g., beef), while others (e.g., fish) include beneficial oils that can influence cardiovascular health (Fig. 3.16).
Structural diversity and organization:
The structures of cells differ by the proteins they contain (e.g., muscle cells with actin/myosin, red blood cells with hemoglobin, support cells with collagen).
Dietary sources of proteins are shown in Fig. 3.16; small servings can provide all essential amino acids if varied.
Amino Acids
Proteins are polymers whose monomers are amino acids.
Amino acids have a common core structure: a central carbon (alpha carbon) bonded to
a hydrogen atom,
an amino group (–NH₂),
a carboxyl group (–COOH),
a variable side chain, or R group.
There are 20 different amino acids, differing by their R groups, which range from a single hydrogen atom to complex ring structures.
Properties of R groups determine amino acid behavior: some are polar, some are charged, and some are nonpolar/hydrophobic.
The order and composition of amino acids in a polypeptide determine its final three-dimensional shape and function.
Size examples:
Ribonuclease (a small protein) contains barely more than ext{approximately } 100 amino acids.
Titin (a very large protein) contains over 3.3 imes 10^{4} amino acids, and is a key part of muscle structure.
The concept of sequence variety:
A protein’s amino acid sequence is unique for each polypeptide, and most proteins contain one or more polypeptide chains.
Even a small change in the amino acid sequence can produce a different fold and loss of function.
Peptides and Peptide Bonds
A peptide forms when two amino acids are joined by a dehydration synthesis reaction between the carboxyl group of one amino acid and the amino group of another:
\text{AminoAcid}1-COOH + \text{AminoAcid}2-NH2 \rightarrow \text{AminoAcid}1-CO-NH-AminoAcid}2 + H2O.The covalent bond formed is a peptide bond; the atoms involved share electrons unevenly because oxygen is more electronegative than nitrogen, making the bond polar.
A chain of many amino acids linked by peptide bonds is a polypeptide; a protein is one or more polypeptide chains folded into a functional 3D shape.
Some proteins are small; others are extremely large (e.g., Titin cited above).
The primary structure is the linear sequence of amino acids; this sequence determines higher levels of structure and ultimately function.
Examples: different proteins with diverse functions arise from different amino acid sequences.
Levels of Protein Structure
All proteins have multiple levels of structure: primary, secondary, tertiary, and quaternary.
Primary structure: the sequence of amino acids in the polypeptide chain.
Secondary structure: local folding patterns stabilized mainly by hydrogen bonding between nearby peptide bonds.
Alpha helix (helical regions).
Beta pleated sheet (pleated, accordion-like regions).
Tertiary structure: the overall three-dimensional shape of a single polypeptide, determined by interactions among the R groups (side chains) within the chain. Types of interactions include
Ionic bonds,
Hydrogen bonds,
Covalent bonds (disulfide bridges),
Hydrophobic interactions leading to tight packing of nonpolar R groups.
The tertiary structure is sensitive to environmental conditions (pH, temperature); changes can disrupt interactions and alter the shape.
Quaternary structure: the arrangement and interaction of multiple polypeptide chains in a protein that has more than one chain.
Example: hemoglobin has four polypeptide chains; each chain has its own primary, secondary, and tertiary structure.
Quaternary structure can affect function; disruptions can impair activity, such as oxygen transport by hemoglobin if its quaternary structure is altered.
Fibrous vs globular proteins:
Fibrous proteins have rodlike shapes and often provide structural support (e.g., keratin, collagen).
Globular proteins have rounded 3D shapes and include many enzymes and hemoglobin.
Protein Denaturation and Function
Protein function depends on correctly folded structure; environmental changes can denature proteins.
Denaturation occurs when the tertiary (and sometimes quaternary) structure is disrupted, often by changes in pH or temperature.
Example: frying an egg denatures albumin in the egg, causing it to solidify and change color.
Denaturation can render proteins nonfunctional, though their amino acid sequence remains the same.
Nucleic Acids: DNA and RNA
Nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
They are polymers made of monomers called nucleotides.
Each nucleotide has three parts:
A phosphate group,
A five-carbon sugar (deoxyribose in DNA; ribose in RNA),
A nitrogen-containing base.
The sugar differences give DNA the name deoxyribose (one less oxygen) and RNA the name ribose.
DNA bases: A,\ G,\ C,\ T (adenine, guanine, cytosine, thymine).
RNA bases: A,\ G,\ C,\ U (uracil replaces thymine).
DNA structure:
DNA acts as the storage location for genetic information inside the cell.
Information is stored in sequences of nucleotides called genes, which specify the amino acid sequence in proteins.
DNA is a double helix: two strands spiral around; the backbone is phosphates bound to sugars; bases project inward.
Complementary base pairing holds the two strands together: A\text{-}T with two hydrogen bonds, G\text{-}C with three hydrogen bonds.
Complementary base pairing is crucial for replication (copying DNA).
RNA structure and role:
RNA processes the genetic information contained in DNA to produce proteins.
RNA is usually single-stranded.
RNA structure and interactions with DNA are explored in later sections (e.g., Section 11.1–11.2).
DNA for humans:
The Human Genome Project revealed a complete sequence of about 3\times 10^9 bases and just under 2.0\times 10^4 genes.
ATP as an energy molecule (a nucleotide derivative):
In addition to forming parts of nucleic acids, the nucleotide adenine is a component of ATP, which acts as an energy carrier in cells (to be discussed in Section 5.2).
RNA structure figure (concept): RNA is single-stranded and contains uracil (U) instead of thymine (T).
Connecting the Concepts: Proteins and Nucleic Acids
The R group of an amino acid determines its behavior and the interactions within the polypeptide.
The order of amino acids in a polypeptide determines its shape, and the shape determines function.
DNA contains the information for the sequence of amino acids in polypeptides; genetic differences lead to differences in proteins across organisms.
Small genetic changes can cause large changes in protein function and can lead to disease.
Example: sickle-cell disease arises from a single amino acid substitution in hemoglobin:
One of the hemoglobin chains is 146 amino acids long.
In sickle-cell disease, valine (Val) replaces glutamate (Glu) at the sixth amino acid position: at position 6 the codon change leads to the substitution ext{Glu}
ightarrow ext{Val}.This single substitution alters the red blood cell shape from normally round and flexible to sickled and rigid, causing blockages in small vessels, pain, organ damage, anemia, and can be fatal if untreated.
Root cause: inherited faulty DNA code for a single amino acid in the beta chain of hemoglobin.
Overall: proteins and nucleic acids are interdependent in biology: nucleic acids encode protein structure, and proteins execute cellular functions that enable life.
Real-World and Educational Relevance
Proteins perform diverse roles from structural support to catalysis and signaling; understanding their structure helps explain function and disease.
Nucleic acids store and transmit genetic information, guide protein synthesis, and underlie inheritance and variation across populations.
The distinction between DNA (double-stranded, deoxyribose, thymine) and RNA (single-stranded, ribose, uracil) is foundational for understanding gene expression and regulation.
The Human Genome Project highlighted the scale of genetic information and its link to human biology, evolution, and medicine.
The sickle-cell example demonstrates how genotype influences phenotype and disease risk, reinforcing the link between molecular biology and clinical outcomes.
Quick Review Prompts (Check Your Progress 3.3)
1. Summarize the roles of proteins in the body.
2. Describe the levels of protein structure (primary, secondary, tertiary, quaternary).
3. Explain how nucleic acids differ in structure from other biological molecules (DNA vs RNA; bases, sugar, backbone; replication and transcription concepts).
Key Equations and Notation Used in This Section
Peptide bond formation (dehydration synthesis):
\text{AminoAcid}1-COOH + \text{AminoAcid}2-NH2 \rightarrow \text{AminoAcid}1-CO-NH-AminoAcid}2 + H2O.Base pairing in DNA:
A \leftrightarrow T \quad (two\;H-bonds), \quad G \leftrightarrow C \quad (three\;H-bonds).Protein structure levels (conceptual):
Primary: sequence of amino acids (Aa1, Aa2, \dots, Aa_n)
Secondary: local folding (alpha helix, beta pleated sheet) stabilized by hydrogen bonds
Tertiary: overall 3D shape determined by interactions among R groups
Quaternary: interactions between multiple polypeptide chains
Genome scale references:
Human genome bases: \approx 3 \times 10^9
Human gene count: \approx 2.0 \times 10^4
Protein example sizes:
Titin amino acid length: \approx 3.3\times 10^{4}
Hemoglobin polypeptide chain length: \approx 146 amino acids
3.1 Organic Molecules
Definition: To be organic, a molecule must contain both carbon and hydrogen.
Carbon chemistry contributes to the diversity of organic molecules because carbon forms four covalent bonds, enabling complex and variable structures.
Functional groups determine chemical reactivity and properties of organic molecules.
Some functional groups are nonpolar (hydrophobic).
Some functional groups are polar (hydrophilic).
Biological molecules in cells are called biological molecules or biomolecules.
Isomers: molecules with the same molecular formula but different structures, leading to different properties and functions.
3.2 Carbohydrates and Lipids
Biological molecules are synthesized by dehydration synthesis (condensation) reactions and degraded by hydrolysis (water-added) reactions.
Four major classes of biological molecules: carbohydrates, lipids, proteins, nucleic acids.
Polymers and monomers:
Polymers: polysaccharides, proteins, nucleic acids are formed by linking monomers in long chains.
Lipids are varied and do not have a single monomer.
Table 3.1 overview (summary):
Carbohydrates: Examples — monosaccharides, disaccharides, polysaccharides; Monomer — monosaccharide units; Functions — immediate energy and stored energy; structural roles.
Lipids: Examples — fats, oils, phospholipids, steroids; Monomer — no single monomer; Functions — long-term energy storage; membrane components.
Proteins: Examples — structural, enzymatic, carrier, hormonal, contractile; Monomer — amino acids; Functions — support, metabolism, transport, regulation, motion.
Nucleic acids: Examples — DNA, RNA; Monomer — nucleotides; Functions — storage of genetic information and processing to form proteins.
Carbohydrates details:
Glucose: a monosaccharide that serves as blood sugar and as a monomer for starch, glycogen, and cellulose.
Isomers: Fructose and galactose.
Ribose and deoxyribose: monosaccharides found in nucleic acids.
Sucrose: a disaccharide (glucose + fructose); other disaccharides include maltose and lactose.
Polysaccharides (all polymers of glucose):
Starch: stores energy in plants.
Glycogen: stores energy in animals.
Cellulose: structural component in plant cell walls.
Chitin: polysaccharide that contains amino groups.
Lipids:
Lipids are hydrophobic and often serve as long-term energy storage.
Fats and oils are triglycerides (glycerol + three fatty acids).
Saturated fatty acids (no double bonds) → fats (solid at room temperature).
Unsaturated fatty acids (one or more double bonds) → oils (liquid at room temperature).
Trans fats: unsaturated fats with a trans configuration in the fatty acid chain.
Phospholipids: glycerol backbone with two fatty acids and a phosphate group; phosphate-containing head is polar, tails are nonpolar; form the plasma membrane and other cellular membranes.
Steroids: lipids with four fused hydrocarbon rings.
Cholesterol: a steroid; component of the plasma membrane.
Sex hormones (testosterone and estrogen) are steroids.
3.3 Proteins and Nucleic Acids
Proteins:
Proteins are polymers of amino acids.
A peptide is composed of two amino acids linked by a peptide bond; a chain of many amino acids forms a polypeptide.
Functions: enzymes (catalyze chemical reactions), structural roles, transport, signaling, regulation, motion, etc.
Protein structure has multiple levels:
Primary structure: the linear sequence of amino acids.
Secondary structure: helices (alpha) or pleated sheets (beta).
Tertiary structure: three-dimensional folding of a single polypeptide chain.
Quaternary structure: assembly of multiple polypeptides into a functional protein.
Denaturation: loss of protein structure and function due to conditions like heat, pH changes, or chemicals.
Nucleic Acids:
Nucleic acids are polymers of nucleotides.
DNA (deoxyribonucleic acid):
Sugar: deoxyribose.
Structure: double-stranded and forms a double helix.
Bases: Adenine (A), Guanine (G), Thymine (T), Cytosine (C).
Complementary base pairing: A ext{ pairs with } T,\quad G ext{ pairs with } C.
RNA (ribonucleic acid):
Sugar: ribose.
Bases: Adenine (A), Guanine (G), Uracil (U), Cytosine (C).
Structure: single-stranded and does not form a double helix inherently.
Genes: sequences of nucleotides that store information to synthesize proteins.
ATP (adenosine triphosphate): a modified nucleic acid used as the main energy carrier in cells.
Table 3.2 compares DNA and RNA structures:
Sugar: DNA uses Deoxyribose; RNA uses Ribose.
Bases: DNA {A, G, T, C}; RNA {A, G, U, C}.
Strands: DNA is double-stranded; RNA is single-stranded.
Helix: DNA is a helix; RNA is not inherently helical.
DNA vs RNA (Table 3.2) – Key contrasts
DNA: ext{Sugar} = ext{Deoxyribose}, ext{ Bases} = ext{A, G, T, C}, ext{ Strands} = ext{Double-stranded}, ext{ Helix} = ext{Yes}
RNA: ext{Sugar} = ext{Ribose}, ext{ Bases} = ext{A, G, U, C}, ext{ Strands} = ext{Single-stranded}, ext{ Helix} = ext{No}
Thinking Critically About Biology
Question 1: We often hear physicians refer to cholesterol as “good” and “bad.” Why is this done, and why is it not accurate to describe any organic molecule as good or bad?
Answer sketch: There is only one chemical entity called cholesterol; health effects depend on context (e.g., transport and receptor interactions). The labels “good” and “bad” reflect associations with cardiovascular risk factors (e.g., LDL vs HDL pathways), not intrinsic moral attributes of the molecule. The material emphasizes that classifying any single molecule as inherently good or bad oversimplifies its diverse roles in physiology and pathology.
Question 2: Why study mutations that swap one amino acid for another to understand the relationship between enzyme structure and function?
Answer sketch: Amino acid substitutions can alter the chemical environment of an active site or stability of the protein. Replacing a residue with a nonpolar R group may preserve core interactions, while replacing with a polar R group can disrupt active site geometry, electrostatics, or hydrogen-bond networks, affecting activity.
Question 3: Why do more distantly related species show greater changes in amino acid sequences of the same protein?
Answer sketch: Over evolutionary time, sequences accumulate substitutions. Distant relatives have diverged longer, accumulating more neutral and sometimes adaptive changes, while essential functional constraints preserve key residues. This pattern helps infer evolutionary relationships and functional conservation.
Making It Relevant to You
Question 1: Explain how knowledge of triglyceride saturation affects healthier grocery choices.
Points to consider:
Saturated fats (no double bonds) tend to be solid at room temperature and are linked to higher LDL cholesterol in some contexts.
Unsaturated fats (one or more double bonds) tend to be liquid and are generally considered healthier for heart health when replacing saturated fats.
Trans fats are associated with negative health effects and are typically avoided.
Reading nutrition labels helps identify sources of saturated versus unsaturated fats and trans fats.
Question 2: When scientists search for evidence of life on other planets/moons, besides water, which molecules are looked for?
Key idea: carbon-containing (bioessential) molecules and potential biomarkers such as simple organic compounds (e.g., amino acids, nucleotides, lipids), especially those showing chiral or functional group patterns consistent with known biochemistry.
Relevance: Presence of complex organic molecules could indicate chemical processes compatible with life or past life.
Question 3: Why is it unlikely that an individual has an immune sensitivity to carbohydrates?
Explanation: Immune responses commonly target protein antigens because peptides are presented by MHC molecules and recognized by immune receptors. Carbohydrates can be antigens, but many immune responses to foods are against proteins (e.g., gluten-containing proteins) rather than simple carbohydrate moieties. Gluten is a protein, not a carbohydrate, despite its name.
Answer Key
Answer Key: Thinking Critically About Biology questions have an accompanying answer key referenced in the material. Click the provided link for the official solutions and explanations.
Connections to foundational principles and real-world relevance
Chemical basis of life: Carbon’s tetravalence drives the diversity of biomolecules and underpins macromolecular complexity.
Structure–function relationships: The specific arrangement of atoms in carbohydrates, lipids, proteins, and nucleic acids determines their roles in energy storage, membranes, catalysis, information storage, and regulation.
Metabolism and energetics: Dehydration synthesis and hydrolysis are fundamental reaction types in building and breaking down macromolecules; ATP as an energy currency integrates metabolism with cellular processes.
Health and disease: Lipid saturation and cholesterol management influence cardiovascular risk; protein mutations inform understanding of enzyme deficiencies and genetic diseases.
Evolution and biology: Comparative sequence analysis across species informs evolutionary relationships and the conservation of essential biological functions.