Chapter 3 Notes - The Chemical Basis of Life II: Organic Molecules
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Chapter 3 – The Chemical Basis of Life II: Organic Molecules
Chapter Outline
1. The carbon atom and carbon-containing molecules
2. Synthesis and breakdown of organic molecules
3. Overview of the 4 major classes of organic molecules found in living cells
4. Carbohydrates
5. Lipids
6. Proteins
7. Nucleic acids
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3.1 The Carbon Atom and Carbon-Containing Molecules
Section 3.1 Learning Outcomes
Explain the properties of carbon that make it the chemical basis of all life
Describe the variety and chemical characteristics of common functional groups of organic compounds
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3.1 The Carbon Atom and Carbon-Containing Molecules
Carbon Forms Four Covalent Bonds with Other Atoms
Organic molecules contain carbon.
Carbon has 4 electrons in its outer (valence) shell and needs 4 more electrons to fill the shell, allowing it to form up to four covalent bonds.
Bonds can be single, double, or triple, and can be polar or nonpolar depending on the bonding partner.
From carbon’s bonding versatility, many diverse molecules can be built, typically using other common atoms such as oxygen, hydrogen, and nitrogen.
Hydrocarbons (composed of C–C and C–H bonds) are nonpolar, hydrophobic, and poorly soluble in water.
Oxygen and nitrogen form polar bonds with carbon, rendering those portions of molecules more hydrophilic and water-soluble.
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3.1 The Carbon Atom and Carbon-Containing Molecules
Carbon Forms Four Covalent Bonds with Other Atoms (continued)
Carbon can form polar or nonpolar covalent bonds depending on the electronegativity of the bonding partner.
Hydrocarbons are nonpolar and hydrophobic.
Oxygen and nitrogen form polar bonds with carbon, contributing to hydrophilicity and water solubility.
Functional Groups
Carbon atoms may be arranged into functional groups.
Functional groups are groups of atoms with characteristic chemical structures and properties.
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3.1 The Carbon Atom and Carbon-Containing Molecules
Functional Groups (continued)
A functional group exhibits similar chemical properties in all molecules in which it occurs.
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3.2 Synthesis and Breakdown of Organic Molecules
Section 3.2 Learning Outcomes
Diagram how small organic molecules are assembled into larger ones by dehydration reactions
Diagram how hydrolysis reactions break down larger organic molecules into smaller ones
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3.2 Synthesis and Breakdown of Organic Molecules
Some important macromolecules found in cells (proteins, carbohydrates, nucleic acids) are formed by linking many small monomers to form polymers.
Polymers are formed by dehydration reactions: a molecule of water is removed each time a new monomer is added, repeating to form long polymers. Dehydration reactions are catalyzed by enzymes.
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3.2 Synthesis and Breakdown of Organic Molecules
Polymers are broken down into their constituent monomers by hydrolysis reactions: a molecule of water is added back each time a monomer is released, repeating to break down polymers. Hydrolysis is catalyzed by enzymes.
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3.3 Overview of the 4 Major Classes of Organic Molecules
Section 3.3 Learning Outcomes
Compare and contrast the structures and functions of carbohydrates, lipids, proteins, and nucleic acids
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3.3 Overview of the 4 Major Classes of Organic Molecules
The 4 major classes of organic molecules are carbohydrates, lipids, proteins, and nucleic acids.
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3.4 Carbohydrates
Section 3.4 Learning Outcomes
Describe the structure and function and give examples of monosaccharides, disaccharides, and polysaccharides
Relate the functions of plant and animal polysaccharides to their structure
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3.4 Carbohydrates
Carbohydrates are composed of carbon, hydrogen, and oxygen in a predictable ratio: Cn (H2O)n where n is a whole number.
Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group.
Particular carbons are identified with numbers (e.g., carbon-1, carbon-2, …).
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3.4 Carbohydrates
Monosaccharides and Disaccharides Are Simple Carbohydrates
Monosaccharides (1) are the simplest sugars and the monomers used to construct larger carbohydrates.
Most common monosaccharides contain 5 or 6 carbons.
Pentoses: includes ribose (C5H10O5) and deoxyribose (C5H10O4).
Hexoses: includes glucose (C6H12O6) and fructose (C6H12O6).
Isomers: molecules with identical chemical formulas but different structures (e.g., galactose, glucose, fructose).
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3.4 Carbohydrates
Monosaccharides and Disaccharides Are Simple Carbohydrates
Monosaccharides can be joined to form disaccharides.
Disaccharides are formed through dehydration reactions and broken down through hydrolysis reactions.
Sucrose (table sugar) is formed from glucose + fructose.
Lactose and maltose are also disaccharides.
The covalent bond formed between two sugars is called a glycosidic bond.
Monosaccharides and disaccharides often function as an energy source.
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3.4 Carbohydrates
Polysaccharides Are Carbohydrate Polymers
Storage = For later, Source = Right away
Polysaccharides are formed when many monosaccharides are linked together. Examples include:
starch: energy storage in plant cells
glycogen: energy storage in certain animal cells
cellulose: provides strength to plant cell walls
peptidoglycans: found in cell walls of certain bacteria
chitin: found in cell walls of fungi and in exoskeletons of arthropods
glycosaminoglycans: found in connective tissues surrounding animal cells (e.g., abundant in cartilage)
Starch, glycogen, and cellulose are built from glucose monomers.
Other polysaccharides are built from different sugar monomers that may have additional functional groups, such as amino groups.
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3.4 Carbohydrates
Polysaccharides Are Carbohydrate Polymers (continued)
The bonds that form in polysaccharides are between specific carbon atoms of each molecule.
The overall structure can range from straight to highly branched.
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3.5 Lipids
Section 3.5 Learning Outcomes
List the different classes of lipid molecules important in living organisms
Diagram the structure of a triglyceride, and explain how it is formed and how its structure is affected by the presence of saturated and unsaturated fatty acids
Explain why some fats are solid at room temperature and others are liquid
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3.5 Lipids
Section 3.5 Learning Outcomes Cont’d
Discuss how triglycerides function as energy-storage molecules
Explain why phospholipids form a bilayer when dissolved in water
Describe the chemical structure of steroids and give an example of their biological importance
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3.5 Lipids
Lipids are composed predominantly of hydrogen and carbon atoms. (Nonpolar, hydrophobic)
A defining feature is that they are nonpolar and thus insoluble in water.
Lipids can be described as hydrophobic hydrocarbons.
Lipids are structurally diverse and do not adhere to a monomer/polymer scheme like other macromolecules.
Examples include triglycerides (fats & oils), phospholipids, steroids, and waxes.
Lipids comprise about 40% of the organic matter in the average human body.
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3.5 Lipids
Triglycerides Are Made from Glycerol and Fatty Acids
Triglycerides (fats and oils) are formed by bonding glycerol to 3 fatty acids.
Fatty acids are long hydrocarbon chains with a carboxyl group at one end.
Joined by dehydration; broken apart by hydrolysis.
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3.5 Lipids
Triglycerides: Saturation and Fatty Acids
Fatty acids in triglycerides may differ in length and in the presence/absence of C=C.
(S)aturated fatty acids have no C=C bonds; all carbons are connected by single bonds and have (S)traight structures.
Monounsaturated fatty acids have one C=C, introducing a kink (bent).
Polyunsaturated fatty acids have two or more C=C.
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3.5 Lipids
Consequences of Saturation
Straight saturated fatty acids pack more tightly than unsaturated fatty acids.
More energy(heat) is required to melt saturated fatty acids compared to unsaturated ones.
Animal fats typically have higher levels of saturated fatty acids; plants typically have more unsaturated fatty acids.
Examples:
Stearic acid in beef fat melts at 70^{\degree}{C}^{} (solid at room temperature).
Oleic acid in olive oil melts at 16^{}{°C} (liquid at room temperature).
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3.5 Lipids
Phospholipids Are Amphipathic Lipids
Phospholipids are similar in structure to triglycerides but are formed from glycerol, 2 fatty acids, and a phosphate group.
Phospholipids are amphipathic: the phosphate "head" is polar and hydrophilic, while the fatty acid "tail" is nonpolar and hydrophobic.
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3.5 Lipids
Phospholipids and the Bilayer
In water, phospholipids organize into a double layer called a bilayer; phospholipid bilayer fundamental for forming the basis of cell membranes.
The bilayer promotes stable chemical interactions: non-polar tails interact with other nonpolar structures; polar heads interact with water and other polar structures.
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3.5 Lipids
Steroids
Steroids contain four interconnected rings of carbon atoms.
They are primarily carbon and hydrogen and are usually insoluble in water.
Example: cholesterol.
Tiny structural differences can lead to distinct biological properties (e.g., estrogen vs. testosterone).
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3.5 Lipids
Waxes
Waxes are complex lipids that prevent water loss from organisms.
They are long structures resembling a fatty acid attached to another long hydrocarbon chain and are very nonpolar.
Uses include protecting organisms from water loss or serving structural roles (e.g., waxy leaf surface, beeswax in honeycombs).
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3.6 Proteins
Section 3.6 Learning Outcomes
Describe the general functions of proteins
Diagram the structure of an amino acid
Describe how amino acids are joined to form a polypeptide
Diagram and explain the 4 levels of protein structure
Outline the factors that determine protein shape and function
Define protein domain
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3.6 Proteins
Proteins are composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of sulfur.
Proteins perform a variety of diverse functions in cells.
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3.6 Proteins
Amino Acids Are the Building Blocks of Proteins
Proteins are polymers made up of 20 different amino acids.
Each amino acid has a common core structure plus a variable side chain (R).
Core features include: a central
α-carbon,
amino group,
carboxyl group,
hydrogen.
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3.6 Proteins
Amino Acids: Side-Chain Properties
Side chains (R groups) categorize amino acids as polar or nonpolar.
Nonpolar (hydrophobic) amino acids include: Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, Trp (and others).
Polar (uncharged) amino acids include Ser, Thr, Asn, Gln, Tyr among others.
Polar (charged) amino acids include:
Acidic: Asp (D), Glu (E)
Basic: His (H), Lys (K), Arg (R)
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3.6 Proteins
Continued: Amino Acids and Side Chains
Diagrammatic representations show functional groups such as hydroxyl (OH), amino (NH2), carboxyl (COO- or COOH), and various side chains.
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3.6 Proteins
Amino Acids Are Joined by Dehydration to Form Peptide Bonds
A dehydration reaction links the carboxyl group of one amino acid to the amino group of another.
The covalent bond formed between carbon and nitrogen is called a peptide bond.
Polymers of amino acids are polypeptides; proteins may be composed of one or more polypeptides.
Polypeptides are broken down by hydrolysis.
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3.6 Proteins
(start) N-Terminus and (end) C-Terminus
The N-terminus is the end with a free amino group; the C-terminus is the end with a free carboxyl group.
Amino acids are numbered from the N-terminus to the C-terminus.
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3.6 Proteins
Protein Structure: A Hierarchy of 4 Levels
Primary structure: linear sequence of amino acids encoded by genes; peptide bonds contribute to primary structure.
Secondary structure: hydrogen bonds between NH and CO groups of the backbone promote folding into an α-helix or β-pleated sheet; turns and loops can form.
Tertiary structure: the overall 3D folded shape of a single polypeptide; R groups participate in chemical interactions and all types of bonds can contribute.
Quaternary structure: assembly of two or more polypeptide subunits into a functional protein; all types of bonds can contribute.
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3.6 Proteins
Protein Structure Is Determined by Several Factors
Hydrogen bonds
Ionic bonds
Hydrophobic effect (nonpolar side chains tend to be in the protein's interior or within membranes)
Van der Waals dispersion forces
Disulfide bridges (covalent bonds between cysteine —SH groups)
Protein–protein interactions are also influenced by their shapes.
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3.6 Proteins
Diagrammatic notes show examples of hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces, and disulfide bonds that stabilize structure.
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3.6 Proteins
Functional Domains
Many proteins have a modular design with distinct regions called domains that have their own structures and functions.
Domains can be duplicated during evolution; the same domain may be found in different proteins.
A single protein can have multiple domains with unique functions (e.g., nuclear receptor proteins with a ligand-binding domain, a DNA-binding domain, a nuclear localization domain, and an activation domain).
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3.7 Nucleic Acids
Section 3.7 Learning Outcomes
Describe the 3 components of a nucleotide
Distinguish between the structures of DNA and RNA
Explain how certain bases pair with others in DNA
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3.7 Nucleic Acids
Nucleotides Are the Building Blocks of DNA and RNA
Nucleic acids store, express, and transmit genetic information.
Two classes: DNA and RNA.
DNA stores genetic information in the sequence of nucleotide monomers; RNA decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain.
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3.7 Nucleic Acids
Nucleotides: Components
Each nucleotide is composed of three components:
a phosphate group
a pentose sugar (ribose or deoxyribose)
a nitrogenous base
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3.7 Nucleic Acids
Bases in DNA and RNA
DNA bases: purines (adenine A, guanine G) and pyrimidines (cytosine C, thymine T).
Nucleotides are linked via phosphate groups; the 3' carbon of one nucleotide links to the 5' carbon of the next, forming the sugar-phosphate backbone.
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3.7 Nucleic Acids
DNA Structure
DNA consists of two strands of nucleotides forming a double helix.
Strands are held together by hydrogen bonds between complementary base pairs: A pairs with T via 2 hydrogen bonds; C pairs with G via 3 hydrogen bonds.
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3.7 Nucleic Acids
RNA Structure
RNA is usually single-stranded.
RNA nucleotides contain the sugar ribose.
RNA uses uracil (U) in place of thymine (T).
RNA exists in several forms, including mRNA, rRNA, and tRNA, all involved in using DNA information to synthesize a polypeptide chain.
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Chapter 3 Summary
3.1 The carbon atom and carbon-containing molecules:
Carbon forms 4 covalent bonds (polar or nonpolar depending on partners);
Carbon atoms can be arranged into functional groups with specific properties.
3.2 Synthesis and breakdown of organic molecules:
Dehydration reactions link monomers into polymers; enzymes catalyze them.
Hydrolysis breaks polymers into monomers; enzymes catalyze this as well.
3.3 Overview of the four major classes of organic molecules:
Carbohydrates, lipids, proteins, nucleic acids.
3.4 Carbohydrates:
Monosaccharides and disaccharides are simple carbohydrates; polysaccharides are polymers built from glucose or other sugars.
3.5 Lipids:
Triglycerides formed from glycerol and 3 fatty acids; phospholipids are amphipathic; steroids have ring structures; waxes prevent water loss.
3.6 Proteins:
Amino acids are the building blocks; proteins have primary, secondary, tertiary, and quaternary structures; factors include hydrogen bonds, ionic bonds, hydrophobic effect, van der Waals forces, disulfide bridges; many proteins have functional domains.
3.7 Nucleic Acids:
Nucleotides are the building blocks; DNA is double-stranded with A–T and C–G base pairing; RNA is typically single-stranded and uses uracil; roles of mRNA, rRNA, and tRNA in protein synthesis.
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Chapter 3 Summary (continued)
Recap of key concepts: carbon chemistry; polymers via dehydration and hydrolysis; the four major macromolecule classes; detailed structure-function relationships in carbohydrates, lipids, proteins, and nucleic acids; and the molecular basis of genetic information flow.