Chapter 3 – The Chemical Basis of Life II: Organic Molecules

The Carbon Atom and Carbon-Containing Molecules

• Organic molecules contain carbon.

• Carbon has 4 electrons in its outer shell.

• It needs 4 more electrons to fill the valence shell.

• Carbon can form up to four covalent bonds, which may be polar or nonpolar, depending on the bonding partner.

• It can form single, double, or even triple bonds.

• Many diverse molecules can be built from carbon and a few other atoms like oxygen, hydrogen, and nitrogen due to carbon's bonding capacity.

• Carbon can form polar or nonpolar covalent bonds depending on the electronegativity of the bonding partner.

• Hydrocarbons are nonpolar, containing only C-C and C-H bonds, making them hydrophobic and poorly soluble in water.

• Oxygen and nitrogen form polar bonds with carbon, making them hydrophilic and soluble in water.

• Functional groups are groups of atoms with characteristic chemical structures and properties.

• A functional group exhibits similar chemical properties in all molecules in which it occurs.

Synthesis and Breakdown of Organic Molecules

• Important macromolecules found in cells (proteins, carbohydrates, nucleic acids) are formed by linking many small monomers together to form a polymer.

• Polymers are formed by dehydration reactions where a molecule of water is removed each time a new monomer is added; the process repeats to form long polymers.

• Dehydration reactions are catalyzed by enzymes.

• Polymers are broken down into their constituent monomers by hydrolysis reactions where a molecule of water is added back each time a monomer is released; the process repeats to break down a long polymer.

• Hydrolysis reactions are catalyzed by enzymes.

Overview of the 4 Major Classes of Organic Molecules

• The 4 major classes of organic molecules are carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

• Carbohydrates are composed of carbon, hydrogen, and oxygen atoms 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.

• Monosaccharides are the simplest sugars and are the monomers used to construct larger carbohydrates.

• The most common types of monosaccharides contain 5 or 6 carbons.

  • Pentoses include ribose (C5H{10}O5) and deoxyribose (C5H{10}O4).

  • Hexoses include glucose (C6H{12}O6) and fructose (C6H{12}O6).

• Isomers are molecules with identical chemical formulas but different structures (e.g., galactose, glucose, and fructose).

• Monosaccharides can be joined together 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 2 sugars is called a glycosidic bond.

• Monosaccharides and disaccharides often function as an energy source.

• Polysaccharides are formed when many monosaccharides are linked together. Examples include:

  • Starch: functions as energy storage in plant cells.

  • Glycogen: functions as energy storage in certain animal cells.

  • Cellulose: provides strength to plant cell walls.

  • Peptidoglycans: found in the cell walls of certain bacteria.

  • Chitin: found in cell walls of fungi and exoskeletons of arthropods.

  • Glycosaminoglycans: found in connective tissues surrounding animal cells (e.g., abundant in cartilage).

• Starch, glycogen, and cellulose are all built from glucose monomers.

• Other polysaccharides are built from different sugar monomers that may have additional functional groups, such as amino groups.

• The bonds that form in polysaccharides are between specific carbon atoms of each molecule.

• The overall structure can range from straight to highly branched.

Lipids

• Lipids are composed predominantly of hydrogen and carbon atoms.

• A defining feature of lipids is that they are nonpolar and therefore very insoluble in water and are described as hydrophobic hydrocarbons.

• Lipids are structurally diverse and do not adhere to the monomer/polymer structure that occurs in other biological macromolecules.

• Examples include triglycerides (fats & oils), phospholipids, steroids, and waxes.

• Lipids comprise about 40% of the organic matter in the average human body.

• Triglycerides are the molecules commonly known as fats and oils, formed by bonding a glycerol to 3 fatty acids.

• Fatty acids are long hydrocarbon chains with a carboxyl group at one end and are joined by dehydration and broken apart by hydrolysis.

• The fatty acids found in triglycerides and other lipids may differ in their length and the presence/absence of C=C.

  • Saturated fatty acids do not have any double-bonded carbons (C=C) within the hydrocarbon chain; all carbons are connected by single bonds (C-C) and the molecule has a straight structure.

  • Monounsaturated fatty acids contain one C=C, which introduces a kink into the shape.

  • Polyunsaturated fatty acids contain two or more C=C.

• Due to their straight structure, saturated fatty acids can pack together more tightly than unsaturated fatty acids.

• It takes more energy (heat) to melt saturated fatty acids than unsaturated fatty acids.

• Animal fats typically contain a high level of saturated fatty acids whereas plants typically contain more unsaturated fatty acids.

  • Stearic acid (found in beef fat) melts at 70°C (solid at room temp) whereas oleic acid (found in olive oil) melts at 16°C (liquid at room temp).

• Phospholipids are similar in structure to triglycerides but are formed from glycerol, 2 fatty acids, and a phosphate group.

• Phospholipids are amphipathic molecules with a polar and hydrophilic phosphate "head" and nonpolar and hydrophobic fatty acid "tail".

• In water, phospholipids become organized into a double layer, called a bilayer, which is fundamental for forming cell membranes.

• The bilayer configuration promotes stable chemical interactions where nonpolar tails can interact with other nonpolar structures, and polar heads can interact with water and other polar structures.

• Steroids have four interconnected rings of carbon atoms, are primarily composed of carbon and hydrogen, and are usually insoluble in water (e.g., cholesterol).

• Tiny differences in structure can lead to profoundly different, specific biological properties (e.g., estrogen vs. testosterone).

• Waxes are long structures that resemble a fatty acid attached to another long hydrocarbon chain and are very nonpolar, excluding water.

• Waxes are used to protect organisms from water loss or as structural elements (e.g., waxy surface on leaves, beeswax in honeycombs).

Proteins

• Proteins are composed of carbon, hydrogen, oxygen, nitrogen (and small amounts of other elements, notably sulfur).

• Proteins perform a variety of diverse functions in cells.

• Proteins are polymers composed of 20 different amino acids.

• Each amino acid has a common core structure containing:

  • α-carbon

  • amino group

  • carboxyl group

  • hydrogen

• Each amino acid also contains a variable side chain (designated R).

• Amino acids are categorized by the chemical properties of their side chains; some R groups are polar while others are nonpolar.

• Amino acids are joined together by a dehydration reaction that links the carboxyl group of one amino acid to the amino group of another.

• The covalent bond formed between the carbon and nitrogen is called a peptide bond.

• Polymers of amino acids are known as polypeptides.

• Proteins may be formed from one or several polypeptides.

• Polypeptides are broken down by hydrolysis.

• The N-terminus is the end with a free amino group, and the C-terminus is the end with a free carboxyl group.

• Amino acids are numbered from the N-term to the C-term.

• Protein structure is characterized at 4 progressive levels:

  • Primary structure is the linear sequence of amino acids (encoded by genes); peptide bonds contribute to primary structure.

  • Secondary structure forms as some chemical groups (NH and CO) of the backbone interact with each other via hydrogen bonds. α helices and β pleated sheets are common; turns and loops can also form as part of secondary structure.

  • Tertiary structure is the overall 3-dimensional folded shape of the protein; R groups participate in chemical interactions, and all types of bonds can potentially contribute to tertiary structure. For some proteins, this is the final level of structure.

  • Quaternary structure occurs when 2 or more protein subunits are assembled together to form a functional complex; all types of chemical bonds can potentially contribute to quaternary structure.

• Many types of chemical interactions influence protein structure and the ability of proteins to interact with each other:

  • Hydrogen bonds

  • Ionic bonds

  • Hydrophobic effect (hydrophobic side chains are likely to be found in the center of a protein or embedded within a membrane)

  • van der Waals dispersion forces

  • Disulfide bridges (covalent bonds that can form between the sulfhydryl —SH groups of cysteine)

• Interactions between proteins are also facilitated by their shapes.

• Many proteins have a modular design where portions of the protein, called domains, have distinct structures and functions.

• Domains have been duplicated during evolution, so the same domain may be found in different proteins.

• A single protein can have multiple domains, each with a unique function; ex: nuclear receptor proteins have a ligand-binding domain, a DNA-binding domain, a nuclear localization domain, and an activation domain.

Nucleic Acids

• Nucleic acids are responsible for the storage, expression, and transmission of genetic information.

• Two classes:

  • Deoxyribonucleic acid (DNA) stores genetic information encoded in the sequence of nucleotide monomers.

  • Ribonucleic acid (RNA) decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain.

• Nucleic acids (DNA & RNA) are polymers; nucleotides are the monomer building blocks of nucleic acids.

• Nucleotides are composed of three components:

  • a phosphate group

  • a pentose sugar (ribose or deoxyribose)

  • a nitrogenous base

• The nitrogenous bases in DNA:

  • The purines, adenine (A) and guanine (G), have a double-ring structure.

  • The pyrimidines, cytosine (C) and thymine (T), have a single-ring structure.

• Nucleotides are linked together via the phosphate groups; the 3’ carbon of one nucleotide is linked to the 5’ carbon of the next, forming a sugar-phosphate backbone.

• A DNA molecule consists of 2 strands of nucleotides, coiled around each other to form a double helix.

• The strands are held together by hydrogen bonds that form between complementary base pairs.

  • A pairs with T through 2 hydrogen bonds.

  • C pairs with G through 3 hydrogen bonds.

• Although they are generally similar, the structure of RNA differs in a few ways from the structure of DNA.

• RNA is usually single stranded.

• RNA nucleotides contain the sugar ribose.

• RNA uses the nitrogenous base uracil in place of thymine; uracil forms hydrogen bonds with adenine.

• RNA comes in several forms including messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).

• mRNA, rRNA, and tRNA are all involved in the process of using the information encoded in DNA to make polypeptides.