The Structure and Function of Large Biological Molecules
Chapter 5: The Structure and Function of Large Biological Molecules
The Molecules of Life
All living organisms are comprised of four classes of large biological molecules:
Carbohydrates
Lipids
Proteins
Nucleic Acids
Macromolecules are characterized as large and complex molecules.
Unique properties of large biological molecules arise from the specific arrangement of their atoms.
Concept 5.1: Macromolecules as Polymers, Built from Monomers
A polymer is described as a long molecule composed of many similar building blocks.
The individual building blocks that form polymers are known as monomers.
Three of the four classes of organic molecules involved in life (carbohydrates, proteins, and nucleic acids) are classified as polymers; while lipids do not fit the true polymer definition.
The Synthesis and Breakdown of Polymers
Enzymes are specialized macromolecules that accelerate chemical reactions, including those that synthesize or degrade polymers.
A dehydration reaction occurs when two monomers bond together with the release of a water molecule, contributing to polymer synthesis.
Conversely, hydrolysis is the reaction through which polymers are disassembled into monomers, representing the reverse of the dehydration process.
Figure 5.2: The Synthesis and Breakdown of Polymers
a) Dehydration reaction: synthesizing a polymer.
b) Hydrolysis: breaking down a polymer.
The Diversity of Polymers
Cells contain thousands of different macromolecules.
Variation of macromolecules can be observed across cells of a single organism, within species, and between different species.
A wide variety of polymers can be formed from a limited set of monomers.
Concept 5.2: Carbohydrates Serve as Fuel and Building Material
Carbohydrates include sugars and polymers of sugars.
The simplest form of carbohydrates, monosaccharides, are also known as simple sugars.
Carbohydrate macromolecules are known as polysaccharides, which comprise long chains of sugar monomers.
Sugars
Monosaccharides have molecular formulas that are typically expressed as multiples of CH₂O.
Glucose is identified as the most prevalent monosaccharide.
Monosaccharides can be classified based on:
The position of the carbonyl group: classified as aldose or ketose.
The number of carbons in the carbon chain.
Figure 5.3: The Structure and Classification of Some Monosaccharides
Aldoses (Aldehyde sugars)
Ketoses (Ketone sugars)
Trioses: Three-carbon sugars
Pentoses: Five-carbon sugars
Hexoses: Six-carbon sugars
Sugars Continued
In aqueous solutions, most sugars typically form ring structures rather than remain in linear configurations.
Monosaccharides play a critical role as a primary fuel source for cellular processes and as raw materials for further macromolecule synthesis.
Figure 5.4: Linear and Ring Forms of Glucose
a) Displays both linear and ring forms.
b) Depicts an abbreviated ring structure.
Disaccharides
A disaccharide is created through a dehydration reaction that connects two monosaccharides.
This covalent bond, known as a glycosidic linkage, is fundamental in sugar polymer connections.
Figure 5.5: Examples of Disaccharide Synthesis
a) Dehydration reaction leading to maltose synthesis.
b) Dehydration reaction involved in sucrose synthesis.
Polysaccharides
Polysaccharides, composed of sugar polymers, are integral due to their storage and structural functions.
The architectural design and functionality of a polysaccharide are dictated by its sugar monomers and the positioning of its glycosidic linkages.
Storage Polysaccharides
Starch serves as the primary storage polysaccharide in plants, consisting exclusively of glucose monomers.
Plants store surplus starch as granules located within chloroplasts and other plastids, with the simplest form identified as amylose.
Storage Polysaccharides Continued
Glycogen denotes an animal storage polysaccharide, primarily stored in liver and muscle cells. The hydrolysis of glycogen releases glucose, fulfilling increased energy demands.
Structural Polysaccharides
Cellulose serves as a crucial structural component of plant cell walls. Similar to starch, cellulose is also a glucose polymer but exhibits different glycosidic linkages.
The distinction in linkages is attributed to the existence of two ring forms of glucose: alpha (α) and beta (β).
Figure 5.7: Structures of Starch and Cellulose
a) Illustrates the α and β glucose ring structures.
b) Depicts starch’s linkage (1–4) of α glucose monomers.
c) Illustrates cellulose’s linkage (1–4) of β glucose monomers.
Structural Polysaccharides Continued
Starch tends to form a helical structure due to the α configuration, while cellulose molecules are characterized as straight and unbranched due to the β configuration.
Some hydroxyl groups in cellulose monomers can engage in hydrogen bonding with adjacent cellulose molecules.
Figure 5.8: Chitin, a Structural Polysaccharide
Chitin is another structural polysaccharide applicable in the exoskeleton of arthropods and used in making strong and flexible surgical threads. It also provides supporting structure for the cell walls of various fungi.
Concept 5.3: Lipids as a Diverse Group of Hydrophobic Molecules
Lipids constitute one class of large biological molecules that do not represent true polymers.
The unifying characteristic of lipids is their poor solubility in water, primarily due to their composition of hydrocarbons that form nonpolar covalent bonds.
The biologically significant lipids include:
Fats
Phospholipids
Steroids
Fats
Fats are constructed from two smaller molecules: glycerol and fatty acids.
Glycerol is a three-carbon alcohol containing a hydroxyl group bonded to each carbon atom.
A fatty acid is composed of a carboxyl group linked to a long carbon skeleton.
Figure 5.9: The Synthesis and Structure of a Fat (Triacylglycerol)
Illustrates a dehydration reaction involved in fat synthesis.
Fats Continued
Fats separate from water because water molecules engage in hydrogen bonds with each other, thereby excluding fats.
In a fat, three fatty acids attach to glycerol via an ester linkage, resulting in a triacylglycerol or triglyceride. This structure allows for the presence of identical or different fatty acids.
Fats Continued-1
Fatty acids exhibit variations in length (the number of carbon atoms) and the presence and positioning of double bonds.
Saturated fatty acids attain the maximum quantity of hydrogen atoms possible and feature no double bonds.
Meanwhile, unsaturated fatty acids have one or more double bonds.
Figure 5.10: Saturated and Unsaturated Fats and Fatty Acids
a) Shows saturated fat.
b) Displays unsaturated fat.
Fats Continued-2
Fats composed of saturated fatty acids are termed saturated fats, remaining solid at room temperature. Most animal-derived fats are saturated.
In contrast, fats originating from unsaturated fatty acids are classified as unsaturated fats or oils, often remaining liquid at room temperature, commonly found in plants and fish.
Fats Continued-3
A high intake of saturated fats may contribute to cardiovascular diseases due to the formation of plaque deposits.
Hydrogenation is the process by which unsaturated fats are converted to saturated fats through the addition of hydrogen, which can occasionally result in the formation of harmful trans fats that may induce cardiovascular diseases.
Fats: Essential Fatty Acids
Some unsaturated fatty acids cannot be synthesized by the human body and therefore must be included in the diet.
These essential fatty acids encompass omega-3 fatty acids, which are vital for normal growth and potentially provide cardiovascular disease protection.
Fats: Function
The primary function of fats is identified as energy storage.
Humans and other mammals reserve long-term food sources in adipose cells, which also provide cushioning for vital organs and body insulation.
Phospholipids
A phospholipid has two fatty acids along with a phosphate group attached to a glycerol backbone.
The hydrophobic nature of the two fatty acid tails contrasts with the hydrophilic properties of the phosphate group, which forms the head of the phospholipid.
Figure 5.11: The Structure of a Phospholipid
Illustrates the chemical composition and structure of a phospholipid molecule, containing hydrophilic heads and hydrophobic tails.
Phospholipids Continued
When phospholipids interact with water, they naturally arrange themselves into double-layered structures referred to as bilayers.
At the cell surface, phospholipids form bilayers whereby the hydrophobic tails direct themselves inward, shielding from water, thus functioning as a boundary between the cell and its external environment.
Steroids
Steroids represent lipids recognized by a carbon skeleton comprised of four fused rings.
Cholesterol, a steroid type, is a significant component within animal cell membranes and serves as a precursor for the synthesis of additional steroids.
Elevated cholesterol levels in the bloodstream may lead to cardiovascular diseases.
Concept 5.4: Proteins Exhibit a Diverse Array of Structures, Leading to Varied Functions
Proteins comprise over 50% of the dry mass of most cells.
Specific functions of proteins include but are not limited to:
Acceleration of chemical reactions,
Defense against pathogens,
Storage of amino acids,
Transport of substances,
Facilitation of cellular communication,
Movement of cells,
Providing structural support.
Figure 5.13: An Overview of Protein Functions
Enzymatic proteins accelerate chemical reactions (e.g., digestive enzymes catalyze the hydrolysis of bonds).
Defensive proteins protect against diseases (e.g., antibodies that neutralize viruses and bacteria).
Storage proteins preserve amino acids (e.g., casein in milk nourishes infant mammals).
Transport proteins carry substances (e.g., hemoglobin transports oxygen in blood).
Hormonal proteins coordinate activities (e.g., insulin regulates blood sugar levels).
Receptor proteins respond to chemical stimuli (e.g., nerve cell receptors detect neurotransmitters).
Contractile and motor proteins allow movement (e.g., actin and myosin in muscle contraction).
Structural proteins provide shape and support (e.g., keratin in hair and collagen in connective tissues).
Proteins Continued
Enzymes are proteins that act as catalysts to expedite chemical reactions, capable of functioning repetitively.
Proteins are constructed from a shared set of 20 amino acids, and polypeptides are unbranched chains of these amino acids.
A functional protein generally consists of one or more polypeptides, meticulously folded into complex shapes.
Amino Acid Monomers
Amino acids are organic compounds containing both amino and carboxyl functional groups, differing due to their varying side chains (R groups).
Figure 5.14: The 20 Amino Acids of Proteins
Classification of amino acids:
Nonpolar side chains: Generally hydrophobic.
Polar side chains: Generally hydrophilic.
Electrically charged side chains: Exhibit hydrophilic properties; can be either basic (positively charged) or acidic (negatively charged).
Polypeptides (Amino Acid Polymers)
Amino acids get linked by covalent peptide bonds to form polypeptides.
A polypeptide emerges as a polymer of amino acids, with lengths ranging from a few to more than 1,000 amino acid monomers.
Each unique polypeptide possesses a specific linear arrangement of amino acids, having a C-terminus (carboxyl end) and an N-terminus (amino end).
Figure 5.15: Making a Polypeptide Chain
Depicts the peptide bond formation and structure of the polypeptide chain.
Protein Structure and Function
The specific functions of proteins originate from their complex three-dimensional architecture.
A functional protein typically consists of one or more polypeptides intricately twisted, folded, and coiled into precise structural shapes.
Figure 5.16: Visualizing Proteins
Various structural models depict the configurations of proteins and their interactions with target molecules.
Levels of Protein Structure
The arrangement of amino acids dictates the three-dimensional structure of proteins. Four levels exist in protein structure:
Primary structure: Defined as the unique sequence of amino acids.
Secondary structure: Consists of coils and folds in the polypeptide chain (e.g., α-helix and β-pleated sheet).
Tertiary structure: Determined via interactions between various side chains (R groups).
Quaternary structure: Results from multiple polypeptide chains forming one macromolecule.
Figure 5.18: Exploring Levels of Protein Structure
Illustrates primary, secondary, tertiary, and quaternary structures, highlighting visualization of protein architecture.
Primary Protein Structure
The primary structure of a protein encapsulates its sequence of amino acids, analogous to the sequential arrangement of letters in a word.
It is dictated by genetic information inherited through inheritance patterns.
Secondary Protein Structure
Secondary structure is defined by hydrogen bonding between repeating constituents of the polypeptide backbone, resulting in specific structural motifs such as α-helices and β-pleated sheets.
Tertiary Protein Structure
Tertiary structure refers to the overall shape of the polypeptide, resulting from interactions among R groups instead of backbone constituents. Important interactions involved include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions. Disulfide bridges can reinforce protein structure.
Quaternary Protein Structure
Quaternary structure arises when two or more polypeptide chains coalesce into one macromolecule. For example, collagen is a fibrous protein consisting of three coiled polypeptides, while hemoglobin consists of four polypeptides: two α and two β subunits.
Sickle-Cell Disease: A Change in Primary Structure
A minor alteration in the primary structure can dramatically influence a protein's overall structure and functionality. An example is sickle-cell disease, a hereditary blood disorder resulting from a single amino acid substitution in hemoglobin that leads to aggregation and deformation of red blood cells into a sickle shape.
What Determines Protein Structure?
Aside from the primary structure, factors like physical and chemical conditions can impact protein structure. Changes in pH, salt concentration, or temperature can trigger protein denaturation, leading to a loss of structure and biological inactivity of proteins.
Protein Folding in the Cell
Predicting a protein's structure from its primary sequence proves challenging, as proteins often progress through various stages to achieve a stable structure. Misfolded proteins are associated with diseases like Alzheimer’s, Parkinson’s, and mad cow disease.
Techniques such as X-ray crystallography are employed to ascertain a protein's structure. An alternative approach is Nuclear Magnetic Resonance (NMR) spectroscopy, which eliminates the need for crystal formation. Bioinformatics assists in predicting protein structures based on amino acid sequences.
Concept 5.5: Nucleic Acids Store, Transmit, and Help Express Hereditary Information
The sequence coding for a polypeptide is determined by units of inheritance known as genes, which are composed of DNA, a nucleic acid formed from monomers called nucleotides.
The Roles of Nucleic Acids
The main types of nucleic acids include:
Deoxyribonucleic Acid (DNA)
Ribonucleic Acid (RNA)
DNA is responsible for providing instructions for its own replication and directing the synthesis of messenger RNA (mRNA), thereby controlling the protein synthesis process known as gene expression.
Figure 5.22: Overview of Gene Expression
Illustrates the process of gene expression where DNA transcribes into RNA and subsequently translates into protein.
The Components of Nucleic Acids
Nucleic acids are long chains called polynucleotides.
Each polynucleotide is composed of smaller units known as nucleotides, each consisting of:
A nitrogenous base.
A pentose sugar.
One or more phosphate groups.
The segment of a nucleotide without the phosphate group is termed a nucleoside.
Nucleoside
A nucleoside comprises a nitrogenous base combined with a sugar. The two families of nitrogenous bases include pyrimidines (cytosine, thymine, and uracil) with a single six-membered ring, and purines (adenine and guanine) with a six-membered ring fused to a five-membered ring.
In DNA, the sugar is deoxyribose, while in RNA, it is ribose.
Figure 5.23: Components of Nucleic Acids
Illustrates the components of nucleic acids including nitrogenous bases and their structures.
Nucleotide Polymers
Nucleotides bond together using phosphodiester linkages to form polynucleotides—these consist of a phosphate group linking the sugars of two nucleotides, creating a sugar-phosphate backbone with nitrogenous bases as appendages.
The sequence of bases within a DNA or mRNA polymer remains unique to each gene.
The Structures of DNA and RNA Molecules
DNA is characterized by two polynucleotides that spiral around each other, forming a double helix structure. The backbones run in opposite 5' to 3' directions, an arrangement known as antiparallel.
Each DNA molecule encompasses numerous genes.
Complementary Base Pairing
Only specific bases in DNA hydrogen bond: adenine (A) pairs with thymine (T), while guanine (G) pairs with cytosine (C). This specificity, termed complementary base pairing, enables the creation of identical DNA copies during cell division.
RNA Structure
Unlike DNA, RNA is predominantly single-stranded. Complementary pairing is also common between two RNA molecules or within the same molecule. In RNA, uracil (U) replaces thymine (T) where A pairs with U, contributing to variable RNA structures.
DNA and Proteins as Tape Measures of Evolution
The sequences of genes and their corresponding protein products trace the hereditary lineage of organisms.
Molecular biology introduces a novel framework to evolutionary biology through molecular genealogy, linking DNA sequences passed from parents to offspring.
Summary of Key Concepts
Carbohydrates
Components:
Monosaccharides (glucose, fructose)
Disaccharides (lactose, sucrose)
Polysaccharides (cellulose, starch, glycogen, chitin)
Functions:
Fuel and carbon sources
Structural integrity in plants (cellulose)
Energy storage (starch and glycogen)
Lipids
Components:
Triacylglycerols (fats or oils)
Phospholipids
Steroids
Functions:
Energy reserve, formation of biological membranes, signaling molecules.
Proteins
Components:
Enzymes, storage proteins, transport proteins, hormones, structural proteins, receptor proteins, and motor proteins.
Functions:
Catalysis, defense against diseases, storage, transportation, communication, movement, and structural support.
Nucleic Acids
Components:
Nucleotides (monomers of nucleic acids)
Functions:
Storage and expression of genetic information, including instruction transfer from DNA to ribosomes for protein synthesis.