The Structure and Function of Large Biological Molecules

Chapter 5: The Structure and Function of Large Biological Molecules

Overview: The Molecules of Life

• All living organisms are composed of four primary classes of large biological molecules:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids

• In cells, smaller organic molecules combine to form larger structures known as macromolecules.

• Macromolecules are large molecules created from thousands of covalently bonded atoms.

• The relationship between molecular structure and function is inseparable.

Concept 5.1: Macromolecules are Polymers, Built from Monomers

• A polymer is defined as a long chain molecule consisting of many similar building blocks.

• These smaller building blocks are referred to as monomers.

• Three out of the four classes of life's organic molecules are classified as polymers:

  • Carbohydrates

  • Proteins

  • Nucleic acids

Synthesis and Breakdown of Polymers

• Condensation Reaction (Dehydration Reaction): Occurs when two monomers bond together with the expulsion of a water molecule (

  • Enzymes, which are macromolecules, facilitate the dehydration process.

• Hydrolysis: The process through which polymers are disassembled into monomers, functioning as the reverse of dehydration reactions.

• Figures Explained:

  • Fig. 5-2 illustrates the process of dehydration creating a longer polymer from unlinked monomers and the hydrolysis stage that breaks the polymer back into monomers.

The Diversity of Polymers

• Each cell hosts a significant variety of macromolecules.

• Variability in macromolecules occurs among different cells within an organism, and even more variability exists between different species.

• A vast range of polymers can arise from a limited set of monomers.

Concept 5.2: Carbohydrates Serve as Fuel and Building Material

• Carbohydrates encompass both sugars and their polymeric forms (polysaccharides).

• The simplest carbohydrates are classified as monosaccharides (single sugars).

• Complex carbohydrate macromolecules are named polysaccharides, consisting of numerous sugar-derived units.

Sugars

• Monosaccharides typically embody molecular formulas that are multiples of the form $ext{CH}_2 ext{O}$.

• Glucose (C6H12O6) is identified as the most prevalent monosaccharide.

• Classification of monosaccharides can be based on:

  • Position of the carbonyl group (as either aldose or ketose)

  • Count of carbons in the skeleton

Ring Formation of Sugars

• Although often depicted as linear structures, many sugars assume ring shapes when in aqueous solutions.

• Monosaccharides function as a primary energy source for cells and as foundational materials for constructing more complex molecules.

Disaccharides

• A disaccharide results from a dehydration reaction that links two monosaccharides.

• The bond formed is known as a glycosidic linkage.

Polysaccharides Overview

• Polysaccharides, acting as polymers of sugars, serve both storage and structural roles in organisms.

• The specific structure and function of each polysaccharide depend on its unique sugar monomers and the specific glycosidic linkages involved.

Storage Polysaccharides

• Starch:

  • A storage polysaccharide found in plants made exclusively of glucose monomers.

  • Plants store additional starch in granules within chloroplasts and various plastids.

• Glycogen:

  • A storage form of polysaccharides in animals; primarily stored in liver and muscle cells of vertebrates.

Structural Polysaccharides

• Cellulose:

  • A key structural polysaccharide component of the plant cell wall.

  • While similar in being a polymer of glucose, the glycosidic linkages in cellulose differ from those in starch.

  • Differentiation arises due to the two distinct ring forms of glucose, alpha (a) and beta (b).

• Polymers with an alpha form exhibit a helical shape; beta form polymers are more linear.

• In linear structures, hydrogen atoms on one strand can interact with hydroxyl groups on adjacent strands, leading to the formation of strong microfibrils contributing to plant structural integrity.

Digestibility of Cellulose

• Enzymes responsible for digesting starch cannot break down the beta linkages found in cellulose, which makes cellulose an insoluble fiber in human diets.

• Some microbes possess enzymes capable of cellulose digestion, establishing symbiotic relationships with various herbivores.

Chitin as a Structural Polysaccharide

• Chitin:

  • Another significant structural polysaccharide constituting the exoskeleton in arthropods and part of cell wall structures in many fungi.

Concept 5.3: Lipids are a Diverse Group of Hydrophobic Molecules

• Unlike other classes of large biological molecules, lipids do not form polymers.

• Lipids are characterized by their minimal to absent affinity for water due to their chemical composition primarily consisting of hydrocarbons.

• The principal lipid types relevant in biological processes are:

  • Fats

  • Phospholipids

  • Steroids

Fats

• Fats are composed of two fundamental smaller molecule types: glycerol and fatty acids.

• Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon atom.

• A fatty acid features a carboxyl group attached to a lengthy carbon skeleton.

Fat Structure and Properties

• Triacylglycerols (Triglycerides):

  • Formed when three fatty acids link to glycerol through an ester linkage.

• The presence of water separates fats from the aqueous environment due to hydrogen bond formation among water molecules that excludes fats.

• Fatty acids can differ in length (number of carbon atoms) and in the number and placement of double bonds:

  • Saturated fatty acids: Have the maximum possible number of hydrogen atoms with no double bonds, solid at room temperature.

  • Unsaturated fatty acids: Contain one or more double bonds, typically liquid at room temperature and often referred to as oils.

Health Implications of Fats

• Diets rich in saturated fats may lead to cardiovascular diseases due to plaque deposits.

• Hydrogenation: A process converting unsaturated fats into saturated fats by adding hydrogen, which can result in the production of trans fats, potentially more harmful than saturated fats in contributing to cardiovascular difficulties.

• Fats serve a critical role in energy storage and are stored in adipose cells in mammals. Additionally, adipose tissue contributes to organ cushioning and body insulation.

Phospholipids

• Phospholipids are unique as they contain two fatty acids and a phosphate group attached to glycerol.

• This unique structure gives them both hydrophobic tails and a hydrophilic head, causing them to spontaneously arrange into bilayers in aqueous environments, a critical structure for cell membranes.

Steroids

• Steroids are a class of lipids identifiable by a carbon skeleton comprising four fused rings.

• Cholesterol is a vital steroid component in animal cell membranes, although excessive levels can contribute to cardiovascular issues.

Concept 5.4: Proteins have Many Structures, Resulting in Diverse Functions

• Proteins represent over 50% of the dry mass of most cells, carrying out varied roles:

  • Structural support

  • Storage

  • Transport

  • Cellular communication

  • Movement

  • Defense against pathogens

Types of Proteins and Their Functions

• Table 5-1 Overview provides a summary of protein types and corresponding functions, including:

  • Enzymatic Proteins: Catalysts for chemical reactions (e.g., digestive enzymes)

  • Structural Proteins: Supportive functions (e.g., collagen, elastin)

  • Storage Proteins: Source of amino acids (e.g., ovalbumin, casein)

  • Transport Proteins: Move other substances (e.g., hemoglobin)

  • Hormonal Proteins: Coordinate activities (e.g., insulin)

  • Receptor Proteins: Chemical stimulus response (e.g., nerve cell receptors)

  • Contractile and Motor Proteins: Facilitate movement (e.g., actin, myosin)

  • Defensive Proteins: Disease protection agents (e.g., antibodies)

Enzymes and Polypeptides

• Enzymes are a vital protein class functioning as catalysts, performing their roles repeatedly.

• Polypeptides: Chains composed of linked amino acids making up proteins, with each protein potentially containing one or more polypeptides.

Amino Acid Monomers

• Amino Acids: Organic molecules characterized by carboxyl and amino groups, differing in properties due to their unique side chains, known as R groups.

Amino Acid Classification

• Exhibit various properties including:

  • Nonpolar: Glycine, Alanine, Valine

  • Polar: Asparagine, Glutamine, Serine

  • Acidic: Arginine, Aspartic acid, Glutamic acid

  • Basic: Active and charged at physiological pH.

Amino Acid Polymers

• Amino acids are linked through peptide bonds, forming polypeptides that can range from a few to over a thousand monomers long. Each polypeptide possesses a unique amino acid sequence.

Protein Structure and Function

• Proteins achieve their function through specific three-dimensional structures derived from polypeptide twisting, folding, and coiling.

• The structure of a protein is intrinsically linked to its amino acid sequence and influences its functional capacity.

Levels of Protein Structure

1. Primary Structure: Linear sequence of amino acids determined by genetic information.

2. Secondary Structure: Regular patterns (e.g., a helices and b pleated sheets) arise from hydrogen bonding between backbone constituents.

3. Tertiary Structure: Overall three-dimensional shape determined by side chain interactions (e.g., ionic bonds, hydrogen bonds, disulfide bridges).

4. Quaternary Structure: Composed of multiple polypeptide subunits merging into one functional macromolecule.

Effects of Primary Structure Changes

• Minor modifications in primary structure can drastically affect protein functionality, as illustrated by sickle-cell disease stemming from a single amino acid substitution in hemoglobin, disrupting normal function and structure.

Determining Factors of Protein Structure

• In addition to primary structure, proteins are susceptible to changes from various physical and chemical conditions (e.g., pH, temperature), which can lead to denaturation, rendering them biologically inactive.

Protein Folding and Chaperonins

• Protein folding is a complex process, often assisted by chaperonins which help ensure proper folding.

• Techniques such as X-ray crystallography and NMR spectroscopy assist scientists in deducing protein structures.

Concept 5.5: Nucleic Acids Store and Transmit Hereditary Information

• Genes, which are segments of DNA, act as units of inheritance directed by nucleic acids.

• There are two main forms of nucleic acids:

  • Deoxyribonucleic acid (DNA)

  • Ribonucleic acid (RNA)

• DNA enables self-replication and serves as the instruction manual for messenger RNA (mRNA) synthesis. mRNA, in turn, plays a central role in protein synthesis.

Structure of Nucleic Acids

• Nucleic acids are polymers known as polynucleotides, composed of monomers termed nucleotides.

• Each nucleotide includes:

  • A nitrogenous base

  • A pentose sugar

  • A phosphate group

• The portion of a nucleotide that lacks the phosphate group is the nucleoside.

Nucleotide Components

• Nucleoside: Composed of a nitrogenous base and sugar.

• Nitrogenous bases fall into two categories:

  • Pyrimidines: Cytosine, Thymine (in DNA), Uracil (in RNA)

  • Purines: Adenine and Guanine

• The sugar in DNA is deoxyribose and in RNA is ribose. A nucleotide consists of a nucleoside plus a phosphate group.

Nucleotide Polymerization

• Nucleotide polymers join together via covalent bonds between the 3' hydroxyl (-OH) of one nucleotide’s sugar and the phosphate group of the 5' of the next, forming a sugar-phosphate backbone with nitrogenous bases as side appendages.

• Each gene has a unique nucleotide sequence along its DNA or mRNA polymer.

The DNA Double Helix

• DNA’s structural configuration consists of two anti-parallel polynucleotide strands forming a double helix.

• Base pairing occurs via hydrogen bonds: Adenine (A) pairs with Thymine (T), and Guanine (G) pairs with Cytosine (C).

Evolutionary Implications of Nucleic Acids

• The nucleotide sequences in DNA are inherited from parental generation to offspring, illustrating kinship through genetic similarities.

• Molecular biology methods can assess evolutionary relationships based on these sequences.