Biological Polymers and Nucleic Acids

Molecular Building Blocks of the Cell

  • Four major classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids.
  • Small organic molecules join to form larger molecules within cells.
  • Building blocks and their corresponding larger units:
    • Sugars -> Polysaccharides
    • Fatty acids -> Lipids/membranes
    • Amino acids -> Proteins
    • Nucleotides -> Nucleic acids

Carbohydrates

  • Include sugars and polymers of sugars.
  • Monosaccharides: Simplest carbohydrates, single sugars.
  • Polysaccharides: Carbohydrate macromolecules, polymers of many sugar building blocks.

Sugars

  • Monosaccharides: Molecular formulas are multiples of CH<em>2OCH<em>2O. Glucose (C</em>6H<em>12O</em>6)(C</em>6H<em>{12}O</em>6) is a common example.
  • Classified by:
    • Location of the carbonyl group (aldose or ketose).
    • Number of carbons in the carbon skeleton (pentose or hexose).
  • Serve as major fuel for cells and raw material for building molecules.

Monosaccharide Examples

  • Glucose: aldohexose
  • Galactose: aldohexose, structural isomer of glucose
  • Fructose: ketohexose, structural isomer of glucose
  • Isomers include structural isomers (e.g., glucose, fructose, galactose) and stereoisomers (α-glucose, β-glucose).

Disaccharides

  • Two monosaccharides linked by dehydration synthesis.
  • Used for sugar transport or energy storage.
  • Examples: Sucrose, Lactose, Maltose
  • Dehydration synthesis (condensation reaction): Two molecules become covalently linked with the loss of a water molecule.
  • Hydrolysis: Reverse reaction where water is added.

Polysaccharides

  • Long chains of monosaccharides linked through dehydration synthesis.
  • Energy storage:
    • Plants use starch (amylose and amylopectin).
    • Animals use glycogen.
  • Structural support:
    • Plants use cellulose.
    • Arthropods and fungi use chitin.

Starch

  • Composed of α-glucose monomers.
  • Amylose: unbranched, with α-1→4 linkages.
  • Amylopectin: branched, with α-1→4 linkages and α-1→6 linkages at branch points.

Glycogen

  • Extensively branched polymer of glucose.
  • Functions as energy storage in animals.

Lipids

  • Diverse group of hydrophobic molecules.
  • Not true polymers.
  • Hydrophobic due to hydrocarbons forming nonpolar covalent bonds.
  • Biologically important lipids: fats, phospholipids, steroids.

Fats

  • Constructed from glycerol and fatty acids.
  • Glycerol: Three-carbon alcohol with a hydroxyl group attached to each carbon.
  • Fatty acid: Carboxyl group attached to a long carbon skeleton.
  • Major function: Energy storage.

Saturated vs. Unsaturated Fats

  • Saturated fatty acids: Have only single bonds, allowing close packing.
  • Unsaturated fatty acids: Have one or more double bonds, causing bending.
  • Cis double bonds in unsaturated fatty acids cause bending.

Hydrogenated Vegetable Oils and Trans Fats

  • Hydrogenation: Synthetic conversion of unsaturated fats to saturated fats by adding hydrogen.
  • Trans fats: Unsaturated fats with trans double bonds, contributing to coronary heart disease. The US FDA ordered food manufacturers to stop producing trans fats in foods by 2021.

Phospholipids

  • Two fatty acids and a phosphate group are attached to glycerol.
  • Fatty acid tails are hydrophobic; phosphate group and its attachments form a hydrophilic head.
  • Essential for cells because they make up cell membranes.

Steroids

  • Lipids characterized by a carbon skeleton consisting of four fused rings.
  • Cholesterol: Important steroid, a component in animal cell membranes. High levels in the blood may contribute to cardiovascular disease.

Proteins

  • Account for more than 50% of the dry mass of most cells.
  • Functions: catalyzing biochemical reactions, structural support, storage, transport, cellular communications, movement, and defense against foreign substances.
  • Polypeptides: Polymers built from the same set of 20 amino acids.
  • A protein consists of one or more polypeptides.

Amino Acids

  • Organic molecules with carboxyl and amino groups.
  • Differ in properties due to differing side chains (R groups).

Side Chains (R groups)

  • Nonpolar side chains: hydrophobic.
  • Polar side chains: hydrophilic.
  • Electrically charged side chains: hydrophilic (acidic - negatively charged, basic - positively charged).

Polypeptide Formation

  • Amino acids are linked by peptide bonds.
  • A polypeptide has an amino end (N-terminus) and a carboxyl end (C-terminus).
  • New peptide bonds form via dehydration reactions.

Protein Structure and Function

  • Primary structure: sequence of amino acids.
  • Secondary structure: α helix and β pleated sheet, stabilized by hydrogen bonding.
  • Tertiary structure: Three-dimensional shape stabilized by interactions between side chains.
  • Quaternary structure: Association of multiple polypeptides.
Examples of Quaternary Structure
  • Collagen (connective tissue protein).
  • Hemoglobin (oxygen transport protein).

Protein Structure Determination

  • Experimentally:
    • X-ray crystallography
    • Electron microscopy
  • Prediction/modeling:
    • DALI
    • AlphaFold

Nucleic Acids

  • Store and transmit hereditary information.
  • Two types: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).
  • Amino acid sequence of a polypeptide is programmed by a gene.
  • Genes are stored as DNA.

Central Dogma of Molecular Biology

  • DNA → mRNA → Protein
  • mRNA moves from the nucleus to the cytoplasm via nuclear pores.
  • Ribosomes synthesize protein.

Structure of Nucleic Acids

  • Polymers called polynucleotides.
  • Monomers called nucleotides.
  • Each nucleotide consists of a nitrogenous base, a pentose sugar (ribose or deoxyribose), and a phosphate group.
  • Nucleoside: Portion of a nucleotide without the phosphate group.
Nucleoside Components
  • Sugars:
    • Deoxyribose (in DNA)
    • Ribose (in RNA)
  • Nitrogenous bases:
    • Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA)
    • Purines: Adenine (A), Guanine (G)

DNA Double Helix

  • Two polynucleotides spiraling around an imaginary axis, forming a double helix.
  • Antiparallel: Two backbones run in opposite 5' → 3' directions.
  • Nitrogenous base pairing: Adenine (A) with Thymine (T), Guanine (G) with Cytosine (C).

DNA and Proteins as Tape Measures of Evolution

  • Linear sequences of nucleotides in DNA molecules are passed from parents to offspring.
  • Closely related species are more similar in DNA than more distantly related species.
  • Molecular biology can be used to assess evolutionary kinship.