Cellular Polymers, Macromolecules, and Nucleic Acids

Chromatin

  • In the nucleus, chromatin is composed of DNA, proteins (including carbohydrates), and lipids.

Cellular Polymers

  • Key components:
    • Plasma membrane: Contains proteins, lipids, and carbohydrates.
    • Ribosome: Contains proteins and RNA.
    • Cell wall: Contains carbohydrates.
    • Mitochondrion: Contains proteins, carbohydrates, lipids, and DNA.
    • Starch grain in chloroplast: Contains carbohydrates, RNA, and proteins.
    • Microtubules: NOT POLYMER.

Cell Monomers and Polymers

  • Monomers:
    • Small organic building blocks of the cell.
    • Include sugars, fatty acids, amino acids, and nucleotides.
  • Polymers:
    • Larger organic molecules of the cell.
    • Include polysaccharides, glycogen, starch (in plants), fats, membrane lipids, proteins, and nucleic acids.

Macromolecules

  • Large molecules made of hundreds to thousands of atoms.
    • Examples: DNA, RNA, proteins, polysaccharides, and lipids.
  • Polymers:
    • Made of similar or identical covalently bound smaller units.
  • Monomers:
    • Small molecules used to build polymers.

Polymer Synthesis

  • Monomers are added to the growing end of a polymer.
  • The process involves a carrier molecule that is recycled.

Biological Polymer Breakdown

  • Hydrolysis:
    • Adding H₂O across a covalent bond, releasing a monomer.
    • Many molecules can undergo hydrolysis.
  • ATP hydrolysis is a major source of cell energy.

Hydrolysis Reaction

  • Condensation:
    • Water is expelled, forming a reactive bond between monosaccharides to create a disaccharide.
  • Hydrolysis:
    • Water is consumed to break the bond in a disaccharide, resulting in monosaccharides.

Disaccharides

  • Cells link sugars to form disaccharides.
  • Glycosidic bond:
    • Linkage between C1 of one sugar and the OH of another.
    • Formed via a condensation reaction.
    • Broken down via hydrolysis.
  • Sucrose:
    • Glucose and fructose joined by an α,β-1,2 glycosidic bond.

Biological Functions of Disaccharides

  • Sucrose:
    • Moved from leaf through "veins" to tissues where needed.
    • Converted to starch (storage) or broken down for energy.
  • Lactose:
    • Primary sugar in mammalian milk.
    • Composed of galactose-β1,4-glucose.
  • Maltose:
    • Hydrolyzed in seed for energy.
    • Composed of glucose-α1,4-glucose.
  • Yeast:
    • Hydrolyze maltose, providing energy for growth and carbon for ethanol production.

Storage Disaccharides

  • Sucrose: Composed of α-glucose and β-fructose with an alpha 1-2 glycosidic bond.
  • Lactose: Composed of galactose and glucose with a β1,4-glycosidic bond.
  • Maltose: Composed of glucose with an α1,4-glycosidic bond.

Components of Starch

  • Amylose:
    • A linear polymer of glucose molecules.
  • Amylopectin:
    • A branched polymer of glucose molecules, with branches occurring every 24-30 units.

Polysaccharides

  • Composed of glucose monomers.
    • Starch: Includes amylose and amylopectin.
      • Amylose: Unbranched helix with α-1,4 glycosidic bonds.
      • Amylopectin: Branched helix with α-1,4 glycosidic bonds and α-1,6 glycosidic bond branches.
    • Plant storage carbohydrate.
    • Hydrolysis produces glucose for energy.

Glycogen

  • Highly branched polysaccharide.
  • Contains α-1,4 glycosidic bonds in the linear chain and α-1,6 glycosidic bonds at branch points.
  • Branching is 2-3 times more frequent than in amylopectin.
  • Helical structure.
  • Animal storage carbohydrate (e.g., liver, muscle).
  • Hydrolyzes food polysaccharides and disaccharides to glucose in the digestive tract.
  • Glycogen (storage) is synthesized in the liver from glucose.
  • When blood glucose is low, liver glycogen is hydrolyzed to glucose.
  • The hormone insulin controls blood sugar levels.

Cellulose

  • Unbranched polysaccharide forming linear rods.
  • Contains β-1,4 glycosidic bonds.
  • Plant cell wall structural component.
  • Forms fibers and wood.
  • Humans are unable to digest cellulose.
  • Some wood rot fungi, bacteria, and protozoa have enzymes that enable them to digest cellulose.
  • Protozoa living symbiotically in termite guts and bacteria in the rumen of cows are able to digest cellulose.

Chitin

  • Unbranched polymer of N-acetylglucosamine.
  • Structural component of insect exoskeletons and fungal cell walls.

Lipids

  • Composed mostly of carbon (C) and hydrogen (H): hydrocarbons.
  • Contain nonpolar covalent C-C and C-H bonds.
  • Hydrophobic: insoluble in water.
  • Soluble in organic solvents.
  • Include fatty acids, steroids, and phospholipids.
  • Major membrane component.
  • Fats are major long-term storage compounds.
  • Breakdown releases 6X energy of glucose breakdown.

Fatty Acids

  • Consist of C-C and C-H bonds with a COOH (carboxyl) group at one end.
  • Amphipathic molecule:
    • Carboxyl end is hydrophilic, interacting with water.
    • Hydrocarbon chain is hydrophobic.
  • Can form droplets or micelles (like soap).
  • Can form a surface film on water.

Saturated vs. Unsaturated Fatty Acids

  • Saturated Fatty Acids:
    • Example: Stearic acid.
    • Have all single C-C bonds.
  • Unsaturated Fatty Acids:
    • Example: Oleic acid.
    • Contain at least one C=C double bond, which is rigid and creates a kink in the chain
    • The rest of the chain is free to rotate about the other C-C bonds.

Fats

  • Glycerol (3-carbon molecule) linked to 1-3 fatty acids.
    • Mono-, di-, or triglyceride.
  • Glycerol has polar covalent C-O-H bonds.
  • The carboxyl group of the fatty acid is linked to glycerol.
  • The longer the fatty acid tail, the more hydrophobic the fat.
  • Fewer fatty acids linked to glycerol make the head more hydrophilic.
    • Monoglycerides are more hydrophilic than triglycerides.

Triacylglycerol

  • Glycerol moiety linked to three fatty acid tails via ester bonds.

Saturated Fats

  • All C-C bonds are single bonds.
  • Straight chain allows maximum interactions of fatty acid tails.
  • Maximum packing.
  • Solid at room temperature.
  • Animal fats.
  • Considered "bad" fats that can clog arteries.

Unsaturated Fats

  • Contain some C=C bonds (double bonds).
  • Bent chain, keeping tails apart.
  • Cis configuration, not trans.
  • Polyunsaturated fats have multiple double bonds and bends.
  • Liquid at room temperature.
  • Vegetable fats.
  • Considered "good" fats that do not clog arteries.
  • Double bonds in unsaturated triglyceride.

Phospholipids

  • Phosphate group on the third OH of glycerol.
  • Have a polar group like choline attached to the phosphate.
  • Increases hydrophilicity.
  • Saturated and unsaturated phospholipid molecular models exist, showing differences in tail packing due to saturation.

Cell Membranes

  • Composed of a phospholipid bilayer.
  • Phospholipid molecules have:
    • A hydrophilic head (polar group and phosphate).
    • Two hydrophobic fatty acid tails.
  • The bilayer arrangement places the hydrophilic heads in contact with water and shields the hydrophobic tails.

Steroids

  • Ring structures.
  • Cholesterol:
    • Major membrane component in animal cells (not in plant membranes).
    • Hormone precursor.
    • Can contribute to artery clogging.

Steroid Hormones

  • Corticosteroids:
    • Anti-inflammatory.
    • Used to treat conditions like arthritis, asthma, and multiple sclerosis.
  • Human sex hormones:
    • Testosterone (produced in testes).
    • Progesterone (produced in ovaries).
    • Estrogen (produced in ovaries).
  • Anabolic steroids:
    • Synthetic male hormone.
    • Builds muscle and body size.
    • Can produce liver damage, mood swings, depression, and death.

Proteins

  • Contain carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and sulfur (S).
  • Polymers of amino acid monomers.
  • Protein Functions:
    • Enzymes: Catalyze reactions.
    • Structural components: Tubulin, actin, laminin.
    • Movement proteins: Dynein, kinesin, myosin.
    • Storage proteins: Egg white, seed proteins.
    • Antibodies: Defense.
    • Transport molecules: Hemoglobin (transports O₂ and CO₂), ions, glucose.
    • Regulatory molecules: Hormones, growth factors.

Amino Acids

  • Monomers of proteins.
  • Amino Acid Structure:
    • Central carbon atom.
    • Hydrogen (H) atom.
    • Amine (NH₂ or NH₃⁺) group.
    • Carboxyl (COOH or COO⁻) group.
    • 20 different R groups.
    • Exist as L isomers, not D isomers.

Types of R Groups

  • Polar Charged (Hydrophilic):
    • Acidic or Basic.
    • Participate in inter- and intra-ionic interactions with other molecules.
    • Positive or negative charge.
    • Chemically reactive, allowing them to act as acid or base catalysts.

Types of R Groups

  • Polar Uncharged (Hydrophilic):
    • Polar covalent bonds lead to partial charges.
    • Capable of forming hydrogen bonds.
    • Participate in chemical reactions.
    • Phosphorylation on serine or threonine:
      • Regulation.
    • Oligosaccharide addition:
      • To asparagine (N-linked glycoprotein).
      • To serine or threonine (O-linked glycoprotein).

Types of R Groups: Polar Uncharged Hydrophilic

  • Examples include:
    • Serine (Ser or S).
    • Threonine (Thr or T).
    • Glutamine (Gln or Q).
    • Asparagine (Asn or N).
    • Tyrosine (Tyr or Y).
  • Properties of side chain:
    • Hydrophilic side chains tend to have partial + or - charge allowing them to participate in chemical reactions, form H-bonds, and associate with water.

Types of R Groups: Nonpolar Hydrophobic

  • Nonpolar covalent bonds.

  • Found in the interior of proteins and within membranes.

  • Examples include:

    • Alanine (Ala or A).
    • Valine (Val or V).
    • Leucine (Leu or L).
    • Isoleucine (Ile or I).
    • Methionine (Met or M).
    • Phenylalanine (Phe or F).
    • Tryptophan (Trp or W).

  • Properties of side chain:

    • Hydrophobic side chain consists almost entirely of C and H atoms. These amino acids tend to form the inner core of soluble proteins, buried away from the aqueous medium. They play an important role in membranes by associating with the lipid bilayer.

Types of R Groups: Other

  • Glycine:
    • Small.
  • Cysteine:
    • Forms S-S crosslink (disulfide).
    • Covalent bond.
  • Proline:
    • Forms bend in chain.
    • Disrupts ordered structure.

Formation of Disulfide Bond

  • Cysteine residues can form disulfide bonds.
  • The process involves oxidation of two cysteine residues to form cystine, creating an S-S bond and releasing 2H+ and 2e-.
  • The reverse process (reduction) breaks the disulfide bond.

Peptide Bond

  • Bond between the carboxyl group (COOH) of one amino acid and the amino group (NH₂) of another amino acid.
  • Formed via a condensation reaction.
  • Amino end (N-terminus) to carboxyl end (C-terminus).

Polypeptide Chain

  • Illustrates the arrangement of amino acids within a polypeptide, demonstrating the N-terminus and C-terminus ends.
  • Highlights different R-groups with varying properties such as:
    • Hydrophobic (Phenylalanine)
    • Hydrophilic (Serine)
    • Acidic (Glutamic acid)
    • Basic (Lysine)

Nucleic Acids

  • Composed of nucleotide monomers.
  • Nucleotide structure:
    • 5-carbon sugar.
    • Phosphate group (phosphate bond is high energy).
    • Nitrogenous base (Adenine, Guanine, Cytosine, Thymine, Uracil).
  • 5’ phosphate joined to 3’ OH to form a polynucleotide.
  • Condensation reaction.
  • Forms repeating sugar-phosphate backbone.
  • Has a 5’ phosphate end and a 3’ hydroxyl end.
  • Grows from the 5’ phosphate end to the 3’ hydroxyl end.
  • Has a negative charge.

Bases in Nucleic Acids

  • The bases are nitrogen-containing ring compounds, either pyrimidines or purines.
  • Pyrimidines:
    • Include cytosine, thymine, and uracil.
  • Purines:
    • Include adenine and guanine.

Phosphodiester Bond Formation

  • Water molecule released during the formation of a phosphodiester bond.
  • Subunits contain high energy, eliminating the need for an activation step.
  • Phosphodiester linkage forms between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of another.

RNA (Ribonucleic Acid)

  • Nucleotide has the 5-carbon sugar ribose.
  • Nucleotides are Adenine, Uridine, Guanine, and Cytosine.
  • RNA is a single nucleotide chain.
  • Blueprint for primary protein structure (sequence of amino acids).

DNA (Deoxyribonucleic Acid)

  • Nucleotide contains the 5-carbon sugar deoxyribose.
  • Nucleotides are Adenine, Thymine, Guanine, and Cytosine.
  • Forms a double alpha-helix structure.
  • Phosphate backbone is on the outside and nucleotides face inside.
  • Adenine and Thymine form hydrogen bonds.
  • Guanine and Cytosine form hydrogen bonds.
  • Antiparallel chains.
  • Genes are made of DNA.
  • The order of the nucleotides encodes information.

H Bond Base Pairs

  • Bases form specific base pairs through hydrogen bonds:
    • A-U in RNA.
    • A-T in DNA.
    • G-C.
  • Forms stable folded structures that allows transmission of genetic information.
  • A 3-nucleotide group specifies the amino acid sequence of a protein.

RNA and DNA

  • Compare and contrast the structures of RNA and DNA.
  • RNA:
    • Ribose sugar.
    • Uracil base.
    • Single-stranded.
  • DNA:
    • Deoxyribose sugar.
    • Thymine base.
    • Double-stranded.

RNA Secondary Structure

  • Illustrates how RNA can fold back on itself to form complex secondary structures.

DNA Double Helix

  • Shows the double helix structure of DNA with:
    • Bases.
    • Sugar.
    • Phosphate groups.
    • Hydrogen bonds.
    • Phosphodiester bonds.
  • Dimensions:
    • Diameter is 2 nm.
    • Distance between base pairs is 0.34 nm.
  • Highlights major and minor grooves.

Importance of H bonds to Information Transfer

  • Hydrogen bonds play a crucial role in:
    • DNA replication.
    • DNA repair.
    • Genetic recombination.
    • RNA synthesis (transcription).
    • Protein synthesis (translation).