Chemical Bonds & Reactions

• Class 03 covers molecules of life, part I

Recap of Introductory Topics

• Scientific Method
• Philosophy of rules and disease
• Usual suspects in biology: Bacteria, Archaea, Eukarya, Viruses, Viroids, and Prions

Today's Focus

• Review of chemistry relevant to living cells
• General molecules shared by all forms of cellular life, including use by acellular agents
• Specific differences will be addressed in later chapters
• Key sections of Chapter 2 (2.1, 2.2, 2.3) for review
• More time on the second part of Chapter 2.4 on Thursday to discuss specialized molecules

Class 03 Agenda

• Overview of atoms, elements, electrons, and bonding
• Expansion on bonding types and their importance
• Expansion on chemical reactions in life
• Focus on water's centrality in solution chemistry
• Concepts of equilibrium and catalysis
• The assembly of biological "legos and tinkertoys," including carbohydrates, lipids, and sterols

Elements and Their Properties

• Chemists and physicists identified 103 elements; more have been added, but not naturally occurring
• Elements have physical laws that define them and their properties
• Elements are composed of protons, neutrons in the nucleus, and electrons in shells
• Elements and their properties were learned through trial and error
• Focus will be on the characteristics and how MOs use them

Key Elements in Molecules of Life (CHONPS)

• Six elements (Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur) form the center of life's compounds
• These six elements form covalent bonds to create complex molecules for life chemistry
• Carbon is emphasized as a central element

Carbon's Bonding Properties

• Carbon is most stable with four covalent bonds, allowing it to form long chains with varied structures and activities
• Organic Chemistry:
  • Hydrogen: 1 covalent bond
  • Oxygen & Sulfur: 2 covalent bonds
  • Nitrogen: 3 covalent bonds
  • Phosphorus: 5 covalent bonds

Biologically Important Functional Groups

• Aldehyde: Found in carbohydrates
• Amino: Found in amino acids, the subunits of protein
• Carboxyl: Found in organic acids, including amino acids and fatty acids
• Hydroxyl: Found in carbohydrates, fatty acids, alcohol, some amino acids
• Keto: Found in carbohydrates and polypeptides
• Methyl: Some amino acids, attached to DNA
• Phosphate: Nucleotides (subunit of nucleic acids), ATP, signaling molecules
• Sulfhydryl: Part of the amino acid cysteine

Water's Importance

• Life can only occur in the presence of water
• The essential chemistry of life is primarily solution chemistry
• Covalent bonds can largely retain their connections between atoms in a water environment

Chemical Reactions

• Atoms are most stable when all possible bonds are in place
• Chemical reactions transfer electrons, rearranging bonds to form stable structures
• Reactions in one direction are defined by reactants changing to products
• Synthesis reaction: A + B → AB
• Decomposition reaction: AB → A + B
• Exchange reactions: AB + CD → AD + CB or AB + C → AC + B
• Most reactions in life chemistry are reversible

Equilibrium in Reactions

• Reactions can run both ways, but favor the most stable compounds
• Extreme example: CH4 + 2O2 <-> CO2 + 2H2O
• Balancing chemical equations requires balancing the number of each kind of atom on each side
• Balancing "redox" elements is important in Life Chemistry, involving reduced or oxidized electrons
• Reactions cannot run if atoms or reduced/oxidized electrons are depleted

Water's Role in Reactions

• In water, reactions proceed more readily
• Water molecules can separate into OH- and H+ ions
• Equilibrium balances products and reactants when the net rate of reaction is the same in both directions
• In pure water, the H+ concentration is 10-7 molar (pH 7)
• Acidified water increases H+ concentration, resulting in a lower pH
• Increase in availability of H+

Covalent Bonds and Stability

• Some compounds are more stable than others (different energy levels)
• Sharing of electrons is not always equal in covalent bonds
  • Nearly equal: C—C, C—H, and H—H
  • Not so equal: O and N hog the electrons
• Dipoles result in slight negative (O—H) and positive charges
• Opposite charges are attracted to each other

Hydrogen Bonds

• Hydrogen Bonds are very weak, roughly 1/100 the strength of a Covalent Bond
• When many hydrogen bonds are formed, molecules will stick...
• Bonds form and unform continuously
• Water is a dipole, creating hydrogen bonding to other water molecules

Covalent Bonds

• Polar covalent bonds result in slight charge separation and are important in biological systems
• May result in formation of hydrogen bonds

Water Properties and Hydrogen Bonding

• Water (H2O) is a polar molecule due to hydrogen bonding
• Liquid water: hydrogen bonds continually form and break, molecules slide
• Solid water (ice): each water molecule forms four hydrogen bonds, creating a less dense structure than liquid water
• Water's polar nature makes it an excellent solvent
• Polar and charged substances are hydrophilic and dissolve in water
• Non-polar substances are hydrophobic and do not dissolve in water
• Water with dissolved substances freezes at lower temperatures

Covalent Bonds in Life Chemistry

• C—C, C—H combinations result in equal sharing with no dipole and are hydrophobic (do not dissolve in water)
• Molecules with O or N have dipoles and are hydrophilic (dissolve in water)
• A molecule contains both hydrophobic and hydrophilic features

Ions and Ionic Bonds

• Some elements don't share electrons, resulting in solid positive or negative charges on each atom
• Salt crystals form a lattice of positive and negative charges but dissolve in water

Water & Electrolytes

• Ions can take on individual lives of their own as “Electrolytes".
• Individual charges can be diffused by hydrogen bonding in water
• Membranes can swap negative ions for OH- and positive ions for H+ via water
• Dissolution of salts in water can alter properties of water by changing the freezing/boiling points of water, changing the pH, changing the concentration of water and by transporting electricity
• Life exploits these properties of water

Chemical Reactions

• Reactions favor the most stable (least energy) compounds
• Life generally wants to go the higher energy compounds and lower entropy structures, but the Second Law of Thermodynamics states that Entropy increases naturally.
• Life links two reactions together, with one being energetically favored and the other not, but still energetically favorable when combined

Enzyme Catalysis

• Higher concentrations of reactants lead to faster reactions
• Reactants and products still diffuse in water
• Catalysis reduces a reaction's activation energy
• Enzymes are biological catalysts that speed the rate of reactions, they bind to reactant molecules
• Enzymes stabilize a transition state, lowering the required activation energy, can also couple unrelated chemical reactions

Major Classes of Compounds Used by Cells

• Carbohydrates
• Lipids/Sterols
• Proteins
• Nucleic Acids
• Building blocks for polymers or structures

Major Classes of Organic Molecules

• Carbohydrates:
  • Subunits: Monosaccharides
  • Major Functions: Structural components of cell walls and energy sources
• Lipids
  • Subunits: Varies, subunits are not always similar
  • Major Functions: Some types are important components of cell membranes; energy storage
• Proteins
  • Subunits: Amino acids
  • Major Functions: Enzyme catalysts; structural portion of many cell components
• Nucleic acids
  • Subunits: Nucleotides
  • DNA: Subunits: Deoxyribonucleotides
  • Major Functions: Genetic information of a cell
  • RNA: Subunits: Ribonucleotides
  • Major Functions: Various roles in protein synthesis; catalysis

Carbohydrates

• Diverse group including sugars and starches
• Serve as energy source, energy storage, and carbon source
• Component of DNA and RNA
• Structural components of cells
• Carbon, hydrogen, oxygen in 1:2:1 ratio
• Building block: CH2O

Monosaccharides

• Basic unit of carbohydrates
• 5-carbon sugars: ribose, deoxyribose
• 6-carbon sugars: glucose, galactose, mannose, fructose
• Structural isomers have the same atoms but different arrangement

Disaccharides

• Composed of two monosaccharides
• Common disaccharides include sucrose, lactose, and maltose
• Dehydration synthesis forms covalent bond between hydroxyl groups of monosaccharides
• Hydrolysis breaks bond and yields two monosaccharides

Polysaccharides

• Chains of monosaccharides
• Structural diversity from branching, linkages
• Important polymers of glucose: cellulose, starch, glycogen, dextran
• Chitin and agar polysaccharides are also important

Lipids

• Non-polar, hydrophobic molecules
• Diverse group defined by slight solubility in water
• Important in structure of membranes
• Not all lipids are composed of similar subunits

Fatty Acids

• Linear carbon skeletons with a carboxyl group (-COOH) at one end
• Saturated fatty acids: no double bonds, tails pack tightly, solid at room temperature
• Unsaturated fatty acids: double bonds between carbon atoms, kinks prevent tight packing, liquid at room temperature (oils)

Lipids Isomers

• Most natural fatty acids are cis: hydrogens bond on the same side of the double bond
• Trans fatty acids: hydrogens bond on opposite sides of double bond

Simple vs. Compound Lipids

• Most common simple lipids: Triglycerides
  • Fats or oils composed of three fatty acids linked to glycerol
  • Fatty acids: linear chains of bonded C, H atoms with carboxyl group at one end

Chemical Reactions and Reactants

• Higher concentration means a faster reaction
• Reactants and products diffuse in water
• Life needs a container that regulates diffusion

Phospholipids

• Compound lipids contain fatty acids and glycerol in addition to a non-lipid component
• Phospholipids contain hydrophilic phosphate group and hydrophobic fatty acid tails
• Phospholipids cluster with polar head in water, fatty acids in oil

Steroids Properties

• Characteristic four-ring structure
• Classified as lipids because they are poorly soluble in water
• Sterols such as cholesterol have hydroxyl group attached to one of the rings
• Often part of eukaryotic plasma membrane, role in Fungal disease treatment
• Other steroids include hormones

Class Assessment Question

• Briefly describe two characteristics of water that are important to Life

Explore covalent bonds, reaction dynamics, and pH. Understand reactants, products, and reversible reactions. Learn about electron transfer and balancing equations, particularly in aqueous and biological contexts.