Chemistry: Atoms, Bonds, Water, and pH

• The lecture covers the structure of atoms, chemical bonds, hydrogen bonds, water ionization, pH, acids, bases and buffers

Atomic Structure

• Essential background knowledge includes subatomic particles, energy levels, orbitals, and valence electrons
• This is covered in Section 2.2

Chemical Bonds

• Atoms combine due to chemical bonds

Types of Chemical Bonds

• Atoms are held together by chemical bonds, there are different types of chemical bonds
• Covalent Bonds: Interaction type where electrons are shared
• Ionic Bonds: Interaction due to attraction of opposite charges
• Hydrogen Bonds: sharing of a H-atom
• Van der Waals Interactions: weak attraction between non-polar molecules

Ionic Bonds

• Ionic bonds form when ions with opposite charges attract each other, such as cations and anions
• An example ionic bond is NaCl or MgCl2
• Valence electrons are not shared; they are fully transferred to the other atom

Covalent Bonds

• Covalent bonds occur when two atoms share a valence electron pair
• Examples include H2, O2, H2O, and CH4
• The bonding capacity is determined by the valence of an atom
• The strength of a covalent bond depends on the number of shared electrons

Types of Covalent Bonds

• Non-polar covalent bonds involve the equal sharing of valence electrons, e.g., H2, O2, N2
• Polar covalent bonds involve unequal sharing of valence electrons, e.g., H2O
• The kind of covalent bond between two atoms is influenced by the electronegativity of the atoms involved

Non-Polar Covalent Bonds

• Methane (CH4) is non-polar covalent

Polar Covalent Bonds

• Water (H2O) is an example of a polar covalent bond

Hydrogen Bonds

• Hydrogen bonds form when a hydrogen atom covalently bonded to an electronegative oxygen or nitrogen atom is attracted to another electronegative oxygen or nitrogen
• A hydrogen bond is a specific type of dipole-dipole interaction, possessing a defined direction

Hydrogen Bonds Between Water Molecules

• Water molecules interact through hydrogen bonds

Role of Hydrogen Bonds in Protein Structure

• Multiple hydrogen bonds stabilize the secondary structure of proteins, like alpha-helices

Van der Waals Interactions

• Van der Waals forces are weak attractive forces between non-polar molecules at very short distances
• Constant electron movement causes temporary accumulation in one part of a molecule
• This leads to transient areas of positive and negative charge

Example of Van der Waals Forces

• Gecko adhesion is an example of the collective strength of Van der Waals interactions

Properties of Water

• Structure: H2O forms through polar covalent bonds between O and 2H
• A water molecule (H2O) is highly polar
• H2O forms hydrogen bonds with other polar molecules
• The unique properties of H2O arise from its ability to form hydrogen bonds

Ice Formation

• In liquid water, hydrogen bonds are dynamic, allowing molecules to slide past each other
• In ice, water molecules are locked into a rigid network due to stable hydrogen bonds

5 Properties of Water

• The capacity of H2O to form hydrogen bonds gives five important characteristics
  • Cohesion
  • Temperature control
  • Frozen H2O (ice) floats
  • Creates polar and non-polar settings
  • Acts as solvent

Cohesion

• H2O adheres to any substance with which it can form hydrogen bonds
• Cohesion refers to the formation of hydrogen bonds with other water molecules
  • Adhesion refers to the creation of hydrogen bonds with other compounds which are not water

Biologoical Consequences of Cohesion

• Surface tension is caused by unbalanced hydrogen bonds
• Spiders utilizes surface tension to walk on water
• Biological consequences of cohesion and adhesion water is pulled from root to leaves

Temperature Control

• Water's high specific heat requires a significant amount of energy to change its temperature
• High heat of vapourization requires a lot of energy to go from liquid to gas
  • This is a driving force in plant cooling and stabilization of water temperature in ponds and rivers

Ice Floating

• H2O is less dense in solid form than in liquid form
• Lower density of ice is because a stable hydrogen bond network forms

Floating of Ice Biological Consequences

• Ice insulates the liquid water that are underneath, thus making life possible

4. Creation of Polar and Non-Polar Environment

• Water resists intrusion because of network
• Creates non-polar association
• Polar /ladded molecules causes competeing pull to create a space
• Krities for the organization of cells by creating the 2 environments

Polarity

• Water is effective solvent because of its polar make up
• Water adheres to polar molecules referred to as "hydrophilic"
• Water repels non-polar molecules referred to as "hydrophobic"

Biologoical Consequences

• Biological fluids involves polar and non-polar moleules which are essential

Water Dissociation and pH

• pH values are used to express the acidity of water
• Water dissociates into H+ and OH-
• pH = -log [H+] is a scale of 0-14 (Logarithmic scale of units with a 10-fold relationship)

pH scale measures

• The pH scale ranges from acid to neutral to base with representative substances as examples

Acids and bases

• An Acid is a substance that increases is [H+] and give H+ and lowers that pH
• A Base is a substance that decreases is [H+] and reduces the H+ and increases to lowers the pH

Buffers

• Buffers lower the concentration of [H+] and [OH-]
• Buffers binds when the concentration is too high and donates when the concentration is too low

Buffers

• Stabilizing of blood pH by carbonic acid
• Carbonic acid donates and deprotonates and bicarbonate intakes proton