Properties of Water

• Topic 1 is on Chemical Constituents of Cells, Part 1 - Water, Acid, Base & Protein
• Learning Objectives include:
  • Describing properties of water
  • Explaining how hydrogen bonding affects water properties
  • Describing acids, bases, pH scale, and how buffers stabilize pH
  • Describing the basic amino acid structure
  • Describing dipeptide formation
  • Explaining how protein bonding gives rise to different levels of protein structure and their functions

Introduction

• Cells, tissues, and organs have chemicals.
• Biochemistry studies chemical compounds in living systems and their reactions.
• Chemical compounds are either inorganic or organic.
• Inorganic include acids, bases, water, and salts.
• Organic include carbohydrates, lipids, and nucleic acids.

Water

• Water is a transparent, odorless, and colorless liquid.
• Each water molecule covalently links two hydrogen atoms and one oxygen atom.
• Water's molecular formula is H₂O.
• Water makes up 75% of brain volume.
• Water regulates internal body temperature.
• Water is 83% blood volume.
• Water removes waste and comprises 22% of bone volume.
• Water cushions joints and helps absorb nutrients.
• Water makes up 75% of muscle volume.
• Water has a bent ('V') shape with an angle of about 104.5°.
• Water is a polar molecule
• The oxygen end is partially negative, while the hydrogen end is partially positive.
• Sharing of electrons is unequal in each O-H covalent bond.
• Each hydrogen shares electrons with oxygen.
• Oxygen's high electronegativity pulls electrons toward the oxygen nucleus.
• Electrons are closer to oxygen, making it partially negative (δ-), while hydrogen becomes partially positive (δ+).
• The asymmetrical electron distribution makes water polar.
• Water molecules form covalent bonds between them.
• The positive end of one water molecule attracts the negative end of another.
• Oxygen attracts two nearby hydrogen atoms from other water molecules.
• A water molecule can form 4 hydrogen bonds with other water molecules.
• Bonds are constantly formed and broken due to weak hydrogen bonds.
• This allows water molecules to maintain a liquid state at ordinary temperature.

Properties of Water

• Water, a universal solvent, is a good solvent because of its polar molecules.
• Water is Important in breakdown of biological molecules.
• Water solubilizes polar and ionic molecules through electrostatic interaction.
• Partial charges on water molecules attract polar molecules.
• Water has high surface tension and the tendency for water molecules to stick together is called cohesion.
• Cohesive forces resulting from hydrogen bonding hold water molecules together, creating a skin at the surface.
• High cohesion creates a 'pulling' force due to water molecules' strong attraction
• Surface tension allows the formation of drops, bubbles, and meniscus.
• Pond surface water molecules stick more closely together, acting like a membrane.
• Small organisms like water striders use surface tension to move on the surface.
• High cohesion helps move water in xylem.
• High specific heat capacity refers to its capability for a molecule to absorb heat energy.
• Specific heat refers to the heat amount one gram of a substance must absorb to change its temperature by 1° C.
• The high specific heat capacity is due to hydrogen bonding.
• More energy is used to break hydrogen bonds.
• As a result, it takes a long time to heat and a long time to cool.
• Water temperature remains stable, even when air temperature changes rapidly.
• Water maintains a stable temperature for cells and aquatic organisms.
• Latent heat of vaporization measures the heat/energy to convert water from liquid into vapor.
• Latent heat of fusion measures the heat that must removed from water to turn it into ice.
• Water acts as a heat transfer medium (ice for cooling) and steam for heating.
• Sweating helps cover the body with water when body temperature rises, promoting cooling
• Water expands when it freezes and becomes less dense than liquid water.
• As water cools, the movement of water molecules slows and the molecules are farther apart.
• Each water molecule can form a maximum of 4 hydrogen bonds with other water molecules.
• Water achieves maximum density at 4°C.
• Ice is less dense than water.
• Floating ice results from lower density.
• This prevents organisms in water from freezing to death in winter.
• The low viscosity of water is due to hydrogen bonds that easily break.
• It allows molecules to slide over each other.
• Plays an important role in efficient transport of water in plants.
• In animals, low viscosity facilitates flow of blood and plasma in circulatory system.
• It is a good medium for movement among earthworms and snails.

Acids, Bases and Buffers

• Acids are substances that donate hydrogen ions when placed in water.
• In acids H+ concentration elevated and OH- concentration decreases
• Acids turn litmus paper from blue to red and have a sour taste
• Acids react with bases to neutralize their properties.
• Hydrochloric acid (HCl → H+ + Cl-) is an example of an acid.
• Bases are substances that receives hydrogen ions.
• In bases OH- concentration elevated and H+ concentration decreases
• Bases are alkaline
• Bases turn litmus paper from red to blue and are slippery.
• Bases react with acids to neutralize their properties.
• Ammonia, is an example of a base.
• pH is a measure of the concentration of hydrogen ions in a solution.
• The pH scale indicates how acidic or basic a substance; it ranges from 0 to 14.
• pH impacts the structure and function of proteins, including enzymes.
• Many cells and organisms can only survive in a specific pH environment.
• Buffers resist pH changes.
• Buffers react with added acid or base to control pH levels.
• A buffer works by donating hydrogen ions if pH increases and accepting them if pH decreases.
• A buffer is a mixture of a weak acid and its conjugate base, or a weak base and its conjugate acid.
• One common buffer component in blood is carbonic acid.
• The equilibrium allows the reaction to go back and forth.
• A consistent internal environment maintains optimal cell function.
• The pH of most living cells is closed to 7.
• Changes to pH can damage or kill cells.

Biological Molecules

• Carbon forms the skeleton of many biological molecules, specifically carbohydrates, proteins, lipids, and nucleic acids
• Monomers serve as the smallest unit of a molecule or micromolecule, e.g. glucose
• Polymers are large structural units of molecules connected via a covalent bond, e.g. carbohydrates and lipids.
• Monomers are combined to form polymers during condensation reactions.
• Polymers broken down during hydrolysis.

Proteins

• Proteins are made of carbon, hydrogen, oxygen, and nitrogen; some contain sulfur and phosphate.
• The monomer of proteins is amino acids.
• There are 20 types of amino acids: essential and non-essential.
• Proteins make up over 50% of dry mass in most cells.
• Amino acids have 4 chemical groups - bonded covalently to a central carbon.
• The amino group (NH2)& carboxylic acid group (COOH) serve as functional groups.
• Amino acids differ depending on their properties as defined by their associated R groups.
• Amino acids include:
  • Non-polar with hydrophobic side chains.
  • Polar with hydrophilic side chains.
  • Electrically charged with hydrophilic side chains.
  • Acidic forms negative ions in water.
  • Basic forms positive ions in water.
• Proteins linked together through formation of peptide bonds
• For amino acids joined through condensation.
• The amino group of one amino acid reacts with the carboxyl group of another, producing a water byproduct.
• Condensation of two amino acids forms a dipeptide
• Forming Dipeptides and Tripeptides via Amino Acids

Levels of Protein Structure

• Protein structure has 4 levels.
  • Primary structure: sequence of amino acids
  • Secondary structure: twist into a helices or beta-pleated sheets.
  • Tertiary structure: folding into 3D structure.
  • Quaternary structure: combination with other 3D protein structures.
• Primary sequences: linear polypeptide chains with associated peptide or covalent bonding that contribute to stabilization.
• Secondary structures in the form of folded primary structures occur as either alpha helices or beta-pleated sheets.
• Attraction results from the interaction of of O of C=O & H of NH of two amino acids
• Hydrogen bonds stabilize through repeating polypeptide backbone constituents.
• Tertiary structures describes precise 3D structures formed from secondary structure folding, through R group attraction.
• Stabilized by hydrogen bonding, hydrophobic interaction/nonpolar R, and ionic bonding and disulphide bonds of cysteine molecules.
• Quaternary structures refer to two or more polypeptide chain associations as determined by the attraction between R-groups.
• A good example is haemoglobin, consisting of two alpha chains (141 amino acids) and beta chains (146 amino acids).
• Fibrous protein include:
  • Long, parallel chains
  • Cross links between molecules, forming strong fibers.
  • Amino acids with non-polar R groups:
  • Stable
  • Providing mechanical & structural support.
  • Found in keratin and collagen.
• Globular proteins include:
  • Polypeptide chains folded
  • Compact spherical shapes
  • Hydrophobic and hydrophilic
  • R groups
  • Soluble with unstable structure, e.g. enzymes, insulin, and hormones.
  • Some globular proteins attached to a non-protein component called conjugated protein, e.g. Haemoglobin.

Protein Functions

• Hair and nails are formed with a form of protein called alpha-keratin that make up hair and fingernails.
• Muscles are created with muscle proteins such as actin and myosin proteins aid muscular contraction.
• They carry oxygen in your blood.
• Nerves rely on ion channel proteins for brain signalling through transporting molecules in and out of cells.
• Cellular messengers transport signals to protein partners.
• Antibodies defend bodies against bacteria and viruses.
• Enzymes in your saliva aid digestion of food.
• Cellular construction workers clusters of proteins that can copy genes and creating new proteins.

This lesson explores the unique properties of water, including its molecular formula, polarity, and high surface tension. It covers the role of hydrogen and oxygen atoms. It also addresses water's solvent capabilities.