General Biology Study Notes: Water and Organic Molecules in Organisms

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Water

Properties and Importance of Water

Water is a unique and essential molecule for life, making up about 70% of the human body. Its chemical and physical properties allow it to support biological processes and act as a medium for chemical reactions.

Polarity: Water is a polar molecule, meaning it has partial positive and negative charges due to the uneven distribution of electrons between hydrogen and oxygen atoms.
Hydrogen Bonding: The polarity of water allows it to form hydrogen bonds, which are weak attractions between the hydrogen atom of one water molecule and the oxygen atom of another.
Cohesion: Water molecules stick to each other due to hydrogen bonding, resulting in high surface tension.
Adhesion: Water molecules can also stick to other substances, aiding processes like capillary action.
Capillary Action: The combined effect of cohesion and adhesion allows water to move through narrow spaces, such as plant xylem.
High Heat Capacity: Water can absorb and retain large amounts of heat, helping organisms maintain stable internal temperatures.

Example: Water's high heat capacity helps regulate climate and body temperature in living organisms.

Acidity, Alkalinity, and pH

The pH scale measures the concentration of hydrogen ions in a solution, indicating whether it is acidic, neutral, or basic.

Acidic Solution: pH < 7; high concentration of H+ ions.
Neutral Solution: pH = 7; equal concentration of H+ and OH- ions.
Basic (Alkaline) Solution: pH > 7; high concentration of OH- ions.

Example: Blood is slightly basic, with a pH around 7.4.

Significance of Water for Life

Water's properties make it an ideal medium for living things, facilitating chemical reactions, nutrient transport, and temperature regulation.

Solvent: Water dissolves many substances, enabling biochemical reactions.
Transport: Water carries nutrients and waste products in organisms.
Temperature Regulation: Water's heat capacity buffers organisms against temperature changes.

Organic Molecules in Organisms

Elements and Atomic Structure

Living organisms are primarily composed of six essential elements: carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), and sulfur (S). Atoms are the basic units of matter, consisting of protons, neutrons, and electrons.

Atom: The smallest unit of an element, containing a nucleus (protons and neutrons) and electrons orbiting the nucleus.
Subatomic Particles: Protons (positive charge), Neutrons (neutral), Electrons (negative charge).

Chemical Bonds

Atoms combine to form compounds through chemical bonds, which include ionic, covalent, and hydrogen bonds.

Ionic Bond: Transfer of electrons between atoms, resulting in charged ions (e.g., NaCl).
Covalent Bond: Sharing of electrons between atoms (e.g., H2O).
Polar Covalent Bond: Unequal sharing of electrons, creating partial charges (e.g., water).
Nonpolar Covalent Bond: Equal sharing of electrons (e.g., O2).
Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom (e.g., between water molecules).

Organic Compounds

Organic compounds contain carbon atoms and form the basis of life. Major classes include carbohydrates, proteins, lipids, and nucleic acids.

Carbohydrates: Provide energy and structural support.
Proteins: Serve as enzymes, structural components, and signaling molecules.
Lipids: Store energy, form cell membranes, and act as signaling molecules.
Nucleic Acids: Store and transmit genetic information.

Carbohydrates

Structure and Function

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically in a 1:2:1 ratio. They serve as energy sources and structural materials.

Monosaccharides: Simple sugars (e.g., glucose, fructose).
Disaccharides: Two monosaccharides joined by a glycosidic bond (e.g., maltose).
Polysaccharides: Long chains of monosaccharides (e.g., starch, cellulose, glycogen).

Example: Starch is a storage polysaccharide in plants; glycogen is a storage polysaccharide in animals.

Hydrolysis and Dehydration Synthesis

Carbohydrates are synthesized and broken down by specific chemical reactions.

Dehydration Synthesis: Formation of a covalent bond between two molecules with the removal of water.
Hydrolysis: Breaking of a covalent bond by adding water.

Equation for Dehydration Synthesis:

Equation for Hydrolysis:

Proteins

Amino Acids and Protein Structure

Proteins are polymers of amino acids, which contain an amino group, carboxyl group, central carbon, and R group. There are 20 different amino acids.

Polypeptide: A chain of amino acids linked by peptide bonds.
Peptide Bond: Covalent bond between the amino group of one amino acid and the carboxyl group of another.

Levels of Protein Structure:

Primary Structure: Sequence of amino acids.
Secondary Structure: Local folding (e.g., alpha helix, beta sheet) stabilized by hydrogen bonds.
Tertiary Structure: Overall 3D shape, stabilized by interactions among R groups.
Quaternary Structure: Association of multiple polypeptide chains.

Protein Functions

Proteins perform a wide variety of functions in cells.

Structural Proteins: Provide support (e.g., collagen).
Storage Proteins: Store amino acids (e.g., ovalbumin).
Transport Proteins: Move substances (e.g., hemoglobin).
Defensive Proteins: Protect against disease (e.g., antibodies).
Enzymes: Catalyze biochemical reactions (e.g., amylase).

Example: Enzymes speed up chemical reactions by lowering activation energy.

Lipids

Structure and Types

Lipids are hydrophobic molecules composed mainly of carbon and hydrogen. They include fats, oils, phospholipids, and steroids.

Triglycerides: Consist of three fatty acids and one glycerol molecule.
Saturated Fatty Acids: No double bonds; solid at room temperature.
Unsaturated Fatty Acids: One or more double bonds; liquid at room temperature.
Phospholipids: Major component of cell membranes, with hydrophilic heads and hydrophobic tails.
Steroids: Four fused carbon rings; function as hormones (e.g., cholesterol).

Phospholipids and Cell Membranes

Phospholipids form bilayers that make up cell membranes, providing selective permeability.

Hydrophilic Head: Attracted to water; faces outward.
Hydrophobic Tails: Repelled by water; face inward.
Lipid Bilayer: Double layer of phospholipids forming the cell membrane.

Example: The lipid bilayer allows only certain substances to pass through, maintaining cellular homeostasis.

Nucleic Acids

Structure and Function

Nucleic acids store and transmit genetic information. The two main types are DNA and RNA.

Nucleotide: The building block of nucleic acids, consisting of a phosphate group, a sugar, and a nitrogenous base.
DNA (Deoxyribonucleic Acid): Contains the bases adenine (A), thymine (T), cytosine (C), and guanine (G).
RNA (Ribonucleic Acid): Contains the bases adenine (A), uracil (U), cytosine (C), and guanine (G).

Type	Pyrimidines	Purines
DNA	Cytosine, Thymine	Adenine, Guanine
RNA	Cytosine, Uracil	Adenine, Guanine

Example: DNA stores genetic instructions; RNA helps in protein synthesis.

Cell Membranes

Structure and Permeability

The cell membrane is composed mainly of phospholipids and proteins, forming a selectively permeable barrier.

Phospholipids: Form the basic structure of the membrane, creating a bilayer.
Proteins: Serve as channels, receptors, and enzymes, facilitating transport and communication.
Permeability: The ability of the membrane to allow certain substances to pass while blocking others.

Example: Transport proteins enable the movement of ions and molecules across the membrane.

Metabolism

Definition and Importance

Metabolism refers to all chemical reactions that occur within living organisms to maintain life.

Anabolism: Building up complex molecules from simpler ones (e.g., protein synthesis).
Catabolism: Breaking down complex molecules into simpler ones (e.g., cellular respiration).

Example: The breakdown of glucose during cellular respiration provides energy for cellular activities.

Additional info:

When an egg is hard-boiled, the proteins denature and coagulate, causing the clear liquid to become white and solid.
Water's role as a solvent and its ability to form hydrogen bonds are critical for biochemical reactions and molecular interactions in cells.