Molecules of Cells - Principles of Biology I

Chapter 2: Molecules of Cells

Principles of Biology I

Overview

  • All living organisms consist of the same types of molecules.

  • Small differences in molecular arrangements can significantly affect health.

    • Example: Artificial trans fats increase the risk of health issues (atherosclerosis, heart attack, diabetes).

    • These trans fats are made by adding hydrogen atoms to liquid vegetable oils.

    • Real Life Application: Fear of Frying - trans fats are used for their long shelf-life, price efficiency, and mild flavor in manufactured foods.

Basic Chemistry

Matter

  • Matter: Anything that occupies space and has mass.

  • Matter can be living (biological) or non-living (inert).

Elements

  • Elements: Substances that cannot be broken down into simpler substances by ordinary chemical means (e.g. melting, reactivity).

  • Molecules: Composed of two or more different atoms.

Elemental Abundances

Earth's Crust and Organisms

  • Breakdown of elements that compose the Earth's crust and living organisms:

    • Major elements include Iron (Fe), Calcium (Ca), Potassium (K), Sodium (Na), Silicon (Si), Aluminium (Al), Magnesium (Mg), and Oxygen (O).

  • Composition indicated in terms of weight percent:

    • Iron (Fe): 20%

    • Calcium (Ca): 40%

    • Potassium (K): 10%

    • Silicon (Si): 67%

Abundance in Different Sources

  • Table 2.2 Some Elemental Abundances (as a percentage of total number of atoms):

    • Hydrogen (H): Human: 62.0%, Earth: 3.1%, Seawater: 66.0%

    • Oxygen (O): Human: 24.0%, Earth: 60.0%, Seawater: 33.0%

    • Carbon (C): Human: 12.0%, Earth: 0.3%, Seawater: <0.1%

    • Nitrogen (N): Human: 1.2%, Earth: <0.1%, Seawater: <0.1%

    • Phosphorus (P): Human: 0.2%, Earth: <0.1%, Seawater: <0.1%

    • Calcium (Ca): Human: <0.1%, Earth: <0.1%, Seawater: <0.1%

    • Sodium (Na): Human: <0.1%, Earth: <0.1%, Seawater: 0.3%

    • Potassium (K): Human: <0.1%, Earth: 0.8%, Seawater: <0.1%

    • Chlorine (Cl): Human: <0.1%, Earth: <0.1%, Seawater: 0.3%

Key Elements in Living Organisms

  • Elements that constitute 95% of living organisms by weight:

    • Carbon (C)

    • Hydrogen (H)

    • Nitrogen (N)

    • Oxygen (O)

    • Phosphorus (P)

    • Sulfur (S)

Atomic Structure

Definition of an Atom

  • Atom: The smallest unit of an element that retains the properties of that element.

    • Atoms of the same element possess the same number of protons.

Subatomic Particles

  • Protons: Positively charged particles (located in the nucleus).

  • Neutrons: Uncharged particles (located in the nucleus).

  • Electrons: Negatively charged particles (located in electron shells around the nucleus).

Example of Atomic Structure: Helium

  • Helium Structure:

    • Contains 2 protons, 2 neutrons, and 2 electrons in its outer shell.

  • The atomic symbol for helium is He, with an atomic mass close to 4.003.

Atomic Number and Atomic Mass

  • Atomic Mass = Number of Protons + Number of Neutrons.

  • Atomic Number = Number of Protons in the nucleus.

Periodic Table

Structure and Organization

  • Elements in vertical columns (groups) share common chemical characteristics.

    • Example: Group VIII elements (Noble gases) rarely react with others.

  • Each horizontal row corresponds to increasing atomic number i.e., the number of protons.

Isotopes

  • Isotopes: Atoms of the same element differing in neutron number.

    • Carbon has 3 isotopes: ^{12}C,^{13}C,^{14}C where:

    • ^{12}C has 6 protons and 6 neutrons,

    • ^{13}C has 6 protons and 7 neutrons,

    • ^{14}C has 6 protons and 8 neutrons (radioactive).

  • Isotopes have the same number of protons but different atomic masses and are essential in various applications including medical scans (e.g., PET scans, thyroid scans).

Chemical Bonds

Electrons and Bonding

  • The arrangement and number of electrons in an atom determine its ability to form bonds.

  • The first electron shell can hold up to 2 electrons, while each subsequent shell can hold up to 8 electrons, filled in lower shells first before moving to higher ones.

Types of Bonds

  • Ionic Bonds: Formed when electrons are transferred from one atom to another resulting in charged ions that attract each other.

  • Covalent Bonds: Involve the sharing of electrons between atoms.

    • Nonpolar Covalent Bonds: Electrons are shared equally.

    • Polar Covalent Bonds: Electrons are shared unequally, resulting in a molecule with partial charges.

  • Hydrogen Bonds: Occur between molecules when a hydrogen atom already bonded to an electronegative atom is attracted to another electronegative atom.

Ionic Bonding Example: Sodium Chloride (Salt)

  • Sodium has 1 electron in its outer shell, functioning as an electron donor.

  • Chlorine has 7 electrons in its outer shell, functioning as an electron acceptor.

  • When sodium transfers an electron to chlorine:

    • Sodium becomes positively charged (Na+) because it loses an electron.

    • Chlorine becomes negatively charged (Cl-) because it gains an electron.

  • This results in the formation of NaCl (sodium chloride).

Covalent Bonding

  • Involves the sharing of electrons between atoms allowing each atom to complete its outer shell.

  • Example: Water (H2O) - consists of two hydrogen atoms covalently bonded to one oxygen atom (H-O-H).

  • Double Covalent Bonds: Occur when two atoms share more than one pair of electrons.

    • Example: Oxygen gas (O2) is formed by a double bond between two oxygen atoms.

Molecular Shape and Function

  • The shape of molecules is critical for their functionality in biological systems.

  • Examples:

    • Hormones have specific shapes recognized by target cells.

    • Antibodies in the immune system recognize and bind to pathogens based on molecular shapes.

Polar and Nonpolar Molecules

  • Polar Molecules: Have unequal sharing of electrons leading to partially positive and negative charges (e.g., water).

  • Nonpolar Molecules: Have equal sharing (e.g., fats and oils).

  • Hydrophobic and Hydrophilic:

    • Hydrophilic substances attract water (e.g., sugars), while hydrophobic substances do not (e.g., oils).

Water as a Biological Molecule

Properties of Water

  1. Excellent Solvent: Facilitates biochemical reactions and dissolves many substances.

  2. Temperature Stability: High specific heat allows water to absorb heat without drastic temperature changes.

  3. Cohesive and Adhesive: Water molecules cling together (cohesion) and can adhere to other polar surfaces (adhesion).

Water Trivia

  • Oceans contain 97% of Earth's water; only 1% is suitable for drinking.

  • Human body: Approximately 66% water.

Acids, Bases, and the pH Scale

Definitions

  • Acids: Substances that release hydrogen ions (H+) when dissolved in water (e.g., hydrochloric acid).

  • Bases: Substances that release hydroxide ions (OH-) or absorb H+ (e.g., sodium hydroxide).

  • pH Scale: Ranges from 0 to 14 -

    • Acidic: pH < 7 (more H+ than OH-).

    • Neutral: pH = 7 (equal H+ and OH-).

    • Basic: pH > 7 (more OH- than H+).

Buffers

  • Buffers: Chemicals that help resist changes in pH, maintaining balance in living systems.

    • Example: Bicarbonate ions (HCO3-) in human blood maintain physiological pH.

Organic Molecules

Definitions

  • Organic Molecules: Always contain carbon (C) and hydrogen (H).

  • Major classes include carbohydrates, proteins, lipids, nucleic acids.

  • Organic molecules can be macromolecules formed from repeating smaller units called monomers.

  • Monomer: A single unit; Polymer: Multiple monomers linked together.

Carbohydrates

  • Composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio.

  • Functions include:

    • Quick energy (e.g., glucose).

    • Short-term energy storage (e.g., glycogen, starch).

    • Structural roles (e.g., cellulose).

Types of Carbohydrates

  1. Monosaccharides: Single sugar units (e.g., glucose, fructose).

  2. Disaccharides: Two monosaccharides joined (e.g., sucrose, lactose).

  3. Polysaccharides: Long chains of glucose subunits (e.g., cellulose, glycogen, starch).

Lipids

Types and Functions

  1. Fats: Long-term energy storage and insulation.

    • Typically solid at room temperature (saturated fats) or liquid (unsaturated fats).

  2. Phospholipids: Make up cell membranes.

    • Composed of glycerol, fatty acids, and phosphate group; have both hydrophilic and hydrophobic regions.

  3. Waxes: Water-repellent and protective coatings.

  4. Steroids: Important biological molecules (e.g., cholesterol).

Proteins

Structure and Function

  • Composed of amino acids linked by peptide bonds.

  • Functions include:

    • Structural support (e.g., collagen).

    • Catalysis (e.g., enzymes).

    • Transport (e.g., hemoglobin).

    • Movement (e.g., muscle contraction).

Levels of Protein Organization

  1. Primary Structure: Sequence of amino acids.

  2. Secondary Structure: Alpha helices or beta sheets formed by hydrogen bonding.

  3. Tertiary Structure: 3D folding due to interactions of R groups.

  4. Quaternary Structure: Assembly of multiple polypeptide chains.

Denaturation

  • Process where proteins lose their 3D structure due to factors like heat or pH changes, leading to loss of function.

Nucleic Acids

Types

  • DNA (Deoxyribonucleic Acid): Carries genetic information.

  • RNA (Ribonucleic Acid): Involved in protein synthesis.

  • ATP (Adenosine Triphosphate): Energy currency of the cell.

Structure of Nucleic Acids

  • Composed of nucleotides (sugar, phosphate group, nitrogenous base).

  • DNA is double stranded with bases A, T, C, and G;

  • RNA is single stranded with bases A, U, C, and G.

Conclusion

  • Understanding molecular biology is crucial for comprehending life processes, biochemical reactions, and systems in health and disease.