Molecular and Cellular Biology

1.1: Introduction to Chemical Composition of Organisms

1.1.1: Reactions & Bonds

  • Matter: Any substance that occupies space and has mass, and is made of elements

  • Elements: Cannot be broken down to other substances

    • Carbon

    • Oxygen

    • Hydrogen

    • The four elements common to all living organisms are oxygen, carbon, hydrogen, and nitrogen

  • Atom: Smallest unit of matter w/ element’s properties

    • Each element has unique atoms composed of three types of subatomic particles

      • neutrons (in nucleus)

      • protons (in nucleus)

      • electrons (orbitals surrounding the nucleus)

  • Compound: 2+ different elements combined in a fixed ratio

  • Molecule: 2+ Same or different elements combined in a fixed ratio

    • Oxygen gas for example

  • Electrons: Found orbiting in shells

    • valence shell: Outermost shell, electrons here called valence electrons

      • only valence electrons interact w/ other atoms

  • Chemical bonds: attractions that keep atoms close together

    • protons and electrons attract like magnets

  • Chemical Bonds - Covalent

    • Sharing pair of electrons, strong bonds

      1. nonpolar: Sharing is equal

        nonpolar example - sharing of electrons is equal

      2. polar: Sharing is unequal, creates partial charges (poles)

  • Chemical bonds - Ionic

    • One atom (anion) steals electron, other atom (cation) loses electron, strong bonds

  • Chemical Bonds - Hydrogen

    • Form between poles of H and O in water molecules, weak bonds

  • Chemical reactions

    • Make and break chemical bonds

    • Reactants react together, start of reaction

    • Products are produced, end of reaction

    • A+B <-> C

  • Energy:

    • 1st Law of thermodynamics: Energy cannot be created or destroyed

    • 2nd law of thermodynamics: reactions tend to increase disorder (make energy less available for cells)

    • Endothermic reactions take energy

    • Exothermic reactions release energy

1.1.2: Properties of Water

  • Solid less dense than liquid

  • Water has adhesion, cohesion and surface tension

    • Adhesion: molecules will stick to molecules other than water molecules well

    • Cohesion: Molecules will stick to molecules of the same type well

    • Surface tension: It’s difficult to break the surface of water

  • All of these characteristics are due to hydrogen bonds

  • Universal solvent

  • High specific heat

  • Evaporative cooling

  • Acids and Bases

    • Acids: dissolve in water and increase relative H+ ion concentration in the solution

      • HCl ←> H+ Cl-

    • Bases: Dissolve in water and decrease the H+ ion concentration in the solution

      • NH3 + H+ ←> NH4+

    • pH scale shows relative amount of H+ ion concentration

      • smaller + means more acidic

        • acidic

      • larger # means more basic

        • alkaline

      • 7 is neutrals

      • substances called buffers can help bring something to neutral

1.1.3 Chemical Structure of Carbohydrates, Lipids, Proteins, Nucleic Acids

  • Any molecule containing carbon is called “organic”

    • Can contain other molecules - oxygen, hydrogen, nitrogen

    • Made of building blocks called monomers

  • Many monomers linked together form polymer (whole molecule)

  • 4 Types of Organic Molecules

    • Carbohydrates

      • carbon, oxygen, and hydrogen

      • Monomer name: monosaccharide

        • ex: glucose

      • Polymer name: polysaccharide

        • ex: starch

    • lipids

      • grouped together because of their hydrophobic properties

        • ex: waxes (water barriers), fats (energy storage), phospholipids (cell membranes), steroids (hormones)

    • proteins

      • Monomer name: amino acids

      • Polymer name: polypeptide (protein)

      • Peptide bond: holds amino acids together

      • function:

        • most enzymes

        • defense - antibodies

        • muscle - fibers

    • nucleic acids

      • monomer name: nucleotide

      • two types:

        • deoxyribonucleic acid (DNA)

        • ribonucleic acid (RNA)

      • Primary function: information storage]

      • Sugar-phosphate “backbone” forms

      • Nucleotides paired (called a base pair) so that DNA or RNA strands are complimentary

        • A-T or A-U

        • C-G

      • Base pairs joined in center by hydrogen bonds

      • nucleotides are made of:

        • 1. Nitrogen base

          • Adenine

          • thymine (only in DNA)

          • uracil (only in RNA)

          • cytosine

          • guanine

        • 1 Sugar (deoxyribose or ribose)

        • 1 Phosphate group

1.2: Introduction to Cells

1.2.1 Structure and Function of Cell Organelles

  • Membrane: Boundary between inside of a cell and surroundings

    • selectively permeable

    • phospholipid bilayer with proteins, other lipids, hybrid molecules

  • Selective Permeability: Membranes regulate cell traffic by only allowing some things to pass freely, transporting others, preventing still others

  • Membrane Transport

    • Passive transport: Diffusion across membrane; no energy required; sometimes need “doorway” protein (which is in membrane)

      • Diffusion: Movement of molecules from high to lower concentrations

        • each molecule moves randomly

        • no energy required; spontaneous

      • Osmosis: Diffusion of water across membrane from higher to lower concentrations

      • Facilitated diffusion: Diffusion with the help of doorway

    Facilitated diffusion

    • Active transport: Movement across membrane requiring energy and doorway protein

      • Useful for moving molecules against their concentration gradients