The Study of Biology

• Eukaryotic cells possess a membrane bound nucleus.
• Prokaryotic cells do not possess a membrane bound nucleus.

3 Domains of Life

• Eukarya are eukaryotes, divided into three multicellular kingdoms: Fungi, Plantae, and Animalia, and a diverse group of mostly unicellular organisms, the Protists.
• Archaea are prokaryotes that are extremophiles.
• Bacteria are prokaryotes.

Fundamental Properties of Life

• Cellular organization – all living things are composed of one or more cells.
• Homeostasis - all organisms maintain constant internal conditions.
• Heredity - all organisms possess genetic system that is based on replication and duplication of DNA.
• Energy utilization - all organisms acquire and use energy to stay alive.
• Growth, development and reproduction - all organisms are capable of growing and reproducing.
• The organization of the biological world is hierarchical – each level builds on the level below it: Cellular, Organismal, Population, and, Ecosystem level.

5 Concepts Unifying Biology

• Life is subject to chemical and physical laws.
• Structure determines function.
• Living systems transform energy and matter.
• Living systems depend on information transactions.
• Evolution explains the unity and diversity of life.

Scientific Method

• It is a procedure consisting of making observations, generating a hypothesis, and designing experiments to test the hypothesis.
• A variable is any factor, trait, or condition that can exist in differing amounts or types.
• The independent variable is the quantity that is being manipulated in an experiment.
• The dependent variable represents a quantity whose value depends on how the independent variable is manipulated.
• A control variable is a quantity that a scientist wants to remain constant.

The Nature of Molecules

• An atom is the smallest unit of matter that retains all chemical properties of an element.
• The Nucleus is the center of the Atom, made up of protons and, neutrons:
  • Protons have a positive charge (+1).
  • Neutrons have a neutral charge.
• Orbiting electrons surround the atom.
  • Electrons have Negative charge (-1).
• Atomic Number = # Protons
  • Atoms are electrically neutral
  • The number of protons equals the number of electrons.
• Atomic Mass = # Protons + # Neutrons
• Ions – the atom or molecule that carries a charge – unbalanced
  • Cation—more protons than electrons → positive charge
  • Anion-fewer protons than electrons → negative charge
• Neutrons in an element may vary, forming elements with different numbers of neutrons (isotope).
  • Isotopes of an element have different masses.
• The valence shell is the outermost shell.
  • Electrons in the valence shell are called valence electrons.
  • Atoms are most stable when the valence shell is full.
• Atoms form chemical bonds with other atoms to fill valence shells.
  • Ionic Bond - an electron is not shared, but is completely transferred from one atom to another.
  • Covalent Bond - form when unpaired valence electrons are shared by two atoms
    • Nonpolar covalent bond: electrons are evenly shared between two atoms.
    • Polar covalent bond: electrons are shared unevenly (asymmetrical).
• Electrons in polar covalent bonds spend most of their time close to nucleus of more electronegative atom.
• Hydrogen bonds - attraction between hydrogen atom with a partial + charge and another atom (usually oxygen or nitrogen) with partial – charge.
• Van der Waals interactions - weak attractions or interactions between two or more molecules due to changes in electron density.

Properties of Water

• Acids - any substance that dissociates in water to increase the H+ concentration and lower pH (proton donor).
  • The stronger an acid is, the more hydrogen ions it produces and the lower its pH.
• Bases - substances that acquire H+ during chemical reactions (proton acceptor).
  • Lowers H+ concentration, thus raising pH.
• pH - a measure of how acidic or basic a solution is.
• Buffers minimize changes in pH.
  • Releasing hydrogen ions when a base is added.
  • Absorbing hydrogen ions when acid is added.
  • Buffers help maintain homeostasis, relatively constant conditions, in organisms.

Chemical Building Blocks of Life

• Except for water, almost all molecules found in organisms have carbon atoms.
• Hydrocarbons – molecules consisting only of carbon and hydrogen, and are nonpolar.
• Functional groups add chemical properties.
• Isomers - Molecules with the same molecular or empirical formula but different arrangements of atoms.
  • Structural isomers – differ in the actual carbon skeleton.
  • Stereoisomers – differ in the spatial arrangement of the groups attached.
    • Enantiomers – D (right) or L (left) based on which direction rotate polarized light.
• Macromolecules: Large molecules made of smaller molecular subunits (monomers) joined together.
• Polymer-large number of monomers bonded together via polymerization (process of linking monomers together).
  • Dehydration synthesis (condensation reaction)- formation of large molecules by the removal of water or joining monomers to form polymers.
  • Hydrolysis- the breakdown of large molecules by the addition of water, polymers being broken down into monomers.
• Four major classes of biological macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic acids.

Carbohydrates

• Molecular formula (C H₂O)„ where n is the number of carbon atoms in the molecule.
• The ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules.
• Polysaccharide - a long chain of monosaccharides linked by dehydration synthesis, used for energy storage:
  • Starch (plants)
  • Glycogen (animals).
• Structural role in:
  • Cellulose (plant cell wall).
  • Chitin (insect exoskeleton and fungi).

Proteins

• Proteins have the most diverse range of functions of all macromolecules: Enzyme catalysis, Defense, Transport, Support, Motion, Regulation, Storage.
• Proteins (polymer) are made up of amino acids (monomer).
  • Composed of a central carbon atom bonded to:
    • H-hydrogen atom
    • N H2-amino functional group
    • COOH-carboxyl functional group
    • R group-variable “side chain”
      • R-group represents part of amino acid core structure that makes each of 20 amino acids unique, and can be: Charged, Acidic, Basic, Polar, Nonpolar, Aromatic, or have a Special Function.
• The peptide bond is a C - N bond covalently through dehydration synthesis
• 4 levels of protein structure:
  • Primary structure - Each protein has a unique sequence of amino acids.
  • Secondary structure - formed by hydrogen bonds between the carbonyl group of one amino acid and the amino group of another amino acid, forming a:
    • α-helix
    • β-pleated sheet
  • Tertiary structure - final folded shape of a globular protein.
    • Results interactions between residues.
  • Quaternary structure - Arrangement of individual chains (subunits) in a protein with two or more polypeptide chains.
• Denaturation - change in protein shape or protein becomes unfolded completely resulting in a nonfunctional protein.

Nucleic Acids

• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA).
• A nucleic acid is a polymer of nucleotide monomers.
  • A phosphate group.
  • A five-carbon sugar.
  • A nitrogenous (nitrogen-containing) base.
    • Purines-contain nine atoms in their two rings:
      • Adenine (A)
      • Guanine (G)
    • Pyrimidines—contain six atoms in their one ring:
      • Cytosine (C)
      • Uracil (U)-found only in ribonucleotides
      • Thymine (T)—found only in deoxyribonucleotides
• Nucleic acids form when nucleotides polymerize via dehydration synthesis and form a phosphodiester linkage.
• DNA strands are antiparallel.
  • One strand runs 3′ → 5′, the other runs 5' → 3'
• DNA strands form a double helix.
  • The sugar-phosphate backbone faces the exterior.
  • Nitrogenous base pairs face the interior.
• Complementary base pairing: A-T, G-C

• of purines = # of pyrimidines

• Equal number of T's and A's; equal number of C's and G's
• The primary structure of RNA differs from DNA:
  • RNA contains ribose instead of deoxyribose
  • 2' -OH group on ribose is more reactive than –H.
  • RNA is much less stable than DNA.
  • RNA contains uracil instead of thymine.

Lipids

• Lipids are diverse groups of hydrocarbon compounds that are hydrophobic.
• Three most important types of lipids found in cells:
  • Steroids - Distinguished by bulky, four-ring structure.
  • Fats - The primary role of fats is energy storage.
    • Composed of three fatty acids linked to glycerol.
    • Saturated - hydrocarbon chains consist of only single bonds between carbons, and has the maximum number of hydrogen atoms.
    • Unsaturated - hydrocarbon chains have one or more double bonds in hydrocarbon chains, forming a "kink" in the chain.
  • Phospholipids - form cell membranes.
    • Hydrophilic “head” composed of: Glycerol, Negatively charged phosphate group, and a Charged or polar group
    • Hydrophobic “tail”, composed of hydrocarbon chains.

Cell Theory

• All living things are composed of one or more cells.
• The cell is the basic unit of life.
• All new cells arise from existing cells.
• As a cell's size increases, its volume increases much more rapidly than its surface area.
  • Small cells have more surface area per unit of volume than larger cells.
  • Smaller cells have a larger surface area : volume ratio.
• All cells share four common components:
  • A plasma membrane – an outer covering that separates the cell's interior from its surrounding environment.
  • Cytoplasm - a jelly-like region within the cell in which other cellular components are found.
  • DNA - the genetic material of the cell.
  • Ribosomes - particles that synthesize proteins.
• Prokaryotic cells do not have a membrane bound nucleus and:
  • Lack a membrane-bound nucleus, but DNA is present in the nucleoid.
  • Have Cell wall outside of the plasma membrane and contain ribosomes.
  • There are No membrane-bound organelles.
  • Two domains of prokaryotes: : Archaea and Bacteria
  • Flagella: A long filament that rotate to propel cell.
  • Fimbriae: Needlelike projections that promote attachment to other cells or surfaces.
• Eukaryotic cells have a membrane bound nucleus.
  • Know organelle functions! Understand function from cellular diagrams.
• Endosymbiosis theory proposes that mitochondria and chloroplast were once free-living bacteria.     - Bacteria were engulfed by an ancestor of modern eukaryotes but were not destroyed, resulting in a mutually beneficial relationship.

Cytoskeleton

• Gives cells shape and structural stability.
• Transports materials within cell.
• 3 types of fibers:
  • Microfilaments (actin filaments).
    • Actin filaments involved in movement with motor protein myosin.
  • Intermediate filaments.
  • Microtubules.
    • Make up filamentous tracks used to transport vesicles and require a motor protein called kinesin
• Cell-cell attachments:
  • Tight junctions - Proteins hold adjacent cells together to form a watertight seal.
  • Desmosomes - Mechanically attach cytoskeletons of neighboring cells.
  • Gap junctions - Connect adjacent cells by forming channels.
    • Example: Plasmodesmata – plants

Membranes

• Fluid mosaic model - Biological membranes are a fluid mosaic of the components - phospholipids, cholesterol, proteins, carbohydrates - in which components flow and change position, while maintaining the integrity of the membrane.
• Cellular membranes have 4 components:
  • Phospholipid bilayer
    • A flexible matrix serving as a barrier to permeability.
  • Integral membrane proteins.
    • Transmembrane protein in transport and communication.
  • Peripheral membrane proteins.
    • Includes an internal protein network for support and cell shape.
  • Cell-surface markers.
    • Glycoproteins and glycolipids.
• Factors that influence fluidity/permeability:
  • Length of hydrocarbon tails.
    • Longer = less fluid/permeable.
    • Shorter = more fluid/permeable.
  • Saturation of state of hydrocarbon tails.
    • Saturated = less fluid/permeable.
    • Unsaturated = more fluid/permeable.
  • Presence of cholesterol molecules.
    • Less fluid/permeable.
  • Temperature.
    • Increase in temp = more fluid/permeable.
    • Decrease in temp = less fluid/permeable.
• Membrane proteins:
  • Transporters: Selective, allow only certain solutes to enter or leave the cell.
  • Enzymes: Carry out chemical reactions on the interior surface of the plasma membrane.
  • Cell-surface receptors: Detect chemical messages.
  • Cell-surface identity markers: Used to identify the cell to other cells.
    • In vertebrates, the immune system must be able to distinguish self from nonself.
  • Cell-to-cell adhesion proteins: Proteins used to glue cells to one another.
  • Cytoskeleton anchors: Often linked to the cytoskeleton via a linking protein.
• Integral membrane proteins - Span the lipid bilayer (transmembrane proteins)
  • Nonpolar regions of the protein are embedded in the interior of the bilayer.
  • Polar regions of the protein protrude from both sides of the bilayer.
• Diffusion - spontaneous movement of molecules from an area of high concentration to a low concentration.
• Osmosis – net diffusion of water across a membrane toward a higher solute concentration.
  • Hypotonic – Solution has a lower concentration than the inside of cell, thus water moves into the cell.
  • Hypertonic – Outside solution has a higher concentration than inside of cell, thus water moves out of cell.
  • Isotonic – solute concentration is equal inside and outside of cell, thus there's no net movement of water.
• Facilitated diffusion - Molecules such as ions that cannot cross the membrane easily may move through via proteins: Move from higher to lower concentration, with No energy requirement, through Channel or Carrier proteins.
• Passive transport occurs when substances diffuse across the membrane in absence of an outside energy source and moves substances down the concentration gradient.
• Active transport is when:
  • Substances move against their gradient.
  • Requires input of energy – ATP is used directly or indirectly to fuel active transport.
  • Protein pumps.
  • Endocytosis.
    • Phagocytosis – cell eating.
    • Pinocytosis – cell drinking.
    • Receptor – mediated endocytosis.
• Exocytosis - its purpose is to expel material from the cell into the extracellular fluid.