Bio notes (combined)

• Matter


  Anything that takes up space and has mass
• Element


  A pure substance that has specific physical/chemical properties and can't be broken down into a simpler substance
• Atom


  The smallest unit of matter that still retains the chemical properties of the element
• Molecule


  Two or more atoms joined together
• Intramolecular forces


  Attractive forces that act on atoms within a molecule
• Intermolecular forces


  Forces that exist between molecules and affect physical properties of the substance
• Monomers


  Single molecules that can polymerize, or bond with one another
• Polymers


  Substances made up of many monomers joined together in chains
• Dehydration reaction

  When monomers bond with each other to form polymers, releasing water
• Hydrolysis


  When polymer bonds are broken using water
• Carbohydrates


  • Used as fuel and structural support
  • Contain carbon, hydrogen, and oxygen atoms (CHO)
  • Can come in the form of monosaccharides, disaccharides, and polysaccharides
• Monosaccharides


  Carbohydrate monomers with an empirical formula of (CH2O)n, where n represents the number of carbons
• Isomers


  Molecules with the same chemical formula but different arrangement of atoms
• Disaccharides


  • Contain two monosaccharides joined together by a glycosidic bond
  • result of dehydration reaction
• Polysaccharides


  Contain multiple monosaccharides connected by glycosidic bonds to form long polymers
• Polysaccharides


  • Starch (alpha bonded, linear amylose and branched amylopectin)
  • Glycogen (alpha bonded, highly branched)

  
• Proteins


  • Contain carbon, hydrogen, oxygen, and nitrogen atoms (CHON)
  • Amino acids link together to build polypeptides (or proteins)
  • A proteome refers to all the proteins expressed by one type of cell under one set of conditions
• Amino acids


  The monomers of proteins, each with a different "R-group"
• Polypeptides


  Polymers of amino acids joined by peptide bonds through dehydration (condensation) reactions
• N-terminus


  The side of a polypeptide that ends with the last amino acid's amino group
• C terminus


  The side of a polypeptide that ends with the last amino acid's carboxyl group
• Conjugated proteins


  Proteins composed of amino acids and non-protein components, including metalloproteins and glycoproteins
• Protein structure


  • Primary structure (sequence of amino acids)
  • Secondary structure (intermolecular forces between polypeptide backbone)
  • Tertiary structure (three-dimensional structure due to interactions between R-groups)
  • Quaternary structure (multiple polypeptide chains come together)
• Protein denaturation


  Loss of protein function and higher order structures, only the primary structure is unaffected
• Protein functions


  • Storage (reserve of amino acids)
  • Hormones (signaling molecules that regulate physiological processes)
  • Receptors (proteins in cell membranes which bind to signal molecules)
  • Structure (provide strength and support to tissues)
  • Immunity (antibodies that protect against foreign substances)
  • Enzymes (regulate rate of chemical reactions)
• Catalysts


  Increase reaction rates by lowering the activation energy of a reaction, without shifting the chemical reaction or affecting spontaneity
• Transition state


  The unstable conformation between the reactants and the products
• Enzymes


  Biological catalysts that bind to substrates (reactants) and convert them into products
• Enzymes


  • Bind to substrates at an active site, which is specific for the substrate
  • Most enzymes are proteins
  • The specificity constant measures how efficient an enzyme is at binding to the substrate and converting it to a product
  • The induced fit theory describes how the active site molds itself and changes shape to fit the substrate when it binds
• Ribozyme


  An RNA molecule that can act as an enzyme (a non-protein enzyme)
• Cofactor


  A non-protein molecule that helps enzymes perform reactions
• Coenzyme


  An organic cofactor (i.e. vitamins)
• Holoenzyme


  Enzymes that are bound to their cofactors
• Apoenzyme


  Enzymes that are not bound to their cofactors
• Prosthetic group


  Cofactors that are tightly or covalently bonded to their enzymes
• Ways enzymes catalyze reactions


  • Conformational changes that bring reactive groups closer
  • The presence of acidic or basic groups
  • Induced fit of the enzyme-substrate complex
  • Electrostatic attractions between the enzyme and substrate
• Enzyme activities


  • Phosphatase (cleaves a phosphate group off of a substrate molecule)
  • Phosphorylase (directly adds a phosphate group to a substrate molecule by breaking bonds)
  • Kinase (indirectly adds a phosphate group to a substrate molecule by transferring a phosphate group from ATP)
• Feedback regulation of enzymes


  The end product of an enzyme-catalyzed reaction inhibits the enzyme's activity by binding to an allosteric site
• Competitive inhibition


  A competitive inhibitor competes directly with the substrate for active site binding, adding more substrate can increase enzyme action
• Noncompetitive inhibition


  The noncompetitive inhibitor binds to an allosteric site that modifies the active site, the rate of enzyme action cannot be increased by adding more substrate