Chapter 2 - Chemistry Comes Alive - Biochemistry

INTRODUCTION - ORGANIC VS INORGANIC

• Organic molecules -contain C and H
  • usually larger than inorganic molecules
  • dissolve in water and organic liquids
  • carbohydrates, proteins, lipids, and nucleic acids
• Inorganic molecules -generally do not contain C
  • usually smaller than organic molecules
  • usually dissolve in water or react with water to release ions
  • water, oxygen, carbon dioxide, and inorganic salts

ORGANIC SUBSTANCES (COMPOUNDS) - living or once living

• Macromolecules (polymers) made up of monomers
  • Dehydration Synthesis - builds polymers - removes ______
  • Hydrolysis - breaks up polymers - adds _______ page 111
• Four major groups + Functional groups
  • Carbohydrates (-OH); lipids (-OH & COOH); proteins (NH₂ & COOH);
    nucleic acids (PO₄ & -OH)
• Isomers - compounds that have the same molecular formula but different structural formulas - examples:
• CARBOHYDRATES - (CH₂O)_n
  • Mainly provide energy, storage of energy, some structural.
  • Mostly polar soluble in water - OH groups (hydroxyl)
  • Are classification based on number of monomers
    • Monosaccharides (monomer) - simple sugar
      • Carbon skeleton varies from 3 - 7 carbons
        • Pentoses - ribose and deoxyribose
        • Hexoses - glucose, fructose & galactos
      • Glucose major cell energy nutrient
    • Disaccharides
      • Two monomers joined by dehydration synthesis
      • Disaccharides are digested by hydrolysis
    • Glucose + fructose ® Sucrose + H₂O
    • ________ + ________® Lactose + H₂O
    • ________ + ________® Maltose + H₂O
  • Polysaccharides - Long chains of glucose molecules covalently bonded (polymer of simple sugars)
    • Storage polysaccharides - starch and glycogen
    • Structural polysaccharide - cellulose (fiber)
      • Found in plant cell walls
      • Indigestible for most organism
• LIPIDS (fats, phospholipids, steroids)
  • Nonpolar, hydrophobic, insoluble in water, soluble in organic solvents
    • Many CH₂ groups (CH3 - methyl on the end)
  • H and O are not in 2 : 1 ratio; much less O, (C₅₇H₁₁₀O₆)
  • Neutral fats - very high energy
    • monomers (building blocks)
      • glycerol - OH groups
      • 3 fatty acids - COOH group
    • glycerol + 3 fatty acids® triglyceride + H₂O
    • saturated fats
      • solid at room temperature
      • no _________ bonds
      • animal fats - linked with _______disease
    • unsaturated fats
      • ___________ at room temperature
      • one or more ___________ bonds
      • extracts usually from ________
  • Phospholipids -modified triglycerides
    • monomer = glycerol + 2 fatty acids + phosphate group(PO₄)
    • hydrophobic on one end and hydrophilic on the opposite end of the molecule
    • bilayer of phospholipids main component in cell membrane
  • Steriods - four fused carbon rings
    • Foundation cholesterol
    • Make up cell membranes and hormones
  • Representative Lipids Found in the Body
    • Neutral fats - found in subcutaneous tissue and around organs
    • Phospholipids - chief component of cell membranes
    • Fat-soluble vitamins - vitamins A, E, and K
    • Lipoproteins - transport fatty acids and cholesterol in the bloodstream (VLDL, LDL, HDL)
    • Eicosanoids include prostaglandins and leukotrienes.
      • Lipid type derived from a fatty acid called arachidonic acid
      • Prostaglandins = wide variety of functions
        • modify responses to hormones
        • contribute to inflammatory response
        • prevent stomach ulcers
        • dilate airways
        • regulate body temperature
        • influence formation of blood clots
      • Leukotrienes = allergy & inflammatory responses
• PROTEINS -contain CHON
  • Monomer - amino acid
    • Amino group ______
    • Acid or carboxyl group ________
    • R group (side chain) unique for each amino acid (20 different)
  • Polymers -peptides, polypeptides and proteins
    • Peptide bond joins amino acids
      • Formed between the ______ group and ______ group
    • Broken up by _____________ and built by _____________
  • Levels of Protein Structure
    • Primary - linear sequence of amino acids
      • Genetically determined
      • Slightly changes can disrupt function of protein
    • Secondary - folding of primary structure
      • Alpha helix or beta pleated sheet
      • Fibrous proteins - held together by H-bonds
      • Examples: keratin, elastin, collagen, and certain contractile fibers
      • Often structural proteins (insoluble in water)
    • Globular protein -Compact, spherical proteins soluble in water
      • Examples: antibodies, hormones, and enzymes
      • Tertiary secondary structure folds more by ionic or hydrophobic interactions within the structure
        • Also sulfur groups can form disulfide bridges
      • Quaternary -polypeptide chains linked together in a specific manner
        • Example hemoglobin- made up of four
        • Form functional enzymes
  • Functions of Proteins - often depends on its ability to "recognize" and bind to some other molecule
    • Structure - keratin and collagen
    • Movement - actin and myosin
    • Transport -hemoglobin
    • Chemical
      • antibodies, antigens, receptors, hormones
      • enzymes to promote metabolism
  • Molecular Chaperones (Chaperonins) and Proteins
    • Help other proteins to achieve their functional three-dimensional shape
    • Maintain folding integrity
    • Assist in translocation of proteins across membranes
    • Promote the breakdown of damaged or denatured proteins
  • Characteristics of Enzymes - Globular proteins with specific shapes
    • Biological catalysts that increase the rate of a chemical reaction without being consumed by the reaction;does not depend on heat instead lowers activation energy
    • specific for substance they act on (substrate)
      • lock and key
      • induced fit (example)
    • names often end with -ase (sucrase, lactase, protease, lipase)
    • only the active site of the enzyme molecule actually binds to the substrate
    • needed only in small quantities
    • Some need a cofactor or coenzyme to activate the enzyme
      • Cofactor -->metal ion - hemoglobin
      • Coenzyme-->vitamins - NADH and FADH
    • Loss of Function ( Denaturation) - - altering enzyme functional 3-D formation.
      • Too high or low pH
      • Too high of a temperature
      • Organic solvents
      • High salt concentrations
      • Harmful chemicals for example cyanide, penicillin
      • Certain drugs that are similar to natural proteins can compete for active site
    • Work in Metabolic Pathways
      • new substrate product of the previous reaction
      • Negative feedback of product to active site of 1st enzyme.
        • Negative feedback to allosteric site
        • Positive feedback to allosteric site
• NUCLEIC ACIDS
  • Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus
  • Monomer - nucleotide -3 parts
    • 1. Pentose sugar
    • 2.Nitrogenous base
      • Purine - adenine and guanine
      • Pyrimidine -thymine and cytosine
    • 3. Phosphate group
  • Polymer
    • Formed by bonding of ___________
    • Bonding forms a sugar/phosphate backbone
  • Types of Nucleic Acids
    • DNA ________________________
      • Structure -handout
      • Function- hereditary instructions; Provides instructions for protein synthesis
      • Double-stranded helical molecule found in the nucleus of the cell
      • Replicates itself before the cell divides, ensuring genetic continuity
    • RNA - ________________________
      • Single-stranded molecule found in both the nucleus and the cytoplasm of a cell
      • Uses the nitrogenous base uracil instead of thymine
      • Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA
    • ATP - universal energy compound
      • Adenine-containing RNA nucleotide with three phosphate groups
      • Functions to transfer chemical energy from one molecule to another in cellular processes

FREE RADICAL - an electrically charged atom or group of atoms with an unpaired electron in its outermost shell.

• Unstable and highly reactive; can become stable
  • by giving up an electron
  • taking an electron from another molecule (example: breaking apart important body molecules)
• Antioxidants are substances that inactivate oxygen-derived free radicals
• Produced in your body by absorption of energy in ultraviolet light in sunlight, x-rays, by breakdown of harmful substances, & during normal metabolic reactions
• Linked to many diseases -- cancer, diabetes, Alzheimer, atherosclerosis and arthritis
• Damage may be slowed with antioxidants such as vitamins C and E, selenium & beta-carotene (precursor to vitamin A)

Helpful Activities to do after you finish reading this chapter

• Dehydration Synthesis and Hydrolysis

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