Ch.2 Chemical Level of Organization Part B

Chemical Level of Organization

  • All organic compounds contain carbon and hydrogen atoms.

Organic Compounds

  • Organic compounds are characterized by:
    • Always containing carbon and hydrogen and generally oxygen.
    • Carbon atoms can bond with one another to form long chains.
    • These chains can carry a variety of different functional groups.
Functional Groups
  • Definition: Attached groupings of atoms that occur commonly in many organic molecules.
  • Importance: Influence the properties of the overall molecule.
  • Functionality: Many functional groups enable cells to transfer and capture energy as high-energy compounds.

Categories of Organic Molecules

  • Biochemists classify organic molecules of life into four primary categories:
    1. Carbohydrates
    2. Lipids
    3. Proteins
    4. Nucleic acids

Important Functional Groups of Organic Compounds

Functional Groups and Their Characteristics

  • Amino group (-NH2)

    • Importance: Acts as a base, can accept H+ depending on pH; forms bonds with other molecules.
    • Examples: Amino acids.

  • Carboxyl group (-COOH)

    • Importance: Acts as an acid, releasing H+ to become R-COO-.
    • Examples: Fatty acids, Amino acids.

  • Hydroxyl group (-OH)

    • Importance: May link molecules through dehydration synthesis; hydrogen bonding between hydroxyl groups and water affects solubility.
    • Examples: Carbohydrates, Fatty acids, Amino acids, Alcohols.

  • Phosphate group (-PO4²-)

    • Importance: Links other molecules to form larger structures; stores energy.
    • Examples: Phospholipids, Nucleic acids, High-energy compounds.
Structural Formula
  • A structural formula shows the covalent bonds within a molecule or functional group. For example:
    • A single bond is represented by a single line (-).
    • A double bond is represented by two parallel lines (=).
    • A triple bond is represented by three parallel lines (=).
    • R represents the organic molecule to which a functional group is attached.

Carbohydrates

Overview

  • Carbohydrates are organic molecules containing carbon, hydrogen, and oxygen.
  • The ratio is usually near 1:2:1 (C:H:O).
  • Common examples include sugars and starches.
  • Carbohydrates account for about 1.5 percent of total body weight.
  • They are most important as energy sources.

Types of Carbohydrates

  1. Monosaccharides:

    • Definition: Simple sugars containing three to seven carbon atoms.
    • Examples: Glucose (most important fuel for the body), fructose.
    • Remarks: Manufactured in the body and obtained from food; distributed in bodily fluids.

  2. Disaccharides:

    • Definition: Two monosaccharides joined together.
    • Examples: Sucrose (table sugar), lactose (milk), maltose (malt sugar).
    • Function: Mainly energy sources.
    • Remarks: Must be broken down into monosaccharides before absorption (e.g., hydrolysis process).

  3. Polysaccharides:

    • Definition: Complex carbohydrates formed from multiple disaccharides and/or monosaccharides.
    • Examples: Glycogen, starches, cellulose.
    • Function: Digested carbohydrates are converted to glucose for ATP production.

Isomers

  • Isomers are molecules with the same molecular formula but different structures, affecting molecular function.
  • Examples: Glucose and fructose (both C6H12O6, but structurally different).

Hydrolysis and Dehydration Synthesis

  • Hydrolysis is the process that breaks down disaccharides into monosaccharides by adding water.
  • Dehydration synthesis is the creation of disaccharides from monosaccharides by removing water.

Lipids

Overview

  • Lipids, often termed fats, consist of carbon, hydrogen, and oxygen.
  • They generally have a carbon-to-hydrogen ratio close to 1:2 and contain much less oxygen than carbohydrates.
  • May also contain small quantities of phosphorus, nitrogen, or sulfur.
  • Common examples include fats, oils, and waxes, most of which are insoluble in water and require special transport mechanisms in the blood.

Types of Lipids

  1. Fatty Acids:

    • Definition: Long carbon chains with attached hydrogen atoms.
    • Structure: Two ends, head (hydrophilic with a carboxyl group) and tail (hydrophobic).
    • Types:
      • Saturated fatty acids: Each carbon in the tail has four attached hydrogens.
      • Unsaturated fatty acids: Contains double bonds in the tail.

  2. Glycerides:

    • Consist of fatty acid chains attached to glycerol.
    • Types include: monoglycerides, diglycerides, triglycerides (also known as triacylglycerols or neutral fats).
    • Created through dehydration synthesis, can be broken down through hydrolysis.

  3. Eicosanoids:

    • Derived from arachidonic acid.
    • Examples include prostaglandins and leukotrienes; they function as chemical messengers.

  4. Steroids:

    • Large molecules with four carbon rings; differ in attached functional groups.
    • Examples include cholesterol and sex hormones (e.g., estrogen, testosterone).

  5. Phospholipids and Glycolipids:

    • Both are diglycerides.
    • Phospholipid: Contains a phosphate grouping; important for cell membranes.
    • Glycolipid: Contains a carbohydrate attached to a diglyceride.

Lipids in the Body

  • Lipids are essential components of all cells, serving as energy reserves (providing twice the energy of carbohydrates) and accounting for 12–18% of total body weight in men and 18–24% in women.
  • Some fatty acids must be obtained through the diet.

Proteins

Overview

  • Proteins are the most abundant organic molecules in the body and account for approximately 20% of total body weight.
  • They contain carbon, hydrogen, oxygen, nitrogen, and possibly sulfur/phosphorus.
  • Basic structural units are long chains of amino acids (20 different amino acids)
  • Typical proteins consist of about 1000 amino acids.

Amino Acids

  • Each amino acid has a central carbon atom connected to four different groups:
    1. Hydrogen atom
    2. Amino group
    3. Carboxyl group
    4. R group (variable side chain influencing chemical properties)
  • Amino acids have both positive and negative charges, resulting in a neutral net charge.

Peptides

  • Formed by linking amino acids through dehydration synthesis, creating peptide bonds:
    • Dipeptide: Two amino acids linked together.
    • Polypeptides: Three or more amino acids linked. Peptides over 100 amino acids in length are considered proteins.

Protein Structure

  1. Primary Structure: Sequence of amino acids in the polypeptide chain.
  2. Secondary Structure: Bonds formed between different parts of the polypeptide (e.g., hydrogen bonds create alpha helix or beta sheets).
  3. Tertiary Structure: Overall 3-D shape from interactions of amino acids and surrounding water molecules.
  4. Quaternary Structure: Interaction between multiple polypeptide chains forming a protein complex (e.g., hemoglobin, collagen).

Denaturation of Proteins

  • Refers to changes in protein tertiary or quaternary structure, which can lead to loss of function.
  • Extreme conditions (e.g., high temperatures) can cause denaturation, which may lead to fatal consequences due to damage in tissues and organs.

Enzymes

Overview

  • Enzymes are proteins that facilitate enzymatic reactions within the body.
  • Each enzyme has an active site where substrates must bind.
  • Substrates lead to specific products due to interactions with enzymes.

Enzyme Functionality

  • The binding of a substrate induces a change in the enzyme's shape, forming an enzyme-substrate complex.
  • Following product formation, the product detaches, allowing the enzyme to catalyze subsequent reactions.
  • Control of Reaction Rates: Each enzyme operates best under specific conditions; activation/inactivation can regulate reactions.
  • Saturation Limit: Relates to substrate concentration and the rate of enzymatic reaction.

High-Energy Compounds

Definition

  • High-energy compounds store and transfer energy; they contain high-energy bonds that release energy when broken.
  • Adenosine triphosphate (ATP) is the most common high-energy compound.

Formation of ATP

  • Begins with adenosine (adenine + ribose).
  • Conversion processes:
    • Adenosine monophosphate (AMP): Adenosine with one phosphate.
    • Adenosine diphosphate (ADP): AMP with a second phosphate (two total).
    • Adenosine triphosphate (ATP): ADP with a third phosphate.

Energy Transfer with ATP

  • Formation of ATP from ADP is reversible.
  • Energy released during the breakdown of ATP to ADP is harnessed for vital body functions:
    • Muscle contraction
    • Synthesis of proteins, carbohydrates, and lipids.

Nucleic Acids

Overview

  • Nucleic acids are large organic molecules composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus.
  • There are two classes:
    1. Deoxyribonucleic Acid (DNA)
    2. Ribonucleic Acid (RNA)
  • They primarily store and transfer information for protein synthesis.

Nucleotide Structure

  • Composed of:
    • Phosphate group
    • Pentose sugar: either deoxyribose or ribose.
    • Nitrogenous base: Purines (adenine, guanine) and pyrimidines (cytosine, thymine in DNA, uracil in RNA).

Nucleic Acid Structure

  • Nucleotides bond via dehydration synthesis to form the backbone of alternating sugar and phosphate units, with nitrogenous bases projecting from the backbone.

DNA and RNA Structures

  • DNA:

    • Composed of two complementary strands forming a double helix, held together by hydrogen bonds between complementary base pairs (A-T, C-G).

  • RNA:

    • Typically a single chain of nucleotides, with various forms including mRNA, tRNA, and rRNA. Different structures and base pairing allow for diverse functions in protein synthesis.