Organic Molecules and Macromolecules

Organic Chemistry

• Organic molecules contain both carbon (C) and hydrogen (H).
• Organic molecules are highly abundant in living things.
• Macromolecules constitute big and complicated organic molecules.
• The four categories include carbohydrates, lipids, proteins, and nucleic acids.
• About 5000 different organic molecules are in bacterial cells, while there are twice as many in plant or animal cells.

Inorganic Molecules

• Inorganic molecules typically have positive/negative ions.
• Generally bound by ionic bonding.
• Have a low amount of atoms.
• They are often associated with nonliving things.

Organic Molecules

• Organic molecules always have both carbon and hydrogen present.
• Bound by covalent bonding.
• Consist of many atoms.
• They are typically associated with living things.

Four Classes of Organic Molecules

• Carbohydrates, lipids, proteins, and nucleic acids get called macromolecules because of their large size.
• Polymers get made of many monomers.
• Protein polymers can hold hundreds of amino acids (monomers) and nucleic acid can hold hundreds of nucleotides.

Polymer Formation: Condensation or dehydration

• Monomers form a bond and release H2O

Polymer Degradation: Hydrolysis

• Monomers are separated by adding H2O

Carbohydrates

• They make up an immediate source of energy in living things.
• The composition is C, H, and O atoms.
• The general formula is Cn(H2O)n.
• Most of the C atoms in a carbohydrate are connected to a H atom and a OH (hydroxyl) group. Plays numerous structural roles in organisms.
• Carbohydrates include single sugar molecules and chains of sugar molecules.

Carbohydrates: Monosaccharides

• These are the Simplest sugars which include (monos, single and sacchar, sugar).
• They are a ready source of energy.
• Molecular formula for a single sugar is a multiple of CH2O.
• Sugars contain many polar hydroxyl groups to make them soluble in water.
• Most common are 5 or 6 carbons
  • Pentoses: consist of 5C as components of RNA and DNA molecules
    • Ribose (C5H10O5): found in RNA
    • deoxyribose (C5H10O4); found in DNA
  • Hexose: consist of 6C
    • Glucose (C6H12O6); is water soluble

Glucose Isomers

• Structural isomers: feature a different arrangement of the same elements.
  • Glucose and fructose
• Stereoisomers: refers to geometric isomers; either above or below ring.
  • α- and β-glucose
• Enantiomers: mirror image.
  • D- and L- glucose

Carbohydrates: Disaccharides

• Consist of two monosaccharides
• Joined together via a dehydration/condensation process to form a glycosidic bond.
• Broken apart by hydrolysis.
  • Sucrose = Glucose (6C – 6 member ring) + Fructose (6C – 5 member ring)
    • Sucrose is the form of sugar transported in plants and used to sweeten food.
  • Maltose = Glucose + Glucose knowns as malt sugar]
  • Lactose = Glucose + Galactose knowns as milk sugar]

Carbohydrates: Polysaccharides

• Formed from the linkage of many monosaccharides to form long polymers
• Short-term energy storage
  • Starch: a mixture of two complex carbohydrates, amylose and amylopectin, that act as polymers of glucose. Plants use it as a way to store excess glucose.
  • Glycogen: used by animals that store glucose as glycogen (granules in the liver). Polysaccharide of glucose serves as the primary short-term energy storage in animal cells.
• Hormones control release and storage of glucose
  • Insulin released from the pancreas promotes the storage of glucose as glycogen, stored.
  • Glucagon released from pancreas stimulates the breakdown of glycogen into glucose.

Carbohydrates: Polysaccharides

• Cellulose: is the most abundant of all carbohydrates
  • Polymer of β-glucose
  • Cell walls in plants contain cellulose.
  • Parallel glucose chains.
• Chitin:
  • Form the external skeleton of insects and the cell wall of fungi.
  • The sugar monomer of chitin has nitrogen-containing groups.
• Glycosaminoglycans:
  • Found in animals, especially in cartilage.
  • Sugar monomers tend to have carboxyl and sulfate groups.

Lipids

• Predominantly made of hydrogen and carbon atoms (hydrocarbon chains)
• Defining feature is that they are nonpolar: hydrogen bonded only to C, gives no ability to form hydrogen bonds with water molecules which makes it insoluble in water.
• Includes fats, phospholipids, steroids, waxes.
• Lipids make up about 40% of the average human body's organic content.

Lipids: Fats

• A mixture of triglycerides, also known as triacylglycerols.
• Serves as long-term energy storage.
• Formed by bonding one glycerol to three fatty acids
• Held together by dehydration or condensation; and broken apart by hydrolysis
• Glycerol forms because it is a compound with three OH groups (OH makes it polar; glycerol is water soluble)
• A typical Fatty acid consists of a long hydrocarbon (R) chain with a carboxyl (-COOH) group at one end.
• Fats and oils are formed via acidic portions react with the OH group of glycerol during a dehydration reaction. The three fatty acids can be all different, all the same, or only two the same.

Lipids: Fats

• Fatty acids are either saturated or unsaturated.
  • Saturated fatty acids: have no double bonds between the carbon atoms where all carbons are linked through single covalent bonds.
    • Tend to be solid at room temperature.
• Unsaturated fatty acids have one or more double bonds in carbon chain
  • 1 double bond: monounsaturated
  • 2 or more: polyunsaturated
  • Tend to be liquids at room temperature (oils).
• Fats play an important component for energy storage where 1g of fat stores twice as much energy as 1g of glycogen or starch
• Fats also provide structural support by providing cushioning and insulation.

Lipids: Phospholipids

• Are formed from glycerol, two fatty acids plus a phosphate group
• The third fatty acid is replaced with a polar phosphate group.
• They are amphipathic molecules
• Hydrophilic heads: phosphate region
• hydrophobic tails: fatty acid chains
• They arrange themselves so only the polar heads make contact with water.
• Cell plasma membranes consists of mainly phospholipid bilayer.

Lipids: Steroids

• Have 4 interconnected carbon rings
• Are typically insoluble in water
• Examples: Cholesterol, estrogen, and testosterone
• Cholesterol forms as the precursor of several other steroids like testosterone and estrogen.
• Even though testosterone and estrogen only differ by what and the structure the groups attach, they have a significant effect on a body and someone's sexuality.

Waxes

• Made of a mixture of hydrocarbons and long-chain fatty acids bonded to long-chain alcohols.
• Secreted onto the surface of plant leaves and of insects in the cuticle
• Waxes are nonpolar so thus they exclude water providing a barrier to water loss
• Have a solid consistency at normal temperatures due to a high melting point
• Water is more resistant.
• They resist degradation.
• Acts as structural elements in colonies like bee hives

Proteins

• Diverse functions:
  • Support: keratin (hair, nail, ligaments..)
  • Enzymes: bring reactants together (e.g. hydrolases, ligases)
  • Transport: channel and career proteins (plasma membrane) which grants substance transport in and around cells. Hemoglobin transports oxygen.)
  • Defense: antibodies (combine with foreign subjects and prevent them from destroying cells)
  • Hormones: eg. insulin regulates blood glucose
  • Motion: eg. actin and myosin allow parts of cells to move and cause muscles to contract
• Composed of C, H, O, N, and small amounts of other elements, like S
• Amino acids act as proteins monomers
  • Common structure with variable R-group
  • 20 amino acids
  • Side-chain determines structure/function
  • Bond to a hydrogen atom, an amino group -NH2, an acidic group -COOH, and an R (remainder) group.

Proteins: Structure of Amino Acids

• Amino acids are commonly classified by properties such as the group into four categories: acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar).

Proteins: peptide bond formation

• Amino acids are combined through a dehydration or condensation reaction, forming a covalent bond known as a "peptide bond".
• Peptide: forms when two or more amino acids join together.
• Polypeptide forms as a chain of many amino acids joined by peptide bonds.
• Proteins consist of either 1 or more polypeptides. Peptide bonds are broken apart by hydrolysis.

Protein Structure

• Primary: sequence of amino acids.
• Secondary: polypeptide folding is a regular fashion as hydrogen bonding is present.
• Tertiary: creates final 3D structure of a polypeptide made through folding and twisting,
• Quaternary: is made of multiple polypeptides.

Protein Structure

• Primary structure: refers to amino acid sequence determined by genes
• Secondary structure: are due by chemical physics interactions causing folding
  • Irregular or repeating
    • α helices and β sheets and key factors for how it functions
  • "Random coiled regions" are parts of it that are not a helix or β sheet but give it properties
• Shape is therefore specific and important to function

Protein Structure

• Tertiary Structure: refers to folding which gives protein their complex 3-D shape and is its final form.
• Quaternary Structurerefers to being is made up of 2 or more polypeptides. Individual chains act as protein subunits that are part Multimeric, where proteins consist of different polypeptides.

Protein folding and Stability

1. Hydrogen bonds: promotes protein folding and stabilty
2. Ionic/polar bonds: ionic and polar interactions fold and stabilty
3. Hydrohpbic effects - avoid water contact
4. Van Dee Waals Forces: atoms that have weak attractions
5. Disulfide bridges: covalent bonds that that line two cysteine amino acids and contain sulflydrl group.

Protein-Protein Interactions

• Cellular processes involve steps that involve two proteins
• Important to structures
• Bonds tightly at surface
• Four factors bind with surface:
  • Hydrogen bonds
  • Ionic/Polar interactions
  • Hydrophobic effects
  • Van der Waals forces

Proteins That Contain Domains

• Contain distinct Structures
• Signal transducer for activators (STAT)
• Function in biological functions
• Proteins shared share domains

Nucleic Acids

• Are Responsible for storage expression and genetic information
• two classes
  • Deoxyribonucleic acid (DNA)
    • Stores genetic information encoded in the sequence of nucleotide monomers
  • Ribonucleic acid (RNA)
    • Decodes DNA into instructions For linking sequence for amion acid to polypeptide chains
• Monomoeris Nucleotide
  • Consist of base. consists of carbon and nitrogen, of sugar and phosphate.
  • Has Sugar Phosphate or backbone.

DNA & RNA

• DNA (Deoxyribonucleic acid )
• Contains "Deoxyribose.
• Has bases : Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) Strands- double helix.
• 1 Form of RNA

RNA (Ribonucleic acid)

• "Robose Has Adenine (A), Guanine (G), Cytosine (C) and Uracil (U) are the nucleotides.
• Single Stratnd
• Several Forms of base groups

Test your knowledge of organic molecule characteristics, breakdown processes, and the roles of macromolecules. Explore carbohydrates, lipids, and their building blocks. Understand triglycerides and phospholipids.