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• Chapter 3 covers Organic Molecules

Organic Molecules

• Organic molecules contain carbon and hydrogen atoms and include biomolecules
• There are four classes of organic biomolecules in living organisms
• The four classes of organic biomolecules are Carbohydrates, Lipids, Proteins and Nucleic Acids
• Functions of the four biomolecules in the cell are diverse

Inorganic vs. Organic Molecules

• Inorganic molecules usually contain positive and negative ions with ionic bonding, a small number of atoms, and are associated with nonliving matter
• Organic molecules always contain carbon and hydrogen with covalent bonding, a large number of atoms, and are associated with living organisms

The Carbon Atom

• C can form 4 covalent bonds
• C bonds with many elements (CHNOPS), including itself
• C-C bond is very stable and allows formation of long C chains

The Carbon Skeleton and Functional Groups

• The carbon chain of an organic molecule is its skeleton or backbone
• Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structures and functions
• Functional groups determine chemical reactivity and polarity of organic molecules
• Replacing H by OH in ethane changes it to ethanol, a hydrophobic molecule, becoming hydrophilic

Functional Groups

• Hydroxyl (R-OH) is alcohol as in ethanol. Significance: Polar, forms hydrogen bond, present in sugars, some amino acids
• Carbonyl (R-C=O-H) is Aldehyde as in formaldehyde. Significance: Polar, present in sugars
• Carbonyl (R-C=O-R) is Ketone as in acetone. Significance: Polar, present in sugars
• Carboxyl (R-C=O-OH) is Carboxylic acid as in acetic acid. Significance: Polar, acidic, present in fatty acids, amino acids
• Amino (R-N-H-H) is Amine as in tryptophan. Significance: Polar, basic, forms hydrogen bonds, present in amino acids
• Sulfhydryl (R-SH) is Thiol as in ethanethiol. Significance: Forms disulfide bonds, present in some amino acids
• Phosphate (R-O-P=O-OH-OH) is Organic Phosphate as in phosphorylated molecules. Significance: Polar, acidic, present in nucleotides, phospholipids

Isomers

• Isomers are organic molecules that have identical molecular formulas but a different arrangement of atoms, so have different functional groups
• Example isomer: glyceraldehyde chemical formula is H-C-C-C-H, OH OH
• Example isomer: dihydroxyacetone chemical formula is H-C-C-C-H, OH OH
• Glucose, Galactose, Fructose are carbohydrate isomers

Biomolecules

• Carbohydrates subunits are Monosaccharide and polymers are Polysaccharide
• Lipids subunits are Glycerol and fatty acids and polymers are N/A
• Proteins subunits are Amino acids and polymers are Polypeptide
• Nucleic acids subunits are Nucleotide and polymers are DNA and RNA
• Biomolecules usually consist of many repeating units called a monomer
• A molecule composed of monomers is a polymer often made of many parts
• Example: amino acids (monomer) are joined together to form a protein (polymer)
• Lipids aren't polymers because contain two different types of subunits

Synthesis and Degradation

• Dehydration reaction joins subunits together by the formation of a covalent bond by producing water
• Hydrolysis reaction adds a water molecule to break a covalent bond
• Both Dehydration and Hydrolysis processes require enzymes
• Forms starch from glucose

Enzymes

• Special molecules called enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions
• An enzyme is a molecule that speeds up a chemical reaction
• Enzymes are not consumed or changed in the reaction
• Enzymes are catalysts

Carbohydrates

• C-H-O occurs at a ratio of 1:2:1
• Can be small soluble chains or long chains or rings
• Carbohydrates act as a short term and long term energy source and have a structural role
• Carbohydrates can take one of the forms; Monosaccharide, Disaccharide, or Polysaccharide

Monosaccharides

• Example, Ribose: chemical formula is 5 CH2OH, 4 H 1, 3 OH 2 H,
• Example, Deoxyribose: chemical formula is 5 CH2OH, 4 H 1, 3 OH 2 H,

Disaccharides

• A disaccharide contains two monosaccharides joined together during a dehydration reaction
• Lactose (milk sugar) is composed of galactose and glucose
• Sucrose (table sugar) is composed of glucose and fructose
• Maltose is composed of two glucose molecules
• Lactose-intolerant individuals lack the enzyme lactase which breaks down lactose into galactose and glucose

Polysaccharide

• Polysaccharide is a polymer of monosaccharides
• Starch is the major form of energy storage in plants
• Glycogen acts as a reserve energy storage in animals
• Cellulose is mainly found in the cell walls of plants
• Animals are unable to digest cellulose, the most abundant organic molecule on earth
• Chitin is found in the cell walls of fungi and exoskeleton of some animals
• Peptidoglycan is found in the cell walls of bacteria containing amino acid chains

Lipids

• Large and nonpolar molecules that are hydrophobic, insoluble in water, and soluble can be found in organic solvents and contain large sections of only C & H
• Lipids function as a long term energy storage - storing more E than CHO and acts as structural components in cell membrane
• It can be used for heat retention, cell communication and regulation and functions as protection in waxes
• Fats, oils, phospholipids, steroids, waxes can be found in lipids

Major types of lipids

• Triglycerides: fats & oils that provide long-term insulation
• Phospholipids
• Steroids
• Waxes

Types of Lipids

• Fats provide long-term energy storage and insulation in animals (butter, lard)
• Oils provide long-term energy storage in plants and their seeds (cooking oils)
• Phospholipids make up major components of plasma membrane (Food additive)
• Steroids components of plasma membrane (Medicines)
• Waxes (cholesterol), sex hormones provide protection, prevention of water (Candles, polishes) loss (cuticle of plant surfaces), beeswax, earwax

Triglycerides

• Acts as long-term energy storage and insulation
• Consist of one glycerol molecule linked to three fatty acids by dehydration synthesis

Fatty acids

• Can be described as unsaturated if one or more double bonds exist between carbons or saturated if no double bonds exist between carbons
• Unsaturated fats exist as a liquid at room temperature (ex: plant oils), and can be on the same chemical groups on the same (cis) or opposite (trans) side of the double bond
• Saturated fats exist as a solid at room temperature (ex.: butter, lard)

Trans-Fats and Cardiovascular Health

• Transfats are a type of fat, or lipid created synthetically through hydrogenation
• They are created by the hydrogenation process which adds hydrogen to unsaturated fats to increase food shelf life and flavor and or texture
• May cause worse health effects than saturated fat which can negatively affect health
• Consuming trans fats as part of the diet can increase risk for cardiovascular diisease

Phospholipids Functions

• Structure is similar to triglycerides.
• They Consist of one glycerol molecule linked to two fatty acids and a modified phosphate group
• The fatty acids are nonpolar and hydrophobic
• The modified phosphate group is polar and hydrophilic
• The plasma membrane of a cell is partly comprised of many phospholipids with:
• Polar phosphate heads are oriented towards the water
• Nonpolar fatty acid tails are oriented away from water and form a hydrophobic core

Steroids

• Testosterone and estrogen are sex hormones differing only in the functional groups attached to the same carbon skeleton,
• Steroid cholesterol is a part of steroids
• The steroid rings are an important class of organic molecules, as well as cholesterol found in the membranes of animal cells

Waxes Facts

• Long-chain fatty acids connected to carbon chains containing alcohol functional groups
• Present as a Solid at room temperature
• Waterproof and resistant to degradation
• Acts as protection such as earwax (contains cerumin), plant cuticle, beeswax

Proteins

• Proteins are polymers of amino acids linked together by peptide bonds
• A peptide bond is a covalent bond between amino acids
• As much as 50% of the dry weight of most cells consists of proteins
• Long chains of amino acids joined together, and are therefore known as polypeptides
• A protein is a polypeptide that has folded into a particular shape, which is essential for its proper functioning

Functions of Proteins

• Metabolism: Enzymes act as catalysts to accelerate chemical reactions within cells
• Support is provided: Structural proteins have a structural function, for example, keratin and collagen
• Transport of molecules: Proteins regulate what substances enter and exit cells. Hemoglobin transports oxygen to tissues and cells
• Defense: Antibodies are proteins of our immune system that bind to antigens and prevent those molecules from destroying cells
• Regulation: Hormones are proteins that that regulate cellular metabolism
• Motion: Microtubules move cell components to different locations. Myosin proteins allow muscles to contract

Amino acids

• There are 20 different common amino acids joined together to form a dipeptide
• Amino acids differ by their R, or variable groups, which vary in complexity

Shape of Proteins and Levels of Protein Structure

• Proteins cannot function properly unless folding occurs resulting in the proper shape
• When a protein loses its unique structure or proper shape- it experiences denaturation
• Exposure protein to the wrong chemicals, a change in pH, or even high temperature can disrupt the proteins shape
• Proteins can have up to four levels of structure classified as:
• Primary, Secondary, Tertiary, Quaternary

Protein Structure

• Polypeptides can have 4 levels of structure before proteins form
• A proteins Primary structure is classified simply as an amino acid chain such as H3N and COO
• A proteins Secondary structures contains fibrous proteins that perform various functions. These proteins can be found in 2 types of folding: a helix, and ẞ sheet
• Hydrogen bonding holds the secondary structure in place
• A proteins Tertiary structure, or Globular proteins function as overall three-dimensional shape of a polypeptide
• Stabilized by hydrophobic interactions, hydrogen, ionic, and covalent bonding
• A proteins Quaternary structure: consists of more than one polypeptide, e.g. hemoglobin

The Importance of Protein Folding and Protein-Folding Diseases

• Chaperone proteins help proteins fold into their normal shapes and may also correct misfolding of new proteins.
• Defects in chaperone proteins may play a role in several human diseases, such as Alzheimer's disease and cystic fibrosis.
• Prions are misfolded proteins that have been involved in TSEs, a group of fatal brain diseases
• Prions may cause folding in other proteins

Nucleic Acids

• Nucleic acids are polymers of nucleotides
• Two varieties of nucleic acids are present:
  • DNA (deoxyribonucleic acid): genetic material that stores information for its own replication and for the sequence of amino acids in proteins
  • RNA (ribonucleic acid): has a wide range of different functions within cells which include protein synthesis and regulation of gene expression

Nucleotide structure

• nucleotide structure contains: phosphate, a nitrogen containing base, and pentose sugar
• A key structure for cell function lies in the nucleotides

DNA vs RNA Structure

• DNA has the deoxyribose sugar, and RNA has the ribose sugar.
• DNA has bases that are adenine, guanine, thymine, cytosine, and RNA contains bases that are adenine, guanine, uracil, or cytosine.
• DNA has strands that are double stranded with base pairing whereas RNA's strands are single stranded.
• DNA forms in a helix shape however RNA does not

ATP: A Special Nucleotide

• ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates
• Energy is created because of the three phosphate groups
• ATP is a high-energy molecule due to the presence of the last two unstable phosphate bonds
• Hydrolysis of the terminal phosphate bond yields the following:
  • The molecule ADP (adenosine diphosphate)
  • An inorganic phosphate
  • Energy to do cellular work
• ATP is therefore considered the energy currency of the cell