Organic Compounds
Introduction to organic compounds
Carbon-based molecules are called Organic compounds
e.g. Methane (CH4) is the simplest organic molecule.
Compounds composed of only carbon and hydrogen are called Hydrocarbon.
e.g. Methane and Propane.
Isomers is the compounds which have same formula but different arrangement.
e.g. Butane and Isobutane.
Carbon skeleton : the chain of carbon atoms in an organic molecule.
Functional groups: is group of atoms.
1- Participate in chemical reactions.
2- Determine the properties of organic compounds.
e.g. Hydroxyl, Carbonyl, Carboxylm and amino group.
Functional groups are Polar and Soluble in water. (except Methyl group)
Functional Groups
Hydrophilic
1- Hydroxyl Group = hydrogen atom bonded to an oxygen atom.
Organic compounds containing hydroxyl groups are called alcohols.
e.g. Ethanol.
2- Carbonyl Group = carbon atom linked by double bond to an oxygen atom.
If the carbonyl group at the end of the carbon skeleton the compound called Aldehyde.
If the carbonyl group at the middle of the carbon skeleton the compound called Ketone.
3- Carboxyl Group = hydroxyl group bonded to a carbonyl group.
act as an acid.
Compounds with carboxyl groups are called Carboxylic Acids.
4- Amino Group = Nitrogen bonded to two hydrogen and carbon skeleton.
Organic compounds with an amino group called amiens.
Amino Acids = amino group and carboxyl group.
is the building blocks of proteins.
5- Phosphate Group = phosphorus atom bonded to four oxygen atoms.
Compounds with phosphate group are called Organic Phosphates.
Often involved in energy transfers.
6- Methyl Group = Carbon bonded to three hydrogens. ( Nonpolar = hydrophobic )
Compounds with methyl group are call Methylated compounds.
Making and Breaking Polymers
Carbohydrates, Proteins, Nucleic Acids are Macromolecules.
Joining smaller molecules into chains called Polymers.
The building blocks of polymers are called Monomers.
Making Polymers ( Dehydration )
Cells link monomers together to form polymers by Dehydration reaction.
Dehydration, reaction that removes a molecule of water.
Dehydration form a covalent bond linking two monomers.
Breaking Polymers ( Hydrolysis )
Digestion process for a polymer call Hydrolysis.
Hydrolysis mean to break with water.
Dehydration and Hydrolysis
Carbohydrates
hydrophilic
Monosaccharide
Monosaccharides are the simplest carbohydrates.
Many monosaccharides form rings.
glucose - fructose - glactose - Ribose - Deoxyribose
Honey consist of monosaccharides (glucose + fructose )
Monosaccharides, particularly Glucose, are the main fuel molecules for cellular work.
Disaccharide
Disaccharide = two monosaccharides link by dehydration.
maltose = glucose + glucose
which is common in germinating seed and milk candy.
sucrose = glucose + fructose
The most common. ( table sugar, plant sap )
lactose = glucose + glactose
Sugar in milk.
Polysaccharide
Starch, energy storage in plants. ( Unbranched )
monomer = glucose
e.g Potatoes and Grains.
Glycogen, energy storage in animals. ( Branched )
monomer = glucose
Most of your glycogen is stored as
granules in your liver and muscle cells.
Cellulose, form plant cell walls.
(abundant organic compound on Earth)
monomer = glucose
Cellulose molecules are joined together by
hydrogen bond ( arranged parallel )
Chitin, 1- form insect exoskeleton.
2- cell walls of fungi.
Each molecule contain Hydroxyl groups and a Carbonyl group.
These molecules typically have a formula that is a multiple of ( CH2O).
An aqueous solution of glucose called Dextrose.
Isomers: They contain the same atoms but in different arrangements.
e.g. Glucose and Fructose .. ( 6 carbon ).
Lipids
hydrophobic
Lipids grouped together because they share one trait
They do not mix mell with water
Lipids consist mainly of Carbon and Hydrogen atoms.
Linked by nonpolar covalent bonds.
Lipids differ from carbohydrates, proteins, nucleic acids in :
Not huge macromolecule.
Not polymers built from similar monomers.
Fats large lipids made from glycerol and fatty acids.
Fats Composed of
Glycerol: is an alcohol with three carbons,
each bearing a hydroxyl group.
Fatty acid: consist of a carboxyl group ( make it an acid ).
and a hydrocarbon chain ( 16-18 atoms on length ) ( make it hydrophobic )
Fats consist Twice the energy as a polysaccharide has.
Main function: energy storage.
Example: Triglycerides ( 1 glycerol linked to 3 fatty acids )
Dehydration reaction linking glycerol molecule and fatty acids molecule.
The nonpolar hydrocarbon chains are the reason fats are hydrophobic.
Fatty acids
1- Saturated
the hydrocarbon chain without double bond(=)
Solid at room temperature.
High melting point.
Occur in most animals fats.
e.g. Butter - Beef.
2- Unsaturated
The hydrocarbon chain contain one or more double bonds.
Liquid at room temperature.
Low melting point.
Occur in most plant cells.
e.g. Corn oil - olive oil.
* Hydrogenated vegetable oil: means that unsaturated fats have been converted to saturated fats by adding hydrogen.
Omega-3 : Unsaturated fatty acids are found in certain nuts, plant oils, and fatty fish and appear to protect against cardiovascular disease.
Phospholipids
The major component of cell membrane.
cell could never exist without phospholipids
Composed of: Phosphate group + Glycerol + 2 Fatty acids.
* negatively charged phosphate group.
Hydrophilic heads : Phosphate group + Glycerol.
Hydrophobic tails : Fatty acids.
Steroids
The carbon skeleton contains four fused rings.
Example:-
Cholesterol :
is an essential structural component of animal cell membranes.
Sex hormones :-
Estradiol in Female.
Testosterone in Male.
Different steroids vary in chemical groups attached to the rings.
Too much cholesterol in the blood may contribute to atherosclerosis.
Proteins
Hydrophilic
Proteins Structure
Protein is a polymer of amino acids.
Nearly every dynamic function in your body depends on proteins.
You have tens of thousands of different proteins in your body.
The most important are Enzymes that speed up all reactions in cells. e.g. Lactase.
lysozyme, an enzyme found in sweat, tears, and saliva.
Lysozyme's general shape is called Globular.
Most enzymes and other proteins are globular.
e.g. Transthyretin, Lysozyme.
Structural proteins are long and thin called Fibrous proteins.
e.g. Collagen.
There are 20 different amino acids that make up all proteins.
The characteristic that distinguishes one amino acid from another is (R group).
Amino acid fundamental design composed of :-
1- Central carbon ( alpha carbon ).
2- Carboxyl group (-COOH) makes it an acid.
3- Amino group ( NH2 ).
4- R-group ( unique side chain ) : differs with each amino acid.
* Carboxyl group and amino group covalently bonded to alpha carbon.
The simplest amino acid is ( glycine ). R= H atom.
The composition and structure of R-group determine
the properties of each 20 amino acids.
Cells join amino acids together in a dehydration reaction.
The resulting covalent linkage is called a peptide bond.
The bonds between amino acid monomers are called peptide bond.
Dipeptide, made from two amino acids.
Polypeptide, chain of amino acids.
Most polypeptides are at least 100 amino acids in length.
Example of amino acids
1- Hydrophilic, Serine (Ser) and Aspartic acid (Asp)
2- Hydrophobic, Leucine (Leu)
A long polypeptide chain of specific sequence is not a protein.
A Functioning protein is one or more polypeptide chains precisely coiled, twisted, and folded into a unique three-dimensional shape.
Proteins Function
Structural Proteins.
Proteins in fibers that make tendons and ligaments.
found in hair too.
Contractile proteins.
Muscle cells are packed with it.
Defensive proteins.
such as antibodies of he immune system.
Signal proteins.
such as hormones.
Receptor proteins.
Transmit signals into cells.
Transport proteins.
such as hemoglobin in red blood cells.
Storage proteins.
ovalbumin ( egg white ).
Milk protein.
plant seeds.
* The functions of all these different types of proteins depend on their specific shape.
* Nearly all proteins must recognized and bind to some other molecule to function.
* A protein loses its specific function when its polypeptides unravel, this process call ( Denaturation ).
Proteins are involved in the following processes :-
1- cellular structure.
2- movement.
3- defense.
4- transport.
5- communication in cells.
Protein's Shape
Primary structure :-
The primary structure of a protein is its unique sequence of amino acids.
Determined by inherited genetic information.
Secondary structure :-
Parts of the polypeptide coil or fold into local patterns called Secondary structure.
Coiling of a polypeptide chain result a Secondary structure called alpha helix.
Folding of a polypeptide chain result a Secondary structure called beta pleated sheet.
The R-groups of the amino acids are not involved in forming these secondary structures.
Transthyretin (protein) has only one alpha helix region.
Tertiary structure :-
The term tertiary structure refers to the overall three dimensional shape of a polypeptide.
Tertiary structure generally result from interactions between the R-groups of the various amino acids.
Disulfide bridges are covalent bonds that further strengthen the protein’s shape
The hydrophobic R-groups are on the inside of the molecule.
The hydrophilic R-groups are on the outside of the molecule.
Quaternary structure :-
Resulting from the association of two ore more polypeptide chains ( subunits ).
Example : Collagen - Hemoglobin - Transthyretin.
Collagen has three helical polypeptides.
Hemoglobin has four polypeptides of two distinct types.
Prions: are infectious misshapen proteins.
it may cause degenerative brain.
Transthyretin is an important transport protein found in your blood.
Transthyretin has four identical polypeptide chains.
each made up from 172 amino acid.
Nucleic Acid
The amino acid sequence of polypeptide is programmed by a directing unit of inheritance known as a genes.
The genetic material that humans and other organisms inherit from their parents consist of DNA.
A gene direct the synthesis of an RNA molecule.
DNA programs cell activities by directing synthesis of protein.
The two types of nucleic acid:-
DNA ( Deoxyribonucleic acid ).
RNA ( Ribonucleic acid )
Nucleic acids (DNA or RNA)are composed of nucleotides .
Genes consist of DNA.
A nucleotide is composed of (3) parts:
5-Carbon sugar ( pentose sugar )
Ribose is RNA
Deoxyribose in DNA
Phosphate group
Nitrogenous bases
Cytosine
Guanine
Thyamine
Adenine
Uracil
*Nitrogenous bases extend from sugar-phosphate backbone
A sugar-phosphate backbone is formed by covalent bonding between
The phosphate of one nucleotide
The sugar of the next nucleotide
Polynucleotide is built from its monomers (nucleotide) by dehydration reaction.
Note that: the nitrogenous bases are not part of the backbone.
RNA usually consists of a single polynucleotide strand.
DNA usually consists of two polynucleotide strand warp around each other called Double Helix.
The two DNA chains are held together by Hydrogen bonds.
between their paired bases.
Complementary, each a predictable counterpart of the other.