Organic Molecules

Organic Chemistry

Branch of chemistry devoted to carbon components

Carbon

Element whose chemical properties are fundamental to the formation of biologically important molecules

Isomers

Organic molecules that have identical molecular formulas but a different arrangement of atoms

Structural Isomers

Organic molecules that differ in the order which their atoms are attached

Stereoisomers

Isomers with identical bonding relationships, but the spatial positioning of their atoms differs

Cis-Trans Isomers

Stereoisomers that differ in the arrangement of substituents around a double bond or ring structure

Enantiomers

Stereoisomers that are mirror images of each other

Polymers

Largest of the biomolecules, constructed by linking together monomers

Monomers

Identical subunits that link together to form polymers

Dehydration Synthesis

Polymerization method that involves removing water from monomers

Hydrolysis

Depolymerization method that involves adding water to a polymer

Carbohydrates, Lipids, Proteins, Nucleic Acids

Four major classes of organic molecules

Carbohydrates

Carbon-containing organic molecules that are often represented by the general formula C_n(H₂O)_n

Monosaccharides

Monomers of carbohydrates, Single sugar molecules that consist of a chain or linked carbs and hydrogen, May be linear or ringed

Disaccharides

Contain two monosaccharides joined together by dehydration synthesis

Glycosidic Bond

The bond between two monosaccharides

Polysaccharides

Polymers of monosaccharides

Glycogen, Starch

Polysaccharides that are used for short-term energy shortage, made of alpha-glucose monomers (2)

Glycogen

Polysaccharides animals use to store glucose

Starch

Polysaccharides plants use to store glucose

Chitin, Peptidoglycan, Cellulose, Glycosaminoglycons

Polysaccharides that are used for structure, Unbranched, Alternating orientation of beta-glucose molecules (4)

Chitin

Polysaccharides that make up animal exoskeletons and fungi cell walls

Peptidoglycan

Polysaccharides that make up bacteria cell walls

Cellulose

Polysaccharides that make up plant cell walls

Glycosaminoglycans

Polysaccharides that make up animal cartilage

Lipids

Nonpolar organic molecules that are insoluble in water

Fatty Acids

Monomers of lipids, Hydrocarbons chains of varying size that terminate a carboxyl group

Saturated Fat

Lipids that have no double bonds between carbon atoms, so the carbon is saturated with a single bond to hydrogen

Unsaturated Fats

Lipids with one or more double bonds between carbon atoms, creating kinks in the chain that prevent tight packing to form a solid

Monounsaturated Fats

Unsaturated fats that contain one double bond

Polyunsaturated Fats

Unsaturated fats that contain more than one double bond

Cis-Fats

Unsaturated fats where the hydrocarbon chain is in the cis conformation across the double bond, naturally found

Trans-Fats

Unsaturated fats where the hydrocarbon chain is in the trans conformation across the double bond, artificially manufactured

Triglycerides

Lipids formed from one glycerol and three fatty acids

Phospholipid

Lipids containing a glycerol bound to two fatty acids and a phosphate group

Phospholipid Bilayer

The formation of cellular membrane and organelles that surround a cell

Steroids

Lipids defined by a four fused ring structure

Waxes

Lipids that are composed of fatty acids bonded to other long hydrocarbon chains by their carboxyl group, resistant to degradation

Proteins

Organic molecules composed of at least one polypeptide, most versatile of the organic molecules

Amino Acids

Monomers of proteins, Structure contains a centralized alpha carbon, amino group, carboxyl group, and a side chain (‘R’)

Peptides

Polymers of proteins, containing at least two amino acids joined together

Peptide Bonds

Bonds that join amino acids together

Polypeptide

Chain of many amino acids (structural unit)

Primary, Secondary, Tertiary, Quarternary

Levels of protein structure

Primary Structure

Protein level that consists of a linear sequence of amino acids forming a polypeptide chain

Secondary Structure

Protein level that occurs due to the folding of the primary structure, either as an alpha helix or a beta pleated sheet held together by hydrogen bonds

Tertiary Structure

Protein level containing a 3-D shape composed to multiple secondary structures and other coils that connect these structures within a single polypeptide chain, Final structure that allows for functionality of some proteins

Quarternary Structure

Protein level that consists of multiple polypeptides (subunits) that form a functional protein

Hydrogen Bond

Bond that promotes protein folding

Hydrophobic Effect

Effect that contributes to major folding force due to nonpolar molecules

Van der Waals Forces

Weak forces that allow attraction between atoms that are close together

Disulfide Bridge

A covalent bond between two cysteine residues

Domains

Structural components within the tertiary structure of most proteins that serve a particular function

Motifs

Common structural components made up of secondary structures and are found in tertiary structures of many proteins

Denaturation

Changes in a protein’s shape due to pH, heat, or chemicals, resulting in loss of functionality

Chaperone Proteins

Proteins that assist in the proper folding of other proteins

Enzymes

A protein that functions as an organic catalyst, Speeds up a chemical reaction without being affected by it, Lowers activation energy of a reaction

Ribozyme

A type of RNA molecule with enzymatic activity

Induced Fit Method

A conformational change to an enzyme that allows its active site to bind to the specific substrate to form the enzyme-substrate complex

Reversible Inhibitors

Noncovalent bonding to an enzyme

Competitive Inhibitor

A reversible inhibitor that binds to the active site of an enzyme

Noncompetitive Inhibitor

A reversible inhibitor that binds to the allosteric site of an enzyme

Irreversible Inhibitors

Covalent bonding to an enzyme

Organic Cofactors

Organic molecules that enhance a chemical reaction

Prosthetic Group

Small organic cofactors that are permanently attached to an enzyme

Coenzymes

Organic cofactors that participate in a chemical reaction

Nucleic Acids

Organic molecule that includes RNA and DNA

Nucleotides

Monomers of nucleic acids, Consists of a phosphate group, pentose sugar (ribose or deoxyribose), and a nitrogenous base

Adenine and Guanine

Purines associated with RNA and DNA

Thymine

Pyramidine associated with DNA

Uracil

Pyramidine associated with RNA

Cytosine

Pyramidine associated with RNA and DNA

Phosphodiester Bond

The bond between the pentose sugar and phosphate group in a nucleotide