From Molecules to Organisms: Structure & Processes Organic Compounds Copyright © Rebecca Rehder Wingerden

Organic Compounds Almost all the molecules a living cell makes are composed of carbon atoms. Carbon is unparalleled in its a ability to form large, diverse molecules. Next to water, carbon containing compounds are the most common substances in living organisms. Organic compounds are compounds containing carbon, – Often synthesized by cells.

Carbon A Carbon atom has 4 outer electrons in a shell that holds 8. It has a strong tendency to complete its outer shell by sharing electrons with other atoms forming covalent bonds. – This allows Carbon to form up to 4 bonds, or bond with 4 different atoms. Carbon is unique in that in likes to bond with itself, capable of forming long chains with a “carbon backbone” (structure). – This diversity in bonding capability allows for an enormous variety of compounds, all with a variety of functions.

Carbon skeletons vary by length, they can be branched or unbranched, they may have double bonds, or they can be arranged in rings. Structure will dictate molecular function. Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons. The chain of carbon atoms in organic molecules is called a carbon skeleton. When two organic compounds have the same molecular formula, but differ in the position of their double bond they are called isomers. Each isomer has unique properties (function).

Functional groups (structure) also contribute to determine the properties (function) of organic compounds. – A group of atoms that participate in a chemical reaction is called a functional group.

Cells synthesize larger molecules (polymers) from a small list of smaller molecules (monomers). – Anabolism Dehydration synthesis- process by which cells links monomers to form polymers. The process is the same regardless of the specific monomers (macromolecules). All unlinked monomers have hydrogen atoms (H) and hydroxyl groups (-OH). For each monomer added to a chain, a water molecule (H2O) is removed. Two monomers contribute to the H2O molecule. As this occurs, a new covalent bond forms, linking the two monomers.

Polymers are also broken down into their monomers by the reverse process, hydrolysis (digestion). – Catabolism The process is the same regardless of the specific monomers (macromolecules). Hydrolysis is the reverse of dehydration synthesis. Hydrolysis means to break (lyse) with water (hydro-) and cells break bonds between monomers by adding water to them. In the process, a hydroxyl group from a water molecule joins to one monomer, and a hydrogen joins to the adjacent monomer. Anabolism + Catabolism Metabolism

Life has a simple yet elegant molecular logic: small molecules common to all organisms are ordered into large molecules, or macromolecules. Macromolecules are very large molecules assembled by living organisms through dehydration synthesis: 1. Carbohydrates: polymer made of monosaccharides 2. Lipids: not true polymer, but are formed by dehydration synthesis from several smaller molecules. 3. Proteins: polymer made from amino acids 4.Nucleic Acids: polymer made of nucleotides

1. Carbohydrates are a class of molecule ranging from small sugar molecules (monosaccharides & disaccharides) to large sugar molecules (polysaccharides). Carbohydrates consist of carbon (C), hydrogen (H), and oxygen (O) in a ratio of CH2O. Carbohydrates are a major source of energy. Glucose C 6 H 12 O 6 Sucrose C 12 H 22 O 11 Why is the ratio of CH 2 O violated in sucrose?

Polysaccharides are polymers made of hundreds to thousands of monosaccharides which are linked through dehydration synthesis. Starch, Glycogen and Cellulose are three functionally different polysaccharides which are made from the same monosaccharide, glucose.

Polysaccharide Structure and Function * Some animals can derive nutrition from cellulose, such as cows and termites, because they have cellulose-hydrolyzing microorganisms inhabiting their digestive tracts.

2. Lipids are not true polymer, but group together because they are hydrophobic (water fearing). Lipids consist mainly of carbon (C) and hydrogen (H) which are linked by non polar covalent bonds. Lipids store energy (triglycerides) and provide structure (phospholipids). Fatty Acid Glycerol Triglyceride Dehydration synthesis links a fatty acids to a glycerol molecule forming a triglyceride, a fat molecule.

The fatty acids of unsaturated fats (plant oils) contain double bonds which prevent these fats from solidifying at room temperature (liquid). Saturated fats (animal fats) lack double bonds, therefore these fats are solid at room temperature.

Phospholipids are a major component of cell membranes and very important biological molecule. They are structurally similar to fats, but contain phosphorus (P) and only two fatty acid tails. Waxes consist of one fatty acid linked to Waxes an alcohol and are very hydrophobic. Steroids are lipids whose carbon skeleton is bent to form four fused rings. How does a lipid’s structure affect its functions?

3. Proteins are essential to the structure and activities of all life. Proteins consist mainly of carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).

The diversity of proteins is based on the specific and unique arrangement of a universal set of 20 amino acids.

Cells link amino acids together by dehydration synthesis forming peptide bonds. Many amino acids linked together will form a polypeptide chain, which is the primary structure of a protein.

Secondary structure is the coiling (alpha helix) or folding (pleated sheet) of the polypeptide. Tertiary structure is the overall three dimensional shape of the protein which can be described as globular or fibrous. Quaternary structure results from bonding interaction with other tertiary proteins. If a protein loses its shape, then it will not be able to function properly (denatured).

4. Nucleic acids are polymers that serve as the blueprints for proteins.Nucleic acids consist mainly of carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and phosphorous (P) There are two types of nucleic acids: -DNA (deoxyribonucleic acid) which is the genetic material (genes) -RNA (ribonucleic acid) intermediary molecule that makes proteins The monomer that makes up nucleic acids are called nucleotides. Each nucleotide is composed of three subunits: – sugar, phosphate, and a nitrogenous base.

DNA nucleotide sugar: deoxyribose DNA nucleotide nitrogenous bases: – adenine (A) – thymine (T) – cytosine (C) – guanine (G) RNA nucleotide sugar is ribose RNA nucleotide nitrogenous bases: – adenine (A) – uracil (U) – cytosine (C) – guanine (G)

DNA polynucleotides form through dehydration synthesis. RNA polynucleotides form through dehydration synthesis.

DNA molecular structure is a double helix (twisted ladder). Two DNA polynucleotides wrap around each other and are held together by hydrogen bonds between their paired bases. DNA base pairing: “A” always pairs with “T” and “C” always pairs with “G”. RNA molecular structure is a single strand.