A Study of the Molecules of Life Biochemistry A Study of the Molecules of Life

Biochemistry is based primarily on the properties of the carbon atom: Because of its electron arrangement, carbon can form more compounds than any other element.

Carbon Can Form Millions of Compounds This is a small sample of carbon-based molecules

Let’s play Organic or Not!!!

Biochemistry also takes place in a water (aqueous) environment Water has many excellent properties as a solvent

Nature uses a few classes of organic molecules to build the structures found in cells Carbohydrates Amino acids lipids Nucleotides

A small molecule that may become chemically bonded to other monomers to form a polymer. Large molecules consisting of large numbers of repeating units connected by covalent bonds. Polymer:

Carbohydrates: Energy molecules of the cell Carbohydrates have the general formula [CH2O]n Glucose (right) has the formula C6H12O6 Other examples are given below:

Glucose is the primary fuel for cells Glucose is broken down in several steps in the cytoplasm and mitochondria of the cell. In these steps, energy is released that the cell can use.

Biological molecules can be linked together to form larger molecules Glucose molecules (monosaccharide) can be linked together to make longer molecules (polysaccharide). In this example, cellulose is formed

Cellulose is the main ingredient in plant fiber

General structure of an amino acid R group H N C OH O R 2.2.2 carboxyl group amino group (acidic) (basic)

Different amino acids have different R groups Their different properties depend on their R groups Hydrophobic (‘Water-hating’) R groups CH2 H N C OH O phenylalanine (aromatic) CH3 H N C OH O alanine Do not need to know names or structure of amino acids – interest only

Hydrophillic (‘Water-loving’) R groups CH2 H N C OH O SH cysteine CH2 H N C OH O serine

First isolated from asparagus juice! CH2 H N C OH O CH2 H N C OH O NH2 asparagine (basic) aspartic acid (acidic) First isolated from asparagus juice!

There are 20 amino acids naturally incorporated into proteins Alanine Arginine Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine You do NOT need to know their names!

These are the essential amino acids: Humans can synthesize some amino acids by altering other amino acids, however… …some amino acids cannot be synthesized and are therefore needed in the diet. These are the essential amino acids: Arginine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine Interest only but see Option A 2.8

Formation of a dipeptide: carboxyl group of one amino acid reacts with amino group of second amino acid H N C OH O R2 R1 water molecule formed H N C O R1 OH R2 H2O 2.2.6 a dipeptide peptide linkage

2 amino acids  dipeptide + water Formation of a dipeptide produces a molecule of water, therefore… H N C OH O R1 R2 H2O …this is a condensation reaction H N C O R1 OH R2 Part of 2.2.5 2 amino acids  dipeptide + water

dipeptide + water  2 amino acids Splitting a dipeptide to form two amino acids consumes one molecule of water, therefore… H N C O R1 OH R2 H2O H N C OH O R1 R2 …this is a hydrolysis reaction Part of 2.2.5 dipeptide + water  2 amino acids

Three amino acids linked together Tripeptide: Three amino acids linked together Oligopeptide: A short chain of a few amino acids Polypeptide: A chain of many amino acids A protein may consist of one or more polypeptide chains Structure of hemoglobin – a protein consisting of four polypeptides

Proteins are tremendously complex structures that perform many functions in cells The protein shown to the right is called myosin. It is one of many proteins that work to make your muscles contract

Some proteins act as chemical signals (hormones) in the body. Insulin is made by cells of the pancreas. When it is released into the blood, it signals other tissues (e.g. muscle) to take glucose from the blood after a meal.

Proteins called enzymes act to speed up chemical reactions in cells The diagram shows a model of trypsin, an enzyme that speeds up the breakdown of proteins during digestion.

Many proteins are important components of cellular structures Membrane channel proteins allow ions to flow in and out of cells.

Proteins can even make the world’s smallest motors This is a model of the flagellum in a bacterium. At the basal body is a small motor that spins the hook and thus moves the flagellum (made of flagelin) through water. This motor is no bigger than 50 nanometers!

 Lipids: a large and varied group of organic compounds.  Lipids include: Triglycerides Phospholipids Waxes Cholesterol and Steroids Lipids are all non-polar and do not dissolve in water, due to this. They are INSOLUBLE.

 Triglycerides are one of the most common types of lipids  Triglycerides consist of one molecule of glycerol bonded to three fatty acid molecules  Each fatty acid is linked to the glycerol molecule by an ester bond C H OH Glycerol Hydroxyl groups

Carboxyl group Fatty Acids: General Formula: CH3 (CH2)n C O OH CH3 H C O OH CH2

H C O OH Can be drawn as: C O OH

This is a condensation reaction Forming a monoglyceride: C O OH C H OH Hydroxyl group and carboxyl group react Ester bond C H OH O + H2O This is a condensation reaction

A triglyceride: C H O Glycerol Fatty acid Can be drawn as: Ester bond

This is a hydrolysis reaction To split these ester bonds and separate a fatty acid from glycerol we need to add a molecule of water C H OH O C H OH + H2O C O OH This is a hydrolysis reaction

Uses of Lipids in Living Things 1. Long-term energy stores Human Adipose Tissue Plant Oils

2. Buoyancy for marine. animals: lipids are less. dense than water so 2. Buoyancy for marine animals: lipids are less dense than water so help animals float 3. Insulation: a layer of fat beneath the skin cuts down heat loss

Phospholipids are modified so that a phosphate group (PO4-) is added to one of the fatty acids. Phospholipids are important components of cell membranes (below).

Cholesterol and steroids are also part of the lipid group Testosterone is an important hormone. Cortisone and vitamin D play important roles in regulating mineral balances in blood. Cholesterol is a part of our diet and is used as a starting point to make the other molecules.

Lipids are also a useful energy source for the cell. The products of fatty acid breakdown can produce energy for the cell. In fact, virtually all biological molecules can produce energy if needed. Lipids produce the most energy per unit mass. Energy

Homework: Compare the relative advantages and disadvantages to an organism of using carbohydrates vs. lipids as energy stores. To be handed in on a separate sheet of paper on Monday (Along with the review packet you’re about to get )