Chapter six : the chemistry of life

It's important to know how does bacteria live? how does it multiply? what does it need to be alive? So biochemistry is very important to micro organisms, we will talk about the organic chemistry of macro molecules : carbohydrates, lipids, proteins and nucleic acids. Organic chemistry : the study of compounds that contain carbon (carbohydrates, lipids, proteins, and nucleic acids) and other organic compounds like O, N & H. they could be in the living cells or out of them. Biochemistry: the chemistry of living cells.

Organic Chemistry - Organic compounds contain carbon, which are carbohydrates, lipids, nucleic acids and proteins. - Organic chemistry is the branch of science that studies organic compounds. - Organic compounds are not necessarily related to living organisms; although some organic compounds are associated with living organisms, many are not. - Organic chemistry involves fossil fuels, dyes, drugs, paper, ink, paints, plastics, gasoline, rubber tires, food, and clothing all of them have carbon atoms. Carbon Bonds - Carbon atoms have a valence of 4, meaning that they can bond to four other atoms. - There are 3 ways in which carbon atoms can bond to each other: single bond, double bond, and triple bond, for example C & N the attach by single ,double or triple bonds and C with H we could have CH3 CH4. - A covalent bond is one in which a pair of electrons is shared, it is one of the strongest bonds that u can find in biochemistry, The covalent bond one of the strongest bonds that you can find in

biochemistry , the outer shell electrons of one atom can be shared with another atom. - When atoms of other elements attach to available carbon bonds, compounds are formed. - A series of carbon atoms bonded together is referred to as a chain(when there is a carbon connected to another carbon and another and another). - If only hydrogen atoms are bonded to the available carbon bonds, hydrocarbons are formed. - Therefore, a hydrocarbon is an organic molecule that contains only carbon and hydrogen atoms; some examples of simple hydrocarbons are shown here: examples of single double & triple bonds of Carbon

Cyclic Compounds - When carbon atoms link to other carbon atoms to close a chain, they form rings or cyclic compounds. - Benzene is a cyclic compound with six carbons and six hydrogen.

Biochemistry Biochemistry is the study of biology at the molecular level; it is the chemistry of living organisms, which related to the structure of the cell, so we look inside the cell to study the chemical reactions, for example the cell membrane is a phospholipid bilayer which is one of the lipid (organic compound), also the proteins imbedded in it are organic contain carbon atoms. Biochemistry involves the study of biomolecules present within living organisms; biomolecules in living organisms are usually large molecules called macromolecules. - Amino acids : they are the building blocks of proteins, we have 20 amino acids in nature, they are grouped acidic ,basic & neutral A.A. each one have different characteristics but all of them share the same atoms mostly C, N & H forming the shared groups ( NH2, H & the R group which is the differential group) - Also there are carbohydrates in the cell ex. Glycoprotein, starch & glycogen which are made of mainly of C & H. - Macromolecules include carbohydrates, lipids, proteins, and nucleic acids. Other examples: vitamins, enzymes, hormones, and energycarrying molecules such as adenosine triphosphate (ATP). - Humans obtain their nutrients from the foods they eat. Carbohydrates, fats, nucleic acids, and proteins contained in the foods are digested; their components are absorbed and carried to every cell in the body, where they are broken down and rearranged by the cells as there need to use in the biological life. - Microorganisms also absorb their essential nutrients into the cell by various means. - The nutrients are then used in metabolic reactions as sources of energy and as building blocks for enzymes, structural macromolecules, and genetic materials. - Glycolysis : is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO + H+.

The free energyreleased in this process is used to form the highenergy compounds ATP (adenosine triphosphate) and, it is different in some steps of aerobic or anaerobic ( it will use another electron acceptor not the O so the ATP will be less) organism or bacteria. - Nucleotides are the building blocks for DNA which are built from nitrogenous base, Phosphate group and d-ribose (pentose ) sugar .. and all these building blocks contain mainly C, H, N, O & P. Carbohydrates - Carbohydrates are biomolecules composed of carbon, hydrogen, and oxygen (in the ratio 1:2:1) 1 C , 2 H & 1 O. - Examples include: - Examples: Glucose, fructose, sucrose, lactose, maltose, starch, cellulose, and glycogen. - Categories of carbohydrates include monosaccharides (Glucose, fructose), disaccharides, and polysaccharides (starch, cellulose). Monosaccharides - Monosaccharides are the smallest and simplest of the carbohydrates. Mono means one, referring to the number of rings in the structure. - Glucose (C6H12O6) is the most important monosaccharide in nature; it may occur as a chain or in alpha or beta ring configurations the dr will not ask us about the structure!! - Monosaccharides contain from 2 to 9 carbon atoms most contain 5 to 6. - A 3 carbon monosaccharide is called a triose; a 4 carbon one is a tetrose; a 5 carbon one is a pentose; a 6 carbon one is a hexose; a 7 carbon is a heptose; and so on.

- The main and the simplest source of energy for body cells is glucose. - The three forms of glucose are shown above. - Glucose is carried in the blood to cells where it is oxidized to produce energy-carrying ATP. ATP is the main energy source used to drive most metabolic reactions.

Disaccharides (di means : two ) Disaccharides are double ringed sugar that result from the combination of two monosaccharides . The synthesis of disaccharides from two monosaccharides by the removal of water molecule is called dehydration synthesis reaction. Example : Sucrose is a disaccharides made by joining together a glucose molecule and a fructose molecule . Disaccharides react with water in a process called a hydrolysis reaction, which causes them to break down into two monosaccharides. (reverse reaction)

Peptidoglycan : Recall that peptidoglycan is found in the cell walls of all members of the Domain Bacteria; peptidoglycan is a repeating disaccharide attached by proteins to form a lattice that surrounds and protects the bacterial cell. ( this layer is a differentiating layer between germ positive and germ negative , we said that germ positive it has a thick layer of peptidoglcan awhile in germ negative this layer is thin .)

Carbohydrates composed of 3 monosaccharides are called trisaccharides; those composed of 4 are called tetrasaccharides; those composed of 5 are called pentasaccharides, and so on until we come to polysaccharides.

Polysaccharides : Carbohydrate polymers containing many monosaccharides that linked to each other by glycosidic bonds , which is a bond that attach two monosaccharides together .

Serve two main function : 1. Storing energy . 2. Structural support and protection. Polysaccharides are examples of polymers molecules that consist of many similar subunits. In the presence of the proper enzymes or acids, polysaccharides may be hydrolyzed or broken down into disaccharides, and then into monosaccharides.

For example starch is a polysaccharide (repetitive glucose units held together by glycosidic bonds ) which is the storage molecule in plants. - Some bacteria produce polysaccharide capsules for protection from phagocytes.

- Plant and algal cells have cellulose (a polysaccharide) cell walls to provide support. - Some protozoa, fungi, and bacteria have enzymes that can break down cellulose. - When polysaccharides combine with other chemical groups (amines, lipids and amino acids), complex macromolecules are formed. For example, chitin, the main component of the hard outer covering of insects, spiders, and crabs and found in the cell walls of fungi.

Lipids - An important class of biomolecules. - Most lipids are insoluble in water, but soluble in fat solvents, such as ether, chloroform, and benzene. - Lipids are essential constituents of most living cells. - Lipids can be classified into the following categories: Waxes Glycolipids Fats and oils Steroids Phospholipids Prostoglandins and leukotrienes

Lipids fatty acids - Fatty acids are the building blocks of lipids; they are long-chain carboxylic acids that are insoluble in water. - Saturated fatty acids contain 1 single bond between carbon atoms; they are solid at room temperature. - Monounsaturated fatty acids have 1 double bond in the carbon chain; found in butter, olives, and peanuts which the best to be used and eaten!

- Polyunsaturated fatty acids contain 2 or more double bonds; found in soybeans, safflowers, and corn. - Essential fatty acids cannot be synthesized in the human body and must be provided in the diet.

Lipid waxes : - A wax consists of a saturated fatty acid and a long-chain alcohol. Examples: the wax coating on fruits; leaves; skin, fur, and feathers of animals. The cell wall of Mycobacterium tuberculosis (the causative agent of tuberculosis) contains waxes. -These waxes protect M. tuberculosis from digestion following phagocytosis by white blood cells , (this capsule help it to survive insde the macrophage !) -These waxes make M. tuberculosis difficult to stain and de-stain; explains why M. tuberculosis is acidfast. Lipids fats and oils - Fats and oils are the most common types of lipids. They are also known as triglycerides because they are composed of glycerol and 3 fatty acids. If its level elevate in the blood may cause closure of artries - Most fats come from animal sources (e.g, beef); most oils come from plant sources (e.g., olive oil).

Phospholipids - contain glycerol, fatty acids, a phosphate group, and an alcohol. There are 2 types: Glycerophospholipids (also known as phosphoglycerides) Sphingolipids Glycerophospholipids are the most abundant lipids in cell membranes.

 A cell membrane is a lipid bilayer, consisting of 2 rows of phospholipids, arranged tail-to-tail.

Glycolipids are abundant in the brain and in the myelin sheath of nerves. Steroids are complex, 4-ringed structures; examples are cholesterol, bile salts, steroid hormones, and fat-soluble vitamins (A, D, E and K). Prostaglandins and leukotrienes are derived from a fatty acid called arachidonic acid. Both have a wide variety of effects on body chemistry such as controlling blood pressure or hormones; leukotrienes can produce long-lasting muscle contractions.

Done by : Baraah Salamat Abeer Dirawi

Good luck

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