BIOCHEMISTRY: The BIOCHEMISTRY: The Chemistry of Life Chemistry of Life

By: Imelda A. Ygan

Why study Chemistry in a Zoology course?

An animal is a multicellular living being. Each cell in an animals body is a bag of chemicals that interact with each other in a variety of ways. Everything an animal is and does relates to its chemistry or chemical component. The various ways animal function and survive in their environment depend on their chemical makeup.

The Chemistry of Cell

Organic compounds compounds that contain carbon ( carbohydrates, proteins, lipids, nucleic acids, and vitamins) Inorganic compounds compounds in which the atoms or radicals consist of elements other than carbon ( mineral compounds: calcium phosphate, sodium chloride, etc. and water)

Organic compounds
Carbohydrates organic compounds containing carbon, hydrogen and oxygen in a ratio of 1:2:1; also known as saccharides. - monosaccharides (gluc, fruc, galac) - oligosaccharides (suc, mal, lac) - polysaccharides(cellulose, starch, gly)

Monosaccharides
Classified based on the number of carbons in its chain, e.g., triose, tetrose, pentose, hexose, heptose, etc. Classified based on the radical group it contains, e.g., aldose ( contains aldehyde group) and ketose (contains keto group)

 Short chains of saccharide units. - Disaccharides - are double-ringed sugars that result from the combination of two monosaccharides. - the synthesis of disaccharide from two monosaccharides by removal of water molecule is called a dehydration synthesis reaction. The bond holding two monosaccharides together is called a glycosidic bond (a typical covalent bond).

Oligosaccharides

Contain many monosaccharide units up to hundreds or thousands. It is an example of a polymer molecules consisting of many similar units. Examples of polysaccharides in the cell are glycogen, starch, and cellulose. When polysaccharides combine with other chemical groups(amines, lipids, and amino acids), extremely complex macromolecules are formed (chitin, peptidoglycan, glucosamine) that serve specific purposes to the cell or to the organism.

Polysaccharides

Lipids
Essential constituents of almost all living cells. Insoluble in water (hydrophobic) but soluble in fat solvents such as ether, chloroform, and benzene. Fatty acids can be thought of as the building blocks of lipids. - saturated fatty acids contain only single bonds between the carbon atoms. Fats containing saturated fatty acids are usually solids at room temperature. - monounsaturated fatty acids have one double bond in the carbon chain, such as butter, olives, and peanuts. - polyunsaturated fatty acids contain two or more double bonds in the carbon chain, like in soybeans, sunflower, and corn.

Classification of Lipids
Waxes consist of a saturated fatty acid and a long chain of alcohol (like wax coating on the fruits, leaves, and stems cutin). Help to prevent loss of water and damage from pests. Waxy secretions protect, lubricate, and impart pliability to skin and to hair.

Fats and Oils

Most common types of lipids. Also known as triglycerides. Composed of glycerol (a three-carbon alcohol) and three fatty acids. Fats are triglycerides that are solid at room temperature while oils are liquid at room temperature. Most animal fats have many saturated fatty acids, which pack together by weak interactions. These remain solid at room temperature. Thick layer of triglycerides are stored under the skin of penguins and other animals which help them resist cold and insulate their body against extreme temperatures of icy habitats.

Phospholipids Contain glycerol, fatty acids, a phosphate group, and an alcohol. There are two types:

glycerophospholipids and sphingolipids.

Glycerophospholipids are the most abundant lipids in the cell membrane.

Sterols and their derivatives

Sterols are among the many lipids with no fatty acids. They differ in the number, position, and type of their functional groups, but all have arigid backbone of four fused-together carbon rings Cholesterol is the most common type in the tissues of animals. Remodelling cholesterol, it makes into vitamin D, steroids, and bile salts. Steroids include sex hormones which govern the formation of gametes and development of secondary sexual traits.

Proteins
The substance of life. A total of 23 different amino acids have been found in proteins, 20 primary or naturally occurring plus 3 secondary amino acids (derived from primary amino acids). Each amino acid is composed of C, H, O, and N. - essential amino acids - non-essential amino acids

The Essential Amino Acids

Pvt. Mat Hill (code used for easy recall of the essential amino acids)
Phenylalanine Valine Threonine Methionine Arginine Tryptophan Histidine Isoleucine Leucine Lysine

Protein structure
When water is removed, by dehydration synthesis, amino acids become linked together by a covalent bond referred to as peptide bond. A chain consisting of more than three amino acids is referred to as a polypeptide. A polypeptide is said to have primary protein structure (linear sequence of amino acids in a chain), secondary protein structure ( helical or sheetlike configuration), tertiary protein structure (globular), and quaternary protein structure (two or more polypeptide chains are bonded together)

Enzymes
Are protein molecules produced by living cells as instructed by genes on the chromosomes. Referred to as biological catalysts. apoenzymes can only function as enzymes after they link up with a nonprotein cofactor. coenzymes require vitamin-type compound to function as enzyme. holoenzymes the combination of the apoenzyme plus cofactor.

Nucleic Acids
Two forms: DNA and RNA DNA (deoxyribonucleic acid) is the hereditary molecule the molecule that contains the genes and the genetic code. It makes up the major portion of the chromosomes. The information in DNA must flow to the rest of the cell for the cell to function properly. This flow of information is accomplished by RNA molecules. RNA (Ribonucleic acid) molecules participate in the conversion of the genetic code into proteins and other gene products.

Differences between DNA and RNA

DNA
Double-helix Found in the nucleus, mitochondria and chloroplasts With A,G,C and T With deoxyribose Carrier of genetic information

vs

RNA

- structuresingle-stranded - location - found in the cytoplasm

- N- bases with A,G,C, and U - pentose sugar - with ribose sugar - function for protein synthesis

Nucleic acid structure

Nucleotides are the building blocks of nucleic acids. Each is made up of: nitrogenous base, pentose sugar, and phosphate group.

Nucleotides of the DNA

Deoxyadenosine triphosphate Deoxyguanosine triphosphate Deoxycytidine triphosphate Deoxythymidine triphosphate

Nucleotides of the RNA

Adenosine triphosphate Guanosine triphosphate Cytidine triphosphate Uridine triphosphate

DNA structure
DNA is a double-stranded molecule formed by the bonding of nitrogenous bases on the two separate strands. It was found that because of the size and bonding attraction between the molecules, A (adenine a purine) always bonds with T (thymine a pyrimidine) via two hydrogen bonds, and G (guanine a purine) always bonds with C (cytosine a pyrimidine) via three hydrogen bonds. The bonding forces of a doublestranded polymer cause it to assume the shape of a double helix.

Inorganic constituents of the Cell

Water Mineral materials such as: calcium, sodium, iron, magnesium, zinc, copper, and many others which are present in different amounts in different kinds of cells Most of these inorganic constituents of the cell occur as compounds . There presence in the cell is important for specific functions; their absence in certain cells where they should be present even in small amounts lead to abnormal functioning of the cell.

Water is essential for life. Cells consist of anywhere between 70 and 95% water. All living organisms require water to carry out their normal metabolic processes, and most will die in environments containing too little moisture. Water has no net charge, but the charge it does carry is unevenly distributed. Its electron arrangements and bond angles make its oxygen end a bit negative and its hydrogen end a bit positive. It has temperature-stabilizing effects, internal cohesion, and a capacity to dissolve many substances. These properties of water influence the structure and functioning of organisms.

Water

Mineral compounds
Salts dissolve into ions that play key roles in cells. - for example, nerve cell activity depends on ions of sodium, potassium, and calcium. - muscles contract with the help of calcium ions. Bone and teeth formation depends also on calcium. - iron is abundant in red blood cell for its function in oxygen transport.

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Important Enzymes required during DNA Replication

DNA Polymerase most important, since it is used to guide the replication. DNA helicase and DNA topoisomeraseinitiate the separation of the two strands of the DNA molecule. Primase synthesizes a short RNA primer. DNA ligase connects fragments of newly synthesized DNA.

Gene expression
A gene is a particular segment of a DNA molecule or chromosome. A gene contains the instructions that will enable a cell to make what is known as a gene product. The genetic code contains four letters(the letters that stand for the four nitrogenous bases found in the DNA). It is the sequence of these four bases that spell out the instructions for a particular gene product.

The Central Dogma

It was Francis Crick who, in 1957, proposed what is referred to as the central dogma to explain the flow of genetic information within a cell: DNA mRNA protein It states that: The genetic information contained in one gene of a DNA is used to make one molecule of mRNA by a process known as transcription. The genetic information in that mRNA molecule is then used to make one protein by a process known as translation.