Chapter one Introduction Biochemistry can be defined as the science concerned with the chemical

basis of life.
The cell is the structural unit of living systems. Thus, biochemistry can also be described as the science concerned with studying the various molecules that occur in living cells and organisms and with their chemical reactions. Biochemical reactions are involved in such areas as breaking down food molecules, generate and store energy, buildup new biomolecules, and eliminate waste. Some biomolecules are small and have only a few functional groups others are big and contain a large number of functional groups. The principal classes of biomolecules are: carbohydrates, lipids, Proteins, enzymes, vitamins and nucleic acids. In general, Biochemistry is the study of the structure, composition, and chemical reactions of substances in living systems.

Branches of biochemistry
Main Branches of biochemistry are: 1- Animal biochemistry 2- Plant biochemistry 3- Molecular biology 4- Cell biology 5- Metabolism 6- Immunology 7- Genetics 8- Enzymology And other branches Molecular chemistry, Enzymatic Chemistry, Endocrinology , Hematology, Pharmaceuticals, , Nutrition and Photosynthesis

Applications of biochemistry:
Biochemistry is applied to medicine, dentistry, and veterinary medicine. In food science, biochemists research ways to develop abundant and inexpensive sources of nutritious foods, determine the chemical composition of foods, and develop methods to extract nutrients from waste products, or invent ways to prolong the shelf life food products. In agriculture, biochemists study the interaction of herbicides with plants. They examine the structure-activity relationships of compounds, determine their ability to inhibit growth, and evaluate the toxicological effects on surrounding life.

Biochemistry spills over into pharmacology, physiology, microbiology, and clinical chemistry. In these areas, a biochemist may investigate the mechanism of a drug action; engage in viral research; conduct research pertaining to organ function; or use chemical concepts, procedures, and techniques to study the diagnosis and therapy of disease and the assessment of health. Also biochemistry is often related to toxicology. Toxicology is the study of the ways in which some organic compounds in the body are changed by enzymes into toxic metabolites.

Elemental compositions for biomolecules are:

1- C, H, O&N ~ (97%) 2- Ca, P, K&S ~(3%) 3- Cl, Na &Fe ~(1%) 4- F, I, Cu, Mn, Mg, Zn..( In small amounts)

Basic components of biomolecules:

1- Organic compounds (8-25%) 2- Inorganic compounds (2-5%) 3- Water (70-90%)

The basic organic compounds in the cell are:

1- Carbohydrates 2- Lipids 3- Amino acids and proteins 4- Enzymes 5- Vitamins 6- Nucleic acids 7- Hormones

The cells:
A cell is the basic unit of life in any organism. They are also the building blocks of life. The cell is the structural and functional of all living organisms. The human body is composed of specialized tissues which in turn consist of vast clusters of cells

Types of cells:
Two general types of cells are recognized in nature. They are prokaryotes and eukaryotes based on the presence and absence of the true nucleus. In prokaryotes, they have no typical nucleus and possess simple structure. Present mainly in the bacteria, blue green algae and certain types of microorganisms.

In eukaryotes, they have nucleus, which is surrounded by nuclear membrane, and are most complex in their structure and function. Present in all higher organisms, (both plant and animal) as well as in fungi, etc

The components of the cells:

A cell has three major components: 1- Cell membrane 2- Cytoplasm with its organelles 3- Nucleus.

Cell membrane (Plasma membrane):

The cell is enveloped (bounded) by a thin membrane called cell membrane or plasma membrane, which is of 750A thickness. The plasma membrane is composed of a double layer (bilayer) of lipids, oily substances found in all cells. Most of the lipids in the bilayer are in the form of phospholipids and they are amphipathic in nature (Amphipathic molecules have both hydrophobic regions and hydrophilic regions). A phospholipid is composed of a head and two tails. The circle, or head, is the negatively charged hydrophilic ("water-loving") polar phosphate group and the two tails are the two highly hydrophobic ("water-fearing") non-polar fatty acid chains of the phospholipid. The fatty acid "tails" of the two-phospholipid layers are oriented towards each other and the phosphate portion; face out to the environment as well as into the cytoplasm of the cell's interior, where they form hydrogen bonds with surrounding water molecules. The cell membrane contains a large amount of protein. Individual proteins may be adjacent to the membrane or may be embedded within it; such proteins are called peripheral and integral membrane proteins, respectively. Membrane proteins and lipids are arranged in a particular fashion, both contributing to containing the cell and to selectively allowing or blocking the traffic of certain substances through the cell. Such arrangement of molecules provides fluidity to the cell membrane. In addition, cell membranes contain a small amount of various polysaccharides as glycoproteins and glycolipids, but no free carbohydrates.

Steroid cholesterol is wedged between phospholipid molecules in the plasma membrane of animals cells.

The plasma membrane performs the following functions:

1- It holds the cells together and makes it a functional unit. 2- The plasma membrane is permeable to specific molecules, however, and allows nutrients and other essential elements to enter the cell and waste materials to leave the cell. Small molecules, such as oxygen, carbon dioxide, and water, are able to pass freely across the membrane, but the passage of larger molecules, such as amino acids, organic acid, inorganic salts, and sugars, must be specifically transported across the membrane by proteins. 3- Plasma membrane proteins function in several different ways. Many of the proteins play a role in the selective transport of certain substances across the phospholipid bilayer, either acting as channels or active transport molecules. Others function as receptors, which bind information-providing molecules, such as hormones, and transmit corresponding signals based on the obtained information to the interior of the cell. Membrane proteins may also exhibit enzymatic activity, catalyzing various reactions related to the plasma membrane.

Mitochondria (power house of cell):

Within the cytoplasm, there are numerous double- layered elongated bodies called mitochondria. A mitochondrion contains inner and outer membranes composed of phospholipid bilayers and proteins. The two membranes, however, have

different properties and functions. Because of this double-membraned organization, there are 5 distinct compartments within mitochondria. There is the outer membrane, the inter membrane space (the space between the outer and inner membranes), the inner membrane, the cristae space (formed by infoldings of the inner membrane), and the matrix (space within the inner membrane). Mitochondria range from 1 to 10 micrometers (m) in size. 1- Outer mitochondrial membrane is smooth and composed of a phospholipid and cholesterol with an equal amount of protein. The outer membrane also contains many copies of proteins. 2- Inner mitochondrial membrane is folded to form cristea, which give it a large surface area and the inner membrane of mitochondria contains the enzymes of electron transport chain. The region enclosed by the inner membrane is known as the matrix, and the matrix contains the enzymes of Krebs cycle, urea cycle, hem and steroid synthesis. Mitochondria are called "power house" of the cell because they generate most of the cell's supply of ATP, used as a source of chemical energy.

Some mitochondrial functions are performed only in specific types of cells. For example, mitochondria in liver cells contain enzymes that allow them to detoxify ammonia, a waste product of protein metabolism.

Golgi apparatus:
The Golgi apparatus (body) is compact and consists of parallel membrane plates and tubules. It is the site for enzyme secretion. It participates in the formation of lysosomes.

Endoplasmic Reticulum and Ribosomes:

Endoplasmic Reticulum is divided into rough and smooth types; 1- Rough Endoplasmic Reticulum is lined on the cytoplasmic surface with multitude particles called ribosomes. The function of rough Endoplasmic Reticulum is protein synthesis. 2-Smooth Endoplasmic Reticulum is in continuation with the Rough Endoplasmic Reticulum. It is distinguishable from the rough by the absence of ribosomes. The function of smooth Endoplasmic Reticulum: 1- Mainly concerned with the synthesis of lipids. 2- It is also the location of glycosyl transferase involved in the synthesis of glycoprotein's and glycolipids. 3-It is responsible for the detoxification of xenobiotics.

Lysosomes:
Lysosomes are tiny organelles in the cell containing homogeneous fluid. The Lysosomes have the thickest covering membrane to prevent the enclosed hydrolytic enzymes from coming in contact with other substances in the cells. Also they have chemicals in them that digest the wastes and other bad organelles. When the cell dies the lysosmes work swiftly with their chemicals and digest the dead cell. Without lysosomes living organisms would become filled with dead cells.

Microtubules:
These are tubular structures composed of globular protein and held in intracellular transport.

Peroxisomes:
Peroxisomes are small organelles also called Micro bodies. All eukaryotes are comprised of one or more cells that contain peroxisomes. Peroxisomes contain a variety of enzymes, which primarily function together to rid the cell of toxic substances, and in particular, hydrogen peroxide (a common byproduct of cellular metabolism). These organelles contain enzymes like catalase that convert the hydrogen peroxide to water, rendering the potentially toxic substance safe for release back into the cell. Some types of peroxisomes, such as those in liver cells, detoxify alcohol and other harmful compounds by transferring hydrogen from the poisons to molecules of oxygen (a process termed oxidation). Others are more important for their ability to initiate the production of phospholipids, which are typically used in the formation of membranes. Recently it has been shown the liver peroisomes have an unusually active -oxidation system capable of oxidizing long chain fatty acids (C16 & C18).

Nucleus and Nucleolus:

A dense spherical structure called nucleus is present in the centre of the cell. It has a double-layered nuclear membrane called nuclear envelope. Nucleus contains a dense body known as the nucleolus. The nucleolus is composed of two important nucleic acid (the Deoxyribonucleic acid DNA) and (Ribonucleic acid RNA). DNA in the nucleus is coiled into a dense mass called chromatin. The major functional role of the nucleus is that of: 1- The synthesis of new DNA. 2- The synthesis of three major types of RNA (mRNA, rRNA, and tRNA).

Review Questions: a- Give structure and function of: Mitochondria -1 Golgi apparatus -2 Endoplasmic Reticulum -3 Lysosomes -4 Peroxisomes -5 Nucleus -6 Cell membrane -7