Introduction to Cell Structure, Lecture notes of Biology

Introduction to biochemistry and cell biology. Cell structure and function.

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INTRODUCTION
Biochemistry is the systematic study of the chemicals of the living systems, their organization, and the principles of their
participation in the processes of life. Its importance is due to the increasing recognition that underlying each and every
biological function is a chemical reaction. Hundreds/thousands of chemical reactions are taking place in our cells every minute
of our lives. Biochemical investigations have been directed towards the study of the chemical composition of cells and the
chemical processes in which they participate.
Several principles are central to the understanding of living organisms:
1) Cells, the basic structural units of all living things, are highly organized.
2) Living processes consist of hundreds of chemical reactions.
3) Certain fundamental reaction pathways are found in all living organisms.
4) All organisms use the same type of molecules.
5) The instructions for growth, development, and reproduction are encoded in an organism’s nucleic acids.
The life of a cell requires materials, information, and energy:
A cell in particular, and a whole organism in general, has three basic needs: materials, information, and energy.
Without the daily satisfaction of these, human life would be severely constrained.
The organic materials of life will be considered, starting with the three main classes of foodstuffs carbohydrates,
lipids, and proteins. Humans use these molecules to build and run their bodies and to try to stay in some state of repair. Plants
rely heavily on carbohydrate for cell walls, and animals obtain considerable energy from carbohydrates made by plants. Lipids
serve many purposes. They are used, both by plants and animals, as materials to make cell membranes and as sources of
chemical energy. Proteins are particularly important in both the structures and functions of cells. Because of the catalytic role
of proteins in regulating chemical events in cells, the study of proteins will be immediately followed with an examination of
enzymes, which make up a particular family of proteins.
Every cell has an information system enzymes, hormones, and neurotransmitters are components of the intricate
information system in the body. Without information, the materials and energy delivered to the body could produce only
rubbish. Although enzymes are major players in the cells’ information system, they do not originate the cellular script. They
only help to carry out directions that are encoded in the molecular structures of the nucleic acids, which are compounds that are
able to direct the synthesis of enzymes. Hormones & neurotransmitters, two other components of cellular information, depend
on the presence of right enzymes not only for their existence but for their functions. Thus the study of the enzyme makers, the
nucleic acids, is included in any study of the molecular basis of life.
All life processes consist of chemical reactions catalyzed by enzymes. The reactions of a living cell, which are known
collectively as metabolism, result in highly coordinated and purposeful activity. Among the most frequent reactions
encountered in biochemical processes are:
1) nucleophilic substitution 4) isomerization
2) elimination 5) oxidation reduction
3) addition 6) hydrolysis
To supply materials for any use parts, information, or energy each organism has basic nutritional needs. These
include not just organic materials, including vitamins, but also mineral, water, and oxygen. Thus, together with learning about
the materials of life and how they are processed and used, the need for vitamins, minerals, water, and oxygen will also be
considered.
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INTRODUCTION

Biochemistry is the systematic study of the chemicals of the living systems, their organization, and the principles of their participation in the processes of life. Its importance is due to the increasing recognition that underlying each and every biological function is a chemical reaction. Hundreds/thousands of chemical reactions are taking place in our cells every minute of our lives. Biochemical investigations have been directed towards the study of the chemical composition of cells and the chemical processes in which they participate.

Several principles are central to the understanding of living organisms:

  1. Cells, the basic structural units of all living things, are highly organized.
  2. Living processes consist of hundreds of chemical reactions.
  3. Certain fundamental reaction pathways are found in all living organisms.
  4. All organisms use the same type of molecules.
  5. The instructions for growth, development, and reproduction are encoded in an organism’s nucleic acids.

The life of a cell requires materials , information , and energy: A cell in particular, and a whole organism in general, has three basic needs: materials, information, and energy. Without the daily satisfaction of these, human life would be severely constrained.

The organic materials of life will be considered, starting with the three main classes of foodstuffs – carbohydrates, lipids, and proteins. Humans use these molecules to build and run their bodies and to try to stay in some state of repair. Plants rely heavily on carbohydrate for cell walls, and animals obtain considerable energy from carbohydrates made by plants. Lipids serve many purposes. They are used, both by plants and animals, as materials to make cell membranes and as sources of chemical energy. Proteins are particularly important in both the structures and functions of cells. Because of the catalytic role of proteins in regulating chemical events in cells, the study of proteins will be immediately followed with an examination of enzymes , which make up a particular family of proteins.

Every cell has an information system – enzymes, hormones, and neurotransmitters are components of the intricate information system in the body. Without information, the materials and energy delivered to the body could produce only rubbish. Although enzymes are major players in the cells’ information system, they do not originate the cellular script. They only help to carry out directions that are encoded in the molecular structures of the nucleic acids , which are compounds that are able to direct the synthesis of enzymes. Hormones & neurotransmitters, two other components of cellular information, depend on the presence of right enzymes not only for their existence but for their functions. Thus the study of the enzyme makers, the nucleic acids , is included in any study of the molecular basis of life.

All life processes consist of chemical reactions catalyzed by enzymes. The reactions of a living cell, which are known collectively as metabolism, result in highly coordinated and purposeful activity. Among the most frequent reactions encountered in biochemical processes are:

  1. nucleophilic substitution 4) isomerization
  2. elimination 5) oxidation – reduction
  3. addition 6) hydrolysis

To supply materials for any use – parts, information, or energy – each organism has basic nutritional needs. These include not just organic materials, including vitamins, but also mineral, water, and oxygen. Thus, together with learning about the materials of life and how they are processed and used, the need for vitamins , minerals , water , and oxygen will also be considered.

Organel l e Prokaryotes Eukaryotes Nucl eus

Cel l membrane Mi tochondri a

Endopl asmi c reti cul um Ri bosomes Chl oropl asts

No defi ni te nucl eus; DNA present but not separate from the rest of the cel l

Present

Present Present None; enzym es for oxi dati on are on pl asma membrane None

Present None; photosynthesi s l ocal i zed i n chromatophores

Present

Present

Present Present i n green pl ants

I. CELL STRUCTURE

Based on their cell structures, organisms are divided into two main groups:

  1. Prokaryote: Greek derivation meaning “before the nucleus”; single-celled organisms
  2. Eukaryote: Greek derivation meaning “true nucleus”; contain a well-defined nucleus surrounded by a nuclear membrane; can be single celled, such as yeasts and Paramecium , or multicellular, such as animals and plants

Five kingdoms:

1) Monera - only prokaryotic organisms; includes bacteria and cyanobacteria 2) Protista - includes unicellular eukaryotes: yeast, Euglena , Volvox , Amoeba , and Paramecium 3) Fungi - includes molds and mushrooms 4) Plantae Fungi, plants, and animals are multicellular eukaryotes 5) Animals (with few unicellular eukaryotes)

The main difference between prokaryotic and eukaryotic cells is the existence of organelles, especially the nucleus, in eukaryotes. An organelle is a part of the cell that has a distinct function; it is surrounded by its own membrane within the cell.

  1. Mitochondria
    • the second largest organelle; usually ellipsoidal in shape; the powerhouse of the cell where carbohydrates, lipids, and amino acids are oxidized to CO 2 and H (^) 2O by molecular O 2 and the energy set free is converted into the energy of ATP
    • has a double-membrane structure, an outer membrane and an inner membrane. The inner membrane, in which the enzymes of electron transport and energy conversion are located, is convoluted to form shelves termed cristae; site for cellular respiration.
  2. Endoplasmic reticulum
    • appears to be a system of interconnected tubules or canaliculi extending throughout the cell cytoplasm and is continuous with the outer nuclear membrane; two types: rough and smooth er
    • rough er is lined with a number of small, spheric, electron-dense particles called ribosomes; primarily involved in synthesis of membrane proteins and proteins for export from the cell
    • smooth er lacks ribosomes; appears to be involved in the biosynthesis of steroids, phospholipids, and complex polysaccharides; functions also include biotransformation, a process in which water-soluble organic molecules are prepared for excretion
  3. Ribosomes
    • consist of ~50% RNA (rRNA) and 50% protein; involved in protein synthesis in the cell and are sometimes referred to as the “workbench” for protein synthesis
    • complex structures containing two irregularly shaped subunits of unequal size; they come together to form whole ribosomes when protein synthesis is initiated, when not in use, the ribosomal subunits separate
  4. Golgi apparatus (Golgi complex)
    • structures composed of flattened sacs with vesicles, located near the nucleus, probably continuous with er
    • the organelles to which synthesized proteins are transported and temporarily stored before release from the cell
    • the “packaging stations” of the cell, the primary site for packaging and distribution of cell products to internal and external compartments
    • there is a continuous flow of substances through the Golgi apparatus
    • responsible for sorting and packaging several types of proteins, small molecules, and new membrane components
  5. Lysosomes
    • membrane-bound organelles containing a variety of hydrolytic and degradative enzymes and having an optimum pH of 5.
    • has regulatory and defense function; function in the digestion of materials brought into the cell by phagocytosis and pinocytosis; also serve to digest cell components after cell death; the “suicide bags” of the cell
    • upon death of the cell or its exposure to environmental conditions, the lysosomal membrane disintegrates, releasing its contents, which cause the self-digestion or autolysis of the cell constituents
  6. Peroxisomes
    • contains oxidative enzymes that oxidize amino acids, uric acid, and various 2-hydroxyamino acids using O 2 with the formation of H (^) 2O (^) 2, which is then converted to H (^) 2O and O 2 by the enzyme catalase

The study of the composition of the living matter is necessary for the intelligent understanding of the chemical processes taking place in the body. The protoplasm , the living matter, is composed of:

also present in the peroxisomes – thus the cell protects itself from the toxicity of H (^) 2O (^2)

a) bioinorganic substances that include water (70-90%) and inorganic salts (chloride, sulfate, phosphate, carbonate, etc. salts of Na, K, Ca, Mg, NH (^) 4) and

b) bioorganic compounds that include proteins, lipids, carbohydrates, and nucleic acids.

Some importance of water in the cell :

  1. the solvent
    • the agency that enables water-soluble, water-miscible, or emulsifiable substances to be transferred in the body not only in the blood but also intercellularly and intracellularly
  2. in biochemical reactions
    • ionization is a prerequisite to many biochemical reactions and ionization takes place in water
  3. in physiologic regulation of body temperature
    • high specific heat (amount of heat required to raise the temperature of 1g of H (^) 2O 1 oC) enables the body to store heat effectively without greatly raising its temperature
    • high heat conductivity permits heat to be transferred readily from the interior of the body to the surface
    • high latent heat of evaporation causes a great deal of heat to be used in its evaporation and thus cools the surface of the body

Chemical reactions occurring in vivo have the following properties:

  1. mildness
    • energy is taken up and released in a gentle way, nor violently as those occurring in vitro (because of high specific heat of water which makes up a large proportion of the protoplasm)
  2. speed
    • glucose, for instance, is oxidized in the body with surprising speed, while in vitro , the same reaction is quite a long and tedious process. This is due to the presence of enzymes, without which life as we know it would not be possible
  3. orderliness
    • a high degree of orderliness is due to the existence of cell specialization within the different organs of the body