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2.4: Inorganic Compounds - Biology

2.4: Inorganic Compounds - Biology


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2.4: Inorganic Compounds

2.4 Inorganic Compounds and Solutions

Their molecules also have only a few atoms and cannot be used by cells to perform complicated biological functions.

They include water and many salts, acids, and bases.

Inorganic compounds may have either ionic or covalent bonds.

Water makes up 55-60% of a lean adult's total body mass all other inorganic compounds combined add 1-2%.

Most are large molecules, many made up of long carbon atom chains.

Although you might be able to survive for weeks without food, without water you would die in a matter of days.

Nearly all the body's chemical reactions occur in a watery medium.

Water has many properties that make it such an indispensable compound for life.

We have already mentioned the most important property of water, its polarity—the uneven sharing of valence electrons that confers a partial negative charge near the one oxygen atom and two partial positive charges near the two hydrogen atoms in a water molecule (see Figure 2.5e).

They found nothing that worked as well as water.

Although it is the most versatile solvent known, water is not the universal solvent sought by medieval alchemists.

If it were, no container could hold it because it would dissolve all potential containers!

What exactly is a solvent?

In a solution, a substance called the solvent dissolves another substance called the solute.

Usually there is more solvent than solute in a solution.

For example, your sweat is a dilute solution of water (the solvent) plus small amounts of salts (the solutes).

The versatility of water as a solvent for ionized or polar substances is due to its polar covalent bonds and its bent shape, which allows each water molecule to interact with several neighboring ions or molecules.

Solutes that are charged or contain polar covalent bonds are hydrophilic (hydro = water philic = loving), which means they dissolve easily in water.

Common examples of hydrophilic solutes are sugar and salt.

Molecules that contain mainly nonpolar covalent bonds, by contrast, are hydrophobic (phobic = fearing).

They are not very water soluble.

Examples of hydrophobic compounds include animal fats and vegetable oils.

To understand the dissolving power of water, consider what happens when a crystal of a salt such as sodium chloride (NaCl) is placed in water (Figure 2.10).

The electronegative oxygen atom in water molecules attracts the sodium ions (Na+), and the electropositive hydrogen atoms in water molecules attract the chloride ions (Cl−).

Soon, water molecules surround and separate Na+ and Cl− ions from each other at the surface of the crystal, breaking the ionic bonds that held NaCl together.

The water molecules surrounding the ions also lessen the chance that Na+ and Cl− will come together and reform an ionic bond.

Figure 2.10 How polar water molecules dissolve salts and polar substances.

When a crystal of sodium chloride is placed in water, the slightly negative oxygen end (red) of water molecules is attracted to the positive sodium ions (Na+), and the slightly positive hydrogen portions (gray) of water molecules are attracted to the negative chloride ions (Cl−).

In addition to dissolving sodium chloride, water also causes it to dissociate, or separate into charged particles, which is discussed shortly.


Organic and Inorganic Compounds Present in Living Body

These are represented by A. Water and B. Inor­ganic salts.

A. Water:

This is most important for the living body. Major bulk of protoplasm is made up of water (66% in man nearly 90% in jelly fish).

It does the following functions:

(i) acts as solvent for other inorganic and organic substances,

(ii) serves as a medium of every chemical reaction that occurs within the living body,

(iii) remains as a liquid for considerable range of temperature and is an excellent transporting medium and

(iv) plays a great role in regulating the effects of exter­nal temperature.

B. Inorganic Salts:

Though often present in insignificant quantity, the inorganic salts play following important roles:

(i) help in certain chemical reactions,

(ii) serve as pre­cursor material for’ the synthesis of certain essential molecules (e.g., DNA),

(iii) take part in the formation of supporting and protect­ing structure of the soft parts (e.g., bone).

Organic Compounds:

Following types of organic compounds exist in living substances—A. Carbohydrates, B. Lipids, C. Proteins, D. Nucleotides, E. Vitamins. In addition to these there are organic acids, alcohols and steroids, which are synthesised from other molecules.

A. Carbohydrates:

These compounds contain carbon, hydrogen and oxygen atoms in their molecules, and the common trend of chemical composition is Cn(H2O)n. The carbohydrates serve as fuel and structural material.

Most of the carbohydrate molecules are very large with a molecular weight of 5,00,000 or more. Each molecule is made up of numerous similar units. Each unit is called sugar. The carbohydrates may be 1. Monosaccharide’s, 2. Disaccharides and 3. Polysaccharides.

Carbohydrate molecules which contain six or lesser number of carbon atoms are included in this group. The best examples are glucose, galactose and fructose (Fig. 2.3). All of them have the same molecular formula and are called isomers.

They differ only in the arrangement of their hydrogen atoms. Of these three, glucose is most important, because it is the, basic transportable form of fuel. It is used as fuel to be utilised during cellular respiration and to supply the energy to the organism for performing its life activities.

These are formed by linking up of two monosaccharides by an oxygen atom between them. The well-known disaccharides are sucrose and maltose (Fig. 2.4). Sucrose is composed of a glucose unit and a fructose unit maltose results during the breakdown of starch (a polysaccharide).

These are very large carbohydrate molecules, containing series of monosaccharide units. Three important polysaccharides are (a) starch, (b) glycogen and (c) cellulose.

These are storage products in plants and are formed by the conversion of excess sugar (Fig. 2, 5). Starch is insoluble in water. When needed for the body in a watery medium starch is digested in the presence of enzymes called amylase and maltase, into simple sugar.

The breaking down of starch or any other organic compound with the inter­action of water is called hydrolysis. Starch provides the richest source of carbohydrate to mankind.

Instead of starch animals store sugar as glycogen. Excess sugar ob­tained from the plant starch is converted into glycogen which differs in structure from the plant starch. Glycogen is kept stored in muscles and liver. When required, it is quickly broken down into glucose. In lower animals, glycogen serves as the only source of reserve energy but in higher animals major energy reserves are the fats.

This is a very important polysaccharide which is responsible for the formation of structural elements in plants. It is generally absent in animals except in a few cases (small quantities of cellulose are repor­ted to be present in the skin of man). These are very long molecules, each of which may contain three thousand simple sugar units.

Cellulose is digested only by an enzyme called cellulase, which is produced by cer­tain organisms. In ruminants, the cellulose in the ingested plant material is digested by cellulase producing bacteria, which reside within their alimentary canal. Within the gut of termite, a flagellate, Triconympha, performs similar function.

B. Lipids:

Lipids are the most common energy reserves in animals. It is stored as round droplets in special kind of tissue called adipose tissue and serves the following important func­tions: (1) as reserved potential energy, (2) as heat insulating layer beneath the skin, (3) as protector of vital organs from mechanical damages and (4) as to meet the water re­quirements in many animals.

Each molecule contains carbon, hydrogen and oxygen at­oms, but their arrangements are entirely different from that of carbohydrates (Fig. 2.6).

Here, in each molecule hydrogen atoms are in greater proportion to oxygen than that in the carbohydrates and thus are concen­trated source of potential energy. Moreover, during its burning (oxidation), more water is produced. The animals living in arid zones and un-hatched chicks meet their water requirements from this water produced as a by-product of the breakdown of lipids.

Each lipid, molecule is made up of one alcohol molecule and three molecules of fatty acid. The three fatty acids in one molecule of fat may be identical or may be different. The number of carbon atoms in fatty acid varies from 4-24, and the number is always even.

Lipids may be of three types:

Fatty acids are com­bined with alcohols to form simple lipids. When the alcohol is glycerol it is called true fat and when it is other than glycerol it is called wax. The common examples of waxes are (a) Beeswax—Fatty acids are combined with myricil. (b) Lanoline—Fatty acids are united with cholesterol.

When fats are com­bined with other non-fatty groups like phos­phates, sulphates, sugar and amino acids. The examples are (a) Phospholipids—Fats with phosphoric acid and nitrogenous base, (b) Glycolipids—Fats with sugar and nitrog­enous base, (c) Amino lipids—Fats united with amino acids, (d) Sulpholipids—Fats united with sulphur.

These are products which are obtained from the breakdown of simple and compound lipids.

Fats which are eaten as food, are first emulsified by the action of bile salts produced in the liver. It is then hydrolysed by the action of an enzyme lipase which converts it into fatty acids and glycerol. As fats are insoluble in water, emulsification is a necessary prereq­uisite for transporting it through a watery medium.

The water-soluble form is also ob­tained by replacing one of the three fatty acid molecules with a phosphorus-containing molecule. The resulting substance is called phospholipid. It may be mentioned here that in man and some other animals, sometimes the carbohydrates are converted into fats.

C. Proteins:

Proteins are the most important compounds which provide the building blocks of the living body. From hair to the nail of the toe, each and every part is made up of protein. It remains dissolved or suspended, either singly or with others in the living substance. When united with other kinds of molecules, they are known as conjugated proteins.

Be­fore entering into the details of protein struc­ture, it is important to note that the diversity of protein in a living body is unique. Each structure in a living body is made up of a specific kind of protein.

Nature of protein not only differs in each species but also no two individuals (excepting identical twins) possess proteins of identical structure. Such uniqueness of proteins in each individual is believable only when the complexities and possibilities of variety of protein molecules are understood.

Each protein molecule contains nitrogen in addition to carbon, hydrogen and oxygen atoms. Other elements, i.e., sulphur, phos­phorus, iron and copper may also be present. The structure of protein molecule is very large and is folded into three dimensional shapes. The two simpler proteins—insulin and beta-lacto-globulin have the molecular formulae—C254 H377 N65 O75 S6 and C1864 H3012 O576 N463 S21.

In spite of their large size the protein molecules are built up in an orderly fashion. Each chain is built up with simpler units called amino acids. Out of nearly eighty known amino acids, twenty are common in all living organisms.

These twenty amino acids are built up in the fol­lowing pattern. An amino group (-NH2) unites with the acid group (COOH), by removing a molecule of water. Figure 2.7 shows the general plan of amino acids.

The letter R represents the particular chemical group which remains associated with the amino acid. The structure of R varies in different amino acids (Fig. 2.8). In a molecule of protein the amino acids are linked together in such a way that amino end unites with the acid end of an­other after removing the water molecules between them.

When it is a combination of two amino acids it is called dipeptide and when many amino acids are united they form a polypeptide. Thus, like the twenty- six alphabets making a voluminous diction­ary, innumerable combinations of amino acids form the diverse kinds of proteins.

During the breaking down of protein, by the action of proteolytic enzymes, the long chains of amino acids are broken into shorter chains. Finally, the shorter chains are broken into constituent amino acids.

A water molecule is inserted at the broken end. The chain of protein molecules which remain folded is extremely sensitive to various physical and chemical agents. When in contact with these agents they lose their characteristic folding. It is called denaturation.

D. Nucleotides:

Each nucleotide consists of a pentose sugar, a phosphate and one of the four bases. The pentose sugar is either ribose or deoxyribose. The ribose contains one oxygen atoms more than deoxyribose.

The phosphate is derived from phosphoric acid. Four bases which are present in the nucleic acids are nitrogenous and two of them are in the group called Purines and two are Pyrimidines. The pruines are adenine and guanine, the pyrimidines are cytosine and thymine or uracil.

Thus, there are four types of nucleotides, each type is characterised by a particular base. When one base unites with one pentose unit, they form a nucleoside, e.g., thymine with ribose = Thymidine ad­enine with ribose = Adenosine.

The sugar end of a nucleoside unites with the phos­phate group to form a nucleotide unit, e.g., Adenosine monophosphate or AMP, Thymi­dine monophosphate or TMP. Nucleotides act as (1) components of genetic system, (2) as energy conveyor and (3) as coenzymes.

1. Nucleotides in Genetic system:

Here nucleotides unite to form complex macro- molecules called nucleic acids. Two types of nucleic acids are found (a) Deoxyribonu­cleic acid (DNA) and (b) Ribonucleic acid (RNA).

(a) Deoxyribonucleic acid:

Deoxyribonu­cleic acid or DNA is the most important chemical substance present in the living sys­tem. The chemical basis of heredity depends upon the working of this substance which is called the key molecule of life. The DNA is localised in the nucleus (on the chromo­somes) and sometimes is seen in other parts, i.e., mitochondria.

Each molecule of DNA is made up of two strands or chains, each of which is formed by the alternate arrangement of deoxy sugar and phosphate groups (Fig. 2.9).

The two chains are helically coiled as in a spiral staircase. This brings the two bases in be­tween the two strands and in front of each other. Space between the two chains is such that one purine and one pyrimidine can fit together by the force of a weak hydrogen bond.

This again is possible when adenine pairs with thymine and guanine pairs with cytosine. Though the sequence of base in one strand varies in different organisms, the pairing of base is always the same. From microbes to man, everywhere adenine fits with thymine and guanine couples with cytosine.

Thus the sequence of base in one strand acts as a template of the other strand. The findings of molecular biology in recent years have established that in the arrange­ment of pairing of purine and pyrimidine bases lies the code of blue print of ‘building and working’ of the living system. These codes are first of all transcribed into the nitrogen base sequence of RNA.

That instruc­tion is again translated to arrange different amino acids in proper sequence to form protein. The DNA can multiply and this involves self-replication. This property serves as the basis of reproduction in all living organisms.

Another important property of DNA is that it is mutable. The sequence of nitrogen base pairing may undergo change. This results into the production of a code of different kind which results into the appear­ance of changed traits.

In most living forms ribonucleic acid or RNA is responsible for the synthesis of proteins. In a group of viruses, it acts like DNA to serve as the material basis of inheritance.

Long, thread-like molecules are arranged usually in single strand but it may be coiled in several places to form helices. Sugar in the nucleotide is ribose sugar and of the pyrimidine bases the thymine is replaced by uracil, but the plan of pairing is same as in DNA, i.e., adenine with uracil and. guanine with cytosine.

According to their functional role in the process of protein synthesis, RNAs are classified into— messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA).

Nucleotides as Conveyors of Energy:

Nucleotides exhibit a tendency to couple with additional phosphate group. For exam­ple, Adenosine monophosphate (AMP) with a second phosphate group becomes Adeno­sine diphosphae (ADP), while the addition of a third phosphate group makes Adenos­ine triphosphate (ATP).

This addition or union of additional phosphate groups re­quires a large quantity of energy which is available from respiratory fuels. This linking energy is called high energy bond. When ATP breaks into ADP and finally into AMP, this bounded form of energy is released and utilised by the cell.

Nucleotides as Coenzymes:

The nucleotides which work as coenzymes, are complex substances which accompany the activity of an enzyme. In a chemical reaction within the body certain atoms are often transferred from one compound to ano­ther. An enzyme hastens the process and a coenzyme actually helps in transfer.

Most of the coenzymes are produced from nucleo­tides, e.g., Flavin mononucleotide (FMN) and Flavin adenine dinucleotide (FAD). Both are formed by the union of flavin parts of vitamin B, Riboflavin with nucleotide derivatives. They work in transferring hydrogen atoms.

E. Vitamins:

These organic substances are never produced from carbohydrates, fats, proteins or nucleo­tides, but mostly taken directly from external sources. Some vitamins are of course synthesised in the body or are supplied secondarily by the micro-organisms living inside.

The vitamins are required in very small quanti­ties but are essential for the individual. Till the chemical nature of the vitamins was unknown, these substances were called in alphabetical names like, Vitamins A, B and so on.

Formerly, it was detected that lack of vitamins in the diet produces various kinds of deficiency diseases. In recent years, it has been established that vitamins act by uniting with the protein part of the enzymes. It is also understood that vitamin requirement is not same in all organisms.

A particular vitamin which is essential for a particular organism, may not be required by some other forms. The latter groups may be capa­ble of synthesising it within their body. A list of vitamins with their chemical names, sources and deficiency diseases produced by them are mentioned in Table 2.1.


TRANSPORT

PHASE ACTIVITY

Metaphase Centromeres of chromatid pairs line up at metaphase plate.

Anaphase Centromeres split identical sets of chromosomes move to opposite poles of cell.

Telophase Nuclear envelopes and nucleoli reappear chromosomes resume chromatin form mitotic spindle disappears.

Cytokinesis Cytoplasmic division contractile ring forms cleavage furrow around center of cell, dividing cytoplasm into separate and equal portions.

Table 3.4 Comparison Between Mitosis and Meiosis

POINT OF COMPARISON MITOSIS MEIOSIS

Cell type Somatic. Gamete.

Number of divisions

Stages Interphase. Interphase I only.

Prophase. Prophase I and II.

Metaphase. Metaphase I and II.

Anaphase. Anaphase I and II.

Telophase. Telophase I and II.

Copy DNA? Yes, interphase. Yes, interphase I No, interphase II.

Tetrads? No. Yes.

Number of cells 2. 4.

POINT OF

COMPARISON MITOSIS MEIOSIS

Number of chromosomes per cell

46, or two sets of 23 this makeup, called diploid (2 n ), is identical to the chromosomes in the starting cell.

One set of 23 this makeup, called haploid ( n ), represents half of the chromosomes in the starting cell.

A cell is the basic, living, structural and functional unit of the body.

Cell biology is the scientific study of cellular structure and function.

Figure 3.1 provides an overview of the typical structures in body cells.

The principal parts of a cell are the plasma membrane the cytoplasm, the cellular contents between the plasma membrane and nucleus and the nucleus.

The plasma membrane, which surrounds and contains the cytoplasm of a cell, is composed of proteins and lipids.

According to the fluid mosaic model, the membrane is a mosaic of proteins floating like icebergs in a lipid bilayer sea.

The lipid bilayer consists of two back-to-back layers of phospholipids, cholesterol, and glycolipids. The bilayer arrangement occurs because the lipids are amphipathic, having both polar and nonpolar parts.

Integral proteins extend into or through the lipid bilayer peripheral proteins associate with membrane lipids or integral proteins at the inner or outer surface of the membrane.

Many integral proteins are glycoproteins, with sugar groups attached to the ends that face the extracellular fluid. Together with glycolipids, the glycoproteins form a glycocalyx on the

small alcohols diffuse through the lipid bilayer of the plasma membrane via simple diffusion.

In channel-mediated facilitated diffusion, a solute moves down its concentration gradient across the lipid bilayer through a membrane channel. Examples include ion channels that allow specific ions such as K+, Cl−, Na+, or Ca2+ (which are too hydrophilic to penetrate the membrane's nonpolar interior) to move across the plasma membrane. In carrier-mediated facilitated diffusion, a solute such as glucose binds to a specific carrier protein on one side of the membrane and is released on the other side after the carrier undergoes a change in shape.

Osmosis is a type of diffusion in which there is net movement of water through a selectively permeable membrane from an area of higher water concentration to an area of lower water concentration. In an isotonic solution, red blood cells maintain their normal shape in a hypotonic solution, they swell and undergo hemolysis in a hypertonic solution, they shrink and undergo crenation.

Substances can cross the membrane against their concentration gradient by active transport. Actively transported substances include ions such as Na+, K+, H+, Ca2+, I−, and Cl− amino acids and monosaccharides. Two sources of energy drive active transport: Energy obtained from hydrolysis of ATP is the source in primary active transport, and energy stored in a Na+ or H+ concentration gradient is the source in secondary active transport. The most prevalent primary active transport pump is the sodium–potassium pump, also known as Na+–K+ ATPase. Secondary active transport mechanisms include both symporters and antiporters that are powered by either a Na+ or H+ concentration gradient. Symporters move two substances in the same direction across the membrane antiporters move two substances in opposite directions.

In endocytosis, tiny vesicles detach from the plasma membrane to move materials across the membrane into a cell in exocytosis, vesicles merge with the plasma membrane to move materials out of a cell. Receptor-mediated endocytosis is the selective uptake of large molecules and particles (ligands) that bind to specific receptors in membrane areas called clathrin-coated pits. In bulk-phase endocytosis (pinocytosis), the ingestion of extracellular fluid, a vesicle surrounds the fluid to take it into the cell.

Phagocytosis is the ingestion of solid particles. Some white blood cells destroy microbes that enter the body in this way.

In transcytosis, vesicles undergo endocytosis on one side of a cell, move across the cell, and undergo exocytosis on the opposite side.

Cytoplasm—all the cellular contents within the plasma membrane except for the nucleus— consists of cytosol and organelles. Cytosol is the fluid portion of cytoplasm, containing water, ions, glucose, amino acids, fatty acids, proteins, lipids, ATP, and waste products. It is the site of many chemical reactions required for a cell's existence. Organelles are specialized structures with characteristic shapes that have specific functions.

Components of the cytoskeleton, a network of several kinds of protein filaments that extend throughout the cytoplasm, include microfilaments, intermediate filaments, and microtubules. The cytoskeleton provides a structural framework for the cell and is responsible for cell movements.

The centrosome consists of pericentriolar material and a pair of centrioles. The pericentriolar material organizes microtubules in nondividing cells and the mitotic spindle in dividing cells.

Cilia and flagella, motile projections of the cell surface, are formed by basal bodies. Cilia move fluid along the cell surface flagella move an entire cell.

Ribosomes consist of two subunits made in the nucleus that are composed of ribosomal RNA and ribosomal proteins. They serve as sites of protein synthesis.

Endoplasmic reticulum (ER) is a network of membranes that form flattened sacs or tubules it extends from the nuclear envelope throughout the cytoplasm. Rough ER is studded with ribosomes that synthesize proteins the proteins then enter the space within the ER for processing and sorting. Rough ER produces secretory proteins, membrane proteins, and organelle proteins forms glycoproteins synthesizes phospholipids and attaches proteins to phospholipids. Smooth ER lacks ribosomes. It synthesizes fatty acids and steroids inactivates or detoxifies drugs and other potentially harmful substances removes phosphate from glucose-6- phosphate and releases calcium ions that trigger contraction in muscle cells.

The Golgi complex consists of flattened sacs called cisternae. The entry, medial, and exit regions of the Golgi complex contain different enzymes that permit each to modify, sort, and package proteins for transport in secretory vesicles, membrane vesicles, or transport vesicles to different cellular destinations.

Lysosomes are membrane-enclosed vesicles that contain digestive enzymes. Endosomes, phagosomes, and pinocytic vesicles deliver materials to lysosomes for degradation. Lysosomes

associated with a wide variety of diseases and disorders.

In sexual reproduction, each new organism is the result of the union of two different gametes, one from each parent. Gametes contain a single set of chromosomes (23) and thus are haploid ( n ).

Meiosis is the process that produces haploid gametes it consists of two successive nuclear divisions, called meiosis I and meiosis II. During meiosis I, homologous chromosomes undergo synapsis (pairing) and crossing-over the net result is two haploid cells that are genetically unlike each other and unlike the starting diploid parent cell that produced them. During meiosis II, two haploid cells divide to form four haploid cells.

The sizes of cells are measured in micrometers. One micrometer equals

. Cells in the body range from to in size.

Aging is a normal process accompanied by progressive alteration of the body's homeostatic adaptive responses.

Many theories of aging have been proposed, including genetically programmed cessation of cell division, buildup of free radicals, and an intensified autoimmune response.

A tissue is a group of cells, usually with similar embryological origin, specialized for a particular function.

The tissues of the body are classified into four basic types: epithelial, connective, muscular, and


3d9b Inl a and b only (2) b and c only (3) b and d only (4) a, b and d only Which of the following pairs will show the same magn

3d9b Inl a and b only (2) b and c only (3) b and d only (4) a, b and d only Which of the following pairs will show the same magnetic moment ("spin only')? U Cr (H,0)J+ and [Fe (H,0), NO32+ (2) [ Mn (CN), 14- and [ Fe (CN), 13 - (3) [ Ni (CO), J and [ Zn (NH), 12+ (4) All of these. us 3ddus² 31845 3 45

78 8. For the reaction INH, NH ANH, NINH =/NHI dt di 1-2/NHI dt then the relation between kk, and is (a) k - - (b) k-34, 28, (e) 1.5k, = 3k, ki (d) 22k, = 3k Comid

Which of the following compound cannot show co-ordination isomerism? (A) [Pt(NH3)4][PtCl4] (B) (Co(NH3)4Cl2][Cr(NH3)2(C2O4)2] (C) [Pt(NH3)4Cl2][Pt(SCN)2Cl2] (D) [Zn(en)2][Zn(OH)4]

103. Which of the following complexes involves d’sp3 hybridization ? (A) [FeF613 (B) (CO(NH3)61+ (C) [Fe(CN)613- (D) [Mn(CN)614-. ill! fit 3d


2.4: Inorganic Compounds - Biology

Hi. Thanks for stoppin' by. This area of my "biology help pages" is about biochemistry, an area that many students find pretty challenging (difficult). While the ideas are abstract, much of the material boils down to memorization. Memorization boils down to studying. Studying boils down to work. Work boils down to effort. So, put your best effort forward & let's get to work !


Page Index
1. Organic vs Inorganic
2. Chemical Formulas
3. Dehydration Synthesis vs Hydrolysis
4. Review of Items #1-3
5. Carbohydrates
6. proteiNs
7. Lipids
8. Nucleic Acids

Organic vs Inorganic compounds:

"All living things are composed of one or more cells and the products of those cells."

Now where have you seen that before ? That is 1/3 of the cell theory, right ? The chemical compounds that make up the structures in cells are a mixture of organic compounds and inorganic compounds. To keep it simple, remember it this way : organic compounds always contain carbon and hydrogen (and maybe some other elements), inorganic compounds do not contain carbon and hydrogen together.

Organic compounds are found in living things, their wastes, and their remains.

Examples of inorganic compounds : water, carbon dioxide.

The elements (atoms) in organic compounds are held together by covalent bonds, which form as a result of the sharing of two electrons between two atoms.

For now, let's save any other nitty-gritty chemistry details for chemistry, OK ?

There are three kinds of chemical formulas we should understand. The simplest is the "molecular formula", which tells you the number of atoms of each element present in a compound. An "empirical formula" is basically a molecular formula with the numbers of atoms shown in the smallest possible ratio. A structural formula is like a diagram of the compound. It shows the atoms present and how they are arranged and bonded together in the compound.

Here are the molecular, empirical, & structural formulas for one compound that we will all learn to love --- GLUCOSE.

CHEMICAL FORMULAS FOR GLUCOSE

Molecular Formula Empirical Formula Structural Formula
C6H12O6 CH2O
Glucose is an example of a "monosaccharide", a small carbohydrate.

  • The molecular formula tells us that there are 6 carbon atoms, 12 hydrogen atoms, & 6 oxygen atoms in one single glucose molecule.
  • Notice that if you look at the structural formula & tally up each letter (element) you get the molecular formula.
  • Each line (dash) represents the covalent bond holding the atoms together.
  • The ratio of the elements in the molecular formula is 6:12:6, which reduces to 1:2:1 (the number expressed in the empirical formula : CH2O --- we don't bother writing the "1"s).

Dehydration Synthesis vs Hydrolysis :

All of the organic compounds we will study are examples of polymers. A polymer is a large chemical compound composed of smaller repeating units --- over & over & over again. Like a long choo-choo train is made up of smaller connected, repeating, choo-choo cars.

The chemical process that connects the smaller subunits to form large organic compounds is called dehydration synthesis. Remember "synthesis" from chapter 1 ? It still means the same thing : build. The "dehydration" part of the term refers to the fact that water is lost during the chemical process that bonds the subunits together. We will "see" this in a minute when we get more specific.

Hydrolysis is the process that breaks large organic compounds into their smaller subunits. It is the opposite of dehydration synthesis. In HYDROlysis, water (hydro) is added and the large compounds are split ("lysis" means split). The process of hydrolysis is involved in digestion --- when food is broken down into nutrients.

So, to summarize :

PROCESS STARTS WITH . ENDS WITH . EXAMPLE
dehydration synthesis small molecules
(subunits)
large molecules & water
hydrolysis water &
large molecules
small molecules
(subunits)
digestion
You will do yourself a BIG favor if you can keep these two processes straight.

QUESTIONS - Organic Compounds, Formulas, Dehydration Synthesis & Hydrolysis

Before we get into specific kinds of organic compounds, let's try some questions about what we've done so far.

1. Which is an example of an organic compound ?

    NOTES:
  • The 2:1 ratio of hydrogen to oxygen atoms in all carbohydrates is a very important identifying characteristic.
  • Another clue to identifying carbohydrates is their structure. Monosaccharides have a ring-like structure, kind of like a hexagon. So if you are looking at structural formulas and you see "rings", it's probably a carbohydrate especially if only carbon, hydrogen, & oxygen are present in the molecule. Want to see what I mean ?
    LOOK . RINGS .
  • The ring-thing is a big deal. It will help you. Memorize it.
  • What we have in the equation above is two single rings (monosaccharides) on the left becoming chemically combined to form the two-ringed molecule on the right (a disaccharide). It is a synthesis reaction --- the product is bigger than the individual reactants.
  • In order to combine the two glucose molecules, bonds must become available. This is accomplished by removing a hydrogen ion (H + ) from one glucose & a hydroxyl ion (OH - ) from the other (the dashed box in the equation illustrates this point). These ions bond to form the water molecule that appears on the far right. This happens in every dehydration synthesis reaction --- water is lost as a waste product.
  • If we were to turn the arrow in the equation around & read from right to left, we would be looking at the HYDROLYSIS of maltose. In the hydrolysis of maltose, water would be added to the disaccharide (maltose) causing it to split into its smaller subunits --- the two monosaccharides (glucose molecules).
  • Not to beat a dead horse, but the fact that only C, H, & O are in the molecules, and that the molecules have a ring-like structure should make you very confident in identifying them as carbohydrates.
  • Getting back to the carbohydrate table, chitin and cellulose are examples of carbohydrates with structural functions. Chitin is the material that makes up the exoskeletons of all arthropods (insects, spiders, lobsters, etc.). Cellulose is what the cell wall in plant cells is made of.
  • Starch is the form by which plants store extra carbohydrates. Glycogen (sometimes referred to as "animal starch") is the form by which animals store extra carbohydrates. We store glycogen in our livers.

dipeptide = two connected amino acids

  • Well, where to start. Did you notice the "N" in the amiNo group ? Since big proteiN molecules (which we call polypeptides) are long chains of amino acids, every (every) proteiN has nitrogen in it. Always.
  • You are responsible for recognizing & identifying the smaller parts of an amino acid. The NH2 on the left is the amino group, the COOH on the right is called a carboxyl group. The carboxyl group is responsible for giving the amino acids its "acid" properties.
  • The "R" is not an individual atom or element. Instead, the "R" spot is the location at which one of a number of groups of atoms connect to the rest of the amino acid. They are called "variable groups". There are 20 different variable groups --- so there are 20 different amino acids. So what I am trying to say is that the basic structure of all amino acids is the same except for the variable group ("R") spot. And whichever of the 20 variable groups you have bonded there determines which of the 20 amino acids you're dealing with. Let me illustrate with an example:
  • Both of these are amino acids because they have an amino group (NH2) on the left & a carboxyl group (COOH) on the right. They are two different amino acids because they have different atoms bonded at the "R" group spot. See ? That's not so bad, is it ?
  • Now, tell me something. By what process are individual amino acids combined to from larger proteiNs ? Very very good . dehydration synthesis. This is THE process by which ANY small organic molecules are combined to form BIG organic molecules. The dehydration synthesis of a protein is typically illustrated like so:
  • There are two clues that what you are looking at in the above equation is dehydration synthesis. The first is that water is at the end --- a waste product in this process ("dehydration" = loss of water !). The 2nd clue is that the one molecule on the right (the dipeptide) is bigger than the individual reactants (amino acids) on the left (synthesis = build).
  • Now, just like with putting 2 monosaccarides together, we can't combine the two amino acids until we have freed some bonds up. This is accomplished by removing an OH from one amino acid & an H from the other. These atoms bond & live happily ever after as H2O (water). The yellow in the diagram above is my attempt to emphasize this idear. The removal of OH's & H's & the formation of water as a waste product happens in EVERY dehydration synthesis reaction --- whether it involves carbohydrates, proteins, or lipids.
  • Notice please that the bonds "freed up" after the removal of water form the "peptide bond".
  • "Dipeptide" is just a word for two amino acids that are bonded together. If we continued to add more & more amino acids to the dipeptide we would then call the molecule a POLYpeptide.
  • If you haven't noticed already, "peptide" is a protein word. Dipeptide, polypeptide, peptide bond, --- all protein stuff.
  • The hydrolysis (breakdown) of a dipeptide could be summarized like this:

i THinK THat wE'vE TRied to STUFF eNOUGh inTo yOur BRAIN for nOW. WE'd bETTEr maKe surE SoMe STuFF is STICkiNG . InterESTeD IN a quiz ? it'S on carbOhyDRAtes & prOTEiNs. C'mon, give it a shot.

LIPIDS : (Fats, Oils, & Waxes)

Lipids are our 3rd group of organic compounds. Again, organic just means the compound contains carbon & hydrogen together. In the case of lipids, the compounds contain C, H, & O, and that's it. No other elements in lipid molecules. Nada, none, zippo, zilch. Just those 3. OK?

Do you recall another group of organic compounds that are also built with those same 3 elements ?
Yes, carbohydrates. So how do we keep from confusing our lipids & carbohydrates? No need to panic, it's quite simple. Carbohydrates always have twice as many hydrogen atoms as oxygen atoms (H:O ratio = 2:1). Lipids never do. Also, the structural formulas of carbohydrates have the "ring thing" (remember?) and lipids do not.

  • A fatty acid is nothing more than a long C-H chain with a carboxyl group (COOH) on the end. The 3 "dots" in the diagram above illustrate that the chain is very long.
  • Remember the carboxyl group from amino acids? The carboxyl group gives a molecule an acidic property. Both of the organic acids you need to remember (fatty ACIDS & amino ACIDS) have carboxyl groups .
  • Glycerol is classified as an alcohol (due to the OH's). It always looks the same: 3 C's with 3 OH's and everything else H's.
  • To build one lipid molecule, we combine 3 fatty acids with 1 glycerol by the process of . DEHYDRATION SYNTHESIS !
  • Like other dehydration synthesis reactions, we must free some bonds before we combine the 3 fatty acids & glycerol. And like before, this is accomplished by removing water molecules. We remove 3 waters in this reaction because we are bonding 3 fatty acids to the glycerol (we need 3 free bonds).
  • Notice that there is no Nitrogen anywhere, so this is definately not a proteiN reaction.
  • Notice also that there are no ring-shaped molecules, so we are not dealing with carbohydrates either.
  • The hydrolysis (digestion) of a lipid could be summarized like so:

NUCLEIC ACIDS: DNA & RNA

  • DNA & RNA (like proteins, carbohydrates, & lipids) are polymers --- long chains of smaller repeating units. The repeating unit in nucleic acids is called a nucleotide.
  • Every nucleotide has the same basic structure:
      • the phosphate is a PO4
      • the sugar (see the ring?) has 5 carbons (one at each corner)
      • the N-base is one of four possibilities (more on that in a second . )
      • so DNA & RNA are alike in that they are both nucleic acids composed of nucleotides
      • their differences lie in their funcstions and structure
      • the main structural differences are the number of strands in the molecule, the sugar structure, and one of the N-bases (thymine in DNA, uracil in RNA)

      Back to Biology Topics Outline

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      ANSWERS : THE CHEMISTRY OF LIVING THINGS

      QUESTIONS : Organic Comp., Formulas, Dehydration Synth. & Hydrolysis Answers & explanations are in black.

      1. Which is an example of an organic compound ?

      C12H22O11 + H2O ---> C6H12O6 + C6H12O6

      * hydrolysis. we know for two reasons : 1) the two molecules we end up with (on the right) are smaller than the one on the left & 2) water is added


      Inorganic Chemical Biology: Principles, Techniques and Applications

      Understanding, identifying and influencing the biological systems are the primary objectives of
      chemical biology. From this perspective, metal complexes have always been of great assistance
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      Applications is a must-have for bioinorganic, bioorganometallic and medicinal chemists as well as
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      2.4: Inorganic Compounds - Biology

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      Dichromium and dimolybdenum compounds of 2,6-dimethoxyphenyl and 2,4,6-trimethoxyphenyl ligands

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      Inorganic Thallium Compounds

      CAS: 7791-12-0 Molecular Formula: ClTl Molecular Weight (g/mol): 239.83 MDL Number: MFCD00011274 InChI Key: GBECUEIQVRDUKB-UHFFFAOYSA-M Synonym: thallium chloride, thallium i chloride, thallous chloride, thallium monochloride, thallium 1+ chloride, tlcl, thallium chloride tlcl, thallium chloride van, rcra waste number u216, rcra waste no. u216 PubChem CID: 24642 ChEBI: CHEBI:37117 IUPAC Name: chlorothallium SMILES: Cl[Tl]

      Alfa Aesar&trade Thallium(I) fluoride, 97%

      CAS: 7789-27-7 Molecular Formula: FTl Molecular Weight (g/mol): 223.38 MDL Number: MFCD00049607 InChI Key: CULOEOTWMUCRSJ-UHFFFAOYSA-M Synonym: thallium i fluoride, thallium fluoride, thallium monofluoride, thallium fluoride ic PubChem CID: 62675 IUPAC Name: λ¹-thallanylium fluoride SMILES: [F-].[Tl+]

      Alfa Aesar&trade Thallium(I) acetate, 99.995% (metals basis)

      CAS: 563-68-8 Molecular Formula: C2H6O2Tl Molecular Weight (g/mol): 266.448 MDL Number: MFCD00013045 InChI Key: CNWGLQAFFSLHRX-UHFFFAOYSA-N Synonym: thallium i acetate PubChem CID: 131675083 IUPAC Name: acetic acidmolecular hydrogenthallium SMILES: [HH].CC(=O)O.[Tl]

      Alfa Aesar&trade Thallium(I) hexafluorophosphate(V), 97% min

      CAS: 60969-19-9 Molecular Formula: F6PTl Molecular Weight (g/mol): 349.344 MDL Number: MFCD00049807 InChI Key: FRZBCOUMLHRKRT-UHFFFAOYSA-N Synonym: thallium hexafluorophosphate, tlpf6, thallium i hexafluorophosphate, thallium 1+ hexafluorophosphate, thallium 1+ hexafluoro-$l^ 5-phosphanuide, $l^ 1-thallanylium hexafluoro-$l^ 5-phosphanuide PubChem CID: 10904204 IUPAC Name: thallium(1+)hexafluorophosphate SMILES: F[P-](F)(F)(F)(F)F.[Tl+]

      Alfa Aesar&trade Thallium(I) bromide, ultra dry, 99.998% (metals basis)

      CAS: 7789-40-4 MDL Number: MFCD00011273 Synonym: Thallous bromide

      Alfa Aesar&trade Thallium(III) oxide, 96%

      CAS: 1314-32-5 Molecular Formula: O3Tl2 Molecular Weight (g/mol): 456.757 MDL Number: MFCD00011276 InChI Key: QTQRFJQXXUPYDI-UHFFFAOYSA-N Synonym: oxo oxothallanyloxy thallane, tl2o3, thallium iii oxide, oxo oxothallanyl oxy thallane, thallium oxide ic, thallium iii oxide trace metals basis PubChem CID: 3579754 IUPAC Name: oxo(oxothallanyloxy)thallane SMILES: O=[Tl]O[Tl]=O

      Alfa Aesar&trade Thallium(III) trifluoroacetate, 95%

      CAS: 23586-53-0 Molecular Formula: C6F9O6Tl Molecular Weight (g/mol): 543.426 MDL Number: MFCD00000414 InChI Key: PSHNNUKOUQCMSG-UHFFFAOYSA-K Synonym: thallium iii trifluoroacetate, acetic acid, trifluoro-, thallium 3+ salt, acetic acid,2,2,2-trifluoro-, thallium 3+ salt 3:1, thallium 3+ 2,2,2-trifluoroacetate, thallium tris trifluoroacetate, trifluoroacetic acid thallium iii, thallic trifluoroacetate, tech, thallium 3+ tritrifluoroacetate PubChem CID: 90200 IUPAC Name: thallium(3+)2,2,2-trifluoroacetate SMILES: C(=O)(C(F)(F)F)[O-].C(=O)(C(F)(F)F)[O-].C(=O)(C(F)(F)F)[O-].[Tl+3]

      Thallium(I) sulfate, 99.5% min (metals basis), Alfa Aesar&trade

      CAS: 7446-18-6 Molecular Formula: O4STl2 Molecular Weight (g/mol): 504.816 MDL Number: MFCD00011278 InChI Key: YTQVHRVITVLIRD-UHFFFAOYSA-L Synonym: thallous sulfate, thallium sulfate, thallium i sulfate, tharattin, zelio, bonide antzix, th-universal, unii-u9f9qir12t, rcra waste number p115, sulfuric acid, dithallium 1+ salt PubChem CID: 24833 ChEBI: CHEBI:81836 IUPAC Name: thallium(1+)sulfate SMILES: [O-]S(=O)(=O)[O-].[Tl+].[Tl+]

      Thallium(I) iodide, ultra dry, 99.999% (metals basis), Alfa Aesar&trade

      CAS: 7790-30-9 Molecular Formula: ITl Molecular Weight (g/mol): 331.28 MDL Number: MFCD00011279 InChI Key: CMJCEVKJYRZMIA-UHFFFAOYSA-M Synonym: thallium iii iodide, thallium iodide tli2, thallium iodide ous, thallium i iodide, anhydrous, ampuled under argon trace metals basis 10g, tli IUPAC Name: λ¹-thallanylium iodide SMILES: [I-].[Tl+]


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