Cytology I: the Chemicals of Life

S.6 Bio notes 09-10 Cytology I -Chem of Life P.1

Cytology I: The Chemicals of Life

Cells, tissues and organs are composed of chemicals. The study of chemical compounds found in living systems, and the reactions in which they take part, is known as bio______. Studies on the structure and behaviour of individual molecules constitute mole______biology.

Chemical compounds are conventionally divided into two groups: organic and inorganic. In 1828 the organic compound u____ was synthesized in the laboratory. Until then it was believed that organic compounds could only be formed in living organisms.

S.6 Bio notes 09-10 Cytology I -Chem of Life P.1

The principal organic compounds found in organisms are carbohydrates, fats, proteins and nucleic acids. Of the inorganic constituents, minerals and water are among the most important.

We shall see that the fun____ of a particular compound in the cell is often related to its str______.

Percentage of body mass
Substance / Woman / Man
Water / 57 / 64
Fat / 23 / 15
Protein / 16 / 17
Carbohydrate / 2 / 2
Other organic sub. / I / I
Inorganic sub. / I / I

S.6 Bio notes 09-10 Cytology I -Chem of Life P.1

1)Inorganic Components

a)Water and its Biological Significance

Water is by far the most ab______ component of organisms. Most human cells are approximately 80% water. Life probably orig______in water. Water provides the m______ in which all biochemical reactions take place, and it has played a key role in influencing the evol______of living things on land and in aquatic env______.

The importance of water as a medium for life springs from five of its properties: its sol_____ properties, h_____ capacity, s______tension, fr______properties and its activities as an rea____.

Solvent properties

Water is an excellent solvent for p_____ substances. These include i_____ substances like salts, and some non-ionic substances like sugars and simple alcohols which contain ch_____ (polar) groups.

Once a substance is in solution its molecules or ions can move about fr_____, thus making it more chemically reactive than if it were solid. Thus the majority of the cell's ch______reactions take place in aqueous solutions.

Non-polar substances, such as lipids, are immiscible with water and can serve to separate aqueous solutions into comp______(with membrane structures), thus allowing meta____ reactions to take place without affecting one another.

Water's solvent properties also mean that it acts as a tr______medium, as in the blood, lymphatic and excretory systems, the alimentary canal and in xylem and phloem.

High heat capacity

Water has a high heat c______. This is because much of the energy is used in breaking the h______bonds. Temperature changes within water are min______. Biochemical processes proceed at more con____ rates and are less likely to be inhibited by extremes of temperature. Water also provides a very constant external env______for many cells and aqua___ organisms.

High heat of vaporisation

As a result of the hydrogen bonding, water has an unusually high b______point. There is also a c______effect when water molecules vaporise. This is made use of in s______and panting of mammals, the opening of the mouth of some reptiles in sunshine, and may be important in cooling tran______ leaves. The high heat of vaporisation means that a large amount of heat can be lost with minimal l___ of water from the body.

High heat of fusion

Liquid water must lose a relatively large amount of heat energy to freeze. Contents of cells and their environments are therefore less likely to fr______. Ice cry____ are particularly damaging if they develop inside cells. WHY?

Density and freezing properties

The density of water decreases below 4°C and ice therefore tends to fl____ It is the only substance whose solid form is less dense than its liquid form. Since ice floats, it forms at the s______firstand the bottom last. Ice ins_____ the water below it, thus increasing the chances of survival of organisms in the water. This is important in cold climates and cold seasons, and must have been particularly so in the past, such as during I___ Ages.

The fact that water below 4°C tends to rise also helps to maintain cir______in large bodies of water. This may result in nu______cycling and colonisation of living things to water to greater depths.

High surface tension and cohesion

Co______ is the force whereby individual molecules stick together. Water has a higher surface tension than any other liquid. The high cohesion of water molecules is important in mo______of water through xylem. Many small organisms rely on surface tension to settle on water or to skate over its surface.

Water as a reagent

Water is biologically significant as an essential meta_____ ; it participates in the chemical reactions of metabolism. In particular, it is used as a source of hydrogen in photo______and is used in hydroly____ reactions.

Water and evolutionary change

Its shortage appears to have been a major sel______pressure in the development of species. All terrestrial organisms are adapted to obtain and cons____ water, and the extreme ad______of xerophytes, desert animals and so on, provide some fascinating examples of biological design.

Give some of the biologically important functions of water :

All organisms

Plants
Animals

b)Minerals and their General Functions

Q.What are the possible benefits of isotonic drinks?

• As constituents of large organic molecules. Proteins contain n______and often sul____ as well. Enzymes, which are nearly always proteins, often contain m_____ ions such as copper, iron or zinc which function as act_____. Phospholipids, as their name suggests, contain p______. Nucleic acids contain phosphorus and nitrogen.

• As constituents of smaller molecules. Adenosine triphosphate (ATP) contains phosphorus. Phosphorus is also often required for the activation of small organic molecules. For instance, glucose is phosphorylated (has phos_____ added to it) before it is broken down in respiration. The hormone thyroxine contains i______.

• As constituents of certain pigments. The two best-known biological pigments are haemoglobin and chlorophyll, which contain i____ and mag______respectively. I_____ is also found in the cytochromes, a group of pigments of great importance in energy transfer.

• As constituents of structures. Cal____ and ph______are found in bones. Calcium is found in plant c___ walls.

• As determinants of the anion-cation balance in cells. Sodium, potassium and chloride ions are particularly important in this regard, especially in nerves, muscles and sensory cells where they are involved in the transmission of im______.

• As determinants of water potential. Mineral salts, together with other solutes, determine the water p______.

2)Organic COMPONENTS and Macromolecules

A macromolecule is a g______molecule made from many repeating units; it is therefore a poly___. There are three types of macromolecule, namely polysaccharides, proteins and nucleic acids. Macromolecules account for over 90% of the dry mass of cells.

Nucleic acids and proteins can be regarded as 'in______' molecules. This means that the seq______of subunits is important in proteins and nucleic acids. Lipids, although generally much smaller molecules and are not polymers (average Mr 750-2,500), are included since they generally associate with each other into much larger groups of molecules.

A)Carbohydrates (saccharides)

Carbohydrates are substances with the general formula Cx (H2O)y. All carbohydrates are ald______or ket_____ and all contain several hy______(-OH) groups. Aldehydes are very easily oxidised and hence are powerful r______agents. Carbohydrates are divided into mono-, di- and polysaccharides.

a)Monosaccharides

Monosaccharides are single sugar units. They are classified according to the number of carbon atoms as trioses (3C), tetroses (4C), pentoses (5C), hexoses (6C) and heptoses (7C). Monosaccharides are important as e______sources and as b______blocks for the synthesis of larger molecules.

Aldoses and ketoses (Reference)
In monosaccharides, all the carbon atoms except one have a hydroxyl group attached. The remaining carbon atom is either part of an aldehyde group, in which case the monosaccharide is called an aldose or aldo sugar, or is part of a keto group, when it is called a ketose or keto sugar. The two simplest monosaccharides are the trioses glyceraldehyde and dihydroxyacetone.

Chief functions of Monosaccharides

Monosaccharide / Example / Functions
Trioses C3H6O3 / glyceraldehyde / Intermediates in resp______, and photo______
Pentoses C5H10O5 / ribose, ribulose / Synthesis of nu_____ acids; ribose is a constituent of RNA, deoxyribose of DNA, Synthesis of some coenzymes, e.g. NAD, NADP, coenzyme A, FAD, Synthesis of AMP, ADP, and ATP
Ribulose bisphosphate is the CO2 acceptor in photosynthesis
Hexoses C6H12O6 / glucose, fructose, galactose / Source of energy when oxidised in respiration; synthesis of disaccharides and polysaccharides

Derivatives of Monosaccharides

Chemical changes involved / Derivatives / Examples and Functions
Sugar reduction / sugar alcohols / glycerol, used in lipid synthesis.
Sugar oxidation / sugar acids / Vitamin C (ascorbic acid) is a sugar acid derived from a hexose.
Sugar acids are important intermediates in carbohydrate metabolism
Removal of O / deoxy sugars / deoxyribose, formed by removal of oxygenfrom ribose, and used in DNA synthesis.
Add NH2 / amino sugars / glucosamine, used in synthesis of chitin and joint catilage
Optical isomers (Reference)
If two different compounds have the same molecular formula, they are said to be isomers of each other. Two types of isomerism occur, structural and stereoisomerism. Structural isomerism is due to different link___ of the atoms or groups within the molecules. Thus all hexoses C6H12O6are structural isomers of each other (glucose, mannose, galactose and fructose).
Stereoisomerism occurs when the same atoms or groups are joined together but are arranged differently in spa___.
Certain solid compounds when in solution (and certain liquid compounds) possess the power torotate the plane of vibration of plane-polarised light, and aresaid to be op______active. If the substance rotates the plane of polarisation to the right, it is said to be dextro-rotatory and if to the left laevo-rotatory. Dextro-rotatory compounds are given the prefix 'd'- or more recently (+) and laevo-rotatory compounds 'l'- or more recently (-)
Optical isomerism is a property of any compound which can exist in two forms whose structures are mirror images. Like right- and left-handed gloves, such structures cannot be superimposed on each other. In organic compounds this occurs when a carbon atom has four different atoms or groups attached to it. Such a carbon atom is called an asymmetric carbon atom. The tetrahedral arrangement of bonds about the central, asymmetric carbon atom means that there are two possible arrangements of the groups in space, forming two mirror images.

All naturally occurringmonosaccharides are virtually D-isomers. Although D- and L-isomers of the same substance have the same chemical and physical properties, theirthree-dimensional differences have biologicalsignificance in one important respect, namely that enzymes, which depend on recognition by sh____, can distinguish between the mirror images. It is possible that early in evolution an arbitrary bias to accept the D-isomers of sugars was established since their L-isomers are rare in nature. Naturally occurring amino acids in proteins, however, are all L-isomers.

Ring structures, -and -isomers

Pentoses and hexoses can exist in r____ forms in addition to straight chain molecules. The ring structures of pentoses and hexoses are the usual forms, with only a small proportion of the molecules existing in the 'open chain' form at any one time. The ring structure is the form incorporated into disaccharides and polysaccharides.

S.6 Bio notes 09-10 Cytology I -Chem of Life P.1

The ring structures results in 2 more isomers. Carbon One has a hydroxyl group (-OH) attached to it. This may be below the plane of the ring (-isomer), or above the plane of the ring (-isomer). The existence of -& -isomers is important in the formation of st______and cell______.

S.6 Bio notes 09-10 Cytology I -Chem of Life P.1

b) Disaccharides

They are formed by condensation reactions between two monosaccharides. The bond formed between two monosaccharides is called a glycosidic bond and it normally forms between carbon atoms 1 and 4 of neighbouring units (a 1-4 gly______bond). The most common disaccharides are maltose, lactose and sucrose:

glucose + glucose = maltose, glucose + galactose = lactose, glucose + fructose = sucrose.

Reducing sugars

All mono______and most di______, including maltose and lactose, are reducing sugars. Suc____ is non-reducing. Non-reducing sugars are non-reducing because their aldo and keto groups are not available since they are linked together in the glycosidic bond. Two common tests for reducing sugars, Benedict's test and Fehling's test, both contain copper(II) sulphate (CuSO4) which can be reduced to insoluble copper(I) oxide (Cu2O) ----therefore the observation : b___ solution to b_____-r____ precipitate)

c)Polysaccharides

The process of linking together monosaccharides can be repeated indefinitely to build up the gi___ molecules of polysaccharides. Polysaccharides function chiefly as food and e______stores (e.g. starch and glycogen) and as stru______materials (e.g. cellulose). They are convenient storage molecules for several reasons: their large size makes them more or less insoluble in water, so they exert no os______or chemical influence in the cell; the solid form can be folded into compact shapes thus taking up less sp_____ and they are easily converted to sugars by hy______ when required.

i)Starch

Starch is a polymer of-glucose(-glycosidic linkage). It is a major fuel storage in plants, but is absent from animals where the equivalent is glycogen. Starch may have straight chain or branched structure consisting of several thousand glucose residues. Branches if present are formed by 1-6 glycosidic bonds.

The chain coils helically into a compact shape. H-bonds point inwards within the coil. (intramolecular). There is little inter______force and so starch is brittle.

Starch molecules accumulate to form starch gr______. These are visible in many plant cells, notably in the chloroplasts of leaves, in storage organs such as the potato tuber, and in seeds of cereals.

S.6 Bio notes 09-10 Cytology I -Chem of Life P.1

ii)Glycogen

Glycogen is theanimal equivalent of starch, being a storage polysaccharide made from glucose; many fu_____ also store it. It is very similar in structure to starch, but shows more branching.

iii)Cellulose

Cellulose is a polymer of -glucose. It is the most abundant organic molecule on Earth. Its abundance is a result of its being a structural component of all plant c___ walls, constituting about 20-40% of the wall on average.

It consists of long chains of glucose residues(-glycosidic linkage) with ~ 10,000 sugars per chain.

Hydroxyl groups (-OH) project outwards from each chain in all directions and form hy______b____ with neighbouring chains, thus establishing a rigid cross-lin____ between chains.

The chains associate in groups to form micro_____ -- which have tremendous tensile strength.

Microfibrils are arranged in layers in a cementing matrix of other polymers e.g. lignin, pectic substances.

Despite their combined strength, the layers are fully perm_____ to water and solutes.

Apart from being a structural compound, cellulose is an important f____ source for herbivorous animals, bacteria and fungi. The enzyme cell_____, which catalyses the digestion of cellulose to glucose, is relatively rare in nature and most animals, including Man, cannot utilise cellulose despite its being an abundant and potentially valuable source of glucose. Herbivorous mammals like cattle and rats, however, have micro______living sym______ in their guts which digest cellulose.

B) Lipids

Lipids are sometimes classified loosely as those water-in______organic substances which can be extracted from cells by org_____ solvents such as ether, chloroform and benzene. They cannot be defined precisely because their chemistry is so variable, but we could say that true lipids are esters of fatty acids and an alcohol.

Fatty acids

They have the general formula R.COOH where R is hydrogen or an alkyl group. R usually has many carbon atoms in lipids. Most fatty acids have an even number of carbon atoms between 14 and 22.

The long chain of C and H atoms forming a h____c_____ tail. Many of the properties of lipids are determined by these tails, including their insolubility in water. The tails are hydro______.

Fatty acids sometimes contain one or more doublebonds –un______. Fatty acids and lipids lacking double bonds are said to be saturated. Unsaturated fatty acids melt at much l____ temperatures than saturated fatty acids.

Q.Cells of poikilothermic animals usually have a higher proportion of unsaturated fatty acids than homeothermic animals. Can you account for this?

Formation of a lipid

G1ycerol has three hydroxyl (OH)groups, all of which can condense with a fatty acid to form an ester, and the lipid formed is therefore called a tri______.

Triglycerides are classified as fats or oils, according to whether they are solid (fats) or liquid (oils) at 20º C. The higher the proportion of unsaturated fatty acids, the ______their melting points.Triglycerides are non-p____ and therefore relatively insoluble in water.

A major function of lipids is to act as e_____ stores. They have a higher calorific value than carbohydrates, this is because lipids have a higher proportion of hy______ and an almost insignificant proportion of oxygen compared with carbohydrates.

Animals store extra fat when hib______, and fat is also found below the dermis of the skin of vertebrates where it serves as an in______. Plants usually store oils rather than fats. Seeds, fruits and chloroplasts are often rich in oils. When fats are oxidised, water is a product. This meta_____ water can be very useful to some desert animals.

Q.A camel stores fat in the hump as a water source as well as an energy source. By what metabolic process would water be made available from fat?

Carbohydrate could also be used as a water source in the same process. What advantage does fat have over carbohydrate?

Waxes

Waxes are esters of fatty acids with long-chain alcohols.

Phospholipids

Phospholipids are lipids containing a ph_____group. They are formed when one of the alcohol groups of glycerol forms an ester with phosphoric acid instead of a fatty acid. The molecule consists of a p______head with two h______tails (the fatty acids).

Steroids

S.6 Bio notes 09-10 Cytology I -Chem of Life P.1

Steroids do not contain fatty acids. They are derived from hydrocarbon building blocks. All steroids contain a nucleus composed of 17 carbon atoms. /

In Man, the steroid present in largest amounts is chol______, a key intermediate in the synthesis of