IBDP 2011 Biology Core Topic 3 The Chemistry of Life

ACS(I) Menon 2011

Most Common Elements

Earths Crust % (by mass)
47

Human Body

% (by mass)
63

Oxygen

Hydrogen

Silicon
Aluminium Iron Calcium

28
7.9 4.5 3.5

Oxygen
Carbon Nitrogen Calcium

25.5
9.5 1.4 0.31

Sodium

2.5

Phosphorus

0.22
2

Primordial Soup Theory

Primordial Soup Theory

In 1920, chemist A.I. Oparin and geneticist J.B.S Haldane first

proposed that life began ~ 3.8 billion years ago in a warm pond/ocean. In 1953, chemist Stanley Miller and physicist Harold Urey constructed an apparatus that supposedly re-created those early conditions. They mixed gases thought to be present on primitive Earth: Methane, Ammonia, Water Vapour, Hydrogen Electrically sparked the mixture to signify lightning. Resulted in the production of amino acids, building blocks of proteins.
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Primordial Soup Theory

Is it time to throw out the Primordial Soup Theory?

Problems with the theory: Early atmosphere contained gases different from those used by Miller/Urey Amino acids have to become proteins. How?

New Research Rejects 80-Year Theory of 'Primordial Soup' as the Origin of Life
ScienceDaily (Feb. 3, 2010) For 80 years it has been accepted that early life began in a 'primordial soup' of organic molecules before evolving out of the oceans millions of years later. Today the 'soup' theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth's chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.

Most Common Elements

Earths Crust % (by mass)
47

Human Body

% (by mass)
63

Oxygen

Hydrogen

Silicon
Aluminium Iron Calcium

28
7.9 4.5 3.5

Oxygen
Carbon Nitrogen Calcium

25.5
9.5 1.4 0.31

Sodium

2.5

Phosphorus

0.22
8

IBDP 2011 Biology Core Topic 3: The Chemistry Of Life

3.1 Chemical elements and water 3.2 Carbohydrates, lipids and proteins 3.3 DNA structure 3.4 DNA replication 3.5 Transcription and translation 3.6 Enzymes 3.7 Cell respiration 3.8 Photosynthesis
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Most Common Elements

Earths Crust % (by mass)
47

Human Body

% (by mass)
63

Oxygen

Hydrogen

Silicon
Aluminium Iron Calcium

28
7.9 4.5 3.5

Oxygen
Carbon Nitrogen Calcium

25.5
9.5 1.4 0.31

Sodium

2.5

Phosphorus

0.22
10

3.2.1 Distinguish between organic and inorganic compounds

Organic compounds
Compounds derived from living things Carbon is uncommon in earths crust but most abundant element

by dry weight in living things

Compounds of carbon; often also contains hydrogen Exceptions CO2, hydrogen carbonates (CO2 dissolved in water),

mineral salts eg calcium carbonate are NOT organic

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Carbon compounds
Carbon forms 4 strong covalent bonds
Can bond with each other to form extended chains straight or

branched chains, or rings

Can bond with other atoms, such as O2, H2, N2 and S (sulphur) Carbon compounds may be unsaturated ie. contain double or triple

bonds

cysteine

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Carbon compounds: Macromolecules

Can form macromolecules (polymers) from

smaller building blocks called monomers

Monomer Polymer Supra Molecular Structure Cellulose cell wall Protein Complex Chromosome Cell membranes

Monosaccharides Polysaccharides Amino acids Nucleotides Fatty acids Polypeptides Nucleic acid Fats

Carbon compounds: Macromolecules

Polysaccharides : polymers of monosaccharides

Polypeptides: polymers of amino acids

Carbon compounds: Macromolecules

Nucleic acids : polymers of nucleotides

Carbon compounds
Theory diversity of organic compounds made possible the diversity of life

IBDP 2011 Biology Core Topic 3: The Chemistry Of Life

3.1 Chemical elements and water 3.2 Carbohydrates, lipids and proteins 3.3 DNA structure 3.4 DNA replication 3.5 Transcription and translation 3.6 Enzymes 3.7 Cell respiration 3.8 Photosynthesis
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3.2 Carbohydrates: Learning Objectives

1. Identify glucose and ribose from diagrams showing their structure.

2. List three examples each of monosaccharides, disaccharides and polysaccharides.

3. State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants. 4. Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides

and polysaccharides.

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3.2.2. List three examples each of monosaccharides, disaccharides and polysaccharides.

Carbohydrates
General formula: Cx(H2O)y
H:O generally 2:1

Monosaccharide (singe sugars)

(eg. glucose, galactose, fructose) Disaccharide (double sugars) (eg. maltose, lactose and sucrose) Polysaccharide (Complex sugars) (eg. starch, glycogen, cellulose)
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Monosaccharides
Cannot be broken down into smaller units General formula: Cx(H2O)y where x=y Have a maximum of 6-carbon atoms, ie. x=y=6

eg. Glucose, fructose C6H1206 Sweet & water soluble molecules

3-carbon : triose sugar 4-carbon : tetrose sugar 5-carbon : pentose sugar 6-carbon : hexose sugar
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Triose: eg. Glyceraldehyde

Pentose: eg. Ribose

Hexose: eg. Glucose

When C in carbonyl group (C=O) is at the very end of the chain it becomes an aldehyde group (H- C=O) and the monosaccharide is I called an aldose. C eg. Aldotriose, aldopentose, aldohexose

Hexose: eg. Fructose (Ketohexose)

When C in carbonyl group (C=O) is at the second position of the C I chain and it becomes a ketone group (C=O) and the I monosaccharide is called a ketose. C

Cyclic Structures: Anomers

In general, alcohols can attack the C=O group in sugars to form hemiacetals Since sugars have OH groups, they can form hemiacetals by an intramolecular reaction, forming closed rings Hexoses and pentoses are able to form closed rings

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Under physiological conditions, glucose exists in a cyclic hemiacetal form where the C-5 hydroxyl reacts with the C-1 aldehyde group The 2 isomers that are formed are called anomers since they only differ in the location of the OH on the acetal carbon, C-1. ie. and forms of D-glucose are anomers of D-glucose 25

Animation: Cyclization of Glucose into Anomers

3.2.1 Identify glucose from diagrams showing its structure

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Note:

Ring consists of 5 carbon atoms and an oxygen atom

Structure of Glucose
Molecular formula: C6H12O6 An aldohexose Common names: Dextrose, blood sugar Structure of the molecule cannot be determined from

molecular formula (due to existence of isomers, anomers)

Each carbon arranges it four bonds into a tetrahedon, so

the molecule is not flat

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3.2.3 State one function of glucose & lactose in animals, and of fructose & sucrose in plants.

Some Functions of Glucose

Especially important in energy production and formation of macromolecules in cells

During photosynthesis, light energy is trapped and stored as chemical energy in the form of glucose
All cells use glucose as substrate in respiration, producing chemical energy ATP Building block for many larger molecules eg. Monomer for glycogen, starch, cellulose

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Glucose & Diabetes

Glucose & Diabetes

Video: Type 1 and Type 2 Diabetes

Reducing Sugars
The aldehyde groups of aldoses and ketone group of fructose are oxidized by Benedicts reagent, an alkaline copper(II) solution The clear blue color of the reagent fades as it is replaced by a red-orange precipitate when Cu2+ is reduced to Cu+

Test can measure glucose in urine

All monosaccharides and disaccharides except sucrose are reducing sugars

C H C OH +2 Cu2+ CH2OH

C H C OH CH2OH

+ Cu2O (red-orange)
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Other Monosaccharides
Fructose (ketohexose) Galactose (aldohexose)

Ribose and Deoxyribose (aldopentoses)

- components of nucleic acids RNA, DNA respectively

Trioses (early products of photosynthesis)
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Fructose
Fructose is also called
Levulose Fruit sugar

Found in large amounts in

Honey Corn syrup Fruits

The sweetest of all sugars Ketohexose An intermediate of glucose metabolism during respiration

CH2OH CO 3 HO 4C H H 5C OH H 6C OH CH2OH
2

CH2OH CH OH O 2 OH H OHH CH2OH OH O CH2OH H OHH

D-fructose

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Relative sweetness of sugars and sweeteners

Galactose
Galactose is the principal sugar found in mammalian milk Aldohexose -D-galactosamine is a component of the blood group antigens

CHO 2 NH2 H C OH 3 HO 4C H HO C H 5 H C OH 6 CH2OH

CH2OH HO O OH H H OH H H OH H NH2 H OH -D-galactose -D-galactosamine

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Ribose
Aldopentose Exists mainly in the cyclic form Component of ribonucleic acid (RNA).

1 2 3 4 5

1 -D ribose

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Deoxyribose
Aldopentose Exists mainly in the cyclic form Component of deoxyribonucleic acid (DNA).

1 2 3 4 5 H

1 -D deoxyribose

2 H

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Structure of DNA and RNA

DNA : Polymer of deoxyribonucleotides

Disaccharides
Consists of 2 molecules of monosaccharides joined together General formula Cx(H2O)y

Maltose: glucose + glucose

Sucrose: glucose + fructose

Lactose: glucose + galactose

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3.2.4 Outline the role of condensation and hydrolysis in the relationships between monosaccharides and disaccharides.

Formation of Disaccharides
2 monosaccharides
Condensation

disaccharide
Hydrolysis

HO

OH

HO

OH

H2O

H2O

HO

OH

Glycosidic bond
Definition: A condensation reaction is a chemical reaction in which two simple molecules are joined together to form a larger molecule with the removal of one molecule of water.
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Formation of Maltose
Maltose is formed by joining -D-glucose to -D-glucose to give an 1,4-glycoside Also known as malt sugar Formed as an intermediate of starch hydrolysis Source: Germinating grains
6 5 4 3 D1 6 5

4
3 D2

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Lactose
Lactose is formed by joining -D-galactose to -D-glucose to give a

-1,4-glycoside Also known as milk sugar Principle source of energy in the diet of young mammals Must be hydrolyzed to glucose and galactose for use as an energy source Lactose intolerance results from lack of lactase to hydrolyze the glycosidic link of lactose

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Lactose Intolerance
Inability to digest lactose Caused by a deficiency of the enzyme lactase, produced by the cells lining the small intestine. Primary lactase deficiency develops over time and begins after about age 2 when the body begins to produce less lactase. Most children who have lactase deficiency do not experience symptoms of lactose intolerance until late adolescence or adulthood. A possible genetic link to primary lactase deficiency. Some people inherit a gene from their parents that makes it likely they will develop primary lactase deficiency. Some racial/ethnic populations are more affected than others

Global Distribution of Lactose Intolerance

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Sucrose
Sucrose is formed by linking -D-glucose with -Dfructose to give a 1,2 glycosidic linkage Sucrose if NOT a reducing sugar because the aldehyde and ketone groups in its component monosaccharides have been lost in the formation of the glycosidic bond
6 5 4 3 D1 1 2

5 3 4
6

D-

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Sucrose
Plants can synthesize sucrose. Animals cannot.

Sucrose is Water soluble Easily transported in plant circulatory system

Sucrose called: Table sugar Cane sugar Beet sugar

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3.2 Carbohydrates: What we have learnt today

1. Identify glucose and ribose from diagrams showing their structure.

2. List three examples each of monosaccharides, disaccharides and polysaccharides.

3. State one function of glucose & lactose in animals, and

of fructose & sucrose in plants.

4. Outline the role of condensation and hydrolysis in the relationships between monosaccharides &

disaccharides.
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Test yourself!
1. Why does cyclization of D-glucose give 2 isomers

called anomers, - and - D- glucose?

2. What is the difference between Type 1 and Type 2 diabetes?

3. What is the major difference between lactose intolerance and galactosemia?

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Polysaccharides
Polymer of monosaccharides
Built by many monosaccharide units condensed together, all linked by glycosidic bonds

Condensing process = polymerisation

Can be divided into 2 groups A. Storage polysaccharides 1. Starch 2. Glycogen B. Structural polysaccharides 1. Cellulose 2. Chitin
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Starch
Energy storage in plants A mixture of amylose & amylopectin Amylose is a linear polymer of hundreds of glucose units, with all the residues linked together by (1-4) bonds

Amylopectin is a highly branched chain polymer of several thousand glucose units, with (1-6) linkages creating branches along the chain of (1-4) linkages
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56

 Before starch can enter (or leave) cells, it must be digested

The hydrolysis of starch is done by amylases.

With the aid of an amylase, water molecules enter at the (1-4) linkages, breaking the chain & eventually producing a mixture of glucose & maltose A debranching enzyme is needed to break the (1-6) bonds of amylopectin

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Glycogen
Energy storage polysaccharides in animals Also made by fungi

58

 Animals store excess glucose by polymerizing it to form glycogen The structure of glycogen is similar to that of amylopectin, although

the branches in glycogen tend to be shorter & more frequent

Glycogen is broken back down into glucose when energy is needed (a

process called glycogenolysis)

Glucose units are released by the enzyme glycogen phosphorylase to produce glucose-1-phosphate, which is then used to generate energy

59

Starch & glycogen good storage substances. Why?

Hydroxyl (OH) groups project into the interior of helix

1. Insoluble in water - Does not affect water potential of cells - Large amounts can be stored without gain of water 2. Can be compacted - Branched structure allows for extensive coiling & entangling - > carbohydrate stored per unit volume
3. Easily hydrolysed - No cross-linkages between chains - Easily broken down into monosaccharides
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STARCH

Cellulose
Structural polysaccharides in plants Like starch, cellulose is a polysaccharide made from

glucose monomers However, cellulose differs profoundly from starch in its properties The glucose units are linked by (1-4) glycosidic linkages, which cannot be digested by mammalian enzymes

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 Because the glycosidic bonds are (1-4), the rings of

glucose are arranged in a flip-flop manner This produces a long, straight, rigid molecule There are no branches in cellulose as there are in starch The absence of side chain allows these linear molecules to lie close together Because of the many OH groups, as well as the oxygen atom in the ring, there are many opportunities for hydrogen bonds to form between adjacent chains The result is a series of stiff, elongated fibrils the perfect material for building the cell walls of plants
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Parallel arrangement of unbranched cellulose molecules

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Functions of Cellulose

Spaces in cellulose

Adds strength to cell walls - macrofibrils arranged in layers - 90o orientation - glue-like matrix (pectin) Prevents cells from bursting Helps determine shape of cells Enable development of turgidity Has gaps between chains & layers - channels for water - can be filled with lignin for extra tensile strength (eg. 65 xylem vessels)

Since both starch and cellulose are made of glucose units joined together, why then only starch can be digested in our bodies but not cellulose?
CELLULOSE

STARCH

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Test Yourself!
1. What is the difference between a condensation and a hydrolysis reaction? Give an example of each. 2. What are the key features of biological macromolecules? 3. What is the significance of hydrogen bonds in fibres of cellulose?
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3.2 Carbohydrates:Learning objectives

1. Distinguish between organic and inorganic compounds 2. Identify glucose and ribose from diagrams showing their structure 3. List three examples each of monosaccharides, disaccharides and polysaccharides 4. State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants 5. Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides and polysaccharides
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Further Reading
Biology Clegg Biology Concepts and Connections

Campbell Advanced Biology Principles and Applications Clegg with Mackean Biological Science Green Stout Taylor

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THE END!

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