IBDP Biology - Biological Molecules

In this IBDP Biology topic, you can learn different biological molecules.

• Monomer – single molecule, e.g. monosaccharide (glucose), amino acids and nucleotides.
• Polymer – long, complex chain of repeating monomers chemically joined together by covalent bonds, e.g. polysaccharides (carbohydrate polymers).

• Condensation reactions join monomers together to make polymers. A water molecule is released for every chemical bond made.
• Hydrolysis reactions use water to break down polymers and release individual

• Carbohydrates are made from monosaccharide and are substances used as energy and structural materials.
• All carbohydrates contain: carbon, hydrogen and oxygen.

There are three main groups of carbohydrates:

• Monosaccharide – simple sugars, e.g. glucose, fructose and galactose
• Disaccharides – “double sugars” formed from two monosaccharides, e.g. maltose, sucrose and lactose
• Polysaccharides – large molecules formed from many monosaccharides, e.g. cellulose, starch and glycogen

Glucose

• Hexose sugar (has six carbon atoms)
• Major energy source for most cells
• Highly soluble
• Transported around the body

• Two common isomers of glucose are alpha glucose and beta glucose.
• They have the same chemical formula, however the atoms are arranged differently. On C1 the OH and the H group have swapped over in the beta glucose molecule.

Maltose

Join together by a glycosidic bond – a glycosidic bond is a bond between two sugars that involves oxygen.

Formation of disaccharides:

1. Maltose: Two Alpha-Glucose molecules
2. Sucrose: Glucose and Fructose
3. Lactose: Glucose and Galactose

Starch

• Storage molecule
• A mixture of two polysaccharides of alpha glucose: amylose and amylopectin

Amylose

• 1-4 glycosidic bonds
• Unbranched chains
• Coiled/helical structure
• It is compact – more stored (fit more in)

Amylopectin

• 1-4 + 1-6 glycosidic bonds
• Highly branched chains – so they can be broken down more easily by the enzymes and glucose can be released quickly.

Plants store excess glucose as starch. When a plant needs more glucose for energy, it breaks down starch to release the glucose.

• In animal cells –excess glucose is not stored as starch but as glycogen.
• Glycogen has a similar structure to amylopectin, containing many alpha 1-6 glycosidic bonds that produce even more branched structures; so glucose can be released quickly and it is very compact (good for storage).
• This is due to the fact that there is a higher metabolic rate in animals than in plants – so animals have a greater energy demand. So, being more highly branched means that it can be hydrolysed even more rapidly.
• It is stored as granules, particularly in the muscles and liver.

• Cellulose is the main part of plant cell walls.
• It is very strong and prevents cells from bursting (due to osmotic pressure).
• Contains long, unbranched chains of beta glucose.
• Every other glucose molecule rotates 180°, so that the hydroxyl (OH) groups on each molecule are adjacent to each other.
• Hydrogen bonding between chains give cellulose molecules great tensile strength and structural support for cells (cell walls).
• Microfibrils are formed when many cellulose molecules are linked together by hydrogen bonds.

• A polymer of nitrogen-containing polysaccharide rendering a tough, protective covering or structural support in certain organisms and makes up the cell walls of fungi and exoskeleton of insects.
• It is made up of chains of the monosaccharide N-acetylglucosamine, which is derived from glucose. The polysaccharide chains are long, unbranched and linked together by weak hydrogen bonds.
• Chitin can be broken down by the enzyme called chitinase, which catalyse hydrolysis reactions. Some organisms are able to make their own chitinases.

Triglycerides are a kind of lipid and are made up of:

• One glycerol molecule
• Three fatty acids

• •Fatty acid molecules have long ‘tails’ made out of hydrocarbons. The tails are hydrophobic (they repel water molecules). These tails make lipids insoluble in water. All fatty acids have the same basic structure, but the hydrocarbon tail varies.

The diagram shows a fatty acid joining to a glycerol molecule. When the ester bond is formed a molecule of water is released per bond made – it’s a condensation reaction.

There are two kinds of fatty acids – saturated and unsaturated.

The difference is in their hydrocarbon tails (R group).

• Saturated fatty acids don’t have any double bonds between their carbon atoms. The fatty acid is ‘saturated’ with hydrogen.
• Unsaturated fatty acids have at least one double bond between carbon atoms, which cause the chain to kink.

• The lipids found in cell membranes aren’t triglycerides – they’re phospholipids.
• Phospholipids are pretty similar to triglycerides except one of the fatty acid molecules is replaced by a phosphate group.
• The phosphate group is hydrophilic (attracts water). The fatty acid tails are hydrophobic (repel water). This is an important feature in cell membranes.

Triglycerides – are mainly used as energy storage molecules. They’re good for this because:

• The long hydrocarbon tails of the fatty acids contain lots of chemical energy – a load of energy is released when they’re broken down. Because of these tails, lipids contain about twice as much energy per gram as carbohydrates.
• They’re insoluble, so they don’t affect the water potential of the cell and cause water to enter the cells by osmosis (which would make them swell). The triglycerides clump together as insoluble droplets in cells, because the fatty acid tails are hydrophobic (water repelling) – the tails face inwards, shielding themselves from water with their glycerol heads.

Phospholipids – make up the bilayer of cell membranes. Cell membranes control what enters and leaves a cell.

• Their heads are hydrophilic and their tails are hydrophobic, so they form a double layer with their heads facing out towards the water on either side.
• The centre of the bilayer is hydrophobic, so water–soluble substances can’t easily pass through it – the membrane acts as a barrier to those substances.

• Made from long chains of amino acids (monomers).
• A dipeptide is formed when two amino acids join together.
• A polypeptide is formed when more than two amino acids join together.
• Proteins are made up of one or more polypeptides.

• Amino acids have the same general structure – a carboxyl group, an amino group, and a carbon-containing variable group.
• They contain the elements: carbon, hydrogen, oxygen and nitrogen.
• All living things share a bank of only 20 amino acids.
• The only difference between them is their variable group.

• Amino acids are linked together by condensation reactions to form polypeptides. A molecule of water is released during the reaction. The bonds formed between amino acids are called peptide bonds.
• The reverse reaction happens during digestion (hydrolysis).

• Biological catalysts – speed up a reaction (by providing an alternative path which is easier and requires less energy), and without being used up.
• Enzymes catalyse metabolic reactions – both at a cellular level (e.g. respiration) and for the organism as a whole (e.g. digestion in mammals).
• Enzymes can affect structures in an organism (e.g. enzymes are involved in the production of collagen, an important protein in the connective tissues of animals) as well as functions (like respiration).
• Enzyme action can be intracellular (within cells), or extracellular (outside cells).
• Enzymes are proteins.

1. Very specific – usually only catalyse one reaction, e.g. maltase only breaks down maltose. This is because only one complementary substrate will fit into the active site.
2. The active site’s shape is determined by the enzyme’s tertiary structure (which is determined by the enzyme’s primary structure). Each different enzyme has a different tertiary structure and so a different shaped active site. If the substrate shape doesn’t match the active site, an enzyme-substrate complex won’t be formed and the reaction won’t be catalysed.
3. If the tertiary structure of the enzyme is altered in any way, the shape of the active site will change. This means the substrate won’t fit into the active site, an enzyme-substrate complex won’t be formed and the enzyme will no longer be able to carry out its function.
4. The tertiary structure of an enzyme may be altered by changes in pH or temperature.
5. The primary structure (amino acid sequence of a protein) is determined by a gene. If  mutation occurs in that gene, it could change the tertiary structure of the enzyme produced.

• Chromosomes are made from DNA
• DNA and RNA are macromolecules (very large molecule)
• They are also polymer, made up of many similar, smaller molecules joined together in a chain
• The smaller molecules are nucleotides
• DNA and RNA are therefore a polynucleotides

DNA and RNA are both types of nucleic acid. They’re found in all living cells and they both carry information.

•DNA (deoxyribonucleic acid) is used to store genetic information – that’s all the instructions an organism needs to grow and develop from a fertilised egg to a fully grown adult.

•RNA (ribonucleic acid) is similar in structure to DNA. One of its main functions is to transfer genetic information from the DNA to the ribosomes. Ribosomes are the body’s ‘protein factories’ – they read the RNA to make polypeptides (proteins) in a process called translation. Ribosomes themselves are made from RNA and proteins.

Two polynucleotide chains of DNA are held together by hydrogen bonds between complementary base pairs:

• Adenine pairs with thymine (A=T) via two hydrogen bonds
• Guanine pairs with cytosine (G=C) via three hydrogen bonds

This means that there are always equal amountsof both pairs in a DNA molecule.

In order for bases to be facing each other and thus able to pair, the two strands must run in opposite directions (i.e. they are anti-parallel). These twist to form a double helix.

Each gene in a molecule of DNA contains:

• A different sequence of bases
• Codes for a particular protein
• Proteins are made in the cytoplasm of a cell, not in the nucleus. Genes cannot leave the nucleus, so a copy of the gene is needed. This copy is able to leave the nucleus to go into the cytoplasm so that proteins can be made by the cell.

• A Water molecule consists of two hydrogen atoms covalently bonded to an oxygen atom.
• Because oxygen is more electronegative than hydrogen, it has a greater pull on the shared electrons.
• This that the oxygen atom is slightly negative (δ-) and can pull the electrons towards itself. The unshared distribution of electrons, means hydrogen becomes slightly positive (δ+).
• Water is therefore called a polar molecule.

• Water is a metabolite in loads of important metabolic reactions, including condensation and hydrolysis reactions.
• Water is a solvent which means some substances dissolve in it. Most metabolic reactions take place in solution (e.g. cytoplasm of eukaryotic and prokaryotic cells).
• Water helps with temperature control because it has a high latent heat of vaporisation and a high specific heat capacity.
• Water molecules are very cohesive (they stick together), which helps water transport in plants as well as transport in other organisms.

ATP is the immediate source of energy in a cell.

• Plants and animal cells release energy from glucose – this process is called respiration.
• A cell can’t get its energy directly from glucose.
• So, in respiration the energy released from glucose is used to make ATP (adenosine triphosphate).
• ATP is made from the nucleotide base adenine, combined with a ribose sugar and three phosphate groups. It’s what's known as a nucleotide derivative. Because it’s a modified form of a nucleotide:

Once made, ATP diffuses to the part of the cell that needs energy.

The energy in ATP is stored in high energy bonds between the phosphate groups. Its release via hydrolysis reactions.

• ATP releases energy in small amounts
• It is broken down in one step (single bond broken between phosphate groups)
• It provides immediate energy (makes energy available rapidly)
• Can phosphorylate other molecules (add phosphate to other molecules) – this makes substances more reactive/lowers the activation energy.
• It can be reformed and made again – i.e. ADP + Pi > ATP

Benedict's test

Non-reducing sugar:

• Add dilute hydrochloric acid to sample and boil for one minute.
• Allow the tube to cool and then neutralize the acid with sodium hydrogen carbonate.
• Carry out Benedict’s test.
• Observe colour change.

Iodine dissolved in potassium iodide solution is added to a sample. A positive result (starch is present), changes the solution from an brown-orange to a blue-black colour.

• Add biuret reagent to a sample.

If protein is present then the solution turns purple.

If there’s no protein, the solution will stay blue.

1. Add a suitable volume of ethanol to the test substance. Then shake the mixture.
2. Next add a equal volume of distilled water. Shake the mixture again.
3. A milky-white emulsion forms if the test substance contains lipids

• The more lipid there is the more noticeable the colour will be.

This is the end of the topic

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Drafted by Eva (Biology)

Photo references:

1. https://sugar.ca/sugar-basics/carbohydrate-and-sugars-terminology
2. http://nnhsbiology.pbworks.com/w/page/109329280/Honors%20Lipids
3. https://www.sciencedirect.com/topics/engineering/triglycerides
4. https://www.nutritionaldoublethink.com/protein-structure.html
5. https://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/26-structure-of-dna-and-rna/dna-structure.html
6. https://www.khanacademy.org/science/high-school-biology/hs-biology-foundations/hs-water-and-life/a/hs-water-and-life-review
7. https://onlinesciencenotes.com/benedicts-test-principle-requirements-procedure-and-result-interpretation/
8. https://www.toppr.com/ask/question/iodine-gives-blue-colour-with/
9. http://biocheminfo.com/2020/04/01/biuret-test/
10. https://socratic.org/questions/what-should-you-use-to-test-if-a-type-of-food-has-starch-sugar-or-fat