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AS Biology Section B – Biological Molecules 1
AS BiologySection B – Biological Molecules
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What are Biological Molecules?What type of molecules are Biological Molecules?
Which elements do you find in Biological Molecules?
The elements join together to make molecules. Each element can make a different number of bonds:
• Carbon – C – 4
• Hydrogen – H – 1
• Oxygen – O – 2
• Nitrogen – N – 3
• Sulphur – S – 4
Using this information draw the following molecules:
CH4 CO2 NH3 H2O
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WaterSyllabus point (i): describe and explain the roles of water in living organisms and as an environment for organisms.
Molecular Structure of Water
H2O
What is a dipole?
What causes the dipole?
What significance does the dipole have in the properties of water?
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Hydrogen bonding
Hydrogen bonds are not ‘real bonds’. They are interactions, or attractive forces. The dipole on the water means that the slightly negative oxygen atoms are attracted to the slightly positive hydrogen atoms.
Hydrogen bonds on their own are extremely weak, but when there are a lot of them together they are strong.
Effects of hydrogen bonding:
Due to the attraction of the dipole, many hydrogen bonds form between water molecules. This large number means that overall strong ‘bonds’ are formed. This means that more energy is required to move water molecules apart and this contributes to many of the properties of water.
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Properties of WaterProperty What this is Why it occurs EffectHigh Specific Heat Capacity
High MP/BP
Anomalous expansion
Universal Solvent
Cohesion
High Surface Tension
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Explain how the structure of water enables it to carry out its functions in living organisms
(8 marks)
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Carbohydrates
The elements found in carbohydrates are:
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In dietary terms carbohydrates are often referred to as complex or simple carbohydrates. The ‘simple’ carbohydrates are generally sugars – they are digested quickly and release a short burst of energy. The ‘complex’ carbohydrates are generally starchy type products like pasta – they are digested more slowly and can result in energy being stored in the body.
However, biochemically we classify carbohydrates differently. We refer to them as:
Monosaccharides Disaccharides Polysaccharides
Mono means one, Di means two, poly means many and saccharide means sugar. Therefore a monosaccharide is literally ‘one sugar’ a disaccharide ‘two sugars’, and polysaccharide ‘many sugars’.
General Formula
All carbohydrates have the following general formula where n is the number of carbon atoms
(CH2O)n
Given this general formula, what would the specific formula be for a:
Triose (3C) sugar
Pentose (5C) sugar
Hexose (6C) sugar
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MonosaccharidesThe monosaccharides that we are most interested in at this juncture are the hexose sugars:
C6H12O6
Although all of these sugars have the same molecular formula they have different structural formulae and are therefore described as isomers of each other:
Fructose Glucose
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In addition to the isometry that results in different molecules, there is isometry within many of the sugars too. For this purpose we will look only at glucose:
Straight chain form Ring form
Naming Carbons
It is often important for us to know exactly which carbon in a molecule is involved in a bond. To do this we number the carbons in a clockwise direction from the Oxygen atom when the molecule is in ring formation. If the molecule is in straight chain formation the carbons are numbered from the top down as you can see above.
Add the carbon numbers to the ring form of gluose shown above.
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There is further isometry within glucose which is to do with the position of the hydroxyl (-OH) group on carbon number one in the ring formation.
An acronym to help you to remember this is ABBA: Alpha Below, Beta Above.
Having an understanding of these different isomers is critical as it impacts on the way that the molecule behaves and particularly on the way that the molecule forms bonds with other molecules.
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Glycosidic BondsThese are strong covalent bonds that form between the functional groups of each monosaccharide unit. Any bond joining monosaccharides together is called a glycosidic bond – they are then more precisely named depending on exactly where the bond has occurred.
Glycosidic bonds are formed by condensation reactions. These occur when a molecule of water is eliminated through the formation of a bond. Conversely glycosidic bonds are broken by hydrolysis reactions. These occur when a molecule or water is replaces through the breaking of a bond:
This diagram shows the formation (and breaking) of an α1-4 glycosidic bond.
α because it is between two α glucose units
1-4 because the bond is formed between carbon 1 on one unit and carbon 4 on the other.
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Draw the formation of an α1-6 glycosidic bond and a β1-4 glycosidic bond:
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DisaccharidesMeaning ‘two sugars’ these are formed when two monosaccharide units are joined together. They exist naturally in living organisms and have important roles. The most common three disaccharides are:
Sucrose: Glucose + Fructose
Maltose: Glucose + Glucose
Lactose: Glucose + Galactose
Each of these disaccharides have unique properties that are different from the properties of the individual monosaccharide units. A lot of the differences are due to the functional groups being involved in the glycosidic bonds. Most specifically this will affect the reducing capabilities of the sugar.
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Homework
1) Review notes on Monosaccharides and bonding. Make additional annotation and construct a glossary of key words from these notes – ensure you are comfortable with the definitions.
2) Complete the following passage by using the most suitable word(s) in each of the blank spaces:Water is essential for life. It makes up a high proportion of the cytoplasm in a cell. Many different compounds can dissolve in it and it is therefore described as an excellent ______. Water remains in the ______ state over a wide range of environmental temperatures.As it cools below 4C it becomes less _____ than warmer water. Ice floats on water, forming a layer that _______ the water beneath with the result that large bodies of water rarely freeze entirely.The ____________ bonds that form between water molecules are responsible for its high _______, which allows small insects such as pond skaters to move on its surface without sinking.
[6]
3) How would you perform a hydrolysis reaction in a laboratory? Why is it not possible to replicate this in cells? What do they use instead?
[3]4) What is a reducing sugar? Use diagrams to illustrate your answer
[3]5) What is the biochemical test for a reducing sugar? Describe the procedure in detail making
sure you explain why the colour change occurs.[6]
6) What is the biochemical test for a non-reducing sugar? Describe the procedure in detail making sure you explain why you have to do each step.
[6]
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PolysaccharidesPolysaccharides are large insoluble molecules made of repeated monosaccharide units. The polysaccharides that we are going to look at are all polymers of glucose. Each polysaccharide has different properties as a result of their structure.
Storage compoundsPolysaccharides that are used as storage compounds need to be: compact, insoluble, able to hydrolyse themselves easily.
Structural compounds
Polysaccharides that are structural compounds need to be: high in tensile strength, tough and flexible.
What features would provide these characteristics?
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STARCH
Starch is the storage compound for glucose in plants. It is made up from two polysaccharides: amylose and amylopectin.
Amylose:
α glucose Joined by 1-4 glycosidic bonds Unbranched Several thousand glucose units Helical in structure
Amylopectin:
α glucose Main chain joined by 1-4 glycosidic bonds Branches every 24-30 glucose units The branches are joined by 1-6 bonds
Starch is made of a mixture of amylose and amylopectin. The ratio of the two varies in different types of starch.
Chemical tests for starch:
The test for starch is iodine. In the presence of starch iodine will go from brown to blue-black.
WHY does Iodine change colour?
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Glycogen
Glycogen is the storage compound in animals. It is structurally very similar to amylopectin:
α glucose Main chain joined by 1-4 glycosidic bonds Branches every 8-12 glucose units The branches are joined by 1-6 bonds
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Cellulose
This is a structural polymer that is found in the cell walls of plants. It has to have structural integrity as this provides the skeleton for the plant.
β glucose 1-4 glycosidic bonds Every other unit is inverted 180C This makes long chains with many hydrogen bonds in between them. This means that the
fibres form tendrils.
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Tasks
1) Make a poster to show the key points of each of the polysaccharides, comparing and contrasting how the structure relates to the function.
2) Write an essay (at least 2-3 sides) to answer the question:
Describe and explain how the molecular structure of polysaccharides relates to their functions. Use examples to illustrate your answer.
3) Use the text book, the syllabus and the notes you have from class to make your own summary notes on water and carbohydrates. These should include:
a. Key wordsb. Structuresc. Functionsd. How structure relates to functione. Biochemical testsf. Diagrams
You should cross reference your notes with the relevant syllabus statement.
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Carbohydrates Questions
1) What is the general formula for a carbohydrate?2) What is the formula for a) a triose and b) a pentose?3) Draw α and β glucose.4) What role do monosaccharides have in living organisms?5) What is the name of the type of bond which joins monosaccharides together?6) What is the name of the type of reaction?7) Draw out the formation of maltose.8) What is the difference between a reducing and a non-reducing sugar?9) How can you test for these biochemically?10) Describe in detail the structure of starch.11) Describe in detail the structure of glycogen.12) Describe in detail the structure of cellulose.13) How does the structure of cellulose enable it to form long, strong, fibres?14) The table below shows statements about 4 carbohydrates. Put a if the statement is true
and a if the statement is false:
Sucrose Maltose Glycogen CelluloseOnly glucose molecules joined togetherA branched chainSoluble in water
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Protein StructureStructure of Amino Acids:
Features of Amino Acids:
How do Amino Acids join together?
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What is the name of the class of enzyme that catalyses this reaction?
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Protein Structure
Primary Structure:
What is it?
What bonds are involved?
How does this contribute to the overall structure of the protein?
What would be the effect of changing the primary structure on the overall shape and function of the protein?
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Secondary Structure:
What is it? Draw diagrams
What are the differences between the α-helices and the β-pleated sheets?
What bonds are involved?
How does the secondary structure contribute to the overall structure and therefore function of the protein?
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Tertiary Structure:
What is it?
What bonds are involved?
How does the tertiary structure contribute to the overall structure and therefore function of the protein?
What impact does changing the primary structure have on the tertiary structure and why?
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Quarternary Structure:
What is it?
What bonds are involved?
Compare and contrast how the structure of collagen and haemoglobin contribute to their function.
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1. Explain what is meant by the primary and secondary structure of a protein.
primary structure
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secondary structure
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2. The diagram below represents part of a collagen molecule.
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(i) Collagen is a protein made of three chains of amino acids, twisted together like a rope. State the name given to a chain of amino acids.
.........................................................................................................................[1]
(ii) Name the amino acid that forms a high proportion of the collagen molecule.
.........................................................................................................................[1]
(iii) Collagen has tremendous strength, having about one quarter of the tensile strength of mild steel.Using information given in the diagram to help you, explain how the structure of collagen contributes to its strength.
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[Total 4 marks]
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Haemoglobin and Collagen
Fibrous and Globular Proteins
Proteins can be put into two broad categories that reflect their structure and function:Fibrous protein: a protein with a relatively long, thin, structure, which is insoluble in water and metabolically inactive, often having a structural role within the organism.Globular protein: a protein with a relatively spherical molecule, soluble in water, often having metabolic roles in organisms.
Collagen
Structure:• Made up from 3 polypeptide chains that twist around each other like a rope• Each polypeptide chain is, itself, a helix made up from approximately 1000 amino acids.• Hydrogen bonds form between the chains giving the protein strength• This is further increased as covalent bonds (disulphide bridges) can form between the
collagen molecules.• This results in a collagen fibril forming. The fibrils then join to form a fibre
Function:• Main protein of connective tissue in animals making up 25-35% of whole body protein
content• High tensile strength• Makes up cartilage, ligaments, tendons, bone and skin• Contributes to the external structure of cells, but can also be found within them.•
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Haemoglobin
Structure:• Made up from 4 polypeptide subunits – 2 -chains and 2 -chains.• Join together to make a water soluble globular protein.• The 4 subunits are held together by the 4 types of bonds and interactions which stabilise
the tertiary structure.• Contains a prosthetic group – the haem group – that the oxygen combines with.
Function:• Makes up 97% of the dry content of a red blood cell• Transports oxygen from the lungs/gills to the tissues• Also involved in the transportation of carbon dioxide.
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The haem group.This is not made up from amino acids –
-chain
-chain
LipidsUse these headings to make your own notes
The difference between a fat and an oil Triglycerides: what are they made up from? What type of bond is used? What type of
reaction forms the bond? What are the properties of triglycerides? Fatty Acids: What is the difference between a saturated and unsaturated fatty acid? What
impact does that have on the function of the lipid? Roles: What are the roles of triglycerides in living things? Phospholipids: What are they? What is their structure? What properties do they have?
Why? What is the biochemical test for a lipid?
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