BIOLOGICAL MOLECULES

Water

WATER.
Describe how H-bonding occurs between water molecules and relate this and other properties to role of water in living organisms Water consists of 2 hydrogen atoms covalently bonded to 1 oxygen. Dipolar molecule; -vely charged at oxygen end and +vely charged hydrogen ends (because oxygen attracts electrons more) In water, molecules form hydrogen bonds with each other. They form a network that allows molecules to move around, continually making and breaking bonds. Negative O atom can H bond to positive H atom Hydrogen bonds are relatively weak bonds (but one of the strongest intermolecular forces of attraction).

Feature Solvent

Description Solvent for polar/ionic substances, because water is attracted to them, because of its dipolar nature. Water clusters around molecules and keeps them apart. Metabolic processes rely on this. Ice is less dense than water, so it floats. Insulates water underneath. Provides living surface, and animals can still swim. As temperature is reduced, more hydrogen bonds form, but they dont break so easily as less kinetic energy). The water molecules space out to allow the increased H bonds High energy is needed to raise temperature; H bonds restrict water movement, because continually making and breaking bonds. This provides a constant and stable temperature, because much energy is needed to break H bonds. Evaporation uses lots of heat energy, so is cooling. So high specific heat capacity High surface tension: Cohesion- water molecules stick together. H bonds pull water molecules in at surface, which can help draw water up in xylem. Surface tension makes long thin columns very strong and difficult to break

Density in freezing

Thermal stability

Surface tension

Liquid

Water is a liquid transport medium for movement of materials, e.g in respiration Transparent to light so plants can photosynthesize

Transparent

BIOLOGICAL MOLECULES
proteins

PROTEINS.
Describe the structure of an amino acid=]

Made of C,H,O,N,S All have same basic structure, except R groups Amino acids are monomers of proteins and join together to form dipeptides/polypeptides.

Amino group: Basic properties

H
Carboxylic acid group: Acidic properties

Describe formation and breakage of peptide bonds Condensation reaction forms a covalent peptide bond. Water is released. Hydrolyosis reaction breaks peptide bond. Water is used up. Catalysed by protease. http://www.biotopics.co.uk/as/aminocon.html

Explain the term primary, secondary, tertiary, and quarternary structure Primary structure: sequence of amino acids that forms the protein and determines its function. Determines overall shape, and how much coiling/folding. Secondary structure: Coiling/folding of a protein due to hydrogen bonds which stabilise it. For example, may form alpha helix (a right handed spiral), or beta-pleated sheet. Tertiary structure: overall 3D shape of a molecule, specific to its function. Stabilised by:
Hydrogen bonding: Between polar groups. Group w/ +ve charge attracted to group w/ -ve charge. Temp/pH breaks. - Ionic bonds between R groups which ionise to form positively and negatively charged groups that attract each other. pH breaks. - Disulfide bridges: Between the sulfur-containing R groups of the amino acid cysteine. Covalent. Strongest bond. Only broken by reducing agents - Hydrophobic interactions: between non-polar R groups. Polar R groups interact with water by forming hydrogen bonds that face outwards. Non-polar R groups cluster towards the centre, so hydrophobic core. So hydrophobic will be found together- slight attraction between them.
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Quarternary structure: When a protein is made up of 2 or more polypeptides, e.g. Haemoglobin:

y y y y y y

Haemoglobins quarternary structure consists of 4 polypeptide subunits. 2 are alpha chains, 2 are beta chains. It forms a water soluble globular protein. Tertiary structure provides subunits with specific shape that is vital for function. Iron Haem group binds to oxygen. Function is to transport oxygen and carbon dioxide.

Describe the structure of collagen Very strong fibrous protein- because of H bonds, overlapping of molecules, and covalent bonds (between R groups) Every 3rd amino acid is glycine- small to allow tight packing Made of 3 polypeptide chains wound around each other. Each chain is a coil. Forms tight coil. H bonds form between chains Molecules of collagen form covalent bonds between R groups Molecules overlap without any sign of weakness Left handed structure Insoluble due to length of chain and hydrophobic R groups Function is to strengthen tissues

COMPARE THE STRUCTURE AND FUNCTION OF HAEMOGLOBIN (E.G. OF GLOBULAR) AND COLLAGEN (E.G. OF FIBROUS)
Feature Type of protein Solubility Number of polypeptides Shape Function Primary structure Haemoglobin Globular Soluble 4 Complex 3D shape. Much is wound into alpha helix. All globular usually have metabolic roles. structure very precise, usually made up of a non-repeating sequence of amino acids forming a chain that is always the same length Collagen Fibrous Insoluble because of length of chain and hydrophobic R groups 3 Triple helix. Much is left handed structures. All fibrous usually have structural roles. often made up of a repeating sequence of amino acids, and the chain can be of varying length

BIOLOGICAL MOLECULES
Carbohydrates

EXPLAIN HOW THE STRUCTURE OF GLUCOSE RELATES TO ITS

FUNCTION IN LIVING ORGANISMS DESCRIBE THE MOLECULAR STRUCTURE OF ALPHA GLUCOSE AS EXAMPLE OF MONOSACCHARIDE STATE DIFFERENCE BETWEEN A/B GLUCOSE

Glucose is polar, so interacts with water, so it is soluble and suitable for transport in the blood. Glucose provides energy via respiration. Monosaccharides are grouped according to number of carbon atoms in molecule: triose = C3H603, Pentose= C5H10O5, Hexose= C6H12O6, e.g. glucose fructose and galactose Alpha glucose has OH at C1 below the plane of the ring, and H at top. Beta glucose has C1 OH above the plane of the ring, and H below. Alpha and beta glucose are isomers. They have same molecular formula but different structural formula.
Alpha glucose: Henrietta. Only has HO HO.

Describe the formation and breakage of glycosidic bonds in synthesis and hydrolyosis of a disaccharide (maltose) and a polysaccharide (amylose) Hydrolyosis/synthesis: 2 monosaccharides can be joined by condensation reaction to form a disaccharide. A covalent bond called glycosidic bond is formed. Water molecule released In the reverse hydrolyosis reaction, water molecule is added to break the glycosidic bond, catalysed by carbohydrase Disaccharides: 2 monosaccharides can be joined by condensation reaction to form a disaccharide. Maltose is a disaccharide in which the oxygen links carbon 1 and carbon 4 together, made by alpha glucose +alpha glucose. Maltose is an energy source in seeds, and is a reducing sugar Polysaccharides: Cells polymerise glucose to form polysaccharides that are long chain molecules with glucose molecules joined by glycosidic bonds Amylose is a chain of glucose molecules joined by an alpha 1.4 glycosidic bond

Compare and contrast the structure and functions of starch (amylose) and cellulose Amylose: (makes up starch with branched amylopectin): Structure:
y

a chain of glucose molecules joined by alpha 1,4 glycosidic bonds which, by hydrogen bonding, form a helix.

Function:
Insoluble in water, so good storage molecule - Helix forms compact shape which allows tight packing, so good storage molecule - Can be broken down to glucose molecules which may be respired to release energy
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Describe structure of glycogen - Made up of alpha glucose (like starch) - Can be broken down to release glucose to be respired (like starch) - However differs from starch because the 1,4 glycosidic chains are shorter, and has more branches, so more compact than starch - Branches are made by glycosidic bonds between Carob atoms 1 and 6

So starch and glycogen are ideal for energy storage, as they are insoluble and compact, and provide large numbers of glucose molecules when needed for respiration. Glycogen and amylopectin have many ends to which glucose can be added or removed as required, so efficient in energy storage. Functions of glycogen and starch:

Energy storage molecules - Insoluble: They dont dissolve, so water potential isnt affected in cell - They hold glucose molecules in chains so they can be easily broken off from ends to provide glucose for respiration when required.
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Cellulose Structure: Long unbranched chains of glucose, linked by B 1,4 glycosidic bonds. Alternate glucose molecules are turned 180 dg, which means cellulose forms straight chains with many projecting OH groups that form hydrogen bonds along the molecule and with adjacent cellulose molecules. Cellulose molecules are in bundles (microfibrils) and are laid down in cell walls in different directions, to give cell wall strength Function: Forms plant cell walls Hydrogen bonds make cellulose much stronger than starch, preventing plant cell walls from bursting when turgid Bundles give added strength Cell walls give strength to cells Arrangement of macrofibrils determines how cells can grow or change shape, e.g. in guard cells macrofibrils result in opening and closing of stomata Hydrogen bonding prevents water entering, so insoluble.

COMPARE STRUCTURE OF PHOSPHOLIPID/

TRIGYLCERIDE

Glycerol is always the same, fatty acid can differ. They can be
Saturated: single bond; solid at room temperature y Unsaturated: single, double bonded carbon = monounsaturated. More than 1 double bond = polyunsaturated. Unsaturated fatty acids have an unflexible kink, pushing molecules apart so they are more fluid (b/c theres less forces of attraction)
y

Fatty acids bind to glycerols OH group (hydroxyl/Hydrocarbon chain) by their carboxyl group (COOH- acid group)

How do they differ? Phosphilipids have 2 fatty acids, triglycerides have 3. Phospholipids have a phosphate group and another hydrophilic group (e.g. choline), triglycerides dont.

Triglycerides:
1 glycerol molecule bonded to 3 F.A molecules There is a condensation reaction between 3 COOH groups of fatty acid chain and OH group of glycerol molecule. - Water molecule is produces; forms ester bond - Triglycerides are insoluble in water, so hydrophobic, because the charges on the molecule are distributed evenly around the molecules, so H bonds cant form with water molecules to they cant mix together easily.
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Phospholipids:
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Consists of a glycerol molecule that binds to 2 fatty acids and 1 phosphate group bonded by condensation reaction to produce an ester bond, releasing water. 3rd fatty acid group isnt added; instead phosphate group is covalently bonded to the 3rd OH group on glycerol. - The phosphate head is hydrophilic, and the fatty acid chain is hydrophobic. Majority is insoluble

EXPLAIN HOW TRIGLYCERIDES, PHOSPHOLIPID AND CHOLESTEROL MOLECULES RELATE TO THEIR FUNCTIONS IN ORGANISMS.
Lipid Triglyceride Structure Glycerol + 3 fatty acids Main Role Compact energy store: when respired, they release energy to generate ATP Insoluble in water so doesnt affect water potential, so good storage molecules Stored as fat which also has thermal insulation and protective properties (like organs) Source of water when respired

Phospolipid

Glycerol + 2 fatty acids and 1 phosphate group

Forms molecule which is part hydrophobic and part hydrophilic, forming stable bilayers in water with hydrophobic at the base which excludes water Creates hydrophobic barrier. Ideal for CSMs Phosphate group may have carbohydrate parts attached-glycolipids involved in cell signalling Forms small molecule that fits into lipid bilayer, interacting with phospholipids regulating stability and fluidity. Used to form steroid hormones

Cholesterol

4 carbon-based ring structures. OH group makes it polar at 1 end & 4 hyddrocarbon rings and hydrocarbon tail are non polar.

Substan ce Starch

Test Add iodine solution to solution in test-tube Add Benedicts solution to substance in test-tube (same vol of both). Heat in water bath If above is ve Add hydrochloric solution to the test solution Boil in water bath (acts as catalyst and hydrolyses any sucrose). Add alkali to neutralise Carry out Benedicts test again Add biuret to solution in test tube and add equal vol. of both. Mix. Crush test solution in test tube with ethanol Filter ethanol into second test tube containing cold water, discarding solid residue.

Change From orange to blue-black

Reducing sugars

From blue to green/orange/red depending on concentration.

Non reducing sugars

If result is positive, (goes green/orange/red), then non-reducing sugars were present. If negative (no change) neither reducing or non-reducing sugars.

Proteins

Blue to lilac

Lipids

White emulsion

COLORIMETRY- QUANTITATIVE
After boiling sample of test solution with excess Benedicts solution, filter solution to remove ppt. Calibrate colorimeter, using un-reacted Benedicts. A solution that remains blue has no reducing sugar in it and has high absorbance reading. A solution that has no blue colours has high concentration of reducing sugars and a low reading for absorbance The more transmission/less absorbance= more sugar present. Obtain calibration curve Use reading of unknown sugar and read off graph to find conc.