Unit 1: Biological Molecules

• atoms share a pair of electrons in their outer shells
• full outer shell
• more stable
• forms a molecule

• ions with opposite charges attract one another
• electrostatic attraction = ionic bond
• weaker than covalent bonds

• electrons are not evenly distributed
• spend more time at one position - more negatively charged
• uneven distribution of charge = polarised
• polar - positive and negative regions attract each other
• weak electrostatic bond
• alter physical properties, e.g. density of water vs. ice

• monomers join to form long chains - polymers
• process = polymerisation
• industrially produced, e.g. polythene, polyesters
• naturally by living organisms, e.g. polysaccharides, polypeptides, polynucleotides

Examples:

• Polysaccharides - monosaccharides
• Polypeptides - amino acids - joined by peptide bonds
• Polynucleotides - nucleotides

• formation of a polymer
• removal of a molecule of water

e.g.

• nucleotides to nucleic acids
• monosaccharides to polysaccharides (carbohydrates)
• fatty acids + glycerol to lipids
• amino acids to polypeptides (proteins)

+ water

• polymers are broken down into monomers
• addition of a molecule of water

e.g.

• nucleic acids to nucleotides
• carbohydrates (polysaccharides) to monosaccharides
• lipids to fatty acids + glycerol
• proteins (polypeptides) to amino acids

+ water

• all chemical processes taking place in a living organism

• measures amount of substance
• 1 mole contains same number of particles as there are in 12g of carbon-12 atoms 
• 12g of carbon-12 atoms contains 6.022 x 10^23 carbon atoms = Avogadro constant

• contains 1 mole of solute in each litre of solution
• 1 mole - molecular mass expressed as grams

e.g.

1M solution of NaCl 

Mr = 58.5

= 58.5g of NaCl in 1 litre of solution

• smallest unit of chemical elements
• nucleus - protons and neutrons
• electrons orbit the nucleus in shells

• number of protons = number of electrons
• no overall charge

• atomic number - the number of protons in the nucleus
• mass number - number of protons + neutrons in the nucleus
• electron configuration

• nucleus of an atom
• same mass as protons
• no electrical charge

• nucleus of an atom
• same mass as neutrons
• positive charge

• orbit in shells around the nucleus
• small mass
• negatively charged
• number of electrons determines chemical properties, e.g. reactivity

• atoms of the same element
• same number of protons
• different number of protons
• differerent mass
• uses, e.g. radioactive tracers

• loss or gain of an electron
• loss = positively charged ion, e.g. H+
• gain = negatively charged ion, e.g. Cl-

• more than one electron can be lost
• ions with more than one atom = molecular ion

• carbon atoms are extremely versatile
• variety of life
• organic molecules
• few atoms attach to carbon
• life based on a small number of chemical elements

• organic molecule
• monomer = monosaccharide
• pair of monosaccharides = disaccharide
• polymer = polysaccharide

• sweet-tasting
• soluble
• general formula - (CH2O)n

e.g.

• glucose
• galactose
• fructose

• hexose sugar
• C6H12O6
• different arrangement of atoms = isomers
• alpha vs. beta glucose - different position of -OH group and - H group on right side of molecule

• reducing sugars 
• donate electrons to or reduce another chemical
• e.g. maltose
• reduction = gain of electrons or H+

• Benedict's reagent - alkaline solution of copper (II) sulfate
• + heat - insoluble red precipitate of copper (I) oxide

Benedict's Test:

1. Add 2cm3 of the food sample to a test tube (grind up in water if solid) 

2. Add 2cm3 of Benedict's reagent

3. Heat mixture in a boiling water bath for 5 minutes

4. Red precipitate = reducing sugar is present

SEMI-QUANTITATIVE

e.g.

blue - green - yellow - orange - red 

COLORIMETRY - % absorbency of light - concentration

• glucose + glucose -> maltose
• glucose + fructose -> sucrose
• glucose + galactose -> lactose

• monosaccharides join
• 1 molecule of water is removed
• condensation reaction
• GLYCOSIDIC BOND

• hydrolysis reaction
• 1 molecule of water is added
• breaks glycosidic bond

• do not change colour of Benedict's reagent when heated with it
• HYDROLYSE into monosaccharides

1. grind up sample if necessary
2. add 2cm3 sample to 2cm3 of Benedict's reagent in a test tube + filter
3. place test tube in a boiling water bath for 5 minutes
4. no colour change = no reducing sugar
5. add 2cm3 sample to 2cm3 to dilute HCl in a test tube + place in a boiling water bath for 5 minutes
dilute HCl hydrolyses any disaccharide into monosaccharides
6. slowly add sodium hydrogencarbonate to neutralise the HCl
7. test with pH paper to check solution is alkaline
8. re-test solution - heat with 2cm3 of Benedict's reagent
9. heat in a water bath for 5 minutes
10. non-reducing sugar present = Benedict's reagent turns orange/brown

• polymer of monosaccharides
• glycosidic bonds
• condensation reactions
• very large
• insoluble
• storage

e.g. cellulose - structural support in plant cells

e.g. starch - grains in chloroplasts - alpha-glucose

• potassium iodide solution
• yellow to blue-black 
• room temperature

1. add 2cm3 sample into a test tube or two drops into a depression on a spotting tile

2. add 2 drops of iodine solution and shake/stir

3. blue-black = presence of starch

• polysaccharide
• plants - starch grains - high concentration in seeds + storage organs
• food + major energy source
• chains of alpha glucose monosaccharides
• glycosidic bonds - condensation reactions
• branched or unbranched
• unbranched chain - tight coil - helix
• compact
• hydrogen bonds

• energy storage
• insoluble - doesn't affect water potential - no osmosis
• large - doesn't diffuse out of cells
• compact - lots can be stored
• hydrolysed - alpha glucose - easy to transport + used in respiration
• branched form - many ends - enzymes - glucose released rapidly

• animals + bacteria
• shorter chains
• highly branched
• carbohydrate storage
• small granules - muscles + liver
• fat = storage molecule
• insoluble - doesn't affect water potential - no osmosis
• doesn't diffuse out of cells
• compact - lots can be stored in a small space
• more highly branched than starch - more ends - enzymes - broken down more rapidly - glucose released more rapidly
• important in animals - higher metabolic rate + respiratory rate than plants
• more active

• polymer of beta glucose
• straight + long unbranched chains
• parallel
• hydrogen bonds - cross linkages between adjacent chains
• lots of hydrogen bonds - strong
• microfibrils - fibres
• plant cell walls + structural rigidity
• prevents the cell bursting as water enters by osmosis 
• exerts inward pressure - stops influx of water
• plant cells - turgid - provide maximum surface area for photosynthesis

• support + rigidity
• beta glucose - long + straight + unbranched chains
• cross links - hydrogen bonds
• molecules grouped together - microfibrils - fibres - stronger

• carbon + hydrogen + oxygen
• insoluble in water
• soluble in organic solvents, e.g. alcohols + acetone
• e.g. TRIGLYCERIDES + PHOSPHOLIPIDS
• fats - saturated fatty acids - solid at rtp
• oils - unsatuated fatty acids - liquid at rtp

• membranes - cell surface membranes + organelles
• phospholipids - flexibility of membrane + transfer of lipid-soluble substances

• source of energy - oxidised - double the energy released by carbohydrate - release water
• waterproofing - insoluble in water - e.g. waxy cuticles of insects + plants - conserve water / animals - oily secretion - sebaceous glands in skin
• insulation - fat - slow conductors of heat - retain body heat + electrical insulators e.g. nerve cells
• protection - fat around delicate organs, e.g. kidney

• 3 fatty acids + 1 glyercol molecule
• ester bond between a fatty acid + glycerol
• condensation reaction
• hydrolysis = glycerol + 3 fatty acids

• glycerol is the same
• variations in the fatty acids = change properties
• -COOH group
• no double C=C bonds = saturated
• 1 double C=C bond = mono-unsaturated
• >1 double C=C bonds = polyunsaturated 

• high ratio of energy storing C-H bonds to C atoms - excellent source of energy
• low mass to energy ratio - good for storage - lots can be stored in a small volume
• animals - less to carry
• large + non-polar molecules - insoluble in water - doesn't affect osmosis or water potential
• high ratio of H to O atoms - release water when oxidised - important source

• 2 fatty acids + 1 glycerol + 1 phosphate group
• fatty acids - repel water = HYDROPHOBIC 'tail' - mixes with fat
• phosphate - attract water = HYDROPHILIC 'head' - not fat

POLAR - two ends behave differently

• dissolve in water

• polar
• hydrophilic phosphate head + hydrophobic fatty acid tails
• bilayer in cell-surface membrane = hydrophobic barrier
• hydrophilic phosphate heads hold at surface of cell-surface membrane
• form glycolipids - carbohydrates + cell-surface membrane = cell recognition

links to defence mechanisms

EMULSION TEST

1. add a 2cm3 sample to a dry + grease-free tube

2. add 5cm3 ethanol

3. shake tube throughly to dissolve any lipid

4. add 5cm3 water + shake gently

5. cloudy white colour = presence of a lipid

CONTROL - repeat experiment using water - clear solution

• any lipid in the sample is evenly dispersed in the water

= EMULSION

• light is refracted from oil to water droplets

• very large molecules
• e.g. enzymes
• lots of different types of proteins

• monomer = amino acid
• polymer = polypeptide
• combine polypeptides - protein
• 20 amino acids in proteins

Carbon atom attached to 4 different chemical groups:

• amino group (-NH2) - basic
• carboxyl group (-COOH) - acidic
• hydrogen atom (-H)
• R (side) group = variety of different chemical groups - difference in amino acids

amino acids join - DIPEPTIDE

CONDENSATION REACTION

H2O - OH group from the carboxyl group + H from the amino group

PEPTIDE BOND - between a C and N atom

POLYMERISATION - amino acid monomers join up to form a polymer

= POLYPEPTIDE

PRIMARY STRUCTURE

• sequence of amino acids in a polypeptide chain
• DNA
• lots of different types of primary protein structure
• - 20 different amino acids in proteins
• determines shape + function of protein
• change in sequence = change shape or stops functioning
• protein shape is very specific to its function
• 1 or more polypeptides

• -NH + -C=O groups on each amino acid
• H = + charge / O = - charge
• WEAK HYDROGEN BONDS
• TWIST
• 3D SHAPE
• coil = ALPHA HELIX
• BETA PLATED SHEETS

• -NH + -C=O groups on each amino acid
• H = + charge / O = - charge
• WEAK HYDROGEN BONDS
• TWIST
• 3D SHAPE
• coil = ALPHA HELIX
• BETA PLATED SHEETS

• MORE TWISTING + FOLDING
• 3D STRUCTURE

BONDS:

• DISULFIDE BRIDGES = STRONG
• IONIC BONDS = BETWEEN CARBOXYL + AMINO GROUPS
• WEAKER
• EASILY BROKEN BY CHANGES IN pH
• HYDROGEN BONDS = LOTS BUT WEAK
• IMPORTANT FOR FUNCTION
• SPECIFIC STRUCTURE

• COMPLEX
• many polypeptide chains
• prosthetic groups, e.g. Fe haem group in HAEMOGLOBIN

• BIURET TEST
• detects PEPTIDE BONDS

1. Add NaOH to the sample

2. Add a few drops of very dilute COPPER (II) SULFATE AND MIX

3. PURPLE = PROTEIN / BLUE = NO PROTEINS

• OR ADD BIURET REAGENT

• FIBROUS - e.g. COLLAGEN = STRUCTURAL
• GLOBULAR - e.g. ENZYMES + HAEMOGLOBIN = METABOLISM
• SPECIFIC STRUCTURE = SPECIFIC FUNCTION

• parallel long chains
• CROSS BRIDGES
• VERY STABLE

e.g. COLLAGEN - TENDONS

e.g.

PRIMARY STRUCTURE - UNBRANCHED POLYPEPTIDE CHAIN

SECONDARY STRUCTURE - TWISTING

TERTIARY STRUCTURE - HELIX

QUATERNARY STRUCTURE - 3 POLYPEPTIDE CHAINS

• GLOBULAR PROTEINS
• CATALYSTS - SPEED UP REACTIONS

• LOWER ACTIVATION ENERGY
• COLLIDE WITH SUFFICIENT ENERGY
• FREE ENERGY OF PRODUCTS MUST BE LESS THAN SUBSTRATES

energy of a system that is avaliable to perform work

• INTRACELLULAR AND EXTRACELLULAR
• LOWER ACTIVATION ENERGY
• LOWER TEMPERATURE

• ACTIVE SITE - FUNCTIONAL REGION OF ENZYME
• made up of amino acids
• SUBSTRATE

= ENZYME-SUBSTRATE COMPLEXES

• BONDS

• active site forms as enzyme and substrate collide
• change in enzyme that forms the active site - change shape
• enzyme is flexible - mould around substrate
• enzymes strains substrate - distorts bonds
• lowers activation energy
• INDUCED FIT

substrate has a complementary shape to active site

• SPECIFIC SHAPE - SUBSTRATE + ACTIVE SITE
• EXACT FIT
• BUT ... the shape of the enzyme is altered by the substrate
• earlier model
• ALL enzymes - ACTIVE SITE
• PROTEINS - binding/receptor sites - e.g. HORMONES

• enzymes MUST collide with substrate
• active site MUST fit substrate

• TIME COURSE

1. formation of products, e.g. volume of oxygen

2. disappearance of substrate, e.g. concentration of starch with amylase

• enzyme substrate complexes
• substrate breaks down = more product
• more and more active sites are filled = slower rate of reaction
• PLATEAU - GRAPHS

• any point on the curve of a graph
• measure the gradient - tangent
• change in y / change in x
• ENZYME + SUBSTRATE = COMPLEMENTARY
• per unit time

• HIGHER TEMPERATURE
• GREATER KINETIC ENERGY
• molecules move more quickly
• increased collision frequency
• more ENZYME-SUBSTRATE COMPLEXES
• faster rate of reaction = RISING CURVE
• BREAK BONDS - changes shape of active site
• harder for susbtrate to fit = SLOWER RATE OF REACTION
• DENATURATION = enzyme can't function = FALLING CURVE

e.g. human body temperature

• higher temperatures - energy to maintain temperature + faster metabolic rate
• proteins may be denatured at higher temperatures

• pH = measure of H+ concentration
• enzyme - OPTIMUM pH
• increase or decrease in pH reduces rate of reaction
• too low or too high = DENATURED

• change in pH = alters charges on amino acids of active site
• substrate can't bind to active site = NO ENZYME-SUBSTRATE COMPLEX
• OR break bonds of enzyme = changes SHAPE OF ACTIVE SITE
• ONLY small fluctuations in pH - less likely to DENATURE

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