Biological Molecules

• Defining monomer & polymer

  monomer = smaller units which form larger molecules

  polymer = chain of monomers joined together
• Ionic, covalent & hydrogen bonding

  ionic bonding = bonding between atoms via electrostatic attraction caused by the loss or gain of an electron

  - are weaker than covalent bonds

  covalent bonding = atoms share pairs of electrons on their outer shell & form molecules

  hydrogen bonding = the uneven distribution of electrons in an atom causing electrostatic attraction between itself & the nucleus of another atom
• Condensation & Hydrolysis reactions

  Condensation reaction = when 2 molecules join through the formation of a chemical bond and involves the elimination of a molecule of water

  
  

  Hydrolysis = breaking down of a bond between 2 molecules and involves the use of a water molecule
• Carbohydrate basics

  • monomer = monosaccharide
  • general formula = (CH2O)n
  • no. of carbons = no. of oxygens
  • white crystalline solids
  • if n = 5 -> pentose (ribose)
  • if n = 6 -> hexose (glucose, galactose, fructose)
• Alpha glucose

  isomer = versions of a molecule with same chemical formula but different structural formula

  A) H

  B) H

  C) OH

  D) OH

  E) H

  F) OH

  G) H

  H) H

  I) OH

  J) O

  K) CH2OH

  
• Beta glucose

  A) H

  B) OH

  C) OH

  D) H

  E) H

  F) OH

  G) H

  H) H

  I) OH

  J) CH2OH

  K) CH2OH

  
• Disaccharides

  • monosaccharides bond via glycosidic bonds
  • disaccharide = 2 monosaccharides bonded
  • glucose + glucose -> maltose + water
  • glucose + fructose -> sucrose + water
  • glucose + galactose -> lactose + water
• Forming glycosidic bonds

  A) OH

  B) HO

  C) H2O

  D) O

  
• polysaccharide

  polymer made of monosaccharides via glycosidic bonds forming via condesation reactions
• Starch (function = energy storage)

  • only found in plants
  • made from alpha glucose monomers
  • made of 2 polysaccharides

  - amylopectin (1-6 bonds & branched)

  - amylose (1-4 bonds & coiled)

  • helical structure -> compact -> can store more in small space
  • insoluble -> doesn't affect water potential
  • large -> can't diffuse out of cell
  • branched -> easily hydrolysed & release glucose quickly
• Glycogen (function = energy storage)

  • found in animal & bacterial cells
  • similar structure to starch except more highly branched & short chains

  - animals have higher metabolic & respiratory rate

  • made of alpha glucose monomers
  • found as small granules in muscles & liver (fat is main storage in animals)
  • large, insoluble, compact
• Cellulose (function = structural support)

  • made of beta glucose monomers
  • monomer flipped 180° each time so glycosidic bond can form
  • straight, unbranched chains parallel to each other

  - hydrogen bonds form between adjacent chains

  - rows form microfibrils & increase overall strength
• Biochemical tests for carbohydrates

  Test for starch

  • Add iodine solution: if present -> turns black/blue

  Test for reducing sugars:

  • Add Benedict's solution & heat: if present -> forms brick red precipitate
  • colour dependent on concentration of sugar in sample
  • can also filter & weigh precipitate to find concentration

  Test for non-reducing sugars (needs to be hydrolysed first):

  • Add HCl & heat gently using water bath
  • Neutralise with sodium hydrogen carbonate
  • Use reducing sugars test
• Lipid basics

  • Contain O, H & C
  • Proportion of O to C&H is smaller than in carbohydrates
  • Insoluble in water
  • Soluble in organic solvent
  • fats solid at room temp but oils liquid at room temp
• Roles of lipids

  • energy source -> provides twice the amount of energy as carbohydrate of the same mass
  • waterproofing -> plants & insects have waxy lipid layer to conserve water
  • insulation -> help retain body heat under skin as lipids are slow conductors of heat

  - also electrical insulators & create myelin sheath around nerves

  • protection of delicate organs
  • cell membranes -> allow flexibility & diffusion of lipid-soluble substances
• Triglycerides

  • lipid formed from 3 fatty acids bonded to 1 glycerol molecule
  • fatty acids form ester bonds to glycerol via condensation react.
  • fatty acids have long, hydrophobic hydrocarbon chain

  - saturated chain = no C=C

  - unsaturated chain = 1 or more C=C
• Formation of a triglyceride

  A) H OH

  B) O-C=O

  C) ester linkage

  D) glycerol

  E) 3 fatty acids

  F) 3 H2O

  G) hydrocarbon chain

  
• Properties of triglycerides related to structure

  • long hydrocarbon tail -> large chemical energy store
  • insoluble in water -> doesn't affect water potential
  • low mass: energy -> don't have to carry as much mass
  • releases water when oxidised
• Phospholipids

  • lipid formed from 2 fatty acids & 1 phosphate molecule bonded to 1 glycerol
  • phosphate replaces 1 fatty acid
  • phosphate is hydrophilic

  - hydrophilic phosphate head -> interacts with water not fat

  - hydrophobic hydrocarbon tail -> interacts with fat not water

  - overall a polar molecule
• Properties of phospholipids related to structure

  • Forms bilayer in cell membrane

  - bilayer = layer 2 molecules thick where hydrophobic end faces inwards & hydrophilic head faces outwards

  • can form glycolipids -> combine in cell-surface membrane & important for cell recognition
• Biochemical test for lipids

  1. Add 5cm^3 of ethanol to 2cm^3 sample
  2. Shake tube thoroughly
  3. Add solution to water

  - if present -> milky emulsion appears (light refraction between oil & water makes it appear cloudy)

  - more milky -> more cloudy
• General structure of an amino acid

  • 20 essential amino acids

  - all have different R groups

  A) H2N

  B) Amine group

  C) COOH

  D) Carboxyl group

  E) R

  F) R group

  
• Dipeptides & Polypeptides

  • dipeptide = 2 amino acids joined by a peptide bond formed via a condensation reaction
  • polypeptide = polymer of amino acids bonded together

  - properties of poly/dipeptide depend on atoms in R group

  A) OH H

  B) O=C-N-H

  C) peptide bond

  D) H2O

  E) amine group

  F) carboxyl group

  
• Primary structure of a protein

  • sequence of amino acids in a polypeptide chain

  - determines structure/shape of protein -> thus function

  • change in amino acid -> change in structure -> change in/can't function
• Secondary structure of a protein

  • local structures in polypeptide formed by hydrogen bonds

  - NH2 = +ve charge & COOH = -ve charge (dipole formed)

  • alpha helix -> polypeptide coils
  • beta pleat -> polypeptide folds

  - 2 or more polypeptides run antiparallel to form H bonds & fold
• Tertiary structure of a protein

  • overall 3D structure of a polypeptide formed from ionic, disulphide, (covalent), or hydrogen bonds between R groups

  - disulphide bridge/bonds = type of covalent bond formed between 2 sulfur molecules

  
  

  all proteins have up to a tertiary structure
• Quaternary structure of a protein

  • the way in which more than 1 polypeptide chain comes together to form a final protein structure
  • formed via covalent, hydrogen or ionic bonds
  • 2 polypeptide chains = dimer, 3 = trimer, 4 = tetramer etc.
  • homomer = made from same polypeptide chains
  • heteromer = made from different polypeptide chains
  • if only 1 polypeptide chain -> no quaternary structure
• Enzymes

  • biological catalysts that speed up the rate of reaction by lowering the activation energy required by creating an alternate reaction pathway
  • are globular (spherical) proteins
  • tertiary structure forms the shape of the active site

  - enzymes are specific -> active site is complementary to their own specific substrate

  - substrate = reactants activated by enzyme
• Induced fit hypothesis

  1. Substrate binds to enzyme & induces conformational change in enzyme's active site
  2. Active site then molds to exact shape of substrate & forms an enzyme-substrate complex
  3. Bonds of substrate manipulated to make reaction easier lowering activation energy

  enzymes then return to original shape

  denaturing of enzyme = disulphide, ionic & hydrogen bonds in tertiary structure break
• Fibrous proteins

  • very long, strong & insoluble proteins which often have a structural role in organisms
  • tertiary & quaternary structure of protein has repeating sequences
  • have non-polar R groups -> making them insoluble
  • form fibres -> make protein stronger
• Collagen

  • forms tendons -> allow skeleton to move
  • found in artery walls to prevent vessels bursting from high pressure
  • made of 3 polypeptides -> quaternary structure
  • have very strong fibres
• Keratin

  • used for hard body parts e.g. nails, hooves, horns
  • primary structure uses cysteine -> disulphide bridges
  • has a quaternary structure
• Elastin

  • can stretch & recoil -> elastin molecules coil & form cross-links to keep molecules together
  • found in lungs to allow inflation & deflation during ventilation
  • found in blood vessels to maintain blood pressure by stretching & recoiling
  • found in bladder to help it expand
• Biochemical test for proteins

  Add Buiret's reagent to sample

  • if present -> blue to purple
• Factors affecting enzymes: temperature

  • increase temp -> increase kinetic energy of reactants -> increase chance of successful collisions
  • High temp breaks H bonds & disrupts tertiary structure of enzyme -> active site changes permanently
  • Optimal temp is around 40°C but body temp is at 37°C

  - requires more energy
• Factors affecting enzymes: pH

  • changes to pH -> alters charges on amino acids making active site -> change to active site
  • Significant change to pH -> breaks bonds in tertiary structure
• Factors affecting enzymes: Enzyme concentration

  • increase enzyme conc. with constant amount of substrate -> proportional increase
  • Will eventually plateau as there is more enzyme than needed

  - enzyme conc. is no longer the limiting factor -> substrate concentration is
• Factors affecting enzymes: substrate concentration

  • increase conc. of substrate with constant amount of enzymes -> proportional increase
  • Will also plateau as there won't be enough enzymes for all of the substrate
  • substrate concentration is no longer the limiting factor -> enzyme conc. is
• Competitive inhibition

  • competes with substrate to bind to active site
  • has similar shape to substrate -> complementary to active site
  • will bind to active site instead of substrate & prevent enzyme-substrate complexes from forming
• Non-competitive inhibition

  • binds to another part of the enzyme NOT THE ACTIVE SITE (called the binding site instead)
  • causes tertiary structure to change -> changing shape of active site
  • prevents formation of enzyme-substrate complexes