2.1.2 biological molecules
Tuesday, 17 September 2024 23:36
- Hydrogen atoms bonded to oxygen atom with covalent bonds
- Water is a polar molecule because the electrons in covalent bonds are not equally shared,
closer to oxygen nucleus
- Hydrogen bonding in water between molecules, attraction between opposite charges
- Weak interaction between slightly negative and slightly positive charged atoms -
intermolecular force
- Water is a solvent, transport medium (high shc, cytoplasm), coolant ( high latent heat of
vaporisation, sweat), habitat (high surface tension, liquid at room temp)
- Colourless, high transmission - light passes through cells photosynthesis
- Monomers join to form polymers in a condensation reaction, where water is produced
- Polymer broken down into monomer requires addition of water, in hydrolysis reaction
- Carbohydrates - C,H,O
- Lipids - C,H,O
- Proteins - C,H,O,N and sometimes sulphur
- Nucleic acids - C,H,O,N,P
- (Carbon is the skeleton for all organic compounds/biological molecules
- Biological molecules contain large numbers of atoms, called macromolecules)
- Carbohydrates have monosaccharides as their monomers, polysaccharides as their
polymers
- Glucose is a monosaccharide with 6 carbons - therefore is a hexose monosaccharide
- Glucose has an alpha form and a beta form, alpha has H above OH on 1st carbon/other way
for beta
- Ribose is a monosaccharide with 5 carbon atoms, pentose
- Synthesis/breakdown of di/polysaccharides are dependent on glycosidic bonds
- Sucrose - a-glucose + fructose
- Maltose - 2 a-glucose
- Lactose - galactose + alpha or beta glucose
- Starch are the Main energy storage in plants, consist of polysaccharides amylose and
amylopectin
- Is insoluble in water so it doesn’t allow osmosis, no swelling - good for storage
- Amylose - long unbranched chain of a-glucose, coiled/compact good for storage
- Amylopectin - long branched chain of a-glucose, side branches allow enzymes to break
down glycosidic bonds to release glucose quickly
- Glycogen - main energy storage in animals, a-glucose long and branched
- Has many more branches, glucose released very quickly, good for energy release, compact
and also good for storage
- Cellulose is the main component of plant cell walls
- It’s made of long unbranded chains of b-glucose, they bond and form straight cellulose
chains.
- These chains are linked by hydrogen bonds to form strong fibres called micro fibrils,
structural support
-
-
- Proteins have amino acids as their monomers, polymers are polypeptide
- Amino acids have the general structure of: a carboxyl group (COOH), amino group (NH2),
and a variable R group attached to a carbon atom.
- The R group distinguishes each one
- Amino acids are joined by peptide bonds to form di/polypeptides, releasing water and is a
condensation reaction
- Hydrolysis adds water to break the bond
- Primary structure: sequence of amino acids in a polypeptide chain, peptide bonds
- Secondary structure: hydrogen bonds forming between nearby amino acids in the chain,
coiling into alpha helix or folding into a beta pleated sheet
- Tertiary structure: secondary structured further folded to form precise 3D structures, often
due to R group interactions. Ionic, disulphide bonds, hydrophobic/hydrophilic interactions,
hydrogen bonds
- Quaternary structures: polypeptide chains further bonding and forming its final 3D
structure
- Globular proteins have its hydrophilic R groups on the outside of the molecule, due to
hydrophilic and hydrophobic interactions in the tertiary structure
- They are therefore soluble and easily transported in fluids
- Example:
- Haemoglobin is a globular protein that carries O2 in rbcs, it is a conjugated protein due to
having a prosthetic groups attached to it (non-Protein group) in this case it is haem which is
bonded to each of the 4 polypeptide chains
- Insulin is a hormone which is secreted to lower blood glucose levels, it has 2 polypeptide
chains held together by disulphide bonds, soluble so carried in blood
- Amylase is an enzyme that catalyses the breakdown starch, single chain of amino acids and
a secondary structure of both alpha/beta
- Fibrous proteins are insoluble and strong, structural and unreactive.
- Collagen is strong and flexible and used for connective tissue in animals
- Keratin is flexible or hard/tough and found in external structures of animals
- Elastin is elastic and returns to its original shape and found in elastic connective tissue
(blood vessels, ligaments)
- Lipids are macromolecules but NOT polymers as they don’t have repeating units
- Have one glycerol and 3 fatty acids = triglyceride
- Fatty acid molecules have long tails made of hydrocarbons, are hydrophobic and make
lipids insoluble in water
- Fatty acids have a COOH group and a variable R group hydrocarbon tail
- Synthesis/breakdown of triglycerides dependent on formation/breakage of ester bonds
between fatty acids and glycerol.
- Ester bonds made by condensation reaction (produces water), broken by hydrolysis
- Saturated fatty acids have no double bonds, saturated with H
- Unsaturated fatty acids have at least one double bond between C atoms, causing chain to
kink
- Phospholipids are a type of lipid, with 2 fatty acids and a phosphate group bonded to a
glycerol
- Phosphate groups are hydrophilic, fatty acids are hydrophobic
- Triglyceride function - energy storage molecules. Long hydrocarbon tails of fatty acids
contain a lot of energy and can be broken down. Are insoluble in water as they bundle
together as insoluble droplets, fatty acid tails are hydrophobic, no osmosis swelling -
compact
- Phospholipid function - cell membranes to form phospholipid bilayer. Double layer with
hydrophilic heads facing outwards and hydrophobic tails inwards, not allowing water-
soluble substances easily through - barrier
- Cholesterol function - small flattened shape makes it fit between phospholipid molecules.
At high temp, they bind to hydrophobic tails of phospholipids, packs closer togetehr - less
fluid and more rigid. At lower temps, prevents phospholipids from packing to closely - inc
membrane fluidity
- Inorganic ions:
- CATIONS:
- Ca2+ - nerve impulse transmission/muscle contraction
- Na+ - nerve impulse transmission, kidney function
- K+ - nerve impulse transmission, stomatal opening
- H+ - catalyst of reactions, pH determination
- NH4+ - production of nitrate ions by bacteria
- ANIONS:
- NO3- - supplies nitrogen to plants for amino acid/protein formation
- HCO3- - maintenance of blood pH
- Cl- - balance positive charge of sodium and potassium ions in cells
- PO4 3- - cell membrane formation, nucleic acid and ATP formation, bone formation
- OH- - catalyst of reactions, pH determination
- Quantitative methods such as colorimetry can be use to determine concentration of a
chemical substance
- A colorimeter is used to measure the strength of a coloured solution by measuring the
absorbance (higher conc, colour, higher absorbance)
- Glucose conc can be tested by having different concentrations in a serial dilution and
ensuring all precipitate is removed through a centrifuge, and measure the absorbance and
make a calibration curve
- Paper chromatography can be used to identify amino acids in a mixture, solutes/amino
acids move up at different rates spreading out
- Pencil drawn line, concentrated spot of mixture on line, prepared solvent with paper
dipped slightly - in a fume cupboard with lid to prevent evaporation, once solvent nearly at
top, mark solvent front and leave dry. Ninhydrin solution must be added (fume cupboard,
gloves) to make colourless amino acids purple
- Rf = distance by solute / distance by solvent To identify amino acids
- Mobile phase - where molecules can move, in tlc/paper is a liquid solvent
- Stationary phase - where molecules can’t move, paper or thin layer of solid (silica gel)
- Mobile phase moves through stationary phase, components spend different amounts of
time in each phase distinguishing them
- Benedict’s test for reducing sugars-
- Reducing sugars are all monosaccharides, and some disaccharides - they can reduce
another molecule
- Benedict’s reagent is an alkaline solution of copper (II) sulfate
- Sample placed in boiling tube, should be liquid and add an equal volume of Benedict’s
reagents, heat in boiling water bath for 5 mins gently.
- Copper ions in Benedict’s is reduced from blue to brick red
- More reducing sugar present the more precipitate is formed, overall blue or brick red ions
present makes it qualitative to identify colour
- Benedict’s can be used for non-reducing sugars, but would have to be boiled first with
dilute HCl to be hydrolysed into its monosaccharides, then heated with Benedict’s solution
- It will be positive as Benedict’s solution identifies reducing sugars, monosaccharides
- Iodine solution is used to test for starch, turns from yellow/brown to purple/black
- Lipids are identified by the emulsion test, where the sample is mixed with ethanol then
with water and shaken. If a white emulsion forms, lipids are present
- Proteins are identified by the Biuret test. Peptide bonds form a violet coloured complex
with copper ions in the alkaline solution (sample+NaOH). Blue - violet
Tuesday, 17 September 2024 23:36
- Hydrogen atoms bonded to oxygen atom with covalent bonds
- Water is a polar molecule because the electrons in covalent bonds are not equally shared,
closer to oxygen nucleus
- Hydrogen bonding in water between molecules, attraction between opposite charges
- Weak interaction between slightly negative and slightly positive charged atoms -
intermolecular force
- Water is a solvent, transport medium (high shc, cytoplasm), coolant ( high latent heat of
vaporisation, sweat), habitat (high surface tension, liquid at room temp)
- Colourless, high transmission - light passes through cells photosynthesis
- Monomers join to form polymers in a condensation reaction, where water is produced
- Polymer broken down into monomer requires addition of water, in hydrolysis reaction
- Carbohydrates - C,H,O
- Lipids - C,H,O
- Proteins - C,H,O,N and sometimes sulphur
- Nucleic acids - C,H,O,N,P
- (Carbon is the skeleton for all organic compounds/biological molecules
- Biological molecules contain large numbers of atoms, called macromolecules)
- Carbohydrates have monosaccharides as their monomers, polysaccharides as their
polymers
- Glucose is a monosaccharide with 6 carbons - therefore is a hexose monosaccharide
- Glucose has an alpha form and a beta form, alpha has H above OH on 1st carbon/other way
for beta
- Ribose is a monosaccharide with 5 carbon atoms, pentose
- Synthesis/breakdown of di/polysaccharides are dependent on glycosidic bonds
- Sucrose - a-glucose + fructose
- Maltose - 2 a-glucose
- Lactose - galactose + alpha or beta glucose
- Starch are the Main energy storage in plants, consist of polysaccharides amylose and
amylopectin
- Is insoluble in water so it doesn’t allow osmosis, no swelling - good for storage
- Amylose - long unbranched chain of a-glucose, coiled/compact good for storage
- Amylopectin - long branched chain of a-glucose, side branches allow enzymes to break
down glycosidic bonds to release glucose quickly
- Glycogen - main energy storage in animals, a-glucose long and branched
- Has many more branches, glucose released very quickly, good for energy release, compact
and also good for storage
- Cellulose is the main component of plant cell walls
- It’s made of long unbranded chains of b-glucose, they bond and form straight cellulose
chains.
- These chains are linked by hydrogen bonds to form strong fibres called micro fibrils,
structural support
-
-
- Proteins have amino acids as their monomers, polymers are polypeptide
- Amino acids have the general structure of: a carboxyl group (COOH), amino group (NH2),
and a variable R group attached to a carbon atom.
- The R group distinguishes each one
- Amino acids are joined by peptide bonds to form di/polypeptides, releasing water and is a
condensation reaction
- Hydrolysis adds water to break the bond
- Primary structure: sequence of amino acids in a polypeptide chain, peptide bonds
- Secondary structure: hydrogen bonds forming between nearby amino acids in the chain,
coiling into alpha helix or folding into a beta pleated sheet
- Tertiary structure: secondary structured further folded to form precise 3D structures, often
due to R group interactions. Ionic, disulphide bonds, hydrophobic/hydrophilic interactions,
hydrogen bonds
- Quaternary structures: polypeptide chains further bonding and forming its final 3D
structure
- Globular proteins have its hydrophilic R groups on the outside of the molecule, due to
hydrophilic and hydrophobic interactions in the tertiary structure
- They are therefore soluble and easily transported in fluids
- Example:
- Haemoglobin is a globular protein that carries O2 in rbcs, it is a conjugated protein due to
having a prosthetic groups attached to it (non-Protein group) in this case it is haem which is
bonded to each of the 4 polypeptide chains
- Insulin is a hormone which is secreted to lower blood glucose levels, it has 2 polypeptide
chains held together by disulphide bonds, soluble so carried in blood
- Amylase is an enzyme that catalyses the breakdown starch, single chain of amino acids and
a secondary structure of both alpha/beta
- Fibrous proteins are insoluble and strong, structural and unreactive.
- Collagen is strong and flexible and used for connective tissue in animals
- Keratin is flexible or hard/tough and found in external structures of animals
- Elastin is elastic and returns to its original shape and found in elastic connective tissue
(blood vessels, ligaments)
- Lipids are macromolecules but NOT polymers as they don’t have repeating units
- Have one glycerol and 3 fatty acids = triglyceride
- Fatty acid molecules have long tails made of hydrocarbons, are hydrophobic and make
lipids insoluble in water
- Fatty acids have a COOH group and a variable R group hydrocarbon tail
- Synthesis/breakdown of triglycerides dependent on formation/breakage of ester bonds
between fatty acids and glycerol.
- Ester bonds made by condensation reaction (produces water), broken by hydrolysis
- Saturated fatty acids have no double bonds, saturated with H
- Unsaturated fatty acids have at least one double bond between C atoms, causing chain to
kink
- Phospholipids are a type of lipid, with 2 fatty acids and a phosphate group bonded to a
glycerol
- Phosphate groups are hydrophilic, fatty acids are hydrophobic
- Triglyceride function - energy storage molecules. Long hydrocarbon tails of fatty acids
contain a lot of energy and can be broken down. Are insoluble in water as they bundle
together as insoluble droplets, fatty acid tails are hydrophobic, no osmosis swelling -
compact
- Phospholipid function - cell membranes to form phospholipid bilayer. Double layer with
hydrophilic heads facing outwards and hydrophobic tails inwards, not allowing water-
soluble substances easily through - barrier
- Cholesterol function - small flattened shape makes it fit between phospholipid molecules.
At high temp, they bind to hydrophobic tails of phospholipids, packs closer togetehr - less
fluid and more rigid. At lower temps, prevents phospholipids from packing to closely - inc
membrane fluidity
- Inorganic ions:
- CATIONS:
- Ca2+ - nerve impulse transmission/muscle contraction
- Na+ - nerve impulse transmission, kidney function
- K+ - nerve impulse transmission, stomatal opening
- H+ - catalyst of reactions, pH determination
- NH4+ - production of nitrate ions by bacteria
- ANIONS:
- NO3- - supplies nitrogen to plants for amino acid/protein formation
- HCO3- - maintenance of blood pH
- Cl- - balance positive charge of sodium and potassium ions in cells
- PO4 3- - cell membrane formation, nucleic acid and ATP formation, bone formation
- OH- - catalyst of reactions, pH determination
- Quantitative methods such as colorimetry can be use to determine concentration of a
chemical substance
- A colorimeter is used to measure the strength of a coloured solution by measuring the
absorbance (higher conc, colour, higher absorbance)
- Glucose conc can be tested by having different concentrations in a serial dilution and
ensuring all precipitate is removed through a centrifuge, and measure the absorbance and
make a calibration curve
- Paper chromatography can be used to identify amino acids in a mixture, solutes/amino
acids move up at different rates spreading out
- Pencil drawn line, concentrated spot of mixture on line, prepared solvent with paper
dipped slightly - in a fume cupboard with lid to prevent evaporation, once solvent nearly at
top, mark solvent front and leave dry. Ninhydrin solution must be added (fume cupboard,
gloves) to make colourless amino acids purple
- Rf = distance by solute / distance by solvent To identify amino acids
- Mobile phase - where molecules can move, in tlc/paper is a liquid solvent
- Stationary phase - where molecules can’t move, paper or thin layer of solid (silica gel)
- Mobile phase moves through stationary phase, components spend different amounts of
time in each phase distinguishing them
- Benedict’s test for reducing sugars-
- Reducing sugars are all monosaccharides, and some disaccharides - they can reduce
another molecule
- Benedict’s reagent is an alkaline solution of copper (II) sulfate
- Sample placed in boiling tube, should be liquid and add an equal volume of Benedict’s
reagents, heat in boiling water bath for 5 mins gently.
- Copper ions in Benedict’s is reduced from blue to brick red
- More reducing sugar present the more precipitate is formed, overall blue or brick red ions
present makes it qualitative to identify colour
- Benedict’s can be used for non-reducing sugars, but would have to be boiled first with
dilute HCl to be hydrolysed into its monosaccharides, then heated with Benedict’s solution
- It will be positive as Benedict’s solution identifies reducing sugars, monosaccharides
- Iodine solution is used to test for starch, turns from yellow/brown to purple/black
- Lipids are identified by the emulsion test, where the sample is mixed with ethanol then
with water and shaken. If a white emulsion forms, lipids are present
- Proteins are identified by the Biuret test. Peptide bonds form a violet coloured complex
with copper ions in the alkaline solution (sample+NaOH). Blue - violet
