2.1.2 Biological Molecules Flashcards
Hydrogen bonding
Water is a polar molecule with regions of partial positivity and negativity.
The difference in electronegativity between the oxygen and the hydrogen means the oxygen attracts a greater share of electrons in the covalent bond, giving it a slightly negative charge.
Interactions of opposite charges within water molecules form relatively weak bons called hydrogen bonds
Break and reform as water molecules constantly moving
Main Properties of Water
Solvent properties Surface tension High specific heat capacity Freezing properties Transparent
Water as a Solvent
Polarity- regions of partial electropositivity (hygrogens) and electronegativity (oxygen) due to hydrogen bonds
Molecules in cells that are either charged (salt ions) or polar can interact with the charges in water molecules, as water hydrates polar ions
- essential elements required by organisms are obtained in ionic form
- acts as the transport medium (via blood, lymph) in multi-cellular organisms
- removes metabolic waste e.g. urea, ammonia in urine
- secretion (via digestive juices, tears)
- allows movement of minerals to lake and sea
Cohesion
Cohesion- attractive forces that hold the molecules of the liquid together
In water there is cohesion due to the hydrogen bonds.
High surface tension when the surface of a liquid contracts so that it occupies the least possible area. This occurs as water molecules on the surface have fewer surrounding molecules to bond with, so they form stronger bonds with the ones they do have.
High surface tension allows organisms e.g. pond skaters to sit on the surface of the water, allows spherical droplets to form
Adhesion
Adhesion- Attraction of molecules of one kind to molecules of a different kind
Adhesion is strong for water, especially with other charged/polar molecules
Capillary action- adhesion enables water molecules to climb upwards in capillary tubes in an upward motion against gravity
Water molecules are more strongly attracted to glass walls of a tube compared to other water molecules (due to glass being more polar than water).
Meniscus- curved surface formed by liquid in a cylinder. Water extends higher where it contacts the edge of the tube and dips lower in the middle.
Important for:
- secretion of tears from tear ducts
- transpiration of water up the xylem tube in plants
Transparency
The transmission of light into depth of water is important for the role of water as a habitat
- sun is the primary source of energy for biological organisms (light required for photosynthesis)
- allows visibility for aquatic creatures
- can be used as an indicator for water quality
Lubricant
Water acts as a lubricant
- during digestion water in saliva lubricates the food molecules to make the passage to the small and large intestine easier
- water around eyeballs, in synovial fluid (joints) and muscles move without friction
Latent Heat of Vaporisation
Water has a high latent heat of vaporisation - the amount of energy needed to change one gram of a liquid substance to a gas at constant temperature
Water acts as a coolant
- evaporation of water from the surface of the body e.g. sweat, panting, transpiration
Specific Heat Capacity
Water has a high specific heat capacity - energy required to raise the temperature of a substance by one degree Celsius (4.18 joules/gram C in water)
- can minimise changes in temperature (e.g. Cars, warm-blooded animals)
- Water is a metabolite that takes part in many reactions in the body, allows enzymes to function correctly
- organisms can se less energy on temperature control
- provide thermally stable environment for aquatic organisms
Freezing Properties
water forms hydrogen bonds
When water freezes - water molecules form a crystalline structure where they are in fixed positions further apart than in liquid water
Water expands when frozen so ice has a lower density than water
- water can act as an insulating layer protecting aquatic organisms
Monomer
Single/individual unit that bonds with other monomers to form a polymer
Polymer
Multiple individual monomers bonded in a repeating pattern to form a larger molecule.
Chemical elements in biological molecules
Carbohydrates
C, H, O
Lipids
C, H, O
Proteins
C, H, O, N, S
Nucleic Acids
C, H, O, N, P
Condensation reaction
Reaction between 2 molecules resulting in the formation of a larger molecule and the release of a water molecule. Reverse of the hydrolysis reaction.
Hydroxyl groups interact and a new bond is formed
Hydrolysis
The breakdown of a molecule into 2 smaller molecules requiring the addition of a water molecule. Reverse of the condensation reaction.
Glucose structure + properties
Hexose monosaccharide 6 carbons in a ring shaped single unit Mono - monomer Saccharide - sugar a.k.a carbohydrates Polar Soluble in water due to hydrogen bonds
Ribose structure
Pentose monosaccharide
Contains 5 carbon atoms in a ring shaped single unit
Present in RNA nucleotides
Glucose synthesis
Condensation
2 monosaccharides side by side so hydroxyl groups at carbon 1 and 4 interact. Bonds break to release a water molecule and a new bond forms between the 2 glucose molecules to form a disaccharide. The covalent bond formed is called a (1,4) glycosidic bond
Hydrolysis
Addition of water molecules catalysed by enzymes
Converts polysaccharides/disaccharides into monosaccharides by breaking the glycosidic bonds
E.g. starch/glycogen converted to glucose for respiration
Amylose
Polysaccharide formed by many a-glucose molecules joined together by 1,4 glycosidic bonds
Allow the chain to twist to form a helical structure
Compact (for storage in plants)
Insoluble in water due to coiled structure encourages intermolecular bonds - blocks access by solvent
Amylopectin
Polysaccharide formed by many a-glucose molecules joined together by 1,4 glycosidic bonds as well as 1,6 glycosidic bonds approx. every 25 units
Branched structure with many free ends for glucose to be added or removed for storage and release
Accessible to enzymes so faster hydrolysis
Soluble in water due to branched open structure that encourages hydrogen bonding
Less compact than amylose - Coil to form spiral molecules for storage
Glycogen
Polysaccharide that contains many a-glucose molecules joined together by 1,4 glycosidic bonds as well as 1,6 glycosidic bonds approx. every 8-12 units
More highly branched with with shorter branches
More compact than starch so can be broken down rapidly to release and store glucose molecules required e.g. liver and muscle cells in animals
Cellulose
Polysaccharide formed by many b-glucose molecules joined together by 1,4 glycosidic bonds
Alternating beta molecules are reversed so the hydroxyl groups are close enough to interact
Form a strait-chain molecule which allows hydrogen bonding between OH groups of adjacent chains
Pack closely into a parallel arrangement (microfibrils - macrofibrils - fibres)
Insoluble a most OH groups are already bonded to each other so limited reaction with water and other solvents
High tensile strength e.g. plant cell walls
Triglycerides
One glycerol molecule (-OH) and to 3 fatty acids (-COOH) joined together by ester bonds
Formed through esterification (condensation reaction) as OH groups interact
Macromolecules - large complexes built from repeating monomers
Non-polar
Long-term energy storage
Thermal insulation to reduce heat loss e.g. penguins
Cushioning to protect vital organs e.g. heart + kidney
Buoyancy for aquatic animals e.g. whales
Phospholipids
Modified triglyceride with a charged phosphate head (PO4-3), 1 glycerol molecule and 2 fatty acids
Phosphate head is hydrophilic (polar) and fatty acid tails are hydrophobic (non-polar)
Form a layer on the surface of the water (surface active agents)
Or bilayer (for cell surface membranes)
Create hydrophobic barriers e.g. to separate cytosol from the aq environment in cells
Sterols
Complex alcohol molecules made of 4 carbon rings (non-polar) and a hydroxyl group at one end (polar)
Electrical insulation necessary for impulse transmission
Cholesterol is a sterol used to add stability to cell membranes, regulate fluidity
Used in hormone production
Essential and non-essential fats
Essential fatty acids
Required for biological processes but not synthesised by the human body
Have to be supplemented through ingestion in the diet
Non-essential fatty acids
Can be synthesised by the human body
Amino acid
COOHC(R)HNH2 Amine group Carboxyl group R group (variable side chains) All bonded to the a-carbon
Polypeptide synthesis
Condensation reaction
Many amino acids bonded together by peptide bonds between an amine group and a carboxyl group to form a dipeptide or polypeptide
Hydrolysis
Addition of water molecules to break the peptide bonds into amino acids
Catalysed by protease enzymes
Primary protein structure
Primary structure
sequence of amino acids to form a polypeptide
Secondary protein structure
Secondary
Interaction along the protein molecules forming hydrogen bonds within the polypeptide chain
Parallel polypeptide chains with hydrogen bonds form a sheet-like structure - beta pleated sheets
Hydrogen bonds within the polypeptide chain at every 4th amino acid pulls the chain into a helical structure - alpha helix
Tertiary protein structure
Tertiary Folding the protein into its final shape involving interactions between different R-groups - hydrogen bonds - hydrophilic/hydrophobic interactions Between polar and non-polar R-groups - ionic bonds Between oppositely charged R-groups - Disulphide bonds Covalent bonds between R-groups that contain sulphur atoms (e.g. cysteine)
Quaternary protein structure
Interactions between multiple subunits (peptide chains) of different protein molecules
Can be identical sub units or different
Globular proteins
Water soluble
Hydrophilic R-groups on the outside and hydrophobic R-groups on the inside
Compact
Distinctive (spherical) shape that determines function
Unusually majority alpha helix shapes
Conjugated protein- contains a prosthetic group (non-protein component) e.g. a haem group
Fibrous proteins
Long chain molecules
Limited amino acid range and small R-groups in a repetitive, organised structure
Insoluble
High proportion of hydrophobic R-groups in primary structures
Insulin
Globular protein
Hormone involved in the regulation of blood glucose concentration
Made of 2 sub units (alpha chain and beta chain) linked by disulphide bridges
Haeomoglobin
Globular protein
Binds with oxygen to transport it around the body via the bloodstream (pick up and release)
4 polypeptide chains - 2 alpha type sub units and 2 beta type sub units each contains a prosthetic haem group
Haem group made of Fe+2 ions which combines with oxygen (reversible reaction - unstable bond) for transport
Catalase
Globular protein
Enzyme that catalyses the conversion of hydrogen peroxide (dangerous as it has radicals that attack/mutate DNA, damaging to cells if accumulates) to water and oxygen (less reactive and not dangerous)
Contains 4 identical polypeptide chains interwoven, each containing a prosthetic haem group which causes the transfer of H+ and speeds up the breakdown of H2O2
Collagen
Fibrous protein
Connective tissue in tendons, ligaments and nervous system (high tensile strength to can withstand force and be stretched without breaking)
3 coiled polypeptide chains of 2 alpha type sub units and 1 beta type sub unit form a triple helix structure
Repeating small amino acids with abundance of glycine, proline and hydroxyproline
Glycine is small so can closely pack to form long ropes
Proline and hydroxyproline repel which increases stability
Many hydrogen bonds form a long quaternary protein with staggered ends joining end to end to form fibrils called tropocollagen
Cross link to form strong fibres which can aggregate into larger bundles
Keratin
Fibrous protein
Found in hair, skin and nails, structural protein that is strong, insoluble and inflexible
2 different polypeptide chains
Large proportion of sulphur containing cysteine amino acids in primary structure leading to many disulphide bonds
Degree of flexibility depends on number of sulphide bonds
More cysteine leads to hard keratin for nails, less flexible
Less cysteine leads to soft keratin for hair, more flexible
Tightly wound structure for stability when exposed to mechanical stress, retains shape and protects surroundings
Elastin
Fibrous protein found in elastic fibres confers strength and elasticity to skin
Present in blood vessel walls and alveoli in lungs for flexibility to expand and contract
Many linked tropoelastin molecules to form a stable structure containing cross-links
Able to stretch and recoil without breaking
Elastin formed due to multiple tropoelastin molecules aggregating via interactions between hydrophobic areas
Stabilised by covalent bonds involving lysine
Inorganic ions
Ca+2 Na+ K+ H+ NH+4
NO3- HCO3- Cl- PO4-3 OH-
Biuret test for proteins
1) mix sample with equal volume of 10% sodium hydroxide solution
2) add a few drops of 1% copper sulphate solution at a time until sample turns blue
3) leave to stand for 5 minutes
If colour changes to purple then protein is present
Benedict’s test for reducing and non-reducing sugars
Reducing sugars - monosaccharides and some disaccharides that can donate electrons
1) place sample in boiling tube and add equal volume of Benedict’s reagent
3) heat mixture in water bath for 5 minutes
Sugar will react with the Cu+ ions to reduce the ions from blue to brick red. The more reducing sugar present, the more precipitate formed
Non-reducing - sucrose
Remain blue and do not react with Benedict’s solution
1) boil with dilute hydrochloric acid to hydrolyse the sucrose into glucose and fructose (reducing sugars)
2) repeat Benedict’s test for reducing sugars
Reagent test strips for reducing sugars
Used to test for presence of reducing sugars (e.g. glucose) Using a colour coded chart to determine the concentration of the sugar
Qualitative method
Iodine test for starch
1) mix a few drops of iodine dissolved in potassium iodide solution with the sample
If positive solution turns from yellow/brown to blue/black
Emulsion test for lipids
1) mix sample with ethanol to dissolve the sample
2) mix resulting solution with water and shake vigorously
If positive a white emulsion forms as a layer on top. If remains clear it is negative.
Colorimeter
Quantitative method to measure concentration
Uses colorimeter to measure absorbance/transmission of light
The more concentrated solution absorbs more light and transmits less - higher Abs value
1) place filter of complementary colour into colorimeter and calibrate using distilled water
2) filter glucose solutions following Benedict’s test to remove any precipitate using filter paper
3) pour sample into cuvette and measure % transmission/absorption using colorimeter
4) plot calibration curve of absorption / concentration
Chromatography
Used to separate individual components of a mixture
Variables
Time measured
Solubility of stationary phase
TLC
Stationary phase: thin layer of silica gel on sheet of glass/metal
Mobile phase: solubility of solvent
Paper:
Stationary phase: thin sheet of paper
Mobile phase: solubility of solvent
Rf = distance travelled by solute / solvent front
E.g. amino acids, carbohydrates, proteins
