2.1.2 Biological Molecules

Question 1

Hydrogen bonding

Answer 1

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

Question 2

Main Properties of Water

Answer 2

Solvent properties
Surface tension
High specific heat capacity
Freezing properties 
Transparent

Question 3

Water as a Solvent

Answer 3

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

Question 4

Cohesion

Answer 4

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

Question 5

Adhesion

Answer 5

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

Question 6

Transparency

Answer 6

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

Question 7

Lubricant

Answer 7

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

Question 8

Latent Heat of Vaporisation

Answer 8

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

Question 9

Specific Heat Capacity

Answer 9

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

Question 10

Freezing Properties

Answer 10

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

Question 11

Monomer

Answer 11

Single/individual unit that bonds with other monomers to form a polymer

Question 12

Polymer

Answer 12

Multiple individual monomers bonded in a repeating pattern to form a larger molecule.

Question 13

Chemical elements in biological molecules

Answer 13

Carbohydrates
C, H, O

Lipids
C, H, O

Proteins
C, H, O, N, S

Nucleic Acids
C, H, O, N, P

Question 15

Condensation reaction

Answer 15

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

Question 16

Hydrolysis

Answer 16

The breakdown of a molecule into 2 smaller molecules requiring the addition of a water molecule. Reverse of the condensation reaction.

Question 17

Glucose structure + properties

Answer 17

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

Question 18

Ribose structure

Answer 18

Pentose monosaccharide
Contains 5 carbon atoms in a ring shaped single unit
Present in RNA nucleotides

Question 19

Glucose synthesis

Answer 19

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

Question 20

Amylose

Answer 20

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

Question 21

Amylopectin

Answer 21

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

Question 22

Glycogen

Answer 22

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

Question 23

Cellulose

Answer 23

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

Question 24

Triglycerides

Answer 24

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

Question 25

Phospholipids

Answer 25

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

Question 26

Sterols

Answer 26

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

Question 27

Essential and non-essential fats

Answer 27

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

Question 28

Amino acid

Answer 28

``` COOHC(R)HNH2 Amine group Carboxyl group R group (variable side chains) All bonded to the a-carbon ```

Question 29

Polypeptide synthesis

Answer 29

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

Question 30

Primary protein structure

Answer 30

Primary structure | sequence of amino acids to form a polypeptide

Question 31

Secondary protein structure

Answer 31

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

Question 32

Tertiary protein structure

Answer 32

``` 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) ```

Question 33

Quaternary protein structure

Answer 33

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

Question 34

Insulin

Answer 34

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

Question 35

Haeomoglobin

Answer 35

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

Question 36

Catalase

Answer 36

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

Question 37

Collagen

Answer 37

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

Question 38

Keratin

Answer 38

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

Question 39

Elastin

Answer 39

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

Question 40

Inorganic ions

Answer 40

``` Ca+2 Na+ K+ H+ NH+4 ``` ``` NO3- HCO3- Cl- PO4-3 OH- ```

Question 41

Biuret test for proteins

Answer 41

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

Question 42

Benedict’s test for reducing and non-reducing sugars

Answer 42

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

Question 43

Reagent test strips for reducing sugars

Answer 43

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

Question 44

Iodine test for starch

Answer 44

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

Question 45

Emulsion test for lipids

Answer 45

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.

Question 46

Colorimeter

Answer 46

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

Question 47

Chromatography

Answer 47

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