Biology 2.2- Biological Molecules (copy)

What are the 4 main biological roles of water?

What are the 4 main biological roles of water?

• Habitat

• Solvent

• Coolant

• Transport medium

Why is water a polar molecule?

• The oxygen atom attracts the electrons more strongly than the hydrogen atoms

• This gives the oxygen a weak negative charge (δ^-) and the hydrogen a weak positive charge (δ⁺)

• This means water has a dipole

How do hydrogen bonds work in water and why are they useful?

• Weak hydrogen bonds form between the hydrogen and oxygen atoms of adjacent water molecules, due to it’s polarity

This means that water:

• Is a good solvent as it attracts other polar molecules

• Has a high specific heat capacity + latent heat of vaporisation

• Is less dense when it freezes

• Has a high cohesion to itself and high surface tension

How do the properties of water relate to it’s role as a solvent, and what are the examples of it?

• Water is a polar molecule, so it attracts other polar molecules and dissolves them

• Eg. Water can carry mineral ions in plant xylem + blood plasma carries blood cells and other substances

How do the properties of water relate to it’s role as a coolant, and what are the examples of it?

• Water has a high specific heat capacity, so it can take in a lot of energy before changing temperature

• It also has a high latent heat of vaporisation, so it takes in a lot of energy when boiling

• Eg. Evaporation is used to cool down, by sweating or panting

How do the properties of water relate to it’s role as a habitat, and what are the examples of it?

• Water has a high specific heat capacity, so it can take in a lot of energy before changing temperature

• Freezes in a crystalline structure, so it is less dense when solid, meaning ice floats and can insulate water bodies

• Polar molecule, so it attracts other polar molecules and can dissolve them

• Eg. Creates a stable environment in ponds, with a constant temperature (for enzyme activity) and dissolved nutrients

How do the properties of water relate to it’s role as a transport molecule, and what are the examples of it?

• Water is a polar molecule, so it attracts other polar molecules and can dissolve them

• This also means it has high cohesion to itself and adhesion to surfaces, so can easily flow

• Eg. Water can carry mineral ions in plant xylem + blood plasma carries cells and dissolved substances

What chemical elements make up carbohydrates, lipids, proteins and nucleic acids?

Carbohydrates = C, H and O

Lipids = C, H and O

Proteins = C, H, O, N, P and S

Nucleic acids = C, H, O, N and P

What are the biological cations calcium, sodium, potassium, hydrogen and ammonium each used for?

Calcium (Ca 2+) - nerve impulses and muscle contractions

Sodium (Na +) - nerve impulses, transport of substances across cell membranes and kidney function

Potassium (K +) - nerve impulses, kidney function and stomata

Hydrogen (H +) - catalysts and pH determination

Ammonium (NH4 +) - used in protein synthesis

What are the biological anions nitrate, hydrogen carbonate, chloride, phosphate and hydroxide each used for?

Nitrate (NO3 -) - amino acid formation

Hydrogen carbonate (HCO3 -) - maintains blood pH

Chloride (Cl -) - balance sodium and potassium ions in cells and maintains blood pH

Phosphate (PO4 3-) - cell membranes, bone formation, and is a component of DNA, RNA and ATP

Hydroxide (OH -) - catalysts and pH determination

What are the structures of alpha and beta glucose?

Glucose is a hexose sugar with two isomers- they both have the formula C6H12O6

What are the structures of ribose and deoxyribose?

Ribose and deoxyribose are pentose (5 carbon) sugars, with similar formulas except that deoxyribose has one less oxygen than ribose (lost from the second carbon)

What three properties do monosaccharides have in common?

• Soluble in water

• Sweet tasting

• Forms crystals

How can disaccharides and polysaccharides be formed and broken down?

They can be formed by condensation reactions- when two hydroxyl (OH) groups from different saccharides interact to produce a water molecule and a glycosidic bond between the two saccharides

• This can be catalysed by enzymes

They can be broken down by hydrolysis- when water is added to a di or polysaccharide, breaking the glycosidic bond to form a hydroxyl group on each saccharide

• This can be catalysed by (different) enzymes

• We use this to test for non reducing sugars

What are the three most common disaccharides made from?

Maltose- two glucose molecules (alpha x alpha)

Sucrose- glucose + fructose (alpha x fructose)

Lactose- glucose + galactose (alpha x beta)

What are reducing sugars?

Reducing sugars can give away electrons via the oxidisation of a carbonyl (C=O) group

• This is why reducing sugars can be detected using Benedict’s solution- they reduce the soluble blue copper sulphate to insoluble brick-red copper oxide

• All monosaccharides and some disaccharides are reducing sugars- polysaccharides aren’t

What is the structure of starch?

Starch is made from two different alpha glucose structures :

• Amylose (20%)- a straight chain linked by 1,4-glycosidic bonds- amylose curls into a helix shape which allows it to be more compact

• Amylopectin (80%)- a branched chain linked by 1,4 and 1,6-glycosidic bonds

What is starch used for and how is it well suited?

• Starch is the main carbohydrate store in plants

• Stored in the plastids- amyloplasts and chloroplasts

This because it is:

• Compact, so large quantities can be stored

• Insoluble, so it won’t change the water concentration in cells and affect osmosis

• Amylopectin (80%) is linked by some 1,6-glycosidic bonds, so it has many terminal glucose molecules that can be hydrolysed for respiration or added for storage

What is the structure of glycogen?

• Made up of alpha glucose molecules linked by 1,6 and 1,4-glycosidic bonds

• Glycogen has a similar structure to amylopectin but is more branched, because it has more 1,6-bonds

What is glycogen used for and how is it well suited?

• Glycogen is used for storage in animals

• Stored in liver and muscle cells

This because it is:

• Compact but relatively large, so large quantities can be stored (more 1,6-bonds means it is more compact than amylopectin)

• Insoluble, so it won’t change the water concentration in cells and affect osmosis

• Linked by many 1,6-glycosidic bonds so it has many terminal glucose molecules that can be hydrolysed for respiration or added for storage

What is the structure of cellulose?

• Made up of beta glucose molecules linked by 1,4-glycosidic bonds

• To bond together, every other beta glucose molecule is flipped

• This means that hydrogen bonds can form between strands, to create microfibrils

• These make up the cellulose fibres that link into a network

What is cellulose used for and how is it well suited?

• Cellulose makes up the majority of plant cell walls

This is because it is:

• Held together by many hydrogen bonds between strands, so it has a very high tensile strength and is able to withstand the pressure from turgidity of the cell

• Linked to other molecules like lignin, which increases the strength of the cell walls

• Permeable, so water and solutes can enter or leave the cell

trigkycer

functions of lipids

energy yield, energy storage, insulation and hormonal communication

how do the properties of a triglyceride relate to function

• non polar, hydrophobic

• made up of glycerol [alcohol] and fatty acids [methyl group and a R group plus a carboxyl group]

• energy storage - more can be stored as they are hydrophobic,

  • plants - oils in seeds and fruits

  • mammals - oil drops in adipose tissue, help survive when food is scarce

• insulation -

  • composition of myelin sheath - helps transmission speed

  • adipose tissue insulates against heat loss

• buoyancy - low density of fat tissue increases animals ability to float

• protection

sketch the formation of triglycerides

esterification

types of fatty acids

• saturated - no double bonds

• mono-unsaturated - one double bond/kink or bend in the chain. -

• polyunsaturated - more than one double bond - bends molecule so less able to pack closely, and therefore are liquid at room temp

phospholipids - structure + function

• amphipathic - both phobic and philic

• 2 fatty acid tails

• cell surface membranes - phosphate head - hydrophilic [amphipathic] , form bilayers in water

• fluidity of cell membrane - more saturated = less fluid

biological roles of lipids

• energy source

• adipose tissue - heat insulation, and protection

cholesterol - function

• both hydrophobic and hydrophilic regions

• synthesised in the liver.

• cell membrane

  • disrupts the packing of phospholipids, making it more rigid

  • barrier between phospholipids

• produce steroid based hormones

emulsion test - method

• label food test tubes

• chop solids foods/grind using pestle and mortar

• add food to a depth of 1cm

• add 3cm of ethanol to each tube

• put a clean bung and shake

• allow the food to settle

• dispense 3cm of distilled water

• should turn cloudy if positive

biological roles of protein

• structural - main components of muscle, skin and hair

• catalytic - all enzymes are proteins

• signalling - receptors and hormones

• immunological - all antibodies are proteins

general amino acid structure

what is lipid bond

ester bond

what is protein bond

peptide bond

how do amino acids form long chains?

condensation reaction

what is two amino acid together for

dipeptide

polypeptide - four level of structure

primary, secondary, tertiary, and quaternary

primary polypeptide

long chains with no bonds or interactions, order of sequence

secondary polypeptides

hydrogen bonds form - causing either a alpha helix (every fourth peptide bond) or a beta pleated sheet [folds so parts are parallel]

tertiary polypeptide

• hydrophilic/phobic interactions - non polar R groups

• hydrogen bonds - r groups

• ionic bond - charged R groups

• Disulphide bonds [between two cysteine amino acids]

quaternary polypeptide

same as tertiary but with two separate polypeptide chains interlinked

how to denature proteins

bonds that maintain a shape are broken - change in temp, pH, salt concentration.

fibrous proteins lose structural strength, whereas globular become insoluble and inactive

types of proteins

globular [spherical], conjugated [parallel, cross links], fibrous [long insoluble molecules]

globular proteins - structure

• spherical shape

• tightly folded polypeptide chains

• hydrophobic groups are on the inside, making them soluble - easily transported for metabolic reactions

• the folding results in specific shapes - enzymes and antibodies.

globular - function/ examples

• transport - proteins in membranes, haemoglobin, iron, containing prosthetic group

• enzymes - catalase

  • speed up rate of reaction, decomposing hydrogen peroxide

  • active site where substrate binds

• hormones - insulin

  • controls/lowers blood glucose levels

  • 2 polypeptide chain with 3 disulphide bridges

fibrous - structure

parallel polypeptide chains held together by cross links. forming long, rope like fibres, with high tensile strength and are generally insoluble

fibrous - example

collagen - 3 polypeptide chains in a triple helix, high proportion of glycine, covalent bonds form cross links

• connective tissues - many hydrogen bonds = high tensile strength

keratin - hard structures, e.g. hair, nails, lots of disulphide bridges

silk - spiders webs and silkworms cocoons, elastic fibres, stretch and recoil. crosslinks between chains

ester bond - how does it form

esterification - condensation reaction

three water molecules are released

alpha helix shape

hydrogen bonds every fourth peptide bond - oxygen and hydrogen)

beta pleated sheet

two parts of polypeptide chain are parallel to each other

collagen vs haemoglobin

collagen -

• 3 chains

• long n thin

• fibrous

• structural

• repetitive

• no prosthetic group

• insoluble

haem - transports oxygen

• 4 chain - 2x alpha-globin, 2x beta-globin

• spherical

• globular

• functional

• haem prosthetic group

• soluble

how to distinguish between proteins

SAFES (Shape, Amino acid sequence, Function, Examples and Solubility)

inorganic ions - function

doesn’t contain ions

• essential in cellular processes

test for proteins

• Add Biuret ‘reagent’ contains [sodium hydroxide, to make the solution alkaline And a few drops of copper (II) sulfate solution ]

• If a colour change is observed from blue to lilac/mauve, then protein is present.

  • hold the test tubes up against a white tile when making observations

limitations to protein test

• The Biuret test is qualitative - it does not give a quantitative value as to the amount of protein present in a sample

• If the sample contains amino acids or dipeptides, the result will be negative (due to lack of peptide bonds)

semi-quantitative test for glucose

• setting up standard solutions with known concentrations of reducing sugar (such as glucose)

• using a serial dilution

• add the same volume of Benedict’s solution to each sample and heat in a water bath

• Any colour change observed for each solution of a known concentration in that time can be attributed to the concentration of reducing sugar present in that solution

• The same procedure is carried out on a sample with an unknown concentration of reducing sugar which is then compared to the stock solution colours to estimate the concentration of reducing sugar present

colourimeter - how to use

• must be calibrated before taking measurements

  • placing a blank into the colorimeter

  • This step should be repeated periodically whilst taking measurements to ensure that the absorbance is still 0

how are colourimeter results displayed

• plot a calibration or standard curve

  • Absorbance/transmission of light against the known concentrations can be used

  • Unknown concentrations can then be determined from this graph

benedict’s test - reducing sugars

• Add Benedict's reagent (contains copper (II) sulfate ions) to a sample solution in a test tube

• Heat the test tube in a water bath

• If a reducing sugar is present, a coloured precipitate will form as copper (II) sulfate is reduced to copper (I) oxide which is insoluble in water

• It is important that an excess of Benedict’s solution

• A positive test- blue to brown/brick-red

non-reducing sugars food test

• Add dilute hydrochloric acid and heat in a water bath

• Neutralise the solution with sodium hydrogencarbonate

  • Use a suitable indicator such as red litmus paper to identify when the solution has been neutralised

• Then carry out Benedict’s test as normal

  • Add Benedict’s reagent to the sample and heat in a water bath that has been boiled – if a colour change occurs, a reducing sugar is present

how does the non-reducing sugars test work?

• The addition of acid will hydrolyse any glycosidic bonds present in any carbohydrate molecules = monosaccharides

what is a non-reducing sugar example?

sucrose

biosensors

• Glucose oxidase uses FAD to oxidise glucose, forming FADH₂

• FADH₂ is then oxidised by the electrode in the device and this produces a current

• The current is a measurement of the glucose concentration

reagent test strip

for reducing sugars, changes colour if urine has glucose, used by doctors to test for diabeties