Topic 1: Biological Molecules

polymer

molecule made from larger number of monomers joined together

monomer

smaller units from which larger molecules are made

condensation

reaction that joins two molecules together with the formation of a chemical bond and involves the elimination of water molecule

hydrolysis

reaction breaks a chemical bond between two molecules and involves the use of a water molecule

monomer of carbohydrates

monosaccharide

2 monomers of carbohydrates

disaccharide

more than 2 monomers of carbohydrates

polysaccharide

bond between two monosaccharides

glycosidic bond

maltose

alpha glucose + alpha glucose

reducing sugar, disaccharide

sucrose

alpha glucose + fructose

non-reducing sugar, disaccharide

lactose

beta glucose + galactose

reducing sugar, disaccharide

starch

polysaccharide used for storage in **plants**, made from alpha glucose molecules

helical so compact, fit lots of energy in small area

insoluble so osmotically inactive

larger molecule so cannot cross cell-surface membrane

branched so can be hydrolysed quickly from multiple ends

glycogen

polysaccharide used for storage in **animal and bacteria**, made from alpha glucose molecules

helical so compact, fit lots of energy in small area

insoluble so osmotically inactive

larger molecule so cannot cross cell-surface membrane

highly branched so can be hydrolysed quickly from multiple ends

cellulose

polysaccharide used in the structure of cell walls in plants

long, straight, and unbranched chains of beta glucose that are rotated by 180° alternatively

joined by lots of hydrogen bonding

to provide rigidity and form (micro)fibrils

test for **reducing** sugars

add Benedict’s solution and boil

positive = blue turns to brick-red precipitate

test for **non-reducing** sugars

1. add Benedict’s solution and boil
2. negative result, stays blue
3. add acid and boil, to hydrolyse poly/disaccharides into monosaccharides
4. add alkali, to neutralise solution
5. add Benedict’s solution and boil
6. positive result, blue turns brick-red

test for starch

add iodine

positive result = brown to blue-black

triglyceride

1 glycerol molecule bonded to 3 fatty acid molecules

hydrophobic

found in fats and oils

phospholipid

1 glycerol molecule bonded to 2 fatty acid molecules and 1 phosphate group

hydrophobic tail

hydrophilic head

structure of fatty acids

R-COOH

R = hydrocarbon chain

COOH = carboxyl group

bond between glycerol and fatty acids

ester bond

difference between saturated and unsaturated

saturated = R-group/fatty acid chain which there is no C=C bonds

unsaturated = contains at least one C=C bond in the R-group

test for lipids

emulsion test

ethanol then water and shake

positive = cloudy-white emulsion

monomer of proteins

amino acid

2 monomers of proteins

dipeptide

more than 2 monomers of proteins

polypeptide

bond between two amino acids

peptide bond

between carboxyl and amine groups

how many amino acids are there

20

primary structure

series of condensation reactions leads to a sequence of amino acids/polypeptide chain

determines shape and function of protein

secondary structure

many hydrogen bonds form between amine and carboxyl groups

either alpha helix or beta pleated sheets

tertiary structure

secondary structure is twisted to for 3D complex shape

hydrogen, disulphide, and ionic bonds form between R-groups of amino acids

quaternary structure

more than one polypeptide chain

and non-protein groups like carbon

test for proteins

add Biuret solution

positive = blue to purple

how enzymes work

enzymes have an active site which is complementary to substrate

they bind to each other forming an enzyme-substrate complex

lowering the activation energy of the reaction, by distorting/bending the bonds of the substrate

products no longer fit the active site so it is released

enzyme remains unchanged

lock and key hypothesis

one substrate fits into active site

active site does not change shape and is complementary

induced fit hypothesis

active site is not initially complementary to substrate

the shape of active site then changes, so that it fits around the substrate

caused by the distorted bonds in the substrate, leading to a reaction

rate of enzyme activity: temperature

**as temperature increases**:

more kinetic energy, more frequent collisions, increase in enzyme-substrate complexes forming, rate increasing

temperature increases **above optimum**:

hydrogen bonds break, change in the 3D tertiary shape, change in shape of the active site, can no longer form enzyme-substrate complexes, enzymes denatures

rate of enzyme activity: pH

pH changes from optimum:

(hydrogen/ionic) bonds are broken, 3D tertiary shape is altered, active site changes shape, can no longer form enzyme-substrate complexes, enzyme denatures

rate of enzyme activity: substrate/enzyme concentration

more substrate/enzyme = faster rate

until no longer the limiting factor

competitive inhibitor

similar shape to the substrate so can bind to active

if it blocks the active site, fewer enzyme-substrate complexes form, lower rate of reaction

temporary and no overall damage to enzyme so reaches same final point at slower rate

to increase rate add more substrate

non-competitive inhibitor

attaches to enzyme away from the active site, altering the 3D tertiary structure, changing the shape of the active site and can no longer form enzyme-substrate complexes

adding more substrate has no effect due to enzymes being permanently altered

enzyme practical: control tubes

milk and water

= indicate colour of absence of enzyme activity

milk and hydrochloric acid

= indicate colour of complete hydrolysis of sample

enzyme practical: why are test tubes placed in water bath of set temperature for 5 mins before enzyme is added

to equilibrate temperature

enzyme practical: rate of reaction equation

rate of reaction = 1 / mean time to turn completely colourless

monomer of nucleic acid (DNA/RNA)

nucleotide

bond between nucleotides

phosphodiester

between pentose sugar and phosphate group

nucleotide structure

phosphate group

pentose sugar (deoxyribose, ribose)

nitrogen-containing base

double-helix structure of DNA

DNA nucleotides join to form 2 polynucleotide strands

nucleotides join up between phosphate and pentose sugar, creating sugar-phosphate backbone

hydrogen bonds between 2 strands

how is DNA a stable molecule

2 strands with specific base pairing

large number of hydrogen bonds

helix shape, reduces molecular damage

strong sugar-phosphate backbone

specific base pairing

each base only pairs with one specific base/one complementary base pairing

adenine to thymine

cytosine to guanine

DNA replication

1. occurs through semi-conservative replication
2. DNA helicase breaks hydrogen bonds between DNA strands
3. DNA uncoils, exposing the bases, and both strands act as a template
4. free DNA nucleotides are attracted to and bind with exposed bases
5. bases bind through specific base pairing: adenine to thymine and cytosine to guanine
6. DNA polymerase joins adjacent nucleotides by condensation reactions

semi-conservative replication

new strand of DNA is built on each of the original 2 strands so that the new DNA molecules are identical to original

each of the two new molecules of DNA has one of the original strands and one new strands

scientists that discovered model of DNA and DNA replication

Watson and Crick

Rosalind Franklin

ATP structure

adenosine triphosphate consists of

adenine, nitrogen-containing base

ribose sugar

3 phosphate groups

ATP hydrolysis enzyme

ATP hydrolase

ATP → ADP + Pi

ATP resynthesis enzyme

ATP synthase

(during photosynthesis and respiration)

why a large amount of ATP is required

ATP cannot be stored/immediate source of energy

release small amounts of energy at a time

why ATP is a suitable source of energy

small amount of energy lost as heat

releases energy instantaneously, immediate source

phosphorylates other compounds, makes them more reactive

rapidly re-synthesised

is not lost/does not leave cell

properties of water

**metabolite** in metabolic reactions like condensation and hydrolysis

**solvent** so reactions can occur, allowing transport of substances

**high heat capacity** so buffers changes in temperature

**latent heat of vaporisation** so provides cooling effect with loss of water through evaporation

**cohesion** so supports column of water in tube-like transport cells of plants and produces surface tension where water meets air

examples of inorganic ions

hydrogen ions related to pH

iron ions related to haemoglobin

sodium ions related to co-transport of glucose and amino acids

phosphate ions related to DNA, RNA, and ATP