main elements:

- carbon
- hydrogen
- oxygen
- nitrogen
- phosphorus
- sulphur
carbohydrates: CHO
lipids: CHO
proteins: CHONS
nucleic acids:
CHONP

chemical group role

carbohydrates - 18% of humans

- makes up skeleton of most biological molecules
- 4 valence electrons allows most types of bonds
- monosaccharides make up carbohydrates
- fast source of energy

proteins - muscle development + immune system + enzymes

- genes
- monomer: amino acid, polymer: polypeptide

lipids - fatty acids and glycerol

- insulation + long term energy source

nucleic acids - monomer: nucleotides, polymer: RNA/DNA

- coding of traits

biochemicals and bonds

- covalent bonds join atoms together to form molecules
- carbon can make four covalent bonds
- carbon can bond to form chains/rings with other atoms bonded to the chain
- carbon can also form double bonds
- oxygen can form two bonds
- hydrogen can form two bonds
- nitrogen can form three bonds

CATION ANION

calcium Ca2+ nitrate NO3-

sodium Na+ hydrogen carbonate HCO3-

potassium K+ chloride Cl-

hydrogen H+ phosphate PO4 3-

ammonium NH4+ hydroxide OH-

macromolecule subunit (monomer)

polysaccharide monosaccharide

proteins amino acids

lipids fatty acid & glycerol

nucleic acid nucleotides

hydrogen bonds:
hydrogen bonds form when negatively charged sections of the molecule comes close to
the positively charged hydrogen atoms within the molecule itself
- weak and easily broken

water
- polar molecule (slight positivity for
hydrogen, slight negativity for oxygen)
- oxygen electrons are not spread equally, so
nucleus is exposed (slightly negative)
- intermolecular forces / hydrogen bonds
between molecules are weak (between two
water molecules)
- hydrogen bonding to another oxygen atom

characteristics:
- is cohesive, water sticks to itself (capillary action - process where water can rise up a
narrow tube against force of gravity)
- adhesive properties, sticks to other surfaces
- high boiling point
- transport medium
- coolant, reduces thermal energy
- surface tension (resists external force)
- high SHC
- stable environment for aquatic organisms
- good solvent

carbohydrates
- contains carbon, hydrogen and oxygen
monosaccharide: single sugar unit (e.g glucose, fructose, ribose)
polysaccharide: two or more monosaccharides linked (e.g glycogen, cellulose, starch)

basic building blocks (monomers) of carbohydrates are glucose molecules

glucose: six carbons -> hexose monosaccharide (hexose sugar)

- OH group on carbon 1 is in
opposite positions
- glucose molecules are polar,
soluble in water (hydrogen
bonds form between
groups) -> glucose is
dissolved in cytosol of cell
- a: ants b: bats

condensation reactions
covalent bond (glycosidic bond) is formed between two alpha glucose molecules
water molecule is formed as a product (oxygen bridge)
alpha glucose molecules can be joined by glycosidic bonds to form starch (chemical
energy store in plant cells)

amylose: starch polysaccharide

- formed by alpha glucose molecules joined by 1-4 glycosidic bonds
- angle of bond -> long chain of glucose twists, forms a helix -> compact and less
soluble
amylopectin: starch polysaccharide
- formed by alpha glucose molecules joined by 1-4 glycosidic bonds,
- (unlike amylose) some glycosidic bonds formed by condensation reactions between c1
+ c6 on two glucose molecules
- has a branched structure (occurring approx. once in every 25 glucose subunits) ->
insoluble

glycogen: energy storage molecule to starch in animals + fungi

- forms more branches than amylopectin (free ends where glucose molecules can be
added / removed, speeds up processes of storing / releasing glucose)
- more compact due to coiling, less space storage, insoluble

hydrolysis reactions
- glucose is stored until needed for respiration (biochemical energy in stored nutrients
is converted into useable energy)
- undergoes hydrolysis: requires water molecules (catalysed by enzymes)

cellulose
- beta glucose molecules cannot join together (OH groups too far to react)
- some turned upside down (inverted) -> cannot coil / form branches
- straight chain molecule formed -> cellulose
- molecules make hydrogen bonds with each other (microfibrils)
- microfibrils join together to form macrofibrils -> combine to produce fibres
- cellulose is hard to break down into monomers

examples of sugars
- sucrose - is a disaccharide (made of glucose and fructose)
- lactose - a disaccharide (made of glucose and galactose)
- maltose - is a disaccharide (made of two alpha-glucose)
- pentose monosaccharides: sugars containing five carbon atoms
- ribose: pentose sugar, present in RNA nucleotides
- deoxyribose: pentose sugar, present in DNA nucleotides

polymerisation
in a condensation reaction:
- 2 molecules are joined together to make a larger + complex molecule with loss of
water
- a water molecule is released
- a new covalent bond is formed
- a larger molecule is formed by bonding together of smaller molecules

in a hydrolysis reaction:
- a large molecule is split into smaller sections by breaking a bond, adding -H to one
section and -OH to another
- water molecule is used
- covalent bond is broken
- smaller molecules are formed by the splitting of a larger molecule
 testing for carbohydrates
reducing sugars: reducing agents, can donate electrons / reduce another
molecule
(all monosaccharides, some disaccharides are reducing sugars)
reduction reaction: electrons gained
reducing sugars donate electrons to another chemical (copper 2 sulphate / benedicts
solution) -> forms red precipitate of copper 1 oxide

copper 2 sulfate is an alkaline solution / base (benedicts reagent)

test for reducing sugars

1. add 2cm³ of food sample (liquid form) to test tube
2. add 2cm³ of benedicts reagent
3. heat mixture in gentle boiling water bath for 5 mins

test for non-reducing sugars (sucrose)

1. confirm sample is not a reducing sugar
2. add 2cm³ of food sample (liquid) to 2cm³ of dilute
HCl and place in gentle boiling water bath for 5 mins
3. slowly add NaOH solution, check solution is neutral
4. retest solution again with benedicts

test for starch

iodine test (positive = blue black)

to check conc: filter + weigh precipitate

biosensors
- use biological components (e.g enzyme) to determine
presence and concentration of molecules (e.g glucose)
colorimeters
- quantitatively measures absorbance / transmission of light by a coloured solution
- use a standard solution
- red filter for benedicts, test water to 0 first (calibrate)

proteins
structure of proteins
monomer: amino acid
polymer of amino acids: polypeptide
one or more polypeptides as a complex
macromolecule: protein

amino acids are made up of...

- an amino group (NH2)
- acidic group -> carboxyl group (-COOH)
- R group
 - 20 amino acids found in cells
- 5 are non essentials
- 9 are essential
- 6 are conditionally essential

- glycine (R group = H)
- alanine (R group = CH3)
- valine (R group = C3H7)

formation of dipeptide:
carboxyl group of one amino acid
reacts with amino group of
second amino acid
- water molecule is formed
during a condensation reaction
- peptide bond between both
amino acids
- polypeptide (a chain of many
amino acids)
- a protein may consist of one or
more polypeptide chains
-
-
haemoglobin consists of four polypeptides
hydrolysis reaction:
dipeptide + water -> two amino acids

levels of protein structure

primary structure
- sequence of amino acids in a polypeptide chain
(polypeptide bond)
secondary structure
- formation of secondary structures (α-helices and β-
pleated sheets)
- formed as a result of hydrogen bonding between
different amino acids in the chain
- hydrogen bonds can form between
● the CO (carboxyl group) of one amino acid and the
NH (amine group) of another amino acid
● the CO of one amino acid and the OH of another
amino acid

tertiary structure
- secondary structures fold up to form a very precise 3d
structure
- R group interactions:
● hydrophobic and hydrophilic interactions (weak)
 ● hydrogen bonds (weak) -> can be split by high temp and altered pH
● ionic bonds (stronger than H bonds) -> can be split by changing pH
● disulfide bonds / bridges (covalent and strongest) -> can be split by reducing agents
quaternary structure
- some proteins have more than one polypeptide chain held together in a 3D structure
- polypeptide chains held together in quaternary structures by same type of forces
responsible for formation of tertiary structures
- can also involve addition of non-amino acid derived groups (prosthetic groups)
- globular proteins form a spherical mass with a specific 3D shape (both tertiary and
quaternary)
- fold up so hydrophilic groups on outside, hydrophobic groups inside

biuret test
protease: enzyme catalysing reverse reaction - turning peptides to amino acids
biuret reagent: solution + sodium hydroxide (to turn alkaline) + copper sulfate solution
negative: blue, positive: purple
- identifies peptide bonds
- different proteins have different numbers of peptide bonds
- degree of colour change: number of peptide bonds
amino acids won’t react to biuret test (only peptide bonds)

types of proteins
1. enzymes 1. amylase, protease, lipase
2. transport 2. haemoglobin
3. movement 3. actin, myosin
4. cell recognition 4. antigens
5. channels 5. membranes
6. structure 6. collagen, keratin
7. hormones 7. insulin, thyroxine
8. protection 8. antibodies

globular (insulin)
conjugated proteins (haemoglobin / catalase)
fibrous proteins (keratin / elastin / collagen)

globular proteins:
- compact
- spherical in shape
- soluble -> tertiary structure folding -> hydrophobic R groups inside, hydrophilic R
groups outside
insulin:
- hormone involved in regulation of blood glucose
- soluble, transported in blood
- specific shape to fit receptors on cell membranes
- disulfide bonds
conjugated proteins:
- type of globular protein
- contains a prosthetic group

haemoglobin:
- 4 polypeptide chains
- 2 identical α-chains and 2 identical β-chains
- nearly spherical -> hydrophobic chains point inwards
- helical
- outward pointing hydrophilic side chains
maintain solubility
- each polypeptide chain contains a haem
group
- haem group: prosthetic group
- haem group has Fe2+ in centre
- function: oxygen carrying pigment found in
rbc

catalase: catalyzes the decomposition of

hydrogen peroxide to water and oxygen

prosthetic group: non-amino acid component

that is part of the structure of conjugated
proteins (may be vitamin, sugar, lipid or
metal ion)

fibrous:
- long parallel polypeptide chains
- cross linkages at intervals forming long fibres or sheets
- usually insoluble
- many have structural roles (e.g keratin, collagen, elastin)
collagen:
- skin, teeth, tendons, cartilage, bones + walls of blood vessels
- 3 polypeptide chains, each in shape of helix
- each chain contains 1000 amino acids (every third amino acid is glycine) -
> triple helix
- 3 helical chains wind around each other -> three stranded ‘rope’
- glycine (small) allows the 3 polypeptides to lie close together to form tight
coil
- 3 strands held together by H bonds
- bonding causes fibres to form
- adjacent molecules of collagen held together by covalent bonds formed
between carboxyl group of one amino acid and amine group of another
- ends of parallel molecules are staggered -> prevents weak areas from
running across collagen fibre
- very strong (¼ strength of mild steel)
lipids
- carbon + hydrogen + oxygen
- fats are lipids that are solid at rtp, oils are lipids that are liquids at rtp
- non polar molecules (electrons in outer orbitals more evenly distributed -> no + or -
areas within molecules -> lipids not soluble in water)
- large complex molecules: macromolecules (repeating units / monomers)
- macromolecules: triglycerides, phospholipids, sterols

triglycerides
- one glycerol molecule + three fatty acids
- glycerol: alcohol (OH)
- fatty acids: carboxylic acids (carboxyl group COOH with hydrocarbon chain)
- glycerol + fatty acids contain OH groups
- 3 ester bonds formed, 3 water molecules formed
- condensation reaction (esterification)
- hydrolysis reaction: uses 3 water molecules to break down to fatty acids + glycerol

- saturated: no double bonds between carbons (max no. of bonds with H)

- monounsaturated: one double bond between carbons
- polysaturated: two or more double bonds between carbons
- double bonds cause molecule to kink / bend -> cannot pack closely together -> liquid
at rtp
- plants: unsaturated triglycerides (oils) - healthier in human diet than saturated
triglycerides (solid fats)

phospholipids
- contains phosphorus, CHO
- 2 fatty acid tails (non-polar, repelled by
water, hydrophobic)
- phosphate ion heads (polar, attracted to
water, hydrophilic)
 - distribution of charge across the molecule

- phospholipids mix with water -> form layer at water surface (phosphate heads stick
into water, fatty acid tails stick out of water) = surface active agents
- inorganic phosphate ions found in cytoplasm of every cell
- phosphate ions have extra electrons -> negatively charged -> soluble in water
triglyceride phospholipid

difference 3 fatty acids 2 fatty acids

difference 3 ester bonds 2 ester bonds

difference absence of phosphate presence of phosphate

similarity - contain glycerol

- contain fatty acids
- contain ester bonds
- contain C, H and O

sterols:
- lipid found in cells
- little structural similarity to lipids
- type of alcohol
- complex alcohol molecules based on complex ring structure with polar OH group at
one end

cholesterol
- is a sterol
- small molecule with 4 carbon rings (C27H46O)
- made in intestine and liver
- -OH group is polar
- 4 hydrocarbon rings and hydrocarbon tail are non polar
- found in biological membranes
- steroid (e.g testosterone, oestrogen, progesterone made from cholesterol)
- excess cholesterol form gallstones in bile + cause atherosclerosis in blood vessels
- small, narrow and hydrophobic -> helps regulate fluidity and strength of cell
membranes (keep fluid at low temp, stops from becoming too liquid at high temp)
- formation of vitamin D, bile and steroid hormones

role of lipids:
biological roles
- membrane formation, creation of hydrophobic barriers
- hormone production
- electrical insulation necessary for impulse transmission
- waterproofing (e.g birds nests, plant leaves)
 long term energy storage
- thermal insulation to prevent heat loss
- cushioning to protect vital organs (heart + kidneys)
- buoyancy for aquatic animals

testing for lipids:

emulsion test
1. few drops of liquid food sample to test tube
2. add 2cm3 ethanol, shake
3. 2cm3 of deionised water
4. cloudy white suspension at top of solution (dont write precipitate)

sudan III (red fat-soluble dye)

1. few drops of liquid food sample to test tube
2. mix sample with water
3. add few drops of sudan 3 stain
4. mix -> sudan turns lipids red

translucency grease mark test

- lipid wiped on filter paper
- if has grease stain, contains lipids

nucleic acids
DNA: stores information (base ATGC)
RNA: reads and translates information (base AUGC)
- mRNA - messenger ribonucleic acid
- tRNA - transfer ribonucleic acid
- rRNA - ribosomal ribonucleic acid

monomers: nucleotide
polymers: nucleic acids
nucleotides linked by
condensation reaction ->
polymer (polynucleotide)

deoxyribose and ribose:

pentose sugars

phosphate group: acidic and

negatively charged (PO4²-)

nitrogenous base:
purine (large) pyrimidine (small)

- adenine - thymine
- guanine - cytosine
- uracil
(each nitrogen is connected to carbon)

condensation of DNA:
- double helix structure
- two antiparallel sugar phosphate backbones
- phosphodiester bonds form between phosphate group of one nucleotide and OH
group of another nucleotide
- sugar phosphate backbone forms
- 2 hydrogen bonds between A and T
- 3 hydrogen bonds between G and C
- complementary base pairing: purines always pair up with pyrimidines
- bonds broken by hydrolysis

- antiparallel: backbone runs parallel but in opposite directions

- parallel bc small pyrimidine base always binds to larger purine base -> constant
distance between backbones
DNA RNA

- 2 strands - 1 strand
- thymine base - uracil base
- deoxyribose - ribose
- 4 bases - 4 bases
- pentose sugar - pentose sugar

DNA replication & The Genetic Code

- happens in the nucleus
- replicates in interphase
- ensures mitosis results in genetically identical daughter cells
- semi-conservative - each new DNA molecule consists of one conserved (original)
strand plus one newly built strand

how DNA replicates (semi-conservative)

1. double helix unwinds
2. DNA helicase (enzyme) unwinds the two strands
3. both strands act as templates for the formation of new strands
4. free nucleotides align
5. complementary base pairing occurs (purine & pyrimidine / A-T & G-C)
6. H bonds reform
7. sugar phosphate backbone forms - DNA polymerase
- one = unwinds
- two = two strands
- three = templates
- four = free nucleotides

protein synthesis
- gene: sequence of DNA nucleotides that codes for a protein
- nuclear envelope protects DNA from damaging in cytoplasm

the genetic code

triplet code:
- read in groups of three bases
- three bases = one codon
- one codon represents one amino acid

ATGCGGATC = 9 bases
ATG CGG ATC = three codons
Met Arg Ile = three amino acids

valine: GTT, GTC, GTA, GTG

universal code: all organisms use the same code (ATGCU)

degenerate code: amino acids can be coded for by more than one codon
 64 combinations -> 20 amino acids

mRNA = messenger RNA (complementary to DNA)

- made in nucleus
- carries genetic code to cytoplasm, used to make a protein in translation
rRNA = ribosomal RNA (found in ribosomes)
- forms two subunits in a ribosome
- moves along mRNA strand in synthesis, helps catalyse formation of peptide bonds
tRNA = transfer RNA (found in cytoplasm - carries amino acids to ribosomes)
- found in cytoplasm
- has amino acid binding site
- carries amino acids to ribosomes during translation

transcription:
- strand of DNA identical to mRNA transcribed: sense strand (5’ to 3’)
- antisense strand (3’ to 5’): complementary copy, non coding, strand acting as a
template
- generates mRNA from 5’ to 3’
1. DNA unwinds, unzips
2. mRNA strand built
3. free RNA nucleotides pair up (complementary)
4. sugar phosphate backbone bonded by RNA polymerase
5. hydrogen bonds break (mRNA + DNA)
6. mRNA leaves nucleus

translation:
1. mRNA moves to ribosomes, binds to
subunit of ribosome
2. tRNA (with complementary anticodons)
binds to mRNA start codon
3. specific amino acids attached to tRNA, start
codon codes for methionine (AUG)
4. peptide bonds formed between amino acids
(condensation reactions)
- catalysed by peptidyl transferase
5. stop codon - end of polypeptide chain

- maximum of 2 tRNAs can be bound at same

time
- amino acids are added one at a time
- proteins may undergo further modifications at golgi

ATP
metabolic processes requiring energy:
- exocytosis
- movement (e.g protein fibres in muscle contraction)
- chemical reactions (respiration)
- synthesis (e.g protein synthesis)
- dna replication
- phagocytosis
- transport (e.g pumping ions across membranes active transport)

phosphates:
- 1 = AMP
(monophosph
ate)
- 2 = ADP
(diphosphate)
phosphorylated:
when a
phosphate
group is
added
adenosine =
adenine +
ribose
ATP = universal energy currency

ATP can be hydrolysed to

form ADP + P
ADP can be hydrolysed
to form AMP + P
AMP can be hydrolysed
to form adenosine +
P

P = inorganic phosphate
bonds between phosphate groups: phosphoanhydride bonds (high energy bond)

hydrolysis of ATP / ADP / AMP releases energy -> energy used to synthesise molecules
ATP + H2O -> ADP + Pi + energy

1. energy released from respiration

2. ADP + P undergo a condensation reaction to form ATP
3. ADP becomes phosphorylated to form ATP
4. ATP is hydrolysed releasing some energy
5. remaining ADP is free to become phosphorylated again using energy released from
respiration
made in mitochondria and cytoplasm
enzyme catalysing reaction: ATP synthase

properties of ATP
- good immediate energy store
- not good for long term energy storage
small moves easily into / out of / within cells

water soluble reactions occur in aqueous environments

bonds between intermediate energy released - large enough to be useful, not so large
phosphates that energy is lost as heat

releases energy in suitable for cellular reactions, energy not lost as heat
small quantities

easily regenerated can be recharged with energy