Topic 1: Biological Molecules

Contents (checklist)
1.1 Monomers and polymers ..................................................................................................................2
Monomers and polymers ....................................................................................................................... 2
Condensation and hydrolysis reactions ................................................................................................. 2
1.2 Carbohydrates ..................................................................................................................................3
Monosaccharides and disaccharides ..................................................................................................... 3
Isomers of glucose: - and -glucose .................................................................................................... 3
Polysaccharides ...................................................................................................................................... 4
Biochemical tests ................................................................................................................................... 5
1.3 Lipids ................................................................................................................................................6
Triglycerides ........................................................................................................................................... 6
Phospholipids ......................................................................................................................................... 6
Saturated & unsaturated fatty acids...................................................................................................... 6
Emulsion test for lipids .......................................................................................................................... 6
1.4.1 Proteins: general properties of proteins..........................................................................................7
Amino acids, dipeptides and polypeptides ............................................................................................ 7
Structural levels of proteins and the role of bonds ............................................................................... 7
Biuret test for protein ............................................................................................................................ 7
1.4.2 Proteins: many proteins are enzymes .............................................................................................8
Introduction to enzymes ........................................................................................................................ 8
Factors affecting rate of enzyme-controlled reactions ......................................................................... 8
1.5.1 Nucleic acids: structure of DNA & RNA..........................................................................................10
Function of DNA & RNA .......................................................................................................................10
Structure of DNA & RNA nucleotides and polymers............................................................................10
Maths ...................................................................................................................................................10
1.5.2 Nucleic acids: DNA replication ......................................................................................................12
Process of DNA replication ..................................................................................................................12
Evidence for semi-conservative replication (Meselson and Stahl) ......................................................12
1.6 ATP .................................................................................................................................................13
The structure of adenosine trisphosphate (ATP) .................................................................................13
ATP/ADP hydrolysis and condensation ................................................................................................13
The properties of ATP make it a suitable immediate source of energy ..............................................13
1.7 Water .............................................................................................................................................14
How hydrogen bonding occurs between water molecules .................................................................14
Properties of water that are important in biology ..............................................................................14
1.8 Inorganic ions .................................................................................................................................15
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1.1 Monomers and polymers

Monomers and polymers
• Monomer: small, single molecule, many of which can be joined together to form a polymer
• Polymer: large molecule made up of many similar / identical monomers joined together

Condensation and hydrolysis reactions

A condensation reaction:
• Joins 2 molecules together
• Eliminates a water molecule
• Forms a chemical bond e.g. glycosidic bond

A hydrolysis reaction:
• Separates 2 molecules
• Requires addition of a water molecule
• Breaks a chemical bond

Exam tip: to get full marks for a diagram of a condensation or hydrolysis reaction, you need to include the
H2O molecule that is added or removed

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1.2 Carbohydrates
Carbohydrates can be classified into 3 groups based on how many units they are made of (1, 2 or many)

Monosaccharides Disaccharides Polysaccharides

The monomers from which Formed by the condensation Formed by the condensation
larger carbohydrates are made of 2 monosaccharides of many monosaccharides

Monosaccharides and disaccharides

Monosaccharides and disaccharides are simple carbohydrates (sugars)

Monosaccharides Structure of glucose

• Monosaccharides are the • 6 carbon atoms, labelled in red on diagram (a)
monomers from which larger • Learn how to draw glucose in as much detail as diagram (b)
carbohydrates are made
• E.g. glucose, fructose and
galactose
(a) (b)
Disaccharides
• Glucose + glucose = maltose
• Glucose + fructose = sucrose
• Glucose + galactose = lactose

A condensation reaction between 2 monosaccharides forms a glycosidic bond

Isomers of glucose: - and -glucose

• Isomer: same molecular formula but
differently arranged atoms
• Difference in structures: OH group is
below C1 on -glucose but above C1 in
-glucose

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Polysaccharides
Examples: starch, glycogen and cellulose

Glycogen
• Function: energy store in animal cells
• Structure: polysaccharide of -glucose with C1-C4 and C1-C6
glycosidic bonds so branched

Structure of glycogen related to its function:

Branched; can be rapidly hydrolysed to release glucose for respiration to provide energy
Large polysaccharide molecule; can’t leave cell
Insoluble in water; water potential of cell not affected i.e. no osmotic effect

Starch
• Function: energy store in plant cells
• Structure: polysaccharide of -glucose. Mixture of
amylose and amylopectin; amylose has C1-C4
glycosidic bonds so is unbranched, while amylopectin
has C1-C4 and C1-C6 glycosidic bonds so is branched

Structure of starch related to its function (amylose):

Helical; compact for storage in cell
Large polysaccharide molecule; can’t leave cell
Insoluble in water; water potential of cell not affected i.e. no osmotic effect

Cellulose
• Function: provides strength and structural support to plant cell walls

Structure related to function:

Every other beta-glucose molecule is
inverted in a long, straight,
unbranched chain
Many hydrogen bonds link parallel
strands (crosslinks) to form micro
fibrils (strong fibres)
H bonds are strong in high numbers
Provides strength and structural
support to plant cell walls

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Biochemical tests
Benedict’s test for sugars
Reducing sugar Non-reducing sugars
• All monosaccharides e.g. glucose • No monosaccharides
• Some disaccharides e.g. maltose / lactose • Some disaccharides e.g. sucrose

Benedict’s test for reducing sugars

1. Add benedict’s reagent
(blue) to sample
2. Heat in a boiling water bath
3. Positive = green / yellow / orange / red
precipitate (reducing sugar present)

Benedict’s test can also be used to test for non-

reducing sugars, indirectly:

Benedict’s test for non-reducing sugars

1. Add a few drops of dilute hydrochloric acid (hydrolyse sugar into its constituent reducing sugars)
2. Heat in a boiling water bath
3. Neutralise with sodium bicarbonate
4. Add Benedict’s reagent and heat again
5. Non-reducing sugar present = green / yellow / orange / red precipitate

Determining glucose concentration

1. Produce a dilution series of glucose solutions of known concentrations
2. Perform a Benedict’s test on each sample
• Heat with Benedict’s solution
• Use same amount of solution for each test
• Use excess Benedict’s
• Remove precipitate by filtering
3. Using a colorimeter, measure the absorbance of each sample and plot a calibration curve
• Calibrate colorimeter using unreacted Benedict’s
• Use a red filter
• Less absorbance of filtrate = more sugar present (as removed precipitate)
• Plot absorbance against glucose concentration
4. Repeat with unknown sample (find absorbance) and use graph to determine glucose concentration

Iodine test for starch

1. Add iodine dissolved in potassium iodide to solution and shake/stir
2. Blue-black colour = starch present

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1.3 Lipids
Triglycerides and phospholipids are 2 groups of lipids

Triglycerides
Triglycerides are formed by the
condensation of 1 molecule of
glycerol and 3 fatty acids

A condensation reaction between

glycerol and a fatty acid (RCOOH) forms
an ester bond

Properties related to structure Zig zags represent a simplified hydrocarbon

tail, also sometimes represented as ‘R’
Triglycerides: energy storage molecules
• High ratio of C-H bonds to C atoms in hydrocarbon tail
so release more energy than the same mass of carbohydrates
• Insoluble in water (clump together as droplets)
so no effect on water potential of cell

Phospholipids
In phospholipids, one of the fatty acids of a triglyceride
is substituted by a phosphate-containing group

Properties related to structure

Phospholipids: form bilayer in cell membrane, allowing diffusion of non-polar / small molecules
• Phosphate heads are polar / hydrophilic
so are attracted to water orient to aqueous environment either side of membrane
• Fatty acid tails are non-polar / hydrophobic
so are repelled by water orient to interior of membrane repels polar / charged molecules

Saturated & unsaturated fatty acids

• Saturated: no C=C double bonds in hydrocarbon
chain; all carbons fully saturated with hydrogen
• Unsaturated: one or more C=C double bonds in
hydrocarbon chain

Emulsion test for lipids

1. Add ethanol and shake (dissolves lipids)
To get the marks in the exam, you must
2. Then add water
state steps 1 and 2 in the correct order
3. Positive: milky/cloudy white emulsion

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1.4.1 Proteins: general properties of proteins

General structure of an amino acid
Amino acids, dipeptides and
Variable side chain / group
polypeptides
Amino acids are the monomers
from which proteins are made
Amine group Carboxyl group
20 amino acids are common in all organisms –
differ only in their side group
Amino acid Amino acid
H R O H R O
A condensation reaction between 2
amino acids forms a peptide bond H N C C OH H N C C OH

H H
• Dipeptide – 2 amino acids joined H2O Dipeptide
• Polypeptide – many amino acids joined H R O H R O
H N C C N C C OH
• A functional protein may contain one or more polypeptides
H Peptide H
bond
Structural levels of proteins and the role of bonds
o
Primary (1 ) structure
• Sequence of amino acids in a polypeptide chain primary
structure
o
Secondary (2 ) structure
• Hydrogen bonding between amino acids (between
carbonyl O of one and amino H of another) secondary
• Causes polypeptide chain to fold into a repeating pattern structure
e.g. alpha helix or beta pleated sheet
o
Tertiary (3 ) structure
tertiary
• Overall 3D structure of a polypeptide held together by
structure
interactions between amino acid side chains:
• Ionic bonds / disulfide bridges / hydrogen bonds
o
Quaternary (4 ) structure quaternary
• Some proteins are made of 2+ polypeptide chains structure
• Held together by more hydrogen, ionic and disulfide
bonds

Proteins have a variety of functions

Biuret test for protein within all living organisms. You need
• Add biuret solution: sodium hydroxide + copper (II) sulfate to be able to relate the structure of
• Protein present: purple colour (negative = stays blue) proteins to properties of proteins
• Detects presence of peptide bonds named throughout the specification
e.g. enzymes / antibodies

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1.4.2 Proteins: many proteins are enzymes

Introduction to enzymes
• Each enzyme lowers the activation energy of the reaction it
catalyses (see diagram) speed up rate of reaction
• Enzymes are biological catalysts; they catalyse a wide range
of intracellular (within cells) and extracellular (outside cells)
reactions that determine structures and functions from
cellular to whole-organism level.

Models of enzyme action

Lock and Key model Induced Fit model

Old, outdated Recent, accepted
• Active site is a fixed 1. Before reaction, enzyme active site not completely complementary to
shape / doesn’t substrate / doesn’t fit substrate
change shape; it is 2. Active site shape changes as substrate binds and enzyme-substrate
complementary to complex forms
one substrate 3. This stresses / distorts bonds in substrate leading to a reaction
• After a successful
collision, an enzyme-
substrate complex
forms leading to a
reaction

The specificity of enzymes

• Enzymes have a specific shaped tertiary structure and active site
• Sequence of amino acids (primary structure) determines tertiary structure
• Active site is complementary to a specific substrate
• Only this substrate can bind to the active site, inducing fit and forming an enzyme-substrate complex

Factors affecting rate of enzyme-controlled reactions

Enzyme concentration
• Increasing enzyme conc. rate of reaction increases
• Enzyme conc. = limiting factor (substrate in excess)
• More enzymes more available active sites
• More successful E-S collisions and E-S complexes
• At a certain point, rate of reaction plateaus
• Substrate conc. = limiting factor (all substrates in use)

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Substrate concentration
• Increasing substrate conc. rate of reaction increases
• Substrate concentration = limiting factor (too few
enzyme molecules to occupy all active sites)
• More successful E-S collisions and E-S complexes
• At a certain point, rate of reaction plateaus
• Enzyme conc. = limiting factor (all active sites
saturated; excess substrate)

Temperature
• Increasing temp. up to optimum rate of reaction increases
• Increase in kinetic energy
• More successful E-S collisions and E-S complexes
• Increasing temp. above optimum rate of reaction falls
• Enzymes denature; tertiary structure and active site
change shape (hydrogen / ionic bonds break)
• Fewer E-S collisions and E-S complexes (substrate no
longer binds to active site)
• Rate of reaction 0 when all enzymes denatured

pH
• pH above / below optimum pH rate of reaction decreases
• Enzymes denature; tertiary structure and active site change
shape (hydrogen and ionic bonds break)
• Complementary substrate can no longer bind to active site
• Fewer E-S collisions and E-S complexes
• pH = - log10 [H+]

Concentration of competitive and non-competitive inhibitors

Competitive inhibitors decrease rate of reaction
• Similar shape to substrate
• Competes for / binds to / blocks active site so
substrates can’t bind
• Fewer E-S complexes
• Increasing substrate conc. reduces effect of inhibitor
(level of inhibition dependent on relative concs. of
substrate and inhibitor)
Non-competitive inhibitors decrease rate of reaction
• Binds to site away from the active site (allosteric site)
• Enzyme tertiary structure / active site change shape
so substrate can’t bind to active site
• Fewer E-S complexes
• Increasing substrate concentration has no effect on
rate of reaction as causes permanent change to active
site

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1.5.1 Nucleic acids: structure of DNA & RNA

Function of DNA & RNA
• Deoxyribonucleic acid (DNA) holds genetic information
• Ribonucleic acid (RNA) transfers genetic information from DNA to ribosomes
Ribosomes are formed from RNA and proteins

Structure of DNA & RNA nucleotides and polymers

The differences between DNA
and RNA nucleotides
• DNA nucleotides have the
pentose sugar deoxyribose,
whereas RNA nucleotides have
the pentose sugar ribose
• DNA nucleotides can have the
• Nucleotides contain a pentose sugar, a nitrogenous base base thymine, whereas RNA
and a phosphate group nucleotides have uracil instead
• Nucleotides (monomers) make DNA or RNA which are
nucleic acids (polymers)
• DNA or RNA nucleotides are joined together by
condensation reactions forming phosphodiester bonds
• DNA: 2 strands joined in anti-parallel, held together by
hydrogen bonds between specific complementary base
pairs (A-T and C-G), twisting into a double helix
• RNA: singe RNA polynucleotide strand

The differences between DNA and RNA molecules

• DNA molecules are double stranded (double helix),
whereas RNA molecules are single stranded
• DNA is longer whereas RNA is shorter

Exam tip: examiners can be picky when it comes to comparison questions. To get the marks, try and
include ‘whereas’ to ensure you have covered both sides

Structure of DNA related to its functions

• Double stranded both strands can act as templates for semi-conservative replication
• Weak hydrogen bonds between bases can be unzipped for replication
• Complementary base pairing accurate replication
• Many hydrogen bonds between bases stable / strong molecule
• Double helix with sugar phosphate backbone protects bases / H bonds
• Long molecule store lots of (genetic) information (that codes for polypeptides)
• Double helix (coiled) compact

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Maths
Use incomplete information about the frequency of bases on DNA strands to find the
frequency of other bases
Key idea…
• % of adenine in strand 1 = % of thymine in strand 2 (and vice versa)
• % of guanine in strand 1 = % of cytosine in strand 2 (and vice versa)
• Because of specific complementary base pairing between 2 strands
Worked example:

• A piece of DNA consists of 74 base pairs

C G A T
• The 2 strands of the DNA, strands A and B, were analysed to find the
Strand A 26
number of bases of each type that were present
Strand B 19 9
• Some of the results are shown in the table. Fill in the gaps

G in strand B = 26; G in strand A = 19; T in strand A = 9; A in strand A = 74(total) – 19 – 26 – 9 = 20; T in

strand B = 20

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1.5.2 Nucleic acids: DNA replication
Process of DNA replication
1. DNA Helicase breaks hydrogen bonds between bases, unwinds double helix
2. = two strands which both act as templates
3. Free floating DNA nucleotides attracted to exposed bases via specific complementary base
pairing, hydrogen bonds form (adenine-guanine; guanine-cytosine)
4. DNA polymerase joins adjacent nucleotides on new strand by condensation, forming
phosphodiester bonds (= sugar phosphate backbone)
5. Replication is semi-conservative – each new strand formed contains one original / template strand
and one new strand
6. Ensures genetic continuity between generations of cells

DNA polymerase moves in opposite directions along the DNA strands

• DNA has antiparallel strands
• DNA polymerase is an enzyme with a specific shaped active site which can only bind to substrate with
a complementary shape
• Can only bind to and add nucleotides to the phosphate (3’) end of the developing strand (so works in a
5’ to 3’ direction)
• Note - 5’ (“5 prime”) and 3’ (“3 prime”) indicate the carbon numbers in DNA’s sugar backbone; 5’
carbon has a phosphate group attached and 3’ carbon has a hydroxyl (-OH) group

Evidence for semi-conservative replication (Meselson and Stahl)

• Bacteria grown in a nutrient solution containing heavy nitrogen (15N)
for several generations
• Nitrogen incorporated into bacterial DNA bases
• Bacteria then transferred to a nutrient solution containing light
nitrogen (14N) and allowed to grow and divide twice
• During this process, DNA from different samples of bacteria was
extracted, suspended in a solution in separate tubes and spun in a
centrifuge

Sample 1. DNA from bacteria grown for several generations in

a nutrient solution containing 15N
DNA molecules contain 2 ‘heavy’ strands
Sample 2. DNA from bacteria grown originally in a nutrient
solution containing 15N, then transferred for one division
to a solution containing 14N
DNA molecules contain 1 original ‘heavy’ and 1 new
‘light strand
Sample 3. DNA from bacteria grown originally in a nutrient
solution 15N, then transferred for two divisions to a solution containing 14N
50% DNA molecules contain 1 original ‘heavy’ and 1 new ‘light’ strand, 50% contain both ‘light’
strands
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1.6 ATP
The structure of adenosine trisphosphate (ATP)
• Ribose, a molecule of adenine, 3 phosphate groups
• Nucleotide derivative (modified form of nucleotide)
• The structure of ADP (adenosine diphosphate) is the same as
ATP, minus a phosphate

ATP/ADP hydrolysis and condensation

ATP hydrolysis (ATP ADP + Pi) ATP condensation
• Catalysed by the enzyme ATP hydrolase (ADP + Pi ATP)
• Can be coupled to energy requiring reactions within cells, • Catalysed by the enzyme
to provide energy for active transport, protein synthesis, ATP synthase
etc. (energy released when bonds between inorganic • Happens during respiration
phosphate groups are broken) or photosynthesis
• The inorganic phosphate released can be used to • Also called phosphorylation
phosphorylate other compounds e.g. glucose, often of ADP
making them more reactive (i.e. lowers activation energy)

The properties of ATP make it a suitable immediate source of energy

Important – ATP cannot me stored

• ATP releases energy in small, manageable amounts (so no energy wasted)

• Only one bond is hydrolysed (single reaction) to release energy (which is why energy release is
immediate)

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1.7 Water
How hydrogen bonding occurs between water molecules
• Water is a polar molecule (oxygen molecule has a partial negative
charge; hydrogen atoms have a partial positive charge)
• Slightly negatively charged oxygen atoms attract slightly positively
charged hydrogen atoms of other water molecules
• So hydrogen bonds (weak attractive force) form between water
molecules

Properties of water that are important in biology

Property Explanation of property
High • Polar so many H bonds form
specific between water molecules
heat • These allow water to absorb
capacity a relatively large amount of
heat energy before its
temperature changes
High latent • Polar so many H bonds form
heat of between water molecules
evaporation • These can absorb a lot of
energy before breaking,
when water evaporates
Cohesive • Polar so many H bonds form
between water molecules
• So water molecules tend to
stick together
Solvent • Polar (has a slightly positive
and negative ends)
• Can separate (dissolve) ionic
compounds e.g. NaCl as +ve
end attracted to -ve ion (Cl-)
and negative end attracted
to positive ion (Na+)
Metabolite • Water is reactive
Importance in biology
• Good habitat for aquatic organisms e.g. lakes as
temperature more stable than land
• Organisms mostly made of water so helps maintain
a constant internal body temperature – important
as temperature affects enzyme activity
• Evaporation of small amount of water (e.g. sweat)
is an efficient cooling mechanism
• Helping organisms maintain a constant body
temperature
• Column of water doesn’t break when pulled up a
narrow tube e.g. xylem during transpiration
• Produces surface tension at an air-water surface so
invertebrates can walk on water e.g. pond skaters
Can dissolve other substances e.g. inorganic ions,
enzymes, urea, etc. so water…
• Acts as a medium for metabolic reactions (which
can happen in water)
• Acts as a transport medium e.g. in xylem to
transport nitrates which are needed to make
amino acids
Condensation releases H2O and forms a chemical
bond; hydrolysis requires H2O to break a bond; e.g.
amino acids joined by condensation reactions to
form polypeptides

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1.8 Inorganic ions

• Occur in solution in the cytoplasm and body fluids of organisms
• Some in high concentrations and others in very low concentrations
• Each type of ion has a specific role, depending on its properties and these roles are relevant in a range
of topics across the A Level

Ion Chemical Role

symbol
Phosphate PO43- Attached to other molecules as a phosphate group, for example:
• in DNA nucleotides, enabling nucleotides to join together forming
phosphodiester bonds
• in ATP – bonds between these store / release energy
Hydrogen H+ Maintain pH levels in the body
• Too much H+ = acidic (low pH)
• Too little H+ = alkaline (high pH)
• Affects rate of enzyme-controlled reactions as can cause enzymes to
denature
Iron Fe 2+
• Component of (haem group of) haemoglobin which is contained in red
blood cells
• Transports oxygen around the body – oxygen temporarily binds to it, so it
becomes Fe3+
Sodium Na+ • Co transport of glucose and amino acids across cell membranes
• Involved in generating nerve impulses and muscle contraction (year 2)

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