This document describes the structure and functions of proteins. It explains that proteins are made up of amino acids, which join together via peptide bonds to form polypeptide chains. Proteins then have four levels of structure - primary, secondary, tertiary, and sometimes quaternary. The primary structure is the sequence of amino acids, while secondary structure involves coiling or folding due to hydrogen bonds. Tertiary structure results from further coiling or folding from interactions between amino acid side chains. Quaternary structure applies to proteins made of multiple polypeptide chains. The document emphasizes that a protein's unique 3D structure determines its specific function in the body.

1. Revision

2. 2 BIOLOGICAL MOLECULES

3. LO
• describe and explain the roles of water in
living organisms and as an environment for
organisms;
• describe the ring forms of α-glucose and β-
glucose
• describe the formation and breakage of a
glycosidic bond with reference both to
polysaccharides and to disaccharides including
sucrose;

4. • carry out tests for reducing and non-reducing
sugars (including using colour standards as a
semi-quantitative use of the Benedict’s test);
• describe the molecular structure of
polysaccharides including starch (amylose and
amylopectin), glycogen and cellulose and
relate these structures to their functions in
living organisms;
• carry out the iodine in potassium iodide
solution test for starch;

5. • describe the molecular structure of a
triglyceride and a phospholipid and relate
these structures to their functions in living
organisms;
• carry out the emulsion test for lipids
• describe the structure of an amino acid and
the formation and breakage of a peptide
bond;
• carry out the biuret test for proteins;

6. • explain the meaning of the terms primary
structure, secondary structure, tertiary structure
and quaternary structure of proteins and describe
the types of bonding (hydrogen, ionic, disulfide
and hydrophobic interactions) that hold the
molecule in shape;
• describe the molecular structure of haemoglobin
as an example of a globular protein, and of
collagen as an example of a fibrous protein and
relate these structures to their functions (the
importance of iron in the haemoglobin molecule
should be emphasised);

7. WATER
describe and explain the roles of water in living organisms and as an environment for
organisms
• Most important biochemical – life would not
exist without it
• Major component of all cells (70 – 95%);
humans 60%
• Provides an environment for water organisms
• Three quarters of the planet is covered in
water

8. PROPERTIES OF WATER
• HYDROGEN BONDING

9. • The attractive force between the hydrogen
attached to an electronegative atom of one
molecule and an electronegative atom of a
different molecule

10. • The hydrogen, which has a partial positive
charge tries to find another atom of oxygen or
nitrogen with excess electrons to share and is
attracted to the negative partial charge – this
forms basis for the hydrogen bond
• Because oxygen has two lone pairs, two
different hydrogen bonds can be made to each
oxygen

11. • Hydrogen bonding is usually stronger than
normal dipole forces between molecules but
not as strong as normal covalent bonds within
a molecule
• It is strong enough to have many important
ramifications on the properties of water

12. a closer look at WATER

13. • Thanks to hydrogen bonding water has
– a relatively high boiling point,
– high specific heat capacity,
– high surface tension and
– high latent heat of vaporisation

14. • WATER AS A SOLVENT
– Water is a good solvent due to its polarity
• When an ionic or polar compound enters water, it is
surrounded by water molecules
• The relatively small size of water molecules typically
allows many water molecules to surround one
molecule of solute
• The partially negative dipoles of the water are attracted
to positively charged components of the solute and vice
versa

15. • Ionic and polar substances (e.g. acids, alcohols, salts)
are easily soluble in water
• Nonpolar substances (e.g. fats, oils) are not soluble.
Their molecules stay together in water because it is
energetically more favourable for the water molecules
to hydrogen bond to each other than to engage in van
der Waals interactions with non polar molecules
• Depending on the relative electronegativities of the
two atoms sharing electrons, there might be partial
transfer of electron density from one atom to another
• When the electronegativities are not equal, electrons
are not shared equally and partial ionic charges develop

16. Difference between polar and non-polar
molecules
• Depending on the relative electronegativities of the
two atoms sharing electrons, there might be partial
transfer of electron density from one atom to another
• When the electronegativities are not equal, electrons
are not shared equally and partial ionic charges develop
– Polar covalent bonds – bonds that are partially ionic
– Nonpolar covalent bonds – bonds with equal sharing of the
bond electrons, arise when the electronegativities of the two
atoms are equal

17. How water dissolves salt

18. • WATER AS A TRANSPORT MEDIUM
– Water is the transport medium in blood, in
lymphatic, excretory and digestive systems of
animals, and in vascular tissues of plants

19. • THERMAL PROPERTIES
– Hydrogen bonding restricts the movement of
water molecules – relatively large amount of
energy is needed to raise the temperature of
water – slow environmental change in oceans and
lakes = more stable habitats

20. • DENSITY AND FREEZING PROPERTIES
– Solid form is less dense then liquid form
– Below 4 degrees the density of water starts to
decrease – ice floats on water and insulates the
water underneath
– Changes in density of water with temperature
causes currents – maintaince of circulation of
nutrients in ocean

21. • HIGH SURFACE TENSION AND COHESION
– Water molecules have very high cohesion – they
tend to stick together
– High cohesion results in high surface tension at
the surface of water – important for small
organisms such as pond skaters

22. • WATER AS A REAGENT
– It is used as reagent in photosynthesis – hydrogen
is used to provide energy for making glucose,
oxygen is source for the atmosphere

23. activity

24. THE BUILDING BLOCKS OF LIFE
• Most common elements in living organisms:
– Hydrogen
– Carbon – is important because carbon atoms can
join together to form long chains or ring
structures; all organic molecules contain carbon
– Oxygen
– Nitrogen

25. MONOMERS, POLYMERS AND
MACROMOLECULES
• Macromolecule – giant molecule;
polysaccharides, proteins and nucleic acids
• Polymers – made of many repeating subunits
that are similar or identical; cellulose and
rubber, polyester, PVC
• Monomers – subunits of polymers that are
joined together; monosaccharides, amino
acids and nucleotides

26. CARBOHYDRATES
• Contain C, H and O
• General formula:
• Divided into three groups:
– Monosaccharides
– Disaccharides
– Polysaccharides

27. MONOSACCHARIDES
• Are sugars – dissolve easily in water to form
sweet solutions
• General formula: (CH2O)n
• Consist of a single sugar molecule; name
always ends with -ose
• Main types:
– Trioses (3C) - glyceraldehyde
– Pentoses (5C) – ribose, deoxiribose
– Hexoses (6C) – glucose, fructose

28. GLUCOSE
– Molecular formula: C6H12O6
- Structural formula:

29. • Ring structures
– Chain of carbon atoms
is long enough to close
up on itself and form a
more stable ring
structure
– Carbon atom 1 joins to
the oxygen on carbon
atom 5
– The ring contains
oxygen and carbon
atom 6 is not part of
the ring

30. • The hydroxyl group (-OH) on carbon atom 1
may be above or below the plane of the ring
– α-glucose (below)
– β-glucose (above)

32. • Roles of monosaccharides
– Source of energy in respiration
• Carbon-hydrogen bonds can be broken to release a lot
of energy which is transferred to help make ATP from
ADP and phosphate
– Building blocks for larger molecules
• Glucose is used to make starch, glycogen and cellulose
• Ribose is used to make RNA and ATP
• Deoxyribose is used to make DNA

33. DISACHCARIDES
LO: describe the formation and breakage of a
glycosidic bond with reference both to
polysaccharides and to disaccharides including
sucrose;

34. Disaccharides
• Are sugars
• They are formed by two monosaccharides
joining together
– Maltose (glucose + glucose)
– Sucrose (glucose + fructose) – transport sugar in
plants and the sugar commonly bought in shops
– Lactose (glucose + galactose) – is the sugar found
in milk

35. Formation of disaccharides
• Condensation
– Two hydroxyle groups line up alongside each other
– One combines with a hydrogen atom from the
other to form a water molecule
– Oxygen bridge is formed between the two
molecules = GLYCOSIDIC BOND

38. • Hydrolysis
– Reverse of condensation
– Addition of water
– Takes place during digestion of disaccharides and
polysaccharides – they are broken down to
monosaccharides

41. POLYSACCHARIDES
LO:
• describe the molecular structure of
polysaccharides including starch (amylose and
amylopectin), glycogen and cellulose and
relate these structures to their functions in
living organisms;

42. POLYSACCHARIDES
• Polymers whose subunits are monosaccharides
• Are NOT sugars
• Made by joining many monosaccharide
molecules by condensation
• May be several thousand monosaccharide units
long, forming a macromolecule
• Most important:
– starch,
– Glycogen
– cellulose

43. • Source of glucose
– Glucose is very reactive and soluble, makes the
contents of cell too concentrated = has to be
stored in other form
= polysaccharide which is compact, inert and
insoluble
- starch in plants
- glycogen in animals

44. STARCH
• Amylose + amylopectin
• Amylose
– Condensation between α-glucose molecules
– Long unbranching chain of several thousand 1,4
linked glucose molecules
– The chains are curved and coiled up to helical
structures

46. • Amylopectin
– made of many 1,4 linked α-glucose molecules
– Chains are shorter than in amylose and branch out
to the sides
– Branches are formed by 1,6 linkages

50. • Amylase and amylopectin build up into large
starch grains, found in chloroplasts and in
storage organs (potato tubers, seeds of cereals
and legumes)
• Starch is never found in animal cells

52. GLYCOGEN
• Is like amylopectin – made of 1,4 linked α-
glucose with 1,6 linkages forming branches
• More branched than amylopectin molecules
• Glycogen molecules clump together to form
granules which are visible in liver cells and
muscle cells
• Form energy reserve

55. CELLULOSE
• Most abundant organic molecule on the
planet
• In plant cell walls
• Slow rate of breakdown in nature
• Mechanically strong
• Polymer of β-glucose and α-glucose

58. • In the β-isomer, the OH group on carbon atom 1
projects above the ring
• In order to form glycosidic bond with carbon
atom 4 where the OH group is below the ring,
one glucose molecule must be upside down
relative to the other
– successive glucose units are linked at 180°
 strong molecule as atoms of OH are
attracted to oxygen atoms in the same
cellulose molecule (hydrogen bonds)

59. • 60 – 70 cellulose molecules become tightly
cross-linked to form bundles = microfibrils
– These are held together in bundles called fibres by
hydrogen bonding

60. LIPIDS
• describe the molecular structure of a
triglyceride and a phospholipid
• relate these structures to their functions in
living organisms;

61. LIPIDS
• Diverse group of chemicals
• Most common are triglycerides = fats (solid)
and oils (liquid)

62. TRIGLYCERIDES
• Made of three fatty acid molecules with one
glycerol molecule
– Fatty acids have –COOH group attached
– Glycerol is alcohol
• Fatty acids joins to glycerol by a condensation
reaction – fatty acid + glycerol = glyceride

64. • Insoluble in water; soluble in ether,
chloroform and ethanol – due to the long
hydrocarbon tails of fatty acids
• Non-polar and hydrophobic

65. SATURATED AND UNSATURATED FATTY ACIDS AND LIPIDS
• Unsaturated
– Have double bonds between neighbouring carbon
atoms: -C=C-; they do not contain the maximum
possible amount of hydrogen
– Double bonds make lipids melt more easily (most
oils are unsaturated)
– If there’s more than one double bond –
polyunsaturated, if there’s one double bond –
monounsaturated
– Plant lipids

66. • Saturated
– Animal lipids,
– No double bonds

68. Roles of triglycerides
• Energy reserve – contain many carbon-
hydrogen bonds – higher caloric value than
carbohydrates
• It is stored below the dermis of the skin and
around the kidneys
• Insulator against loss of heat
• Whales – buoyancy
• Metabolic source of water – desert kangaroo
rat (never drinks water)

70. PHOSPHOLIPIDS
• Each molecule has one end which is soluble in
water – one of the fatty acids is replaced by a
phosphate group which is polar – hydrophilic
• Important function in membranes

72. Protein Structure & Function

73. What are proteins?
• Proteins are made up of C, H, O, N and some S
and P
• Proteins are the building blocks of life
• There are millions of different proteins
• Proteins are the most abundant molecules in
cells
• Proteins make up more than 50% of a cell’s
dry mass

74. What do proteins do?
Proteins perform a wide range of biological functions:
• As enzymes they catalyse reactions.
• Carrier proteins transport molecules across
membranes.
• Antibodies defend against disease.
• Structural proteins support cells and tissues.
• Hormones transmit information.
• Transport proteins such as haemoglobin carry oxygen.
• Contractile proteins enable muscles to contract.

75. How do proteins do all this?
Proteins can carry out all these different
functions because each different protein has a
specific molecular shape which enables the
protein to do its job.
It is structure of a protein that allows it to carry
out its function.

76. So, what goes into a protein?
• Proteins are polymer molecules.
• The monomer molecules making up proteins
are called amino acids.
• There are 20 different naturally occurring
amino acids.
• There are over 100,000 combinations of
amino acids forming known proteins.

77. What is an amino acid?
All amino acids have the same general structure:
• A carboxyl group (-COOH)
• An amino group (-NH2) attached to a C atom
• A variable group called R
It is the R group that differs from one amino acid
to another

79. Are all amino acids ‘equal’?
No, of the 20 naturally occurring amino acids 8
are known as ‘essential amino acids’. These 8
cannot be synthesised by the body and must
be obtained from the diet.
The remaining 12 can be synthesised by the
body.

80. Joining amino acids together
When amino acids join together, they do so by a
condensation reaction.
This means one water molecule is removed,
using the
OH group from the carboxyl group of one
amino acid, and one H from the amino group
of another.
The resulting bond is called a peptide bond.

82. Peptides
• Two amino acids joined together form a
dipeptide.
• Three amino acids joined together form a
tripeptide.
• A polypeptide is made up of many amino acids
joined together.
• When a polypeptide bonds with other
polypeptides it forms a protein containing
thousands of amino acids.

83. Proteins have 4 structural levels.
Proteins are big, complicated, 3-dimensional
molecules.
The structure is described in four ‘levels’:
• Primary
• Secondary
• Tertiary
• Quaternary

84. Primary structure
• The primary structure of a protein is the
sequence of amino acids in the chain.
• The primary structure determines the
eventual shape of the protein, hence its
function.

85. Secondary structure
• The amino acids in the primary structure of a
protein do not lie flat and straight.
• Hydrogen bonds form between the amino
acids in the chain.
• This makes the protein coil into an a helix or
fold into a b pleated sheet.
• This is the secondary structure.

87. Tertiary structure
• The coiled or folded chains often coil or fold
further.
• More bonds form due to interactions between
the R-groups of the polypeptide chain.
• This is called the tertiary structure.
• For proteins formed from a single polypeptide
chain this is the final 3D structure of the
protein.

88. Quaternary structure
• Some proteins are made up of several
polypeptide chains held together by bonds.
• The quaternary structure is how these chains
are put together.
• The best known example is haemoglobin,
which is made of four polypeptide chains
bonded together. For proteins such as
haemoglobin, the quaternary structure
determines the final 3D structure.

89. Haemoglobin

90. Protein bonds
The four structural levels in proteins are held together by
different bonds:
• Peptide bonds (primary)
• Hydrogen bonds (secondary and tertiary)
• Ionic bonds (tertiary)
• Disulphide bonds (tertiary)
• Hydrophobic and hydrophilic interactions (tertiary)
• Quaternary structure depends on the tertiary structure
of the individual polypeptides, and so is influenced by
all these bond types.

91. Types of protein
• There are two different types of protein and they
are different shapes. The shape of a protein
molecule is related to its function.
• Globular proteins – these are round, compact and
easily soluble so they can be transported in fluids.
Examples are haemoglobin and enzymes.
• Fibrous proteins – these are tough and rope-
shaped. They tend to be found in connective
tissues such as tendons. Collagen is an example
of a fibrous protein.

92. Haemoglobin
• Haemoglobin is a globular protein.
• It’s structure is curled up so that hydrophilic
side chains face outwards and hydrophobic
side chains face inwards.
• This makes haemoglobin soluble and
therefore good for transport in the blood.

93. Collagen
• Collagen is made of three polypeptide chains,
tightly coiled in a strong triple helix.
• The chains are interlinked by strong covalent
bonds.
• Minerals can bind to the triple helix to
increase its strength.

94. Bonds in proteins
• Hydrogen bonds
– Form between strongly polar groups (-NH, -CO, -
OH)
• Disulfide bonds
– Form between cysteine molecules, strong covalent
bonds, can be broken by reducing agents
– oxidation

95. • Ionic bonds
– Form between ionised amine NH3
+ groups and
ionised carboxylic acid COO- groups
– can be broken down by pH changes
• Weak hydrophobic interactions
– Occur between non-polar R groups

96. Plenary
• Name the two groups found in all amino acid
molecules.
• Name the bond that joins amino acids
together in proteins.
• Name the four types of bond that determine
the structure of a protein.
• Name the four structural levels of a protein.