The document details the structure and diversity of proteins, emphasizing the role of amino acids, specifically their R-groups, in determining protein function and conformation. It explains the synthesis of essential and non-essential amino acids, the different levels of protein structure, including primary, secondary, tertiary, and quaternary formations, and how interactions between amino acids affect stability and function. Additionally, it discusses the importance of protein folding, denaturation, and the role of chaperones, alongside the distinction between fibrous and globular proteins.

1. B1-2 PROTEINS

5. Chemical diversity in the R-groups of amino acids

8. http://commons.wikimedia.org/wiki/File:Amino_Acids.svg
“OMG I HAVE TO LEARN THE
NAMES OF ALL 20 !?!?”
“Relax, no you don’t, you just
need an awareness of the
concepts as outlined.”
2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

9. Enantiomers of amino acids
cells use only the L forms to synthesize proteins,
• D- and L-enantiomers

14. • Non-essential amino acids are made from other amino
acids. Humans can only synthesize10 of [he 20 standard
amino acids.
• Tyrosine and cysteine. for example, are synthesized from
the essential amino acids phenylalanine and methionine,
respectively.
• The liver has enzymes such as transaminases and is
responsible for non-essential amino acid synthesis through
a process called transamination.

15. Conversion of an essential amino acid into non essential amino
acid ( structure not expected )
phenylalanine is converted into tyrosine
by the enzyme phenylalanine hydroxylase,

16. 2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.
Hydroxyproline is an
example of an amino acid
created not by the genetic
code, but modification, after
polypeptide formation, of
proline (by the enzyme prolyl
hydroxylase).
http://chempolymerproject.wikispaces.com/file/view/collagen_%28alpha_chain%29.jpg/34235269/collagen_%28alpha_chain%29.jpg
• This modification of proline to
hydroxyproline increases the
stability of the collagen triple
helix.
• Collagen is a a structural protein
used to provide tensile strength in
tendons, ligaments, skin and
blood vessel walls.
prolyl
hydroxylase

17. Essential Amino acids

19. 2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A
protein may consist of a single polypeptide or more than one polypeptide linked together.
Proteins may consist of a single polypeptide
or multiple polypeptides that fold together.

20. If a polypeptide contains just 7 amino acids there can be 207
= 1,280,000,000 possible polypeptides generated.
Given that polypeptides can contain up to 30,000 amino acids (e.g.
Titin) the different possible combinations of polypeptides are
effectively infinite.
2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

23. It is possible to eat a protein rich diet and still be
deficient in an essential amino acid.
Animal based foods like fish , meat, milk,eggs have a
balance of amino acids .
wheat has low lysine content and peas and beans are
low in methionine both are essential amino acids ..

24. The level a protein conforms to is
determined by it’s amino acid sequence.
(Polypeptide)
• The order / sequence of the
amino acids of which the protein
is composed
• Formed by covalent peptide
bonds between adjacent amino
acids
• Controls all subsequent levels of
structure
• The chains of amino acids fold or
turn upon themselves
• Held together by hydrogen bonds
between (non-adjacent) amine
(N-H) and carboxylic (C-O) groups
• H-bonds provide a level of
structural stability
• Fibrous proteins
• The polypeptide folds and
coils to form a complex
3D shape
• Caused by interactions
between R groups (H-
bonds, disulphide
bridges, ionic bonds and
hydrophilic / hydrophobic
interactions)
• Tertiary structure may be
important for the
function (e.g. specificity
of active site in enzymes)
• Globular proteins
• The interaction
between multiple
polypeptides or
prosthetic groups
• A prosthetic group
is an inorganic
compound
involved in a
protein (e.g. the
heme group in
haemoglobin)
• Fibrous and
Globular proteins
n.b. although you don’t need to be able to outline the different
levels of structure for knowing of them helps to understand the
difference between globular and fibrous proteins. This is though
required knowledge for AHL (7.3.U7 to 7.3.U10)
The four levels of protein structure.

25. Primary structure of proteins
• The order / sequence of the amino acids of which the protein is
composed
• Formed by covalent peptide bonds between adjacent amino acids
• Controls all subsequent levels of structure

27. Secondary structure of proteins
• The most common types of secondary structures
are the α helix and the β pleated sheet.
Both structures are held in shape by hydrogen bonds,
which form between the carboxyl O of one amino acid
and the amino H of another.

29. Super-secondary structure
• Super-secondary structure describes the different patterns
that a-helices or beta-sheets commonly adopt in proteins.
For example, four alpha-helices often form a coiled-coil
arrangement known as a four-helix bundle
• Pairs of adjacent helices are often additionally stabilized by
salt bridges (ionic bonding) between charged amino acids.

30. • Two beta-sheets may stack on top of each other in a 'beta sandwich'
such as in the immunoglobulin fold

31. Tertiary structure of a protein
• The tertiary structure of a protein consists of the
way a polypeptide is formed of a complex molecular
shape. This is caused by R-group interactions such
as ionic and hydrogen bonds, disulphide bridges,
and hydrophobic & hydrophilic interactions.

34. Amino acid Cysteine

35. • disulphide bridges between cysteine( amino acid)

37. Effect of polar and non-polar amino acids on tertiary structure of proteins

38. Chaperones are a functionally related group of
proteins assisting protein folding in the cell
under physiological and stress conditions. They
share the ability to recognize and bind
nonnative proteins thus preventing unspecific
aggregation.

40. Quaternary structure of a protein
• The quaternary structure of a protein is the
association of several protein chains or subunits
into a closely packed arrangement. Each of the
subunits has its own primary, secondary, and
tertiary structure. The subunits are held together
by hydrogen bonds and van der Waals forces
between nonpolar side chains.

42. Non conjugated quaternary structure
Eg Insulin has two polypeptides linked by sidulphide
bonds
eg 2 Collagen consists of 3 polypeptides wound
together to form a rope like structure with high
tensile strength.

47. Conjugated Proteins
Have one or more non-polypeptide subunits in
addition to their polypeptides.
Eg Haemoglobin molecule consists of 4 polypeptide
chains each associated with a heme group .The
inclusion of non-polypeptide subunits increases the
chemical and functional diversity of proteins. The
haem group binds oxygen , allowing oxygen transport.
Eg many enzymes have a non-polypeptide component
that contributes to the catalytic activity of their active
site.

49. Cryo- electron microscopy
A protein sample is applied to a sample grid and is
plunged into liquid ethane to flash freeze it .
The protein molecules are trapped in a thin layer of
ice and images can then be obtained using a beam of
electrons .
Software has been developed for processing the
images to increase the resolution.
Cryo EM also enables function to be investigated .The
freezing technique allows conformation change to be
revealed as a protein carries out its task.

51. In globular proteins the hydrophobic R groups are folded into the core of the molecule, away from
the surrounding water molecules, this makes them soluble. In fibrous proteins the hydrophobic R
groups are exposed and therefore the molecule is insoluble.
Proteins are commonly described as either being fibrous ( Insoluble )or
globular (Soluble )in nature.
Fibrous proteins have structural roles whereas globular proteins are functional (active in a
cell’s metabolism).
2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein.

52. Relationship of form and function in globular and
fibrous proteins
FIBROUS PROTEIN - COLLAGEN
Collagen consists of 3 polypeptides wound together in a triple helix.
Primary structure of the polypeptide consists of repeating sequence
of 3 amino acids P-G-X.
P-is proline or hydroxy proline which prevents formation of α helix,
since winding of the 3 polypeptides would be impossible if there
were α helix.
G- Glycine - since the R group of every 3rd amino acid faces inwards
towards the centre of the triple helix , glycine is the only amino acid
with an R group as a single H small enough to fit.
X-The R group of this amino acid faces outward and is variable
producing variations of collagen present in
skin,tendons,ligaments,cartilage , etc. .

53. GLOBULAR PROTEINS
Have a round shape formed by folding up of
[polypeptides,stabilised by bonds between the R
groups of amino acids .that have been brought
together by folding.
Eg Active site of enzymes .

54. Denaturation
• Denaturation: a structural change in a protein
that results in a loss (usually permanent) of its
biological properties
• Denaturation occurs when the ionic
interactions, hydrogen bonds and other weak
intermolecular forces within tile globular
protein, formed between different amino acid
residues, break, changing the shape of the
protein, including the active site in enzymes,