Download Page 1 Proteins - Made up of amino acid monomers (yep, you got it

SICM Tuition
Biology AS
Proteins
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Made up of amino acid monomers (yep, you got it…that makes it a polymer!)
Contain Carbon, Hydrogen, Oxygen and Nitrogen. Some also have Sulphur
Amino acids join together to form polypeptides
A protein consists of one or more polypeptide chains
R is a variable group – it
varies with each amino acid
Structure of an amino acid
R
H
NH2 is the functional
group for an amine
O
N
C
C
COOH is the functional
group for a carboxylic acid
OH
H
Each amino acid contains a carboxyl group
o Can you think of something else that you know that contains a carboxyl
group?
H
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o (Those of you who thought of carboxylic acids are correct, but that really would be
TOO easy now wouldn’t it! I mean something we’ve done in Biology recently!)
o Lipids also contain a carboxyl group
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The R group is different in every amino acid. It can be polar, non-polar, contain
carboxyl or hydroxyl groups in it.
o Can you explain what the words in bold mean?
Polar molecules are generally able to dissolve in water (hydrophilic) due to the
polar nature of water. Polar molecules have slightly positive and slightly
negatively charged ends.
Non-polar molecules are mostly water insoluble (hydrophobic) at room
temperature. However many non-polar organic solvents, such as turpentine, are
able to dissolve non-polar substance
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Some amino acids can be produced by the human body. However, there are some
that have to be retrieved from the diet. These cannot be made by humans and are
known as “essential amino acids”.
Condensation of amino acids
Two amino acids condense to form a dipeptide. This happens with the formation of a
PEPTIDE BOND. Show how this occurs below.
R
R
H
H
O
O
C
C
C
C
N
N
H
OH
OH
H
H
H
H2O
CONDENSATION
R O
R
H
H
O
N C C
N C C
H
H
H
PEPTIDE BOND
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OH
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Biology AS
Further condensation reactions create polypeptides
All polypeptide chains have similar backbones with an amino end and a carboxyl
end
There are 20 different common amino acids and, as there can be any number of
them within a polypeptide chain, and as they can be in any order, there are an
infinite number of different polypeptide chains possible
Levels of Protein structure
Proteins can be arranged in various ways. This is determined by the structural formation of
the molecule.
1.
Primary Structure
This is simply the arrangement of the amino acids in a chain. The amino acids are the
fundamental units and are arranged in a chain by peptide bonds.
2.
Secondary Structure
The shape taken by the polypeptide chain as a result of the formation of hydrogen
bonds is known as the secondary structure. The secondary structure contains
hydrogen bonds which are not joined to the variable R groups and so the secondary
structure is not specific to particular polypeptides.
There are two common types:
Alpha Helix:
Hydrogen bonds are formed between the CO of one amino acid with the NH of an
amino acid further along the chain. This twists the shape and a spiral is formed which
is held in place by H-bonds.
Keratin (hair and nails) has molecules
which are largely this shape.
H2N
Hydrogen
bonds
H2N
O
Beta-pleated sheets:
If polypeptide chains are formed in opposite directions to each other (anti-parallel)
then they form a beta-pleated sheet. In the same way as the alpha helix, hydrogen
bonds hold the CO to NH but this
time they are in separate chains.
The beta pleated sheets are
therefore stronger, but less elastic
than the alpha-helix.
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3.
Biology AS
Tertiary structure
This refers to the shape taken up by polypeptide chains as a result of the bonds
formed between R groups. Every polypeptide has a different order of R groups and
so bonds form in different places. This makes the proteins various shapes.
This is of particular importance when looking at enzymes, who require specificity for
their active site.
Three types of bonds form to form this tertiary structure:
Hydrogen bonds:
common, but weak
formed when δ+ H from –OH or –NH of the R group attract the δ- O of
a –CO group, or another R group
Ionic bonds:
form between amino and carboyl groups on some R groups
stronger than hydrogen bonds, but are weaker than disulphide bonds
Disulphide bonds:
covalent bond that is formed between R-groups which contain –SH
groups
This is the strongest bond of the three
All of these bonds and interactions cause the protein to have an irregular shape
compact globular shapes are formed with hydrophilic parts on the outside
(when in an aqueous environment)
one molecule may become surrounded by water and form what is known as a
colloidal solution. This forms a globular protein (an example of this is
insulin)
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BUT….some (e.g. keratin, collagen and fibroin) have hydrophobic amino
groups and do not form a tertiary structure. Instead, as they are insoluble, they
remain unfolded and have a non-specific structure. These are known as
fibrous proteins.
Fibrous Proteins
Polypeptide chains parallel with little or no
tertiary folding
Different proteins may have similar shapes and
lengths of chains of same proteins may vary
Insoluble in water
Stable and tough
Have structural functions
4.
Globular Proteins
Polypeptide chains have structure and fold
to impact shape
Each protein has its own specific shape and
length of chains
Soluble in water (make colloidal solutions)
Easily changed chemically – not so stable
Have metabolic (chemical) functions
Quaternary structure
This is just how the polypeptide is fit into a protein molecule and how they are linked
together.
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Biology AS
SYLLABUS CHECKLIST
Unit 1.1 – Molecules
Proteins
understand the nature of amino acids as monomers in the formation of
polypeptides and proteins; recall the general formula and general structure of
amino acids (details of the structures and formulae of specific amino acids are not
required);
understand that amino acids are linked by peptide bonds to form polypeptides;
describe the formation of a peptide bond;
understand the meaning of the terms primary, secondary, tertiary and quaternary
structure and their importance in the structure of enzymes;
understand that condensation and hydrolysis reactions are involved in the
synthesis and degradation of polypeptides and proteins;
understand the role of ionic, hydrogen and disulphide bonds in the structure of
proteins as illustrated by insulin and collagen;
understand the nature and roles of fibrous and globular proteins as illustrated by
collagen and insulin.
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