Download Unit 2.1.1a - Biological Molecules

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Biology AS
Biological Molecules
I won’t lie. This is probably the most boring topic you have ever done in any science. It’s
pretty much as simple as this: learn the material…deal with it. Enjoy…don’t say I didn’t
warn you.
Revision from GCSE and earlier…
Cells contain many small molecules such as:
water (approximately 80% of the mass of a typical cell)
inorganic ions (e.g. sodium and calcium – essential for cell function)
large molecules (e.g. carbohydrates, lipids and proteins – made up of lots o
small molecules)
Carbohydrates, lipids and proteins found in living organisms are described as organic
because the contain carbon. Many of these organic molecules are very large in size and so
are called macromolecules. Often the smaller molecules that make up the macromolecule
are identical (or similar) to each other and so are described as monomers. Monomers join
together to form polymers.
Right, so let’s see how much you remember with a childish, yet still useful, fill in the gaps!
Starch, protein and lipids are all large molecules. Starch is made up of many ___________
molecules and proteins are made up of __________ __________. A lipid consists of a
molecule of _______ and three _________ _________.
Now just to add a little variety into the mixture…
Which of the molecules in the above short paragraph is:
1.
a monomer (1)
2.
a polymer (2)
3.
a macromolecule (3)
OK…that was so easy, if you didn’t get 100% you should be worrying. But don’t worry too
much, we have a year to work on these basic principles.
Condensation and Hydrolysis reactions
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two monomers can be joined together by a condensation reaction. As you
may have guessed from the name, in this process, water is formed. (And if
you didn’t guess…never mind…maybe next time)
o the water molecule comes from a hydrogen on one monomer and a
hydroxyl group (OH) on the other
the remaining monomers now remain as residues
joining many monomers together by condensation reactions form polymers
polymers can be broken back into monomers by a hydrolysis reaction.
o In this reaction, water is added
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General example of condensation and hydrolysis
HO
OH
HO
condensation
linked with the
removal of a
molecule of water
OH
hydrolysis
broken down with
the addition of a
molecule of water
As you can see, the monomers get
joined together by condensation to
form a polymer.
The diagram shows two monomers
joining together. When a large
number of monomers are joined
like this, we get a polymer.
A polymer can be broken down into
its monomers by hyrolysis.
HO
O
OH
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
Structure of an amino acid
R is a variable group – it
varies with each amino acid
R
H
NH2 is the functional
group for an amine
N
H
-
C
C
O
OH
H
COOH is the functional
group for a carboxylic acid
Each amino acid contains a carboxyl group
o Can you think of something else that you know that contains a carboxyl
group?
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 ____________ ___________ also contain a carboxyl group
-
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:
Non-polar:
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Biology AS
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.
(Muhahaha…yep…YOU can work – shock shock horror!)
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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.
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Keratin (hair and nails) has molecules
which are largely this shape.
H2N
Hydrogen
bonds
H 2N
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.
3.
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
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All of these bonds and interactions cause the protein to have an irregular shape: a
quartenary structure
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 or haemoglobin)
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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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