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1: Biochemistry of macromolecules and metabolic pathways
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Nucleotides and lipids
We inherit our DNA from our parents – we inherit 23 pairs of chromosomes
that contain millions of genes. These genes code for our characteristics and all
the proteins necessary for our body to function.
On successful completion of this topic you will:
•• understand the chemical principles that apply to the structures of
biological building block molecules (LO1)
•• understand the structures of biological macromolecules and the
relationships to biological functions (LO2).
To achieve a Pass in this unit you need to show that you can:
•• explain the principal properties and classification of nucleosides and
nucleotides (1.3)
•• explain the principal properties and classification of fatty acids (1.4)
•• outline briefly the roles of the nucleic acids in protein biosynthesis with
reference to the structural differences between DNA and different types
of RNA (2.4)
•• explain the structural features and properties of phospholipids that
enable them to form membranes (2.5).
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1: Biochemistry of macromolecules and metabolic pathways
1Nucleotides
Before you start
If you find some parts of this unit challenging, remember you are working at a higher level than
you may be used to. In this unit it is important that you fully understand the following themes and
topics before you begin:
•• structure and function of biological molecules
•• enzyme structure and function
•• aerobic respiration.
If you need to check your understanding of proteins, carbohydrates, lipids and nucleic acids,
Unit 2 Module 1 of OCR AS Biology (P. Kennedy and F. Sochacki, 2008), offers a good introduction
to the topic.
If you need to check your understanding of aerobic respiration and the stages of glycolysis, link
reaction, the Krebs cycle and the electron transport chain, you may find Unit 1 Module 4 of OCR A2
Biology (S. Hocking, 2008) useful.
Phosphate
Base
Deoxyribonucleic acid (DNA)
A nucleotide is a monomer made from a sugar, a phosphate group and a base. The
nucleosides are the bases that form part of the nucleotide.
Deoxyribose sugar
Figure 1.6.1: Structure of a nucleotide.
Figure 1.6.2: Structures of
purines and pyrimidines.
Figure 1.6.1 shows the basic structure of a nucleotide and Figure 1.6.2 shows the
structures of different types of nucleosides known as pyrimidines and purines.
Pyrimidines
NH2
Purines
NH2
N
7
8 9
N
5
4
6
3
N
R
N
1
2
O
N
7
8 9
N
5
4
6
3
N
R
Adenine
N
H
1
2
Guanine
NH2
5
6
4
N
3
1 2
N
R
Cytosine
O
5
6
O
4
1
O
3N
H
2
N
R
Uracil
O
H3C
5
6
4
1
3N
H
2
O
N
R
Thymine
Deoxyribonucleic acid (DNA) is a large molecule made from a chain of nucleotides
bonded together, a condensation reaction between the phosphate group of one
nucleotide and the sugar of another producing ester bonds. This produces a long
sugar-phosphate backbone and the attached bases protrude into the centre of the
structure – this is called a polynucleotide.
DNA consists of two long polymers that run in opposite directions to each other
and are therefore anti-parallel, one backbone being 3’ (three prime) and the other
5’ (five prime) (the direction of the 3rd and 5th carbon on the sugar molecule is
known as three prime or five prime).
Key term
Double helix: The structure formed
by double-stranded molecules of
nucleic acids.
1.6: Nucleotides and lipids
Inside the sugar phosphate backbone are bases. It is the sequence of these
bases along the backbone that codes for our characteristics. Purines pair with
pyrimidines – adenine (A) and guanine (G) are both purines, thymine (T) and
cytosine (C) are pyrimidines.
In DNA, A pairs with T and they are held together by two hydrogen bonds and
C pairs with G, held together by three hydrogen bonds. As these bases bond
together the DNA molecule starts to form a double-stranded helix. As the DNA
strand grows larger, the double helix twists 360°.
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1: Biochemistry of macromolecules and metabolic pathways
Figure 1.6.3: Structure of
the DNA double helix.
Sugar
phosphate
backbone
GC
Base pair
G C
T A
Adenine
A T
Nitrogenous
base
G C
Thymine
T A
A T
Guanine
G)C
T A
A T
Cytosine
C )G
T A
A T
Ribonucleic acid (RNA)
Ribonucleic acid (RNA) is usually single stranded and smaller than DNA, consisting
of just hundreds of nucleotides rather than thousands (like DNA). RNA contains
the base uracil in place of thymine and therefore is a different macromolecule from
DNA. RNA is less stable and only has a short-term function. It exists in three forms:
•• messenger RNA (mRNA): a small molecule that is made inside the nucleus by
copying a template DNA strand. Once it is constructed it moves outside the
nucleus to the ribosomes where protein synthesis takes place. Figure 1.6.4
shows the structure of a single strand of mRNA synthesised inside the nucleus.
•• ribosomal RNA (rRNA): found in ribosomes
•• transfer RNA (tRNA): transfers amino acids to the ribosomes where protein
synthesis is taking place, i.e. where polypeptides are built. Figure 1.6.5 shows
the structure of tRNA including the specific amino acid.
Figure 1.6.4: Single strand of mRNA
synthesised inside the nucleus.
C
TA
DNA template strand
U
A
U
A
U
T
A
G
C
G
C
T
C
mRNA
T
G
T
T
G
G
G
C
A
A
C
T
A
G
1.6: Nucleotides and lipids
C
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1: Biochemistry of macromolecules and metabolic pathways
Figure 1.6.5: Structure of tRNA,
including the specific amino acid.
3’
A
C
C
A
C
C
U
G
C
U
C
Ester bond
A U U C C G G A
G
G G C C
C
Ψ T
C
G
Intramolecular
base-pairing
O
CHR
G C G C G
C G C G A
G A G
A
G
G
G
Ψ
G
Amino acid
NH+3
5’
G
G
A
C
G
U
G
U
C
mRNA
C
O
C
U
C
C
C
U
U
G
U A G
D
C
D G G
Anticodon
G C C
Protein synthesis
Genes are a length of DNA that code for particular proteins. The sequence of the
bases on the DNA code for a specific sequence of amino acids that join together
with peptide bonds to make specific proteins. The DNA inside the nucleus cannot
leave, so the sequence of bases in a particular gene must be copied for protein
synthesis to occur.
Transcription
Transcription is the first stage of protein synthesis – the length of DNA unzips,
breaking the hydrogen bonds between the complementary bases. This exposes
the bases, so that free RNA nucleotides can bind to the complementary bases on
the template DNA strand.
The reaction is catalysed by the enzyme RNA polymerase. G binds with C and U
binds with A and this makes a strand of mRNA, which is complementary to the
original DNA sequence. The mRNA strand is released from the DNA; it passes out
of the nucleus, through pores in the nuclear envelope and to the ribosomes.
Translation
Translation is the second stage of protein synthesis. During this stage the amino
acids assemble to make a polypeptide. The succession of the amino acids depends
on the sequence of the codons on the mRNA strand. tRNA molecules are uniquely
shaped into a hairpin structure, so that there are three exposed bases at one end
where amino acids bind, and at the other end is the anticodon.
1.6: Nucleotides and lipids
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1: Biochemistry of macromolecules and metabolic pathways
Key term
Codon: Triplet of nucleotide bases,
for example, AAG.
Link
The organisation of DNA,
transcription and translation are also
discussed in detail in Unit 7: Molecular
biology and genetics.
Each anticodon binds with a complementary codon on the mRNA strand. As each
tRNA molecule arrives at the ribosome, peptide bonds are formed between the
adjacent amino acids until a stop codon is reached (UAA, UAC, UGA), producing a
polypeptide.
Activity
The RNA polymerase enzyme moves along a DNA sequence reading TATTGGGCTTATACAGGC.
1 What would the sequence of the mRNA be?
2 How many amino acids are assembled in this sequence?
Portfolio activity (2.4)
You can generate evidence for your portfolio by:
•• producing a table of differences between DNA and RNA
•• describing the roles of each in protein synthesis.
Checklist
In this topic you should now be familiar with the following ideas about nucleotides:
 a nucleotide is a monomer made from a sugar, a phosphate group and a base
 nucleoside bases found on nucleotides are adenine, thymine, cytosine, guanine
 pyrimidines are cytosine and thymine
 purines are adenine and guanine
 DNA is a polynucleotide
 the DNA structure is described as a double helix
 RNA is a single-stranded molecule
 mRNA is messenger RNA that carries the genetic code from the nucleus to the ribosome
 rRNA is ribosomal RNA found in ribsomes during protein synthesis
 tRNA is transfer RNA that assembles specific amino acids according to the triplet codon
 genes are lengths of DNA
 protein synthesis is the production of proteins according to the DNA code
 transcription is the process of copying the original DNA code
 translation is the process of amino acid assembly.
2 Lipids
Lipids have many functions, which include energy source, energy storage,
biological membranes, insulation and hormones. There are many types of lipid,
including triglycerides, phospholipids and cholesterol. Triglycerides are made from
a glycerol molecule and fatty acids – the fatty acid molecules differ depending
on the molecule. The fatty acids are composed of an acid group at one end and a
hydrocarbon chain of between 2–20 carbons in length.
1.6: Nucleotides and lipids
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1: Biochemistry of macromolecules and metabolic pathways
Saturated and unsaturated
Too much saturated fat is considered to be bad for human health. Saturated fats
are saturated with hydrogen atoms whereas unsaturated fats contain double
bonds so have fewer hydrogens.
If a single double bond is present between two carbons this produces a
monounsaturated fatty acid. If two or more double bonds are present it produces
a polyunsaturated fatty acid. The presence of the C=C bond changes the shape of
the hydrocarbon chains. This makes the substance more fluid so they are usually
found as oils.
Figure 1.6.6 shows the structural difference between saturated and unsaturated
fats. Notice the presence of a double bond (and therefore fewer hydrogen atoms)
on the unsaturated fat molecule.
Figure 1.6.6: Saturated
and unsaturated fats.
O
O
C
H
O
O
H
H
H
H
C
C
C
H
O
O
O
H
C
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
C
H
H
H
H H H
Saturated
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
H
H
H
H H
Unsaturated
H
C
H
C
H
H
H
C
H
O H
H
H
H
H
C
C
C
C
C
C
H
H
H
H
H
Triglycerides
O H
H
H
H
H
C
C
C
C
C
C
Animals store energy in the form of triglycerides; these are made from one glycerol
molecule bonded to three fatty acid tails.
H
H
H
H
H
O H
H
H
H
H
C
C
C
C
C
C
H
H
H
H
H
H
H
H
Triglycerides are described as hydrophobic lipids because they are insoluble in
water – the hydrogen bonds cannot form with water and therefore the two do not
combine.
H
Triglyceride
Figuremolecule
1.6.7: Chemical
structure of a triglyceride.
Phospholipids
A phospholipid also consists of one glycerol molecule but it differs from a
triglyceride molecule because only two ester bonds form, allowing two fatty acid
tails to bond. The third fatty acid tail does not bond; instead a phosphate group is
covalently bonded to the third –OH group of the glycerol molecule.
The phosphate head is polar but the fatty acid tails are non-polar. When placed
in water they arrange themselves so that the tails are pointing inwards and their
phosphate heads point outwards.
The water solubility of the head enables the molecules to form membranes in
double layers called bilayers. Bilayers consist of proteins and other biological
molecules. Membranes are very fluid, constantly moving.
Scientists Singer and Nicholson introduced the Fluid Mosaic model to describe the
structure of biological membranes. The correct ratio of saturated to unsaturated
fatty acids keeps the membrane fluid at any temperature necessary. The presence
of cholesterol lowers the requirement for unsaturated fatty acids and helps
maintain fluidity of biological membranes at body temperature.
1.6: Nucleotides and lipids
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1: Biochemistry of macromolecules and metabolic pathways
Cholesterol
Cholesterol is a lipid but it is structurally different from those discussed previously.
It is made from four carbon-based rings and it is also smaller than other lipids.
Cholesterol provides strength and fluidity to biological membranes, placed
between hydrocarbon chains of phospholipids.
See the Case study for a real life example of cholesterol in the human body.
H3C
Figure 1.6.8: Structure of cholesterol.
CH3 CH
CH3
H2
C
C
H2
H2
C
CH
CH3
H3C
HO
Link
Checklist
You can find out more about
phospholipid membranes and see
some diagrams in Unit 14: Cell biology.
In this topic you should now be familiar with the following ideas about lipids:
 lipids are fats and oils
 lipids have many functions in living organisms
 lipids are found in fats, oils and membranes
 saturated fats have the full allocation of hydrogen atoms and are therefore said to be
saturated with them
 unsaturated fats contain C=C and have less hydrogen atoms
 phospholipids contain only two fatty acid tails, a phosphate head and one glycerol molecule
 phospholipids make biological membranes in bilayers because of the hydrophilic and
hydrophobic properties
 cholesterol is present in membranes to give strength and fluidity.
Case study
The genetic disorder familial
hypercholesterolemia (FHC) refers
to people who have high cholesterol
levels in their body. This is because
cells do not respond to the stop
signals of cholesterol production and
therefore keep producing it even
when there are sufficient amounts
in the blood. This disorder can cause
myocardial infarction (heart attack)
in those as young as 2 years.
Take it further
There are several suitable books or
websites that show you the Fluid
Mosaic model. Try this website:
http://telstar.ote.cmu.edu/biology/
MembranePage/index2.html
1.6: Nucleotides and lipids
Further reading
Boyle, M. & Senior, K. (2008) Biology, 3rd Edition, HarperCollins
Campbell, M.K. & Farrell, S.O. (2011) Biochemistry, Cengage Learning
Kennedy, P., Sochacki, F. & Hocking, S. (2008) OCR Biology AS, Heinemann (Pearson Education
Limited)
Kennedy, P., Sochacki, F., Winterbottom, M. & Hocking, S. (2008) OCR Biology A2, Heinemann
(Pearson Education Limited)
Moran, L., Horton, R., Scrimgeour, G., Perry, M. & Rawn, D. (2011) Principles of Biochemistry
(International Edition), 5th Edition, Pearson
Acknowledgements
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