Y1 Nucleotides and Nucleic Acids Notes
AQA Y1 #3 Nucleic Acids Notes
3.1.5.1 Structure of DNA and RNA
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are important information-carrying molecules.
In all living cells, DNA holds genetic information and RNA transfers genetic information from DNA to the ribosomes.
Ribosomes are formed from RNA and proteins.
Both DNA and RNA are polymers of nucleotides. Each nucleotide is formed from a pentose, a nitrogen-containing
organic base and a phosphate group:
The components of a DNA nucleotide are deoxyribose, a phosphate group and one of the organic bases adenine,
cytosine, guanine or thymine.
The components of an RNA nucleotide are ribose, a phosphate group and one of the organic bases adenine,
cytosine, guanine or uracil.
A condensation reaction between two nucleotides forms a phosphodiester bond.
A DNA molecule is a double helix with two polynucleotide chains held together by hydrogen bonds between specific
complementary base pairs.
An RNA molecule is a relatively short polynucleotide chain.
Students should be able to appreciate that the relative simplicity of DNA led many scientists to doubt that it carried
the genetic code
MS 0.3 Students could use incomplete information about the frequency of bases on DNA strands to find the frequency
of other bases.
3.1.5.2 DNA Replication
The semi-conservative replication of DNA ensures genetic continuity between generations of cells.
The process of semi-conservative replication of DNA in terms of:
- Unwinding of the double helix
- Breakage of hydrogen bonds between complementary bases in the polynucleotide strands
- The role of DNA helicase in unwinding DNA and breaking its hydrogen bonds
- Attraction of new DNA nucleotides to exposed bases on template strands and base pairing
- The role of DNA polymerase in the condensation reaction that joins adjacent nucleotides
Students should be able to evaluate the work of scientists in validating the Watson–Crick model of DNA replication.
3.1.6 ATP
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Y1 Nucleotides and Nucleic Acids Notes
A single molecule of adenosine triphosphate (ATP) is a nucleotide derivative and is formed from a molecule of ribose,
a molecule of adenine and three phosphate groups.
Hydrolysis of ATP to adenosine diphosphate (ADP) and an inorganic phosphate group (Pi) is catalysed by the enzyme
ATP hydrolase.
- The hydrolysis of ATP can be coupled to energy-requiring reactions within cells.
- The inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate other
compounds, often making them more reactive.
ATP is re-synthesised by the condensation of ADP and Pi. This reaction is catalysed by the enzyme ATP synthase
during photosynthesis, or during respiration.
Revision
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Y1 Nucleotides and Nucleic Acids Notes
Monomers are the smaller units from which larger molecules are made; polymers are molecules made from
many monomers joined together. Monosaccharides, amino acids and nucleotides are examples of monomers. A
condensation reaction joins two molecules together with the formation of a chemical bond and the elimination of a
water molecule. A hydrolysis reaction breaks a chemical bond between two monomers and involves the use of a
water molecule.
Proteins are made from monomers known as amino acids joined together by peptide bonds.
Polysaccharides are made from monomers known as monosaccharides, joined together by glyosidic bonds. The
three most important polysaccharides in plants and animals are starch, cellulose and glycogen.
Triglycerides are not polymers because they are not made from monomers; they are made from three fatty acids
attached to a glycerol molecule by three ester bonds.
The monomers which form DNA, RNA and ATP are made are called nucleotides. In DNA and RNA, these
nucleotides join to form “nucleic acids” joined together by phosphodiester bonds.
Nucleotide Structure
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Y1 Nucleotides and Nucleic Acids Notes
Each nucleotide is made from 3 basic components: a “nitrogenous base”, a “sugar” and a “phosphate”. All
nucleotides contain the elements C, H, O, N and P.
Whilst both DNA and RNA are made from nucleotides like the one shown below, there are also structural
differences between them:
In each DNA nucleotide:
- The phosphate group does not change
- The sugar molecule is always “deoxyribose” leading to the name Deoxyribose Nucleic Acid
- The “nitrogenous base” can be one of 4 molecules: adenine (A), thymine (T), cytosine (C) or guanine (G)
In each RNA nucleotide:
- The phosphate group does not change
- The sugar molecule is always “ribose” leading to the name Ribo Nucleic Acid
- The “nitrogenous base” can be one of 4 molecules: adenine (A), uracil (U), cytosine (C) or guanine (G)
Sugars
The sugars in both DNA and RNA nucleotides are pentose sugars. There is only 1 small difference between the two
sugars; the hydroxyl group on carbon 2 is a hydrogen atom in DNA and a hydroxyl group in RNA
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Y1 Nucleotides and Nucleic Acids Notes
Nitrogenous Bases
The organic bases which make up nucleotides contain carbon, hydrogen, oxygen and nitrogen.
There are 4 different nitrogenous bases in DNA:
There are 4 different nitrogenous bases in RNA:
NOTE: Thymine swaps for uracil in RNA
Purines have a double ring structure and therefore are large and include Adenine and Guanine
Pyrimidines have a single ring structure and therefore are titchy and include Thymine and Cytosine (and uracil)
Adenosine Triphosphate and Adenosine Diphosphate
A single molecule of adenosine triphosphate (ATP) is a nucleotide derivative and is formed from a molecule of
ribose, a molecule of adenine and three phosphate groups.
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Y1 Nucleotides and Nucleic Acids Notes
Glucose cannot be used as an immediate source of energy in cells; it must be oxidised during respiration, where it
releases energy. This energy is used to phosphorylate ADP into ATP, catalysed by the enzyme ATPsynthase.
When a cell requires energy eg for active transport, muscle contraction and biosynthesis, ATP is hydrolysed by
ATP hydrolase. The process uses a water molecule to hydrolyse ATP into ADP and Pi, releasing energy. The
inorganic phosphate is used to phosphorylate other compounds, often making them more reactive. Note that the
second phosphate group can also be removed, but this releases less energy; it leaves adenosine monophosphate
(AMP) and Pi.
Nucleotides Summary
Complete the table below by placing ticks into the appropriate columns in each row:
DNA Nucleotides RNA Nucleotides Phosphorylated
Nucleotides
(ADP and ATP)
Contains Nitrogen
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Y1 Nucleotides and Nucleic Acids Notes
Contains Carbon
Contains Hydrogen
Contains Phosphorous
Can contain Adenine
Only base is adenine
Can contain Guanine
Can contain Thymine
Can contain Cytosine
Can contain Uracil
Contains Ribose sugar
Contains Deoxyribose sugar
Contains phosphate
Contains > 1 phosphate group
Contains a purine only
Can contain a purine or pyrimidine
Used as an immediate energy source
A monomer which can form a polymer
Forming Polynucleotides
A condensation reaction between the hydroxyl group on the phosphate of one nucleotide and the hydroxyl group
of the pentose sugar of another nucleotide, forms a molecule of water and a “phosphodiester” bond. The reaction
is catalysed by either DNA polymerase or RNA polymerase. The resulting molecule is known as a dinucleotide.
Further condensation reactions form a polynucleotide of alternate sugar and phosphate molecules joined by
“phosphodiester” bonds; this is the name for the entire bond between one pentose and the next. The side of the
molecule is known as the sugar – phosphate “backbone”.
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Y1 Nucleotides and Nucleic Acids Notes
Note that these phosphodiester bonds can be broken again by hydrolysis reactions, where a molecule of water is
used to break the bond.
DNA Structure
DNA stands for Deoxyribonucleic Acid. DNA is a very simple molecule; so simple, that Scientists did not think it
could be the information carrying molecule for a long time. Its function is to hold genetic information.
DNA consists of two polymers of nucleotides joined by hydrogen bonds between specific complimentary bases.
Adenine binds to thymine with two hydrogen bonds and cytosine binds to guanine with three hydrogen bonds.
Each polymer is made up of nucleotides joined by phosphodiester bonds. Each nucleotide consists of a
nitrogenous base, a pentose sugar and a phosphate group. The hydrogen bonds form the “rungs” of the ladder.
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Y1 Nucleotides and Nucleic Acids Notes
The molecule is then twisted round to form a double helix shape (not a spiral). The two DNA strands are described
as being “anti-parallel”, since one strand is upside down relative to the other.
Extension: the end of the strand where the “point” of the pentose sugar is, is the “5 prime” (5”) end, , whilst the end of
the strand where the “base” of the pentose sugar is, is known as the “3 prime” (3”). In the diagram below, the left
strand is running 5” to 3” top to bottom and the right strand is running 3” to 5” top to bottom.
In a DNA molecule, a purine always bonds with a pyrimidine since the two polynucleotide molecules must always be
the same distance apart.
The pairings are in fact even more precise than this. Adenine always pairs with Thymine by two hydrogen bonds
and Guanine always pairs with Cytosine by three hydrogen bonds
This base pairing is specific because adenine is complementary to thymine and guanine is complimentary to
cytosine. The quantities of A and T are always the same and C and G are always the same. The ratio of AT to CG
varies from species to species and the order of bases varies from organism to organism.
RNA Structure
RNA molecules are made from RNA nucleotides, which each contain ribose sugar, a phosphate group and a
nitrogenous base which can be adenine, guanine, cytosine or uracil. There is no thymine in RNA nucleotides.
The RNA nucleotides join during condensation reactions to form ribonucleic acid (RNA). RNA molecules are
made from a single polynucleotide. There are three different types, all of which have a different function in protein
synthesis.
Messenger RNA (mRNA)
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Y1 Nucleotides and Nucleic Acids Notes
mRNA transfers genetic information from DNA to the ribosomes. It is a single polynucleotide strand made in
the nucleus during transcription. mRNA molecules are the “photocopy"; they carry the genetic code from the DNA
in the nucleus to the cytoplasm, where it’s used to make a protein during translation. A group of three bases in
mRNA is called a codon.
Transfer RNA (tRNA)
tRNA transfers amino acids to the ribosome. It is also a single polynucleotide chain folded into a clover leaf
shape held by hydrogen bonds which occur between complimentary base pairs. At one end of every tRNA
molecule is a sequence of three bases known as the anticodon. At the opposite end is an amino acid binding site.
Ribosomal RNA (rRNA)
rRNA combines with proteins to form ribosomes. Each ribosome is made from 2 subunits.
DNA Replication
When new cells are produced for growth and repair, the DNA must be replicated to ensure that each new daughter
cell receives a full copy of the entire genome of the organism; the process ensures genetic continuity between
cells. The process of DNA replication must be very accurate to ensure all new DNA molecules are identical to the
original one, enabling DNA to be conserved from one generation to the next, remaining unchanged.
Occasionally, a random, spontaneous mutation can occur, which changes the base sequence. This may have a
positive, negative or neutral effect, depending on if or how it alters the sequence of amino acids.
Semi-conservative Model
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Y1 Nucleotides and Nucleic Acids Notes
DNA replication is semi-conservative; each new DNA molecule contains one template and one new strand
- The enzyme DNA helicase breaks the hydrogen bonds between complimentary bases
- The double helix unwinds to form two separate strands
- Each exposed polynucleotide strand then acts as a template
- Free-floating DNA nucleotides are activated by phosphorylation
- Free-floating DNA nucleotides line up with complimentary bases
- Hydrogen bonds form between the bases on the original and new strand
- DNA polymerase joins adjacent nucleotides in condensation reactions forming phosphodiester bonds
- The strand twists to form a double helix
- Each of the new DNA molecules contain one template strand and one new strand
Evidence
There were three possible mechanisms proposed for how DNA replicated:
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Y1 Nucleotides and Nucleic Acids Notes
Scientists debated for many years about how DNA replicated; eventually, the semi-conservative method proposed
by Meselsohn and Stahl became widely accepted. Their work was based on several key facts:
- All bases in DNA contain Nitrogen which has 2 forms: 14N is lighter than 15N, a heavier isotope
- Bacteria will incorporate Nitrogen from their growing medium into any new DNA that they make
- DNA grown on 14N would be lighter than DNA grown on 15N
Stage 1: They labelled all bacterial DNA with the
heavy 15N by culturing in a medium containing 15N
Stage 2: When spun in a centrifuge tube, this DNA
settles at the bottom of the tube.
Stage 3: They then transferred the bacteria to a second
culture containing 14N for a single generation only to
allow it them replicate once. The mass of each “new”
DNA molecule would depend upon which method of
replication which had taken place; to separate the
original and new DNA molecules they centrifuged the
extracted DNA in a special solution; if replication was
semi-conservative, each new molecule would weigh
14.5N and only one band would be seen in the middle; if
replication was conservative then each new molecule
would weigh 14N and two bands would be seen, one
heavy one, towards the bottom and one lighter one,
towards the top. They also analysed the DNA after two,
then three, then four generations growing with 14N.
Results
After the first replication one band was obtained. This ruled out conservative replication because there would have
been two bands. After the second replication there were two bands. This was consistent with the semi-conservative
model but not the dispersive model since this would still have had only one, higher band. This is because this model
predicts all molecules would have contained approximately ¼ heavy DNA and ¾ light DNA. The semi-conservative
model was consistent with their findings; one band at the original height and a second higher band for new DNA
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Y1 Nucleotides and Nucleic Acids Notes
Evaluation
Students should be able to evaluate the work of scientists in validating the Watson–Crick model of DNA replication.
Watson and Crick proposed a model for the structure of DNA in 1953 and it is widely believed that they “discovered”
DNA; they did not. Many other Scientists, including Rosalind Franklin, had already discovered crucial information
about the structure of DNA, including the composition of nucleotides, the base pairing etc. Watson and Crick proposed
the double helix model for the structure of DNA and are given much of the credit.
Rosalind Franklin: A Crucial Contribution | Learn Science at Scitable (nature.com)
Nucleic Acid Single Answer Questions
1 What does DNA stand for? Deoxyribonucleic Acid
2 Name the classic shape of a DNA molecule: Double helix
3 State the term which describes a molecule made from monomers Polymer
4 Name the monomers used to produce DNA DNA Nucleotides
5 Name the pentose sugar in DNA molecules Deoxyribose
6 Name the 4 nitrogenous bases which can be found in DNA nucleotides ATCG
7 Name the bond forms between a sugar and phosphate in a nucleotide Ester
8 Name the bond which includes the two sugars in a polynucleotide Phosphodiester
9 State the type of reaction which occurs between 2 nucleotides Hydrolysis
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Y1 Nucleotides and Nucleic Acids Notes
10 State the number of polynucleotides which join to form a DNA molecule 2
11 Name the bonds which form between polynucleotide strands Hydrogen
12 State the number of bonds formed between bases A and T 2
13 State the number of bonds formed between bases C and G 3
14 State the collective name of the larger bases Purines
15 Name the 2 larger bases which are found in DNA molecules A and G
16 State the collective name of the smaller bases Pyrimidines
17 Name the 2 smaller bases which are found in DNA molecules C and G
18 State the term which describes base pairing between C and G and A and T Complimentary
19 What does RNA stand for? Ribonucleic acid
20 Name the pentose sugar in RNA molecules Ribose
21 Name the 4 nitrogenous bases which can be found in RNA molecules AUCG
22 Name the type of RNA molecule which is a “copy” of DNA mRNA
23 Name the type of RNA molecule which takes information from the “copy” of tRNA
DNA and links this to the amino acids
24 State 3 similarities between DNA and RNA Both contain pentose sugar,
Both contain pentose sugar, nitrogenous bases and phosphate nitrogenous base, phosphate
25 State 3 differences between DNA and RNA DNA contains T, RNA U, DNA
DNA contains deoxyribose, RNA contains ribose; DNA contains thymine, double stranded, RNA single
RNA contains uracil; DNA is double stranded and RNA is single stranded and DNA contains deoxyribose
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Y1 Nucleotides and Nucleic Acids Notes
Compare and contrast DNA and RNA
➔ Write the following terms into the section of the circles which overlap, or the sections which do not. Label one circle DNA and one RNA:
Single stranded, double stranded, shorter, longer, made from nucleotides, contain deoxyribose sugar, contain ribose sugar, contain nitrogenous bases,
contain nitrogenous bases A, C, G and T, contain nitrogenous bases A, C, G and U, twists to form a double helix, involved in protein synthesis.
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Y1 Nucleotides and Nucleic Acids Notes
Y1 Nucleotides and Nucleic Acids Revision Summary
Nucleotides are monomers from which polynucleotides are made. Another name for polynucleotides is nucleic
acids. The nucleic acids important in cells are DNA (deoxyribonucleic acid) made from DNA nucleotides and RNA
(ribonucleic acid) made from RNA nucleotides.
All nucleotides are composed of a pentose sugar, at least one phosphate group and a nitrogenous base. The
pentose sugar in DNA is deoxyribose and the four different nitrogenous bases are adenine, thymine, cytosine
and guanine. The pentose sugar in RNA is ribose and the four different nitrogenous bases are adenine,
cytosine, guanine and uracil.
The largest bases are known as purines; they have a double carbon ring and include A and G. The smaller bases
are known as pyrimidines; they have a single carbon ring and include T and C in DNA and U and C in RNA. There
is also a third, special type of nucleotide known as ATP and ADP. These are phosphorylated nucleotides, which
means that they have 1 or 2 additional phosphate groups added. They are each made up of the base adenine, the
sugar ribose and then ATP has 3 phosphate groups whilst ADP only has 2. ATP is our immediate source of energy in
cells. Glucose (or any other relatively large molecule) cannot be used as an immediate energy source; first it has to be
oxidised during the process of respiration. During this process, it releases energy; this energy is used to
phosphorylate ADP using Pi to make ATP. When a cell requires energy, a hydrolysis reaction occurs where a
water molecule is used to break the phosphate bond and release energy.
In order to form polynucleotides, nucleotides join together in condensation reactions to produce a
phosphodiester bond between the hydroxyl group on the pentose sugar from one nucleotide and the hydroxyl
group on the phosphate group of another. A molecule of water is also produced.
DNA is a nucleic acid made from DNA nucleotides. It is actually made up of two polynucleotides joined together by
hydrogen bonds between the nitrogenous bases of each molecule. The deoxyribose sugars and the phosphate
groups form the sugar-phosphate backbone or the “sides” of the ladder whilst the hydrogen bonds form the
“rungs”. The molecule is then twisted into a double helix shape. The two strands are described as being “anti -
parallel” since one strand is upside down relative to the other (one strand has the “point” on the pentose sugar
pointing up and the other has the “point” on the pentose sugar pointing down; the “point” end is known as the 5’ end).
The nitrogenous base pairing is specific; A always binds with T with 2 hydrogen bonds and C always binds with G
with 3 hydrogen bonds.
DNA replication must be very accurate to ensure each new daughter cell has an identical DNA strand. This means
that DNA can be conserved from generation to generation and remains unchanged. DNA replicated using the semi-
conservative model, where each new strand contains one copy of the original DNA and one copy of the new DNA.
The enzyme DNA helicase breaks the hydrogen bonds between the two polynucleotides, so the DNA molecule
unwinds to form two strands. Each strand then acts as a template to which free-floating DNA nucleotides can bind to
their complimentary bases joined by hydrogen bonds between the bases. The enzyme DNA polymerase joins the
nucleotides together by phosphodiester bonds. The strand then twists to form a double helix shape. A source of
energy is required for the process. The meselsohn-stahl experiment provides evidence to support the theory that
DNA replication is semi-conservative.
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