DP Biology SL A1.2 Nucleic Acids

DP Biology SL A1.2 Nucleic Acids - Full notes

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DP Biology SL | A1.2 Nucleic Acids

DP BIOLOGY · THEME A: UNITY AND DIVERSITY

A1.2

Nucleic Acids

Full notes for SL · IB-style

Contents

1	DNA as the genetic material of all living organisms
2	Nucleotides: the building blocks
3	From nucleotides to strands: the sugar-phosphate backbone
4	The double helix and complementary base pairing
5	RNA and how it differs from DNA
6	Diversity, information and the genetic code
7	Nucleotide structure in detail
8	Purines and pyrimidines
9	The sugar–phosphate backbone
10	Antiparallel strands and the double helix
11	Complementary base pairing and hydrogen bonds
12	Chargaff's rules and base calculations
13	DNA versus RNA
14	The role of DNA: information storage
15	The universal genetic code
16	Watson, Crick, Franklin and the double helix
17	Directionality and its importance
18	ATP: a nucleotide for energy
19	Mixed review: worked problems
20	Additional exam-style practice
21	DNA profiling and nucleic acid technology
22	Nucleic acids and viruses
23	Practical: extracting DNA
24	Common misconceptions and links
25	Exam-style question with markscheme
26	Check your understanding
27	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
state that DNA is the genetic material of all living organisms and that some viruses use RNA
draw and label a nucleotide
explain how nucleotides are linked into a strand by condensation
describe the double helix and explain complementary base pairing
compare the structure of DNA and RNA
explain why the sequence of bases can store an almost unlimited amount of information

This booklet covers the SL content of this subtopic. Additional Higher Level material is not included.

Guiding questions

How does the structure of DNA allow it to store and copy information? What makes DNA and RNA different, and why does it matter?

How this topic is examined

Nucleic acids are central to Themes A and D. Paper 1 questions test the structure of nucleotides, base pairing and DNA/RNA differences; Paper 2 asks you to draw a section of DNA, calculate base percentages, or (at HL) analyse classic experiments.

Accurate diagrams and precise vocabulary (deoxyribose, phosphodiester, complementary, antiparallel) earn most of the marks.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 DNA as the genetic material of all living organisms

One molecule carries the instructions for every living thing.

Think about it

Bacteria, oak trees and humans look completely different. What is surprising about the fact that all three store their genetic information in the same molecule?

Deoxyribonucleic acid (DNA) is the genetic material of all living organisms. It carries the hereditary information that is passed from parents to offspring and that controls the development and functioning of cells. The fact that every organism uses DNA, with the same four bases and essentially the same genetic code, is strong evidence that all life shares a common ancestor.

Some viruses use ribonucleic acid (RNA) as their genetic material instead (influenza, HIV, SARS-CoV-2). Viruses are not considered living organisms because they cannot carry out metabolism or reproduce outside a host cell (A2.3), so the statement that DNA is the genetic material of all living organisms still holds.

DNA and RNA are nucleic acids: polymers built from monomers called nucleotides.

Quick check

1. What is the genetic material of all living organisms?

2. Name a virus that uses RNA as its genetic material.

Answers: 1. DNA 2. e.g. influenza, HIV, SARS-CoV-2

2 Nucleotides: the building blocks

Phosphate, sugar, base: three parts in every nucleotide.

A nucleotide has three components: a phosphate group, a pentose sugar (five carbon atoms) and a nitrogenous base. The phosphate is attached to one side of the sugar and the base to another.

In DNA the sugar is deoxyribose; in RNA it is ribose. Deoxyribose has one fewer oxygen atom than ribose (hence 'deoxy').

There are four bases in DNA: adenine (A), guanine (G), cytosine (C) and thymine (T). RNA has adenine, guanine, cytosine and uracil (U) instead of thymine. The base is the part of the nucleotide that varies, so it carries the information.

Figure 1. A DNA nucleotide: phosphate, deoxyribose sugar and one of four nitrogenous bases.

Common mistake

Drawing the base attached to the phosphate. In a nucleotide the base and the phosphate are both attached to the sugar, on different carbons.

Quick check

1. Name the three parts of a nucleotide.

2. Which sugar is found in DNA?

3. Which base is found in RNA but not DNA?

Answers: 1. phosphate, pentose sugar, nitrogenous base 2. deoxyribose 3. uracil

3 From nucleotides to strands: the sugar-phosphate backbone

Condensation reactions link nucleotides into long chains.

Nucleotides are joined by condensation reactions: the phosphate of one nucleotide bonds to the sugar of the next, and a molecule of water is released. The covalent bond formed (between the phosphate and the sugar) is part of a phosphodiester linkage.

Repeating this produces a long strand with an alternating sugar-phosphate backbone. The bases project from the backbone to one side. The backbone is the same along the whole strand; only the sequence of bases varies. Strong covalent bonds in the backbone make DNA chemically stable, which suits a molecule that must store information for a lifetime.

Key point

The backbone is sugar-phosphate-sugar-phosphate. The information is in the sequence of bases attached to it.

Quick check

1. What type of reaction joins nucleotides?

2. What forms the backbone of a nucleic acid strand?

Answers: 1. condensation 2. alternating sugar and phosphate groups

4 The double helix and complementary base pairing

Two strands, held together by base pairs, wound into a helix.

Think about it

If you knew the base sequence of one strand of DNA, could you work out the other strand? What rule would you use?

DNA consists of two strands of nucleotides wound around each other to form a double helix, a structure worked out by James Watson and Francis Crick in 1953, using X-ray diffraction images produced by Rosalind Franklin and Maurice Wilkins.

The two strands are held together by hydrogen bonds between bases on opposite strands. Bases pair in a fixed way, called complementary base pairing: adenine pairs with thymine (A–T) and guanine pairs with cytosine (G–C). A–T pairs are joined by two hydrogen bonds and G–C pairs by three.

Complementary base pairing has two key consequences. First, the sequence of one strand determines the sequence of the other, so DNA can be copied accurately during replication (D1.1): each strand acts as a template. Second, it allows information to be transcribed into RNA (D1.2).

Figure 2. Two strands of DNA joined by complementary base pairs (A–T, G–C).

WORKED EXAMPLE 1 Complementary strand and base percentages

(a) Write the complementary strand to 5' ATGCCTA 3'. (b) A DNA sample contains 22% adenine. Calculate the percentage of guanine.

Solution

(a) A pairs with T, G with C: TACGGATA1

(b) A = T, so T = 22%; A + T = 44%M1

G + C = 56%, and G = C, so G = 28%A1

This works only for double-stranded DNA, where every A has a partner T and every G a partner C.

Common mistake

Saying A pairs with U in DNA. Uracil is found only in RNA; in DNA, A pairs with T.

Quick check

1. Which bases pair in DNA?

2. What holds the two strands together?

3. A sample has 30% cytosine. What percentage is thymine?

Answers: 1. A–T and G–C 2. hydrogen bonds between complementary bases 3. 20%

5 RNA and how it differs from DNA

One strand, a different sugar, and uracil instead of thymine.

RNA is also a polymer of nucleotides, but it differs from DNA in three main ways. It is usually single-stranded; its sugar is ribose; and it contains uracil instead of thymine. RNA molecules are generally much shorter than DNA molecules.

Cells make several types of RNA with different roles in protein synthesis: messenger RNA (mRNA) carries a copy of a gene to the ribosome; transfer RNA (tRNA) brings amino acids; and ribosomal RNA (rRNA) forms part of the ribosome. You will study these in D1.2.

Feature	DNA	RNA
Number of strands	two (double helix)	usually one
Sugar	deoxyribose	ribose
Bases	A, T, G, C	A, U, G, C
Length	very long	shorter
Location (eukaryotes)	mainly nucleus (also mitochondria, chloroplasts)	nucleus, cytoplasm, ribosomes
Function	stores genetic information	uses information to make proteins

Quick check

1. Give three structural differences between DNA and RNA.

2. What is the role of mRNA?

Answers: 1. strands, sugar, thymine vs uracil 2. carries a copy of a gene to the ribosome

6 Diversity, information and the genetic code

Four letters, endless messages.

DNA can store an enormous amount of information because there is no restriction on the sequence of bases along a strand. With four possible bases at each position, a sequence of n bases has 4ⁿ possible combinations. Even a short sequence of 10 bases has over a million possibilities; the human genome has about 3 billion base pairs.

The information is read in groups of three bases called codons, each of which specifies an amino acid. This genetic code is almost universal: the same codon codes for the same amino acid in bacteria, plants and animals, which is why a human gene can be inserted into a bacterium to make human insulin.

WORKED EXAMPLE 2 Counting possible sequences

How many different base sequences are possible for a DNA section 3 bases long, and for one 6 bases long?

Solution

3 bases: 4³ = 64A1

6 bases: 4⁶ = 4 096A1

In the real world

Because the genetic code is universal, bacteria engineered with the human insulin gene have produced human insulin for diabetics since 1982, replacing insulin extracted from pigs and cattle.

7 Nucleotide structure in detail

Three components.

Each nucleotide contains a pentose sugar (deoxyribose in DNA, ribose in RNA), a phosphate group attached to carbon 5′ of the sugar, and a nitrogenous base attached to carbon 1′. The carbons of the sugar are numbered 1′ to 5′.

WORKED EXAMPLE 3 Drawing (standard)

Describe how to draw a simple diagram of a DNA nucleotide.

Solution

Pentagon for deoxyribose; circle for phosphate linked to C5′R1

Rectangle for base linked to C1′R1

Quick check

1. Which carbon of the sugar carries the base?

2. What is the difference between ribose and deoxyribose?

Answers: 1. C1′ 2. deoxyribose lacks an oxygen (OH) at C2′

8 Purines and pyrimidines

Two families of bases.

Adenine and guanine are purines (double-ring bases). Cytosine, thymine and uracil are pyrimidines (single-ring bases). Complementary pairs always contain one purine and one pyrimidine, so the double helix has a constant width.

Base	Type	Found in	Pairs with
adenine (A)	purine	DNA, RNA	T (DNA), U (RNA)
guanine (G)	purine	DNA, RNA	C
cytosine (C)	pyrimidine	DNA, RNA	G
thymine (T)	pyrimidine	DNA only	A
uracil (U)	pyrimidine	RNA only	A

WORKED EXAMPLE 4 Constant width (standard)

Explain why DNA has a constant diameter.

Solution

Each base pair contains one purine (two rings) and one pyrimidine (one ring)R1

So every rung is the same lengthR1

9 The sugar–phosphate backbone

Covalent links between nucleotides.

Nucleotides are linked by condensation reactions forming covalent phosphodiester bonds between the phosphate of one nucleotide and the 3′ carbon of the sugar of the next. This creates a strong backbone with the bases projecting from it. Each strand has a 5′ end (free phosphate) and a 3′ end (free OH).

WORKED EXAMPLE 5 Bond types (exam level)

Distinguish the bonds that hold the backbone together from those that hold the two strands together.

Solution

Backbone: covalent phosphodiester bonds (strong)R1

Between strands: hydrogen bonds between complementary bases (weak individually)R1

Quick check

1. What molecule is released when two nucleotides join?

Answers: 1. water (condensation)

10 Antiparallel strands and the double helix

5′ to 3′ opposite 3′ to 5′.

The two strands of DNA run in opposite directions (antiparallel): one 5′→3′, the other 3′→5′. They coil around each other to form a double helix, with the bases stacked inside and the backbones outside.

WORKED EXAMPLE 6 Antiparallel (standard)

Write the complementary strand to 5′-ATGCCGTA-3′ with its ends labelled.

Solution

3′-TACGGCAT-5′A2

Quick check

1. Write the complementary DNA strand to 5′-GGATCC-3′.

Answers: 1. 3′-CCTAGG-5′

11 Complementary base pairing and hydrogen bonds

Two and three hydrogen bonds.

A pairs with T by two hydrogen bonds; G pairs with C by three. DNA with a higher proportion of G–C pairs is more stable and needs a higher temperature to separate the strands.

WORKED EXAMPLE 7 Stability (exam level)

DNA sample X is 60% G–C pairs; sample Y is 40%. Which has the higher melting temperature? Explain.

Solution

XA1

G–C pairs have three hydrogen bonds; more energy needed to separate strandsR1

12 Chargaff's rules and base calculations

A = T and G = C.

In double-stranded DNA, the amount of A equals T and G equals C. Therefore purines = pyrimidines = 50%. If one base percentage is known, the others can be calculated.

WORKED EXAMPLE 8 Calculation (standard)

A DNA sample contains 22% adenine. Find the percentages of the other bases.

Solution

T = 22%A1

G + C = 56%: G = C = 28%A1

Quick check

1. A DNA sample is 31% guanine. Find % thymine.

2. Why do Chargaff's rules not apply to single-stranded RNA?

Answers: 1. 19% 2. no complementary strand, so bases need not be in equal amounts

13 DNA versus RNA

Three key differences.

Feature	DNA	RNA
sugar	deoxyribose	ribose
bases	A, T, G, C	A, U, G, C
strands	double (helix)	usually single
length	very long	short
function	stores genetic information	protein synthesis (mRNA, tRNA, rRNA), regulation

WORKED EXAMPLE 9 Distinguishing (standard)

State three differences between DNA and RNA.

Solution

Deoxyribose vs ribose; thymine vs uracil; double vs single strandA3

14 The role of DNA: information storage

The genetic code.

The sequence of bases in DNA stores genetic information. Because there are four bases, a sequence of n bases can have 4n combinations, giving enormous storage capacity. The information is copied (replication) and expressed (transcription and translation).

WORKED EXAMPLE 10 Storage capacity (standard)

How many different sequences are possible for a stretch of 10 bases?

Solution

410M1

= 1 048 576A1

Quick check

1. Why are three bases (a codon) needed to code for 20 amino acids?

Answers: 1. 42 = 16 is too few; 43 = 64 is enough

15 The universal genetic code

Evidence for common ancestry.

The same codons code for the same amino acids in almost all organisms. This universality allows genes from one organism to be expressed in another (genetic modification) and is strong evidence that all life shares a common origin.

WORKED EXAMPLE 11 Universality (standard)

Explain how the universality of the genetic code supports common ancestry.

Solution

The code is arbitrary yet shared by almost all organismsR1

Best explained by inheritance from a common ancestorR1

In the real world

Human insulin is produced by bacteria containing the human insulin gene; the bacteria read the human gene using the same genetic code.

16 Watson, Crick, Franklin and the double helix

Nature of science.

Watson and Crick built a model of DNA in 1953 using X-ray diffraction images from Rosalind Franklin and Maurice Wilkins, Chargaff's base ratios, and model-building. Franklin's 'Photograph 51' showed a helical structure with regular spacing. The story illustrates collaboration, competition, and the use of evidence to test models.

WORKED EXAMPLE 12 Evidence (standard)

State two pieces of evidence used by Watson and Crick.

Solution

X-ray diffraction images (helix, dimensions)A1

Chargaff's rules (A = T, G = C)A1

17 Directionality and its importance

Enzymes read 3′ to 5′.

Because nucleic acids have direction, enzymes act in specific directions: DNA polymerase adds nucleotides only to the 3′ end, so new strands grow 5′→3′; RNA polymerase also synthesizes RNA 5′→3′ by reading the template 3′→5′.

WORKED EXAMPLE 13 Direction (standard)

In which direction is a new DNA strand synthesized?

Solution

5′ to 3′A1

18 ATP: a nucleotide for energy

Not only information.

Adenosine triphosphate (ATP) is a nucleotide with three phosphate groups. Hydrolysis of the terminal phosphate (ATP → ADP + Pi) releases energy for cellular processes. Other nucleotides act as coenzymes (NAD+, FAD).

WORKED EXAMPLE 14 ATP (standard)

State two differences between ATP and a DNA nucleotide.

Solution

ATP has ribose, not deoxyriboseA1

Three phosphate groups, not oneA1

19 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 15 Mixed problem (exam level)

A section of DNA has 300 base pairs, 90 of which are A–T pairs. Calculate the number of (a) cytosine bases; (b) hydrogen bonds between the strands.

Solution

(a) G–C pairs = 210: 210 cytosinesA1

(b) 90 × 2 + 210 × 3 = 810M1 A1

Quick check

1. How many phosphodiester bonds join 20 nucleotides in a single strand?

Answers: 1. 19

20 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 16 Paper 1 question (standard)

Which bonds link complementary bases? A. covalent B. ionic C. hydrogen D. phosphodiester

Solution

CA1

WORKED EXAMPLE 17 Paper 2 question (exam level)

Outline how the structure of DNA allows it to be copied accurately.

Solution

Two strands separated by breaking weak hydrogen bondsR1

Each strand acts as a templateR1

Complementary base pairing ensures accurate copyingR1

21 DNA profiling and nucleic acid technology

Applications.

Knowledge of DNA structure underpins modern biotechnology: PCR copies DNA using its base-pairing; gel electrophoresis separates DNA fragments by size (DNA is negatively charged due to its phosphate groups); DNA profiling compares short tandem repeats to identify individuals.

WORKED EXAMPLE 18 Electrophoresis (standard)

Explain why DNA moves towards the positive electrode in gel electrophoresis.

Solution

Phosphate groups are negatively chargedR1

22 Nucleic acids and viruses

RNA and DNA genomes.

Viruses may have DNA or RNA genomes, single- or double-stranded. Retroviruses such as HIV have RNA and use reverse transcriptase to make DNA. The SARS-CoV-2 genome is single-stranded RNA of about 30 000 nucleotides.

Quick check

1. What does reverse transcriptase do?

Answers: 1. makes DNA from an RNA template

23 Practical: extracting DNA

From fruit to fibres.

DNA can be extracted from strawberries or onions: mash the tissue with detergent (breaks membranes) and salt (helps DNA clump), filter, then add ice-cold ethanol, in which DNA is insoluble and precipitates as white strands.

WORKED EXAMPLE 19 Explaining steps (standard)

Explain the role of detergent in DNA extraction.

Solution

Dissolves phospholipids in cell and nuclear membranesR1

Releases DNAR1

Try this

Extract DNA from a strawberry using washing-up liquid, salt and cold ethanol. Spool the white strands onto a glass rod.

24 Common misconceptions and links

Students often think…	Actually…
DNA contains uracil	uracil is found only in RNA
base pairs are held by covalent bonds	they are held by hydrogen bonds; the backbone is covalent
A + T always equals G + C	A = T and G = C, but A + T need not equal G + C
RNA is always double-stranded	RNA is usually single-stranded

How A1.2 connects to the rest of the course

Topic	Connection
D1.1 DNA replication	base pairing allows semi-conservative replication
D1.2 Protein synthesis	transcription and translation use RNA
A2.1 Origins of cells (HL)	the RNA world hypothesis
D1.3 Mutations	changes in base sequence
A3.1 Diversity	genome size and variation

25 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Text A. Analysis of DNA extracted from wheat gave the following base composition: adenine 27.3%, thymine 27.1%, guanine 22.7%, cytosine 22.8%.

(a) Draw and label a single DNA nucleotide. [3]

(b) Using the data for wheat, show that the data support complementary base pairing. [2]

(d) Explain how the structure of DNA allows it to store a large amount of information. [2]

Markscheme

Part	Answer	Marks
(a)	phosphate attached to sugar	A1
	sugar labelled deoxyribose / pentose	A1
	base attached to the sugar (not to phosphate)	A1
(b)	A (27.3) ≈ T (27.1)	A1
	G (22.7) ≈ C (22.8)	A1
(c)	double vs single strand; deoxyribose vs ribose; thymine vs uracil	A3
(d)	any sequence of bases is possible	R1
	4ⁿ combinations for n bases; long molecules	R1

Examiner's comments. In (a), many drawings attached the base to the phosphate. In (b), the best answers compared both pairs with figures.

26 Check your understanding

Section A: multiple choice

1. The sugar in DNA is

A. deoxyribose B. ribose C. glucose D. ribulose

2. Which base pairs with guanine?

A. adenine B. thymine C. cytosine D. uracil

3. Nucleotides are joined by

A. hydrolysis reactions B. condensation reactions C. hydrogen bonds only D. ionic bonds

4. RNA differs from DNA in having

A. deoxyribose B. two strands C. no phosphate D. uracil instead of thymine

5. The two strands of DNA are held together by

A. phosphodiester bonds B. hydrogen bonds between bases C. peptide bonds D. ionic bonds

6. A DNA sample has 18% thymine. The percentage of cytosine is

A. 32% B. 18% C. 36% D. 64%

7. The genetic material of all living organisms is

A. RNA B. protein C. lipid D. DNA

8. How many sequences are possible for 4 bases?

A. 16 B. 64 C. 256 D. 4

Section B: structured

9. Describe the structure of a DNA molecule. [5]

10. Explain the importance of complementary base pairing. [3]

11. Compare and contrast DNA and RNA. [4]

Answers

1. A 2. C 3. B 4. D 5. B 6. A 7. D 8. C

9. Two strands, sugar-phosphate backbone, bases inward, A–T and G–C, hydrogen bonds, double helix.

10. One strand is a template for the other; accurate replication; transcription into RNA.

11. Both nucleotide polymers with A, G, C and phosphate; DNA double, deoxyribose, T; RNA single, ribose, U.

27 Summary and topic map

Idea	Remember
Genetic material	DNA in all organisms; RNA in some viruses
Nucleotide	phosphate + pentose + base
Strand	sugar-phosphate backbone by condensation
Double helix	two strands; A–T, G–C; hydrogen bonds
RNA	single strand, ribose, uracil
Information	unlimited base sequences; universal code

Before the exam, make sure you…

•draw nucleotides with base and phosphate both on the sugar
•use complementary pairing for strand and percentage questions
•list DNA/RNA differences in a table
•use precise terms: deoxyribose, condensation, hydrogen bonds

Nucleic Acids on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 3. Topic map for Nucleic Acids.

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