Nucleic Acids

Learning Objective A1.2.1 - DNA as the Genetic Material of All Living Organisms

DNA – The Universal Genetic Code

• Deoxyribonucleic acid (DNA) is the molecule that stores the long-term genetic information in all living organisms.

  • This information provides the instructions for building proteins, which determine how cells function.

Because DNA can be accurately replicated, it allows genetic information to be:

• passed from cell to cell during growth

• passed from parent to offspring during reproduction

  
  

DNA as Evidence of Common Ancestry

• All living organisms use DNA as their genetic material.

  • This universality suggests that all life shares a common evolutionary origin.

  • This supports the idea that:

    • life evolved from a common ancestor

    • the genetic code is fundamentally shared across all species

Gene Expression: Same DNA, Different Cells

In multicellular organisms:

• all cells contain the same DNA

• but only specific genes are expressed in each cell

This leads to:

• cell specialization

• different structures and functions despite identical genetic material

What About Viruses?

Some viruses use:

• DNA as genetic material

• others use RNA

Examples:

• DNA viruses → bacteriophages

• RNA viruses → HIV, coronaviruses

Why This Does NOT Contradict the DNA Rule

• A virus is simply:

  • a nucleic acid core (DNA or RNA)

  • surrounded by a protein coat

  • with no cellular machinery of its own

• Because of this, viruses:

  • cannot reproduce independently

    • they must infect a host cell

  • do not carry out metabolism

  • do not respond to stimuli independently

So Why Doesn’t RNA in Viruses Falsify the DNA Claim?

• Since viruses are not living, they are not exceptions to the rule.

  • therefore, the presence of RNA in some viruses does not contradict the idea that DNA is the genetic material of all living organisms.

• In fact, the dependence of viruses on host cells highlights that only living cells with DNA have the full capacity for independent life.

🔍 IB EXAM FOCUS

• ⚠️ Always state: “viruses are not considered living”

• Be ready to explain:

  • DNA as evidence for common ancestry

  • Why universality of DNA supports evolution

• You MUST be able to link: DNA → genes → proteins → cell function

  • This is the foundation of gene expression and cell differentiation

• Common exam traps:

  • Saying “all organisms use DNA” ❎

    → Must say all living organisms ✅

A1.2.2 - Components of a nucleotide

What is a Nucleotide?

A nucleotide is the basic building block (monomer) of nucleic acids (DNA and RNA).

• Each nucleotide is made of three components:

  • Phosphate group - circle

  • Pentose sugar (5-carbon sugar) - pentagon

  • Nitrogenous base - rectangle

Key Structural Details

• The pentose sugar has 5 carbon atoms:

  • Base attaches to Carbon #1 (C1)

  • Phosphate attaches to Carbon #5 (C5)

• This positioning is what allows nucleotides to link together to form long chains (polymers)

🔍 IB EXAM FOCUS

You may be asked to:

• draw a nucleotide from memory

• identify components in a diagram

• label phosphate, sugar, and base correctly

Common mistakes:

• Not showing correct relative positioning

A1.2.3 - Sugar - Phosphate Bonding & Backbone

How Nucleotides Join Together

• Nucleotides are linked by covalent bonds called phosphodiester bonds.

• These form between:

  • phosphate of one nucleotide

  • sugar of the next nucleotide

• Formation of the Backbone

  • Repeating linkage creates a:

👉 sugar–phosphate backbone

• This backbone:

  • runs along the length of the DNA/RNA strand

  • is made of alternating:

sugar → phosphate → sugar → phosphate

Key Functional Importance

• The backbone:

  • is strong and stable (covalent bonds)

  • protects the sequence of bases

  • gives structure to the molecule

• The bases project inward, allowing base pairing and genetic coding

Reminder: Polymer Formation

• Nucleic acids are polymers formed by condensation reactions

• Each bond formation:

  • releases a molecule of water

🔍 IB EXAM FOCUS

• IB LOVES asking:

  • What type of bond joins nucleotides → covalent bond, specifically a phosphodiester bond

  • What forms the backbone → alternating sugar-phosphate chain

• Common mistake:

  • Saying “bonds between bases form the backbone”

→ backbone is ONLY sugar-phosphate

A1.2.4 – Nitrogenous Bases & the Genetic Code

The Nitrogenous Bases

DNA bases:

• Adenine (A)

• Thymine (T)

• Cytosine (C)

• Guanine (G)

RNA bases:

• Adenine (A)

• Uracil (U) (instead of thymine)

• Cytosine (C)

• Guanine (G)

Key Differences (DNA vs RNA)

• DNA uses thymine (T)

• RNA uses uracil (U)

This is the ONLY base difference

Bases Form the Genetic Code

• Each nucleotide contains one base

• The sequence of bases stores genetic information

• This sequence:

• forms genes

• determines amino acid sequences

• ultimately determines protein structure and function

Why Base Sequence Matters

• Different sequences → different proteins

• Different proteins → different:

• cell structures

• cell functions

This is the basis of biological diversity

IB EXAM FOCUS

• You MUST:

5/23

• know all base names (not just letters)

• distinguish DNA vs RNA bases

• IB often asks:

• role of base sequence → genetic information storage

• link: base sequence → gene → protein → phenotype

• Always phrase as:

• “The sequence of nitrogenous bases forms the genetic code”

• Then link to protein synthesis

6/23

A1.2.5 – Structure of RNA

RNA as a Polymer

• RNA (ribonucleic acid) is a single-stranded polymer made of nucleotide monomers

• Nucleotides are joined by condensation reactions

• Forms phosphodiester bonds

• Water is released each time a bond forms

If a chain has n nucleotides, it forms (n − 1) bonds & (n − 1) water molecules

For example a if an RNA chain has 4 nucleotides:

• it forms 3 phosphodiester bonds and 3 water molecules are released

Key Structural Features

• RNA consists of:

• Ribose sugar

• Phosphate backbone

• Nitrogenous bases (A, U, C, G)

Recognising RNA in Diagrams

• Look for:

• Single strand (NOT double)

• Presence of uracil (U) instead of thymine

IB EXAM FOCUS

• IB commonly tests:

• Condensation reactions → water released

• Identification of RNA vs DNA from diagrams

• Common mistakes:

• Forgetting uracil replaces thymine

Always phrase as:

“RNA is a single-stranded polymer formed by condensation of RNA nucleotide monomers

via phosphodiester bonds”

7/23

A1.2.6 – Structure of DNA

DNA as a Double Helix

• DNA (deoxyribonucleic acid) consists of two strands of nucleotides.

• Each strand has a sugar–phosphate backbone

• The nitrogenous bases face inward & form “rungs” of the ladder

• These strands:

• twist into a double helix

• are held together by hydrogen bonds between bases

Antiparallel Structure

• The two strands run in opposite directions:

• one strand: 5’ → 3’

• other strand: 3’ → 5’

Complementary Base Pairing

• Bases pair specifically:

• Adenine (A) Thymine (T) - with 2 hydrogen bonds

• Guanine (G) Cytosine (C) - with 3 hydrogen bonds

• This ensures accurate replication and a stable structure.

Diagram Expectations (VERY important)

You should be able to:

• draw two strands

• show antiparallel orientation

• show correct base pairing (A–T , G–C)

IB EXAM FOCUS

• IB LOVES asking:

• define antiparallel

• explain complementary base pairing

• identify errors in DNA diagrams

• Common mistakes:

• Both strands drawn in same direction 🆇

8/23

A1.2.7 – Differences Between DNA and RNA

Key Structural Differences

Feature DNA RNA

Strands Double-stranded Single-stranded

Sugar Deoxyribose Ribose

Bases A, T , C, G A, U, C, G

Sugar Structure Difference: Ribose vs. Deoxyribose

• Ribose (RNA):

• has –OH group on carbon 2

• Deoxyribose (DNA):

• has H instead of OH

• → one less oxygen

This is the ONLY structural sugar difference

Functional Differences

• DNA:

• long-term genetic storage

• stable structure

• RNA:

• involved in protein synthesis

• shorter-lived and more flexible

Examples of RNA (IMPORTANT)

• mRNA (messenger RNA) → carries genetic code from DNA

• tRNA (transfer RNA) → brings amino acids

• rRNA (ribosomal RNA) → forms ribosomes

IB EXAM FOCUS

• IB frequently asks:

• compare DNA vs RNA (table or structured answer)

• identify differences in strands, bases, sugar

• For “compare” questions, ALWAYS structure answers like:

• DNA is

___, whereas RNA is

___

9/23

• DNA contains

___, whereas RNA contains

___

Direct comparison = higher marks

10/23

A1.2.8 – Importance of Complementary Base Pairing

Reminder: DNA bases pair in a specific and predictable way:

• Adenine (A) Thymine (T)

• Cytosine (C) Guanine (G)

• This pairing occurs due to hydrogen bonding

• weak individually, but strong collectively

Why Complementarity Matters

1. Accurate DNA Replication

• During replication, DNA strands separate and each strand acts as a template

• Free nucleotides pair with complementary bases on the template strand

• This ensures:

• exact copying of genetic information

• production of identical DNA molecules

2. Gene Expression (Protein Synthesis)

• Complementary base pairing is also essential in:

• Transcription (DNA → RNA)

• Translation (RNA → protein)

• This ensures:

• correct amino acid sequence

• correct protein structure and function

Key Idea

Complementarity = information is preserved AND accurately used

IB EXAM FOCUS

• IB commonly asks:

• explain how complementary base pairing ensures accuracy

• link base pairing to replication AND transcription

A1.2.9 – DNA’s Capacity to Store Information

DNA Stores Information in Base Sequences

• Genetic information is stored in the sequence of nitrogenous bases

• Each sequence:

• represents a gene or regulatory region

11/23

Enormous Diversity of Sequences

• There are 4 possible bases:

• A, T , C, G

• For a sequence of length n : possible combinations = 4ⁿ

Examples:

• 1 base → 4 possibilities

• 3 bases → 64 possibilities

• 10 bases → over 1 million possibilities

Real DNA molecules:

• contain millions to billions of bases

“Limitless” Storage Capacity

• DNA can vary in length AND vary in sequence

• This creates virtually unlimited combinations

Efficiency of DNA Storage

• DNA stores massive information in a very small space

Example:

• DNA molecules are extremely thin (~2 nm wide), yet can encode entire organisms

• Therefore it has high information density

Key Idea

DNA = high-capacity, compact information storage system

IB EXAM FOCUS

• IB LOVES questions like:

• “Explain why DNA has a large capacity for storing information”

• Common mistakes:

• only saying “DNA is long”

• not explaining how combinations arise

• Full-mark phrase:

“The sequence of four bases can vary in any order and length, producing an exponential

number of possible combinations (4ⁿ), giving DNA a large capacity to store information.

”

12/23

A1.2.10 – Universal Genetic Code & Common Ancestry

The Genetic Code is Universal

• The genetic code is the way base sequences are translated into amino acids

• In ALL living organisms:

• the same codons code for the same amino acids

What This Means

All organisms use the same molecular “language”

• DNA → RNA → protein works the same way in bacteria, plants & animals

Evidence for Common Ancestry

• If all organisms share the same genetic code:

they must have inherited it from a common ancestor

• This suggests:

• life originated once

• and diversified through evolution

Small Variations

• There are minor exceptions

• some codons may differ slightly in rare organisms

• BUT overall the genetic code is highly conserved

Key Idea

Universal code = strong molecular evidence for evolution

IB EXAM FOCUS

• IB commonly asks:

• explain how the genetic code supports common ancestry

• Must include:

same codon → same amino acid

shared across all life

implies inheritance from a common ancestor

• Common mistakes:

• just saying “all organisms use DNA” (too vague)

• not linking to evolution/common ancestry

13/23

Additional HL

A1.2.11 – Directionality of RNA and DNA

What Does “Directionality” Mean?

• DNA and RNA strands have polarity (direction) due to how nucleotides are linked

• Each strand has:

• a 5′ (five-prime) end → phosphate group attached to C5

• a 3′ (three-prime) end → hydroxyl (–OH) group on C3

These ends are chemically different, giving the strand direction

3′

–5′ Linkage (Phosphodiester Bond)

• Nucleotides are joined by a phosphodiester bond between:

• 3′ carbon of one sugar

• 5′ phosphate of the next nucleotide

This creates a:

• sugar–phosphate backbone

• repeating 3′

–5′ linkage pattern

Key Consequence: Synthesis is ALWAYS 5′ → 3′

• New nucleotides are always added to the:

3′ end of the growing strand

• Therefore:

strands are synthesized in the 5′ → 3′ direction

Why Directionality Matters

1. DNA Replication

• DNA polymerase adds nucleotides only to the 3′ end

• Result:

replication proceeds 5′ → 3′

• Leads to:

• leading strand (continuous)

• lagging strand (discontinuous)

2. Transcription (DNA → RNA)

• RNA polymerase:

• also adds nucleotides to the 3′ end

RNA is synthesized:

14/23

• 5′ → 3′

3. Translation (RNA → Protein)

• Ribosome:

• reads mRNA in the 5′ → 3′ direction

Directionality ensures:

• correct reading of codons

• correct amino acid sequence

Big Picture Link

• Directionality = enzymes only work in one orientation

• ensures accuracy and consistency across all processes

IB EXAM FOCUS

• IB LOVES:

• “Explain why DNA/RNA synthesis occurs in a 5′ → 3′ direction”

• Must include:

nucleotides added to 3′ end

phosphodiester bond (3′

–5′ linkage)

applies to replication AND transcription

15/23

A1.2.12 – Purine–Pyrimidine Pairing & DNA Stability

Two Types of Nitrogenous Bases

Purines (double-ring structure)

• Adenine (A)

• Guanine (G)

Pyrimidines (single-ring structure)

• Cytosine (C)

• Thymine (T)

One purine ALWAYS pairs with one pyrimidine

Why This Matters for Structure

Constant Width of DNA

• Purines = large (2 rings)

• Pyrimidines = small (1 ring)

Pairing:

• purine + pyrimidine = constant width

What If Pairing Was Different?

• Purine + purine → too wide

• Pyrimidine + pyrimidine → too narrow

• this would distort the DNA structure

Result: Stable Double Helix

• Uniform base pairing ensures consistent spacing between strands & stable double helix

shape

Key Idea

• DNA stability depends on:

• complementary base pairing

• purine–pyrimidine matching

IB EXAM FOCUS

• IB commonly asks:

• “Explain why purine–pyrimidine pairing is important”

• Must include:

16/23

difference in size (double vs single ring)

ensures constant distance between strands

maintains stable double helix structure

17/23

A1.2.13 – Structure of a Nucleosome

Why DNA Needs Packaging

• DNA is an extremely long molecule (~2 metres in a single human cell)

• It must:

• fit inside the nucleus (~µm scale)

• remain organized and accessible

Solution: DNA is packaged efficiently using proteins called histones

What is a Nucleosome?

• A nucleosome is the basic unit of DNA packaging

• Structure:

• DNA wrapped around a core of histone proteins

Core Structure

• The nucleosome core contains:

• 8 histone proteins (histone octamer)

• DNA:

• wraps around this core ~2 times

Linker DNA & Additional Histone

• Between nucleosomes:

• linker DNA connects them

• An additional histone protein (H1):

• helps hold DNA in place

• stabilizes the nucleosome structure

“Beads on a String” Model

• Nucleosomes appear like beads on a string

Where:

• beads = nucleosomes

• string = DNA

Higher-Level Packaging

• Nucleosomes:

• coil further → form chromatin

• condense → form chromosomes

18/23

• This allows DNA to be:

• tightly packed

• still accessible when needed

Key Functional Ideas

• Histones are positively charged

• DNA is negatively charged

• This allows strong attraction → DNA wraps tightly around histones

Prokaryote vs Eukaryote Link

• Eukaryotes:

• DNA packaged with histones → nucleosomes

• Prokaryotes:

• no histones

• DNA is “naked”

Key Idea

Nucleosomes allow DNA to be:

• compact

• organized

• functionally accessible

IB EXAM FOCUS

• IB typically asks:

• “Describe the structure of a nucleosome”

• Must include:

DNA wrapped around 8 histone proteins

presence of linker DNA

role of additional histone (H1)

19/23

A1.2.14 – Evidence from the Hershey–Chase Experiment

The Big Question

Before the 1950s, scientists were unsure:

What is the genetic material?

• DNA

• or proteins

Why proteins seemed likely:

• proteins have 20 amino acids → more complex

• DNA has only 4 bases → seemed too simple

The Key Idea of the Experiment

Hershey and Chase used:

• bacteriophages (viruses that infect bacteria)

Structure of a virus:

• protein coat

• DNA inside

When a virus infects a cell:

• it injects its genetic material into the bacterium

Experimental Design

• They used radioactive labeling to track what enters the cell:

Two separate experiments:

Protein-labelled virus

• labelled with ³⁵S (sulfur)

• sulfur is found in proteins, NOT DNA

DNA-labelled virus

• labelled with ³²P (phosphorus)

• phosphorus is found in DNA, NOT proteins

Key Procedure Steps

• Viruses infect bacteria

• Mixture is blended → removes viral coats

20/23

• Centrifuged:

• pellet = bacteria

• supernatant = viral coats

Then measure radioactivity

Results

• ³²P (DNA):

found in the pellet (inside bacteria)

• ³⁵S (protein):

found in the supernatant (outside cells)

Conclusion

• DNA enters the cell and controls replication

• Protein does NOT enter the cell

• Therefore: DNA is the genetic material

Why This Works (Critical Logic)

• Only the material that enters the cell and directs production of new viruses

• can be the genetic material

That material = DNA

Nature of Science (NOS)

• This experiment was only possible because of:

radioisotopes (³²P and ³⁵S)

• Shows:

• advances in technology → enable new discoveries

• science builds on tools + methods

IB EXAM FOCUS

• IB will NOT ask you to just “describe the experiment”

• They ask:

• “Explain how the results support DNA as genetic material”

What You MUST Include

• DNA labelled with ³²P → found inside cells (pellet)

• Protein labelled with ³⁵S → remains outside (supernatant)

• Only DNA enters the cell

• Therefore DNA controls viral replication

21/23

Common Mistakes

• just describing steps without linking to conclusion

• forgetting which isotope labels what

• not mentioning pellet vs supernatant

• saying “DNA is important” instead of explicit conclusion

A1.2.15 – Chargaff’s Rule

Chargaff’s Key Findings

• Erwin Chargaff analysed DNA from many different organisms and measured the

proportions of the four bases:

• Adenine (A)

• Thymine (T)

• Guanine (G)

• Cytosine (C)

He discovered two consistent patterns:

• The amount of adenine ≈ thymine

• The amount of guanine ≈ cytosine

This became known as Chargaff’s Rule

Important Insight

Although: A = T & G = C

The overall proportions vary between species

This shows:

DNA is NOT identical across organisms → genetic diversity exists

Why This Was a Big Deal

Before Chargaff:

• Scientists believed the tetranucleotide hypothesis

• DNA = repeating pattern: A-T-G-C-A-T-G-C-A-T-G-C...

This would mean:

• DNA is too simple

• Cannot store complex genetic information

Chargaff’s data showed:

• Base proportions are NOT equal overall

22/23

• DNA is NOT repetitive

Therefore:

• DNA sequence is variable

Link to DNA Structure

Chargaff’s findings helped explain: complementary base pairing

This directly supported:

• the double helix model

• base pairing rules used in replication & transcription

Nature of Science (NOS)

Problem of Induction vs Falsification

• Induction: forming general conclusions from observations

→ always uncertain

• Falsification: proving an idea is wrong

→ much stronger scientifically

In this case:

• Scientists assumed DNA had a repeating structure

• Chargaff’s data contradicted this

Therefore:

The tetranucleotide hypothesis was falsified

IB EXAM FOCUS

What IB expects you to state:

• No. of A = T and G = C

• Base composition varies between species

• DNA is not repetitive

• This falsified the tetranucleotide hypothesis

High-Scoring Answer Structure

3–4 mark answer:

“Chargaff found that the proportion of adenine equals thymine and guanine equals

cytosine in DNA. However, the overall proportions of bases vary between species. This

showed that DNA is not composed of a repeating tetranucleotide sequence, thereby

falsifying the tetranucleotide hypothesis."