A1.2 nucleic acids

What are nucleic acids and what is their main function?

• Nucleic acids are polymers made from nucleotide monomers.

• The two main types are DNA and RNA.

• DNA stores and transmits genetic information.

• This information can be used to make RNA and ultimately proteins.

• DNA also allows hereditary information to be passed from parent to offspring.

What are the three components of a nucleotide?

Every nucleotide contains:

1. Phosphate group

2. Pentose (5-carbon) sugar

3. Nitrogenous base

The sugar is:

• Deoxyribose in DNA

• Ribose in RNA

⭐ Nucleotide = phosphate + sugar + base

What is the difference between ribose and deoxyribose?

• Both are 5-carbon (pentose) sugars.

• Ribose is found in RNA.

• Deoxyribose is found in DNA.

• At the 2′ carbon:

  • Ribose has an –OH group

  • Deoxyribose has an –H

→ Deoxyribose therefore has one less oxygen than ribose.

What nitrogenous bases are found in DNA and RNA?

DNA:

• Adenine (A)

• Thymine (T)

• Guanine (G)

• Cytosine (C)

RNA:

• Adenine (A)

• Uracil (U)

• Guanine (G)

• Cytosine (C)

⭐ RNA has uracil instead of thymine.

What is the difference between purines and pyrimidines?

Purines = 2 rings

• Adenine (A)

• Guanine (G)

Pyrimidines = 1 ring

• Cytosine (C)

• Thymine (T)

• Uracil (U)

Memory trick:

PURe As Gold → PURines = A + G

How are nucleotides joined together to form a nucleic acid?

• Nucleotides are joined by strong covalent phosphodiester bonds.

• The bond forms between the phosphate group of one nucleotide and the sugar of the next nucleotide.

• More specifically, it links the 3′ carbon of one sugar to the 5′ carbon of the next nucleotide via phosphate.

• This creates the sugar-phosphate backbone.

⭐ Bases project from this backbone.

How do condensation and hydrolysis relate to nucleic acids?

Condensation:

• Joins nucleotide monomers together.

• Forms a phosphodiester bond.

• Water is removed.

Hydrolysis:

• Breaks polymers into smaller units.

• Water is added to break covalent bonds.

What are the main structural features of DNA?

DNA is:

• A polymer of nucleotides

• Double-stranded

• Twisted into a double helix

• Made with deoxyribose

• Has a sugar-phosphate backbone on the outside

• Has nitrogenous bases facing inward

• The two strands are antiparallel

• The strands are held together by hydrogen bonds between complementary bases

What is complementary base pairing in DNA?

Bases only pair with specific complementary bases:

A — T

• Adenine pairs with thymine

• 2 hydrogen bonds

G — C

• Guanine pairs with cytosine

• 3 hydrogen bonds

Therefore, knowing the sequence of one DNA strand allows the sequence of the other to be determined.

What bonds are found within and between DNA strands?

Within each strand:

• Strong covalent phosphodiester bonds

• Join nucleotides in the sugar-phosphate backbone

Between the two strands:

• Hydrogen bonds

• Form between complementary nitrogenous bases

Why are hydrogen bonds useful for holding the two DNA strands together?

• Each individual hydrogen bond is relatively weak, allowing the strands to separate during processes such as replication and transcription.

• However, there are many hydrogen bonds along a DNA molecule.

• Together they provide enough stability to hold the double helix together.

Why does DNA always pair a purine with a pyrimidine?

Complementary pairs contain:

• A (purine) + T (pyrimidine)

• G (purine) + C (pyrimidine)

A purine has 2 rings, while a pyrimidine has 1 ring.

Pairing one of each maintains a constant distance between the two sugar-phosphate backbones, giving DNA a uniform width and stable double helix.

What do the 5′ and 3′ ends of a DNA strand mean?

The numbers refer to carbon atoms in the pentose sugar.

• 5′ end → associated with the phosphate attached to the sugar's 5′ carbon

• 3′ end → has a free –OH group on the 3′ carbon

What does it mean that DNA strands are antiparallel?

The two DNA strands run in opposite directions.

One strand:

5′ → 3′

The complementary strand:

3′ → 5′

This is called antiparallel.

Why is the 5′ → 3′ direction important when synthesizing DNA?

• New nucleotides can only be added to the 3′ end of a growing DNA strand.

• Therefore, new DNA is synthesized in the:

5′ → 3′ direction

What are the major differences between DNA and RNA?

DNA	RNA
Usually double-stranded	Usually single-stranded
Deoxyribose	Ribose
Contains thymine	Contains uracil
A pairs with T	A pairs with U
Long-term genetic information storage	Important in gene expression/protein synthesis

Both contain A, G and C and are polymers of nucleotides.

What are the three major types of RNA?

• mRNA — messenger RNA: carries genetic information from DNA for protein synthesis.

• tRNA — transfer RNA: carries amino acids to the ribosome.

• rRNA — ribosomal RNA: forms an important structural/catalytic component of ribosomes.

How can DNA store huge amounts of genetic information using only four bases?

DNA uses four bases:

A, T, G, C

But they can occur in an enormous number of different sequences.

For a DNA sequence containing n bases:

Number of possible sequences = 4ⁿ

Example:

3 bases → 4³ = 64 possible sequences

Because DNA molecules can contain millions or billions of bases, the number of possible sequences is enormous.

Why is the sequence of bases in DNA important?

• Genetic information is encoded in the order of bases.

• Different base sequences contain different genetic information.

• Through gene expression, this information can determine the amino acid sequence of proteins.

• Therefore, changing the DNA sequence can potentially change the protein produced.

What is gene expression?

Gene expression is the use of information in a gene to produce a functional product, commonly a protein.
For protein-coding genes:

DNA → RNA → Protein

1. Transcription: DNA → RNA

2. Translation: RNA → protein

Complementary base pairing is essential during this process.

What is a codon?

• A codon is a sequence of 3 bases on mRNA.

• During translation, codons are read to determine which amino acids are added to a protein.

Because there are 4 bases:

4³ = 64 possible codons

What are the start and stop codons?

Start codon:

• AUG

• Codes for methionine

• Usually marks where translation begins

Stop codons:

• UAA

• UAG

• UGA

Stop codons do not code for an amino acid and signal the end of translation.

⭐ There are 61 amino-acid coding codons + 3 stop codons = 64 total.

What does it mean that the genetic code is nearly universal?

• In almost all organisms, a particular codon specifies the same amino acid.

• This includes organisms that are very distantly related.

This strongly supports the idea that life shares a common evolutionary ancestor.

⭐ Say nearly universal, rather than absolutely universal, because a small number of exceptions exist.

Why is complementary base pairing biologically important?

Complementary base pairing allows genetic information to be accurately copied and expressed.

During replication:

• Each original DNA strand acts as a template.

• Complementary nucleotides are added.

• This allows accurate copying of the DNA sequence.

During transcription:

• A DNA strand acts as a template for the formation of complementary RNA.

What does semiconservative DNA replication mean?

During replication:

1. The two parental DNA strands separate.

2. Each parental strand acts as a template.

3. A new complementary strand is synthesized.

Therefore, each resulting DNA molecule contains:

1 original/parental strand + 1 newly synthesized strand

This is called semiconservative replication.

What did Chargaff discover about DNA bases?

In double-stranded DNA:

%A ≈ %T

%G ≈ %C

Therefore:

total purines = total pyrimidines

because:

• Purines = A + G

• Pyrimidines = T + C

The overall percentages of A+T versus G+C can differ between species, showing that DNA is not simply a repeating sequence.

How do you calculate missing base percentages using Chargaff's rule?

For double-stranded DNA:

A = T
G = C

All four must total 100%.

Example:

If A = 20%:

• T = 20%

• A + T = 40%

• G + C = 60%

• G = 30%

• C = 30%

How did Chargaff's findings challenge the tetranucleotide hypothesis?

The tetranucleotide hypothesis suggested DNA contained equal amounts of A, T, G and C in a simple repeating pattern.

Chargaff found:

• Base composition varied between species.

• The four bases were not always present in equal amounts.

• However, A ≈ T and G ≈ C.

This showed DNA was much more variable and information-rich than previously thought.

What was the purpose of the Hershey–Chase experiment?

Scientists knew chromosomes contained DNA and protein, but did not know which molecule carried hereditary information.

Hershey and Chase used bacteriophages to determine whether DNA or protein entered bacterial cells and directed production of new viruses.

Why did Hershey and Chase use ³²P to label DNA and ³⁵S to label protein?

DNA contains phosphorus but essentially no sulfur
→ label DNA with ³²P

Proteins can contain sulfur in amino acids such as cysteine and methionine
→ label protein with ³⁵S

This allowed DNA and protein to be tracked separately.

What happened in the Hershey–Chase experiment and what did it show?

1. Bacteriophages with labelled DNA or protein infected bacteria.

2. A blender separated viral protein coats from the bacteria.

3. Samples were centrifuged.

Results:

• ³²P-labelled DNA → mainly in the bacterial pellet

• ³⁵S-labelled protein → mainly in the supernatant

Conclusion:
DNA entered the bacteria and directed production of new viruses.

→ DNA is the genetic material.

How did the Meselson–Stahl experiment provide evidence for semiconservative DNA replication?

• E. coli were first grown with ¹⁵N, producing heavy DNA.

• They were then transferred to ¹⁴N, so newly synthesized DNA contained lighter nitrogen.

• DNA was separated based on density.

After one replication, all DNA had intermediate density.

After two replications, there were:

• Intermediate-density DNA molecules

• Light DNA molecules

This pattern supports semiconservative replication: each new DNA molecule initially contains one old strand and one new strand.

What is a nucleosome?

A nucleosome consists of:

• DNA wrapped around a core of 8 histone proteins (histone octamer)

• DNA wraps around the histone core about 1.7 turns

• Linker DNA connects neighbouring nucleosomes

• Histone H1 associates with linker DNA and helps promote further DNA packing

Nucleosomes help package and organize DNA in eukaryotic chromosomes.

Why does DNA need to be packaged around histones?

DNA molecules are extremely long compared with the size of the nucleus.

Wrapping DNA around histones:

• Compacts the DNA

• Allows long DNA molecules to fit inside the nucleus

• Helps organize DNA into chromatin

• Also contributes to regulation of DNA accessibility and gene expression

How does the structure of DNA allow it to perform its function?

Several features work together:

• Strong phosphodiester bonds → create a stable sugar-phosphate backbone.

• Base sequence → stores genetic information.

• Complementary base pairing → allows accurate replication and transcription.

• Hydrogen bonds → hold strands together but allow them to separate when necessary.

• Antiparallel strands → important for DNA replication.

• Purine–pyrimidine pairing → maintains a uniform helix width.

• Double helix → provides a stable structure.

• Histone packaging → allows large DNA molecules to fit inside eukaryotic nuclei.