Chapter 11: The Instructions for Life—DNA and RNA (Structure, Function, and Gene Expression)

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11.1 DNA and RNA Structure and Function

DNA as the Genetic Material

Early studies in genetics led to the discovery that DNA, not protein, is the hereditary material responsible for transmitting genetic information. The Hershey-Chase experiment using bacteriophages and Escherichia coli demonstrated that only DNA enters the bacterial cell and directs the formation of new viruses.

Capsid: Protein shell of a virus.
DNA: Located inside the capsid, carries genetic instructions.
Key Experiment: Radioactive tracers showed DNA, not protein, enters the bacterium.
Conclusion: DNA is the genetic material.
Example: Hershey-Chase experiment (1952).

Structure of DNA

The structure of DNA was determined through a combination of chemical analysis and X-ray diffraction studies. Chargaff's rules and the work of Watson, Crick, and Franklin were pivotal.

Nucleotides: Building blocks of DNA, each containing a phosphate group, a 5-carbon sugar (deoxyribose), and a nitrogenous base.
Chargaff's Rules: In any species, the amount of adenine (A) equals thymine (T), and the amount of guanine (G) equals cytosine (C).
Double Helix: DNA is structured as a twisted ladder, with sugar-phosphate backbones forming the sides and base pairs forming the rungs.
Base Pairing: A pairs with T, G pairs with C via hydrogen bonds.
Example: Watson and Crick's model (1953).

DNA Replication

DNA replication is the process by which DNA is copied before cell division. It is semiconservative, meaning each new DNA molecule consists of one parent strand and one new strand.

Unwinding: Helicase enzyme separates the two DNA strands.
Complementary Base Pairing: New nucleotides are added according to base pairing rules.
Joining: DNA polymerase synthesizes new strands; DNA ligase seals breaks in the backbone.
Semiconservative Replication: Each daughter DNA molecule contains one old and one new strand.
Replication in Eukaryotes: Begins at multiple origins, forming replication bubbles that expand until they meet.
Example: Okazaki fragments on the lagging strand.

RNA Structure and Function

RNA (ribonucleic acid) is a nucleic acid similar to DNA but with key differences in structure and function.

Sugar: Ribose (not deoxyribose).
Bases: Uses uracil (U) instead of thymine (T); also contains A, C, and G.
Single-Stranded: Unlike the double-stranded DNA.
Types of RNA:
- Messenger RNA (mRNA): Carries genetic information from DNA to ribosomes.
- Transfer RNA (tRNA): Transfers amino acids to ribosomes during protein synthesis.
- Ribosomal RNA (rRNA): Combines with proteins to form ribosomes.

Table: Comparison of DNA and RNA

Similarities	DNA	RNA
Both are nucleic acids, composed of nucleotides, have a sugar-phosphate backbone, and four types of bases.	Found in nucleus, genetic material, sugar is deoxyribose, bases are A,T,G,C, double-stranded, transcribed to give RNA molecules.	Found in nucleus and cytoplasm, helper to DNA, sugar is ribose, bases are A,U,G,C, single-stranded, translated to make proteins.

11.2 Gene Expression

Central Dogma of Molecular Biology

Gene expression is the process by which information from DNA is used to synthesize proteins. The flow of genetic information follows the sequence: DNA → RNA → Protein.

Transcription: DNA serves as a template to make mRNA.
Translation: mRNA directs the sequence of amino acids in a protein, assisted by rRNA and tRNA.
Example: Synthesis of hemoglobin from the globin gene.

The Genetic Code

The genetic code translates nucleotide sequences into amino acid sequences in proteins.

Triplet: Three-nucleotide sequence in DNA.
Codon: Three-nucleotide sequence in mRNA; each codon encodes a specific amino acid.
Start and Stop Codons: Signal the beginning and end of translation.

Table: Messenger RNA Codons

First Base	Second Base U	Second Base C	Second Base A	Second Base G	Third Base
UUU	Phenylalanine	Serine	Tyrosine	Cysteine	U, C, A, G
UAA	Stop	Stop	Stop	Stop	U, C, A, G
AUG	Start (Methionine)	Threonine	Asparagine	Serine	U, C, A, G
Additional info:	Table lists all 64 codons and their corresponding amino acids, including start and stop signals.

Transcription

Transcription is the synthesis of RNA from a DNA template.

RNA Polymerase: Enzyme that synthesizes RNA.
Process: DNA unwinds and unzips; complementary RNA nucleotides are added.
Product: Pre-mRNA, which must be processed before translation.

Processing Pre-mRNA

Pre-mRNA undergoes several modifications before becoming mature mRNA.

Capping and Poly-A Tail: Added for stability.
Introns: Noncoding regions removed.
Exons: Coding regions joined together.
Alternative Splicing: Allows for different proteins from the same gene.

Translation

Translation is the process by which ribosomes synthesize proteins using mRNA as a template.

tRNA: Brings amino acids to the ribosome; contains anticodon complementary to mRNA codon.
Ribosome: Composed of rRNA and protein; has P and A sites for tRNA binding.
Stages:
- Initiation: mRNA binds to small ribosomal subunit; large subunit joins.
- Elongation: Peptide chain grows one amino acid at a time.
- Termination: Stop codon reached; release factor causes dissociation and release of polypeptide.

11.3 Gene Regulation

Levels of Gene Expression Control

Gene expression is tightly regulated to ensure proper cell function and specialization.

Specialization: Only certain genes are active in specialized cells.
Housekeeping Genes: Govern functions common to all cells.
Selected Genes: Activity accounts for cell specialization.

Gene Expression in Prokaryotes

Prokaryotic gene expression is often regulated by operons, such as the lac operon in E. coli.

Operon: Cluster of genes with a single promoter and operator.
lac Operon: Controls metabolism of lactose; repressor binds operator when lactose is absent, preventing transcription.
Inducible System: Lactose inactivates repressor, allowing transcription.
Example: François Jacob and Jacques Monod (1961 Nobel Prize).

Gene Expression in Eukaryotes

Eukaryotic gene expression is regulated at multiple levels, both in the nucleus and cytoplasm.

Promoter: Each gene has its own promoter.
Mechanisms: Chromatin condensation, mRNA transcription, mRNA processing, translation delay, and protein duration.
Chromatin Condensation: Tightly packed chromatin (heterochromatin) is inactive; unpacked (euchromatin) is active.
Transcription Factors: Proteins that help RNA polymerase bind to promoters; combinations allow for complex regulation.
Alternative mRNA Processing: Multiple proteins from one gene.
Protein Activity: Some proteins require processing before becoming active (e.g., insulin).
Cell Signaling: Chemical signals coordinate cell behavior and development.

Additional info:

Equations: DNA replication can be summarized as:
Central Dogma: