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

11.1 DNA and RNA Structure and Function

DNA as the Genetic Material

Early experiments established DNA as the hereditary material responsible for genetic information in living organisms.

• Hershey-Chase Experiment: Used viruses (bacteriophages) to show that DNA, not protein, enters bacteria and directs viral replication.

• Capsid: Protein shell of a virus; DNA is contained inside.

• Conclusion: DNA is the genetic material, not protein.

• Example: Escherichia coli infected by bacteriophage.

Structure of DNA

The structure of DNA was determined through a combination of chemical analysis and X-ray diffraction studies.

• Chargaff's Rules: DNA contains four nucleotides (A, T, G, C); amount of A = T and G = C in any species.

• Nucleotide: Composed of a phosphate group, a 5-carbon sugar (deoxyribose), and a nitrogen-containing base.

• Rosalind Franklin: X-ray diffraction data revealed DNA is a helix with repeating structures.

• Watson and Crick Model: DNA is a double helix; sides are sugar-phosphate backbone, rungs are base pairs.

• Complementary Base Pairing: A pairs with T, G pairs with C via hydrogen bonds.

DNA Structure

• Double Helix: Twisted ladder shape.

• Sugar-Phosphate Backbone: Forms the sides of the ladder.

• Base Pairing: A&T and G&C held together by hydrogen bonds.

Replication of DNA

DNA replication is essential for cell division, ensuring genetic continuity.

• Semiconservative Replication: Each new DNA molecule consists of one parent strand and one new strand.

• Steps:

  1. Unwinding by helicase

  2. Complementary base pairing

  3. Joining by DNA polymerase and DNA ligase

• Result: New DNA molecules are identical to the original.

DNA Replication in Eukaryotes

• Replication begins at multiple origins, forming replication bubbles.

• Bubbles expand in both directions until they meet.

RNA Structure and Function

RNA Structure

RNA (ribonucleic acid) is a nucleic acid similar to DNA but with distinct differences.

• Sugar: Ribose (not deoxyribose)

• Bases: Uses uracil (U) instead of thymine (T); also contains A, C, G

• Single-stranded

Types of RNA

• Messenger RNA (mRNA): Carries genetic information from DNA to ribosomes.

• Transfer RNA (tRNA): Transfers amino acids to ribosomes during protein synthesis; each tRNA carries one type of amino acid.

• Ribosomal RNA (rRNA): Combines with proteins to form ribosomes, the site of protein synthesis.

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 genetic information is used to synthesize proteins.

• DNA → RNA → Protein: Information flows from DNA to RNA to protein.

• Transcription: DNA serves as a template to make mRNA.

• Translation: mRNA directs the sequence of amino acids in a protein; rRNA and tRNA assist.

The Genetic Code

• Triplet: Three-nucleotide sequence in DNA.

• Codon: Three-nucleotide sequence in mRNA; each codon encodes a single amino acid.

• Start and Stop Codons: Signal initiation and termination of translation.

Codon	Amino Acid
AUG	Methionine (Start)
UAA, UAG, UGA	Stop
UUU, UUC	Phenylalanine
UUA, UUG, CUU, CUC, CUA, CUG	Leucine
... (Additional info: See full codon table for all 20 amino acids)	...

Transcription

• Complementary RNA is synthesized from a DNA template.

• RNA polymerase binds to DNA, unwinds it, and assembles RNA nucleotides in the order dictated by the DNA sequence.

Processing Pre-mRNA

• Capping and Poly-A Tail: Added for stability.

• Introns: Noncoding regions removed.

• Exons: Coding regions joined together.

• Alternative Splicing: Allows production of different proteins from the same gene.

Translation

• tRNA: Brings amino acids to the ribosome; anticodon matches mRNA codon.

• Ribosome: Composed of rRNA and protein; site of protein synthesis.

• Three Phases:

  1. Initiation: mRNA binds to small ribosomal subunit; large subunit joins.

  2. Elongation: Peptide chain lengthens one amino acid at a time.

  3. 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.

• Only certain genes are active in specialized cells.

• Housekeeping Genes: Govern functions common to all cells.

• Activity of selected genes accounts for cell specialization.

Gene Expression in Prokaryotes

• Operon: Cluster of genes with a common regulatory sequence.

• lac Operon: Controls metabolism of lactose in E. coli.

• Regulation:

  • Lactose absent: Repressor binds operator, blocks transcription.

  • Lactose present: Lactose binds repressor, inactivates it, transcription proceeds.

  • System can also repress genes normally turned on (e.g., tryptophan operon).

Gene Expression in Eukaryotes

• Each gene has its own promoter.

• Regulation occurs at multiple levels:

  • Nucleus: Chromatin condensation, mRNA transcription, mRNA processing.

  • Cytoplasm: Delay of translation, duration of mRNA/protein activity.

Chromatin Condensation

• Heterochromatin: Tightly packed, inactive chromatin (e.g., Barr body in female mammals).

• Euchromatin: Loosely packed, active chromatin; contains genes being transcribed.

• Nucleosome: DNA wrapped around histone proteins.

Transcription Factors

• DNA-binding proteins that help RNA polymerase bind to promoters.

• Multiple factors required for transcription initiation.

• Defects can lead to disease (e.g., Huntington disease).

• Can speed up transcription by binding to enhancer regions.

mRNA Processing and Translation

• Alternative splicing allows multiple proteins from one gene.

• Translation can be delayed or regulated by cytoplasmic proteins and environmental conditions.

• Longevity of mRNA affects amount of protein produced.

Protein Activity and Cell Signaling

• Some proteins require processing to become active (e.g., insulin).

• Cell signaling pathways coordinate cell behavior and development.

• Signals bind to receptors, initiate transduction pathways, and affect cell function.

Additional info: For full codon tables and more detailed mechanisms, refer to molecular biology textbooks or resources.