Chapter 7: DNA Structure and Gene Function

What is DNA?

• DNA is a molecule of nucleic acid.
• It is made up of many monomer subunits called nucleotides.
• DNA stores the information that the cell needs to produce proteins.
  • This is the foundational link between DNA and gene expression.

DNA is composed of nucleotides

• Each nucleotide consists of:
  • One phosphate group
  • One 5-carbon sugar: deoxyribose
  • One nitrogenous base: Adenine (A), Guanine (G), Cytosine (C), or Thymine (T)
• Overall, the nucleotide composition gives DNA its chemical properties and coding potential.

Nucleotides join together into strands of DNA

• The nucleotide sequence of DNA is the order of the nitrogenous bases in a strand.
• One DNA molecule is made of two strands of nucleotides.
• The two strands wind together into a helical shape (double helix).

DNA strands are held together by base pairing

• Base pairing rules:
  • A \leftrightarrow T
  • G \leftrightarrow C
• These complementary pairings stabilize the DNA double helix and enable accurate replication and transcription.

Protein production starts with DNA

• A gene is a small region of a chromosome.
• The sequence of DNA in each gene encodes a specific protein.
• Genes are the functional units of heredity that link DNA to protein production.

Making proteins is like making brownies (two stages)

• Protein production occurs in two stages:
  • Transcription = RNA synthesis
  • Translation = Protein synthesis
• Diagram concept (simplified):
  • DNA --mRNA--> Ribosome --Protein
• Key players in translation: DNA, mRNA, ribosome, protein product.

Transcription is RNA synthesis

• Transcription uses DNA as a template to produce RNA.
• The nucleotide sequence of the DNA determines the nucleotide sequence of the RNA that is transcribed.
• RNA sequence is complementary to the DNA template.
• Base pairing rules (RNA vs DNA):
  • A \text{-} U
  • C \text{-} G
  • G \text{-} C
  • T \text{-} A
• Note: RNA uses uracil (U) instead of thymine (T).

Translation is protein synthesis

• Translation takes place at ribosomes.
• Three types of RNA interact to carry out translation:
  • Messenger RNA (mRNA) brings the genetic information from DNA
  • Ribosomal RNA (rRNA) makes up the ribosome
  • Transfer RNA (tRNA) brings the amino acids
• Translation converts the nucleotide language of mRNA into the amino acid language of proteins.

Transcription uses DNA to create RNA

• Transcription occurs in the nucleus.
• To make RNA, base pairing occurs between RNA and DNA:
  • A \text{-} U
  • C \text{-} G
  • G \text{-} C
  • T \text{-} A
• The product is a primary RNA transcript that may require processing before it becomes functional.

Transcription occurs in three steps

• Initiation
• Elongation
• Termination
• These steps coordinate the opening of the DNA, synthesis of RNA, and release of the new RNA molecule.

RNA is processed in the nucleus

• RNA is not ready yet and must be modified before it can function.
• Processing includes splicing and other modifications to produce mature mRNA.

RNA processing removes extra sequences

• Introns are sequences in genes that are not used for producing a protein.
• Exons are sequences that specify amino acids.
• Introns are removed from the mRNA.
• After processing, mRNA leaves the nucleus to be translated in the cytoplasm.

Translation builds the protein

• Translation uses the information in the mature mRNA to assemble a protein.
• Ribosomes coordinate the interaction of rRNA and tRNA to form a polypeptide chain.

Translation occurs by reading one codon at a time

• A codon is a three-nucleotide sequence that encodes one amino acid.
• The genetic code maps codons in mRNA to specific amino acids.
• Example concept: several codons can code for the same amino acid (degeneracy not shown in every example here).

mRNA “codes” for proteins

• The genetic code shows which mRNA codons correspond to which amino acids.
• This code is read in sets of three nucleotides (codons).

Translation (like transcription) occurs in three steps

• Initiation
• Elongation
• Termination
• These steps occur at the ribosome and drive the assembly of the protein.

Each step in translation happens at ribosomes

• Ribosomes are the molecular machines for translation.
• The large subunit binds to tRNA; the small subunit binds to mRNA.
• The interaction of ribosomal subunits with the three RNA types enables protein synthesis.

Translation is efficient

• Multiple ribosomes can attach to a single mRNA molecule simultaneously.
• This allows the cell to synthesize many copies of the same protein at once (polyribosome effect).

Mutations change DNA

• A mutation is a change in a cell’s DNA sequence.
• Mutations come in several varieties.
• Visual example: a mutation can cause a dramatic phenotype change (e.g., legs growing where antennae should be).

Mutations change the DNA sequence

• Table 7.2 (Types of Mutations) illustrates several forms:
  • Substitution (missense)
  • Nonsense
  • Insertion
  • Deletion
  • Expanding repeat
• Note: In the provided examples, each "word" represents one codon; base changes alter codons and potentially amino acids.
• Wild type = original nucleotide sequence; Substitution = changed nucleotide(s); often only one codon is altered, so only one amino acid may be affected.

Nucleotide substitutions cause small changes in protein structure

• Substitution mutations can alter a single codon, leading to a single amino acid change (missense) or a premature stop codon (nonsense).
• The table emphasizes that a single codon change can have limited or significant effects depending on the altered amino acid and protein context.
• Key takeaway: Wild type = original sequence; Substitution = changed nucleotide(s); typically only one codon is affected.

Some mutations cause disease

• A single base substitution in the hemoglobin gene can cause sickle cell disease.
• This illustrates how a seemingly small change can have major physiological consequences.

Frameshift mutations cause large changes in protein structure

• Frameshift mutations result from inserting or deleting nucleotides in numbers other than a multiple of three.
• They shift the reading frame, altering downstream codons and typically changing every amino acid encoded after the mutation.
• Diagrammatic idea: substitutions shift reading frame differently than single-nucleotide indels that are not multiples of three.

Frameshifts affect multiple amino acids

• Example progression (conceptual):
  • Original DNA: GAC GAC GAC GAC GAC GAC
  • One nucleotide added (frameshift): GAC TGA CGA CGA CGA CGA CGA
  • Two nucleotides added (frameshift): GAC TTG ACG ACG ACG ACG ACG
  • Three nucleotides added (reading frame restored): GAC TTT GAC GAC GAC GAC GAC
• Insertion or deletion of a single nucleotide disrupts the reading frame for all subsequent codons.
• With three-nucleotide insertions, the reading frame can be restored, potentially lessening the impact, depending on the context.

Mutations create genetic variety

• Mutations generate different versions of alleles, which are alternative versions of the same gene.
• Genetic variation is important for evolution.
• Plant breeders sometimes induce mutations to create new plant varieties.
• Visual references show diverse examples of mutation-driven variation.

Notation and references

• Throughout the notes, base-pairing and coding rules align with the commonly taught concepts in modern biology textbooks (McGraw Hill press as cited in the material).
• Key concepts to remember:
  • DNA structure: double helix, nucleotides, phosphate-sugar backbone, base pairing
  • Central dogma steps: transcription (DNA -> RNA) and translation (RNA -> protein)
  • RNA processing (introns/exons) and nuclear export of mature mRNA
  • Codons and the genetic code
  • Mutations and their phenotypic consequences (substitution, insertion, deletion, frameshift, expanding repeats)
  • Evolutionary and practical relevance of genetic variation