DNA & Protein Synthesis Guide Summary & Study Notes

🧬 13.1 Identifying the Substance of the Gene

Griffith identified a transforming factor that could convert harmless bacteria into deadly ones. He worked with two forms: the rough (R) form and the smooth (S) form, and observed that a factor could pass from S to R bacteria, making them virulent. He named this process transformation, noting that the form changed permanently due to the factor carrying genetic information.

Avery identified DNA as the transforming factor. By purifying Griffith’s transforming factor, Avery showed that DNA was responsible for the transformation, not other cellular components.

Hershey & Chase (1952) confirmed that DNA is the genetic material. They studied bacteriophages (viruses that infect bacteria) and showed that the material injected into bacteria was DNA, not protein.

Watson & Crick (1953) proposed a double-helix model of DNA. They built the first accurate physical model and showed two strands twisted around each other, carrying genetic information and capable of replication.

🧬 13.2 The Structure of DNA

DNA is composed of four nucleotides and is built from a long chain of nucleotides. Each nucleotide has three parts: a phosphate group, a deoxyribose sugar, and a nitrogenous base. The four bases are adenine ($A$), thymine ($T$), cytosine ($C$), and guanine ($G$).

The bases are the only difference among the four nucleotides and determine the genetic code. The nitrogen bases pair specifically: A with T and G with C (base pairing rules). The backbone of DNA is the sugar–phosphate chain on the outside, held together by phosphodiester bonds; the bases are on the inside, held together by hydrogen bonds.

Rosalind Franklin used X-ray diffraction to determine the shape of DNA. Her data suggested this molecule is a helix with uniform width.

The discovery of base pairing led to the notion that DNA has a uniform width: a purine (two-ring) must pair with a pyrimidine (one-ring) to maintain this width. This pairing also explains how DNA can be replicated faithfully.

🧬 13.3 DNA Replication

The central dogma describes the flow of genetic information: DNA → RNA → protein. DNA replication copies genetic information so that each new cell inherits a complete set of genes.

Replication uses the two DNA strands as templates to make new copies, and occurs during the S phase of the cell cycle. Steps:

1. The enzyme helicase unwinds and separates the two DNA strands.
2. The single strands separate further, creating a gap where primers provide starting points.
3. The enzyme DNA polymerase adds nucleotides to the growing strands following base-pairing rules ($A$ with $T$, $G$ with $C$).
4. Two new DNA molecules form, each consisting of an original (parent) strand and a new (daughter) strand.

🧬 14.1 RNA

RNA carries DNA’s instructions and participates in the three steps of the central dogma: Replication (not typically a direct RNA role), Transcription, and Translation. RNA to protein is the essential link in expressing genes.

RNA is typically single-stranded and is made of nucleotides with three parts: a phosphate group, a ribose sugar, and a nitrogenous base. The four bases are adenine ($A$), guanine ($G$), cytosine ($C$), and uracil ($U$) (uracil replaces thymine).

RNA differs from DNA in several ways: RNA is usually single-stranded, contains ribose, uses $U$ instead of $T$, and has several types, including mRNA, tRNA, and rRNA.

🧬 14.2 Protein Synthesis

Transcription copies DNA instructions into RNA. RNA polymerase binds to DNA and unwinds it to read a gene and synthesize an RNA strand using base-pairing rules.

RNA editing in eukaryotes removes introns and splices exons to form the mature mRNA. Transcription resembles replication in using base-pairing rules, but it yields RNA, not a DNA copy.

Translation converts mRNA codons into a sequence of amino acids. A codon is a sequence of three nucleotides that codes for an amino acid.

tRNA transfers specific amino acids to the ribosome, carrying an anticodon that base-pairs with the mRNA codon. Ribosomes consist of two subunits with three tRNA-binding sites on the large subunit and mRNA binding on the small subunit.

Genetic code: Codons correspond to amino acids, and there are 64 codons, including a start codon (AUG) and three stop codons (UAA, UAG, UGA).

Translation steps:

1. mRNA exits the nucleus to the ribosome. 2) The start codon (AUG) initiates translation.
2. tRNA brings amino acids and their anticodons pair with mRNA codons. 4) The ribosome forms peptide bonds between amino acids. 5) tRNA translocates with the ribosome moving along the mRNA. 6) Translation ends at a stop codon.

🧬 14.4 Mutations

Mutations can affect a single gene or an entire chromosome. A mutation is a change in an organism’s DNA and can be caused by UV light, radiation, chemicals, etc. Mutations occur at two levels: gene mutations and chromosomal mutations.

DNA/Gene mutations include:

• Substitution: one nucleotide is replaced by another. Example: Our big dog bit the man may involve a single-base change.
• Insertion or deletion: a nucleotide is added or removed, causing a frameshift.

Chromosome mutations involve changes in chromosome structure during cell division, such as duplications, deletions, inversions, translocations, or even aneuploidy (e.g., Turner’s syndrome XO, Kleinfelter’s XXY) or trisomy (e.g., Down syndrome, Trisomy 21).

Significance: Mutations can be neutral, harmful, or beneficial. In populations, many mutations are removed over time when they are deleterious.