DNA Replication, Transcription, and Translation: Comprehensive Notes

Enzymes in DNA Replication

• Helicase:

  • Unwinds and unzips the DNA molecule.
  • Breaks the hydrogen bonds that hold the strands of nucleotides together.

• Primase:

  • Adds an RNA primer to the DNA template to initiate replication.

• DNA Ligase:

  • Joins Okazaki fragments on the lagging strand.
  • Joins newly synthesized strands of DNA together.

• DNA Polymerase:

  • Synthesizes new DNA strands by adding nucleotides to the template strand.
  • Functions on either strand.

• DNA Topoisomerase:

  • Prevents supercoiling of the DNA ahead of the replication fork.

Lagging Strand Formation

• DNA polymerase can only synthesize DNA in the 5' to 3' direction.
• Nucleotides are always added to the 3' hydroxyl group, catalyzing a dehydration reaction.
• The leading strand is synthesized continuously towards the replication fork.
• The lagging strand is synthesized in fragments (Okazaki fragments) because it must wait until enough of the template is exposed.

Telomeres

• Telomeres are short, repeating sequences at the ends of chromosomes that protect them from degradation.
• DNA polymerase removes primers from the ends of strands but cannot synthesize DNA in the 3' to 5' direction, leaving a gap.
• Telomeres are present in eukaryotic organisms because their chromosomes are linear and have ends that cannot be fully replicated.
• Prokaryotes do not have telomeres because their chromosomes are circular.

DNA to Protein: Unlocking Genetic Information

• DNA contributes to phenotype through protein production.
• Proteins underlie observable phenotypes, including physical traits and metabolic functions.
• Metabolic processes are catalyzed by enzymes, which are proteins.

Amino Acids: Building Blocks of Proteins

• Amino acids are the monomers that make up proteins (polymers).
• Each amino acid consists of:
  • A central carbon atom.
  • An amine group ($\NH_2$).
  • A carboxyl group (\COOH).
  • A hydrogen atom.
  • An R-group (variable).
• The carboxyl group is acidic because it can lose a hydrogen ion.
• There are 20 different amino acids.
• Proteins range in size from 50 to 1000 amino acids, leading to millions or billions of possible combinations.
• A protein made of only five amino acids would have over 3,000,000 possible combinations.

From DNA to mRNA: Transcription

• DNA is the instruction book (recipe book) for life, containing recipes for proteins.
• Cells make a copy of a recipe (gene) when they want to produce a specific protein.
• DNA remains protected in the nucleus.
• mRNA (messenger RNA) carries the recipe from the nucleus to the ribosome.
• RNA polymerase synthesizes mRNA by making a copy of the DNA template.

Ribosomes: The Chefs

• Ribosomes are the chefs that read the mRNA recipe and assemble the protein.
• tRNAs (transfer RNAs) bring the ingredients (amino acids) to the ribosome.
• tRNAs attach to specific amino acids and match sequences on the mRNA.
• The ribosome puts the amino acids together in the correct order to form a protein.

Protein Synthesis: Two-Step Process

• Transcription: Copying a gene to produce mRNA. In eukaryotes, this occurs in the nucleus.
• Translation: Using mRNA to assemble a protein. This occurs in the cytoplasm, specifically at the ribosomes on the rough endoplasmic reticulum (ER) or free ribosomes.

Differences Between RNA and DNA

Types of RNA

• mRNA (messenger RNA): Made during transcription; carries information from DNA to the ribosome.
• tRNA (transfer RNA): Brings amino acids to the ribosome during translation.
• rRNA (ribosomal RNA): Part of the ribosome.
• Other types include: small nuclear RNA, signal recognition RNA, microRNA, and siRNA (silencing RNA).

Transcription

• Transcription is facilitated by RNA polymerase, which makes RNA from a DNA template.
• One DNA strand is used as a template, and RNA polymerase synthesizes an RNA molecule complementary to the DNA template in the 5' to 3' direction.
• Base pairing changes: adenine (A) on DNA pairs with uracil (U) on RNA, instead of thymine (T).
• RNA polymerase:
  • Does not need helicase, topoisomerase, or primase.
  • Can start synthesizing mRNA without needing anything to attach to.
  • Unwinds and unzips DNA as well as builds the complementary strand.
• Template Strand: The DNA strand used to make the mRNA.
• Coding Strand: The other DNA strand, which has the same sequence as the mRNA (except T is replaced by U).

Transcription Process

• Initiation:
  • Transcription factors (in eukaryotes) or sigma factors (in prokaryotes) connect to the DNA at the start of the gene (promoter) to signal where to start copying.
• Elongation:
  • RNA polymerase runs along the DNA sequence and makes an mRNA copy, synthesizing the mRNA in the 5' to 3' direction.
  • The mRNA sequence does not stay attached to the DNA template; it is released.
• Termination:
  • RNA polymerase reaches a terminator sequence (in prokaryotes) or a polyadenylation sequence (in eukaryotes).
  • The polymerase drops off, and the mRNA molecule is released.

Eukaryotic mRNA Editing

• The initial mRNA transcript (primary transcript) undergoes editing before translation.
• Splicing:
  • Introns (non-coding sequences or Intervening sequences) are removed.
  • Exons (expressed sequences) are joined together by spliceosomes.
• 5' Capping:
  • A 5' bonding cap is added to the beginning of the mRNA.
• Poly A Tail:
  • A poly-A tail (a string of adenine bases) is added to the 3' end.
  • Helps protect the transcript from degradation and helps it find the ribosome.

Structural vs. Nonstructural Genes

• Structural genes code for mRNAs that are translated into proteins.
• Nonstructural genes code for RNAs that have other functions.

Translation

• Translation occurs when the mRNA leaves the nucleus and interacts with a ribosome.
• The ribosome reads the mRNA code and translates it into a specific amino acid sequence.
• Each three-base sequence on the mRNA is called a codon.
• The genetic code is universal; it is the same in bacteria, plants, and animals.
• There are 64 possible codons, but only 20 amino acids, so the genetic code is redundant.
• Some codons are stop codons (UAA, UAG, UGA), which signal the end of translation.
• There is also a start codon.

The Role of tRNA

• tRNAs are helper molecules that bring amino acids to the ribosome.
• Each tRNA has an anticodon sequence that is complementary to a codon on the mRNA.
• tRNA also has a site where a specific amino acid can attach.

The Ribosome in Translation

• The ribosome is made up of a large subunit and a small subunit.
• It is an rRNA protein complex that acts as the chef, taking the mRNA and making the protein.

Translation Process

• Initiation:
  • tRNA with an amino acid binds to the ribosome, and the anticodon lines up with the start codon on the mRNA.
• Elongation:
  • The ribosome cycles through tRNAs, adding amino acids to the growing polypeptide chain.
  • This requires energy (GTP).
• Termination:
  • A stop codon is reached, and a release factor binds to the ribosome, cleaving the bond that holds the polypeptide.

The Central Dogma of Molecular Biology

• Summarized as the process of how DNA makes protein.