Protein Synthesis Notes

DNA Replication Review

• Helicase unwinds DNA.
• Single-stranded binding proteins hold the DNA strands open.
• Primase adds RNA primer.
• DNA polymerase III binds to the primer and builds new DNA.
• Okazaki fragments are created on the lagging strand.
• DNA polymerase I removes the RNA primer and replaces it with DNA.
• Ligase connects Okazaki fragments.
• Eukaryotic cells use DNA polymerase I and III.
• Prokaryotic cells use DNA polymerase II.

Protein Synthesis Overview

• Two main steps:
  • Transcription: Copying DNA information into RNA.
  • Translation: Decoding RNA information to create a polypeptide (protein).
• Polypeptide: a chain of amino acids.
• Protein synthesis creates proteins.
• Genes are like recipes for proteins, found in DNA.

Codons

• RNA information is in a code of three-letter "words" called codons.
• Each codon specifies a particular amino acid.
• The genetic code is universal across organisms.

Codon Dictionary

• A table showing which codons correspond to which amino acids.
• Example: UUU codes for phenylalanine (phe).
• AUG codes for methionine (met) and also serves as the start codon.
• UAA, UAG, and UGA are stop codons, signaling the end of translation.

Transgenic Organisms

• Organisms that receive a gene from another species.
• This is possible because the genetic code is universal.
• Not a natural process, but a human-driven transfer.
• Mutation is an error in existing genes; transgenic is a new gene.

Location of Transcription and Translation

• Eukaryotic Cells:
  • Transcription happens in the nucleus (where DNA is).
  • Translation happens in the cytoplasm (where ribosomes are).
• Prokaryotic Cells:
  • Both transcription and translation happen in the cytoplasm.
• Ribosomes are the key organelle for translation.

Transcription: Detailed Steps

• Enzyme: RNA Polymerase.
• It makes RNA by reading DNA nucleotides and linking RNA nucleotides together.
• Uracil (U) in RNA pairs with adenine (A) in DNA.
• Occurs in the 5' to 3' direction.
• Three main steps:
  • Initiation: Setting up at the promoter region.
  • Elongation: Building the RNA molecule.
  • Termination: Ending the process at the terminator region.

Transcription Initiation

• Starts at promoter region.
• Transcription factors (proteins) bind to the promoter region, enabling RNA polymerase to bind.
• RNA polymerase attaches and starts making RNA.

Transcription Elongation

• RNA polymerase adds nucleotides to the growing RNA strand in the 5' to 3' direction.

Transcription Termination

• RNA polymerase reaches the terminator region.
• Chemical signals cause the complex to disassemble.

RNA Processing (Eukaryotic Cells Only)

• Occurs inside the nucleus.
• Two key steps:
  1. RNA ends protected with caps:
     • 5' cap and poly-A tail. Protect the ends of the molecule from damage.
  2. RNA splicing: introns are removed, and exons are joined together.
     • Finished mRNA does not include introns.
• Spliceosomes and ribozymes are involved in RNA splicing.
  • Spliceosomes are made of RNA and proteins.
• Finished mRNA includes the coding segment, leader, and trailer sequences.
• After processing, the finished mRNA transcript moves to translation

Translation: Detailed Steps

• Occurs in the cytoplasm.
• Ribosomes read mRNA and create a polypeptide.
• Three stages:
  • Initiation: Setting up the ribosome and tRNA at the start codon.
  • Elongation: Making the polypeptide chain.
  • Termination: Releasing the polypeptide.

Translation Initiation

• Small subunit binds to mRNA.
• tRNA with methionine (met) attaches at the start codon (AUG).
• Large subunit binds, forming the complete ribosome.
• Three slots on the ribosome:
  • A (acceptor) site: Receives new tRNA.
  • P (peptidyl) site: Holds tRNA with the growing polypeptide.
  • E (exit) site: tRNA exits.

tRNA and Codon Recognition

• tRNA has an anticodon that matches the mRNA codon.
• Each tRNA carries a specific amino acid.
• Example: If the codon is UUC, the anticodon is AAG, and the amino acid is phenylalanine (phe).

Translation Elongation

• tRNA comes into the A slot.
• The amino acids in the P slot jump over and join to the amino acid in the A slot.
• Ribosome shifts over one codon:
  • tRNA in the A slot shifts to the P slot.
  • tRNA in the P slot shifts to the E slot and exits.
  • A slot is now open for the next tRNA.
• Polypeptide grows longer one amino acid at a time.
• Codons are the code that actually codes for each amino acid.

Translation Termination

• Ribosome reaches a stop codon (UAA, UAG, UGA).
• A release factor protein binds to the stop codon.
• The complex disassembles.
• Polypeptide is released.
• The machinery can be used again.

Product of Translation

• The polypeptide, which will fold into a protein.

Polyribosomes

• Multiple ribosomes translating the same mRNA simultaneously.
• Increases protein production.

Bound Ribosomes

• Ribosomes that are attached to a membrane (e.g., endoplasmic reticulum).
• Bound ribosomes are actively elongating a polypeptide.
• Signal recognition particles (SRPs) move ribosomes to membranes via signal peptide the polypeptide.
  • All ribosomes start as free ribosomes.
  • Grab the polypeptide which drags where it should be for bonding:
    • E.g. The ER for transport and secretion.

Protein Synthesis in Prokaryotic Cells

• Transcription and translation occur simultaneously in the cytoplasm.
• Ribosomes bind to mRNA while it is still being transcribed.

Mutations and Alleles

• Mutations in genes can lead to new alleles.
• Mutations alter the genetic code.
• Every allele that is in us originated from a mutation in cells.

Point Mutations

• Change in one nucleotide pair.
• Two types:
  • Base pair substitution: One pair replaced by another.
  • Base pair insertion or deletion: Adding or removing a pair.

Missense Mutations

• A base pair substitution that causes a change in the amino acid sequence.
• An example is sickle cell anemia.

Silent Mutations

• A point mutation that has no impact on the amino acid sequence.
• May happen because multiple codons code for the same amino acid.

Nonsense Mutations

• A point mutation that changes a normal codon into a stop codon.
• Results in a truncated, non-functional protein.

Frameshift Mutations

• Caused by base pair insertion or deletion.
• Changes all codons downstream from the mutation.
• Leads to massive missense or nonsense.

Mutagens

• X-rays.
• UV radiation.
• Chemicals.
• Cause mutations by altering DNA.

Inheritance of Mutations

• Mutations must occur in sperm or egg cells (gametes) to be passed to future generations.
• Otherwise they are not passed to offspring.
• That is why during radiation in the waist areas are blocked to protect egg/sperm cells.