MOLBIO DX LE 1

• Central Dogma:

  • DNA contains the complete genetic information that defines the structure and function of an organism
  • Proteins are formed using the genetic code of the DNA
• Foundations of the Central Dogma: Replication, Transcription, Translation
• DNA Replication:

  • A double-stranded nucleic acid (DNA) is duplicated to give identical copies
  • This process perpetuates the genetic information
• Transcription:

  • A DNA segment that constitutes a gene is read and transcribed into a single-stranded sequence of RNA
  • The RNA moves from the nucleus into the cytoplasm
• Translation:

  • The RNA sequence is translated into a sequence of amino acids as the protein is formed
  • The ribosome reads 3 bases (a codon) at a time from the RNA and translates the codons into 1 amino acid
• DNA:

  • Deoxyribonucleic Acid serves as the genetic material in all living organisms on Earth, except in some viruses that use RNA
  • DNA is an extraordinarily stable molecule, losing its normal conformational structure only at extremes of heat, pH, and presence of destabilizing agents
  • DNA is assembled in units of nucleotides composed of a phosphorylated ribose sugar and a nitrogen base
  • The information system of DNA is based on the order of sequence of molecules called nucleotides
• DNA Structure:

  • Watson and Crick model of the DNA
  • Sugar-phosphate backbone: phosphorylated ribose sugar forms the backbone and is found at the side of the DNA structure
  • Nitrogenous bases are inside the DNA structure
  • Pyrimidines: Thymine (1 ring) and Cytosine
  • Purines: Adenine (2 rings) and Guanine
• Chargaff’s Rule:

  • Adenine pairs with Thymine (AT)
  • Guanine pairs with Cytosine (CG)
  • Pyrimidines should not pair with another pyrimidine
  • Purines should not pair with another purine
• Nucleotide Composition:

  • Nitrogenous base attaches to the 1st carbon of pentose sugar
  • Phosphate group attaches to the nucleoside of the 5th carbon and makes the phosphodiester bond
  • Phosphodiester bond is the backbone that bonds all phosphate groups from one nucleoside to another
• Sugar-Phosphate Backbone:

  • Hydrophilic (water-loving) and located outside the axis where both components may interact with water
  • Direction: 5’ to 3’
  • PO4 attaches to the 5th Carbon
  • Next PO4 attaches to the 3rd Carbon
• Complementary Strand:

  • Anti-parallel to the original strand = DNA double helix structure
  • Complementary strand is 5’ to 3’
  • Anti-complementary strand is 3’ to 5’
• RNA:

  • Ribonucleic Acid exists predominantly as a single-stranded molecule and in much shorter lengths than DNA
  • Once RNA synthesizes the mRNA during transcription, its complementary strand will contain methylated Uracil (U) instead of Thymine (T)
  • Structurally, the ribose contains 1 hydroxyl group at the 2’ position, unlike DNA
• Messenger RNA (mRNA):

  • Carries genetic information from the DNA of the gene to the ribosomes after transcription
  • Varies in sizes reflecting the range of protein sizes encoded by the mRNA and the gene sizes that serve as templates
  • Creates the codons and carries instructions from DNA to Ribosomes
• Ribosomal RNA (rRNA):

  • Important components of ribosomes which are nonspecific workbenches where proteins are synthesized during translation
  • Combines with proteins to make up ribosomes
• Transfer RNA (tRNA):

  • Smallest class that carries amino acids to the ribosomes during translation and brings the anticodons to the mRNA
  • Brings amino acids to ribosomes
• 3 major steps of DNA replication:

  • DNA unwinding
  • DNA unzipping (hydrogen bond break)
  • New strands made
• 2 Different kinds of DNA Replication:

  • Semi-conservative: only one strand (original) is conserved
  • Conservative: both strands are conserved
• Replication Fork:

  • Created when the strands of the helix are unwound at each point along the chromosome where replication is occurring
  • Initially appear at the point of origin of synthesis
• Bidirectional:

  • Two replication forks will be present migrating in opposite directions away from the origin
• Classes of Proteins:

  • DNA polymerase III
  • DNA Polymerase I
  • RNA primer
  • Okazaki fragments: short DNA fragments found on lagging strand
  • DNA ligase: Seal the single strand nick between the nascent chain and Okazaki fragment on lagging strand
  • DNA primase: Anneal RNA primer to nucleotide so DNA polymerase III know where to start
• DNA Polymerase III and I:

  • Deoxynucleotide polymerization
  • Initiates nascent, daughter strand synthesis
• PROCESS of DNA Replication:

  • Helicase
  • Topoisomerase
  • Leading strand
  • Lagging strand
  • DNA polymerase III
  • Primase
• Transcription:

  • Only specific portion of the DNA strand is exposed
  • RNA molecules are produced by coping part of a nucleotide sequence of DNA into a complementary sequence in RNA
  • Requires the enzyme RNA polymerase
• Transcription strand formed:

  • Coding strand
  • Template strand
  • Travels 3’ to 5’
  • Makes complementary strands (antiparallel) from 5’ to 3’
• STAGES of transcription and translation:

  • Initiation
  • Elongation
  • Termination
• Translation:

  • Decoding of an mRNA message into a polypeptide chain (protein)
  • tRNA transfers RNA
  • On ribosomes in the cytoplasm
  • Cell uses information from mRNA to produce proteins
• CODONS:

  • Travels from 5’ to 3’
  • Start codon: AUG - Methionine (Met)
  • Stop codons: UGA, UAA, UAG
• HELICASE:

  • Enzyme responsible for the unwinding of the DNA strand
• TOPOISOMERASE:

  • Helps the helicase in unwinding the strands
  • Cuts the DNA strand in front of the Helicase, twist, and attach it again to the strand
• LEADING STRAND:

  • Formation of complementary strand from 3’ to 5’
  • Enzyme: DNA Polymerase 3
  • Only 1 RNA primer - 5-10 nucleotides long
• LAGGING STRAND:

  • Anti-parallel
  • Enzyme: DNA polymerase 1
  • Okazaki fragment (100-200 nucleotides long)
  • Okazaki fragment per RNA primer
• DNA POLYMERASE III:

  • Enzyme responsible for making the complementary strand in the leading strand
• PRIMASE:

  • Enzyme that synthesizes an RNA primer and attach to a certain nucleotide
• TRANSCRIPTION INITIATION:

  • RNA Polymerase binds to the promoter and starts to unwind the DNA strand
• TRANSCRIPTION ELONGATION:

  • RNA polymerase moves along the DNA template strand from 3’ to 5’ and produces the RNA transcript by adding nucleotides to the 3’ end of the growing RNA
• TRANSCRIPTION TERMINATION:

  • Specific sequences of DNA signal termination of transcription
  • RNA transcript/complementary strand is released from the DNA and will move to the ribosome
  • The double helix DNA will zip up again
  • When RNA polymerase reaches the termination site, the RNA transcript is set free from the template
• TRANSLATION INITIATION:

  • mRNA attaches to a small ribosomal unit from 5’ – 3’
  • The large ribosomal unit arrives
• TRANSLATION ELONGATION:

  • An initiator tRNA carries an anti-codon UAC pair with the start codon AUG
  • tRNA anti-codon is complementary to mRNA codon
  • mRNA codon read & tRNA brings matching amino acid to ribosome
  • Amino acids are strung together like beads on a necklace to form a polypeptide chain
  • Amino acids are held together by peptide bonds
• TRANSLATION TERMINATION:

  • Stop codon (UAA, UAG, UGA) signals the termination of the polypeptide chain
  • The polypeptide chain leaves the ribosome for further packing and protein synthesis
  • Proteins with more than 1000 amino acids are produced