Central Dogma of Molecular Biology

• DNA is a sequence of nucleotides made up of sugar, phosphate, and nitrogenous bases
• Nucleotide: phosphate + sugar + base
• Nucleic acids consist of many nucleotides that are composed of a sugar-phosphate backbone and nitrogenous bases
• Families of sugar: deoxyribose and ribose
• Families of nitrogenous bases:

  • Pyrimidines: cytosine, thymine (only in DNA), and uracil (only in RNA)
  • Purines: adenine and guanine
• Nucleotide monomers are joined together to form a polynucleotide/nucleic acid by a covalent bond, phosphodiester bond, between the OH group (3’ C) and P (5’ C of the next nucleotide)
• Hydrogen bonds between N-bases hold DNA strands together:

  • 2 HB for AT pair
  • 3 HB for CG pair
• Prime (‘) denotes where a carbon is located

  • P is attached to the 5’ end
  • Nitrogenous bases are attached to the 1’ end
  • -OH (hydroxyl) is attached to 3’ carbon (as well as the phosphate of the next nucleotide)
• DNA and RNA differences:

  • DNA: Adenine, guanine, cytosine, thymine, 2 strands, located in the nucleus, sugar is deoxyribose, stores genetic materials
  • RNA: Adenine, guanine, cytosine, uracil, 1 strand, located in the cytoplasm, sugar is ribose, transforms and transports proteins
• Proteins involved in DNA replication:

  • Helicase: breaks hydrogen bonds between nitrogenous bases
  • Single-strand binding proteins: prevent re-binding of unwound parental strands
  • Topoisomerase: relaxes the strain on the strand caused by unwinding to prevent supercoiling
  • Primase: synthesizes RNA primers on both strands
  • DNA polymerase: responsible for elongating the DNA strand by adding nucleotides to the free 3’ end
  • Ligase: joins Okazaki fragments together
• DNA replication occurs in the S-Phase (eukaryotes)
• Start of replication:

  • Replication of DNA molecule begins at the gene, origin/s of replication
  • Replication bubble forms and each bubble will have two replication forks
  • Helicase is the enzyme that opens up the DNA at the origin of replication
• Models of DNA replication:

  • Semiconservative is the best model that represents DNA
• Elongation process of transcription:

  • Adds nucleotides from 5’ to 3’ direction
  • RNA primer initiates the process, activating the DNA polymerase
  • Leading strand is continuously synthesized in the direction of the replication fork
  • Lagging strand is formed in short fragments
  • Okazaki fragments are fragments of the lagging strand
  • DNA ligase joins the Okazaki fragments together
• Transcription:

  • RNA polymerase creates a matching set of bases based on a selected DNA segment, forming a strand called mRNA
• mRNA: RNA that corresponds to the sequence of a gene synthesized by RNA polymerase

  • Carried from the nucleus to the ribosome to create protein
• RNA polymerase: moves along the DNA strand making mRNA
• Promoter: segment of DNA that signals the initiation of RNA polymerase's job to start RNA synthesis

  • Located before the transcription start site
• σ factor/transcription factor: proteins that help RNA polymerase recognize promoter sequences
• In RNA synthesis, only a portion of the DNA will be replicated
• INITIATION:

  • Transcription factors bind to promoters
  • RNA polymerase recognizes and binds to the promoter sequence with the assistance of transcription factors
• ELONGATION:

  • RNA polymerase moves along the DNA template synthesizing mRNA in the 5' — 3' direction
  • DNA unwinds and rewinds as the RNA polymerase reads
  • Elongation occurs at a rate of 40 nucleotides per second
• TERMINATION:

  • mRNA is released and the RNA polymerase detaches
  • Prokaryotes couple transcription and translation, happening simultaneously in the cytoplasm
• EUKARYOTES: mRNA PROCESSING

  • Guanine nucleotide cap added at 5' end
  • Poly-A tail added at 3' end
  • RNA splicing removes introns and joins exons to form mature mRNA
  • Alternative splicing allows for multiple splicing methods
  • Mature mRNA can leave the nucleus and undergo translation
• TRANSLATION terms:

  • Peptide: two or more amino acids joined by peptide bonds
  • Polypeptide: chain of many amino acids
  • Protein: contains one or more polypeptides
• TRANSLATION MACHINERY:

  • mRNA
  • tRNA (transfer RNA)
  • Ribosome synthesizes proteins by translating the genetic code transcribed in mRNA into an amino acid sequence
  • Ribosomal subunits are made of rRNA
• THE GENETIC CODE CHART:

  • Start codon: AUG (methionine/Met)
  • Stop codons: UAG, UAA, UGA
• INITIATION:

  • mRNA attaches to the small ribosomal sub-unit
  • tRNA base-pairs with the start codon AUG on the P site
  • Large subunit arrives
  • A site is available for the next tRNA bearing the next amino acid
• ELONGATION:

  • New tRNA binds on the A site
  • Polypeptide on the P site binds to the new tRNA on the A site through a peptide bond
  • Process repeats
• SAMPLE READING OF SEQUENCES:

  • Codons are 3 nucleotide portions
  • There are 64 codons representing 20 amino acids and 3 stop signals
• POST-TRANSLATIONAL MODIFICATIONS:

  • Proteins are modified in the Golgi apparatus for them to become useful
  • After translation, proteins undergo modifications like phosphorylation, glycosylation, and lipidation
  • Release factor promotes hydrolysis of the bond between tRNA and the last amino acid of the polypeptide
• The Central Dogma of Molecular Biology:

  • DNA undergoes replication, transcription to RNA, then translation to proteins
  • Nucleic acids are formed from nucleotides (monomers) which consist of N-bases, sugar-phosphate backbone
  • Nucleotide composition: phosphate + sugar + base
  • Nucleoside composition: sugar + base
  • DNA sugar: deoxyribose (lacks Oxygen on 2')
  • RNA sugar: ribose (contains Oxygen on 2')
  • Nitrogenous bases:
  • Pyrimidines: Cytosine, Uracil (only in RNA), Thymine (only in DNA)
  • Purines: Adenine, Guanine
  • Complementary bases: Pyrimidines pair with purines
  • Nucleotides are linked by phosphodiester bonds to form nucleic acids
  • N-bases are bonded by hydrogen bonds
  • Sugar-phosphate bonds form the backbone, while nitrogenous bases are the appendages
  • DNA strands are anti-parallel, with the sequence depending on the N-bases
• DNA Replication:

  • Models: conservative, semi-conservative (best model), dispersive
  • Proteins involved: Helicase, Single-strand binding proteins, Topoisomerase, RNA Primase, DNA polymerase I and III, Ligase
  • Process: Initiation, Elongation, Termination
• Transcription:

  • RNA polymerase synthesizes mRNA from DNA
  • Terms: mRNA, Promoter, σ/transcription factor
  • Process: Initiation, Elongation, Termination
• Termination Processes in Prokaryotes and Eukaryotes:

  • Prokaryotes couple transcription and translation
  • Eukaryotes involve mRNA processing
• Translation:

  • Terms: codon, amino acid, peptide, polypeptide, protein
  • Machineries: mRNA, tRNA, Ribosome, rRNA, Initiation factors, Release factor
  • Process: Initiation, Elongation, Termination
• Post-Translational Modifications:

  • Proteins undergo modifications in the Golgi apparatus