GENE2230

• Central dogma and relevance to flow of info?

  • States that information in biological systems only flows in one direction: from DNA to RNA to proteins
  • Transcribes into RNA, translates into protein
• Exceptions to central dogma:

  • Major info pathway:

  1. Info transferred from one DNA molecule to another (DNA pol.)
  2. Transcription (RNA pol): Info transferred from DNA TO RNA
  3. Translation (Ribosome): Info transferred from RNA to protein

  • Special info. Pathway: 1. In some viruses, info is transferred from RNA to DNA or to another RNA
• Key characteristics of genetic material:

  ➢ Must contain complex info

  ➢ Must replicate faithfully

  ➢ Must encode phenotype

  ➢ Must have the capacity to vary
• DNA is the source of genetic information.
• The discovery that DNA is the genetic material was made through a series of experiments by scientists such as Frederick Griffith, Oswald Avery, Colin MacLeod, and Maclyn McCarty.
• In the 1940s, Avery and his team at the Rockefeller Institute in New York City helped establish that DNA is the genetic material.
• The Hershey-Chase experiment in 1952 confirmed that DNA is the genetic material of viruses that infect bacteria, providing further evidence that DNA is the molecule responsible for inheritance.
• The Human Genome Project, which began in 1990, revolutionized our understanding of DNA and genetics.
• DNA

  1. Primary: nucleotide structure
  2. Secondary: DNA’s stable three-dimensional configuration
  3. Tertiary: packing of double-stranded DNA in chromosomes
• RNA

  1. Single-stranded molecule that is similar in structure to DNA
  2. Plays a crucial role in protein synthesis by carrying the genetic information from DNA to the ribosomes
  3. RNA secondary structures are formed by the base-pairing of complementary nucleotides, making a helix between two strands
• Special secondary structures:

  1. Can Form in DNA and RNA
  2. Hair, stem, complex secondary structure
• • Overrotated: positive supercoiling
  • Underrotated: negative supercoiling
  • Topoisomerases add/remove rotations by breaking the nucleotide strands
  • Most DNA found in cells is negatively supercoiled
  • Separation of the two strands of DNA is easier during replication and transcription
  • Supercoiled DNA can be packed into a smaller space than relaxed DNA
• Within eukaryotic cells, DNA is organized into long linear structures called chromosomes.

  Chromosomes are made up of DNA and proteins called histones. Histones compact and organize DNA into a dense structure called chromatin.

  Chromatin helps prevent DNA damage, tightly packs the DNA to fit into the cell, and controls DNA replication and gene expression
• The different types of chromatin (euchromatin and heterochromatin)

  1. Euchromatin: Most of the chromosome, condensation and decondensation with the cell cycle, transcriptionally active
  2. Heterochromatin: Remains highly condensed throughout the cell cycle, even during interphase; Constitutive (permanent) heterochromatin at the telomeres and centromeres; Facultative heterochromatin at certain developmental stages; Repeated sequences, few genes
• The dynamic nature of chromatin involves its condensation and decondensation with the cell cycle and with replication & gene activity (transcription).
• For most of the life of the cell, chromatin is relatively uncondensed, allowing the DNA to be accessed relatively easily by cellular machinery.
• Condensation takes place when the cell is about to divide, progressing chromosomes from a highly packed state to a state of extreme condensation necessary for chromosome movement in mitosis and meiosis.
• DNA packing also changes locally during replication and transcription, when the two nucleotide strands must unwind so that particular base sequences are exposed.
• Sensitivity to DNase I shows that chromatin structure changes with gene activity

  • DNase I is an enzyme that digests DNA ➢ Its ability to digest DNA depends on chromatin structure (histone-bound DNA is less sensitive)
  • Globin genes encode hemoglobin & are expressed in the erythroblasts of chicks at different stages of development
  • Experiments on globin genes in chick embryos show that DNase sensitivity is correlated with gene activity
• Semiconservative replication= process by which DNA replicates in all known cells. In this model, the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand. Two copies of the original DNA molecule are produced, each copy conserving (replicating) the information from one half of the original DNA molecule
• Replication fork = point where leading and lagging strands meet
• Leading strand = continuous strand of newly synthesized DNA that grows continuously away from the origin of replication. The leading strand can grow continuously because it has a free 5' end that allows primers to be added ahead of the advancing replication fork
• Lagging strand = discontinuous strand of newly synthesized DNA that grows only in short fragments called Okazaki fragments. These fragments are joined together later to form a complete lagging strand
• Leading strand = continuous strand of newly synthesized DNA; synthesis occurs continuously toward the replication fork
• Lagging strand = discontinuous strand of newly synthesized DNA; synthesis occurs in short fragments called Okazaki fragments
• Okazaki fragment = small piece of DNA formed during semiconservative replication of lagging strand
• Okazaki fragment = small piece of DNA formed during the synthesis of the lagging strand
• Primer = short RNA sequence that provides a starting point for DNA polymerization. Primers are made by RNA primase, which attaches them to the parental DNA strand using ribonucleotides
• Primer = short RNA sequence that serves as starting material for DNA polymerization
• Ribonuclease H = enzyme that degrades RNA within RNA/DNA hybrids
• DNA polymerases = enzymes responsible for adding nucleotides to growing chains of DNA
• The different modes of replication include three main types: conservative, semi-conservative, and dispersive replication. However, the mode of replication for linear eukaryotic chromosomes is primarily semiconservative replication.
• Semi-conservative replication begins with the unwinding of the DNA double helix by helicase enzymes, creating two separated strands referred to as the leading and lagging strands.
• Replication origins, specific regions of DNA, act as starting points for the replication process.
• On the leading strand, DNA polymerase III synthesizes a continuous new DNA strand in the 5' to 3' direction, which matches the existing parental strand in the 3' to 5' direction.
• This process occurs in a continuous manner, as there is a continuous template strand available.
• On the lagging strand, DNA polymerase III synthesizes short DNA fragments called Okazaki fragments.
• The RNA primase enzyme first synthesizes a small RNA primer that serves as the starting point for DNA synthesis.
• DNA polymerase III elongates the RNA primer with DNA nucleotides, forming an Okazaki fragment.
• This process is discontinuous because the template strand is only exposed in short stretches, requiring the synthesis of multiple fragments.