11 + 12 Control of Genome (DIY)

• Where is the Prokaryotic Genome located

  Nucleoid Region
• Where is the Eukaryotic Genome located

  Nucleus
• Define Genome

  • the complete set of genetic material in a particular cell
• Define Gene

  • the entire specific nucleotide sequence encoding the synthesis of a polypeptide chain (functional protein) or RNA product
• Size of Genome

  • Prokaryotes: Smaller (10^5 - 10^7 base pairs)
  • Eukaryotes: Larger (10^7 - 10^11)
• Number of genes

  • Prokaryotes: Fewer
  • Eukaryotes: More
• Number of Genes

  • Prokaryotes: Only 1 set of genes in a bacterial chromosome
  • Eukaryotes: Sister chromatids contain identical copies of each gene located at the same gene loci along the chromosome
• Number of origins of replication

  • Prokaryotes: One
  • Eukaryotes: Multiple (Increases the speed of replication due to larger genome size)
• Chromosomes

  • Prokaryotes: 1 (Circular)
  • Eukaryotes: More than 1 (Multiple, Linear)
• Association with proteins involved in organisation of genome

  • Prokaryotes: Associates with histone-like proteins
  • Eukaryotes: Associates with a large number and type of histone proteins
• Prokaryotes


  Lower degree of DNA condensation
• Prokaryotes


  1. Circular DNA folded into chromosomal looped domains by histone-like protein-DNA associations

  2. Folding is further compacted by supercoiling
• Eukaryotes

  Higher degree of DNA condensation
• Eukaryotes

  1. DNA double helix is associated with histone proteins by electrostatic interactions (ionic bonds)

  2. Most of the DNA is wound around octamers of 8 histone proteins (2 of each histone: H2A, H2B, H2 and H4) to form nucleosomes (approximately 10nm)

  3. Remainder of DNA (linker DNA) joins adjacent nucleosomes

  4. Nucleosomes coil around itself to form a 30nm chromatin fibre with the help of histone H, later forming loops called looped domains (300nm fibre) when associated with scaffold proteins

  5. Supercoiling present as the loops further coil and fold to produce characteristic metaphase chromosomes in dividing cell
• DNA is negatively-charged and histones are positively-charged due to amino acids
• Promoter Region

  • Prokaryotes: Pribnow Box (TATAAT sequence)
  • Eukaryotes: TATA Box (TATAAA sequence)
• Location of Transcription

  • Prokaryotes: Cytoplasm
  • Eukaryotes: Nucleus
• Location of Translation

  • Prokaryotes: Cytoplasm
  • Eukaryotes: Cytosol (Free ribosomes)/ RER (Bound ribosomes)
• Post-transcriptional modification

  • Prokaryotes: Does not occur (no pre-mRNA)
  • Eukaryotes: Occurs (pre-mRNA forms mature mRNA before being translation)
• Location of functionally-related genes on chromosomes

  • Prokaryotes: These genes are grouped together in a single operon
  • Eukaryotes: These genes are located on different chromosomes
• Control by promoter

  • Prokaryotes: Single promoter controls the structural genes grouped in an operon
  • Eukaryotes: Each gene is under the control of its own individual promoter
• Presence of introns

  • Prokaryotes: Present but not as extensive as eukaryotes (very low in number)
  • Eukaryotes: Present and more extensive than prokaryotes (interspersed between exons of a gene)
• Extrachromosomal DNA (Plasmids)

  • Prokaryotes: May be present
  • Eukaryotes: Usually absent (but may be present in some species of yeast)
  • However, mitochondria and chloroplast have their own circular DNA
• Centromere Structure

  • Found in linear chromosomes located anywhere along the length of a chromosome
  • Visible during the metaphase stage as constricted regions on chromosomes where spindle fibres attach to during nuclear division (where 2 sister chromatids join - each has its own centromeric DNA sequences)
  • Special DNA sequence in centromeric region is important for binding of kinetochore protein
  • Consist of large arrays of non-coding repetitive tandem DNA where the sequence within the individual repeat unit is similar but not identical
• Without centromere, what occurs?

  Improper chromosomal alignment and segregation will result in aneuploidy
• Kinetochore

  Being the site of kinetochore assembly, centromeres allow the attachment of spindle fibres at kinetochore found at centromere of sister chromatids
• Spindle fibres attached to kinetochore proteins


  Required to pull homologous chromosomes to opposite poles during anaphase of mitosis and anaphase I and II of meiosis
• What happens when centromeres divide

  Allows for equal separation of sister chromatids to opposite poles of cell during anaphase of mitosis or anaphase II of meiosis
• Functions of Centromeres

  • Facilitate chromatin organisation by enabling sister chromatids adhesion during mitosis (prophase and metaphase)
• Telomeres

  Non-coding regions of DNA consisting of a series of short tandem repeat sequences
• Telomeres

  • Found in linear chromosomes
  • Can only be found at the ends of linear chromosomes
  • 5' TTAGGG 3' in humans
  • Have a single-stranded DNA at their 3' ends known as the 3' overhang
  • Does not have a complementary strand
  • Loops back and displaces the same sequence in the upstream region of the telomere and binds to the complementary sequence of the other strand via the action of special telomere-binding proteins
• Formation of Telomeres

  • Single-stranded DNA at their 3' ends - 3' overhang
  • Does not have a complementary strand
  • Loops back and displaces the same sequence in the upstream region of the telomere and binds to the complementary sequence of the other strand via the action of special telomere-binding proteins
  • Formation of the T-loop and D-loop

  
• Functions of Telomeres

  • Ensures genes are not lost/ eroded with each round of DNA replication due to the end-replication problem
  • Serves a buffer DNA to protect the organism's genes from being eroded after successive rounds of DNA replication
  • Shortening of chromosomal ends leads to shortening of the telomeres without any deleterious effects (non-coding)
  • Plays a protective function by preventing chromosomes ends from degradation by cellular nucleases via the formation of telomeric caps
  • Prevents chromosomal ends from activating the cell’s system for monitoring DNA damage
• Functions of Telomeres (2)

  • Serves as a signal for apoptosis when they are critically short
  • There is a limit to which the telomeres are shortened before regions of chromosome containing essential genes are degraded
  • Once the length of the telomere reaches a critical length, it will signal for programmed cell death (apoptosis)
  • The shortening of telomeres indirectly prevents the development of cancer
  • Apoptosis prevents accumulation of mutations
• Functions of Telomeres (3)

  • Protects and stabilise the terminal ends of chromosomes
  • The single stranded 3’ overhang may cause
  • anneals to a complementary single-stranded region of the terminal end of another chromosomes
  • Ends are similar to DNA damage formed due to double stranded breaks (broken chromosome ends) and sends signals to trigger cell arrest and cell death (apoptosis)
  • Formation of D-loop and T-loop by telomeres is essential - prevents fusion with other chromosomes and prevents the DNA repair machinery from recognising the ends of chromosomes as DNA breaks and trigger apoptosis
• Telomerase Structure + Function

  • A ribonucleoprotein (a complex or RNA and proteins) that functions as a reverse transcriptase (a protein that synthesises DNA using an RNA template)
  • Maintains the length of telomeres
  • In humans: contains a single RNA molecule, which provides the template sequence (AAUCCC) to guide the synthesis and insertion of the telomeric DNA sequence (TTAGGG)
• Process of synthesis of DNA sequence via Telomerase (Steps 1-2)

  1. A short segment of RNA within telomerase binds to part of a tandem DNA repeat in the 3’ overhang of the parental strand via complementary base pairing
  2. The adjacent part of the RNA within the telomerase is used as a template to add 6 DNA nucleotides to the 3’ end of the parental DNA strand (catalysed by the reverse transcriptase activity of the telomerase)
• Process of synthesis of DNA sequence via Telomerase (Steps 3-4)

  3. After the repeat is made, telomerase begins to make another 6 nucleotide repeat, extending the 3’ overhang of the parental DNA strand in the 5’ to 3’ direction

  4. Primase synthesises an RNA primer near the end of the telomere, DNA polymerase adds nucleotides to the 3’ OH end of the RNA primer and hence synthesises a complementary DNA strand, RNA primer is removed and the nick is sealed by DNA ligase 
• Chromatin Modification (Genomic Control)

  Organisation of DNA into chromatin helps to:

  1. Pack DNA into a compact form that fits inside the nucleus of a cell
  2. Regulate gene expression - physical state of DNA/near a gene to determine if the gene is accessible for transcription 

  Functions to control gene expression by making regions of DNA more or less accessible for transcription through the enzymatic addition or removal of chemical groups from chromatin
• Chromatin types

  1. HETEROCHROMATIN (dark-coloured)

  • highly compact form of DNA where DNA wide more tightly around histone --> Promoter inaccessible to RNA polymerase and transcription factors --> TIC unable to form --> trascription does not occure

  2. EUCHROMATIN (light-coloured)

  • less compact form of DNA where DNA winds less tightly around histones --> Promoter accessible to RNA polymerase and transcription factors --> TIC can form --> transcription occurs