BIO282 Lecture Notes - Lecture 2: Lytic Cycle, Dna Supercoil, Bacteriophage
Definitions
Genomes
Viruses that infect bacterial cells are called bacteriophages or just phages.
Life cycles of bacteriophages
Lytic cycle: phage DNA enters inside the cell, replicates and produces more phage particles that
are released by cell lysis.
The phages that reproduce strictly through lytic cycle are called virulent phages; they kill their
host cells, eating bacteria.
Phage means a virus that infects a bacterium.
Plaques are the clear patches of lysed cells on a lawn of bacteria
Lysogenic cycle: phage DNA enters the cell and then get inserted into the bacterial
chromosome. It remains inactive without any disruption in the host cell.
There is no harm to the cell so that It can continue to replicate
The integrated phage is called a prophage; the phages having the ability of the lysogenic cycle
are called temperate phages.
RNA viruses
o The positive-sense RNA, is like mRNA, can be directly translated into viral proteins.
o The negative-sense must first produce complementary strand before it can be translated to
produce viral proteins.
o Ambi-sense are not fully active, they have some genes on the mRNA directly and some genes on
the complimentary strand
RNA viruses capable of integrating into host genome are called retroviruses. The integrated
virus is called a provirus. (once it has already entered)
o Supercoiling
o There are several levels of organization, one of which is the supercoiling of the double-stranded
DNA helix.
o When circular DNA is wound up multiple time it becomes more compact
Topoisomerase
Topoisomerases are required for DNA unwinding and rewinding during transcription and
replication
Chromatin and compaction into a chromosome
Histones are small proteins with lots of basic (Lys, Arg) amino acids
o DNA wraps around histones to form nucleosomes; giving an appearance of beads on a string.
o Nucleosomesare~146 bp DNA wrapped around 8 histones(the “core particle”). The linker DNA
of ~54 bp joins nucleosomes
o Chromatosome is the fundamental unit of chromatin, it consist of nucleosome and the linker
histone H1.
Heterochromatin describes regions of the genome that are highly condensed. These are not
transcribed (silent)
Euchromatin is less tightly coiled than heterochromatin, and contains most of the active or
potentially active genes. (expressed)
Concepts
o Genomes
o Double stranded (ds) DNA is the genetic material for all prokaryotes and eukaryotes.
o Viruses may have DNA or RNA as the genetic material which could be single or double
stranded, linear or circular.
o
• Viruses are obligate parasites; can grow only in their host cells that could be a
bacterium, an animal or a plant cell.
o They only have DNA, therefore they only contain the genetic material in order
to multiply and grow
• Neither the total length of DNA, nor the number of chromosomes correlates strongly with
the complexity of an organism (i.e. Plants have more genes than humans_
• The correlation between genome size and complexity is poor because most of eukaryotic
DNA is non-coding
• Genomes of prokaryotes
• Bacterial genomes are double-stranded circles
• E. coli genome has 4.5 million bp, the total length of DNA is 850× longer than the cell!
• Genome of eukaryotes
• Genomic DNA in eukaryotes combines with proteins to form chromatin which condenses
to form chromosomes.
• Eukaryote DNA is in multiple discrete linear chromosomes.
o Most of the bacterial chromosome has a single circular chromosome, while
eukaryote have many linear chromosomes
• The number of chromosomes in eukaryotes varies with species.
o Life cycles of bacteriophages
Lytic and Lysogenic cycle
o Lytic cycle: phage DNA enters inside the cell, replicates and produces more phage particles
that are released by cell lysis.
o Lysogenic cycle: phage DNA enters the cell and then get inserted into the bacterial
chromosome. It remains inactive without any disruption in the host cell.
The phage DNA becomes part of the bacterial DNA and is replicated generation after
generation when the cell is replicated. They are happy there but when something happens
to the cell, the viral DNA comes out and goes through the lysogenic phase to reproduce.
The prophage in certain conditions can dissociate from the chromosome and enter into
the lytic cycle.
o RNA viruses
• The genetic material of RNA viruses is either a double stranded RNA or a single stranded
RNA.
• Single strands are positive or negative sense and negative sense has to replicate before
translation.
• The single stranded RNA viruses could further be classified as negative-, positive- or ambi-
sense RNA viruses.
Something should happen before the viruses integrate – they change from RNA to DNA so
they can be inserted into the bacterial DNA.
o Packaging of DNA
DNA is heavily negatively charged because of the Phosphate ions and so is difficult to pack. The
proteins help to pack it.
• Viral genomic DNA may be associated with capsid proteins, very small amount of protein
there
• Prokaryotic DNA is associated with proteins in the nucleoid, some proteins involved but
not many
• Eukaryotic DNA is organized with proteins into a complex called chromatin which further
condenses to make chromosomes.
o Supercoiling
• DNA must be organized to allow:
o Packing of large DNA within the cells
o Access of proteins to read the information in DNA sequence
o There should be a way to access different genetic material at different times when
required
• Supercoiling is achieved with the help of topoisomerases.
Document Summary
Viruses that infect bacterial cells are called bacteriophages or just phages. Lytic cycle: phage dna enters inside the cell, replicates and produces more phage particles that are released by cell lysis. The phages that reproduce strictly through lytic cycle are called virulent phages; they kill their host cells, eating bacteria. Phage means a virus that infects a bacterium. Plaques are the clear patches of lysed cells on a lawn of bacteria. Lysogenic cycle: phage dna enters the cell and then get inserted into the bacterial chromosome. There is no harm to the cell so that it can continue to replicate. The integrated phage is called a prophage; the phages having the ability of the lysogenic cycle are called temperate phages. Rna viruses capable of integrating into host genome are called retroviruses. The integrated virus is called a provirus. (once it has already entered: supercoiling, there are several levels of organization, one of which is the supercoiling of the double-stranded.
