Test practice (Unit 5 & 6)

Microbial Genetics

• Heredity is based on DNA
• DNA is made up of nucleotides, which comprise of a sugar (deoxyribose), phosphate, and a nitrogenous base
• Four nitrogenous bases exist: Adenine, Thymine, Guanine, and Cytosine
• Nucleic acids store and transfer information, holding the instructions for all proteins and metabolic reactions, defining an individual organism or cell
• Nucleic acids are reproducible, passing information from DNA to RNA, leading to protein formation
• Chromosomes, composed of DNA, are circular in prokaryotes and linear in eukaryotes
• A gene, a sequence of nucleotides located at a specific locus on a chromosome, can have different versions, called alleles
• Genotype represents the complete set of genes an organism possesses
• Phenotype encompasses the physical characteristics of an individual, influenced by both the genes and the environment

Protein Synthesis

• Transcription, the process of reading a specific section of the genome to create proteins, involves the conversion of DNA to messenger RNA (mRNA)
• Translation interprets mRNA to synthesize a specific protein (mRNA to Protein)
• The codon table, a tool used to decipher the relationship between mRNA codons and amino acids, reveals that every three bases code for a specific amino acid

Mutations

• Mutations are heritable changes in an organism's DNA sequence
• Mutants may exhibit phenotypic differences compared to the "wild type", the most prevalent form in nature
• Mutations can affect protein function:
  • Silent mutation: no effect on protein function
  • Missense mutation: a different amino acid is incorporated into the protein
  • Nonsense mutation: converts a codon into a stop codon, often leading to a non-functional protein

Adaptation and Mutations

• Mutants can be:
  • Successful: advantageous (mutant surpasses non-mutants)
  • Neutral: no difference in success compared to non-mutants
  • Deleterious: less successful than non-mutants
• Adaptation occurs when a beneficial mutation arises within a population and eventually becomes the dominant form due to increased success of mutant individuals

DNA/Chromosome Replication

• Consists of three stages: Initiation, Elongation, and Termination

Initiation

• Replication starts at the origin of replication (oriC)
• oriC is a specific sequence of bases on DNA that marks the beginning of DNA replication
• DNA strand unwinds at oriC, generating two strands
• Helicase unwinds the DNA, creating two replication forks

Elongation

• Polymerase replicates the two strands, but can only extend existing strands
• Primase primes the strands for replication by adding a primer recognized by the polymerase
• Replication initiates simultaneously in both directions: leading and lagging strands
• Okazaki fragments, short DNA segments created during lagging strand replication, are joined by ligase to create a contiguous strand
• Topoisomerases (gyrase) manage DNA winding problems

Termination

• Replication halts when the polymerase encounters the termination (Tus-Ter) sequence
• Two new loops form and migrate to the bacterial ends
• A septum forms to create two new cells

Gene Transfer

• Binary fission is simple asexual cell division, lacking genetic diversity
• Bacterial conjugation involves a donor cell transferring genetic information to a recipient cell, promoting genetic diversity
• Bacterial transformation involves cells acquiring genetic information from the environment, leading to the acquisition of new traits and genetic diversity
• Bacterial transduction occurs when a bacterial cell is infected by a bacteriophage
• Viral DNA integrates into the bacterial DNA, replicating and carrying portions of bacterial and viral DNA
• The infected phage then infects other bacteria, transferring the combined DNA

Biotechnology

• Biotechnology is the science of using living systems to improve humankind
• Genetic engineering involves altering an organism's genetics to produce desirable traits

What is a Virus?

• A virus is an acellular infectious agent that cannot self-replicate.
• Viruses must infect a cell to reproduce.
• Examples of viruses include Influenza, HIV, and Ebola.

Viral Structure

• Viral structure varies but has common elements.
• All viruses have a genome made of either RNA or DNA.
• Viruses have a protein coat called a Capsid.
• Some viruses also have an envelope composed of a lipid bi-layer.
• Viruses have surface receptors, often spikes of protein or glycoprotein.

Viral Replication Cycle

• Viral replication depends on the type of genome a virus possesses.
• Different types of viruses have distinct replication strategies.

Viral Attachment

• Proteins on the viral envelope or Capsid bind to specific receptors on host cells.

Viral Penetration

• There are three main ways a virus enters a host cell:
  • Direct penetration (naked viruses): Only the viral genome enters the host cell.
  • Fusion: The viral envelope fuses with the host membrane, allowing the capsid containing the genome to enter.
  • Receptor-mediated endocytosis: Attachment stimulates endocytosis of the entire virus.

Viral Uncoating

• The virus removes its Capsid (uncoats), exposing the nucleic acid genome to the cytoplasm.

Viral Transport to Nucleus

• The viral genome enters the host cell nucleus.

Viral Synthesis

• The viral genome is reproduced through transcription in the nucleus.
• Viral proteins are produced through translation in the cytoplasm.

Viral Assembly

• Newly produced viral components (genome and Capsid) assemble into new viruses.

Viral Release

• Viruses are released from the host cell through one of three mechanisms:
  • Apoptosis: The host cell lyses, releasing mature viral particles. The host cell dies.
  • Budding: The virus buds through the nuclear or plasma membrane, acquiring an envelope. The host cell survives.
  • Exocytosis: Viruses leave the host cell using vesicles; the host cell survives.

Influenza Virus

• Influenza virus is an enveloped RNA virus.
• RNA viruses mutate more frequently than DNA viruses.
• RNA viruses can adapt to environmental changes more readily due to their high mutation rates.
• Influenza has two surface proteins: Hemagglutinin (H) and Neuraminidase (N).

Hemagglutinin (H)

• This glycoprotein binds the virus to cells with sialic acid on their membranes.
• Sialic acid is a receptor found on most vertebrate cells.
• Hemagglutinin helps the virus enter the cell.

Neuraminidase (N)

• This enzyme aids in penetration of the respiratory tract mucus and viral shedding.
• Neuraminidase cleaves sialic acid from host glycoproteins during viral release (budding).

Antigenic Variation

• There are two main types of antigenic variation in Influenza viruses:
  • Antigenic drift: This occurs due to point mutations in the genes coding for Hemagglutinin and Neuraminidase.
  • Antigenic shift: This occurs due to reassortment of viral genes from two different viruses infecting the same cell.

Antigenic Drift

• Mutations in Hemagglutinin and Neuraminidase genes alter the antigens.
• This makes it harder for the host's immune system to recognize and fight the virus.
• Antigenic drift causes new flu epidemics (localized flu) and necessitates annual flu vaccine updates.

Antigenic Shift

• Two different viruses exchange large portions of their genomes.
• The resulting virus is antigenically distinct from both parent viruses.
• Antibodies against the parent viruses are ineffective against the new virus.
• This can lead to pandemics.
  • Examples:
    • H5N1 (bird flu)
    • H1N1 (swine flu)

Swine Flu Viroid Re-assortment

• This is an example of antigenic shift where the genes of a swine flu virus re-assort, leading to a new, potentially pandemic strain.

What is a Virus?

• A virus is an acellular infectious agent that cannot self-replicate.
• Viruses must infect a cell to make copies of themselves.
• Examples of viruses include Influenza, HIV, and Ebola.

Viral Structure

• Viruses have varied structures, but there are common features.
• Viral structures include RNA or DNA genomes, protein capsids, envelope lipid bi-layers, and surface receptors (spikes) made of protein or glycoprotein.

Viral Replication Cycle

• The replication cycle of a Virus depends on its genome.

Viral Replication Cycle (Steps)

• Attachment: Proteins on the viral envelope or capsid recognize and bind with target host cell receptors.

• Penetration: Entry can occur in three ways:

  • Direct penetration (naked viruses): Only the viral genome enters the host (typical of bacteriophages);
  • Fusion: Viral envelope fuses with the host membrane, the capsid containing the genome enters the cell (e.g. HIV);
  • Receptor-mediated endocytosis: Attachment stimulates endocytosis of the whole virus (e.g. Influenza).

• Uncoating: The virus removes the capsid and the nucleic acid of the genome is exposed to the cytoplasm.

• Transport to Nucleus: Viral genome enters the nucleus.

• Synthesis (Transcription & Translation): Reproduction of the viral genome (transcription in the nucleus) and viral proteins (translation in the cytoplasm).

• Assembly: Assembly of new virions (complete virus). The genome and capsid are put together to form a new virus.

• Release: Release of the virus from the host cell (viral shedding). Release occurs by one of three mechanisms:

  • Apoptosis: The host cell lyses and releases mature viral particles (naked viruses); The host cell dies.
  • Budding: Through the nuclear or plasma membrane, creating an envelope; Does not kill the host.
  • Exocytosis: Viruses leave the host cell using vesicles; Does not kill the host.

Influenza Virus

• Influenza virus is an enveloped RNA virus.
• RNA viruses have higher mutation rates than DNA viruses as they don't have self-regulation and DNA correction mechanisms.
• This makes RNA viruses highly adaptable to environmental changes.
• The envelope of the influenza virus is covered with two proteins (antigens) essential for the infection process:
  • Hemagglutinin (H) spike
  • Neuraminidase (N) spike

Hemagglutinin (H) spike

• Glycoprotein on the surface of the Influenza virus binds the virus to cells with sialic acid on host cell membranes, such as cells in the upper respiratory tract or erythrocytes.
• This helps the virus enter the cell.
• Sialic Acid is a receptor found on most vertebrate cells.

Neuraminidase (N) spike

• Enzyme that helps the virus penetrate the mucus of the respiratory tract & aids in viral shedding of influenza (budding).
• It does this by cutting sialic acid from host glycoproteins as the virus is being released.

Antigenic Variation

• Mutations in genes that code for these two proteins (H and N) are responsible for the development of new strains of Flu.
• Antigenic variation occurs in two ways with the Flu Virus:
  • Antigenic drift results from point mutation of genes coding for Hemagglutinin & Neuraminidase.
  • Antigenic shift is caused by re-assortment of viral genes.

Antigenic Drift

• Mutations in genes that code for Hemagglutinin & Neuraminidase.
• These two proteins are the antigens that cause the formation of host antibodies.
• It produces new strains of flu virus that host antibodies won't recognize.
• If enough of an antigenic drift occurs, it will cause a new flu epidemic (localized flu).
• Antigenic drift causes new formulations of flu vaccine every year.

Antigenic Shift

• Results from gene re-assortment from two different viruses that infect the same cell.
• Viruses exchange a large part of their genome.
• The virus that emerges is antigenically different from either of the two viruses.
• Antibodies formed from the two viruses are ineffective against the new combined virus genome.
• For example:
  • H5N1 = bird flu
  • H1N1 = swine flu
• Can lead to Pandemics.