Bio 120 MT3

start oct 5 Egan 120 USC

Gene duplication

increases the number of genes in genome, providing more opportunities for evolutionary change

Gene Families

repeated gene duplications making groups of related genes within a genome

homologous genes

genes inherited by two species that evolved from the same ancestor categories: orthologous genes or paralogous genes

paralogous genes

the homology results from gene duplication and occurs between gene copies within a species

Otohrologous genes

genes that arrived from a common ancestor, used for inferring phylogeny because they reflect the history of speciation events

Paralogous genes

can diverge within a species if present in more than 1 copy

Genome Evolution

lineages that diverged long ago often shared many orthologous genes

Molecular Clock

an approach used to estimate the absolute time of evolutionary change, the estimate is based on the observation that some genes evolve at a constant rate

Assumption for molecular clock

An assumption of the molecular clock concept is that the number of nucleotide substitutions is proportional to the time since

– the split from a common ancestor for orthologous genes

– gene duplication for paralogous genes

Molecular clock calibration

calibrated by graphing the number of genetic differences in a gene against dates of a branch

Limitations of Molecular Clock

• Some genes evolve in irregular bursts, rather than clocklike precision

• the rate of evolution deviates from the average periodically even in reliable clocklike genes

• the same gene may evolve at different rates in different taxa

• Some clocklike genes evolve at dramatically different rates from each other

Neutral genes

silent mutations, changes in composition in genotype but no change in phenotype

Carolus Linnaeus

classified organisms in either kingdom plantae and Animalia Limitation labels bacteria as plants but it is not autotrophic( lives off sun)

5 kingdom classification

classification based on Cell structure, body organization, and mode and source of nutrition. Groups: (Monera, Protista, Fungi, Plantae and aminalia)

Three domain classification

dived cellular life forms into Archaea, Bacteria, and Eukarya.

• Prokaryotes form two domains because some differ as much from each other as they do from eukaryotes

• Eukarya includes three kingdoms: Plantae, Fungi, and Animalia

• Protista group doesn't exist

Horizontal gene transfer

the movement of one gene to another genome, can occur by exchange of plasmids, viral infection, and possibly fusion of organisms

Conjugation

the transferring of genes from one to another example plasmids (horizontal gene transfer type)

Virus

An infectious particle consisting of genes packed into a protein coat (sometimes can have an outer membrane)

Although not live organism because it cannot reproduce without the help of another organism

Origin of Viruses

Three hypothesis:

1. The progressive or escape hypothesis states that viruses arose from genetic elements that gained the ability to move between cells (nah virus not linked with Luca extra question not important mention)

2. the regressive or reduction hypothesis asserts that viruses are remnants of cellular organisms ( virus could be linked to Luca extra no important mention)

3. the virus- first hypothesis states that viruses predate or coevolved wi their cellular hosts (virus could be linked to Luca not important motion )

Viral Characteristics and diversity

Host, Genome, capsid, and envelope

Viral Genomes

• double or single stranded DNA or double or single stranded RNA

• Genome is either linear or circular molecule of the nucleic acid

Capsid

the protein shell that encloses the viral genome

** Built from protein subunits called capsomeres

Capsomeres

protein sub units in capsid

Viral envelopes

surround the capsid of virus

Bacteriophages also called Phages

• viruses that infect bacteria

• have an elongated capsid head that encloses their DNA

Obligate intracellular parasite

can only replicate within a host cell

Host range

a limited number of host species that it can infect (some viruses can only affect one species)

Central Dogma

DNA (translation)→ RNA (translation) → Protein

Viral Replication

1. Recognition of host cell and attachment

2. Genome Replication and protein Synthesis

3. Protein Synthesis viral mRNA is produced, and viral protein is made

4. Assembly- new viral genomes associate with capsid proteins

5. Release - mature virions leave the cell

Lytic Cycle

the phage replicative cycle that culminates in the death of host cell

virulent phage

A phage that reproduces only by the lytic cycle

Lysogenic cycle

replicates the phage genome without destroying the host

Temperate phages

Phages that use both the lytic and lysogenic cycles

Lambda

a temperate phage

Replicative cycles of Animal Viruses

Two key variables used to classify viruses that infect animals:

• An RNA or DNA genome either single-stranded or double stranded

• The presence or absence of a membranous envelope

Retroviruses

uses reverse transcriptase to copy their RNA genome into DNA

Provirus

the viral DNA that is integrates into the host genome

Viral genetic replication

• RNA polymerase polymerase transcribes the proviral DNA into RNA molecules

• The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles released from the cell

CRISPR-Cas system

Both bacteria and archaea can protect themselves from viral infection with this system that also stands for Cluster Regularly Interspaced Short Palindromic Repeats

Prokaryotic Defense

The Cas proteins use the Phage related RNA to attacked invading phage DNA

Pathogens

Keep the internal body free of disease causing microbes (bacteria and fungus are outside of host and Viruses are inside of host!)

three Major lines of defense

1. First line- Barriers (physical, chemical, and biological)

2. Second line - Innate Immune System

3. Third Line- Adaptive Immune System

Innate Immune System

• operates constantly

• Innate (inborn) - no training needed

• not affected by prior exposure

• Not directed for specific agent (but does have different way for bacterial/viral response)

Pattern Recognition Receptors (PRRs)

• present on host cells

• bind to structures that are unique to microbes (we don’t make them)

Toll-like receptors (TLRs) bind and recognize

• Lipopolysaccharide (TLR4)

• Flagellin protein (TLR5)

• Double-stranded RNA (TLR3)

What happens when a PRR binds to a PAMP

• Cells that recognize PAMPS produce proteins (cytokines) to communicate infection to other cells

Pathogen-associated molecular patterns (PAMPs)

Structures associated with something foreign in our body

Interferon response

trying to interfere to stop this virus from further replicating

Adaptive Immune System

Only present in vertebrates, recognizes a very specific part of the pathogen (antigen)

Antigen

Specific part of pathogen

Anti-body

made by body to attach and attack antigen

lymphocytes

two types of white cells adaptive immune system relies on:

• Lymphocytes that mature in the thymus (gland) above the heart are called T cells

• T cells that mature in bone marrow are called B cells

Antigen receptors

bind to antigens of specific pathogen

Pathogen specific

• Each individual B or T cell is specialized to

  recognize a specific type of molecule

Epitopes

regions on the surface of antigens that have complementary shapes to antigen binding sites

How does the body produce cells

One is selected (the chosen one!)

• Starts to divide (clonal expansion)

• Creates an army of clones to fight the infection

• Plasma cells create and release antibody

• Memory cells persist in body and wait for pathogen to enter again.

primary immune response

• The first exposure to a specific antigen

• During this time, selected B and T cells give rise to their effector forms

secondary immune response

memory cells facilitate a faster, more efficient response

Prokaryotes

Single celled organisms that make up domains bacteria and Archaea

• Adapted to diverse and extreme evironments

Prokaryote Structure Types

Spheres (cocci), Rods (bacilli), and spirals

Prokaryote Cell Wall Functions

Maintains shape, protects the cell, and prevents bursting in a hypotonic environment

Peptidoglycan

A network of sugar polymers cross-linked by polypeptides (Most Bacterial cell walls have this)

Archaean Walls

Contain a variety of polysaccharides and proteins, but lack peptidoglycan

Gram Stain

Scientist use this method to classify bacteria by cell wall composition

Gram positive Bacteria

Bacteria have simpler walls with a large amount of peptidoglycan

Gram Negative Bacteria

Bacteria have less peptidoglycan and are more complex with an outer membrane that contains lipopolysaccharides

Capsule

A sticky layer of polysaccharide or protein surrounding the cell wall (Many prokaryotes have it)

Fimbriae

Some prokaryotes have hairlike appendages that allow them to stick to their substrate or other individuals in a colony

Pili

Longer than fimbriae and function to pull cells together enabling the exchange of DNA

Endospores

Some bacteria form metabolically this inactive layered structure when water or nutrients are lacking

Taxis

The ability to move toward or away from a stimulus

Nucleiod

the prokaryotic region with no membrane where the chromosome is located

Plasmids

Smaller rings of independently replicating DNA in some prokaryotes

Three factors contributing to high levels of genetic diversity observed in prokaryotes

1. Rapid

2. Mutation

3. Genetic Recombination

Binary Fission

When Prokaryotes divide every 1-3 hours under optimal conditions to replicate

How do mutations accumulate in Prokaryotes?

mutations accumulate with short generation times and large populations

Genetic Recombination

The combining of DNA from two sources, contributes to prokaryote diversity

DNA by different individuals can be combined by…

Transformation, transduction, or conjugation

Horizontal gene Transfer

The movement of genes between individual prokaryotes of different species

Transformation

Prokaryotic cells incorporate foreign DNA taken up from their surroundings (harsh conditions promote this)

Competence

A state of more permeable cell well in prokaryotes due to environmental conditions

Transductions

Phages (viruses) carry prokaryotic genes from one host cell to another

Conjugation

The process through which DNA is transferred between two prokaryotic cells

F Factor

A piece of DNA required for production of pili (F is for fertility)

Cells containing F plasmid function as…

DNA donors

Cells that have the F factor in their chromosome (Hfr cells named as high frequency of recombination) function as…

donors during conjugation

Recombines

Homologous segments of the chromosomal DNA from the Hfr cell recombines with that of F- cell

Metabolism

The totality of an organism’s chemical reactions

Emergent property

life arising from interactions between molecules within a cell

Metabolic pathways

begin with a specific molecule(substrate or reactant) and end with product

Catabolic Pathways

Release energy by breaking down complex molecules into simpler compounds

Cellular Respiration

Breaks down glucose in the presence of oxygen

Anabolic Pathways

Consume energy to build complex molecules from simpler ones

Energy and carbon sources are combined to give four majors modes of metabolism in prokaryotes:

• Anabolic Pathways

  Photoautotroph

  Chemoautotroph

• Catabolic Pathways

  Photoheterotroph

  Chemoheterotroph

Chemosynthesis

Use inorganic energy sources to synthesize larger molecules

Chemoautotrophs

• Feed on chemicals that are good electron donors (hydrogen sulfide, sulfur, or iron)

• Most are Extremophiles that live in hostile environments

Photoautotrophs

Feed with oxygenic photosynthesis or anoxygenic photosynthesis to trap light energy and convert it to chemical energy

Chemoheterotrophs

Obtain and Feed on carbons from other living things through using Cellular respiration to break down bonds in complex molecules to harvest energy

The role of oxygen in Prokaryote metabolism

Prokaryotic metabolism varies with respect to O2

Obligate aerobes

Require O2 for cellular respiration