Potts-Santone Gen Bio 2 Exam 2

Previous Classification System

- Until mid-1800s, biologists recognized only 2 kingdoms:

1) Plantae (plants)

2) Animalia (animals)

- Protista (protists) added as 3rd kingdom in 1880s

- Whittaker expanded to 5 kingdoms in 1969 by adding Fungi and Monera

3 Domain System of Classification

1) Bacteria

2) Archaea

3) Eukarya

Bacteria and Archaea Domains

-Bacteria and Archaea are so different they have separate domains

-- Distinguishable by:

--- Differences in rRNA base sequences

--- Plasma membrane history

--- Cell wall chemistry

Eukarya

- Unicellular and multicellular organisms

- Cells with a membrane-bound nucleus

- Sexual reproduction is common

- Contains kingdoms

Virology

- The study of viruses

Viruses

- Over 4,000 different types (3,000 of which are for mammals alone)

- Noncellular

- No binomial nomenclature

- Extremely small:

2 Parts of Viruses

- Capsid

- Nucleic Acid core

Capsid

- Outer layer composed of protein subunits

- Some enveloped by membrane and others are "naked"

- Generally symmetrical

Nucleic Acid Core

- DNA or RNA (around 3-100 genes)

- Single or double stranded linear or circular

- Positive or negative

- RNA transcriptase present with RNA

4 Categories of Viruses

- Icosahedral

- Complex

- Helical

- Spherical

Icosahedral Virus

Complex Virus

Helical Virus

Spherical Virus

Classification of Viruses

- Based on:

1) Type of DNA/RNA

2) Size and shape

3) Presence or absence of outer envelope

- International Committee on Taxonomy of Viruses: uses the ICTV and Baltimore System

International Committee on Taxonomy of Viruses (ICTV) and Baltimore System

- Group I: double stranded DNA

- Group II: single stranded DNA

- Group III: double stranded RNA

- Group IV: positive single stranded RNA

- Group V: negative single stranded RNA

- Group VI: single stranded RNA with reverse transcription

- Group VII: double stranded RNA with reverse transcription

Bacteriophages

- Portions of capsid adhere to specific receptor on host cell

- Not easily recognized by host immune system

-- Animal viruses coat themselves with the host's body proteins

- Viral nucleic acid enters cell

- Once inside, the virus takes over metabolic machinery of host cell

Lytic Cycle

1) Attachment

2) Penetration

3) Viral components synthesized

4) Assembly of viral components

5) Cell ruptures and viruses leave host cell

Lysogenic Cycle

- Used by temperatephage

1) Attachment

2) Penetration

3) Integration: viral DNA integrated into bacterial DNA and then is passed on when bacteria reproduce

4) Activation of virus occurs later

5) Lytic Cycle occurs after activation

Ex: chicken pox --> shingles

Viral Infections

- Best known for causing infectious diseases in plants and animals

- Most common entry: respiratory tract and open wounds

Herpes, HIV, Cancer type Viral Infections

- Viruses lack metabolism

- Antibiotics have no effect

- Controlled by preventing transmission (vaccines and antiviral)

Viroids

- Naked strands of RNA

- Many crop diseases come from this

Prions

- Protein molecules with contagious tertiary structure

- Some human and other animal diseases: TSE's (transmissible spongiform encephalopathism) , scrapie, kufu, and mad cow disease

Emerging Diseases

- One that has appeared in a population for the 1st time or one that may have existed previously but is rapidly increasing in incidence or geographic species

- Highly mutative

Human Immunodeficiency Virus (HIV) and Acquired Immune Deficiency Syndrome (AIDS)

- Primarily spread through sexual contact

- Also spread by:

-- Transfusion of infected blood

-- Sharing infected needles in drug use

-- From infected mother to child

- Affects helper T-cells and compromises the immune system

- Treated with AZT

- Around 36.7 million infected (1/100 adults)

- 2.2 new people infected per year

- 65% of new infections occur in Sub-Sharan Africa

- Around 1.1 million people died in 2015

Influenza Virus ("The Flu")

- Viral respiratory disease

- Symptoms included fevers, head ache, cough, muscle pain, and runny nose

- 4 types: A, B, C, and D

-- Humans only affected by A and B

- Characterized by surface antigens

- Increases change of heart attack by 6x

- Widespread in the continental US

Surface Antigens of Influenza Virus

- H=hemagglutinin

- N=neuraminidase

The Influenza Virus in 2018

- 80% are H3N2

- More health complications and is more difficult to prevent

- Mutates faster then other types

- Hard to prevent with vaccination

- Difficult to grow in eggs (which makes the vaccine less effective)

- More seniors hospitalized

- 37+ children have died

Zika Virus

- Lots of cases in Central and South America

- Spread by daytime biting mosquitoes

- 80% of infected show no symptoms (asymptomatic)

- Increase in south Florida, south Texas, and Puerto Rico

- Causes microcephaly (a birth defect) in pregnant women

Antony vanLeeuwen Hook

- Danish civil servant around 350 years ago

- Maker of the most powerful microscopes at the time

- 1st person to see microbes/bacteria

- Found microbes in the body

Microbes

- Often have a negative connotation

- Can lead to diseases (although only a small number of species do this)

- Most are benign

- Runs the world

- Influence animal evolution

- Accelerate animal evolution

- Stimulates immune system

- Not inherently good or bad

Microbiomes

- Environment of a microbe

- Shapes the way organisms think

- Can change positively or negatively

- Can be changed in deliberate ways

Why the Human Microbiology is Changing

- Movement of populations

- War on Microbes

- Antibiotics

- Diet includes less plant foods and less fiber

Fecal Transplant

- Transplantation of healthy stool into an unhealthy person

- Good for treating CDif (94% success rate)

Stratification of Medicine

- Look at the microbes found in a person and prescribe based on that

- Use medicine to influence microbes

- Target human and microbe parts

Wolbachia

- Found by Simeon Burt Wolbach and Marshall Hurtig

- Found in 40% of insects and arthropods

- Sometimes a parasite and sometimes an ally

- Causes mosquitoes to not be able to spread viruses

- Good at spreading through mosquito populations

- Cheap, nontoxic, and self-sustaining way to prevent the spread of mosquito born illnesses

Bacteria and Archaea

- Fully functioning prokaryotic cells

- More numerous than all other organisms

- Range in size from 1-10 micrometers in length and .7-1.5 micrometers in width

- Fossils from 3.5 bya

- Have been alone on Earth for 2 by

- Very diverse

Horizontal Gene Transfer

- Movement of genes from one species to another

- Increases diversity

- Can result in large genetic changes

- 80% of prokaryotic genes do this

- Important to bacteria and archaea in regards to evolution and diversity

Structure of Prokaryotic Cells

- Slimy mucilage

- Sex pilus

- Fimbriae

- Flagellum

Slimy Mucilage

- Found in Prokaryotic Cells

- Biofilm

- Quorom Sensing

Quorom Sensing

- When bacteria communicate collectively

Sex Pilus

- Elongated, hollow appendage used for DNA transfer

- Used by Prokaryotic Cells for horizontal gene transfer

Fimbriae

- Hairlike bristles that allow adhesion to surfaces

Flagellum

- Rotating filament present in some bacteria that pushes cell forward

Prokaryotic Cytoplasm

- Inclusion body

- Mesosome

- Ribosome

- Nucleoid

Inclusion Body

- Stored nutrients for later use

Mesosome

- Plasma membrane that folds into the cytoplasm and increases the surface area

Ribosome

- Site of protein synthesis

Nucleoid

- Location of bacterial chromosome

Plasma Membrane

- Sheath around cytoplasm that regulates entrance and exit of molecules

Cell Wall

- Covering that supports, shapes, and protects cell

Glycocalyx

- Gel-like coating outside cell wall

- If compact: capsule

- If diffuse: slime layer

Archaeal Bonds

- Ether bonds holding isoprene chains

Bacterial Bonds

- Ester bonds holding phospholipid chains

Cell Envelope

- Can be either gram positive or gram negative

Asexual Prokaryotic Reproduction

- Reproduce by binary fission

- Methods

1) Conjugation

2) Transformation

3) Transduction

Conjugation

- Sex pilus forms between 2 cells

- Donor cell passes DNA to recipient cell through pilus

Transformation

- Occurs when bacterium picks up free pieces of DNA from other prokaryotes

- Becomes incorporated into genome

Transduction

- Occurs when bacteriophages carry portions of bacterial DNA from 1 cell to another through vectors

Endospores

- Response to unfavorable conditions

- Dormant stage of bacteria

- Resistant to heat, radiation, disinfectants, and desiccation

- Difficult to eliminate from medical and pharmaceutical material

- Frequent cause of contamination

- Some bacteria form these

- Ex: anthrax, tetanus, botulism, and botox

Obligate Aerobes

- Unable to grow in absence of free oxygen

Facultative Aerobes

- Able to grow in the presence or absence of free oxygen

Obligate Anaerobes

- Unable to grow in presence of free oxygen

- Aerotolerant Anaerobes

- Don't use oxygen, but not bothered by the presence of oxygen

Photoautotrophs

- Type of autotrophic prokaryotes

- Some do not produce oxygen (green/purple bacteria)

- Others use solar energy to reduce carbon dioxide to organic compounds

- Photosynthetic

Chemoautotrophs

- Oxidize inorganic compounds to obtain necessary energy

- Use to reduce carbon dioxide to organic compounds

- Chemosynthetic

Heterotrophic Bacteria

- Most are chemoheterotrophs that take in organic nutrients

Chemoheterotrophs

- Aerobic saprotrophs decompose most large, organic molecules to smaller molecules (detritivores)

- Essential components of healthy ecosystem

Free-Living or Symbiotic Heterotrophic Bacteria

- Nitrogen fixation

- Commensalism

- Parasites

Commercial Uses for Bacteria

- Chemicals

- Antibiotics

- Cotton

- Silk

Gram Positive Bacteria

- Many pathogenic

- Vulnerable to antibiotics that interfere with peptidoglycan synthesis

- Stain purple

Gram Negative Bacteria

- Thinner cell wall

- Stains pink

Coccus Bacteria (Round)

Bacillus Bacteria (Rod)

Spirillus Bacteria (Rigid Spirals)

Vibrio Bacteria (Comma)

Spirochete Bacteria (Flexible Spirals)

Salmonella Outbreaks

- One of the most common occurring outbreaks

- Transmitted by fecal/oral route

- Causes typhoid fever

- A rod-shaped enterobacteria

Koch's Postulates

- Test for whether a particular microorganism causes a particular disease

1) Microorganism must be in abundance in sufferers of disease, not in healthy individuals

2) Microorganism must be isolated from diseased organism and grown in pure culture

3) Cultured microorganism should cause disease in a healthy organism

4) Microorganism must be isolated from inoculated disease experimental host and identified as being identical to the original specific causative agent

Pathogenic Bacteria

- Evolving resistance faster than new drugs can develop

- Can be:

-- Sexually transmitted

-- Systemic

-- Respiratory

-- Skin

-- Digestive tract

-- Nervous System

Archaea

- Were considered bacteria before reclassification

- Membrane lipids give resilliance

- Most are chemoautorophs

- Some are mutualistic or commensalistic

- Not parasitic, photosynthetic, or pathogenic

- More like Eukarya biochemically and now thought to be more related

- Extremophiles

- Sometimes found in deep sea vents and floating in the open ocean

Differences between Bacteria and Archaea

- Base sequence of their rRNA differs

- Bacteria have peptidoglycan in their cell walls; archaea have polysaccharides and proteins

How Archaea are Similar to Eukarya

- Both possess:

-- Histone proteins

-- Ribosomal proteins

-- RNA polymerase

Methanogens

- Type of archaea

- Not extremophile

- Produce methane

- Found in anaerobic marshes and in ruminant gut

Halophiles

- Type of archaea

- Found in salty lakes (like the Great Salt Lake)

- Need high salt concentration for growth

Thermo/acidophiles

- Found in hot sulfur springs

- Reduces sulfides and survive best at above 80ºC

Protists

- Part of the Eukarya

- 12 different kingdoms within this catch-all group

- Paraphyletic: very diverse

- Fill evolutionary gaps

- Most unicellular and microscopic (some as large as algae)

- Contain specialized organelles

- All life activities carried on within the limits of one membrane

- Many have amazingly high level of structural and functional complexity

- Enormous ecological importance

- Difficult to classify

- No vaccinations available

Life Cycles of Protists

- Asexual reproduction common

- Sexual reproduction occurs in dire circumstances

- Simple and complex life cycles

Photoautotrophic Forms of Protists

- Produce 20% of Earth's oxygen

-- 1º producers in freshwater and saltwater ecosystems

- Major component of plankton- suspended in water

-- Serve as food for heterotrophic protists and animals

- Found in every food web

Symbiont Protists

- Range from parasitism to mutualism

- Ex: zooxanthellae on coral reefs

- Some with great medical importance: pathogenic and parasitic

Plant-like Protists

- Multicellular algae not plants

- Do not protect gametes/zygote from dessication

Fungi-like Protists

- Lack flagella

- No chitin in cell wall

Animal-like Protists

- AKA Protozoa

- Heterotrophs

- Embryonic development

Eukaryotic Supergroups

- Dicoba

- Land plants and relatives

- Stramenophila

- Alveolata

- Amoebozoa

- Rhizaria

- Opithokanta

Dicoba

- 3 types

1) Metamonda

2) Euglenozoa

3) Kinetoplastids

Euglenids (Euglenozoa)

- Part of the Dicoba

- small freshwater unicellular organisms

- Difficult to classify

- Have 2 flagellae and an eyespot (stigma)

-- 1 flagellum is longer than the other

--- Tinsel flagellum project out of an anterior, vase-shaped invagination

- Bound by flexible pellicle

- Possess chloroplasts

Tinsel Flagellum

- Type of flagellum found in euglenids

- Project out of an anterior vase-shaped invagination

- Possess hair-like projections

Euglenid Chloroplast

- 3 membranes instead of 2

- Pyrenoids produce the carbohydrate paramylon

Kinetoplastids

- Colorless heterotrophs

- Most are symbiotic and parasitic

- Cause various diseases in animals

- Possess one mitochondria

- Have 6 different stages in life cycle

- Ex: trypanosomes and leishmania spp.

Metamonda

- Colorless heterotrophs

- Most are symbiotic and parasitic

- Cause various diseases in animals

- Ex: giardia lamblia and trichomonas vaginalis