Germs 101 Exam 1

Microbes

Anything too small to be seen without a microscope

Components of the Scientific Process

1. Scientific Method

2. Peer Review & Replication

3. Professional Consensus

Components of the Scientific Method

1. Observations

2. Hypothesis

3. Predictions

4. Data Collection

5. Interpretation

Observations

Describes

Hypothesis

Explains an observation

Predictions

Describes results if hypothesis is true

Data Collection

Either a study or experiment

Interpretation

Hypothesis supported or refuted

Study

Observations of something

Experiment

Manipulations to see effects

Peer Review & Replication

Experts decide if a paper is good enough to publish

Preprint

paper not yet peer-reviewed and published

Professional Census

What the experts on a topic collectively agree is most likely true/correct

Six Characteristics that define Life

1. Reproduction & Heredity

2. Individual Growth

3. Metabolic activity

4. Response to light & chemical stimuli

5. Cellular structure

6. Cellular transport/nutrients

Reproduction & Heredity

Life produces more life and passes on traits

Individual Growth

Organisms grow

Metabolic Activity

Some form of energy consumption and excrete waste products

Response to light and chemical stimuli

Organisms have ways to react to light and environmental chemicals

Ways to Organize Life

1. Taxonomy

2. Binomial Nomenclature

3. Genus

Taxonomy

The formal study of organizing life according to some notion of similarity or "relatedness"

7 Nested categories of Taxonomy

1. Kingdoms (largest, ex. animal kingdom)
   2. Phylum (ex. Vertebrates)
   3. Class (ex. Mammals)
   4. Order (ex. Primates)
   5. Family (ex. Hominidae (great apes))
   6. Genus (ex. Homo, in Homo sapiens)
   7. Species (smallest, ex. Sapiens, in Homo sapiens)

Binomial Nomenclature

• A universal system of naming species that reflects their taxonomic organization

• Genus is always capitalized, species in not

• Genus can be abbreviated to 1 letter; species is never abbreviated

• Genus & species are always italicized or underlined

Robert Hooke

• Helped invent the compound light microscope

• Published the first "micrographia", or microscopic pictures in 1665

• In a sample of cork, he took note of a strange, room-like compartments, he named them cells

Compound Light Microscope

• Passes light through a specimen and 2 lenses

• Magnification often 10X -> 400X, 1,000X -> 2,000X with special treatments

• Resolution - 0.2 micrometers

Anthony van Leeuwehoek

In 1674 he discovered single-celled eukaryotes; in 1676, the first bacteria

Traits shared amongst all cells

1. Organic Molecules

2. Cell membrane

3. DNA

Organic Molecules found in all cells

1. Lipids/fats

2. Carbohydrates/sugars

3. Nucleic Acid

Lipids

Fats, energy and membranes

Carbohydrates

Sugars, energy and structure

Nucleic Acid

Stored Information (these make up DNA)

Cell Membrane

Protects cell from environment, Contains liquid cytoplasm, Site of metabolic reactions, Regulates transport

DNA

Stores genetic information

Traits that differ between cells

Eukaryotes vs. Prokaryotes (Bacterium Cell)

Eukaryotes

DNA stored in Nucleus, Often larger in size, have many organelles

Prokaryotes (Bacterium Cell)

DNA lose in cytoplasm, Often much smaller, no organelles

Archaea

Discovered in 1977, Subset of Prokaryotes, Extremophiles

Extremophiles

Cells that live in extreme environments (very hot, cold, salty, pressure, very acidic/basic environments)

Cell Theory

Proposed by Theodor Schwann and Matthias Jakob Schleiden in 1838:

1. All living things are made of cells
2. All cells come from other cells
3. Cells are the fundamental unit of life

Dmitry I. Ivanovsky and Martinus W. Beijerinck

Discovered viruses while studying tobacco plants in the 1890's

Tobacco Mosaic Disease

Discovered by Dmitry I. Ivanovsky and Martinus W. Beijerinck, revealed in 1935 with electron microscope

Electron Microscope

Invented in 1931, uses electron beams to image a target, Magnification ranges from 1,000,000X -> 50,000,000X

Distinct features of Bacteria

1. Membrane Structures (Cell Wall or Capsule/Slime layer)

2. Surfaces/Structures (Pilus/Pilli or Flagellum/Flagella)

Cell Wall

Covers the cell membrane, rigid and provide structural support

Capsule/Slime Layer

Covers the Cell Wall, gel-like and usually made of sugars. Helps bacteria adhere to surfaces and can protect them from desiccation or predators

Pilus/Pilli

Protein tubes extending out from bacteria

Long Pilus

Used for conjugation

Short Pilli (fimbriae)

Cover the capsule of many bacteria, crucial for bacteria to adhere to surfaces

Conjugation

Exchanging DNA between cells via the Long Pilus

Flagellum/Flagella

Long protein tube that rotates for mobility, Not found in all bacteria, greatly improves mobility of a bacterium

Chemotaxis

Flagella drives cell toward or away from a chemical stimulus

Phototaxis

Flagella drives cell toward or away from light

Binary Fission

The basis of bacterial population growth, how bacteria divide

Colony

A visible cluster of bacteria derived from 1 cell, take on different appearances based on species

Culture

Growing colonies of bacteria in a petri dish

Ways to Categorize Bacteria

1. Genetics

2. Size

3. Shape

4. Metabolism

5. Cell wall components

Genetics

Pros:

• As with taxonomy in animals, increasingly preferred method

• Only requires a small number of cells; often quicker and easier than observing or growing bacteria in the lab

• Can accurately ID specific species if genetics are known
  Cons:

• Sequencing machines may not be available

• A LOT of species genetics remain unknown or unclear

• Many other ID techniques are already well established

Size

Pros:

• Can readily identify species of unusual size

  Cons:

• Most bacteria are just "very small" Miniscule differences in size is not a very convenient tool for organizing bacteria

Shape

Pros:

• Easy to identify three major groups

• Shape correlates with evolutionary history; knowing bacteria of similar shape is informative

• Key diagnostic tool in medical applications
  Cons:

• For colony shape, must grow bacteria in a lab

• Only a starting point; won't ID specific species

Coccus

Round, circular form. Often form clusters that can help ID

Bacillus

Rod-like form, can form endospores, reproduction can form chains that can help ID

Curved

3 Subgroups:

1. Spirilla/Spirillum

2. Spirochetes

3. Vibrio

Spirillum/Spirilla

• Rigid corkscrew shape

• Whip-like flagella at cell ends

Spirochete

• Flexible spiral shape

• Flagella embedded in capsule

Vibrio

• Comma shape

• 1-3 flagella at one end

Metabolism

Pros:

• Can provide major clues to bacteria's preferred lifecycle & environment

• Useful diagnostic tool in medical applications

  Cons:

• Must be a bacteria that can be grown in a lab to test

• Many bacteria fall in each category (and subcategories)

Aerobic Respiration

Cell uses oxygen to produce energy

Anerobic Respiration

Cell produces energy through non-oxygen methods

Metabolic Types

1. Obligate Aerobe

2. Facultative Anaerobe

3. Obligate Anaerobe

Obligate Aerobe

The cell can only produce energy when it has oxygen

Facultative Anaerobe

The cell prefers oxygen, but can produce energy using anaerobic respiration

Obligate Anaerobe

The cell can only produce energy when there is no oxygen

Cell Wall Components

Pros:

• Gram staining can quickly differentiate between 2 major groups of bacteria

• Easy and useful starting point for ID & classification

  Cons:

• Need bacteria in the lab to test

• It is only a starting point; cannot ID specific species

Gram Staining

Used to determine Cell Wall Components, Bacteria put through specific chemical stains will change color based on their cell wall

Gram Positive

Shows Purple: Simple cell wall

Gram Negative

Shows Pink: Complex, multi-layered cell wall with 2nd outer membrane

Bacterial Adaptations

1. Biofilm

2. Plasmids

3. Endospores

Biofilm

• Group of microbes that adhere to each other and a surface

• Produced by cell secretions, made mostly of sugars

• Bacteria in this can communicate with each other, act as a population

• Additional microbes are attracted to developing film and create a mature community with complex function

Plasmids

• Additional circles of DNA in a bacterium (NOT part of the nucleoid DNA)

• Can give bacteria valuable traits (drug resistance, enzyme or toxin production)

• Bacteria share these via conjugation, including across species

Endospores

• Only made by some genera of bacteria (eg. Bacillus, Clostridium)

• Inactive structure that stores bacterium's DNA (Like a vault)

• Very Tough; resists high temperatures, UV irradiation, desiccation, chemical damage

• Emergency survival strategy when environment is bad

• When environment improves, it can use its DNA to remake an active bacterial cell

• Made using a septum

• Cell dies once endospore is complete

• An alternative lifecycle pathway

Viral Structure

1. Nucleic Acid

2. Capsid

3. Envelope

4. Spike protein

Nucleic Acid (Viruses)

Contained in the capsid, either DNA or RNA

Capsid

Proteins that protect the nucleic acid, can be Helical or Icosahedral

Helical Capsule

Proteins tightly spiral around nucleic acid, forms tube-like capsid

Icosahedral

Proteins form 20-sided capsid

Envelope

Either a naked virus or envelope

Naked Virus

Has nucleic acid and capsid proteins

Enveloped Virus

Has nucleic acid, capsid proteins, and envelope proteins that surround the capsid

Spike Proteins

Help virus bind to other cells and infect the host

Viral ID in practice

Often via: Patient symptoms or Cellular damage from lytic cycle

Obligate Intracellular Parasites

What viruses are, MUST parasitize a host cell to reproduce

Parasitism

A relationship between two things where the host is harmed and the parasite benefits

Central Dogma of Biology

All cells use DNA (genes) to make RNA, and RNA to make protein, what the virus is after because they do not have the capability themselves

Transcription + Translation

The process of converting DNA to RNA, and RNA to proteins

Lytic Cycle

Steps of a viral Infection:

1. Binding

2. Penetration & Uncoating

3. Synthesis & Assembly

4. Release

Binding

Virus spike proteins attach to cell by recognizing host-specific cell membrane receptors

Penetration & Assembly

Enters cell & dissolves capsid

Synthesis & Assembly

Molecules for transcription and translation hijacked to make viral nucleic acids and proteins

Release

• Virus without envelope ruptures (lyse) cell, killing it

• Viruses with envelopes can bud off cell membrane

Viral Lysogenic Cycle

Used when the host environment of a cell is bad for a virus, viral DNA integrates into the Hosts' DNA until environment improves when the lytic cycle starts

Fungi Structure (Multicellular)

1. Hyphae

2. Mycelium

3. Mold

4. Spores (reproduction)