Microbiology Lecture Exam 1

Microorganism

microbe: any organism you need a microscope to see

• diverse in form/function

• inhabit every environment that supports life

• many single-celled, some form complex structures, some multicellular

• live in microbial communities

What are the kinds of Microorganisms? Name an example of each

Virus: Norovirus, Hepatitis C Virus, Retrovirus

Bacteria: E.coli, Salmonella, Cyanobacteria, Staphylococcus

Fungi: Penicillium, Aspergillus, Stachybotrys, Trichosporon

Protists: Amoeba, Algae, Dinoflagellate, Ciliate

Three fold relationship : Delicate balance

Why do different factors determine the likely hood of illness.

Ex: In regards to age the thymus is smaller in the infants and elderly which could affect T cells because that’s where they mature etc.

How do microobes effect day to day life?

They are everywhere like yeast and food to diseases or in your gut

What’s an Example of Microbiology in the news?

-Food poisoning

-Measles out break

-Vaccines

-Antibiotics

What are examples of Microbial Applications?

-Animal/Human Health

-Ecosystem Health

-Agriculture

-Food

-Industry

How do we study microorganisms?

• microscopy

• culture: cells grown in/on nutrient medium

• medium: liquid/solid mixture containing all required nutrients

• growth to form a visible colony

• Genomic studies

What are some Similarities and differences in Prokaryotes and Eukaryotes?

genome

a cell's full complement of genes

eukaryotic DNA

• linear chromosomes within nucleus

• much larger/more DNA (up to billions of base pairs)

prokaryotic DNA

• generally single circular chromosome that aggregates to form the nucleoid region

• may also have plasmids (extrachromosomal DNA) that confer special properties (e.g., antibiotic resistance)

• small, compact (0.5–10 million base pairs)

Transcription, Translation, DNA Relication

•transcription: DNA information converted to RNA

• translation: RNA used by ribosome protein

• DNA replication: copying genome

What are properties all cells have?

What are properties some cells have?

Differentiation

Some microbes modify structures to form specialized cells

Intercellular communication:

Some microbes respond to chemical signals from other microbes.

advantages to being small

• more surface area relative to cell volume than large cells (i.e., higher S/V ratio)

• support greater nutrient and waste product exchange per unit cell volume • More efficient than larger cells

Major morphologies of prokaryotic cells

• coccus (p l. cocci): spherical or ovoid

• rod/bacillus (p l. bacilli): cylindrical

• spirillum: flexible spiral

• spirochete: rigid spiral

History of Life on Earth

• Earth is 4.6 billion years old.

• First cells appeared between 3.8 and 4.3 billion years ago.

• The atmosphere was anoxic (no O2 ) until ~2.6 billion years ago.

• only anaerobic metabolisms

Extremophiles

live in habitats too harsh for other life forms.

• examples: hot springs, glaciers, high salt, high acidity/alkalinity, high pressure

Ecosystem

refers to all living organisms plus physical and chemical constituents of their environment.

• Metabolic activities can change habitats and affect other organisms.

Microbial ecology

is the study of microbes in their natural environment.

• in humans, 1–10 microbial cells per human cell

Most microorganisms beneficial

• vaccination and antibiotic therapy

• water and wastewater treatment

• food safety (e.g., pasteurization)

Microorganisms and food

negative impacts • can cause food spoilage and foodborne disease • harvest, storage, safety, prevention of spoilage influenced by microbes

positive impacts • improving food safety, preservation • dairy products (e.g., cheeses, yogurt, buttermilk) • other food products (e.g., sauerkraut, kimchi, pickles, chocolate, coffee, leavened breads, beer)

Microorganisms and industry

• biofilms: growth on submerged surfaces (e.g., pipes, storage tanks, implanted medical devices)

• industrial microbiology: massive growth of naturally-occurring microbes to make low-cost products (e.g., antibiotics, enzymes, some chemicals)

• biotechnology: genetically engineered microbes making high-value products in small amounts

• production of biofuels

• examples: methane, ethanol

• wastewater treatment

• bioremediation: cleaning up pollutants

Robert Hooke (1635–1703)

first to describe microbes

Antoni van Leeuwenhoek

first to describe bacteria (used set of lenses)

Described as father of micrbio

magnification

the ability to make an object larger

resolution

the ability to distinguish two adjacent objects as distinct and separate

Louis Pasteur

chemist and microscopist

-Proved vaccinee effective with sheep and anthrax

-Developed vaccines for anthrax, fowl cholera, and rabies

-Pasteurization which led to less GI issues in kids and lower infant death numbers

-Swan neck flask

-Disproved spontaneous generation

(Using the swan-necked Pasteur flask, he disproved theory of spontaneous generation)

What is the theory of spontaneous generation and who disproved it?

Spontaneous generation was the historical belief that living organisms could arise directly from non-living matter. Louis Pasteur disproved it using a swan neck flask that didn’t allow anything into the broth.

Staining

Staining improves contrast

basic dyes: positively charged, bind strongly to negatively-charged cell components (e.g., nucleic acids, acidic polysaccharides, cell surfaces)

Differential stains

Different kinds of cells are different colors.

• Gram-positive bacteria appear purple-violet

• Gram-negative bacteria appear pink

Gram-positive bacteria have a thick peptidoglycan cell wall, retain the crystal violet stain, and appear purple. In contrast, gram-negative bacteria have a thin peptidoglycan layer and an outer membrane, lose the crystal violet stain, and appear pink

Robert Koch (1843–1910)

experimentally demonstrated the link between microbes and infectious diseases (germ theory of infectious disease)

• identified causative agents of anthrax, tuberculosis, and cholera

• Koch's postulates

Koch’s Postulate

1. The microorganism must be found in all cases of the disease, but not in healthy individuals. 

2. The microorganism must be isolated from the diseased host and grown in pure culture. 

3. The cultured microorganism must cause the original disease when inoculated into a healthy, susceptible host. 

4. The same microorganism must be re-isolated from the newly infected host. 

Sergei Winogradsky

proposed concept of chemolithotrophy

• oxidation of inorganic compounds to yield energy

Frederick Griffith

-Streptococcus pneumoniae

-Transformation:the process where a bacterial cell takes up external DNA from its environment and integrates it into its own genetic material, either the chromosome or a plasmid.

James Watson, Francis Crick, Rosalind Franklin:

structure of DNA

Ribosomal RNA (rRNA) made what possible?

present in all cells made it possible to build the first tree of life.

Carl Woese

Carl Woese (1928-2012) realized rRNA sequences could be used to infer evolutionary relationships

Phylogenetic tree

-clearly shows three domains

evolution along two paths to form Bacteria and Archaea

• Archaea later diverged to distinguish Eukarya from Archaea.

Metagenomics

microbial genomes/fragments can be recovered from environmental DNA samples

End of Ch.1 if you’re going in order

End of Ch.1 if you’re going in order

The cyctoplasmic membrane function and components (general)

Main function: selective permeability

Contain

▪ hydrophobic = fatty acids “tails”

▪ hydrophilic = glycerol + phosphate and another functional group (e.g., sugars, ethanolamine, choline)

– Fatty acids associate inward to form hydrophobic environment; hydrophilic “head groups” remain exposed to external environment or the cytoplasm.

embedded proteins: integral membrane proteins

– transmembrane proteins: extend completely across membrane

– peripheral membrane proteins: loosely attached

In detail Cytoplasmic membrane function

– permeability barrier

▪ Polar and charged molecules must be transported. ▪ Transport proteins accumulate solutes against the concentration gradient.

– protein anchor: Holds proteins in place.

– energy conservation and consumption

▪ Generation of proton motive force→ (ATP production ,ATP synthase)

Archaeal cytoplasmic membranes

– Ether linkages in phospholipids of Archaea in contrast to Bacteria and Eukarya that have ester linkages in phospholipids

– Archaeal lipids have isoprenes instead of fatty acids.

Transporting Nutrients into the Cell

-Active transport – how cells accumulate solutes against concentration gradient

– energy-driven (proton motive force, ATP, or another energy-rich compound)

-Simple transport – driven by proton motive force

What does the cell wall do proactive and and actively ?

Need to withstand osmotic/turgor pressure to prevent cell lysis

• Maintains cell shape and rigidity

How are most bacteria separated into two groups?

Most Bacteria separated into two groups based on Gram stain (organization and cell wall structures)

Gram Positive vs Gram negative

• Gram-positives and gram-negatives have different cell wall structures.

– gram-positive cell envelope

▪ Cytoplasmic membrane + thick cell wall

*commonly have teichoic acids (acidic molecules) embedded in cell wall and covalently linked to peptidoglycan

– gram-negative cell envelope

▪ Cytoplasmic membrane, thin cell wall, outer membrane, periplasm (between cytoplasmic and outer membranes)

**Penicillin blocks formation of peptide cross-links

Peptidoglycan:

-It’s rigid polysaccharide layer that provides strength

– Found in all Bacteria with a cell wall

– Not found in Archaea or Eukarya

– Peptidoglycan can be destroyed by lysozyme (cleaves glycosidic bond between sugars)

>▪found in human secretions (tears/saliva), major defense against bacterial infection

Archaeal Cell Walls

– Cytoplasmic membrane structure differs from Bacteria

– Lack peptidoglycan

– Typically lack outer membrane

– Most lack polysaccharide wall, instead have S-layer (protein shell)

-– In methanogens, pseudomurein cell wall

Most of gram-negative cell envelope composed of what?

Outer membrane

»– Outer membrane contains polysaccharides covalently bound to lipids: lipopolysaccharide layer (LPS)

- endotoxin: lipid A, the toxic component of LPS

(Be able to identify LPS, Outer membrane, Cytoplasmic membrane, and Peptidoglycan on a photo)

Alternative Configurations of the Cell Envelope

– Some Bacteria and Archaea lack cell walls, have tough cytoplasmic membranes (e.g., sterols)

▪ Mycoplasmas (Bacteria)

Capsules and slime layers

• Capsules and Slime Layers – sticky polysaccharide coat outside cell envelope

– capsule: if tightly attached, tight matrix; visible if treated with India ink

– slime layer: loosely attached, easily deformed

– functions :

▪ assist in attachment to surfaces

▪ role in development and maintenance of biofilms

▪ contribute to infectivity

▪ prevent dehydration/desiccation

Fimbriae, Pili

Pili: thin filamentous protein structures

Fimbriae: short pili

>Enable organisms to stick to surfaces or form pellicles (thin sheets of cells on a liquid surface) or biofilms

-Conjugative/sex pili facilitate genetic exchange between cells (conjugation)

Cell Inclusions

Inclusions function as energy reserves, carbon or phosphorus reservoirs, and/or have special functions

– glycogen: glucose polymer

Gas Vesicles – Confer buoyancy

Endospores

-Survival structures to endure unfavorable growth conditions

-• Present only in some gram-positive bacteria, (e.g., Bacillus and Clostridium

• Endospore Formation and Germination

– can remain dormant for years but converts rapidly back to vegetative

Ex: C.diff Gram(+),rod shaped, anaerobic bacteria→ release toxins

Flagella/archaella

structure that assists in swimming in Bacteria and Archaea, respectively

– different arrangements: polar, tufts lophotrichous, amphitrichous, peritrichous

Taxis

Taxis: directed movement in response to chemical or physical stimuli

– chemotaxis: response to chemicals

> monitor/sample environment with chemoreceptors that sense attractants and repellents

– phototaxis: response to light

Bacteria and Archaea

Eukaryotes-The nucleus

– Contain a double membrane-enclosed nucleus.

– Other organelles include mitochondria, Golgi complex, lysosomes, endoplasmic reticula, microtubules, and microfilaments. . – Chloroplasts in phototrophs.

– Some have motility (flagella or cilia).

– Some have cell walls.

– DNA is wound around histones forming nucleosomes which are then organized into chromosomes

▪ Archaea also contain histones and nucleosomes;

>Within the nucleus is the nucleolus .

▪ site of ribosomal RNA synthesis

Cell Division (eukaryotes)

– mitosis

▪ results in two diploid (two copies of each chromosome) daughter cells

– meiosis

▪ specialized form of nuclear division

▪ converts diploid into haploid cells

▪ results in four haploid (one copy of each chromosome) gametes

Mitochondria (eukaryotes)

respiration and oxidative phosphorylation for aerobic eukaryotes

ATP

Chloroplasts (eukaryotic)

– chlorophyll-containing organelle found in phototrophic eukaryotes

– site of photosynthesis

Endosymbiotic hypothesis

-Endosymbiotic hypothesis: Mitochondria and chloroplasts descended from respiratory and phototrophic bacterial cells, respectively, associating with nonphototrophic eukaryal hosts.

– Evidence: Mitochondria and chloroplasts contain circular DNA genomes and ribosomes similar to those of Bacteria

. – Eukarya hypothesized to have originated from symbiotic fusion of archaeal host and mitochondrial endosymbiont

– Later, eukaryotic host cell acquired a chloroplast endosymbiont to become ancestor of phototrophic eukaryotes.

microtubules (eukaryotic)

▪ maintain cell shape, facilitate motility; move chromosomes and organelles

Eukaryotic Cell Structures

Endoplasmic Reticulum:

– Rough contains attached ribosomes; smooth does not.

– Smooth ER participates in the synthesis of lipids and carbohydrate metabolism.

– Rough ER produces glycoproteins and new membrane material.

– Golgi complex: stacks of membrane-bound sacs modifying ER products

– Lysosomes : membrane-enclosed compartments containing digestive enzymes and recycling cell components

Flagella and Cilia:

– Function in motility, allowing cells to move by swimming. – Cilia are short flagella that beat in synchrony

– Structurally and functionally differ from prokaryotic flagella

End of Ch.2 If going in order

End of Ch.2 If going in order