Germs 101 Final Exam

Microbes

anything too small to be seen without a microscope

includes:

-bacteria

-single-celled eukaryotes

-fungi

-viruses

Scientific process

more realistic and useful view of how science works

3 major components:

-scientific method

-peer review & replication

-professional consensus

What is peer review?

when experts decide if a paper is good enough to publish

What is replication

when others try the same methods to get the same results

professional consensus

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

Scientific Method

-A framed explanation of good science

-A foundational tool to generate new knowledge

-generally defined by 5 steps:

1) observations

2)hypothesis

3)prediction

4)data collection

5)hypothesis (supported/refuted)

Observations

describes, measures, records

hypothesis

explains an observation, is testable, is specific

prediction

describes results we should see if hypothesis is true

data collection

can be described as numerical

hypothesis (supported/refuted)

interpretation

Traditionally, 4 characteristics were recognized that defined life:

-reproduction and heredity

-individual growth

-metabolic activity

-response to light and chemical stimuli

REPRODUCTION & HEREDITY

life produces more life, and passes on traits

METABOLIC ACTIVITY

Organisms consume energy sources and excrete waste products

INDIVIDUAL GROWTH

Organisms grow:

-they develop

-they age

RESPONSE TO LIGHT & CHEMICAL STIMULI

Organisms have ways to react to light and environmental chemicals

Traditionally, characteristics were recognized that defined life LATER:

-cellular structure

-cellular transport/ nutrients

What is taxonomy?

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

What aspects are considered in taxonomy?

Often traits, appearances, and behaviors

Taxonomy organizes life into 7 nested categories:

Kingdom, phylum, class, order, family, GENUS, SPECIES

BIONOMIAL NOMENCLATURE

A universal system of naming species that reflects their taxonomic organization

Bionomial nomenclature naming rules

-genus is capitalized, species is not

-genus can be abbreviated to one letter, species is never abbreviated

-Genus and species are always italicized or underlined

Ex:

Genus: Homo sapiens: Species (italicized)

Genus: H.sapiens: species

EVOLUTIONARY TREE

Where taxonomic relationships can be visually studied through

What major kingdoms do we recognize?

Plants and animals

What did ROBERT HOOKE invent and discover?

-helped invented the compound light microscope

-published the first "micrographic" (microscopic picture)

-discovered and named cells

COMPOUND LIGHT MICROSCOPE

-passes light through a specimen and 2 lenses

-magnification often 10x-400x, 1,000x-2,000x

-resolution 0.2 micrometers

-most common and affordable microscopes

ANTONY VAN LEEUWEHOEK

-built light microscopes and crafted his own lense

-1674 he discovered single-cell eukaryotes, the first bacteria

-limit of light microscopes is 2000x

WHAT DO CELLS SHARE IN COMMON?

-Some organic molecules

-Cell membrane

-Uses DNA to store genetic information

ORGANIC MOLECULES

-lipids/fats->energy and membranes

-carbohydrates/sugars->energy and structure

-nucleic acid->store information(make up DNA)

CELL MEMBRANE

-contains liquid cytoplasm

-protects cells from environment

-made of lipid bilayer

-site of metabolic reactions

-regulates transport

WHAT ARE DISTINCT DIFFERENCES OF CELLS?

-Eukaryotes

-Prokaryotes

EUKARYOTES

-Fungi cell, animal and plant cell, paramecium (single cell)

-has a nucleus to store DNA

-larger in size

-Have many organelles

PROKARYOTES

-Bacterium Cell

-DNA scattered (loose) in cytoplasm

-much smaller

-No organelles

ARCHAEA

-Bizarre group of cells called "a subset of prokaryotes" in 1977

-known to cause disease

-hottest (hydrothermal vents)

-Often lives in extreme environments

-Saltiest (grows on salt piles)

-Depths of ocean (intense pressure)

-Frozen environments (found in ice core)

EXTREMOPHILES

Cells that often live in extreme environments

What did Theodor Schwann and Matthias Jakob Schleiden do in 1838?

They created the cell theory

CELL THEORY

1) All living things are made of cells

2)All cells come from other cells

3)Cells are the fundamental unit of life

Three most known microbes

Animals, plants and fungi

Can you see virus's with light microscopes?

No

what did DMITRY I. IVANOVSKY & MARTINUS W. BEIJERINCK do?

-Discovered virus's (bacteria)

Found bacterial infections causing disease - Tobacco "Mosaic" disease

-discovered that sap filtered to remove bacteria still caused disease

ELECTRON MICROSCOPE

-1931 the electron microscope was invented

-multiple types; all use electron beams to image a target

-magnifications ranges up to 1,000,000x-50,000,000x

What makes up bacteria?

-cell wall

-capsule or slime layer

-pilus/pilli

-flagellum/flagella

CELL WALL

-coveres the cell membrane

-rigid and provide structural support (unlike membrane)

CAPSULE or SLIME LAYER

-covers cell wall

-gel-like and made of sugars

-helps bacteria stick to surfaces

-can protect them from desiccation or predators

What are PILUS/PILLI?

Protein tubes extending out from bacteria

What are short pilli (fimbriae) responsible for?

Covering the capsule of many bacteria

Why are PILUS/PILLI crucial for bacteria?

They are crucial (with capsule/slime layer) for bacteria to stick to surfaces

What is a flagellum?

A long protein tube that rotates for mobility.

Is a flagellum found in all bacteria?

No, it is not found in all bacteria.

How is a flagellum powered?

It is powered by a multi-protein 'motor'.

-Active motor causes a "run and tumble" movement

What activates a flagellum?

A flagellum can be activated by two mechanisms: chemotaxis and phototaxis.

CHEMOTAXIS

flagella drives cell toward or away from a chemical stimulis

PHOTOTAXIS

Flagella drives cell towards or away from light

In acceptable environments, growth can proceed on two levels

-cell synthesizes new cell components and increase in size

-the number of cells in the population increases

BINARY FISSION

The basis of bacterial growth

How do bacteria divide?

Through binary fission

SEPTUM

Fission occurs by forming septum

What happens as the septum gets bigger during bacterial division?

The cell splits apart

COLONY

-A visible cluster of bacteria derived from 1 cell

-Take on different appearances based on the species

-As the bacterium divides it can form a colony

CULTURE

growing a group of organisms and other cells in the lab to study

-"when scientists culture bacteria in the lab..."

How do we categorize these bacteria?

-genetics

-size

-shape

-metabolism

-cell wall components

Genetic pros

-with taxonomy in animals, genetics is preferred

-only requires a small number of cells

-can accurately ID specific species

Genetic cons

-Sequence machines may not be available

-lots of species' genetics remain unknown

-other ID techniques are established

Size pros

can readily identify species of unsusual size

Size cons

Most bacteria are just "very small", not a very convenient tool

Shape

Gernal bacteria can be sorted into 3 shape groups:

-Coccus (round)

-Bacillus (Rod)

-Curved

Coccus

-circular form

-often form clusters

-cluster shape determined by how species reproduces

-CLUSTER CAN HELP ID GENERA & SPECIES

Bacillus

-rod-like form

-can form endospores

-reproduction can result in distinct chains

-CHAINS CAN HELP ID GENERA & SPECIES

Curved

3 subgroups:

1)Spirilla/spirillum

2)Spirochetes

3)Vibrio

Spirilla/sprillillum

-rigid corkscrew shape

-whip-like flagella at cell ends

Spirochetes

-flexible spiral shape

-flagella imbedded in capsule

Vibrio

-comma shape

-1-3 flagella at one end

Shape pros

-easy to identify

-shape correlates with evolutionary history, informative

-key diagnostic tool in medical applications

shape cons

-for colony shape, must grow bacteria in the lab

-only a starting point, won't ID specific species

Metabolism

All life metabolizes food for energy in 1 of 2 ways:

1)Aerobic respiration

2)Anaerobic respiration

AEROBIC RESPIRATION

cell uses oxygen to produce energy

ANAEROBIC RESPIRATION

cell produces energy through non-oxygen methods

Metabolic types

Different bacteria use different approaches:

1)Obligate aerobe

2)Facultative anaerobe

3)Obligate anaerobe

OBLIGATE AEROBE

the cell an only produce energy when it has oxygen

FACULTATIVE ANAEROBE

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

OBLIGATE ANAEROBE

The cell can only produce energy when there is no oxygen

How do we determine bacterial metabolism?

-test tube filled with fluid thioglycollate

-thioglycollate has a gradient of oxygen

-where bacteria grow in the tube indicates their metabolic process

(bacterial growth has a cloudy appearance)

Metabolism pros

-can provide major clues to bacteria's lifecycle & environment

-useful diagnostic tool in the medical applications

Metabolism cons

-must be a bacteria that can be gown in the lab to test

-many bacteria fall in each category and subcategory

Cell walls

Cell walls can be:

-gram positive

-gram negative

Gram positive

PURPLE

-simple cell wall gets stained darker

-simpler structure

-thick peptidoglycan layer over cell membrane

Gram negative

PINK

-complex cell wall gets stained lighter

-complex structure

-2nd outer membrane after peptidoglycan layer

Gram Staining

-Hans Christian Gram invented staining

-Bacteria put through specific chemical stains will change color based on their cell wall

Cell wall pros

-gram staining can quickly differentiate between 2 major groups of bacteria

-easy and useful starting point for ID & classification

Cell wall cons

-need bacteria in the lab to test

-is only a starting point; cannot ID specific species

Bacterial adaptations

Bacterial has evolved several adaptations that help them survive:

-biofilm

-plasmids

-endospores

Biofilm

-group of microbes that adhere to each other and a surface

-produced by cell secretions, made mostly of sugars

-bacteria in biofilm can communicate with each other, act as a population

Plasmids

-additional circles of DNA in a bacterium (not part of the nucleoid DNA)

-plasmids can give bacteria valuable traits (drugs or toxin production)

-Bacteria share plasmids via CONJUGATION

Endospores

-Only made by some genera of bacteria

-Inactive structure that stores bacterium's DNA

-VERY TOUGH; resists high temperatures, chemical damage

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

Viral structure

-Nucleic acid

-CAPSID proteins

-Envelope

-Spike proteins

NUCLEIC ACID

The nucleic acid contained in a viral capsid is either DNA or RNA

CAPSID SHAPE

-Helical

-Icosahedral

HELICAL

-Proteins tightly spiral around nucleic acid

-forms tube-like capsid

ICOSAHEDRAL

-proteins form 20-sided capsid

ENVELOPE PROTEINS

-Surround capsid

-Envelope can have SPIKED PROTEINS