Germs Exam 1

Microbes

Anything too small to be seen without a microscope

Bacteria (prokaryotes), single-celled eukaryotes, fungi, viruses

The Scientific Method

Famed explanation of good science; foundational tool to generate new knowledge; generally defined by 5 steps

Oberservations

describes, measures, records

Hypothesis

explains an observation, is testable, is falsifiable, specific

Predictions

describe results we should see if the hypothesis is true

Data Collection

a study (observations), an experiment (manipulations), descriptive (qualitative), numerical (quantitative)

Interpretation

hypothesis supported or refuted

Scientific Process

a more realistic and useful view of how science works

Steps of the Scientific Process

1. Scientific method

2. Peer review and replication

3. professional consensus

Preprint

paper not yet peer reviewed and published

Reproduction and heredity

life produces more life and passes on traits

Individual growth

organisms grow:they develop, they age

Metabolic activity

organisms consume energy sources and excrete waste products

Response to light and chemical stimuli

organisms have ways to react to light and environmental chemicals

Characteristics recognized later:

cellular structure, cellular transport/nutrients

Taxonomy

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

Binomial nomenclature

a universal system of naming species that reflects their taxonomic organization

Specifics of binomial nomenclature

genus is always capitalized, species is not; genus can be abbreviated to 1 letter, species never abbreviated; always italicized or underlined

Genus example

"Homo"

Species example

"sapiens"

Robert Hooke

helped invent the compound light microscope

Compound light microscope

passes light through a specimen and two lenses, magnification often 10x-400x

Antony van Leeuwehoek

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

Same organic molecules

Lipids/fats = energy/membranes

carbohydrates/sugars = energy/structure

Nucleic acid = store info (make up DNA)

Cell membrane

protects cell from environment, made of lipid bilayer, site of metabolic reactions, regulates transport

DNA

use DNA to store genetic information

Eukaryotes

DNA in nucleus, larger size, have organelles

Prokaryotes

DNA loose in cytoplasm, smaller size, NO organelles

Archaea

subset of prokaryotes, a brand new type of cell, not known to cause disease (1977), often live in extreme environments ("extremophiles")

Cell theory

1838, Theodor Schwann and Matthias Jakob Schleiden

1. all living things made of cells

2. all cells come from other cells

3. cells = fundamental unit of life

Dmitry I. Ivanovsky & Martinus W. Beijerinck

/ dimitry and martin

1890's microbiolgists were studying tobacco plants; have a strange "mosaic" disease that ends up being a virus

Tobacco Mosaic Disease

Something smaller than bacteria existed, a bacterial infection causing disease, finally revealed in 1935

Electron microscope

was invented in 1931, magnification 1,000,000x-50,000,000x

Cell wall

covers the cell membrane, used to maintain shape of the bacteria

Capsule or slime layer

covers the cell wall, gel-like, usually made of sugars, helps bacteria adhere to surfaces, can protect them from drying out or predators

Pilus/pilli

hair type stuff, protein tubes extending out from bacteria

Short pilli

helps bacteria stick to surfaces

Conjugation

Long pilli used to exchange DNA between cells ('"sexual")

Flagella/flagellum

tail type thing, movement towards stimuli, greatly improves mobility

Chemotaxis

flagella; drives cell toward or away from chemical stimulus

Phototaxis

flagella; drives cell toward or away from light

Binary Fission

the basis of bacterial population growth, bacteria divide, fission occurs by forming a septum, as the septum gets bigger the cell splits apart

Colony

as bacteria divide it can form a colony; a visible cluster of bacteria derived from one cell

Culture

scientists culture bacteria in the lab, and they often grow colonies in a petri dish

Genetics pros

increasingly the preferred method

only requires small number of cells

can accurately ID specific species if genetics are known

Genetics 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

Size cons

most bacteria are very small; miniscule differences in size is not a convenient tool for organizing bacteria

Shape: coccus

circular form. often form clusters, cluster shape determined by how species reproduces, clusters can help ID genera and species

Shape: Bacilus

rod-like form, can form endospores, reproduction can result in distinct chains, chains can help ID genera and species

Shape: Curved: Spirilla/Spirllum

rigid corkscrew shape, whip-like flagella at cell ends

Shape: curved: Spirochete /spirochete

flexible spiral shape, longer spiral, flagella embedded in capsule

Shape:curved: Vibrio / vibrio

comma shape (kidney bean), 1-3 flagella at one end

Shape pros

easy to identify three major groups

shape correlates with evolutionary history(informative)

key diagnostic tool in medical applications

Shape cons

for colony shape, must grow in lab

only starting point, won't ID specific species

Aerobic respiration

cells needs oxygen to produce energy

Anaerobic respiration

cell produces energy without oxygen

Obligate aerobe

the cell can only produce when it was oxygen

Obligate anaerobe

the cell can only produce with NO oxygen

Facultative anerobe

cell prefers oxygen, but can produce oxygen using anaerobic respiration

Metabolism pros

can provide major clues to lifecycle and environment

useful diagnostic tool in medical applications

Metabolism cons

must be grown in a lab to test

many bacteria fall in each category (and subcategories)

Gram positive

purple; simpler structure, thick peptidoglycan layer over cell membrane, one thick layer over cell membrane

Gram negative

pink; complex structure (two layers), second outer membrane after peptidoglycan layer

Gram staining

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

negative = pink (light)

positive= purple (dark)

Gram staining pros

quickly differentiate into two categories, easy/useful starting point for ID/classification

Gram staining cons

need bacteria in a lab, only starting point, cannot ID specific species

Biofilm

group of microbes that adhere to each other and a surface, produced by cell secretions, bacteria in a biofilm can communicate with each other and act as a population, cell communication

Plasmids

additional circles of DNA in a bacterium, can give bacteria valuable traits (drug resistance, enzyme or toxin production), bacteria share plasmids via conjugation, including across species

Endospores

only made by some genera of bacteria (bacillus, clostridium), inactive structure that stores bacterium's DNA, very tough, made using septum, cell dies once endosphere is complete

Nucleic acid

DNA or RNA, the nucleic acid contained in a viral capsid

Capsid shape: Helical / helical

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

Capsid shape: Icosahedral

proteins form 20-sided capsid, geometric shapes

Envelope

envelope proteins surround capsid

Naked virus

No envelope

Viral identification in practice

patient symptoms, cellular damage from lytic cycle, patient cells can be cultured in a dish and observed for viral damage

Parasitism

relationship between two things in which the host is harmed and the parasite benefits

Obligate intracellular parasites

viruses must parasitize a host cell to reproduce

Central Dogma of Biology

all cells use DNA (genes) to make RNA, and RNA to make protein, this is what viruses are after

DNA -(transcription)-RNA-(translation)-protein

Binding

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

Penetration and Uncoating

enters cell and dissolves capsid

Synthesis and Assembly

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

Release

viruses without envelope rupture (lyse) cell, killing it, viruses with envelopes can bud off cell membrane

Bacteriophage

bacteria-specific cells

Multicellular fungi / Hyphae

grow using filaments called hyphae

Mycelium

all hyphae together make up the mycelium (fungal body)

Mold

mycelium big enough to see is often called mold

Spores

reproduction often via airbone spores

Single celled fungi

Yeast

Immunity and Immune System

the biological processes that grant ability to resists pathogenic disease

Pathogen

any disease-causing bioligcal agent

First defense

innate, non-specific physical and chemical barrriers

Skin

keratinocytes: detect microbes, aid immune response, high cell turnover

dry environment, acidic pH (5)

Mucous Membrane

internal mucous-secreting layers, entry points in holes in body, mucous traps and clears microbes

Second defense

innate, non-specific responses, fever, inflammation, phagocytosis, activates when pathogens enter body

White blood cells

must distinguish between "self" and "non-self" entities

Phagocytes

phago=eating, consumes pathogens in body identified as non-self, digestive enzymes break down bacteria, bacteria dissolved into molecules

Natural Killer (NT) Cells

identify pathogens inside cells, checks cell membranes for non-self proteins, if detected NK cell inject enzymes that trigger apoptosis

Apoptosis

programmed cell death

Cytokine proteins

attracts white blood cells to infection, promotes fever or inflammation