Exam 1 outline

Most common bacterial shapes

coccus, bacillus,vibro

coccus

round

bacillus

rod

vibro

curved rod

spirillum

spiral

Diplococcus

pair of 2 cocci

tetrad

group of 4 cells in square

streptococcus

chain of cocci

staphylococcus

cluster id cocci

streptobacillus

chain of rods

Gram staining Step 1

crystal violet → purple or blue

Gram staining Step 2

Iodine → cells remain purple or blue

Gram staining Step 3

Alcohol → gram + remains purple / gram - becomes colorless

Gram staining Step 4

safranin → gram positive purple / gram - pink

Common feature bacteria shares with ALL other cells

plasma membrane separating inner cytosol from outside

ribosomes

DNA → RNA → proteins

some similar metabolic pathways

Distinctive features of bacteria

cell wall incorporating peptidoglycan layer

no nucleus or organelles

absence of membrane bound organelles

smaller mostly unicellular

Nucleoid

bacterial genome: single circular double stranded DNA molecule

DNA chromosome

HUGE

Chromosomal DNA

gen. compacted with nucleoid region contains the DNA and associated proteins

Nucleoid is NOT

membrane bound

Bacteria have homologs of

3 eukaryotic cytoskeletons

FtsZ

Many Bacteria

Tubulin homolog

Forma ring during septum formation in cell division

MreB

Many rod shaped bacteria

Actin Homolog

positions cell wall synthesis machinery

CreS

Rare

Intermediate filament homolog

maintains curved shape

Cytoskeleton

provides shape and structure/ organization

Ribosomes

Macromolecular structure

Composed of proteins and rRNA

protein synthesis

abundant in cytosol

Inclusion: Lipid droplets

carbon storage

Inclusion: Volutin granules

inorganic phosphorous

Inclusion: gas vacuoles

increases buoyancy

Inclusion: magnetosomes

carboxsomes that fix CO2

Inclusion: sulfur granules

sulfur for redox chemistry

Cell envelope

plasma membrane, cell wall, capsule

cell envelope forms boundary

between cell and outside wall

plasmid membrane

phospholipids and proteins

phospholipid properties

Amphipathic

polar head groups

non-polar tails

many varieties

lipid comp. changes with changing conditions

Membrane proteins: peripheral membrane proteins

loosely connected to membrane/ easily wash off

Membrane proteins: transmembrane proteins

Embedded in the bilayer (hydrophobic)

Transporters, enzymes, signaling molecules

Mass of protein

Protein is >50% of mass

Simple diffusion

some small molecules can passively diffuse across the membrane

O2, CO2, some organic

High → Low concentration

Facilitated Diffusion

use a transmembrane transporter to diffuse

Handles specific cargo

only transport along concentration gradient (High → low)

The gradient drives diffusion

Active Transport

Uses energy to move molecule against its concentration gradient

Fueled by chemical energy (ATP)

Can be coupled to diffusion of a second molecule along gradient

Low → High

Group Translocation

modify a molecule once it is transported

Preserves the gradient and traps inside cell

Sugar is transported along gradient → Phosphorylated into cytosol

Peptidoglycan cell wall function

Contains peptidoglycan

Maintains shape of bacterium

Help protect cell form osmatic lysis

blocks entry of toxic material, viruses

May contribute to pathogenicity

Peptidoglycan barrier

mesh like material made form 2 polymers: polysaccharide and polypeptides

What two polymers comprise the cell wall? Which are the long

chains, and which form the crosslinks?

polysaccharide and polypeptides

Sugar units polymerize into chains

Crosslinked by peptides

Structure of peptidoglycan

overall helical structure

Lysozyme disrupt cell wall

Enzyme that breaks bonds between sugars in peptidoglycan backbone

Cause cell lyse (destruction)

Penicillin disrupt cell wall

Antibiotic that prevents crosslinking new peptidoglycan

Cause cell lyse (destruction)

Gram positive

Thick peptidoglycan layer

Thin Periplasmic space

negatively charged teichoic acid

NO outer membrane

Gram negative

Thin peptidoglycan layer

Thick periplasmic layer

Porous outer membrane

outer lipopolysaccharide layer

Crystal violet on gram -

most is washed out of peptidoglycan

Lipopolysaccharide

decorates outside of outer membrane; the “lipid

A” component of this is also toxic to humans; endotoxin

Mycobacteria Gram +

Outer waxy layer mycolic acid

Crystal violet does not penetrate the cell wall

Acid fast Gram +

Has mycomembrane

Glyococalax

capsule is an exterior layer of polysaccharide

important in Griffin experiment

makes bacteria more pathogenic

Capsule

Thin layer on cell wall

Slime layer

diffuse, loosely attached to the layer

Aids in motility, attachment, prevents desiccation

S layer

Tile like layer of protein or glycoprotein

Protect from environment, host, predators

promotes adhesion

Endospores

form in response to stress

-ONLY GRAM + FORM

Pili and Fimbriae

Used for attachment

thin, bristle like fibers

BOTH - + bacteria

Sex pili

Facilitates gene transfer/ conjugation

Longer, thicker, hollow

ONLY GRAM -

Type IV pili

twitching motility

Attaches to surface and retracts, pulling along bacteria (grappling hooks)

Flagella

in GRAM + -

long, thin, rigid/ made of protein

not observable by bright field microscope unless stained

not homologus to eukaryotic flagella

Flagella Functions

motility and swarming behavior

attachment to surfaces

many be a virulence factor

monotrichous

one flagellum

polar flagellum

flagellum at end of cell

amphitrichous

one flagellum at each end

lophotrichous

cluster of flagella at one end or both ends

peritrichous

spread all over entire surface

Endosymbiotic theory

Some organelles share features with bacteria

Mitochondria

Chloroplast

Apicoplast

Shared features

two cell walls

have genome and ribosomes / separate from main

When was massive die off

3 mil years ago

What cause that massive die off

The great oxidation event

The great oxidation event

oxygen is corrosive and toxic

Bacteria learned photosynthesis and began producing oxygen

Terrabacteria / Monoderms

dry environment gram +

Hydrobacteria / diderms

aquatic environments gram -

Gram - Bacteria

Proteobacteria

Alphaproteobacterial

Gram - Bacteria

includes many oligotrophs and some intracellular parasites

Adapted to low nutrients

Caulobacter crescentus

Betaproteobacteria

Gram -

Gammaproteobacteria

Gram -

highly diverse group; includes gut bacteria and pathogens (like e.coli)

▪ includes Legionella pneumophila

Deltaproteobacteria

Gram -

Epsilonproteobacteria

Gram -

Chlamydia

Gram -

These are obligate intracellular pathogens

▪ eg, Chlamydia trachomatis

Spirochetes

Gram -

spiral-shaped bacteria

▪ Includes the tick-born pathogen Borrelia burgdorferi that causes Lyme disease

Gram positive G + C meaning

Guanine and cytosine content in DNA

Actinobacteria

Gram +

High G+C

Some Mycobacterium species are important human pathogens

Firmicutes

Gram +

Low G+C

o This group includes many common human pathogens

o Clostridium difficile (important in the context of Superinfection…)

o Staphylococcus aureus (common cause of hospital acquired drug

resistant infections)

Deeply branching bacteria

These branched off from other larger groups of bacteria early on in

evolution, and have evolved some unusual properties

acetothermus pacivorans

thermophilic

deepest branching bacterium

deinoccus radiodurans

survives in radioactive waste

deep branching bacteria

Core characteristics of viruses

Acellular organism

Obligate intracellular pathogen

Lack genes required for metabolism and reproduction

Genome is surrounded by a protein capsid and maybe membrane

Smaller that bacteria (.05-<1um)

Virion

Complete virus particle

Virion Structure

Contains genome of DNA/ RNA

Surrounded by capsid of protein

May have membrane envelope

Inherit delivery system

Nucleocapsid

genome + capsid

Non enveloped viruses have

enveloped virus

additionally possess host-derived membrane

Spikes

Glycoprotein/ project outward from capsid

Aids in attachment/ entry into host cell

Capsid shapes

Helical, polyhedral, comples

Helical Capsid

Hollow tube with protein walls

Nucleic acid in center

Polyhedral capid

often icosahedral: 20 faces

Different subunits for faces, sides, corners

Complex capsid

May be irregular / no shape

Envelopes

outer membrane layer

Host cell plasma or nuclear membrane

Decorated with viral proteins to aid infection