Download Lecture 1 - Microbiology Intro

Geomicrobiology
Course Goals
• At the end of this course you will be able to…
– Intelligently converse with microbiologists, geologists,
environmental scientists and engineers about the role
microorganisms play in the cycling of elements
– Use several techniques to identify and characterize
microorganisms in any environment
– Relate microbial physiology, genetics, cell structure,
and metabolism to the effect, role, or signature that
microbes uniquely imprint on their surroundings
Grading
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Homeworks
Discussion participation
Mid term exam
Final Exam
Lab/Field Project and Paper
10%
20%
20%
20%
30%
Basic Microbiology Primer
• Microorganisms exist as single cells or cell
clusters – almost all of them are invisible
to the naked eye as individuals but can be
readily seen as communities
• As opposed to most ‘higher order’ life om
earth, microbes can eat and breathe
things besides organic carbon and oxygen
 this makes them critical to cycling of
compounds that are able to be oxidized or
reduced in water
• Classification of life forms:
– Eukaryotic = Plants, animals, fungus, algae,
and even protozoa
– Prokaryotic = archaea and bacteria
• Living cells can:
– Self-feed
– Replicate (grow)
– Differentiate (change in form/function)
– Communicate
– Evolve
Can purely chemical systems do these things?
All of these things? Why do we care to go
through this ?
Microbes and Thermodynamics
• First and foremost, the basic tenet relating
microbial activity with thermodynamic
descriptions of physical and chemical
systems is:
Equilibrium = Death
• Why then are microbes on seemingly every
corner of the planet’s surface? Why might
we expect to find them on other planets?
Cell Composition
• 70-90% water
• Organic chemistry key to the construction of
cells is inherently linked to the properties of
water vs. organic compounds
• Consider 4 groups of monomers (a single,
repeated ‘building block’):
Polysaccharides
Lipids
Nucleic Acids
Proteins
Macromolecules
– Sugars
– Fatty Acids
– Nucleotides
– Amino Acids
Macromolecules
• Informational macromolecules: They carry
information because the sequence of
monomer building blocks is specific and
carries information = Nucleic Acids and
Proteins
• Non-informational macromolecules: The
sequence is highly repetitive and the
sequence has no function to carry
information
• composition and how exactly the sequences
are structures delineate different functionality
Small molecules present in a growing bacterial cell.
Monomers
Approximate ##
of kinds
Amino acids, their precursors and derivatives
120
Nucleotides, their precursors and derivatives
100
Fatty acids and their precursors
50
Sugars, carbohydrates and their precursors or derivatives
250
quinones, porphyrins, vitamins, coenzymes and prosthetic
300
groups and their precursors
Inorganic ions present in a growing bacterial cell.
Ion
Function
K+
Maintenance of ionic strength; cofactor for certain enzymes
NH4+
Principal form of inorganic N for assimilation
Ca++
Cofactor for certain enzymes
Fe++
Present in cytochromes and other metalloenzymes
Mg++
Cofactor for many enzymes; stabilization of outer membrane of Gramnegative bacteria
Mn++
Present in certain metalloenzymes
Co++
Trace element constituent of vitamin B12 and its coenzyme derivatives and
found in certain metalloenzymes
Cu++
Trace element present in certain metalloenzymes
Mo++
Trace element present in certain metalloenzymes
Ni++
Trace element present in certain metalloenzymes
Zn++
Trace element present in certain metalloenzymes
SO4--
Principal form of inorganic S for assimilation
PO4---
Principal form of P for assimilation and a participant in many metabolic
reactions
Molecular composition of E. coli under conditions of balanced growth.
Molecule
Protein
Total RNA
DNA
Phospholipid
Lipopolysaccharide
Murein
Glycogen
Small molecules: precursors,
metabolites, vitamins, etc.
Inorganic ions
Total dry weight
Percentage
of dry
weight
55
20.5
3.1
9.1
3.4
2.5
2.5
2.9
1.0
100.0
Construction, Part 1…
• Sugars (aka carbohydrates) to polysaccharides
• Sugars start out with 4,5,6, or 7 carbons:
– Pentoses (C5) are critical to DNA, RNA (form the
‘backbone’)
– Hexoses (C6) are crucial to cell walls
• Polysaccharides contain hundreds of sugars or
more held together with glycosidic bonds – form
starches, cellulose, glycogen, etc.
Construction, Part 2
• Fatty Acids – long chains with hydrophobic
and hydrophilic parts
• Lipids are made of fatty acids put together
The chemical characteristics
of the fatty acids and
subsequently the lipids make
them ideal for membranes
Construction, Part 3
• Bases – Two types:
Pyrimidine
Purine
• Derivatives
Cytosine, C
Uracil, U
Thymine, T
DNA  C,T,A,G
No U
Adenine, A
RNA  C,U,A,G
No T
Guanine, G
• Bases come together with a pentose sugar
to form a nucleoside
• A nucleoside containing phosphate is a
nucleotide
This P group has a pK 1
of ~1.0, therefore is
acidic  nucleic acid
ATP structure
• A nucleotide with 3 phosphate linkages is ATP, the
principle ‘currency’ of energy  it is a high energy
molecule, energy from P-P bonds drive many
processes…
• Different nucleotide 3 P links (GTP, CTP, UTP) also
provide energy for other cell processes
• Nucleotides are then linked together via a
phosphodiester bond
• Several nucleoties together = oligonucleotide 
deoxyribose bonded together with the
phosphodiester is the backbone…
3’ and 5’ linkages run in
specific directions –
assures directionality for
assembling a strand of
nucleosides i.e. no
bonding though 3’-3’ or 5’5’ bonding
• Strand put
together with
alternating
sequences
• Number
sequences
using a
shorthand:
3’ taagc-p 5’ or
5’ p-cgaat 3’
DNA formation
• Chargaff's Law: [A] = [T], and [G] = [C] (for any DNA) 
ONLY combination possible, G does NOT bond to itself, A or T
– ONLY C !!
• Purine –pyrimidine pairs!
Down-axis view
Construction, Part 4
• Amino acids  monomer units of proteins
All amino acids have 2
functional groups – one
carboxylic acid group (COO-)
and one amino group (NH3)
Some amino acids have
hydrophobic ends, others
are acidic, some
hydrophilic, or ionzable
Bonds between the C and N
form a peptide bond, which
helps form proteins
Proteins
• Proteins are generally
either catalytic proteins
(aka enzymes) or
structural proteins
• Proteins are polymers
of various lengths (20 –
10,000 amino acid
monomer units) and are
folded, with a complex
geometry which also
helps determine
function
Denaturation – excess heat, outside a
pH range, interaction with reactive
chemicals can undo this folding –
destroying protein function
Cell Construction
• OK – using the building blocks we have
described, let’s make a microbe…
Cell sizes and shape
• Most cells are between 0.1 and 5 mm in
diameter
• Several shapes are common:
– Rod or bacilli
– Spherical or cocci
– Spiral
– Other forms – including square, sheathed,
stalked, filamentous, star, spindle, lobed,
pleomorphic forms
100 µm
20 µm
Microbes on the head of a pin, false color SEM images, from j. Rogers,
http://people.westminstercollege.edu/faculty/jrogers/V%20prokaryotes.ppt#298,3,Slide 3
0.5 µm
Figure 27.3 The most common shapes of prokaryotes
http://people.westminstercollege.edu/faculty/jrogers/V%20prokaryotes.ppt#298,3,Slide
Prokaryote Structure
Cell wall
Nuclear material
membrane
Membrane is critical part of how food and waste are transported
- Selectively permeable
Phospholipid layer
Transport proteins
Eubacteria vs. Archaebacteria
Archaeal cell structure
Bacterial cell structure
Difference??
Let’s look more closely at the membrane, though only 8 nm thick,
it is the principle difference between these 2 groups of microbes
Archaea vs bacteria membranes
• Principle difference between these two is
the membrane
• In archaea, lipids are unique  they have
ether linkages instead of ester linkages
Cell Membranes
• The membrane separates the internal part of the cell from
the external  that these environments remain separate,
but under CONTROLLED contact is a key to life
Membrane Components:
•Phospholipid bilayer
•Hopanoids, which provide
additional structural stability
(similar to sterols (cholesterols)
which provide rigidity to
eukaryote cells)
•Proteins – direct transport
between outside and inside the
cell
Membrane function
• SELECTIVELY PERMEABLE
– Passive diffusion  Gases (O2, N2, CO2, ethanol, H2O
freely diffuse through layer
– Osmosis  because solute concentration inside the cell
are generally higher (10 mM inside the cell), water
activity is lower inside, H2O comes in – increased water
results in turgor pressure (~75psi)
– Protein-mediated transport  selective and directional
transport across the membrane by uniporters and
channel proteins, these facilitate diffusion – still
following a gradient and does not require an energy
expenditure from the cell
Membrane function 2
• Active transport  proteins that function to move
solutes against a gradient, this requires energy
• Uniport, Symport, and Antiport proteins guide
directional transport of ions/molecules across
membrane – different versions can be quite
selective (single substance or class of substances)
as to what they carry
Membrane and metabolism
• As the membrane is the focus of gradients, this is where
electron transport reactions occur which serve to power the
cell in different ways
• Many enzymes important to metabolic activity are
membrane bound
H+ gradients across the membrane
• Proton Motive Force (PMF) is what drives
ATP production in the cell
Figure 5.21
Membrane functions (other)
• In addition to directing ion/molecule transport and
providing the locus for energy production,
membranes are also involved in:
–
–
–
–
–
Phospholipid & protein synthesis for membrane
Nucleoid division in replication
Base for flagella
Waste removal
Endospore formation
• Though very small, the membrane is critical to
cell function  Lysis involves the rupture of this
membrane and spells certain death for the
organism
Cell Wall
• Cell wall structure is also chemically quite
different between bacteria and archaea
• Almost all microbes have a cell wall –
mycoplasma bacteria do not
• Bacteria have peptidoglycan, archaea use
proteins or pseudomurein
• The cell wall serves to provide additional
rigidity to the cell in order to help withstand
the turgor pressure developed through
osmosis and define the cell shape as well as
being part of the defense mechanisms
• Cell wall structure
• Two distinct groups of bacteria with very different
cell walls
– Gram negative has an outer lipid membrane (different
from the inner, or plasma membrane)
– Gram positive lacks the outer membrane but has a
thicker peptidogycan layer
Peptidoglycan layer
• This layer is responsible for the rigidity of the cell wall,
composed of N-Acetylglucosamine (NAG) and Nacetylmuramic (NAM) acids and a small group of amino
acids.
• Glysine chains held together with peptide bonds between
amino acids to form a sheet
Outer membrane – Gram (-)
• Lipid bilayer ~7 nm thick made of phospholipids,
lipopolysaccharides, and proteins
• LPS (lipopolysaccharides) can get thick and is
generally a part that is specifically toxic (aka an
endotoxin)
• LPS layers are of potential enviornmental
importance as a locus of chelators and electron
shuttles
• Porins are proteins that are basically soluble to
ions and molecules, making the outer layer
effectively more porous than the inner
membrane, though they can act as a sort of
sieve
External features
• Glycocalyx (aka capsule – tightly bound
and adhering to cell wall, or slime layer –
more unorganized and loosely bound) –
helps bacteria adhere to surfaces as well
as provides defense against viruses
• Flagella – ‘tail’ that allows movement by
rotating and acting as a propeller
• Pili – thin protein tubes for adhesion
(colonization) and adhering to surfaces
Inside the cell
• Cytoplasm – everything inside the membrane
• Nucleoid – DNA of the organism – it is not
contained by a nuclear membrane (as eukaryote
cell)
• Ribosomes – made of ribosomal RNA and protein
 these are responsible for making proteins
• Vacuoles or vesicles – spaces in the cytoplasm that
can store solids or gases
• Organelles – structures specifically for
photosynthesis – a membrane system
Ribosomes
• RNA is a single stranded nucleic acid
– mRNA- messanger RNA – copies information
from DNA and carries it to the ribosomes
– tRNA – transfer RNA – transfers specific
amino acids to the ribosomes
– rRNA – ribosomal RNA – with proteins,
assembles ribosomal subunits