Chemicals needed for life

• Besides chemicals for metabolic energy,

microbes need other things for growth.
– Carbon
– Oxygen
– Sulfur
– Phosphorus – Arsenic can substitute (??)
– Nitrogen
– Iron
– Trace metals (including Mo, Cu, Ni, Cd, etc.)
• LET’S PUT THIS TOGETHER INTO A
MICROBE….
 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’):
– Sugars Polysaccharides

Macromolecules
– Fatty Acids Lipids
– Nucleotides Nucleic Acids
– Amino Acids Proteins
 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 

Molecular composition of E. coli under conditions of balanced growth.

Percentage
Molecule of dry
weight

Protein  55
Total RNA  20.5
DNA  3.1 
Phospholipid 9.1 
Lipopolysaccharide  3.4 
Murein  2.5 
Glycogen  2.5 
Small molecules: precursors, 2.9
metabolites, vitamins, etc.
Inorganic ions  1.0
Total dry weight  100.0
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
Cofactor for many enzymes; stabilization of outer membrane of Gram-
Mg++
negative bacteria
Mn++ Present in certain metalloenzymes
Trace element constituent of vitamin B12 and its coenzyme derivatives and
Co++
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
 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’):
– Sugars Polysaccharides

Macromolecules
– Fatty Acids Lipids
– Nucleotides Nucleic Acids
– Amino Acids Proteins
 Construction, Part 1…
• Sugars (aka carbohydrates) can be linear or cyclic
(if >5 C)
• 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 with
either  or  orientations
• Cn(H2O)n-1 where n is typically 200-2500
 
 Polysaccharides:
• Glycogen – C and energy storage
• Starches – C and energy storage ( poly)
• Cellulose – cellular wall material ( poly)
• Extracellular polysaccharides (aka
glycoproteins or glycolipids) - pathogenic
component of some cells, also useful for
attachment and solubilization
 Construction, Part 2
• Fatty Acids – long chains of C (aliphatic)
• Lipids are made of fatty acids put together
to form hydrophobic and hydrophilic end

The chemical characteristics

of the fatty acids and
subsequently the lipids make
them ideal for membranes
 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’):
– Sugars Polysaccharides

Macromolecules
– Fatty Acids Lipids
– Nucleotides Nucleic Acids
– Amino Acids Proteins
 Construction, Part 3
• Bases – Two types:
Pyrimidine Purine

• Derivatives

Cytosine, C Uracil, U Thymine, T Adenine, A Guanine, G

DNA  C,T,A,G RNA  C,U,A,G

No U No T
•DNA is double-stranded (double helix), while RNA is single stranded
•RNA has a slightly different sugar backbone – ribose instead of
deoxyribose
•RNA has a lot of turns and kinks, more chaotic structure, but some
sections are closer to the outside than others…
RNA

DNA
 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’):
– Sugars Polysaccharides

Macromolecules
– Fatty Acids Lipids
– Nucleotides Nucleic Acids
– Amino Acids Proteins
 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 ionizable

Bonds between the C and N

form a peptide bond, which
helps form proteins
Proteins – ‘key and lock’ concept
 Peptidoglycan (aka Murein)
• Polymer consisting of both sugars and
amino acids
• Rigid material and serves a structural role
in cell wall
 Cell Construction
• OK – using the building blocks we have
described, let’s make a microbe…
 Predominant chemical
Function(s)
composition
Flagella,Pili Swimming movement
Protein

Sex pilus Mediates DNA transfer during conjugation Protein

Common pili or Attachment to surfaces; protection against phagotrophic
Protein 
fimbriae engulfment
Capsules
(includes Attachment to surfaces; protection against phagocytic
Usually polysaccharide;
"slime engulfment, occasionally killing or digestion; reserve of
occasionally polypeptide
layers" and nutrients or protection against desiccation
glycocalyx)
Cell wall
Gram-positive Prevents osmotic lysis of cell protoplast and confers rigidity Peptidoglycan (murein) complexed
bacteria and shape on cells with teichoic acids
Peptidoglycan (murein) surrounded
Peptidoglycan prevents osmotic lysis and confers rigidity
Gram-negative by phospholipid protein-
and shape; outer membrane is permeability barrier;
bacteria lipopolysaccharide "outer
associated LPS and proteins have various functions
membrane"
Plasma Permeability barrier; transport of solutes; energy generation;
Phospholipid and protein
membrane location of numerous enzyme systems
Ribosomes Sites of translation (protein synthesis) RNA and protein
Highly variable; carbohydrate, lipid,
Inclusions Often reserves of nutrients; additional specialized functions
protein or inorganic
Chromosome Genetic material of cell  DNA
Plasmid Extrachromosomal genetic material DNA
 Prokaryote Structure

Cell wall
Nuclear material

membrane

Membrane is critical part of how food and waste are transported

- Selectively permeable

Phospholipid
layer
Transport proteins
 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

~ 40% lipid, 60% protein

Eubacteria vs. Archaebacteria

Bacterial cell structure Archaeal 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
 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 N-
acetylmuramic (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/Chromosome – 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
• Mesosomes/Organelles –a membrane system
internal to the cell which facilitates protein function;
there are these structures specifically for
photosynthesis
Cell structure
 Nucleoid
• Single strand of DNA, usually circular, usually
looks like a big ball of messed up twine…
• Size – smallest organism yet discovered
(Nanoarchaeum equitans) 490,889 base pairs; e.
coli 4.7 Mbp, most prokaryotes 1-6 million base
pairs (1-6 MBp); Humans 3300 MBp
• DNA is around 1000 m long in bacteria, while the
organism is on the order of 1 m long – special
enzymes called gyrases help coil it into a compact
form
 Ribosomes
• Ribosomal RNA is single stranded
• 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

DNA is transcribed to produce mRNA

mRNA then translated into proteins.
 RNA and protein construction
• The nucleotide base sequence of mRNA is encoded
from DNA and transmits sequences of bases used to
determine the amino acid sequence of the protein.
• mRNA (“Messenger RNA”) associates with the ribosome
(mRNA and protein portion).
• RNA (“Transfer RNA”) also required
• Codons are 3 base mRNA segments that specify a
certain amino acid.
• Most amino acids are coded for by more than one
codon: degenerage genetic code.
• Translation ends when ribosome reached “stop codon”
on mRNA.
 Transcription
RNA polymeraze takes the DNA and temporarily unwinds it, templates the
transfer RNA from that, using ribonucleoside triphosphates to assemble…
 Translation
• mRNA is coded for one or more specific
amino acids and moves to the ribosome to
assemble amino acids into proteins
• On mRNA, codons are 3 bases, coded to
specific amino acids
• On tRNA, the anticodon
latches to the codon
on the mRNA
Protein Formation

• The ‘code’ on
mRNA
determines the
sequence of
protein assembly
 rRNA
• Ribosomes are made of proteins and rRNA, the
tRNA and mRNA come to it andassemble the
proteins
• rRNA plays a structural role, serving as a
support for protein construction, and a functional
role
• rRNA consists of two subunits, one 30S in size
(16S rRNA and 21 different proteins), one 50S in
size (5S and 23S rRNA and 34 different
proteins). The smaller subunit has a binding site
for the mRNA. The larger subunit has two
binding sites for tRNA.
Cytoplasmic
Where found Composition Function
inclusions

glycogen many bacteria e.g. E. coli polyglucose reserve carbon and energy source

polybetahydroxy
polymerized hydroxy
utyric acid many bacteria e.g. Pseudomonas reserve carbon and energy source
butyrate
(PHB)

polyphosphate
linear or cyclical reserve phosphate; possibly a reserve of high
(volutin many bacteria e.g. Corynebacterium
polymers of PO4 energy phosphate
granules)

phototrophic purple and green sulfur reserve of electrons (reducing source) in

sulfur globules bacteria and lithotrophic colorless elemental sulfur phototrophs; reserve energy source in
sulfur bacteria lithotrophs

protein hulls or shells buoyancy (floatation) in the vertical water

gas vesicles aquatic bacteria especially cyanobacteria
inflated with gases column

parasporal endospore-forming bacilli (genus

protein unknown but toxic to certain insects
crystals Bacillus)

magnetite (iron oxide) orienting and migrating along geo- magnetic

magnetosomes certain aquatic bacteria
Fe3O4  field lines

enzymes for autotrophic

carboxysomes many autotrophic bacteria site of CO2 fixation
CO2 fixation

phycobilisomes cyanobacteria phycobiliproteins light-harvesting pigments

lipid and protein and

chlorosomes Green bacteria light-harvesting pigments and antennae
bacteriochlorophyll