chemicals needed for life
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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– Fatty Acids– Nucleotides– Amino Acids
Polysaccharides
Lipids
Nucleic Acids
Proteins
Macrom
olecules
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
groups and their precursors
300
Molecular composition of E. coli under conditions of balanced growth.
MoleculePercentage of dry weight
Protein Total RNA DNA Phospholipid Lipopolysaccharide Murein Glycogen Small molecules: precursors, metabolites, vitamins, etc. Inorganic ions Total dry weight
55 20.5 3.1 9.1 3.4 2.5 2.5 2.9
1.0 100.0
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
Mg++ Cofactor for many enzymes; stabilization of outer membrane of Gram-negative 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
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– Fatty Acids– Nucleotides– Amino Acids
Polysaccharides
Lipids
Nucleic Acids
Proteins
Macrom
olecules
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– Fatty Acids– Nucleotides– Amino Acids
Polysaccharides
Lipids
Nucleic Acids
Proteins
Macrom
olecules
Construction, Part 3
• Bases – Two types:Pyrimidine Purine
• Derivatives
Cytosine, C Uracil, U Thymine, T Adenine, A Guanine, G
DNA C,T,A,GNo U
RNA C,U,A,GNo 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…
DNA
RNA
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– Fatty Acids– Nucleotides– Amino Acids
Polysaccharides
Lipids
Nucleic Acids
Proteins
Macrom
olecules
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…
Flagella,PiliFunction(s) Swimming movement
Predominant chemical composition
Protein
Sex pilus Mediates DNA transfer during conjugation Protein
Common pili or fimbriae
Attachment to surfaces; protection against phagotrophic engulfment
Protein
Capsules (includes "slime layers" and glycocalyx)
Attachment to surfaces; protection against phagocytic engulfment, occasionally killing or digestion; reserve of nutrients or protection against desiccation
Usually polysaccharide; occasionally polypeptide
Cell wall
Gram-positive bacteria
Prevents osmotic lysis of cell protoplast and confers rigidity and shape on cells
Peptidoglycan (murein) complexed with teichoic acids
Gram-negative bacteria
Peptidoglycan prevents osmotic lysis and confers rigidity and shape; outer membrane is permeability barrier; associated LPS and proteins have various functions
Peptidoglycan (murein) surrounded by phospholipid protein-lipopolysaccharide "outer membrane"
Plasma membrane
Permeability barrier; transport of solutes; energy generation; location of numerous enzyme systems
Phospholipid and protein
Ribosomes Sites of translation (protein synthesis) RNA and protein
Inclusions Often reserves of nutrients; additional specialized functionsHighly variable; carbohydrate, lipid,
protein or inorganic
Chromosome Genetic material of cell DNA
Plasmid Extrachromosomal genetic material DNA
Prokaryote Structure
Cell wall
membrane
Nuclear material
Membrane is critical part of how food and waste are transported - Selectively permeable
Phospholipid layerTransport 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 mRNAmRNA 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.
TranscriptionRNA 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 inclusions
Where found Composition Function
glycogen many bacteria e.g. E. coli polyglucose reserve carbon and energy source
polybetahydroxyutyric acid (PHB)
many bacteria e.g. Pseudomonaspolymerized hydroxy
butyratereserve carbon and energy source
polyphosphate (volutin granules)
many bacteria e.g. Corynebacteriumlinear or cyclical
polymers of PO4reserve phosphate; possibly a reserve of high
energy phosphate
sulfur globulesphototrophic purple and green sulfur
bacteria and lithotrophic colorless sulfur bacteria
elemental sulfurreserve of electrons (reducing source) in
phototrophs; reserve energy source in lithotrophs
gas vesicles aquatic bacteria especially cyanobacteriaprotein hulls or shells
inflated with gasesbuoyancy (floatation) in the vertical water
column
parasporal crystals
endospore-forming bacilli (genus Bacillus)
protein unknown but toxic to certain insects
magnetosomes certain aquatic bacteriamagnetite (iron oxide)
Fe3O4 orienting and migrating along geo- magnetic
field lines
carboxysomes many autotrophic bacteriaenzymes for autotrophic
CO2 fixationsite of CO2 fixation
phycobilisomes cyanobacteria phycobiliproteins light-harvesting pigments
chlorosomes Green bacterialipid and protein and
bacteriochlorophylllight-harvesting pigments and antennae