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167 Cards in this Set

  • Front
  • Back
Carboxylic Acid Uses
organic, amino, and fatty acids, lipids, and proteins
Aldehyde Uses
Reducing sugars
Alcohol Uses
lipids and carbs
Keto Uses
pyruvate, citric acid cycle (converts carbs, proteins, fats into CO2 and H2O)
Ester Uses
lipid structure, and amino acids attach to tRNA via ester bonds
Phosphate Ester
Nucleic acids in DNA/RNA
Thioester
Energy metabolism and fatty acid synthesis
Ether
lipids of Archaea (single celled prokaryotes) and Sphingoloids (bacteria that make sphingolipids from sphingosine)
Acid Anhydride
Used in energy metabolism (forms acetyl phosphate)
Phosphoanhydride
Also used in energy metabolism (forms ATP)
Pentoses
Important in DNA/RNA nucleic acids (5-membered rings)
Hexoses
Important for cell wall structure and energy conversions
Starch
Stored form of glucose in plants, a polysaccharide with alpha-1,4 bonds, digestible by humans
Glycogen
Polysaccharide of glucose, used for glc storage in humans, have alpha-1,4 and alpha-1,6 bonds
Cellulose
Beta-1,4 bonds of glc, indigestible
NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid)
Glc derivatives that contain N-acetyl groups and are within bacterial cell walls. They alternate with cross-linked oligopeptide bonds forming the peptidoglycan (aka murein) layers. (Thicker in Gram+ bacteria)
Fatty Acid Uses/Fnx
Structure n function of cytoplasmic membranes. The double bond number/location determine the FA's fluidity. FAs are linked to the glycerol via ester bonds.
Phospholipids
Make up cell membranes, transport DNA, and contain a phosphate in place of one of the 3 FAs. i.e. phosphatidyl ethanolamine has a phosphate attached to (CH2)2(NH3) <--ethanolamine
Nucleotide Structure
Phosphates in b/t 5' and 3's, Base attaches to 1' C, and if deoxy (H only instead of OH) is present it occurs on 2' C.
AA structure
Alpha C attaches to:
1. carboxylic acid
2. Amino group
3. R group
4. Hydrogen

AAs bond through dehydration synthesis (gain of H2O)
Types of R groups on AAs
Ionizable acidic
Ionizable basic
Nonionizable polar
Nonpolar (hydrophobic)
Protein Structures
Primary: order of AAs
Secondary: alpha helix/beta sheet
Tertiary: How the helices/sheets fold on themselves
Quaternary: two proteins
? Angstrom = 1nm
10
? nm = 1 micrometer
1,000
? micrometers = 1mm
1,000
List the light path for compound light microscope
IC SO B PO

Illuminator
Condensor
Specimen
Objective Lens
Body
Prism
Ocular Lenses
Resolution (Resolving Power)
the ability to distiguish between two objects
Resolution (d)
Distance that two objects must be separated by for them to be distinct.

d=0.5(wavelength)/NA (Numerical Aperture)
Resolution with oil imm and 1000x
0.2-0.3 micrometers
WHy do Positive Stains work?
Bind to cells because cells have a net negative charge (they are basic).
The dyes are small enough to penetrate the outer membrane and cell wall.
Negative Stains
Do not bind to cell because both are negatively charged (they are acidic), and do not require heat fixing, so they can be used on live or fragile specimens.
Positive Stain Names
Methylene Blue
Crystal Violet (Diff stain)
Malachite Green
A dye used for staining endospores.
Nigrosin
A negative stain dye, also used for capsule visualization.
Immunological Staining
Can use antibodies tagged with fluorescence to identify antigens.
Gram Stain Procedure
1. Crystal Violet (primary stain)
2. Iodine (mordant)
3. Alcohol (decolorizer, Gram neg will be colorless)
4.Safranin (Counterstain, Gram neg will be pink)
Acid-Fast Stain
Used to stain mycobacterium such as the antigens that cause tuberculosis and leprosy
India Ink Stain
A dye used in differential acid-fast staining that dyes acid-fast cells red, while the tissue or other structures will be blue.
Wavelengths and Resolution
As wavelengths get shorter, reolution increases.

More voltage = shorter wavelengths = more resolution.
Dark-Field Imaging
Uses visible light, but only reflected/refracted light given off by the specimen.

Used for live specimens.
Phase Contrast Imaging
Emphasizes slight differences in refractive indexes.

Also used for live, unstained specimens.
Differential Interference Imaging
Like phase-contrast, it uses refractive indeces, and good for live unstained cells.

The light source must be plane polarized light!
Fluorescence Microscopy
Molecular tag becomes excited by UV light and emits visible light. Many colors so multiple can be used at same time.

Tags are often covalently bonded to antibodies.
Acridine Orange
Fluorescent Dye:
Stains DNA orange.
DAPI
Fluorescent Dye:
Stains DNA GREEN.
FITC
Fluorescent Dye:
Stains antibodies and DNA probes GREEN.
TRITC (rhodamine)
Fluorescent Dye:
Stains antibodies red.
Transmission Electron Microscopy (TEM)
Must be in a vaccuum.
Light source = electron beam.
Lenses = electromagnets (seen on a viewing screen).
Can see viruses!
Use of electron dense stains.
Resolution = 0.5nm (small!)
Scanning Electron Microscopy (SEM)
Only difference bt this and TEM is this collects electrons emitted from surface of specimen, no electron beam.
Confocal Scanning Laser Microscopy (CSLM)
Fluorescent dyes used, makes 3D image.
Shapes of Prokaryotes
Cocci = Spherical
Bacilli = Rod
Vibrio = Comma
Spirilla = Spirals (squiggles)
Spirochete = corkscrew (helix)
Pleomorphic = transition in shape or size
Prokaryote Attaching
Diplo = pairs
Tetrad = 4's
Strepto = Chains
Staph = clusters (grape-like)
Filamentous = mixed filaments
PM/CM
Plasma Membrane, aka Cytoplasmic Membrane.
All cells have this.
CW
Cell Wall
Made of Murein (a peptidoglycan) and sometimes an S-Layer
All cells have this as well.
OM
Outer Membrane.
Only Gram Neg bacteria have this. Not considered part of the CW.
Periplasmic Space
The space bt the CW and OM in Gram Neg bacteria only.
Plasma Membrane Structure
Phospholipid Bilayer with integrated Hopanoids.The ehtanolamine, glycerol, and phosphate are hydrophilic, tails are hydrophobic.
Hopanoids
Pentacyclic compounds in prokaryotes that improve PM fluidity such as permeability for diff environments. Cholesterol has same role in eukaryotes.
General Bacterial (+ and -) Cell Wall Structure
Layers of alternating NAG and NAM, and each NAM has a short peptide X linked to another short peptide on another NAM.
Transpeptidase
Attatches the short peptide X links between NAMs. Antibiotics inhibit this enzyme.
Gram + Cell Wall
X-link of D-Alanine to L-Lysine by a glycine interbridge.

Has many layers (20-80nm)
Gram Neg Cell Wall
No glycine interbridges.

X-link D-Alanine to DAP (diaminopimelic acid)

Fewer layers (2-7nm)
Gram + Cell Wall Features
Techoic Acids attach to CW.
Lipotechoic Acids attach CW to PM.
These acids make the cell overall negative charge.
Gram Neg OM Featrues
Made of lipopolysaccharide (LPS), which is made of lipid A, a core polysaccharide, and an O antigen. Has porins, which makes it more permeable than the PM.
Lipid A
Aka endotoxin, it is part of the OM in gram neg bacteria. It is responsible for the shock associated with bacterial infection.
Porins
Also part of the OM, it allows anything with MW <700 to penetrate.
S-Layer
Outermost layer in Bacteria and Archaea, made of protein or glycoprotein and is made by self assembly. Used for nanotech, and campylobacter have them to protect them from our immune systems.
Capsules and Slime Layers Fnx:
Made of high MW polysacc or polypeptide. May help in virulence (disease causing), or for motility.
Protects them against:
attachment, protection, dehyd.
Archaeal Envelope Structure
No Murein
CM contains branched lipids derived from isoprene
No LPS in Gram Neg Archaea
Hyperthermophiles contain:
C40 monolayers, others contain bilayers or combos.
Chemotaxis
Movement toward a chemical stimulus by bacteria.
Monotrichus
one flagella at the end of the cell.
Lophotrichus
Tuft of flagella at one end of cell.
Peritrichus
Flagella all around the cell.
Pili (aka fimbriae)
Used for adhesion to surfaces or other cells, but also may be used for slime production for motility on solid surfaces.
Structure of Flagella
Both Gram+/-
Anchored by rings in each layer of cell envelope.
Flagella Movement
Each is bent and rigid, spins to move, clockwise or CCW by Fli Proteins.

Move H+ into cell (protonmotive) using Mot proteins
Spirochete Flagella
Have AF (axial fibrils) that lie in periplasmic space, and an OS (outer sheath) that propels it like a corkscrew.
Syphilis and Lime Disease
Caused by spirochetes
Pili
Surface structures
Usually Gram Neg
Involved in sex conjugation
Generally not used for motility
Fimbriae
Smaller surface structures
Motility
Usually Gram Neg
Attachment purposes
Filaments made pilin (a fibrous protein)
Nucleoid
Contains condensed chrom, but does not have a nuclear membrane. Transcription/lation occur here.
Plasmid
Extra-chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently of the chromosomal DNA. Can be present in many or few, large or small, and may have non-essential functions.
Prokaryotic Ribosomes
10^4-10^5 ribosomes/cell.
Made up of 70S, eukaryotic cells are made up of 80S. Antibiotics differentially inhibit them, thats one of the reasons they work.
Prokaryotic Cytoskeleton
Used for cell division, protein localization, and cell shape
Tubulin
Helps with cell division
Actin and Crescentin
Work together to determine cell shape
Gas Vesicles in Cyanobacteria (photosynthetic bacteria)
Found in Bacteria and Archaea. Can be few or many, and help with buoyancy. Vary in size.
Structure of Gas Vesicles
1. Waterproof proteins
2. Gvp A = Beta sheet
3. Gvp C = x-linked alpha helix
Permeable to air, not H2O
Types of Cell Inclusions
Usually separated from cytosol by membrane.
1. Storage
2. Carboxysomes
3. Magnetosomes
Energy Storage in Cells
1. PHA (polyhydroxyalkanoates) is enclosed in a membrane.
2. PHB (polyhydroxybutyrate, the most common storage for excess fuel molecules)
3. Glyogen
Magnetosomes
Particles that contain Fe3O4, or Fe3S4. These molecules are magnetic and align with earth's magnetic poles.

Each magnetosome is surrounded by CM.
Other "somes"
Includes carboxysomes and enterosomes that contain high levels of enzymes involved in certain MOAs.
Sulfur Storage
Oxidation of H2S results in S accumulation stored in vesicles.
Endospore Inclusion Locations
Terminal: at end
Subterminal: close to end
Central: center
Swollen sporangium: cell looks dessicated around endospore
Spores Contain:
1. high calcium ions
2. dipicolinic acid
3. SASPs (small acid-soluble proteins, they bind to DNA and protect it)
4. Low H2O

They are metabolically inactive
Requirements for Microbial Nutrition
1. 12-13 specific carbon precursors
2. Energizable electrons
3. Energy source (UV light,etc)
4. N, S, P, Fe, minerals
Movement of high energy electrons leads to production of:
ATP and a PMF (proton motive force)
Classification of Microbes can be based on these types of nutritional requirements:
1. Carbon Source
2. Energy Source
3. Electron Source
Autotrophs
CO2 is their main C source
Heterotrophs
Reduced, preformed, organic molecules from other org's.
Phototrophs
Get their energy source from light.
Chemotrophs
Get energy from the oxidation of organic or inorganic compounds.
Lithotrophs
Get their electron source from reduced inorganic molecules.
Organotrophs
Get their energy source from organic molecules.
Photolithoautotroph
Photo = light energy source
litho = Inorganic e- donor source
auto = CO2 Carbon source
Photoorganoheterotroph
Photo = light energy
organo = Organic e- donor
hetero = Organic molecule C source
Order of Nomenclature for microorg's:
1. Energy Source (photo, chemo)
2. Electron Source (litho, organo)
3. Carbon Source (auto, hetero)

i.e. Chemoorganoheterotroph
Chemolithoheterotroph
Chemo = Chemical energy
litho = inorganic e- source
hetero = Organic C source
Chemolithoautotroph
Chemo = chemical energy
litho = inorganic e- source
auto = CO2 C source
Chemoorganoheterotroph
Chemo = chemical energy
organo = Organic e- source
hetero = Organic C source
Cell membrane (CM) is only permeable to:
Small gas molecules, therefore needs a transport system.
Main Prokaryotic Transport is:
Active transport using a concentration gradient, this requires energy.
Other systems include:
ABC systems
Group Translocation (PTS) systems
Gradient-Driven Active Transport Process:
Cells use energy to create a gradient, and molecules are transported in by "symport" or "antiport" methods.

Fermenting microbes cannot generate gradients, so does not occur in them.
Symport
A gradient-driven active transport in which sugars, AAs, and anions move into the cell ALONG WITH H+ ions.
Antiport
A gradient-driven active transport in which H+ and other cations move in the opposite direction
ABC transporter stands for:
ATP-Binding Cassette Transporter
ABC transporter steps:
1. Solute-binding protein, AA, or sugar binds to the transporter outside the cell
2. ATP binds to the nucleotide binding site domain on the opposite end of the transporter inside the cell
3. ATP --> ADP + Pi
4. Solute binding protein (or sugar, AA, etc) is transported into the cell.
Group Translocation System
Used by anaerobic or facultative anaerobic bacteria to transport sugars into cell bc they cannot use symport systems.

Uses the phosphoenolpyruvate (PEP) sugar phosphotransferase system.
Group Translocation System Method
Transported sugar is phosphorylated once it reaches the cytoplasm by PEP.
3 methods to measuring microbial growth:
1. Petroff-Hausser counting chamber = immediate answer, need microscope (live and dead cells)
2. Plating to count colonies (count directly or dilute and plate, live cells only!!)
3. Spectrophotometer to measure cell mass (live and dead cells)
Dilutions
1. Start with original volume
2. Add 1ml to 9ml water (this will be 10^-1
3. repeat and plate each one up until your final plate has 10^-6
4. To determine count, divide colonies counted (must be less than 300) by dilution.
5. 159/10^-3 = 159 x 10^3 = (1.59 x 10^5 cfu/ml) <-- final answer
Environmental factors that influence growth:
Osmotic concentration
pH
Temp
O2 levels
Pressure
Microbial Life at Thermal Extremes:
1. AA differences allow protein to remain folded at higher temps
2. More ionic bonds
3. More saturated FAs in CM, whereas psychrophiles have more PUFAs in their CM
4. DNA is positively supercoiled
Classification based on O2 Utilization:
1. Obligate aerobe (needs O2)
2. Facul. anaerobe (does not req O2 but grows better w it)
3. Aerotolerant anaerobe (grows well w/ or w/out O2)
4. Obligate anaerobe (will die if O2 present)
5. Microaerophile (requires low O2 levels)
Aerobic metabolism reactive intermediates (2):
O2- (superoxide anion, very toxic)
H2O2 (peroxide, very reactive)
SOD
SuperOxide Dismutase - turns superoxide anion into H2O2 and hydrogen
Catalase
aka Peroxidase - converts H2O2 into O2 and H2O
SOD and Catalse levels in microorg's:
Microbes contain levels of these enzymes that are proportional to levels or O2 in their environments. If they metabolize more O2, they will have more SOD and catalase.
Org's that do not metabolize O2 (such as obligate anaerobes) will have no SOD or Catalase.
The energy required to run cellular metabolism is derived from:
Redox rxns
Energy from redox rxns is used to:
Make high energy phosphate bonds (ATP) and to generate ion gradients
The 3 central pathways that give rise to all the building blocks of the cell are:
1. Glycolysis
2. TCA cycle
3. Pentose Phosphate cycle

These cycles produce ATP, reducing power (in the form of NADH and NADPH), and the 12-13 Carbon precursors needed to make the building blocks.
Respiring Org's use this pathway:
Glycolysis and the TCA cycle (aka the krebs cycle along with the electron transport chain).

Non-respiring org's use fermentation to produce ATP.
Movement of e-'s liberates energy w/in the cell to produce:
ATP and PMF (proton motive force)
Movement of e-'s to NAD+ and NADP+ generates reducing power in the form of:
NADH and NADPH (reducing agents that are involved in e- transfer and biosynthesis and photosynthesis).
FAD, O2, NAD+, cytochromes, and glucose are all used in:
Electron transport, redox rxns to eventually generate ATP. They produce the best "bang for the buck."
Aerobes extract maximal energy by using this as the final electron acceptor:
O2
My Glycolysis Overview:
1. Glucose is phosphorylated
2. Glucose converted to Fructose -1,6-biphosphate
3. split in half to two glyceraldehydes w/ Phosphates
4. Phosphorylated to 1,3-glyceraldehyde
5. ATP is made by loss of phosphate
6. Result is two pyruvate molecules (precursor metabolites)
Ogden's Glycolysis Overview:
1. Glucose oxidized
2. Energy released to NAD+ and trapped by forming phosphate bonds
3. P-bond is used to make ATP via substrate level phosphorylation (SLP)
4. Phosphoenolpyruvate (PEP) is also used to make ATP via SLP.
TCA cycle
Generates ATP
1. Pyruvate from glycolysis converted to AcSCoA
2. AcSCoA enters the TCA cycle
3. Fermenting org's use only the steps needed to produce carbon precursors
4. Respiring org's complete the entire cycle, generating GTP, NADH, and FADH2
Pentose Phosphate Pathway
Interconnects with glycolysis, produces reductive equivalents, pentose sugars to make nucleotides, and precursors for AAs and vitamins.
Entner-Duodoroff Pathway
Used by few microbes.
Generates 1 of each per glc metabolized: ATP, NADH, NADPH
Fermentation
Usually (not always) carried out under anaerobic conditions.
H+ and NADH build up, must use ATP to pump out.
Energy only generated by SLP.
NAD+ must be regenerated somehow.
Pyruvate is commonly fermented into various products.
Homolactic fermentation
produces lactic acid and also regenerates NAD+, thats why it is so common.
Respiration def.
The movement of e-'s through an e- transport chain to harness energy.
Aerobic org's use O2 as final e- acceptor, anaerobic do not.
Energy is used to produce a PMF and pump H+ out of the cell.
Coenzyme Q as an e- carrier:
aka Ubiquinone, transfers 2 e-'s and 2 H+'s at a time.
Heme as an e- carrier
Attached to cytochromes, the Fe core transfers one e- at a time.
ATPase
enzyme that sits in CM and spins as H+ ions enter cell and creates ATP.
It also reverses its spin to transport excess H+ out of the cell.
Aerobic respirators produce this as a final product:
H2O.
Includes all aerobic bacteria, fungi, and protists.
Chemolithotrophs
- Use inorganics as electron donors
- Usually aerobic, sometimes anaerobic
- Can use reverse respiration to produce NADPH
Phototroph PMF Production
- Use chlorophyll (oxygenic) or bacteriochlorophyll (nonoxygenic) and light to elevate reduction potentials of electrons.
- Some contain rhodopsin
Rhodopsins
Light driven H+ pumps in phototrophs that move H+ to create PMFs
In Chl and BChl (diff types of chl)
- Many differnt types used to absorb different wavelengths of light.
- Accessory pigments in Bchl are also used to absorb diff wlengths and transfer the energy to "reaction centers" (only in BChl)
Cyclic Photophosphorylation
- Initial and final e- acceptor is Bchl
- NAD+ is produced and exits the system
- Anoxygenic and always use Bchl
Non-Cyclic Photophosphorylation
Chls are used (oxygenic)
- H2O is initial e- acceptor, producing O2
- NADP+ is the final acceptor
Bacteriorhodopsins
All use light absorbed by retinal
- Light induces conformational changes in these cells and H+ to be pumped out
- Some bacteriorhodopsins act as photoreceptors
Anabolic reactions utilize large amounts of:
ATP and NADPH
Monomers aka building blocks are and made with:
precursor metabolites and N,S,P,Fe, and others
- Amino acids, nucleotides, sugars, FAs
Accumulation of monomers makes:
Macromolecules
- proteins, polysaccs, lipids
Supramolecular structures are:
Accumulation of Macromolecules
- Membranes, enzyme complexes
- These make up organelles
Calvin Cycle
Most common pathway for CO2 fixation
- These systems contain Rubisco (an enzyme) that completes the first step in the calvin sycle
-Rubisco is the most common enzyme in nature
N2 Assimilation
- N2 not able to be used except by bacteria/archaea
- Converted to NH3/NH4+ first, then incorporated using Glu/Gln
- N2 + 8H + 16ATP --> NH3 + H2 + 16 ADP/Pi
- Most N2 fixers are aerobes, free living, or work with legumes.
Glu
Provides N for amino acids
Gln
Major provider for other building blocks than AAs.
- Made by Gln synthetase
NO3- to NH3
- Nitrate Reduction
- Uses Nitrate Reductase enzyme
- Contains MO and FAD
- Uses NADPH to make Nitrite
- Nitrite reductase produces NH3, then it is used
Sulfur Assimilation
- Mostly converted to Cysteine, which serves as a donor for biosynthesis
P Assimilation
- All is transported in as PO4-2 or as a part of other small molecules, then catabolized.