MIC 102 UC Davis Study #2

Last Universal Common Ancestor (LUCA)

Was a microbe of unknown type that lived about 4 billion years ago; the origin of all organisms.

What is 16s small unit rRNA used for?

It's used to study construct phylogenetic trees of organisms because it's highly conserved and hasn't changed much over time.

Antonie von Leeuwenhoek

Father of microscopy in 1620

Increased surface area like folded membranes

How do larger cells maximize diffusion across surface membranes?

Resolution

Shortest distance between 2 objects that can be distinguished as seperate objects. Very important specification in microscopes.

360-700nm

Ideal resolution range for light microscopes

Fluorescent microscopy

Fluorochromes emit specific wavelength of light when excited and can be used to tag specific molecules in a cell like a protein. Can also be engineered into genes of living cells.

Electron microscopy

Uses a wavelength of around 0.005nm to magnify object by up to 500000 times. Used to view details of cell structuresor viruses.

Scanning electron microscopy

EM used to see exterior surfaces of cell

Transmission microscopy

EM used to see internal cell views and the smallest structures

Phospholipid bilayer

Structure of a bacteria cell wall. Some are covalently bonded in order to survive high stress environment like extreme temperature

Small polar, uncharged molecules

What type of things can passively cross most cell walls?

Peptidoglycan

Substance in bacteria cell walls that provides shape, rigidity, and protection by forming repeating cross links in its structure

Gram positive bacteria

Have one membrane and a large cell wall with a thick peptidoglycan layer and acids that anchor membrane to cell wall. Stain purple and hold onto stain well.

Gram negative bacteria

Have a second membrane and thin cell wall made of lipopolysaccharides that are often responsible for septic shock in infections. Stain pink in microscope slides.

Porins

Pores that increase outer membrane permeability to hydrophobic compounds like sugars. Passive channels.

Periplasm

Space between cell wall and membrane(s), where much enzymatic activity occurs in prokaryotes.

Archaeal cell envelope

Made of pseudomurein instead of peptidoglycan.

Acid fast bacteria

Possess thin cell wall and a partial second membrane that is resistant to acids and soaps. Grows slowly due to slow nutrient uptake. M. tuberculosis is an example.

S-layers

Crystalline surface bacteria surface that provides more rigidity and can help extremophiles survive conditions

Capsules and Slime Layers

Prevent dessication and phagocytosis of bacteria, limit diffusion of harmful compounds. Mostly made of polysaccharides.

Glycocalyx

Sugar coat slime layer that makes a biofilm for bacteria to stick to surfaces or each other. Common in gum disease bacteria.

Flagella

Motility structure, assembled from rigid flagellin filaments that assemble from bottom up, out of cell.

Pilus

Structure made from pilin monomer that allows for conjugation, adhesive attachment, or limited twitching motility

Nucleoid

Area in prokaryotic cell where DNA is located; not separate from rest of cell by a compartment.

Smaller: intracellular parasites, Larger: more adaptable bacteria or extremophiles.

What type of bacteria might have a smaller or larger genome?

Bacterial chromosome

Exists in circular form with a bottlebrush structure that is wound into negative supercoils. Contains no histones and DNA is bound by cations to neutralize furth reulsion.

DNA Gyrase

Controls negative supercoiling of chromosome in a process that requires ATP

Topoisomerase 1

Lets coiled chromosome relax in a passive process

Ribosomes have immediate access to newly transcibed mRNA at surface of nucleoid.

Why does transcription and translation occur simultaneously in prokaryotes?

Thylakoids

Stacks of membrane sac with a shared lumen that increases surface area for better photosynthesis. Continuous with cell membrane.

Carboxysomes

Structure with a protein shell that helps bacteria fix CO2. Contains enzyme RuBisCo which could harm the bacteria if it were not kept inside structure.

Enterosomes

Similar structure to carboxysomes, but metabolizes compounds other than RuBisCo.

Refractile inclusion bodies

Storage granules that hold useful materials for later use when in abundance, like S, Ca, P, or organic polymers. Allows for growth when resources are scarce.

Magnetosomes

Membrane bound structure that contains iron and allows bacteria to align with magnetic field, to move around and find oxygen, etc.

Turbidity

Amount of light passing through cell culture, and reported as optical density. Easiest method of measuring cell numbers, but not an indicator of living cells since dead bacteria still scatter light.

Viable cell count

Diluted culture spread on plates and each colony counted as one living cell from culture. Counts only living and viable cells.

Direct cell count

Culture loaded on hemocytometer and cells counted under microscope. Flaw: hard to tell if cells are living or dead.

Flow cytometry

Laser assisted direct cell count. Often used with stains to count cells with specific features.

Psychrophile

Bacteria that live in cold places, who have specialized proteins and adjusted fatty acid composition in cells to survive.

Thermophiles

Heat tolerant bacteria that have specialized proteins to withstand denaturing, chaperones for proper folding. Archaea have soecialized membrane bonds to survive heat.

Increased internal concentration of solutes that won't disrupt protein function, likeproline and choline.

How do halophiles grow at saturated salt conditions?

FtsZ (Filamentous temperature sensitive gene)

Gene that helps form a ring at the correct spot on a cell for division. Temperature sensitive and when deactivated, bacteria form long filaments instead of individual cells.

minCD

Protein that polymerizes at poles of a cell, preventing FtsZ from functioning there. When not active, bacteria form minicells by dividing at poles.

minE

Protein that prevents minCD from polymerizing at center of the cell.

Heterotroph vs Autotroph

Use organic vs inorganic carbon source for energy

Chemotroph

Gets energy from a chemical source, rather than light.

Phototroph

Uses light as a source of energy

Fueling

Process by which 13 precursor metabolites are made from carbon/energy sources and redox reactions. (Precursors may also be scavenged from environment)

Building blocks

Synthesized from precursor metabolites and ATP, and used to later make macromolecules. More reduced than precursors.

Macromolecules

Mainly polymerized from building blocks, at high energy cost. Proteins, DNA/RNA, lipids, sugars, etc.

Electrons moving along energy gradients

How is energy produced for fueling and growth processes?

NAD+

Main carrier of electrons for reducing power.

NADH/NADPH

Reduced molecules gained from fueling, needed for biosynthesis. Reducing power.

Transmembrane ion gradient

Flow of e- through channels generates energy. Protons pumped out, e- passed along electron transport chain, and ATP is generated by the proton motive force.

Substrate level phosphorylation

P from substrate is taken up by cell and generates NADH; the more energized bond can be transferred to ADP to make ATP.

Fermentation

Occurs in anaerobic sugar metabolism. Excess NADH from substrate phosphorylation is converted to byproducts like acetate or ethanol. Allows cells to get energy in absence of O2 or ADP.

ATP synthase

Enzyme that bonds P and ADP to F1 complex in ion pump, allowing it to be converted to ATP from rotational energy.

Chemoautotroph

Uses respiration to make enrgy to fix CO2, which requires a LOT of reducing power. Uses inorganic e- donor compound, and can run the electron transport chain backwards.

Photosynthesis

Light enters reaction center and chlorophyll excites electrons, producing energy. Archaea incapable but some bacteria (mostly autotrophs) can do this.

Cyclic photosynthesis

E- acceptor is the same chlorophyll that served as a donor. Excites e- and returns it to ground state.less common form of photosynthesis.

Non-cyclic photosynthesis

E- taken from energy source and is accepted by NADH. Must have an external e- donor source like H2O, lactate, Fe, etc.

Anoxygenic photosynthesis

Photosynthesis used by early bacteria; does NOT generate O2, and currently used by purple and green Sulfur bacteria.

Oxygenic photosynthesis

Used by Cyanobacteria, where H2O is e- donor. Generates O2 and H+, and relies on two reaction centers to make NADPH, and to make and then return new e- to first reaction center.

True

Microbes can either completely make building blocks with nothing but an energy source, or rely on the environment to get them. (T/F)

Sugars, acids, most ions, H2O

What tyypes of molecules will passively diffuse through porins on gram negative outer membrane? (But still dependent on concentration outside of membrane...)

Facilitated diffusion

Uses no ATP, allows diffusion through specific selective protein channels in gram negative porins. Rare in prokaryotes.

Ion coupled transport

Active transport where energy is provided by an ion gradient (H+, N+, etc). Works in both directions.

ABC (ATP Binding Cassette)

Active transport where binding proteins bring solute to membrane protein complex, ATP opens channel, and transporter protein brings molecule in. Very common and useful for large molecules, like galactose.

Group trabslocation

Less common active transport where phosphotransferase brings in a solute while phosphorylating it at the same time. Very useful! Saves energy for later sugar metabolism amd also prevents sugar from diffusing out of cell.

Siderophores

Porins that specifically transport metal ions. Active transport complex, where ions are chelated and bound in 2 or more places so cell won't lose it.

Feeder pathways

The process that converts carbon into central pathway metabolites. Polymer breakdown and isomerization in heterotrophs which convert organic compounds into intermediate molecules, or carbon fixation in autotrophs.

Calvin cycle

Carbon fixation cycle. RuBisCo adds CO2 to 5 Carbon sugar to make 6 Carbon sugar, and it breaks in half. ATP and NADPH then create Fructose-6P. Needs a LOT of energy and occurs in carboxysomes.

RuBisCo is sensitive to Oxygen.

Why does the Calvin Cycle occur in carboxysomes?

Reductive TCA cycle, Acetyl-CoA fermentation, and hydroxyproprionate pathway

Alterntive ways of carbon fixation in autotrophs besides the Calvin cycle

Glycolysis

A central pathway to make some of the 13 precursor metabolites. Starts with glucose and creates 3 precursors, 2 pyruvate, 2 NADH, and 2 ATP via phosphorylation. Reversible and can be stopped at any time to grab a precursor molecule for use.

Pentose-Phosphate Pathway

A central pathway to make some of the 13 precursor metabolites. Generates reducing power in the form of 2 NADPH, glyceraldehyde, and fructose6P. (NOTE: NADPH is one of the metabolites for building DNA.)

TCA (tricarboxylic acid cycle)

Krebs cycle. A central pathway to make some of the 13 precursor metabolites. Makes 3 precursors, 3 NADPH, 2 CO2, and 1 FADH2. Can be run in portions or backwards by anaerobes, or to fix CO2 by autotrophs. Very flexible cycle!

Gluconeogenesis

Reversal of central pathways on certain substrates in order to make glucose from 1,2,3,or 4 carbon sugars like malate.

Phosphorus, Sulfur, and Nitrogen

What other elements are needed to make building blocks alongside the central pathways and precursor metabolites?

Obtaining Sulfur for use to make building blocks

Must be reduced to Sulfide for assimilation, can be obtained directly from excess Cysteine.

Obtaining Nitrogen to make building blocks

N2 gas must be reduced to ammonia via fixation, which only occurs in prokaryotes. Very energy costly, requires nitrogenase reductase complex that is O2 sensitive. Highly conserved genetically.

Ammonia

Used to make glutamate and glutamine, both parts of amino acids.

Amino acids

Building blocks of protein. Different families made from different precursors, and can be used to trace central pathway mutations.

Nucleotides

Make up DNA and RNA. Made to carry all of the energy needed for polymerization within them. Made up of lots of energy, and nitrogen (glutamine).

Sugar

Macromolecule used in capsules, cell wall, membrane, and as energy storage in form of glycogen.

Fatty acids and lipids

Macromolecules used in membranes, lipopolysaccharides. Linked by glycerol, vary in terms of double bonds, branches, and chains.

Rosalind Franklin

Original discoverer of the double helix who was not credited until after her death.

1 pyridimine ring and two purine rings.

Which nucleotide bases make up DNA?

DNA polymerase

Adds nucleotides to synthesize DNA, always adding the 5' end to the 3' end.

oriC

Origin sequence of DNA replication, from which it proceeds outwards in both directions towards ending terC sequence.

Lagging strand

The discontinuous strand of DNA being replicated, initially produced in the form of short Okazaki fragments.

DnaA

Initiator protein that binds to DNA at oriC, melts/seperates strands, and recruits proteins for holding open the strands and replication. Requires ATP.

DnaB (helicase)

DNA replisome protein, which recruits the replication machinery and locks it into place during the process. Helps unwind the two strands as it moves. . (NOTE: DnaA disconnects after machinery is in place.)

DnaC

Chaperone protein that interacts with DnaA to load DnaB onto single strands at oriC and nowhere else along the opened strand. Requires ATP.

Replisome

DNA replication machinery, which move away from the origin bidirectionally.

DnaG (primase)

RNA polymerase that starts DNA synthesis via RNA primers. Needed only once on leading strand but continuously on lagging strand.

Pol 3

Main DNA polymerase, which does the actual work of replication by polymerizing nucleotides in the 5' to 3' direction. Needs to be "clamped" in place by the replisome machinery. Can extend chain but needs RNAP to get it started by making a RNA primer segment it can add to.

Cell-mediated control of DNA replication

Replication can only be initiated when there is enough ATP present, and all of the DnaA binding sites that accumulate as the cell grows are finally full.

SeqA

Protein that prevents premature DNA replication by sequestering normally methylated origin sites of new DNA to prevent DnaA from binding. (Disconnects when other strand is methylated, freeing origin.)