Microbio Midterm 2 Study Guide

bacterial cytoplasm

• site of metabolism

• contains ribosomes

• holds genetic material

Bacterial Cytoskeleton (functions)

functions:

• cell division (pass on genes)

• protein localization (getting things at place at the right time)

• cell shape

What are some homologues to eukaryote cytoskeleton components and their functions

• MreB is like actin: cell division

• Crescentin is like intermediate filaments: shape + hold proteins in place

• FtsZ is like tubulin: microtubels

What makes up the eukaryotic cytoskeleton

• microfilaments

• intermediate

• microtubules

microfilaments are?

• thin filaments

• actin and myosin(motor protein)

what are microfilaments function and bacterial homogloue

• movement, endocytosis, cytokinesis, and secretion

• bacterial homologue= Mre proteins (Mre B)

Intermediate filaments and bacterial homologue

• structural filaments of about 10 nm diameter

• structural in function

• points of attachment for organalles

• highly stable

Bacterial Homologue: crescentin

Microtubles and its bacterial homologue

• helical shaped polar cylinders about 25 nm diameter

• tubulin subunits

  • Bacterial homologue FtsZ proteins

• dynein and kinesin motor proteins (no known bacterial homologue

Describe the movement of a dynein motor protein on microtubles

• turkey legs walking

• not always have two legs

• subsets of both that can move both ways

Inclusions are in bacterial cells what about them

• prokaryotic homologues to membrane bound vesicles

• aggregates of organic and inorganic substances: granules, cystals or globules

Storage:

• carbon: glycogen and poly beta hydroxybutarate

• inorganics: sulfur globules and polyphosphate granules

What is the importance of gas vacuoles

• allow microbes to regulate buoyancy

• found in cyanobacteria and other aquatic prokaryotes and photosyntetic

• protein compartments filled with gas

What are magnetosomes

• contain magnetite (Fe3O4)

• allow bacteria to orient along magnetic fields

• consolidate iron in inclusion bodies

• not true endocytic membranes (single lipid membranes)

• ruffles that allow invagination of phospholipids

Prokaryote Ribosomes

• S*= Svedberg, a unit for sediment

• 70S= 30S small subunit + 50S large subunit

• 60% RNA and 40% protein

• 16S rRNA is found in the 30S small subunit

  • 98.7%= same species

• are soluble polysomes: a group of ribosomes reading the same mRNA simultaneously

• not attached to PM so free floating protein

Compare and contrast Eukaryotic and Bacterial Ribosomes

Euk.

• 80S = 60S + 40S

• 18S rRNA

• slightly larger in molecular weight/layer

Bact.

• 70S = 50S + 30S

• 16S rRNA

• life started int the RNA world

S* = svedberg, a unit for sediment

Both are made of RNA + protein and perform the same core function: protein synthesis — but differ in size, complexity, and evolutionary details.

Endoplasmic reticulum (ER)

• function: syntesis and transport (shuttling system)

• rough (RER): studded w/ ribosomes, sythesis and transport of proteins

• smooth (SER): fewer ribosomes, synthesizes lipids and other macromolecules (some proteins but not as many and lots of lipids)

• endocytic pathway brings it in

Secretory Pathway

funt: move materials throughout to the PM or to the cell exterior

- a way to get things out eukaryotic cells

- some type of signal or hormone that releases this

- generally coated in the phosphlipid bilyer vesicles

WE DO NOT OBSERVED IN PROKARYOTES

• prokaryotes will have some type o channels instead of secretory vesicles

- regulated requires a signal

• triggered/controlled

- unregulated does not require signal

• continuous

Proteasome

• macromolecule

• Quality Assurance: misfolded or otherwise damaged (or excess) protein is carefully stored and discarded

• basically proteosomes destroy misfolded proteins

Difference btwn prokaryotes and eukaryotes

• No phospholipid bilayer membrane compartments in prokaryotic cells 

• But might have single layer of phospholipid coating 

• Prokaryotic cells: dont have internal membrane system 

  • Stuck with diffusion or transport across membrane

What do molecule chaperones do

• they help proteins fold correctly

What does proteasomal degradation of proteins look like in Pro vs Euk

Pro

• Pup proteosome system

• PUP

• single pup

• pupylation

Euk

• ubiquitin proteasome system

• Poly-Ub

• polyubiquitination: protesomeal degredation

• ubiquitin links

• monoubiquination: transport, signaling, DNA repair

What was the missing link

• promodial escort proteins

  • escort systems important for allowing the plasma membrane to form internal phospholipid bilayer membranes

• found in the archea lokiearcheota

Eukaryotic Glycocalyx

• outermost boundary of the cell composed of polysaccharides

• funct: adherence to surfaces and other cells w/in a biofilm protection

Eukaryotic Plasma Membrane and Cell Wall

PM:

• phospholipid bilayer

• contains a high proportion of sphingolipids and sterols (cholesterol) for strength and rigidity

• selective permeable barrier

CW:

• found in fungi and algae

• unlike prokaryotes, generally composed of chitin, cellulose or sillica

Sterols(cholesterol) in which biphospholipid membrane

• eukaryotic cells

• these cholesterol rich regions are a structured system but also regulate exo/endocytosis signal transduction

What are lipid rafts

• cholesterol congregates in specalized micodomains

• these cholesterol rich microdomains are extremely important for endocyotosis

• play critical roles in cell signaling, trafficking, and membrane organization.

What are the proteins called that allow for internalization

• escort proteins

• allow for channels, secretion

• protein with short transmembrane domain cannot enter lipid raft

endocytic pathway

• observed in all eukaryotic cells

• funct: to bring materials into the cell from the outside

• endocytosis is nonspecific but ligand specific

what are diff types of endocytic pathways

• phagocytosis: extends membrane and internalizes macromolecules into the cells

  • solid particles

• macropinocytosis: sampling fluids (EC fluid)

  • all cells

• clathrin and caveolin endocytocis: receptor mediated cytosis

All pathways endup in a degradative lysosome

pathways 2 and 3 turn into early endosomes which turn into late endosomes and then lysosomes

The inside out origin

• theory on how the nucleus is acquired: the inside out origin for the eukaryotic ell (typically outside in thought process)

• membrane blebs surrond symbiotic prokaryotes such as rickettsia ans through blebs, were able to make phospholipid bilayer needed for the nucleus

• nucleus is an extremely protected struture

Prokaryotic Nucleoid

• a singular, circular dsDNA

• The nucleoid is a non-membrane-bound region in prokaryotic cells (like bacteria) that contains the cell’s DNA.

• Unlike eukaryotic nuclei, the nucleoid:

  • Has no nuclear membrane

  • Is not surrounded by a nuclear envelope

  • Is sometimes referred to as “naked DNA”

• prokaryotes have histone like homologues called NAP nucleoid-associated proteins

Even though it’s “naked” (no membrane), the DNA is tightly packed and organized: Supercoiling

• which twists the DNA into tighter structures.

Eukaryotic Nuclear Envelope

• two membranes both consisting of lipid bilayers

• nuclear pore complexes allow for transport in and out of the nucleus

  • requires signals to get in and out

• chromosomes released by ER to get packaged and shipped out

• have protective endomembrane structure

• The outer membrane connects to the ER — allowing for communication and material flow between the nucleus and the rest of the cell.

• funct: Protects genetic material, regulates gene expression access

Eukaryotic Nucleus

• the repository of genetic info

• linear chromosomes: composed of condensed chromatin a complex of DNA, RNA and proteins

• DNA is wrapped around histones (protein) in a bead on string format, yielding multiple nucleosomes

  1. DNA wraps around histones

  2. Nucleosomes coil into chromatin fibers

  3. Higher-order folding

  4. Supercoiling

plasmids (only prokaryotes, not eukaryotes)

prok. cells carry extra copies of this

not required for replication, recommended not needed

• Structure: Small, circular double-stranded DNA molecule

• function:

  • autonomous replication: make multiple copies

  • confers selective advantages: then shares it w/ others w/o losing it

• Impact on host cell:

  • provides selective advantages

  • can have a metabolic burden

Plasmid shared via conjugation

"Shared via conjugation" means that a plasmid can be transferred from one bacterium to another through direct contact, allowing rapid spread of useful traits like antibiotic resistance

• Typically carries ~30 genes, most of which provide a selective advantage (e.g., antibiotic resistance, virulence, or metabolic functions).

Plasmid vs. Episome vs Vector

episome: integrates w/ genome

• goes in and out of cell

• all episomes are plasmids but not vv

• called vectors in lab

Definition

• Plasmid = Independent DNA circle in the cytoplasm

• Episome = Special plasmid that can also insert itself into the chromosomal DNA

• Vector = A lab-modified plasmid (or virus) used to carry and express foreign DNA in cells.

Mitochondria

• semi-independant organelle

• funct: energy production and sysnthesis

• matrix: DNA (circular) and ribosomes 70S

• reproduce by binary fission

Outer Membrane

Smooth and porous; allows small molecules and ions to pass through freely. Contains porins.

Intermembrane Space

Space between the outer and inner membranes; important for proton gradient in ETC.

Inner Membrane

Highly folded into cristae to increase surface area; contains ETC complexes and ATP synthase. Selectively permeable.

Matrix

Innermost compartment; contains enzymes for the Krebs cycle, mitochondrial DNA, and ribosomes

Endosymbiotic Theory

• 2 billion years ago

• evolution from prokaryotic organisms by symbiosis

• organelles from prokaryotic cells trapped inside them

Eukaryotic Cilia

• used for locomotion

• composed of mircotubles

• 2 phase stroke: effective (power) stroke and recovery stroke

Eukaryotic Flagella

• fewer flagella/organism

• longer than cilia

• movement is in an undulating motion (base to tip or tip to base)

ultrastructure

• membrane bound cylinders

• microtubles in a 9+2 pattern

• movement and bending is achieved by doublet dynein arms

movement of a dynein motor protein on microtubles

can move both ways up and down

walking motion

Essential Macronutrients

• 6 essential

• CHNOPS

• carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur

CHO

• components of important macromolecules

• backbone of many biological macromolecules

Elemental makeup of important cell molecules

Proteins —> CHONS

Lipids —> CHOP

Carbohydrates —> CHOP

Nucleic Acids —> CHONP

Why are electrons important

• electrons are vehicles for deriving cellular energy, by two important mechanisms:

  • oxidation-reduction reactions of biomolecules

  • via the movement of electrons along electron transport chains

classification of microorganisms

• Carbon Source: Heterotrophs and Autotrophs

• Energy Source: phototrophs and chemotrophs

• Electron Source: lithotrophs and organotrophs

Major Nutritional Types of Microorganisms

most common *

mutualistic

• microorganisms that inhabit a host, yet provide a mutually beneficial element for survival of the host

• ex: pineseedling mycorrhizal roots from one tree spread to innoculate other tree roots

commensal microorganisms

• microorganisms that derive a benefit from a host, however they may not help nor harm the host

• microorganisms that have co-evolved w/ their host (our epithelial body surfaces)

parasitic microorganisms

• a microorganism that inhabit a host, derives nutrients and in the process harms the host

pathogens

• a parasite that can cause severe harm and death to a host

• exceptions are when a commensal/mutulastic bacteria that become opportunistic

saprobic microorganism

• organisms that decompose organic matter

• generally secrete enzymes to the environment

immobilization

• nutrients converted into biomass become tied-up and are unavailable for nutrient cycling

Nitrogen fixation discovered by…

• fritz haber

• carl bosch

• N2 fixation —> NH3

Nitrogen Fixation

• requires the synthesis of nitrogenase (enzyme inactivated by oxygen)

• organisms that nitrogen fix

  • rhizobium spp. (uses legume nodule)

    • bacteria —> infection thread —> early nodule

      inside nodules they nitrogen using nitrogenase but they need low oxygen conditions

      need a compartment to fix nitrogen

  • clostridium and azotobacter spp. (free-living soil bacteria)

    • enviornment is already anerobic

  • cyanobacteria (heterocysts)

    • heterocysts: thick walled compartments where nitrogenase converts N2 to NH3 (uses energy)

    • they also block oxygen

    • found in water

What is nitrogen fixation

• the process of converting atmospheric nitrogen gas (N2) into ammonia (NH3), which plants and microbes can use

• done by certain microorganisms not by plants of animals

• enzyme that perform this task are called nitrogenous

  • but its inactivated by oxygen

  • this is why bacteria need special environments to use it

  • nitrogenase requires energy

  • N2 —> NH3

mineralization (decomposition)

• the process by which organic matter is decomposed and released as simple, inorganic compounds

• aerobic and anaerobic bacteria, fungi

• recovering sequestered organic nitrogen into Ammonium (NH4+)

• organic N (aa or na) —> NH4+

• aka: Ammonification

nitrification

• a 2 step process that us carried out by two diff genus of bacteria

  • step 1: NH4+ —> NO2- carried out by nitrosomonas

  • step 2: NO2- —> NO3- carried out by nitrobacter

• long membrane tublues: generate a H+ gradient from the oxidation of Ammonium

• assimilatory reduction

• taking (NH4+) into a readily usable oxidized nitrate into usable oxidized (NO3-)

assimilatory reduction

• incorporation of an oxidized (useable) form of molecule into microbial biomass via reduction

• NO₃⁻→NO₂⁻→NH₄⁺→Amino acids

• consumes energy

• Build proteins, nucleic acids, etc.

• reduction of nitrate (NO3-)

denitrification

• uses dissimilatory reduction

• occurs in many bacteria

• dissimilatory reduction: NO3- serves as a terminal electron acceptor during anaerobic respiration; when gases N2 and N2O are produced and released into atmosphere, process called denitrification

• N2O —> N2

• DR:

  • NO3- —> N2

  • NO3- —> N2O

  • NO3- —> NO2-

wastewater

• any water that has been adversely affected by humans

sewage

• subset of water contaminated by feces or urine

whitewater

• potable water

greywater

• household water that has no fecal matter

blackwater

• fecal contaminated water

goals of wastewater treatment

• return to then environment free of pathogens

• decrease the load of nutrients (carbon and nitrogen)

  • the goal is NOT to clean wastewater to drinking water levels

oxygen depletion

Oxygen depletion in water refers to a reduction in the amount of dissolved oxygen (DO) available in a body of water

• caused by things like thermal pollution, runoff, sewage pollution, algae growth

Waste Water Treatment Stages

1. Headworks: removes bulk inorganic solid

2. Primary: removal of bulk organic solid material

3. Secondary: removal of dissolved organic matter by conversion into microbial biomass and CO2 (activated sludge)

4. Tertiary: Final purification and removal of : nitrogen and phosphorous compounds, heavy metals, biodegradable organics and remaining microbes, including viruses

Primary Treatment

1. Screening: use of fine screens to remove smaller debris

2. Sedimentation/clarification: large, still tanks of water allow for removal of about 90% of settleable solids, about 55% suspended solid removed (sludge) oil and grease skimmed from top

Secondary treatment

*nutrient removal

• aeration basin: O2 and activated sludge is mixed w/ clarified water (mixed liquor)

• allows aerobic bacteria to grow and remove organic compounds

• 2ary treatment reduces dissolved organics available to microorganisms by about 90-95%

activated sludge

• first described in the 1914 by E. Ardern and W.T Locket (great britain)

• activated sludge flocs are complex system composed of microbial cells and minerals in a polymeric matrix

  • saprophytic bacteria

  • archea

  • protoza: amoebae, spirotrichs, peritrichs

  • rotifers

• a fraction of the activated sludge is returned to the aeration basin. Excess is removed for further treatment

• healthy flocs are dense, large particulate that settle during sedimentation

• healthy sludge must be maintained and can be disrupted by influent contaminants:

  • toxins, medications, antifreeze, floods

Sludge bulking

• the failure of sludge to seperate during sedimentation

• generally a result of poor aeration, inappropriate microbial communities in the activated sludge. Overgrowth of filamentous bacteria: Sphaerotilus, Thiothrix

• filamentous bacteria have a greater volume and surface areas, resulting in open/porus flocs that dont settle

Secondary Treatment

*microbial removal

• secondary sedimentation/clarification: same as primary, large particulate settle are removed

• other secondary treatment: trickling filter

Tertiary treatment

• wetlands as tertiary treatment

Sludge Treatment

• reduce pathogens, odors and lower concentrations of metals

• Step 1: Dewatering (centrifuge)

• Step 2: Anaerobic digestion

• Step 3: final dehydration and removal

Anaerobic Digestion

1. fermentation: big molecules to small molecules (generally anerobic)

2. acetogenic: makes acetate, H2, CO2 (takes another week)

3. Methanogenic reaction: archea breaks into single carbon molecules

what is a dehydrater

• pressing the remainder of waste

Baby blue syndrome

• when there are inc levels of nitrates in water met hemoglobin goes up

• methemoglobin (ferric)

  • does not bind to oxygen as well

  • 3 bound oxygens instead of 4 bound oxygens

  • Methemoglobin cannot carry oxygen, leading to tissue hypoxia (lack of oxygen)

• adults have the enzyme cytochrome b reductase that converts it back but babies dont have it

energy

• the ability to do work

• displayed in many forms and is transferable, thus converted in form

• thermodynamics is the study of energy

major types of energy

• thermal energy (heat)

• rediant energy (waves)

• electrical energy (flow of e-)

• mechanical energy (physical change in position)

• atomic energy (stored energy in an atomic nucleus)

• chemical energy (stored energy in the bonds of molecules

  • what we focus on

catabolism

• the process and pathways by which larger molecules are broken down and in turn release energy

anabolism

• the process by which larger molecules are built from smaller units, using energy in the process

exergonic reactions

• Products have less free energy than reactants

• energy released is used by the cell

• spontaneous

endergonic

• Products have more free energy than reactants

• energy is supplied (enters) for reaction to occur

• nonspontaneous

Why is ATP important

ATP: cellular energy storage to carry out metabolic reactions

ATP: is a high-energy molecule

ATP: almost completely hydrlyzes to ADP

ATP/ADP cycle

Other important cellular energy storage

GTP

NADH
NADPH

FADH2

• they all have a similar backbone

  • adenine or gaunine

NAD+

• gets reduced to NADH

• they are limiting reagent (especially NAD+)

• recycling NAD+ is much faster and efficient compared to de-novo biosynthesis (generating from scratch)

common monosaccharides

• glucose

• fructose

• galactose

glucose is the most common

Glycolysis

• breaking sugar

• taking a high energy potential molecule and breaking it to get that energy

• glucose is a good e donor

• breaking glucose= few ATP and a lot of potential energy

• NAD+ is a limiting agent

• yields 2 pyruvate

• what is required: ATP, NAD+, glucose, enzymes

Fates of Pyruvate

anaerobic respiration: nonoxygen electron acceptors (ex: SO4²-, NO3-, CO3²-, )

aerobic respiration: O2 is final electron acceptor

fermentation: an organic molecules is final electron acceptor (pyruvate, acetaldehyde, etc.)

• yields the least amount of ATP

Exactly the same till the last step

• aerobic and anaerobic are exactly the same till the last step (different electron donor)

Common features and differences (aerobic respiration, anaerobic respiration, and fermentation

• In aerobic respiration there are 4 complexes and O2 is the final e- acceptor making water

  • yields about > 30 ATPs

• In anaerobic respiration (obligate anaerobes)

  • complex 4’s are different

  • instead of oxygen: Nitrate, Sulfate, Fumarate are the final electron acceptors

• Fermentation (most different)

  • for glycolysis to continue, a limiting reagent must be regenerated (NAD)

  • uses pyruvate as an electron acceptor in the absence of the ETC

    • this is what maintains glycolysis

    • is diverse (soy sauce, vinegar, cheese)

  • all cells; but not all cells carryout for a long time

locations of pathways in Eukaryotes

External to mitochondrion

• glycolysis

• fermentation

Inside mitochondrion inner membrane

• respiratory chain

Matrix

• citric acid cycle

Locations of pathways in Prokaryotes

Cytoplasm

• glycolysis

• fermentation

• citric acid cycle

Inner Face of Plasma Membrane

• respiratory chain

Where is the ETC located

Prokaryotes: along the plasma membrane

Eukaryotes: inner membrane of the mitochondria

H+ concentration gradient role of ATP synthase

• complexes accept electrons gaining energy to pump H+ which creates a high concentration gradient in the inter membrane space and a low concentration gradient in the mitochondrial matrix

• this concentration gradient powers ATP synthase allowing it to generated many ATP molecules

• Describe H+ concentration gradient (proton motive force/stored potential energy) and role of ATP synthase

• the proton motive force causes protons to diffuse back into the mitochondrial matrix through the membrane channel protein ATP synthase

Aerobic vs. anaerobic fermentation (Pasteur vs Crabtree effect)

• Aerobic Fermentation

  • Crabtree Effect

  • abnormal but an increase in sugar concentration pushes the pathway through fermentation to make ethanol

  • seen in organisms such as yeast

• Anaerobic Fermentation

  • Pasteur Effect

  • if O2 is present, most organisms use aerobic respiration

Four Important Observations about Fermentation

1. NADH is oxidized to NAD+

2. The electron acceptor is pyruvate or pyruvate derivative (Fermentation, ETC are respiration)

3. An ETC cannot operate = decreased ATP yield (in general not always)

4. O2 generally not present (where pasteur vs crabtree comes into play)

What must pyruvate be modified to, to enter the TCA cycle?

pyruvate —> acetyl CoA

Binary Fission

• one cell divides into two cells

• specific to prokaryotes and archaea

• asexual reproduction and cell division

• rapid process about 20 min @ RT (not for all microbes)

• some eukaryotes (some yeast) and eukaryotic organelles (mitochondria) divide by binary fission