Microbiology exam 2

What is the relationship between the pine beetle and the fungus Grosmannia clavigera?

Symbiotic: the fungus neutralizes tree toxins for beetles, and beetles transport the fungus to new trees.

What cause blue rot in trees? Why is this bad for climate change?

pine beetles and this is bad for climate change because the beetles thrive in heat and it is not getting as cold the beetles are surviving through winter and killing the forests

What is endocytosis and what are its key features?

Energy-requiring (ATP) eukaryotic process where particles are enclosed in vesicles and destroyed in lysosomes.

what is an example of endocytosis?

cell eating amoeba

What is the endosymbiotic hypothesis for the origin of mitochondria and chloroplasts?

Mitochondria and chloroplasts originated as preliving prokaryotic bacteria engulfed by host eukaryotic cells.

Who proposed the endosymbiotic hypothesis?

Lynn Margulis and Konstantin Mereschkowsky.

What evidence supports the bacterial origin of mitochondria and chloroplasts?

Circular DNA, 70S ribosomes, binary fission reproduction, and bacterial-like double phospholipid membranes.

What is a recent example of an endosymbiotic event?

The pea aphid and Buchnera aphidicola, an endosymbiont transitioning into an organelle.

Why do cells have a nucleus

Separates transcription/translation for gene regulation.

what are two main nucleus origin theories?

Theories: Karyogenetic (membrane envelope formed) and Endokaryotic (guest cell entered host).

What are two main ways to define a microbial species?

Phylogenetic (genetic sequence similarity like 16S rRNA) and Ecological (occupying a distinct ecological niche).

Why is it difficult to define a microbial species?

Microbes reproduce asexually, have massive genetic diversity, and most have never been cultured or isolated. (species --> operational taxonomic unit)

How does the biological species concept compare to microbial species concepts?

Biological concept relies on interbreeding (fails for asexual microbes); microbial concepts rely on genomic similarity and ecological distinctness.

What is the most common operational definition of a microbial species and its limitations?

>97-98.7% 16S rRNA sequence identity; limited by horizontal gene transfer and arbitrary historical thresholds.

What is an Operational Taxonomic Unit (OTU)?

An operational proxy for a microbial species used in sequencing, grouping clusters of similar sequence reads.

What is lateral (horizontal) gene transfer?

The transfer of genetic material between organisms other than vertical transfer from parent to offspring.

What are the main steps in bacterial binary fission?

semi-conservative chromosome replication, partitioning, growth, and septation

In Steps 1&2 o binary fission what occurs?

Origin

Initial replication

Threshold cell length reached

Septum formed and divide

In steps 3&4 of binary fission what occurs?

Formation of new cell wall (Fts Z ring: basic cell wall protein)

Cocci: in center

Bacilli: throughout cell

What molecules give bacilli their rod shape

MreB gene directs peptidoglycan synthesis

What molecules give Vibrio their comma shape?

crescentin protein restricts growth along one curve

How is new peptidoglycan synthesized and incorporated into the cell wall?

NAG-NAM units cross the membrane via lipid carriers and are cross-linked into autolysin breaks by transpeptidases.

How does penicillin inhibit cell wall synthesis?

Mimics D-alanyl-D-alanine, binding transpeptidases (PBPs) to prevent peptidoglycan cross-linking, causing osmotic lysis.

What are the five phases of growth in a batch culture?

Lag phase, log (exponential) phase, stationary phase, death phase, and long-term stationary phase.

lag phase

new components & vary length

log phase

exponential rate of growth, constant, @max rate

stationary phase

growth=death, nutrient limitation, limited oxygen availability, toxic waste accumulation, population density reached

Triggers spirolation: endospore and other stress related mechanism activated

death phase

death > growth

long term stationary phase

growth and death

What equation calculates population size during exponential cell growth?

N = N₀ × 2ⁿ (Starting population × 2^(number of generations)).

What is the difference between an extremophile and an extremotolerant organism?

Extremophiles require and thrive in extreme conditions; extremotolerant organisms survive them but prefer neutral conditions.

halophile

35-40% salt, balance with internal solute levels, pump inorganic ions from environment into cell, synthesis or concentration of organic solutes

osmophiles

organisms that live in environments high in sugar

xerophiles

grow in very dry environment

psychrophiles

cold temp (4C)

mesophiles

(20-45C) mid-range temp, warm-blooded animals

acidophiles

low pH

alkayliophiles

high pH

What is water activity (a_w)

Vapor pressure of air in equilibrium with substance / vapor pressure of pure water

Pure water = 1

what is the theoretical limit for life?

0.700

How do hypertonic solutions affect cell water movement?

higher solute outside (water exits)

How do hypotonic solution affect cell water movement?

lower solute outside (water enters)

How do isotonic solution affect cell water movement?

equal solute concentration

How do microbial cells adapt to high salinity environments?

accumulating compatible solutes internally to balance osmotic pressure

How do microbial cells adapt to acid/base environments?

pumps to expel excess protons (H+) or import them, along with modifications to membrane lipid composition

How do microbes adapt to high and low temperature extremes?

high temp: saturated fatty acids and heat-stable proteins; Low temp: unsaturated fatty acids and cold-shock proteins.

What are the five main categories of microbial oxygen requirements?

aerobes, anaerobes, facultative anaerobes, aerotolerant anaerobes, and microaerophiles.

aerobe

require oxygen to live

anaerobes

do not require oxygen and can be killed by exposure

facultative organisms

can live with or without oxygen

aerotolerant anaerobes

can tolerate but don't use oxygen

microaerophiles

can use oxygen at low levels

What are reactive oxygen species (ROS), and how do cells neutralize them?

Toxic oxygen derivatives (superoxide, hydrogen peroxide, medical hydroxyl); neutralized by enzymes like catalase, peroxidase, and superoxide dismutase.

What is a mesophile?

An organism growing best at moderate temperatures (20-45 °C), such as warm-blooded animals.

What is a biofilm?

A surface-attached microbial community encased in a self-produced matrix with water channels, regulated by quorum sensing. (ex: TOOTH)

What are the functional categories of culture media?

Supportive (general purpose), enriched, selective, and differential media.

supportive general purpose media

(tsa) support growth of many microorganism

enriched media

(blood agar) media supplemented by species

selective media

( MacConkey) favor some growth and inhibit other

differential media

(MacConkey & blood agar) distinguish groups via biological characteristics

What are the 3 main kinds of media covered in lecture

chemical composition, physical nature, function

chemical composition

defined/complex

physical nature media

liquid or solid

function media

supportive, enriched, selective, differential

How do MacConkey agar and blood agar function as differential media?

MacConkey differentiates lactose fermenters (pink vs yellow); blood agar differentiates hemolytic vs non-hemolytic bacteria.

What are common methods for measuring cell growth and their main limitations?

Microscopic (can't tell live/dead), flow cytometry (requires dyes), viable counts (live only), turbidimetric (measures total biomass).

What is the difference between catabolism and anabolism?

Catabolism breaks down complex molecules releasing energy; anabolism synthesizes complex molecules consuming energy.

Why do microbes perform catabolism?

To harvest energy as ATP and reducing power (NADH/NADPH) for cellular maintenance and growth.

What is an enzyme and what are its structural components?

A biological protein catalyst consisting of an apoenzyme (protein part) plus cofactors/coenzymes forming a holoenzyme.

how do enzymes work?

Enzymes bind substrates in an optimal orientation and stabilize the transition state, effectively lowering the activation energy barrier

What is activation energy?

is the energy threshold required to break existing chemical bonds and start a reaction

What is a ribozyme?

A catalytic RNA molecule that functions as an enzyme.

What is metabolic compartmentalization in eukaryotes?

Organizing pathways into membrane-bound organelles to isolate incompatible reactions and concentrate reactants.

How does allosteric regulation control enzyme activity?

Effector molecules bind to an allosteric site, altering the active site structure to increase or decrease activity.

What is the difference between competitive and non-competitive enzyme inhibition?

Competitive inhibitors bind directly to the active site; non-competitive inhibitors bind to an allosteric site.

what's an example of competitive inhibition

ethanol v methanol → (ethanol → acetaldehyde → acetate) works against methanol and can save lives VS (methanol → formaldehyde → formate) is deadly and causes the mitochondria to stop working

What is feedback inhibition?

The end product of a metabolic pathway binds an allosteric site on an early enzyme to stop production.

what are the major nutritional types of microorganisms?

Energy: phototrophs/chemotrophs; Electrons: lithotrophs/organotrophs; Carbon: autotrophs/heterotrophs.

photo

light

chemo

chemicals

litho

inorganic electron donor

organo

organic electron donors

auto

inorganic carbon

hetero

organic carbon source

What nutritional classifications apply to humans and plants?

Humans are chemoorganoheterotrophs; plants are photolithoautotrophs.

What are the inputs and net outputs of the Embden-Meyerhof glycolysis pathway?

Inputs: glucose, 2 ATP, 2 NAD+; Net

outputs: 2 pyruvate, 2 net ATP, and 2 NADH.

How does the Entner-Doudoroff (ED) pathway differ from standard glycolysis (EMP)?

ED yields only 1 net ATP, 1 NADH, and 1 NADPH per glucose, whereas EMP yields 2 net ATP and 2 NADH.

What are the primary products of the pentose phosphate pathway?

NADPH for biosynthesis/redox balance and ribose-5-phosphate for nucleotide synthesis.

How are fats/lipids digested/catabolized for energy?

lipases break down triglycerides into glycerol (enter glycolysis) and fatty acids (broken down via BB-oxidation into acetyl-CoA)

How are proteins digested/catabolized for energy?

proteases break proteins into amino acids, which are deaminated (amino group removed) and enter glycolysis or the citric acid cycle as metabolic intermediates

What six chemical elements (CHNOPS) are pivotal to life?

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur.

Why are silicon and arsenic theorized as alternative elements for life?

Silicon forms 4 bonds like carbon; arsenic is chemically similar to phosphorus below it on the periodic table.

How is pyruvate modified before entering the citric acid cycle?

Decarboxylated and oxidized by pyruvate dehydrogenase into acetyl-CoA, yielding 1 CO₂ and 1 NADH.

What occurs during the Citric Acid (Krebs) Cycle?

Acetyl-CoA combines with oxaloacetate; oxidation steps generate ATP/GTP, NADH, FADH₂, and CO₂ while regenerating oxaloacetate.

What is the difference between substrate-level and oxidative phosphorylation?

Substrate-level directly transfers a phosphate from a substrate to ADP; oxidative uses proton motive force via an ETC.

Substrate-level phosphorylation

direct transfer of a phosphate group from a metabolic intermediate to ADP to form ATP

oxidative phosphorylation

ATP synthesis driven by the proton motive force (PMF) generated as electrons flow down an electron transport chain

What is the main function of the electron transport chain (ETC)?

Passes electrons along carriers to pump protons, generating a proton motive force (PMF) for ATP synthesis.

What is the terminal electron acceptor and theoretical ATP yield of aerobic respiration?

Oxygen (O₂) is the terminal electron acceptor; theoretical yield is 30-32 ATP per glucose.

Why is the theoretical ATP yield of aerobic respiration rarely achieved?

Proton motive force is consumed for active transport and flagellar rotation, and membranes leak protons.