BISC 261 Exam 2

metabolism

total of all chemical reactions in the cell

what are the aspects of metabolism common to all organisms (6)?

* life obeys the laws of thermodynamics
* the energy cells obtain from their environment is most often conserved as ATP
* oxidation-reduction (redox) reactions play a critical role in energy conservation
* the chemical reactions that occur in cells are organized into pathways
* each reaction of a pathway is catalyzed by an enzyme or a ribozyme
* the functioning of biochemical pathways is regulated

in the TCA cycle, two carbons are removed from citric acid in the form of __________, thereby regenerating oxaloacetate to complete the cycle.

carbon dioxide

processes that supply ATP, reducing power, and precursor metabolites are collectively referred to as ___________ reactions.

fueling

a reaction that releases energy is endergonic or exergonic?

exergonic

enzymes are usually named based on _____________

the substrates they act on and the type of reaction they catalyze

cells carry out 3 major types of work; which involves nutrient uptake and waste elimination?

transport work

the TCA cycle begins when…?

a) pyruvate from the glycolytic pathway is added to oxaloacetate

b) NADH is oxidized to NAD+, which provides a source of electrons to drive the cycle

c) ATP from the glycolytic pathway is hydrolyzed, providing the energy to start the cycle

d) pyruvate from the glycolytic pathway is oxidized to acetyl-CoA, which is added to oxaloacetate

pyruvate from the glycolytic pathway is oxidized to acetyl-CoA, which is added to oxaloacetate

aerobic respiration, anaerobic respiration, and fermentation are 3 basic types of what type of organism’s metabolism? (ex: photoorganoautotroph)

chemoorganoheterotrophs

if deltaG is negative, is the reaction spontaneous or not?

spontaneous

holoenzyme = ____________ + ___________

apoenzyme + cofactor

how do enzymes lower Ea (activation energy)?

* increasing concentrations of substrates at active site of enzyme
* orienting substrates properly w respect to each other to form transition state complex
* induced fit for enzyme-substrate interaction

what 3 conditions is enzyme activity significantly impacted by?

substrate concentration, pH, and temperature

what are some things ribozymes can do (3)?

* catalyze peptide bond formation
* self-splicing
* involved in self-replication

what are 3 methods for regulating metabolism in microbes?

* metabolic channeling
* regulation of synthesis of a particular enzyme
* direct controlling of the activity of enzymes

what small molecule is involved in allosteric regulation?

the allosteric effector

what happens when an allosteric effector binds to an enzyme’s regulatory site?

the enzyme’s catalytic site changes, which allows it to either bind to substrates or be inhibited from binding substrates

how does covalent modification of enzymes work?

an addition or removal of a chemical group (phosphoryl, methyl, adenylyl) is added or removed from an enzyme. An enzyme with a chemical group attached has lower activity levels. This is reversible.

what is common among all reproductive strategies?

the copying and segregation of the genome first

what are the three phases of the bacterial cell cycle (binary fission)?

* period of growth after the cell is born
* chromosome replication and partitioning
* cytokinesis and septum formation

where is new peptidoglycan built in spherical cells vs rod-shaped cells?

spherical: only at midcell

rod-shaped: along side of cell but not at poles, then confined to midcell.

what is exponential phase also called?

log phase

what is remarkable about the exponential phase considering chemical and physical properties?

chemical and physical properties of cells are most uniform during this phase

what is the process of long-term stationary phase marked by?

successive waves of genetically distinct variants

what do mechanosensitive channels do and where are they located?

located in the plasma membrane, they allow solutes to leave when the cell finds itself in a hypotonic solution.

what can a cell do in defense when it finds itself in a hypertonic solution?

increase internal solute concentration w compatible solutes

what salt levels do halophiles and extreme halophiles grow optimally in/require?

halophiles optimally grow in salts at a concentration of \~0.2M, while extreme halophiles require concentrations between 3M to 6.2M

alongside salt, extreme halophiles also live in extremely high concentrations of what element?

potassium

what water activity will most microorganisms grow well under?

0\.98 or higher

what is pH a measure of?

relative acidity of a solution

what pH do acidophiles, neutrophiles, and alkaliphiles live between?

Acidophiles: between pH 0 and 5.5

Neutrophiles: between pH 5.5 and 8

Alkaliphiles: between pH 8 and 11.5

are most bacteria and protists acidophiles, neutrophiles, or alkaliphiles?

neutrophiles

most fungi prefer what pH levels?

pH 4 to 6

true or false: alkaliphiles are only found in archaea

false

what do neutrophiles exchange potassium for (to maintain neutral cytoplasmic pH)?

protons (H+)

what can acidic tolerant microbes synthesize to maintain neutral cytoplasmic pH?

acid and heat shock proteins

what temperature range do mesophiles live under?

20 to 45 degrees C.

what temperature ranges do the following organisms live under?

Psychrophiles

Psychrotrophs

Mesophiles

Thermophiles

Hyperthermophiles

Psychrophiles: 0°C to 20°C

Psychrotrophs: 0°C to 35°C

Mesophiles: 20°C to 45°C

Thermophiles: 45°C to 85°C

Hyperthermophiles: 85°C to 100°C

how are protein structures stabilized in thermophiles (3)?

* more H bonds
* more proline
* chaperones

how is the membrane stabilized in thermophiles (4)?

* more saturated
* more branched
* of higher molecular weight lipids
* ether linkages in archaeal membranes

why is oxygen toxic?

oxygen reduces into reactive oxygen species such as hydrogen peroxide

what protective enzymes do aerobes produce?

superoxide dismutase (SOD) and catalase

describe the oxygen needs for the following organisms:

Obligate aerobe

Microaerophile

Facultative anaerobe

Aerotolerant anaerobe

Strict anaerobe

obligate aerobe: need oxygen

microaerophile: need 2-10% oxygen

facultative anaerobe: prefer oxygen

aerotolerant anaerobe: ignore oxygen

strict anaerobe: oxygen is toxic; cannot survive in presence of it

microbial environments are ___________ and constantly ___________

complex, changing

oligotrophic

low-nutrient

what kind of environment do most microbes inhabit?

oligotrophic environments

a surface must be _________________ before a biofilm can form

conditioned

what does enrichment of pure cultures do?

encourages growth of microbes w particular characteristics and inhibiting the growth of other microbes

the methods for isolating pure cultures was developed by who?

robert koch

what is the difference between flow cytometry and the coulter counter?

flow cytometry uses a laser, coulter counter is electronic and measures electrical resistance

what 3 things does life require?

energy, electrons, and carbon

where do chemotrophs obtain energy from?

oxidation of chemical compounds

where do lithotrophs and organotrophs obtain electrons?

lithotrophs from reduced inorganic substances, organotrophs from organic compounds

why does life need carbon?

proteins, carbohydrates, lipids, nucleic acids, and other essential molecules are made up of carbon

true or false: autotrophs’ energy and carbon source is the same.

false

state what these word parts mean when describing a nutritional type of an organism.

Photo-

Chemo-

\-organo-

\-litho-

\-heterotroph

\-autotroph

photo- and chemo- refer to energy source: light, chemical compounds.

\-organo- and -litho- refer to electron source: organic compounds, inorganic substances.

\-heterotroph and -autotroph refer to carbon source: organic, carbon dioxide

organisms all have what 3 same, basic needs that are called fueling reactions?

ATP as energy currency, reducing power to supply electrons for chemical reactions, precursor metabolites for biosynthesis

what is reducing power for?

supplying electrons for chemical reactions

what are precursor metabolites for?

biosynthesis

what are chemoorganotrophs also called?

chemoheterotrophs

what are the two ways ATP can be generated in chemoorganotrophs?

oxidative phosphorylation and substrate-level phosphorylation

what are the three processes chemoorganotrophs can use to catabolize an energy source?

aerobic respiration, anaerobic respiration, and fermentation

what comes together to make pyruvate and ATP during substrate-level phosphorylation? what enzyme does this take place in?

phosphoenolpyruvate (PEP) and ADP, pyruvate kinase

what are some examples of terminal electron carriers in anaerobic respiration?

SO4 2-, NO3-, CO2, fumarate

what is the only way ATP is synthesized in chemoorganotrophic fermentation?

substrate-level phosphorylation

how do enzymes of the Embden-Meyerhof pathways function during glycolysis and glyconeogenesis?

catabolically during glycolysis, anabolically during gluconeogenesis

what 3 steps can aerobic respiration be divided into?

glycolysis & pyruvate oxidation, krebs (TCA) cycle, oxidative phosphorylation (ETC)

what are the three common routes of breaking down glucose?

embden-meyerhof, entner-doudoroff, and penthose phosphate pathways

what are the products of the embden-meyerhof pathway?

2 pyruvate, 2 ATP, 2 NADH, 2 H+

where does the embden-meyerhof pathway occur?

in the cytoplasmic matrix of most microorganisms, plants, and animals

what is the most common pathway for glucose degradation to pyruvate?

emdben-meyerhof

what are the two phases of the embden-meyerhof pathway?

6C and 3C

what microbes use the entner-doudoroff pathway?

some Gram-negative bacteria, especially those found in soil

what does the entner-doudoroff pathway generate per glucose molecule?

1 ATP, 1 NADPH, 1 NADH

what does the pentose phosphate pathway produce that are needed for biosynthesis?

sugars

what does the TCA cycle generate for each acetyl-CoA oxidized?

3 CO2, 3 NADH, 1 FADH, 1 GPT/ATP

when is the most ATP made?

when NADH and FADH2

can proteins diffuse across the membrane?

no

where are bacterial and archaeal ETCs located?

in the plasma membrane

how are bacterial and archaeal ETCs different from mitochondrial ETCs?

* different electron carriers
* different terminal oxidases
* may be branched
* may be shorter--fewer protons and therefore less energy

what oxygen classification is *Paracoccus denitrificans*?

facultative anaerobe

what does *Paracoccus denitrificans* use instead of glucose as a source of energy and electrons?

one-carbon molecules

what are the upper and lower branches of *E. coli*’s ETC used for?

upper-low aeration conditions, lower-high aeration conditions

what is the most widely accepted hypothesis to explain oxidative phosphorylation?

chemiosmotic hypothesis

what is the chemiosmotic hypothesis?

protons move outward from mitochondrial matrix as electrons are transported, forming a concentration gradient of protons as well as a charge gradient. the electrical and chemical potential difference make up the proton motive force, which powers a variety of cell work

what can proton motive force power?

ADP + Pi to ATP, bacterial flagella rotation, active transport

what factors can affect ATP yield (3)?

* bacterial ETCs are shorter
* ATP production may vary with environmental conditions
* PMF in bacteria and archaea is used for other purposes

what is denitrification?

the reduction of nitrate to nitrogen gas

what does denitrification cause?

loss of fertility

is the substrate completely catalyzed in fermentation?

no

what are the steps of fermentation (3)?

1. SLP of 2 ATP
2. 3C pyruvate to 2C acetaldehyde and CO2
3. 2C acetaldehyde converted to 2C ethanol

what are common energy sources other than glucose?

triclycerides

where are fatty acids often oxidized?

the b oxidation pathway

what do proteases do?

hydrolyze protein to amino acids

what is deamination?

removal of amino group from amino acid

what does deamination result in?

organic acids converted to acetyl-CoA, pyruvate, or TCA cycle intermediates

why are plate count results often expressed in colony forming units?

because it’s not possible to be sure that each colony arose from a single cell, it could offput or incorrectly estimate the correct count if measured simply in number of microorganisms

what enzyme hydrolyzes proteins to amino acids?

proteases

how many NADH are generated in the TCA cycle per glucose molecule?

6

what type of phosphorylation does chemiosmosis refer to?

oxidative phosphorylation