Exam 2 study guide

Autotroph

an organism that must obtain its carbon in an organic form

heterotroph

an organism that uses in organic CO2 as its carbon source (convert CO2 to organic compounds and not nutritionally dependent)

chemotroph

microbe that photosynthesis

phototroph

microbe that gets its energy from chemical compound

what do we call any substance that must be provided to an organism

essential nutrient

why do bacteria require trace elements

they act as cofactors for enzymes, which are essential for various biological reactions

photoautotroph

• energy source: sunlight

• carbon source: CO2

• example organism: photosynthesis organisms (ex. plants)

photoheterotroph

• energy source: sunlight

• carbon source: organic

• example organism: purple and green photosynthesis bacteria

chemoautotroph

• energy source: inorganic compounds (minerals)

• carbon source: CO2

• example organism: Thiobacillus, “rock-eating” bacteria

chemoheterotroph

• energy source: metabolic conversion of the nutrients from other organisms

• carbon source: organic

• example organism: protozoa, fungi, many bacteria, animals

chemolithotrophs

oxidize inorganic compounds to get energy and use CO2 from the environment (chemoautotrophs)

saprobes

breakdown dead organic matter for energy and carbon (heterotroph)

parasite

get energy by depleting host’s nutrients (glucose, amino acids, lipids) and get carbon from host through glycolysis (heterotroph)

ectoparasite

live on the body

endoparasite

live in the organs and tissues

intracellular parasite

live within cells

obligate parasites

unable to grow outside of a living host (leprosy bacillus and syphillis spirochete)

carbon

• how elements is obtained: heterotroph = use organic carbon sources and autotroph = use CO2

• used to make: all macromolecules

hydrogen

• how elements is obtained: acquired through organic compounds and several inorganic compounds, including water, salts, and certain naturally occurring gases

• used to make: all macromolecules (help cells maintain pH, form hydrogen bonds, source of free energy)

nitrogen

how elements is obtained:

• most bacteria decompose proteins to get a source of N

• some bacteria use NH4/ammonium or NO3 (nitrated from organic material)

• a few bacteria use N2 gas from atmosphere in nitrogen fixation

used to make: proteins and nucleic acids (ATP)

oxygen

how elements is obtained:

• obtained trough organic compounds and inorganic salts such as sulfates, phosphates, nitrates, and water

• plays an important role in the structural enzymatic function of the cell

used to make: all macromolecules

phophorus

how elements is obtained:

• (PO4)³ (phosphate ion) is a source of phosphorus, found in rocks and oceanic mineral deposits

used to make: nucleic acids (DNA, RNA, ATP) and cell membranes

sulfur

how elements is obtained:

• most bacteria decompose proteins for the sulfur source

• some bacteria use (SO4)²- (sulfate ion) or H2S (hydrogen sulfide)

used to make: amino acids and vitamins

obligate O2

• oxygen requirement: require O2

• Example: pseudomonas aeruginosa - inflections in burn victims and with cystic fibrosis

microaerophile

• oxygen requirement: require low O2 concentrations

• Example: Helicobacter pylori - ulcers

obligate anaerobe

• oxygen requirement: cease growth or die in O2

• Example: Clostridium perfringens = gas gengrene

facultative anaerobe

• oxygen requirement: grow with or without O2, but grow better with O2 (use it when given a choice)

• Example: E. coli - cause of UTI

aerotolerant anaerobe

• oxygen requirement: tolerate O2, but don’t use it (can grow in O2, but don’t use it)

• Example: streptococcus pyogenes = causes strep throat (strict fermenters)

a microorganism that does not have catalase or superoxide dismutase would find it difficult to live in an environment with

oxygen

what is superoxide dismutase use for? what types of organisms produce superoxide dismutase and why

used to neutralize superoxide ions. convert to hydrogen peroxide to O2 gas. used by organisms that grow in the presence of O2

what is catalase used for. what type of organisms produce catalase and why

used to neutralize hydrogen peroxide. types of organisms include organisms that use O2 as their FEA. Produces water and oxygen

what is peroxidase used for. what types of organisms produce peroxidase and why

used to neutralize hydrogen peroxide and produce water. used by organisms that grow in O2, but don’t use it

thioglycolate broth

use a reducing media to create an anaerobic environment

capnophile

organisms that grow best at higher CO2 tension than is normally present in atmosphere (can be grown in a candle jar)

ex: Neisseria (gonorrhea and meningitis), brucella (undulant fever), and streptococcus pneumoniae

minimum growth temperature

lowest temperature that permits a microbe’s continued growth and metabolism → below this temp, activity stops

maximum growth temp

the highest temp at which growth and metabolism can produce before proteins or denatures

optimum growth temp

intermediate between minimum and maximum that promotes the fastest rate of growth

psychrophile

• meaning: cold lover

• growth range: -20-15

• optimal growth temperature: 0-10

• example: n/a

• where organism is found: refrigerator temp, bacteria, fungus, algae like lakes, river, snowfields, polar ice, and the deep ocean

psychotroph

• meaning: cold eater

• growth range: 0-30

• optimal growth temperature: 15-30

• example: listeria monocytogenes cause listeriosis

• where organism is found: room temp, found in deli meat, milk (cows get listeriosis), and unpasteurized cheese

mesophile

• meaning: moderate lover

• growth range: 10-50

• optimal growth temperature: 20-45

• example: E. coli - sepsis infection, UTI, food poisoning and S. aureus - skin infection, sepsis, pneumonia

• where organism is found: animals and plants, soil, water in temperate subtropical and tropical regions

thermophile

• meaning: heat lovers

• growth range: 45-80

• optimal growth temperature: 50-60

• example: n/a (most eukaryotic cells cannot survive above 60 C)

• where organism is found sunlit soil, water with volcanic activity, compost biles, and hot springs

do most psychotrophs cause human disease

no because they don’t grow at 37 C or human body temp

what problems do psychrotrophs cause for humans

can cause sepsis and meningitis for immununocompromised. cause baby to be stillborn or contract meningitides (brain injury, and 60% morality rate)

which temperature requirement organisms cause the most food spoilage and human disease

31 because it is human body temp

why can a fever be useful for the body

increase body temp and mesophiles suffer and fever try to inhibit microbes’ growth

thermoduric microbes

normally mesophiles, but can survive short exposure to high temp (ex. heat resistant endospores like bacillus and clostridum)

what pH range do most bacteria grow at

6.5-7.5

what pH range do most molds and yeast grow at

5-6

acidophiles

• grow in acidic environments

• most food spoilage microbes

neutrophiles

• grow in neutral pH environments

• most normal biota (flora; around 7)

alkaliphiles

• grow in alkaline (basic environments)

which pH requirement organisms are likely to be the case for most food microbes (that cause spoilage)

acidophiles

which pH requirement organisms are likely to be the case for most normal microbiota (flora)

neutrophiles

what happens to most bacteria when placed in hypertonic environments (in a solution with high concentration of salt or sugar)

they experience plasmolysis, or the cell is going to collapse in and inhibit microbial growth

what is the term for organisms that require high osmotic pressure

extreme/obligate halophiles

what is the term for organisms that tolerate high osmotic pressure. example?

• facultative halophiles

• staphylococcus aureus

what is synergy. example?

• members cooperate and share nutrients

• biofilm

chemically defined

was a chemical composition is known. for fastidious organisms and certain assays. ex. Citrate

complex (undefined)

extracts and digests of yeasts, meat, or plants, chemical composition varies batch to batch (nutrient broth and agar)

reducing

used for the cultivation of anaerobic bacteria; contains chemicals (sodium thioglycolate) that reduce O2 → water and combine O2 to deplete it; heated to drive off O2

selective

suppress unwanted microbes and encourage desired microbes and encourage desired microbes; contained inhibitors to suppress growth

differential

allow distinguishing of colonies of different microbes on the same plate

true or false. microbial growth refers to an increase in the size of the microbial cell

false b/c increase in number of cells only

process of binary fission

1. one cell (young)

2. chromosome is replicated and new and old chromosomes move to a different sides of the cell

3. protein band forms in the center of cell

4. septum formation begins

5. when septum is complete, cells are considered divided. Some species will separate completely as shown here, while others remain attached, forming chains or doubts

term for time required for a cell to divide and its population double

generation time

what is the typical generation time for most bacteria

30-60 minutes; number of cells in each generation is 2^n

lag phase

newly inoculated cells require a period of adjustment; cells are not yet multiplied at maximum rate; high metabolic activity; can last to 1 hour to several days

exponential growth phase

fastest rate of divisions; exponential growth, birth rate > death rate, population increases as long as nutrients and environment is favorable

stationary phase

BR = DR (no change in population size); exhaustion of nutrients, acclimation of waste and harmful changes in pH

death phase

BR < DR - cells are dying at an exponential rate

during which phase of the growth curve are endospores most likely to be produced

stationary phase

three metods to analyze population size without culturing the bacteria

1. turbidity/turbidometry

2. counting

3. Gentetic probing

tubridity/turbidometry

a clear nutrient becomes turbid as microbes grow in it; the greater the turbidity, the larger the population rate

counting

• direct cell count: measured microscopically

• coulter counter: electronically scans a fluid as it passes through a tiny pipette

• flow cytometer: works similarity to a counter, but can measure cell size and differentiate between live and dead cells

genetic probing

uses real-time PCR to quantify bacteria and other organisms present in environmental or tissue samples

term for the sum of all chemical reactions in an organism

metabolism

catabolism

provides energy and building blocks for anabolism; breaks down molecules (hydrolysis); exergonic reaction

anabolism

uses energy and building blocks to build large molecules: build molecules (dehydration); endergonic reaction

endergonic

store energy; ex: photosynthesis make energy rich sugar molecules (glucose) using energy sunlight

exergonic

energy is released; ex: cellular respiration

if a chemical bond is formed, does this release or store energy

store energy

does an exergonic or an endergonic reaction require a high amount of potential energy for the reaction to occur

exergonic because the energy gets released and products > reactants

linear metabolic pathway

A → B → C → (ex: starch)

branched metabolic pathway

circular metabolic pathway

why are some organisms be able to do some metabolic processes and other organisms cannot do these processes? for example, yeast can do alcohol fermentation and you cannot

because yeast have enzymes. metabolic pathways are determined by enzymes (proteins) and enzymes are encoded by genes

what is the advantage of organisms performing metabolism? which class of macromolecules provides most of the energy in the cell

• advantage = allows for stored storage and release of energy in the form of ATP

• oxidation of carbohydrates provides the most of cellular energy (doesn’t provide the greatest energy yield, fats do)

what is it about ATP’s structure that allows it to store lots of potential energy? what happens when this energy is transferred to something else

lots of energy stored in bond between phosphate groups (similar to RNA). because of the negative charges that repel each other, energy have to be put in; ATP is hydrolyzed (break bond) and becomes ADP + Pi

true or false. organisms store their energy in the cell as ATP

false because instead, organism store energy rich molecules like glycogen, starch, and fats. ATP is not long-term high energy

collision theory

molecules or atoms must make physical contact in order for a chemical reaction to occur

activation energy

the amount of energy required to get a reaction started

reaction rate

the frequency of collisions containing sufficient energy to bring about a reaction

ways to increase a reaction rate

add heat/raise the temperature, stir the tube, when pressure is increased (molecules collide more often), high concentration of reactants (more concentrated) because the distance between molecules decreases (more collisions), add an enzyme

an _ is a type of protein that accelerates the rate at which a chemical reaction takes place in an organism

enzyme

what type of macromolecules are enzymes usually

3D globular proteins

do specific enzymes usually catalyze only one reaction or many reactions

one reaction

lactose is the _ of the enzyme _

substrate; lactase

how do enzymes work

enzymes are catalyst-substances that can retain their original chemical composition while bringing a change in a substrate. It lowers the activation energy

what is the region of the enzyme called that binds to the substrate

active site

apoenzyme

protein portion