Exam 2 (Micro)

What is anoxigenic photosynthesis?

A type of photosynthesis that does not produce oxygen as an end product.

What is the name of the half of the light reaction that makes ATP? What is the name of the half of the light reaction that makes NADPH?

ATP: Photosystem II NADPH: Photosystem I

What is the difference in catabolism and anabolism?

Anabolism uses energy, whereas catabolism releases energy.

Define anabolism, catabolism, and metabolism

Anabolism: converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy (endergonic metabolic pathways) Catabolism: exergonic pathways that break down complex molecules into simpler ones Metabolism: the term used to describe all of the chemical reactions inside a cell

Define broad spectrum and narrow spectrum as the terms apply to antimicrobial drugs. What are the advantages and disadvantages of using each type?

Broad spectrum- targets a wide variety of bacterial pathogens, including both grampositive and gram-negative species. Disadvantage: also targets a broad spectrum of the normal microbiota, increasing the risk of a superinfection, a secondary infection in a patient having a preexisting infection. Narrow spectrum- targets only specific subsets of bacterial pathogens. For example, some narrow-spectrum drugs only target gram-positive bacteria, whereas others target only gram-negative bacteria. Disadvantages: can only be used if the causative organism is identified, and you have to be 100% sure on the one you choose, because if it's not the right one, the drug may not kill the microorganism you're wanting to kill

Describe the Calvin Benson Cycle. What is its function? What type of organisms use the Calvin-Benson cycle? What is the key enzyme of this cycle?

Calvin Benson Cycle: -Starts with 6- 5 carbon molecules (ribulose biphosphate RuBP) - then the enzyme rubisco that adds 6 CO2 to the RuBP, making 12 3 carbon molecules (phosphoglycerate- PGA), but not very useful because they're low energy - PGA converts 12 ATP to 12 ADP, and 12 NADPH to 12 NADP+ through the light reactions to make it high energy. (still 12-3 carbon molecules but now called phosphoglyceraldehyde (PGAL) which is high energy) - it keeps 10 PGALs (10 3 carbon molecules), and cutt and paste (converting 6 ATP to 6 ADP) to make the 6 RuBPs again. - 2 PGAL of 3 carbon molecules (6 carbons) get let go, and becomes glucose. which is the beginning of essentially all organic molecules - type of organic molecules: photoautotrophs - key enzyme: rubisco

What breaks down cellulose? What breaks down starch?

Cellulose: Cellulase Starch: Amylase

All living organisms require a source of nitrogen. What do organisms use nitrogen for? Note that many of the steps of the nitrogen cycle are carried out by organisms attempting to convert nitrogen to a form that they can use.

- use nitrogen to build proteins (organic molecules) and nucleic acids, to get energy, for cell respiration

Give examples of food preservation using pH

-Pickling food (acidic) -Lactic Acid ferments milk into yogurt

Describe the light reactions of photosynthesis. What is its function? What types of organisms use the light reaction?

-The high energy electron passes down the electron transport chain until its low energy, and then the energy is used to pump H+ in/out. the H+ come back through the ATP synthase to convert ADP+P --> ATP. the electrons are high energy because they're being zapped by light (the chlorophyl in the light harvesting center absorbs the light). when it moves down the chain, it becomes low energy, and then zapped by light again by the second light harvesting center. this time, it stays high energy while moving down the chain and then gets put on a high energy electron carrier (NADPH). - Convert light energy to ATP+NADPH - Photoautotrophs

Define the word roots -cidal and -static

-cidal: to kill -static: inhibiting growth without killing them

Define the following terms and describe how each type of bacteria would grow in a sodium thyoglycolate tube. (flashcard too) 1. Obligate aerobe 2. Facultative anaerobe 3. Aerotolerant anaerobe 4. Microaerophile 5. Obligate anaerobe

1. Obligate aerobe: cannot grow without an abundant supply of oxygen. 2. Facultative anaerobe:thrive in the presence of oxygen but also grow in its absence by relying on fermentation or anaerobic respiration 3. Aerotolerant anaerobe:. They do not use oxygen because they usually have a fermentative metabolism, but they are not harmed by the presence of oxygen (indifferent- don't care either way) 4. Microaerophile: need O2, but do best with low levels 5. Obligate anaerobe:killed by oxygen

Define the following terms relating to the control of microbial growth: Sterilization Disinfection Antisepsis Degerming

Sterilization: the complete removal or killing of all vegetative cells, endospores, and viruses from the targeted item or environment Disinfection: inactivates most microbes on the surface of a fomite by using antimicrobial chemicals or heat Antisepsis: antimicrobial chemicals safe for use on living skin or tissues Degerming: microbial numbers are significantly reduced by gently scrubbing living tissue, most commonly skin, with a mild chemical (e.g., soap) to avoid the transmission of pathogenic microbes

what does it mean when a reaction is thermodynamically unfavorable? thermodynamically favorable?

Thermodynamically unfavorable: energy is absorbed Thermodynamically favorable: doesn't require energy

How is death defined microbiologically?

Unable to grow (divide) even when favorable conditions return

Explain why temperature affects the growth of microbes

there are specific temperatures that specific bacteria/microbes grow at best. if its too hot for the specific microbe, it kills them. if its too cold, it inhibits their growth. Also, the phospholipid bilayer will melt if too hot, and solidify if too cold.

Describe the benefits and costs associated with the presence of oxygen.

there are specific types of bacteria that will thrive with oxygen present. but on the other hand, there are bacteria that die in the presence of oxygen - benefit: lots of ATP - cost: when it doesn't pick up the right number of electrons, it can turn into the superoxide radical (can cause damage - like to DNA, etc.)

Explain why recombination (transduction, conjugation, and transformation) are medically significant.

they are significant because they are a major factor in explaining antibiotic resistance

What is the relationship between penicillin and semi-synthetic penicillins such as methicillin, ampicillin, amoxicillin?

they're all narrow-spectrum against gram-positive bacteria

Describe transduction

viruses transport DNA between bacterial cells

Why do viruses pose particular challenges for the development of effective antimicrobial drugs?

viruses use host enzymes and ribosomes

What pH do most bacteria grow best at?

~ pH 7

Explain how lipids and amino acids are catabolized.

Lipids: - Triglycerides are made of a glycerol and 3 fatty acids. Phospholipid structure is similar to triglycerides except that one of the fatty acids is replaced by a phosphorylated head group. Triglycerides and phospholipids are broken down first by releasing fatty acid chains (and/or the phosphorylated head group, in the case of phospholipids) from the three-carbon glycerol backbone. - the triglycerides are catalyzed by lipases, and the phospholipids are catalyzed by phospholipases. Proteins: - Proteins are degraded through microbial protease enzymes. Extracellular proteases cut proteins internally at specific amino acid sequences, breaking them down into smaller peptides. - After extracellular protease degradation and uptake of peptides in the cell, the peptides can then be broken down further into individual amino acids by additional intracellular proteases, and each amino acid can be enzymatically deaminated to remove the amino group.

what are planktonic cells?

free floating microbial cells that live in an aquatic enviornment

Describe how obligate anaerobes and microaerophiles can be grown in the laboratory.

grown in an anaerobic jar (which includes chemical packs that remove oxygen and release carbon dioxide), and an anaerobic chamber (enclosed box where all oxygen is removed)

Define Fastidious

has lots of growth factor requirements

What does penicillin do?

inhibits cell wall synthesis

Explain why pH affects the growth of microorganisms.

it affects the growth because if its too acidic or basic, it changes the charges of functional groups in active sites, and denatures enzymes

How does heat kill microorganisms?

it alters their membranes and denatures their proteins

What is pasteurization?

kills pathogens and reduces the number of spoilage-causing microbes while maintaining food quality (uses high heat for a short period of time)

Would you expect penicillin or cephalosporin family of antibiotics to work against protists or fungi? Archaea? Viruses? why or why not?

penicillin has no effect on eukaryotic cells

Define obligate

restricted to

Define transposon

"jumping genes" - genes that move around on chromosomes - if they move to plasmid, they're more likely to pass on to other microbes

Fill in the table to differentiate between photoheterotrophs, photoautotrophs, chemoautotrophs, and chemoheterotrophs.

(flash card)

What is anaerobic respiration? How does it differ from fermentation and from aerobic respiration? How is it similar to each of these processes?

- Anaerobic respiration is when some other molecule other than O2 is used as an electron acceptor of ETC - It doesn't use O2, and produces less ATP than aerobic respiration but more than fermentation. - it still uses the krebs cycle - still uses the ETC just with different final electron acceptors

What other methods of bacterial growth are there besides binary fission?

- Budding - Fragmentation

Describe the experiment by Griffith that illustrated transformation

- He first injected the mice with streptococcus pneumonia with a capsule , and the mice died. - He injected the mice with a related strain without a capsule, and the immune system was able to fight it off, and the mice lived - to start his experiment, he took the related strain that doesn't kill mice (without the capsule) and added heat that killed the strain with the capsule (dead bacteria with a capsule), and mixed them together and injected into the mouse= mouse died and found live bacteria in their blood that had a capsule (so this proved the instructions for making the capsule were transferred) - the next part, he took the related strain without the capsule, and the dead strain with the capsule(treated with proteases) and the strain still picked up the instructions, and killed the mice. - the last piece he needed, he mixed the related strain without the capsule and the dead strain with the capsule and treated it with nucleases (break down nucleic acids so the instructions are gone), the mice lived. - IN CONCLUSION: the last two steps showed that the nucleic acids (DNA), not the proteins, were the genetic material

What is fermentation? How is fermentation different in the world of microbes compared to how you first learned about this process?

- Making ATP without oxygen -

explain what occurs in oxidation-reduction reactions, and why they are important to catabolism.

- Reactions that remove electrons from donor molecules, leaving them oxidized, are oxidation reactions; those that add electrons to acceptor molecules, leaving them reduced, are reduction reactions. Because electrons can move from one molecule to another, oxidation and reduction occur in tandem. These pairs of reactions are called oxidation-reduction reactions - They're important because Nicotinamide adenine dinucleotide (NAD+ /NADH) is the most common mobile electron carrier used in catabolism. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule.Nicotine adenine dinucleotide phosphate (NADP+ ), the oxidized form of an NAD+ variant that contains an extra phosphate group, is another important electron carrier; it forms NADPH when reduced

How does cold temperature retard the growth of microorganisms? Is exposure to cold temperatures -cidal or -static?

- Refrigerators used in home kitchens or in the laboratory maintain temperatures between 0 °C and 7 °C. This temperature range inhibits microbial metabolism, slowing the growth of microorganisms significantly and helping preserve refrigerated products such as foods or medical supplies. Freezing below −2 °C may stop microbial growth and even kill susceptible organisms - it would be -static. because heat kills bacteria and cold just inhibits the growth

What are MRSA and VRE?

- Strains of methicillin-resistant S. aureus (MRSA) are widespread opportunistic pathogens and a particular concern for skin and other wound infections, but may also cause pneumonia and septicemia - vancomycin-resistant enterococci (VRE): target modification involving a structural change to the peptide component of the peptidoglycan subunits, preventing vancomycin from binding

The effectiveness of a microbicidal agent is dependent upon the time of exposure. What other factors influence effectiveness?

- The number of microbes (biofilms especially) - Presence of organic matter (dirt, feces, blood, etc.) - temperature (colder=harder)

Streptomycin, tetracycline, and erythromycin inhibit protein synthesis. Why is this selectively toxic? Why is there concern about the effect of these drugs on mitochondria?

- because bacteria have different ribosomes - because mitochondria are structured a lot like bacteria

Physical and chemical microbiological agents (disinfectants and antiseptics) attack four general categories of cellular targets. What are these targets?

- cell wall - cell membrane - proteins - nucleic acids

Explain why osmotic pressure affects the growth of microbes by describing what happens to microbes in hypertonic and hypotonic environments. Give examples of food preservation using osmotic pressure.

- if you put a microbe in a hypertonic solution (more solutes outside of the cell), so the water will flow out of the cell, then the cell membrane will shrivel up away from the cell wall (plasmoysis). - if you put a microbe in a hypotonic solution (more solutes in the cell), the water will flow in. the cell wall keeps bacterial cells from bursting (but some bacteria lack a cell wall) - you can use salt and sugar to preserve food because it kills microbes by pulling the water out of their cells

Give examples of traits carried on plasmids

- often have genes for antibiotic resistance - can have genes for making a sex pilus

What is aerobic respiration? and what is the difference in ATP with aerobic respiration?

Respiration with oxygen. You get the most ATP with aerobic respiration than anything

Microbial metabolism is controlled by enzymes. Review enzyme function by labeling the components of the enzyme-catalyzed reaction shown on the flashcard, and then determining whether each statement listed is true or false. T/F __1__ Enzymes interact with specific substrates __2__ Enzymes make thermodynamically favorable reactions occur at biologically relevant temperatures __3__ One enzyme can be used for many different types of chemical reactions __4__ Enzymes can make thermodynamically unfavorable reactions favorable __5__ Sulfa drugs act by mimicking the substrate of a reaction in folate synthesis. This is an example of allosteric inhibition

1. True 2. True 3. False 4. False 5. False

What are the desirable characteristics of a chemical antimicrobial agent?

1. cheap 2. stable 3. broadly effective 4. fast acting 5. non-corrosive/non-toxic

Many prokaryotic species divide by binary fission. Describe this process. Define generation time. (flashcard too)

1. circular chromosome attached to the cell membrane 2. DNA replication (helicase, DNA polymerase, etc..) 3. Enlargement of cell separates the 2 pieces of DNA 4. Cell division produces identical daughter cells Generation time:the time it takes for the population to double through one round of binary fission

Describe the mechanisms by which bacteria become resistant to antibiotics.

1. enzyme to breakdown antibiotic (like beta lactamase for penicillin) 2. Antibiotic can't get in the cell OR pump to pump it out again 3. Mutuation in target of antibiotic so antibiotic doesn't affect it

Explain how antibiotic resistance can become more common in a population

1. heritable variation (mutation or sex) 2. Not all survive to reproduce because wide spread use of antibiotics kills susceptible bacteria 3. those with favorable characteristics (antibiotic resistance) survive and reproduce 4. over time, antibiotic resistance becomes more common

What are the most common mechanisms of action of antibacterial drugs? Which of these mechanisms do the penicillin and cephalosphorin families of antibiotics go after?

1. inhibit cell wall synthesis (penicillin and cephalosphorin families) 2. inhibit protein synthesis 3. inhibit cell membrane formation 4. inhibit folate synthesis 5. inhibit nucleic acid synthesis

1. Explain how non-ionizing radiation such as ultraviolet light kills microorganisms. 2. What are the main disadvantages of using ultraviolet light as a microbial control? 3. Can ultraviolet light be used to sterilize something?

1. it causes thymine dimers to form between adjacent thymines within a single strand of DNA. When DNA polymerase encounters the thymine dimer, it does not always incorporate the appropriate complementary nucleotides (two adenines), and this leads to formation of mutations that can ultimately kill microorganisms 2. it does not penetrate cells or packaging, the light has to hit directly. 3. No. it can disinfect, but not sterilize

Explain how biofilms form, including the role of quorum sensing.

1. planktonic cells attach to a surface with a conditioning film of organic material (seconds) 2. they become irreversibly attached (seconds/minutes) 3. growth and cell division occurs (hours/days) 4. production of extracellular polymeric substances (EPS) (an extracellular matrix secreted by the organisms) and formation of water channels (hours/days) 5. attachment of secondary colonizers and dispersion of microbes to new sites (days/months) Quorum sensing enables organisms to detect their cell density through the release and binding of autoinducers. when the cell population reaches a quorum (critical threshold), these autoinducers initiate a cascade of reactions

What can be done to reduce the development of antibiotic-resistance in bacteria?

1. reduce antibiotic use (especially in livestock 2. prescribe more carefully - not for viruses - test for susceptibility - use narrowest spectrum antibiotic 3. alternatives- vaccinations, probiotics, bacteriophages (viruses that attack bacteria)

How does chlorophyll replace its lost electron?

2H2O --> 4H+ + 4e- + O2 - the hydrogen ions become part of the H+ gradient - the e- replace chlorophylls lost e- - O2 is the waste product (source of O2 on earth)

Describe the Krebs Cycle. Explain what enters and leaves the Krebs, and the amount and type of energy molecules generated. Where does Krebs Cycle take place in prokaryotes and eukaryotes?

Acetyl CoA is added to a 4 Carbon molecule called oxaloacetate, forming a 6 carbon molecule called citrate. (the coenzyme A is removed as this happens). Two molecules of carbon dioxide are removed from citrate, regenerating the 4C oxaloacetate. Some of the energy that was in the covalent bonds of the acetyl CoA molecule is captured in the form of the high energy electron carriers NADH and FADH2. A molecule of ATP is also produced. Prokaryotes: Cytoplasm Eukaryotes: mitochondrial matrix

What is an autoclave?

Autoclaves rely on moist-heat sterilization. They are used to raise temperatures above the boiling point of water to sterilize items such as surgical equipment from vegetative cells, viruses, and especially endospores, which are known to survive boiling temperatures, without damaging the items

Why does the Gram status of the microbe causing an infection matter when prescribing an antibiotic from the penicillin family?

Because they are all narrow-spectrum against gram-positive bacteria. BUT, Penicillin is against a few gram-negative bacteria, Ampicillin and amoxicillin have increased gram-negative spectrum, and methicillin is against gram-positive bacteria only.

what is the difference is drugs and chemicals with the cell wall?

Drugs: goes after cell wall synthesis Chemicals: goes after cell walls

What is Beta-lactamase, and why is it important?

Enzyme to breakdown antibiotics (beta-lactamase is the enzyme for penicillin)

Define facultative halophile (halotolerant) and obligate halophiles and explain the strategies employed by each group to survive in high salt environments.

Facultative halophile: organism that can grow in high salt concentration but is not dependent of those high salt concentrations for growth. - they accumulate organic molecules (like glycerol) to get isotonic to the environment Obligate halophile: organisms that can only survive in high salt concentrations - they accumulate K+, Na+, and Cl- intracellularly to be isotonic to environment (enzymes adapted to high salt

Describe glycolysis. Explain what enters and leaves glycolysis, and the amount and types of energy molecules generated. (Flash card too)

Glycolysis begins with a 6 carbon glucose molecule with lots of chemical energy in the covalent bonds, and ends in 2 pyruvates where each contain 3 carbon atoms. There is less chemical energy in the 2 pyruvate than there was in the 1 glucose molecule. (there are some amino acids in glycolysis that get deaminated and release NH3, making it alkaline. If this occurs, in lab the phenol red will turn pink) 2 ATP enter in the beginning and converted to 2ADP+P, 2 NAD+ converted to 2 NADH, AND 4ADP+P converted to 4 ATP. The net profit in the end is 2 ATP, 2 NADH and 2 pyruvate molecules

Where does glycolysis take place in prokaryotes and eukaryotes?

Glycolysis takes place in the cytoplasm of prokaryotic and eukaryotic cells

Explain how ionizing radiation kills microorganisms. Can ionizing radiation be used to sterilize something?

Ionizing radiation is strong enough to pass into the cell, where it alters molecular structures and damages cell components. For example, ionizing radiation introduces double-strand breaks in DNA molecules. yes, ionizing radiation is commonly used to sterilize materials that cannot be autoclaved, such as plastic Petri dishes and disposable plastic inoculating loops. for clinical use, things like gloves and plastic and latex are sterilized with ionizing radiation.

Describe and draw a diagram illustrating the stages of the bacterial growth curve: lag, log, stationary, and death. Explain what is happening in the bacterial culture at each stage. (flashcard too)

Lag phase: synthesizing materials (not really dividing yet) Logarithmic phase: exponential growth (growing fastest) Stationary phase: waste accumulation, food becomes limited, rate of division is same as rate of death (population is staying constant because they're growing and dying at the same rate) Death phase: exponential population decline

What characteristics of prokaryotes reduce the potential for variation compared to eukaryotes?

Prokaryotes are haploid- so only have one allele Eukaryotes are diploid- so can have two different alleles.

One of the differences in cell respiration of microbes compared to more familiar organisms is that they can utilize a wider variety of starting compounds. Give examples of compounds that microbes metabolize that animals (like us!) generally do not.

Microbes can convert carbs and lipids to protein using NH3 (ammonia). Humans cannot convert them to protein.

Describe transformation

Microbes pick up DNA from their environment

Classify the following organisms with regards to their difficulty in killing them with an antimicrobial chemical: Enveloped viruses Naked viruses Prions Bacterial cells Bacterial endospores Fungal spores Fungal hyphae Protozoan cysts Protozoan trophozoites

Moderately resistant: - protozoan cysts - naked viruses Most resistant: - bacterial endospores - prions All others are least resistant

what are possible electron acceptors in anaerobic respiration?

NO3-, NO2-, SO4-, etc.

Define: Neutrophile Acidophile Alkalophile (flashcard too)

Neutrophile: grow optimally at a pH within one or two pH units of the neutral pH of 7 Acidophile: grow optimally at pH less than 5.55 Alkalophile:grow best at pH between 8.0 and 10.5

Describe the transitional reaction (also called the preparatory stage). Explain what enters and leaves the transitional reaction, and the amount and type of energy molecules generated. Where does the transitional reaction take place in prokaryotes and eukaryotes? (Flash card too)

One molecule of carbon dioxide is removed. The remaining 2 carbon molecules are attached to coenzyme A, forming acetyl CoA. Some energy is captured in the form of NAD+--> NADH. Prokaryotes: cytoplasm (because they lack membrane-enclosed organelles) Eukaryotes: the matrix of the mitochondrion

Define- Psychrophile Psychrotroph Mesophile Thermophile Hyperthermophile 1. Which of these groups of organisms are most likely to cause food spoilage? 2. Which are most likely to be causative agents for disease? (flashcard too)

Psychrophile:(cold loving) Psychrophiles are microorganisms that can grow at 0 °C and below, have an optimum growth temperature close to 15 °C, and usually do not survive at temperatures above 20 °C Psychrotroph: prefer cooler environments, from a high temperature of 25 °C to refrigeration temperature about 4 °C Mesophile:("middle loving") are adapted to moderate temperatures, with optimal growth temperatures ranging from room temperature (about 20 °C) to about 45 °C Thermophile: grow at optimum temperatures of 50 °C to a maximum of 80 °C are called thermophiles ("heat loving"). They do not multiply at room temperature Hyperthermophile: Higher up on the extreme temperature scale we find the hyperthermophiles, which are characterized by growth ranges from 80 °C to a maximum of 110 °C 1. psychrotrophs 2. mesophiles

What is selective toxicity? Why are there fewer antimicrobial drugs for eukaryotic pathogens (fungi, protests, and helminths)?

Selective toxicity: killing microbes without killing patients Because they're in different domains.

Define growth factor (organic growth factor), and give an example.

Something an organism needs that it can't make itself - examples (for humans): vitamins, essential amino acids, essential fatty acids

Describe the role of superoxide dismutase and catalase/peroxidase in reducing the risks of O2 use.

Superoxide dismutase- takes two superoxide radicals and 4 hydrogen ions and turns it into 2 hydrogen peroxides, then you use a catalase to turn hydrogen peroxide to water and oxygen.

Explain how transformation can be used to make recombinant DNA products. Give an example. (See Fig 12.2)

the human insulin gene is inserted into a bacterial plasmid. This recombinant plasmid can then be used to transform bacteria, which gain the ability to produce the insulin protein

Describe the electron transport system. Include the role of NADH, FADH2, H+, ATP synthase, and oxygen. Where does the electron transport chain take place in prokaryotes and eukaryotes? (flashcard too)

The electron transport system is when NADH/FADH2 energy is converted to ATP energy. The electron transport chain takes the high energy electron carriers and takes the high energy electrons and passes them down the electron transport chain and the energy from those high energy electrons is used to pump hydrogen ions which that gradient then can be used to make ATP or to do other cell work. The low energy electrons use oxygen as the acceptor (which makes water). Prokaryotes: cell membrane of mitochondrion Eukaryotes: inner membrane of mitochondrion

why is inhibiting cell wall synthesis selectively toxic?

because we don't have peptidoglycan, or a cell wall

Define facultative

capable of adapting to different conditions

Explain how ATP acts as an intermediate between catabolism and anabolism

catabolism is energy forming (ADP+P --> ATP), so in catabolism ATP is the product. anabolism: is energy storing (ATP --> ADP +P) in anabolism ATP starts the reaction. SO: ADP + P --> <-- ATP

Describe conjugation

cell to cell transfer of DNA, usually via a sex pilus

Flash card #18

check flashcards