Final exam

Question 1

Describe the contributions Hippocrates made to microbiology and when

Answer 1

• 400 BC
• first to observe immunity
  
  • bubonic plague survivors could care for plague victims
• realized disease particles are transferred through clothing

Question 2

what myth has resulted in low immunization rates and disease resurgence in the U.S.?

Answer 2

• anti-vac movement - Andrew Wakefield (1998)
  
  • vaccinated 12 kids who were already showing signs of autism, then claimed the autism was a result of being vaccinated
  • DUMBASS
  • no study to support his
  • autism develops around age 2, which is about the same age of vaccination
    
    • correlation not causation

Question 3

Describe the contributions Joseph Lister made to microbiology and when

Answer 3

• 1865
• came across writings of Semmelweis
• started sterilizing knives with carbonic acid and drastically reduced infection rates
• he was laughed at but shrugged it off
• Father of modern surgery

Question 4

calculate the amount of energy released from a reaction using Gibbs free energies of formation for the products and reactants.

say whether or not the reaction can proceed spontaneously.

Answer 4

• Gibbs free energy: amount of “useable” energy (energy available to do work)
• when delta G < 0, energy is given off (exergonic)
  
  • sponanteous
• when delta G > 0, energy is added (endergonic)
  
  • not spontaneous

Question 5

Val

Answer 5

Valine

nonpolar (hydrophobic)

Question 6

Describe the chemical structure of peptidoglycan, (including three differences between gram negative and gram positive regarding the chemical composition of the peptidoglycan layer)

Answer 6

• peptidoglycan
  
  • consists of alternating units of N-acetylglucosamine (G) and N-acetylmuramic acid (M)
  • glycan strands are connected by peptide bridge (connects G to M)
  • keeps the cells together by hydrophobic sources
  • PSI = 20 at its softest to hold peptidoglycan together
  • D vs. L amino acids (isomers)
    
    • ​L amino acids are typically seen in proteins, but we see both in peptide linkage
• Differences between gram pos. and gram neg:
  
  • length of interbridge is longer from gram pos. (Gly interbridge)
  • DAP (diaminopimelic acid) is in gram neg.
    
    • two amino acid heads
  • Teichoic acids are in gram pos.

Question 7

describe three early attempts at immunization

Answer 7

• Edward Jenner
  
  • cowpox vaccine
• 900 AD
  
  • Chinese would scrape off the scabs from recovering smallpox victims, powder it, and use a straw to blow it in the nostrils of children
• Louis Pasteur
  
  • rabies vaccine

Question 8

describe the three general functions of glycolysis, beta-oxidation, and the TCA cycles (what cell resources do they produce? how much do they produce?)

Answer 8

• beta-oxidation
  
  • produces a lot of reducing power
  • if a 16C fatty acid were oxidized, it would produce 8 acetyl CoA, 7 NADH, and 7 FADH₂
• glycolysis
  
  • produces a little bit of reducing power
  • produces a little bit of energy
  • net: 2 ATP (4 total but 2 used) + 2 NADH + 2 pyruvates
    
    • 8 ATP total
• TCA cycle
  
  • produces a lot of reducing power
  • produces a little bit of energy
  • pre-TCA cycle: 8 ATP total
  • TCA cycle: 8 NADH + 2 FADH₂ + 2 GTP
    
    • 30 ATP total
• glycolysis + TCA cycle = 38 ATP/mol of glucose
• remember:
  
  • 1 FADH₂ = 2 ATP
  • 1 NADH = 3 ATP

Question 9

Describe the importance of protein conformation and what factors influence it

Answer 9

• change in protein conformation mediates/facilitates what moves in and out of the cell
  
  • environment interacting with DNA sequences affects structures
    
    • pH
    • ionic concentration
    • temperature
    • chaperone proteins (interact with peptide sequence and influence folding of amino acid tails)
      
      • mad cow disease is due to defective chaperone proteins

Question 10

Glu

Answer 10

Glutamate

ionizable; acidic side chain

Question 11

Aromatic side chain amino acids

Answer 11

Question 12

Koch’s postulates

Answer 12

• steps needed to demonstrate microbial cause of disease

1. Association - the microbe must be present in EVERY case of the disease and absent when there is no disease
2. Isolation - the microbe must be isolated in pure culture
3. Causation - innoculation of healthy animal with pure culture should cause disease
4. Reisolation - you should be able to isolate the same microbe from the newly sick animal

Question 13

Define autoclaving and tyndallization

Answer 13

• Autoclaving (sterilize samples) - chamber heated up to 121ºC at 15 PSI for 15-20 min
  
  • endospores will germinate
• Tyndallization - double autoclaving
  
  • incubate sample for 24 hours
  • the 2nd autoclave is used to kill vegetative cells

Question 14

Compare and contrast the structure and movement of prokaryotic and eukaryotic flagella

Answer 14

• eukaryotic flagella:
  
  • membranous sheath with protein tubules embedded
  • flexible
• prokaryotic flagella:
  
  • not flexible - rigid corkscrew protein structure
  • works by rotating
    
    • flow of protons past the disc causes rotation (repels)
    • lower M ring spins and causes shaft to rotate
    • can spin in both directions
      
      • CCW = forward run
      • CW = tumbling motion

Question 15

Describe the contributions Alexander Fleming made to microbiology and when

Answer 15

• 1929
• microbiologist studying bacteria
• made an accidental discovery by leaving agar plates for a few days when he was on vacation. when he came back, he noticed a green fungal contaminate on one
  
  • where there used to be colonies, there were ghost colonies
  • isolated the fungus and found that it could kill bacteria
  • identifed the fungus as penicillium
    
    • later on in the early 1940s, other chemists were able to isolate the compound penicillin (1st antibiotic); there was a boom in the discovery of antibiotics and they felt invincible, so they closed TB hospitals (problem - antibiotic resistance)
      
      • STDs are increasing in the U.S. due to antibiotic resistance and a 40% cut in funding by public health

Question 16

describe the importance of immunization and the role of herd immunity in preventing disease in populations

Answer 16

• if you get enough of the population vaccinated, it immunizes the entire population
  
  • 83-94%
  • important for those who cannot get vaccinated (immunocompromised)

Question 17

describe the reactions necessary to re-establish the TCA cycle when intermediates are withdrawn to be used for building microbial biomass

Answer 17

• Anaplerotic reaction: different way of recreating oxaloacetate to restart TCA cycle (filling in)
  
  • pyruvate carboxylase
    
    • CO₂ + pyruvate + ATP = oxaloacetate
    • used by heterotrophs, but not autotrophs
    • this is the reaction we do
  • PEP carboxylase
    
    • PEP + CO₂ = oxaloacetate
    • this is the reaction many microorganisms do

Question 18

describe the chemical and physical structure of prokaryotic and eukaryotic membranes

Answer 18

• plasma membrane and DNA are not optional
• membrane has a phospholipid bilayer
  
  • the glycerol backbone is the lipid
  • 3 carbon chain, phosphate, and 2 fatty acid chains
    
    • long fatty acid chain (non-polar) is hydrophobic and points inward
    • charge polar head is hydrophilic and points outward
  • proteins in the membrane allow transport

Question 19

Asp

Answer 19

Aspartate

ionizable; acidic side chain

Question 20

Describe how the structure and function of the LPS layer differs from the plasma membrane

Answer 20

• outer membrane is less selective than plasma membrane
  
  • no active transport
• Gram positive
  
  • thick peptidoglycan layer embedded with teichoic acids and lipoteichoic acids
  • periplasmic space is less defined
• Gram negative
  
  • two layers help to define the periplasmic space (contains a lot of enzymes; solute binding protein)
  • porins:
    
    • transmembrane proteins in membrane that allow material to pass back and forth
    • slightly selective - molecular weight and slight charge discrimination
  • Braun’s lipoprotein
    
    • protein inserts into peptidogylcan layer
    • hydrophobic interaction keeps it attached
  • LPS (lipopolysaccharide)
    
    • outer portion of outer membrane
  • O-specific side chains
    
    • disguises bacterial cell from immune systems by modifying
    • can classify organisms based on their side chains
    • changes over time
    • example: E.Coli O157-H7
      
      • exotoxin (produced inside of cell and secreted)
  • Lipid A and polysaccharide (carbohydrate chain) are endotoxins (part of outer membrane of gram negative cells; causes shock)
  • core polysaccharide always stays the same

Question 21

Describe how bacteria behave as they move along a concentration gradient.

Describe the signal transduction that results in this movement.

Answer 21

• extend duration of run when there is a higher concentration of attractant
• signal transduction - biochemical decision making process
  • there are sensory proteins on the surface of the cell - MCP (methyl accepting chemotaxis protein)
    
    • transmembrane protein
    • lock and key mechanism
    • portion outside of the cell binds the substrate
    • the portion inside has these chemotaxis proteins:
      
      • CheW (associated with inside of MCP)
      • CheA (associated with inside of MCP)
      • CheY (floating around inside cell)

Question 22

Aliphatic side chain amino acids

Question 23

name the genus of one of the two ginormous prokaryotes discovered in the past few years

Answer 23

• Epulopiscium fishelsoni
  
  • from gut of surgeon fish
• Thiomargarita namibiensis
  
  • ​found in marine sediments
  • largest prokaryote
  • most of the cell is covered in a vacuole and storage granules (sulfur and nitrate)
• simple organisms can be large
• large prokaryotes have large vacuoles and cytoplasm pressed against plasma membrane

Question 24

Pro

Answer 24

Proline

nonpolar; secondary amino group

Question 25

Define pasteurization

Answer 25

• Treat food products with mild heat to reduce pathogens and increase shelf life
  
  • heated grape juice to 80ºC for 15 min
    
    • killed 98-99% of microorganisms
    • inoculated it back with yeast for flavor

Question 26

how were endospores used as a weapon?

Answer 26

• endospores of Bacillus anthracis in powder form were sent in envelopes to congress
  
  • lesions in lungs
  • wiped walls and gassed with chlorine oxide gas, but there were still endospores
  • a second gassing made it safe
  • biological warfare

Question 27

Gly

Answer 27

Glycine

nonpolar (hydrophobic)

Question 28

Define chemotaxis

Answer 28

• chemotaxis: movement in response to chemical repellent or attractant

Question 29

Ser

Answer 29

Serine

polar; aliphatic hydroxyl side chain

Question 30

explain the importance of pure culture techniques in microbiology

Answer 30

• pure culture is a population that contains only a single species or strain of bacteria
• important for studying cultural, morphological, and physiological characteristics

Question 31

define what a high-energy phosphate bond is, and describe the molecular configuration that results in one

Answer 31

• a very low (negative) delta G is a high energy bond; lower than -30 is needed to produce ATP
• a high energy phosphate bond has more stable resonance states

Question 32

Describe the controversy surrounding spontaneous generation.

When and how was it disproved for microorganisms?

What was the alternative hypothesis (which later became a theory)?

Answer 32

• spontaneous generation - idea that life comes if you simply get the appropriate elements together
• It was disproved by Louis Pasteur’s swan-necked flask experiment in 1861
• alternative hypothesis: germ hypothesis that became the germ theory
  
  • bacteria comes from seeds or germs

Question 33

describe four general mechanisms by which compounds are transported into cells, which require the expenditure of energy, and identify which are more important in prokaryotes or eukaryotes

Answer 33

• Facilitated diffusion
  
  • limited form of diffusion
  • gating mechanism that is partially selective
  • change of shape is solely dependent on interaction with ion; no energy involved
  • cannot concentrate things against its concentration gradient; can only equalize concentration
  • common in eukaryotes
• Group translocation
  
  • compound taken up is modified as it enters the cell
    
    • can no longer interact with the membrane proteins once inside, so it cannot get back out of the cell
      
      • work against concentration gradient and accumulate compound inside
  • PEP/PTS: Phosphoenolpyruvate/Phosphotransferase System
    
    • Series of proteins that help transfer a phosphate to a sugar or other substrate being taken up (intermediate proteins)
      
      • modification requires energy (in the form of high energy phosphate bond associated with PEP)
      • transmembrane protein is unique for substrate
      • example: changing glucose to glucose-6-phosphate
    • associated with prokaryotes
• Active transport (two types)
  
  • ​Primary - ABC transporters
    
    • ​ATP binding cassette
      
      • whole unit: transmembrane protein and outside we have a solute binding protein
    • high affinity for substrate
      
      • Nucleotide-binding protein: binds and hydrolyzes ATP for energy to change conformation and allow intrusion
      • solute changes shape by binding to the substrate
    • requires energy (in form of ATP)
  • Secondary
    
    • requires proton gradient
    • protons are pumped outside of the cell as electrons move down the tower “chain”
    • can flow back in and cause something else to move out
    • sodium gradient is used instead of proton gradient to drive uptake of other compounds like sugars
    • oxidative phosphorylation
• Lipid raft
  
  • phospholipids are aggregated together only for transport

Question 34

Tyr

Answer 34

Tyrosine

polar; aromatic side chain

Question 35

Describe the contributions Robert Koch made to microbiology and when

Answer 35

• 1896
• physician interested in studying disease in animals and later progressed to diseases in humans
• worked with Anthrax (disease that affects livestock)
  
  • saw that sick animals had Bacillus anthracis (produces endospores and used in biological warfare)
  • decided to isolate the bacteria in blood and grow in pure culture, then transfer to a healthy animal. the problem with this was lack of technology (they used methods such as potato as a host to grow bacteria, innoculating a flask with broth, and using a flask with gelatin that gives a hard surface to pick bacteria off but melts at <37ºC)
  • solution - use agar (polysaccharide of algae) that is solid at 37ºC and a petri dish (invented by Richard Petri)
• discovered cause of cholera, TB, and 20+ other human diseases
  
  • received nobel prize
• formalized Koch’s postulates

Question 36

describe the functions of Che A, B, R, W, Y, and Z, and whether the phosphorylated or non-phosphorylated forms are active

Answer 36

• CheR slowly methylates MCP
  
  • affect: changes shape of MCP so it is no longer capable of binding glucose (attractant). As you add more methyl groups, takes higher concentrations of glucose to keep MCP bound to glucose and in the run mode
• when attractant comes off, CheA catalyzes hydrolysis of ATP
• this phosphorylates CheA and produces ADP
• CheA-P phosphorylates CheY
• CheY-P is capable of binding to the flagellar switch and changes the configuration of the switch proteins to change the direction of the flagellum to a CW motion (tumble)
• CheZ dephosphorylates CheY-P
• CheB picks up phosphate from CheA-P
  
  • affect: rapidly demethylates MCP (in phosphorylated state), which allows it to bind glucose again
• CheB and CheY are only active when phosphorylated

Question 37

obligate endosymbionts today

Answer 37

• Proof that there are obligate endosymbionts today:
  
  • Rickettsia - can exist outside the cell
    
    • only grow and reproduce inside the cell
    • Ticks - Rocky mtn spotted fever
    • lost ability to retain/generate energy
  • Chlamydia
    
    • only grow and reproduce inside the cell
    • lost ability to generate energy
  • Cyanophora paradoxa (photosynthetic protozoa)
    
    • remnants of peptidoglycan in primitive chloroplast
• rare and difficult to occur, but is now a theory with all the proof

Question 38

describe the cell wall morphologies of gram negative and gram positive bacteria

Answer 38

• Gram positive
  
  • plasma membrane with a thick peptidoglycan layer
    
    • no outer membrane
• Gram negative
  
  • plasma membrane, an outer membrane (LPS layer), and a thin peptidoglycan layer in the middle

Question 39

describe the glycolysis cycle

Answer 39

• Glycolysis:
  
  • +2 ATP (net)
  • +2 NADH
  • +2 pyruvate
• delta G for ATP and ADP = -31 kJ
• delta G of 1,3-biphosphoglycerate = -52 kJ
• delta G for glucose-6-P = -14 kJ
• substrate level phosphorylation:
  
  • high energy bond made using substrate
  • can use to convert ADP to ATP using kinase (transfers phosphate)
• Can also use PEP instead of ATP

Question 40

Leu

Answer 40

Leucine

nonpolar (hydrophobic)

Question 41

name and describe the process by which fatty acids are converted to acetyl CoA (at the level of detail presented in class - in this case, know the chemical structures of intermediates)

Answer 41

• structure of fatty acid: carboxyl carbon, alpha carbon, beta carbon
• process requires some energy
• steps:
  
  • to attach CoA to fatty acid, burn up two high energy phosphate bonds in ATP, producing two inorganic phosphates and AMP
    
    • remember that sulfur is part of CoA; the high energy bond is where the sulfur links to the carbon
  • oxidize with FAD, forming FADH₂
  • hydration (forms hydroxyl bonded to a C)
  • oxidation with NAD+ (forms C=O bond where hydroxyl was)
    
    • forms NADH + H+
  • thiolysis (another CoA-SH comes in and separates the compound into two)
• Each round of beta-oxidation clips off two carbons
  
  • Acetyl CoA is two carbons
    
    • example: to split an 18 carbon fatty acid
      
      • produce 9 acetyl CoA
      • 8 rounds of beta-oxidation
      • produces 8 FADH₂
      • produces 8 NADH
  • Just lose two high energy phosphate bonds one time

Question 42

Secondary amino group amino acid

other amino acid (uncategorized)

Answer 42

Question 43

Sulfur-containing side chains amino acid

Answer 43

Question 44

Explain the functional difference between glycans that have alpha 1,4 glycosidic linkages and those that have beta 1,4 linkages

Answer 44

• alpha-1,4
  
  • stores energy
  • easy to degrade
  • quick access
  • starch, glycogen, etc.
• beta-1,4
  
  • untouched energy that can last
  • cellulose, chitin, hemicellulose, pectin, microbial polysaccharides
    
    • chitin: long polymers N-acetylglucosamine in insect exoskeleton and fungal cell walls
    • cell wall of plants - cellulose, hemicellulose, pectin, lignin

Question 45

Cys

Answer 45

Cysteine

polar; sulfur-containing side chain

Question 46

Describe the role and structure of endospores

Answer 46

• Endospores: resting structure
  
  • most resistant (heat, chemicals, radiation)
  • impermeable coat
  • one cell produces one spore
  • long-lived (millions of years)

Question 47

Trp

Answer 47

Tryptophan

nonpolar; aromatic side chain

Question 48

Describe the contributions Martinus Beijerinck made to microbiology and when

Answer 48

• 1900s
• described the first virus - tobacco mosaic virus
  
  • passed through filter that retains bacterium
• formed enrichment culture technique
  
  • altered media and incubation conditions

Question 49

Discuss the differences between the nuclear material of prokaryote and eukaryotes

Answer 49

• prokaryotes
  
  • no membrane bound nucleus
  • single circular dsDNA chromosome
    
    • haploid (one copy)
    • chromosome is 4x10⁶ bp
  • no wasted space
  • super coiled
  • 0.4 microns is as small as it can be
  • 70s ribosomes
    
    • 16s subunits (rRNA)
• eukaryotes
  
  • ​double membrane bound nucleus
  • many linear strands of dsDNa
    
    • haploid, diploid, polyploid
  • DNA is packaged around histone proteins => nucleosomes
    
    • nucleosomes aggregate together to form chromosomes
  • lots of information
    
    • 100 to 10,000x as much info as prokaryotes
  • lots of wasted space
    
    • non-coding regions called introns that insert in the middle of genes and have to be clipped out
  • any cell division has to involve mitosis (nuclear division)
  • 80s ribosomes
    
    • 18s subunits (rRNA)

Question 50

Lys

Answer 50

Lysine

ionizable; basic side chain

Question 51

explain why the field of microbiology has seen a resurgence in interest during the past two decades

Answer 51

• emerging diseases
• bioterrorism
• antibiotic resistance
• gut microbiology

Question 52

describe the TCA cycle

Answer 52

• Per 2 pyruvates in TCA cycle:
  
  • 8 NADH
  • 2 FADH₂
  • 2 GTP

Question 53

describe at least three locations in these pathways where amino acids enter when they are broken down for energy and reducing power

Answer 53

• (6C) citrate
• (5C) alpha-ketoglutarate
• (4C) succinyl-CoA
• (4C) succinate

Question 54

Describe the contributions Ignaz Semmelweis made to microbiology and when

Answer 54

• 1840
• in charge of Hungarian hospital
• women were dying from puerperal fever (child bed fever)
  
  • deaths were occurring more often with interns that studied corpses then went straight to women giving birth
  • when they began washing their hands, rates drastically lowered
• his idea of sanitation to reduce infection was laughed at and he disappeared

Question 55

describe the characteristics that typically distinguish eukaryotic and prokaryotic organisms.

what are the definitive characteristics used to separate the two groups?

Answer 55

• eukaryotic cell:
  
  • cell membrane
  • plant or fungus - cell wall
  • double membrane bound nucleus (contains DNA and chromosomes)
  • golgi apparatus
  • mitochondria
  • plant - chloroplast
  • microtubules/microfilaments
  • vacuole
  • flagella
• prokaryotic cell:
  
  • plasma membrane
  • cell wall
  • no membrane bound nucleus
  • storage granules
  • simple organelles
  • flagellum
• the definitive characteristics used to seperate the two groups are:
  
  • membrane bound nucleus
  • compartmentalization

Question 56

describe the three basic groups (domains) of organisms identified by rRNA sequence analysis and how these differ from the classical five kingdom classification system

Answer 56

• the five kingdom classification is based on morphological characteristics
  
  • plants
  • animals
  • fungi
  • protist
  • monera (bacteria)
• three basic domains are based off of DNA sequences
  
  • rRNA - enzyme that produces proteins based on the messenger RNA template
  • different groups have different sizes of RNA in two subunits
    
    • prokaryotes (70S)
      
      • 50S and 30S
        
        • 16S rRNA segment in the 30S
    • eukaryotes (80S)
      
      • 60S and 40S
        
        • 18S rRNA segment in the 40S
  • 3 domains found by Carl Weise:
    
    • bacteria
    • archaea
    • eukarya

Question 57

Acidic side chains amino acid

Answer 57

Question 58

Asn

Answer 58

Asparagine

polar; amide side chain

Question 59

describe two examples of biological warfare used prior to the 1800’s

Answer 59

• mongols attacked a walled city in Ukraine called Caffa
  
  • catapulted dead plague victims over the wall
• european settlers knowingly gave Native Americans blankets contaminated with smallpox
  
  • 30% mortality

Question 60

provide and use the appropriate equation to calculate the amount of energy released from a reaction based on the change in redox potential and oxidation state

Answer 60

• delta G = -(-24e/mol glucose)(F)(1.25V)
  
  • -2895kJ/mol of glucose
  • 1.25 = 0.43+0.82

Question 61

Ala

Answer 61

Alanine

Question 62

Gln

Answer 62

Glutamine

polar; amide side chain

Question 63

Ala

Answer 63

Alanine

nonpolar (hydrophobic)

Question 64

Describe the contributions Edward Jenner made to microbiology and when

Answer 64

• late 1700s
• worked with cowpox virus
  
  • cow maids has a lower incidence of smallpox; he hypothesized that they were being exposed to cowpox
  • he injected people with cowpox, but discovered that cowpox and smallpox are not that similiar, so it provided little immunity
  • he didn’t keep good records, so his work had little impact
• termed “vaccination” (vacca is latin for cow)

Question 65

provide a name for an organism that describes its sources of energy, reducing power, and C

Which combinations are most likely to go together?

Answer 65

• energy
  
  • phototroph - energy from light
  • chemotroph - energy from chemical reactions
• reducing power
  
  • lithotrophs - inorganic compounds
  • organotrophs - organic compounds
• carbon
  
  • autotrophs - plants make carbon skeletons for CO₂
  • heterotrophs - carbon backbone from environment
• combinations:
  
  • all organotrophs are heterotrophs
  • all lithotrophs are autotrophs
• common names:
  
  • humans are chemoorganoheterotrophs
  • plants are photolithoautotrophs
  • chemolithoautotrophs

Question 66

define the terms uniporter, symporter, and antiporter (classes of transmembrane proteins)

Answer 66

• uniporters - tranports one molecule in one direction
• symporters - transport two molecules in the same direction
• antiporters - transport one compound in the cell and another compound out of the cell

Question 67

describe several common storage compounds found in prokaryotes and what they store (i.e. energy, C, P, S, etc.)

Answer 67

• storage granules/inclusion bodies:
  
  • starch - stores carbon
  • glycogen - stores carbon
  • PHB (poly-beta-hydroxybutyrate) - stores carbon
    
    • biodegradable plastic
  • volutin - stores phosphate (phosphorus in bacteria)
  • sulfur granules - store sulfur
    
    • Thiomargarita namibiensis
  • carboxysomes - stores crystalline forms of rubisco (ribulose 1,5-biphosphate)
    
    • carbon fixation in plants

Question 68

Ile

Answer 68

Isoleucine

nonpolar (hydrophobic)

Question 69

His

Answer 69

Histidine

ionizable; basic side chain

Question 70

Discuss at least five of the pieces of evidence discussed in class indicating that mitochondria and chloroplasts evolved from bacterial endosymbionts

Answer 70

• Endosymbiotic hypothesis: origination from free-living bacteria now dependent on another organism
  
  • they have their own DNA and are similar to prokaryotes
  • circular
  • efficient
  • double membrane
  • 70s ribosomes
    
    • 16s rRNA subunits
    • when sequenced, they identified as bacteria (most convincing)
  • functionality
    
    • ribosomes: chloramphenicol, kanamycin, tetracycline
    • bind to ribosomes and prevent production of protein

Question 71

Describe the contributions Anton van Leeuwenhoek made to microbiology and when

Answer 71

• 1680
• invented the 1st microscope
• referred to organisms as “wee animalcules”
• published pictures
• put into question the hypothesis of spontaneous generation

Question 72

Basic side chain amino acids

Answer 72

Question 73

describe a specific example of group translocation

Answer 73

• Phosphoenolpyruvate (PEP) –> pyruvate
  
  • adds phosphate to glucose to prevent it from leaving
  • phosphate goes from PEP –> Enzyme I –> Enzyme III –> Enzyme II (channel protein; passes phosphate to glucose 6-phosphate)
• In the phosphotransferase system (PTS), energy is used from PEP
  
  • requires energy to modify the compound to keep it from associating with the membrane and exiting the cell

Question 74

describe at least five behaviors or practices that have contributed to increased antibiotic resistance in microbes

Answer 74

• over prescriptions by physicians
  
  • antibiotics given for viruses
  • penicillin shots “just in case”
• over the counter availability of antibiotics
  
  • self-diagnosis
• not taking entire dose/treatment
  
  • more sensitive strain is wiped out, but more resistant version is still alive
• inclusion of antibiotics in livestock feed
  
  • 8x as much used
  • now can only use if recommended by veterinarian
• antimicrobial/antibacterial soaps
  
  • only effective if left on for 10 min
• new antibiotics discovered
  
  • results in large profit
  • cannot be saved for vital cases
• vaccination/immunization
  
  • captured Osama Bin Laden by “vaccinating” children for blood samples
    
    • people in middle east and africa think we use it for mass genocide
    • used for politics rather than medical purposes

Question 75

Amide side chains amino acid

Answer 75

Question 76

Phe

Answer 76

Phenylalanine

nonpolar; aromatic side chain

Question 77

identify two inventions by Koch’s lab that allowed the development of pure culture techniques

Answer 77

• Agar (polysaccharide of red jelly)
• petri plate

Question 78

provide terms that describe the arrangement of flagella on the prokaryotic cell

Answer 78

• monotrichous - single flagellum at one end
• amphitrichous - flagella at both ends
• lophotrichous - tuft of flagella
• peritrichous - all around

Question 79

Describe the contributions Louis Pasteur made to microbiology and when

Answer 79

• mid 1800s
• father of microbiology
• worked with chicken cholera
  
  • when chickens were injected with an old culture of cholera, they didn’t get sick
  • when they were injected with a new culture, some got sick and some did not (the ones who were injected with the old culture)
  • came up with the idea of stimulated immune system
  • took good notes
• worked with rabies virus
  
  • weakened the virus by heating it up
  • injected a kid in Paris who had been bitten with the weakened virus and he survived. hundreds of other people infected went to him
  • developed first effective vaccine
• invented swan-necked flask
  
  • if he left the flask, growth occurred
  • if he capped the flask are boiling it, nothing grew
  • with the swan-necked flask, he could boil the broth and use no cap and no growth would occur
  • drove final stake through spontaneous generation
  • made germ hypothesis into the germ theory (particles in the air were leading to microbial growth)
• invented pasteurization
  
  • if you heat up liquids at high temperatures for short periods of time, you can kill off most of the organisms contaminating the solution without significantly affecting the taste
  • original pasteurization - heated grape juice and milk up to 80ºC for 15 minutes
    
    • killed 98-99% of organisms
    • could add yeast to get the fermentation to produce flavors
    • refined today at higher temps for shorter periods of time

Question 80

define “protein conformation”

Answer 80

• Protein conformation: the characteristic 3D shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain
• Primary structure - amino acid sequence
  
  • dictated directly by DNA
    
    • codons are transferred to mRNA
    • ribosomes link the three letter code to the appropriate amino acid
• Secondary structure - folding of sequence
  
  • Two types of structures:
    
    • alpha helices
      
      • hydrogen bonds form between nearby amino acids when it spirals (stabilizes)
    • beta sheets
      
      • hydrogen bond between distant amino acids (stabilizes)
• Tertiary structure - higher level of folding
• Quarternary structure - association of separate peptide units

Question 81

provide the complete names and recognize the structures of two diffusible carriers of e- and two diffusible carriers of high-energy bonds.

identify the subunits that make up these molecules.

Answer 81

• diffusible carriers of reducing powers (e-)
  
  • giant molecules that pick up electrons and take them to another location to dump them off
  • carry them on the nitrogen base that is associated with the nucleotide
    
    • NAD (Nicotinamide adenine dinucleotide)
    • FAD (flavin adenine dinucleotide)
      
      • ​both are electron carriers and do not have electrons yet
        
        • NADH and FADH₂ have 2 electrons each
  • Nucleotide = nitrogen base + 5C sugar + phosphate
• diffusible carriers of high-energy bonds
  
  • ATP (adenosine triphosphate)
  • CoA (coenzyme A)
• subunits:
  
  • NAD: two ribose sugars, one adenine (nitrogenous base), two phosphates bonded together and nicotinamide
  • FAD: one ribose, one adenine, one flavin, 2 phosphates, and a ribitol sugar
  • CoA: one ribose, one adenine, two phosphates, one pantothenate, one acetyl group from cysteine
  • ATP: one adenine, one ribose, 3 phosphates

Question 82

describe the four basic resources needed by organisms to carry out biological processes

Answer 82

• source of carbon
  
  • reduced carbon backbones on which they can create biomass
• source of energy
• source of reducing power
  
  • source of electrons to reduce compounds
• source of inorganic nutrients

Question 83

Describe the contributions Sergei Winogradsky made to microbiology and when

Answer 83

• 1887
• Winogradsky column - model ecosystem used to study a variety of bacteria
• worked with Martinus Beijerinck on environmental microbiology
  
  • enrichment culture technique
• first to demonstrate nitrogen fixation

Question 84

name the disease and disease-causing organism that killed more than a quarter of the population of Europe between 1346-1350

Answer 84

• disease: Bubonic plague (“black death”)
• organism: Yersinia pestis
  
  • flea would bite rat then human

Question 85

Name two genera of organisms that produce endospores.

Steps in spore formation.

Answer 85

• Genera that form endospores:
  
  • Bacillus
  • Clostridium - endospore germinates in absence of oxygen
    
    • C. tetani
    • Botulism (germinates with heat)
• Steps in formation:
  
  • 1) signal - running out of nutrients
  • 2) DNA divides and membrane partitions it
  • 3) the membrane grows back around and encapsulates the cytoplasm and DNA, creating a double membrane

Question 86

Explain how the membranes may be modified during adaptation to different temperatures

Answer 86

• Require a level of fluidity for membranes (except for lipid rafts, which are phospholipids covalently bonded with proteins embedded)
• phospholipids for the most part are not covalently bonded into place, but kept together by hydrophobic interactions. This means that they have to have fluid to function, but not too much
• Cholesterol
  
  • found in animal membranes
  • function: to manipulate fluidity by extending the range of temperatures in which appropriate fluidity exists
  • flat planar compound that fits in hydrophobic region (polar -OH region points out)
• Ergesterol
  
  • found in fungi membranes
• Hopanoid
  
  • function: same as cholesterol
  • found in bacterial membranes
• Double bonds
  
  • saturated double bonds
    
    • push fatty acids out to create a kink, so they cannot get close enough for weak hydrophobic interactions to occur
    • increases fluidity due to more hydrophobic interactions
    • hot temperatures
  • Polyunsaturation
    
    • hydrophobic interactions are minimized
    • cold temperatures
• Fatty acid chains
  
  • extending the length
    
    • increases hydrophobic interactions
    • higher temperatures
    • more stable
  • shorter tails
    
    • less hydrophobic interactions
    • better for cold environment
• linkage of fatty acids
  
  • ​Archaea are adapted to extremely high temperatures because they use ether linkages
    
    • phospholipid monolayer
  • bacteria and eukaryotes use ester linkages

Question 87

Describe how the composition of the cell wall differs among groups such as bacteria, archaea, plants, animals, diatoms, and fungi

Answer 87

• cell wall:
  
  • ​plants
    
    • ​cellulose
    • hemicellulose
    • pectin
    • lignin (glue)
  • animals
    
    • ​none
  • fungi
    
    • ​chitin (long polymers of N-acetylglucosamine)
  • Diatoms
    
    • ​silica
  • archaea
    
    • ​pseudopeptidoglycan (different type of sugar)

Question 88

Thr

Answer 88

Threonine

polar; aliphatic hydroxyl side chain

Question 89

What physical and chemical characteristics make endospores so resistant and long-lived?

Answer 89

• Structure:
  
  • Ex: exosporium
    
    • fragile protein coat
  • SC: spore coat
    
    • protein coat is very resistant and impermeable
  • CX: cortex
    
    • peptidoglycan layer that is loosely cross linked
  • CW: core wall
    
    • inner most part of spore wall
  • cytoplasm
    
    • very dehydrated
      
      • normal vegetative cell is 80-90% water
      • endospore is 10-25% water
      • inactivates enzymes and proteins change shape and become unfunctional to preserve them
    • DNA binding proteins
      
      • protect DNA and absorb hit from radiation
    • calcium dipicolinate
      
      • 25% of weight
      • carbon ring with nitrogen and two carboxyls
      • DNA binding protein
      • absorbs water
    • DNA repair enzymes
      
      • nonfunctional in normal state

Question 90

Discuss the differences between the secondary DNA of prokaryotes and eukaryotes

Answer 90

• secondary DNA: where DNA is found in cells
  
  • prokaryotes:
    
    • viral DNA (virus can inject its own DNA in a cell)
    • plasmids: small circular dsDNA that replicates independently of cell
      
      • 5,000 to 10,000 bp (substantially smaller)
      • nonessential
      • antibiotic resistance gene
      • ability to detoxify
      • ability to deal with heavy metals
  • eukaryotes
    
    • viral DNA
    • very few plasmids
    • mitochondria
    • chloroplasts

Question 91

Chemical “type structure” of an amino acid

Question 92

determine whether or not a compound could donate or accept an e- from another compound, when you are provided with redox potentials

Answer 92

• oxidation: removal of electrons
  
  • looking at H and O can help calculate oxidation state
    
    • H: +1
    • O: -2
  • oxidation is at the top of the tower; these compounds can donate e- to the compounds below them
  • largest free energy at top of tower (most negative/holds on to e- loosely)
• Reduction: addition of electrons
  
  • reduction is at the bottom of the tower; compounds can accept e- from the compounds above them
  • highest attraction for e- is at the bottom of the tower; more positive (volts)
  • the lowest free energy is at the bottom of the tower (most positive/tightly holds e-)
• Redox potential: relative affinity of a compound for electrons; how tightly the electrons are held on (volts)

Question 93

Describe the contributions Jon Snow made to microbiology and when

Answer 93

• 1854
• father of epidemiology
• studied cholera outbreaks in London and decided to try to prevent rather than just treat
  
  • made a map of cholera deaths and water pumps
  • noticed deaths were occurring around one specific water pump
  • took the handle off that pump and disease dwindled

Question 94

Aliphatic hydroxyl side chains amino acids

Answer 94

Question 95

Arg

Answer 95

Arginine

ionizable; basic side chain

Question 96

Describe the contributions Christian Gram made to microbiology and when

Answer 96

• 1884
• gram stain
  
  • gram positive - purple
  • gram negative - pink
  • crystal violet, KI (mordant - keeps stain in bacterial cell), alcohol (wash), safranin (counter stain)

Question 97

provide a list of macro- and micronutrients required by most microorganisms

Answer 97

• plant macronutrients - C HOPKNS CaFe Mighty good
  
  • carbon
  • hydrogen
  • oxygen
  • phosphorus
  • potassium
  • nitrogen
  • sulfur
  • calcium
  • iron
  • magnesium
• plant micronutrients - Mn CuZn MoCloB
  
  • manganese
  • copper
  • zinc
  • molybdenum
  • chlorine (needed by plants, but not microorganisms)
  • boron

Question 98

explain what is meant by “substrate-level phosphorylation.”

explain why some texts identify different steps in pathways as the exact location of s.l.p.

Answer 98

• substrate level phosphorylation is how high energy bonds are made using a substrate
  
  • can convert ADP to ATP using kinase (transfers phosphate)
• some texts think s.l.p. takes place when ATP is created while others think the most important step is when high energy phosphate bonds are created

Question 99

provide names of at least three membrane bound e- carriers, and explain how these function to create a proton gradient

Answer 99

• membrane bound e- carriers:
  
  • flavoprotein
  • quinone
  • cytochrome bc1
  • cytochrome c
  • cytochrome a
• redox potentials rise (becomes more positive) as we go from carrier to carrier
  
  • drop in redox is used to move protons across the membrane
  • outside of the membrane is more protons and inside of the membrane is more hydroxyl which creates a concentration gradient that is a form of energy (ATP synthase or ATPase)

Question 100

explain how reducing power and energy can be converted from one to another

Answer 100

• a series of oxidation/reductions that dump electrons down the tower
  
  • NADH oxidizes to NAD. electrons get dumped down tower on flavoprotein which gets reduced.
  • flavoprotein gets oxidized and dumps electrons onto something down the tower which gets reduced
  • so on and so on
• energy is released every time electrons reach a step because compounds change shape (positive to negative charge) when they go from oxidized to reduced
• as electrons get passed down, it grabs a proton and moves it out of membrane (pumping or shuttle mechanism caused by change in shape)
• since protons come from water, protons are outside of the membrane and hydroxyl is inside of the membrane. the concentration gradient forms energy (drive flagellum, active transport, production of ATP using ATPase)
• electrons are eventually passed to oxygen (terminal electron acceptor), forming water. the energy of electrons is completely dissipated
• • to convert energy to reducing power:
    
    • reduce concentration of one side of the reaction to drive it in the opposite direction
      
      • change concentration = change position on tower (able to reduce NAD to NADH)
        
        • higher concentrations of NAD relative to NADH = drops down the tower
      • lower redox potential -> more likely to give up electron and be oxidized
      • high proton concentration = reduced state = less likely to give up electrons = increasing redox potential
      • use high ATP to pump protons out and electrons are transferred back onto NAD forming NADH

Question 101

explain why oxidation of FADH₂ produces less energy than oxidation of NADH

Answer 101

• FADH₂ comes in lower on the tower, so it only pumps 6-8 protons -> 2 ATP
• NADH pumps 8-10 protons, so when protons flow back into the cell, it can produce a maximum of 3 ATP

Question 102

describe in detail two examples of glucose fermentation, and identify the key characteristics of all fermentation

Answer 102

• two types of glucose fermentation:
  
  • lactic acid fermentation
    
    • dump electrons stripped off carbon skeleton onto pyruvate -> reduce lactate and produce NAD
  • decarboxylate pyruvate
    
    • reduce acetaldehyde and use the electrons from NADH to produce ethanol and more NAD
• key characteristics of all fermentations:
  
  • no net oxidation or reduction of substrate (carbon skeleton)
  • ATP is generated by s.l.p. not oxidative phosphorylation
  • not much energy is harvested (2 ATP versus the 38 ATP from respiration)
  • organic acids and alcohols are produced and secreted from the cell (waste products)

Question 103

explain the differences between aerobic respiration, anaerobic respiration, and fermentation, including differences in the amount of energy harvested during each process

Answer 103

• aerobic respiration
  
  • oxygen is terminal electron acceptor
  • 38 ATP
• anaerobic respiration
  
  • something other than oxygen is used as a terminal electron acceptor (i.e. ferric iron or nitrate)
    
    • will eventually shift to methanogens when all other resources are used
  • cytochrome will stay in reduced state (no place for electrons to go)
  • can’t carry out steps in TCA cycle (NAD will be reduced to NADH and FAD would be FADH₂)
  • not as much energy yielded

Question 104

describe noticeable changes in the environment when anaerobic respiration occurs and either FeOOH, MnO₂, or SO₂^-2 are used as terminal electron acceptors.

describe the environmental impacts that can occur when chemolithotrophs use H₂S or FeS₂ as a source of reducing power

Answer 104

• flooded soils
  
  • FeOOH, MnO₂, or SO₄^-2 becomes more soluble
• swamps
  
  • H₂S or FeS₂ cause odor
  • reduced species are more toxic than oxidized species
• example of methane: compost, dairy, waste
  
  • cows burp because microorganisms are in its rumen, producing methane

Question 105

describe three mechanisms by which the specific activity of an enzyme molecule can be controlled

Answer 105

• product inhibition (fastest)
  
  • A→B (changing concentrations will change direction)
    
    • if it’s a negative delta G, it can go to the right
    • if it’s a positive delta G, it can’t go to the right
    • delta G (real nonstandard) = delta G (standard) + rT log(q)
      
      • ​q = product concentration / reactant concentration
  • works well with delta G around -3 to 0
  • instantaneous - as soon as product increases it shuts down
• allosteric regulation
  
  • ​enzymes act as lock and key with an active site to fix substrate
  • end product must accumulate before enzyme activity is shut down
  • weak bonds
  • allosteric site binds allosteric effectors (have effect of shape of active site)
    
    • allosteric activator - improves shape; positive
    • allosteric inhibitor (feedback inhibition) - make shape worse so substrate can’t bind; negative
  • when it operates:
    
    • immediately following branch points; enough product shuts down enzyme early on
    • good for reaction with very low delta G values
• covalent modification (longest)
  
  • small molecules are attached to the enzyme
    
    • phosphate, methyl groups, ADP (example: CheB)
      
      • acts as a switch to turn on and off (like chemotaxis)
  • long term to shut down enzyme activity
  • more negative delta G

Question 106

give an example of an enzyme found in glycolysis that is controlled by allosteric regulation, and name the allosteric activator and inhibitor for this enzyme in bacteria

Answer 106

• phosphofructokinase (third enzyme of glycolysis)
  
  • activator - ADP
  • inhibitor - PEP

Question 107

identify two types of reactions (or points along a pathway) that are typically regulated by feedback inhibition

Answer 107

• immediately at a branch point within the pathway
• when the change in G of a reaction is too negative to be controlled by concentration of the products

Question 108

describe two ways that the quantity of enzyme in a cell may be negatively controlled.

describe when you would expect one mechanism to be used as opposed to another.

Answer 108

• repression
  
  • corepressor (i.e. arginine) + repressor bind to operator to block transcription
  • used when you have lots of the compound and don’t need enzymes to produce more (biosynthesis reactions)
  • negative control
• induction
  
  • ​operon is normally blocked by repressor
  • inducer binds to the repressor and pulls it away to allow transcription
  • used when you need the energy from the substrate (catabolic reactions)
    
    • i.e. lactose
  • negative control

Question 109

describe in detail one positive control mechanism.

describe an operon that is regulated by both positive and negative control mechanisms.

Answer 109

• Cababolite “repression” - presence of glucose prevents transcription in lac operon
  
  • CAP (catabolite activator protein) = CRP (cyclic AMP receptor protein)
    
    • ​stimulates binding of RNA polymerase

Question 110

describe the three major steps in the process of binary fission

Answer 110

• cell elongation (elongates cell to 2x original size)
  
  • autolysins - enzymes that break peptide bonds in peptidogylcan layer of cell wall
    
    • clips and lays down new material
      
      • penicillin prevents the new material from being laid down (only effective with growing cell)
• chromosome replication (circular chromosome)
  
  • origin of replication - 300 bp region
  • series of enzymes come in:
    
    • DNA helicase - splits apart double helix
      
      • one for each replication fork
    • single stranded DNA binding proteins
      
      • ​keep base pairs from reattaching
      • keep ssDNA from degradation
    • DNA gyrase - ahead of helicase to untie supercoiling caused by helicase
      
      • breaks knots and reattaches
    • primase - RNA polymerase that creates a 10 bp long RNA primer
    • DNA polymerase III
      
      • ​3’ to 5’ exonuclease activity
      • leading strand (continuous)
        
        • new nucleotides are only added to the 3’ carbon of the growing strand
      • lagging strand (okazaki fragments)
        
        • can only grow away from replication fork so primase jumps ahead and new forms backwards
      • proofreading capability
    • DNA polymerase I
      
      • ​5’ to 3’ exonuclease activity (degrades RNA primer and makes new DNA; starts at 5’ end of chain)
      • proofreading capability
    • ligase - seals the nick made by DNA polymerase I to link okazaki fragments together
• cross wall/septum formation
  
  • ​ingrowth of cell wall -> ingrowths meet -> break apart due to brownian motion -> two daughter cells are formed

Question 111

calculate changes in bacterial population size during exponential growth when provided information on initial population size and µ

Answer 111

N_t = N_oe^µt

µ = instantaneous growth rate constant per unit time

Question 112

distinguish between microbial growth rate and the growth rate constant, and provide an equation that shows the relationship between the two

Answer 112

dN/dt = µN

dN/dt = instantaneous rate of increase = “cells per hour”

Question 113

primary impact of pH on microbial growth

Answer 113

• nutrient solubility
• element toxicity

Question 114

provide an equation that describes the effect of substrate concentration on the growth rate constant.

be able to provide appropriate units for the monod constants, µ_max and K_s

describe, using a graph, what the constants in the equation refer to

describe how these constants would differ between copitrophs and oligotrophs

Answer 114

• monod equation - microbial growth rate constant relating substrate concentration
• µ = (µ_max[s]) / (k_s + [s])
  
  • ​k_s = substrate concentration that produces 0.5µ_max (mg x L^-1)
  • µ_max = plateau of the graph; maximum specific growth rate (h^-1)
• copiotroph - adaptation to high substrate concentration
  
  • faster growing
  • higher growth rate
• oligotroph - adapted to low [s]
  
  • slow growing

Question 115

describe the free radical forms of oxygen that are toxic to some microorganisms and how particular enzymes deal with these free radicals

Answer 115

• superoxide
  
  • most common
  • more reactive than hydrogen peroxide but not as reactive as the hydroxyl radical
• peroxide
  
  • weakest oxidizing species and most stable
• hydroxyl radical
  
  • ​strongest oxidizing species and most dangerous

Question 116

describe the typical size of a virus and compare it to a typical bacterium

Answer 116

• virus is 20-400 nm
• bacterium is 0.2-10 micrometers

Question 117

difference between influenza and norovirus (structure)

Answer 117

• influenza is an enveloped helical structure
• norovirus is a naked icosahedral virus

Question 118

name and describe the different phases of a “growth curve” for a virulent bacterial virus and what technique is needed to measure the length of those phases

Answer 118

• phases:
  
  • _​_latent period
    
    • ​includes the eclipse (virus inside bacteria) and early maturation phases
    • viral nucleic acid replicates and protein synthesis occurs
  • maturation period
    
    • ​assemble virions and release
    • number of infectious virions inside host cell rises dramatically
  • burst size - number of virion release per cell