Exam 3

Question 1

What are the functions of the cell wall?

Answer 1

physical barrier, maintains shape of the bacterium, helps protect cells from osmotic lysis, helps protect from toxic materials, and contribute to pathogenicity

Question 2

Where is the cell wall made?

Answer 2

Internally but is supposed to be on the external side

Question 3

What is the cell wall made up out of?

Answer 3

The disaccharide subunit is made on the inside, so the NAM is linked to the UDP. Then the side chain is added and then NAG is added to the NAM. The disaccharide on the outside is added to the peptidoglycan chain.

Question 4

How can the cell wall be broken by lysozyme?

Answer 4

The cell wall can be broken down by lysozyme which breaks the 1,4 bonds between the saccharides. Lysozyme is a nice way to control the number of bacteria that is on the human body.

Question 5

What can the cell wall use to break it?

Answer 5

lysozyme, lysostaphin, B- lactam antibiotics

Question 6

How can the cell wall be broken down by B-lactam antibiotic?

Answer 6

All antibiotics contain the beta lactic ring and this is the reason why the structure cannot be put into heat since the heat will cause the bonds to breaks apart. This antibiotic prevents the enzyme from putting the peptidoglycan cross linkages together by binding to the side chain.

Question 7

How can the cell wall be broken down by lysostaphin?

Answer 7

Lysostaphin targets the peptidoglycan on other species of bacteria and will cause the cell to burst in a hypotonic state.

Question 8

How is antibiotic resistance created? And why do the bacteria choose to keep it?

Answer 8

It is created when the beta-lactamase is cleaving the nitrogen bond so he antibiotic does not work anymore. Bacteria choose to keep it due to the constant creation of mutation (even to medicine that is not created yet) and the environment is the deciding factor on whether or not to keep the mutation.

Question 9

How does Augmentin work?

Answer 9

Augmentin actually contains amoxicillin and clavulanic acid which contains the beta lactic structure so the beta-lactamase does not hydrolyze the amoxicillin but the calvulanic acid

Question 10

How does Vancomycin work?

Answer 10

It works by using macromycin which is a bulky compounds that sits on the peptidoglycan which allows the beta-lactam ring to not be hydrolyzed.

Question 11

What is peptidoglycan?

Answer 11

A rigid structure that lies just outside the cell membrane and a repeating sugar with peptide chain, the alternating sugars are NAG and NAM. Each peptidoglycan disaccharide subunit is NAM with a small peptide chain and NAG. NAG and NAM are both 6 carbon sugars. The side chain never comes off the NAG, only the NAM. The side chain needs to be linked together otherwise the cell wall will just fall off. They are cross linked directly from the 4th which is always alpine to the 3rd. Transpeptidase uses the delaine to make the cross inter bridge. Peptidoglycan take on helical shape because it is important for stability. Peptidoglycan can stretch in response to osmotic pressure and flexibility comes from peptide side chains. It is also porous so things can come into and out of the cell.

Question 12

What are L and D forms and how are they related to the peptidoglycan?

Answer 12

D forms amino acids associated with NAM in peptidoglycan. D forms are stereoisomers of L forms normally found in biological proteins. They are both chirality and are not superimposable. The L form is counterclockwise and the D form is clockwise. L forms are the only ones coded for by amino acids. D forms need to made by racemes which takes L forms and makes them D forms. D forms are made because of denaturation by objects around the plasma membrane since it cannot detect D forms.

Question 13

Gram positive bacteria

Answer 13

They have a thick outer layer of peptidoglycan, a very narrow periplasmic space, and teichoic acids in the peptidoglycan that do not anchor into the plasma membrane, have large pores through its matrix, no porins

Question 14

Teichoic acids

Answer 14

only in gram positive bacteria, carry negative charge which contribute to overall charge of cell envelope, serve as a barrier of harmful substances

Question 15

Lipoteichoic acids

Answer 15

help anchor the peptidoglycan into the plasma membrane

Question 16

Gram negative bacteria

Answer 16

have a varying width in periplasmic space, thin layer of peptidoglycan, and an outer membrane composed of lipopolysaccharides, have porins and TonB proteins in its outer membrane to transfer molecules into periplasmic space

Question 17

Glycoprotein

Answer 17

helps anchor the outer membrane to the peptidoglycan

Question 18

Lipopolysaccharides

Answer 18

composed of lipids and carbohydrates, have lipid A, core polysaccharides, and O antigen

Question 19

Lipid A

Answer 19

the most inner part that contains 3 fatty acids and a phosphate with 2 glucose derivatives

Question 20

Core polysaccharides

Answer 20

made up of about 10 round sugars that tend to be unusual

Question 21

O antigen

Answer 21

the largest chain and makes contact with the outside environment, could contains about 200 sugar and resist phagocytosis

Question 22

Importance of LPS

Answer 22

the contribution to negative charge on cell surface, help stabilize outer membrane structure (adding rigidness), may contribute to attachment to surfaces and biofilm, creates a permeability barrier, protection from his defenses (resists entering of bio salts), and can act as a endotoxin (made inside of the cell and when released it is needed, can create shock and fever from lipid A)

Question 23

Porin proteins

Answer 23

The outer membrane is more permeable than plasma membrane due to porins. They are usually primary proteins together and are nonspecific but molecules that are smaller than 600. They use facultative diffusion

Question 24

How does the cell wall explain how the gram stain works?

Answer 24

Large pores in the gram-positive cell shrink while the outer membrane lipids are stripped in the gram-negative cells

Question 25

Flagella

Answer 25

used for motility, they are usually spiral, hollow, rigid filaments extending from the cell surface

Question 26

Monotrichous

Answer 26

one flagellum

Question 27

Amphitrichous

Answer 27

one flagellum at each end of the cell

Question 28

Polar flagellum

Answer 28

flagellum at the end of the cell

Question 29

Lophotrichous

Answer 29

cluster of flagella at one or both ends

Question 30

Peritrichous

Answer 30

spread over entire surface of cell

Question 31

What are the three part of the flagella?

Answer 31

filament, hook protein, and basal body

Question 32

Filament

Answer 32

a single protein subunit made up of flagellum

Question 33

Hook protein

Answer 33

connects the filament to the basal body

Question 34

Basal body

Answer 34

embedded in the cell wall and is most complex, 4 rings in the gram negative while 2 rings in the gram positive, gram negative have a p ring in the peptidoglycan and c rings in the cytoplasmic part of the membrane

Question 35

Why is the flagellum hollow in bacteria?

Answer 35

They are hollow because the filament extends by the tip so the proteins that the filament is made up out of will go through the center

Question 36

How does the flagellum rotate?

Answer 36

like a propeller and is very rapid rotation up to 1100 rev/sec

Question 37

What does counterclockwise rotation mean in bacteria?

Answer 37

run, move forward

Question 38

What does clockwise rotation mean in bacteria?

Answer 38

tumble, cell stops

Question 39

Chemotaxis

Answer 39

the movement toward a chemical attractant or away from a chemical repellent and changing the concentration of chemical attractants and chemical repellents bind chemoreceptors of the chemo sensing system

Question 40

What happens in the presence of attractant?

Answer 40

tumbling frequency is reduced and runs in the direction of attractant are longer

Question 41

What happens in the presence of repellent?

Answer 41

tumbling frequency is reduced and runs in the direction opposite from repellent are longer

Question 42

How does the flagellum operate?

Answer 42

2 part motor producing torque which is rotor and stator

Question 43

Stator

Answer 43

is an electromagnet so Mot A and Mot B proteins are used to help the energy needed from existing ion gradients used to turn the flagella, the flagellum moves by protons which move through the cell and allow the basal body to turn and that causes the actual turning of the filament

Question 44

Rotor

Answer 44

C ring and MS ring turns and interacts with the stator

Question 45

How do bacteria move without flagella?

Answer 45

gliding (smooth sliding over a surface), polymerization of action (for propulsion of bacteria into adjacent cells) and twitching (slow, jerky process using pili)

Question 46

Pili

Answer 46

a secondary function that some bacteria have evolved to have, adherence molecules stick to surfaces that are mediated by pili, fibers of pili proteins possess other proteins on their tips for sticking, some scientists prefer to use pili only for conjugation structure and fimbrriae for adherence

Question 47

Glycocalyx

Answer 47

outermost layer in the cell envelope, sugar coat, aids in the attachment to solid surfaces, biofilms are considered this, refers to either slime layers or capsules

Question 48

Capsules

Answer 48

composed of polysaccharides, sticky, helps bacteria adhere to different things, and an organized layer helps define the structure of the cell, not easily removed from the cell, can be seen from underneath light microscopes, make it hard for the immune response to recognize you, cannot be phagocytosed from the immune system, allows you to pathogenic, lot of water to prevent desiccation

Question 49

Slime layers

Answer 49

similar to capsules, sticky, can adhere to things, and much more easily removed to the cell, outermost layer, cannot be seen underneath microscope, offer protection from host cell immune response, difference antibiotics get hung up here as well, aids in motility and can cause gilding cause of slime, a lot of water to prevent desiccation

Question 50

S layers

Answer 50

made up of proteins, extremely organized, help adhere to things, and can be found in both positive (adheres to our layer) and negative (adheres to peptidoglycan) bacteria, gives protection, helps with shapes and rigidity, has potential in nanotechnology, protects from ions and pH fluctuation and osmotic stress, enzymes and predation, is self assembly so no energy or enzyme needed

Question 51

Sporulation

Answer 51

complex 7 step process, has to put all layers together, all of nothing response, cannot stop in the middle, and usually occurs up to 10 hours, triggered my nutrient starvation, the master regulator is spo A and once it has phosphorylated it has started

Question 52

Steps in sporulation

Answer 52

axial filament forming so the chromosome is stretching out the entire length of organism, then septum formation which is a forespore development (separation between forespores and the rest of cell) then engulfment of forespore, then cortex formation which is specialized peptidoglycan formation for the cortex, then coat synthesis, then completion of coat synthesis and should be resistant to everything it is supposed to have then release to the environment which kills mother cells

Question 53

Germination

Answer 53

reverse of sporulation and it still a complex multistep process, transformation of sporulation into a vegetative cell

Question 54

Steps of germination

Answer 54

activation - heat for 70 degrees Celsius for 10 minutes, germination - germinate receptor binds certain nutrients when they bind so it trigger a lot of things to happen in the cell, water starts to move back into the cell so calcium increase which starts metabolic activity, the cell will swell and the cortex region degrades, outgrow - emergence of vegetative cell

Question 55

What is the size and shape of Archaea?

Answer 55

usually between 0.5 and 5 micrometers in diameter but can vary greatly, they have similar shapes, are singular, circular chromosomes, and lack a membrane-bound nucleus, shapes can also vary so they can be rods, spheres or spirals just like bacteria

Question 56

Cytoplasm in archaea

Answer 56

Histones form structures that DNA wraps around. Histones are difference in archaea from eukarya. There is a single circular chromosome. The thought is bacteria had branched off from eukarya and archaea then separated from each other. The histone is smaller in archaea since there is only a tetramer so the DNA has to wrap around a smaller space

Question 57

Cytoskeleton in archaea

Answer 57

The cytoskeleton shows that archaea can resemble eukarya but some resemble bacteria. They are playin the same role as bacteria when they are closer in relation to bacteria

Question 58

Plasma membrane in archaea

Answer 58

all archaeans possess a plasma membrane because it is needed, can be bilayer or monolayer, contains hydrocarbons derived from isoprene units, hydrocarbons attached to glycerol by ether linkages, have a transport system, lipid chain has an isoprene unit which is 5 carbon units, fatty acids is attached to the glycerol with ester linkages, fatty acids attach to the 1 carbon in archaea while 3 carbon in bacteria, does play the same role in archaea, not able to use group translocation, so have primary and secondary active transport

Question 59

Cell wall in archaea

Answer 59

most have a cell wall but is not needed, provides physical and osmotic protection, function is the same, look the same as bacteria, uses NAG and NAT which have the peptide side and there is no D forms, only L forms, joined by beta 1,3 linkage, lysozyme and beta lactase antibiotic will not work on archaea

Question 60

Flagella in archaea

Answer 60

Flagellum is similar to bacteria that they rotate to move the cell. They are not evolutionary related to bacteria but more to pili, thinner, usually composed of 2 or more different version of flagellin protein, and likely growing from base rather than tip, not hollow, basal body is much less complex, tend of rotate slower and needs ATP to move the basal body, very stable because it has to withstand various conditions, no tumble, rotation one way gives forward while rotating in the other gives backward

Question 61

S layer in archaea

Answer 61

a single layer of many identical armor like subunits, made up of polysaccharides and use it the same way that bacteria does, sticky so helps with adherence

Question 62

Cannulae in archaea

Answer 62

hollow glycoprotein tube that links cell together to form a complex network, running between archaea and what they are doing is still being researched but it could have something to do with sharing connections or sharing nutrients

Question 63

Metabolism

Answer 63

sum of the chemical reactions in an organism

Question 64

Catabolism

Answer 64

the breakdown of molecules for energy, reducing potential, and building blocks, an energy conserving reaction, fueling reaction, providing a ready source for reducing power, generating precursors for biosynthesis, and they break down macromolecules and store the energy for later as ATP

Question 65

Anabolism

Answer 65

put energy together so it is the energy using process, the synthesis of complex organic molecules from simpler ones, requires energy from fueling reactions, and takes simple sugars and puts them together to make macromolecules

Question 66

How is metabolism, catabolism and anabolism related?

Answer 66

Catabolism proves the building blocks and energy for anabolism and then catabolic reactions transfer energy from complex molecules to ATP, anabolic reactions transfer energy from ATP to complex molecules

Question 67

Metabolic pathways

Answer 67

are long, complex, branched and mediated by enzymes that are encoded by genes

Question 68

Enzymes

Answer 68

acts as catalysts, they are either used up or charged, the active of an enzyme is vital to its function, if it were to lose the structure of the active site, it will lose it function, all enzymes have a turnover number as well, meaning how fast it works, this number is usually between 1-10,000 molecules per second, are not spontaneous because of their high affinity, solely composed of one or more polypeptides, and others are composed of peptides and non protein components

Question 69

Transition state

Answer 69

higher when an enzyme is not added

Question 70

Activation energy

Answer 70

energy requires to bring reacting molecules together in a specific way, the greater the activation energy the slower it occurs, enzymes lower activation energy because of their high affinity, meaning they can pull things towards them, also physically grateful what they need to binds and make it react with each other

Question 71

Lock and key model

Answer 71

enzyme is the lock and substrate is the key and the active state is the key hole, really rigid

Question 72

Induced fit

Answer 72

differs from lock and key, substrate plays a role in shape of the enzyme and the enzyme will hug you a bit, the substrate still has to have a very specific confirmation with the enzyme, when the substrate binds it affects ends conformation of the enzyme so enzyme changes just as much as substrate

Question 73

Apoenzyme

Answer 73

protein component of an enzyme, it is inactive if alone and needs a cofactor to be become active

Question 74

Holoenzyme

Answer 74

active form of an enzyme which is the apoenzyme and cofactor together

Question 75

Co-factor

Answer 75

non protein component that some enzymes need to work

Question 76

Coenzymes

Answer 76

loosely attached to protein portions of the enzyme and organic molecules, they are carrier by moving functional groups substrate to substrate important coenzymes

Question 77

Prosthetic

Answer 77

closely attached and tend to be inorganic

Question 78

Substrate important enzymes

Answer 78

NAD+, NADP+, FAD, Coenzyme A, and most of them are involved in the TCA cycle

Question 79

What are the environmental factors on enzymes?

Answer 79

temperature and pH and the active site becomes denatured

Question 80

How does temperature affect enzymes?

Answer 80

every enzyme has a temperature has an optimal temperature, at high temperatures, the enzyme starts to pull apart, they denature, and the active site disappears, at low temperatures, the enzyme starts to not work fast enough and eventually shuts down

Question 81

How does pH affect enzymes?

Answer 81

has an optimal pH range, they cannot function if it gets too acidic or alkaline, it dentures when it passes the range

Question 82

How does substrate concentration affect enzymes?

Answer 82

It effects product formation and then when you increase, more products will be made

Question 83

Km

Answer 83

when enzymes have to work at half of its capacity, used to measure affinity an enzyme has for its substrate, low Km is good at grabbing substrate in the environment, high Km needs more substrate in the environment and not the best at grabbing it, most enzymes tend to have low Km

Question 84

Vmax

Answer 84

the rate of product formation when the enzymes is saturated with substrate and operating as fast as possible

Question 85

Michaelis Menten Plot

Answer 85

up to a point of adding too much substrate and all enzymes are busy with substrate then it does not matter if you add more substrate because enzymes are saturated with substrates

Question 86

Competitive inhibition

Answer 86

when the competitor directly competes with the binding of substrate to active site so substrate cannot bind to active site since inhibitor is there

Question 87

Example of competitive inhibition

Answer 87

PABA sulfonamides that work at folic acid pathways

Question 88

The ways of overcoming competitive inhibitors

Answer 88

having a higher substrate concentration, enzymes have higher affinity for competitive inhibitors

Question 89

Noncompetitive inhibition

Answer 89

when a competitor binds to enzymes at allosteric sites, this changes the enzymes shape so that it becomes less active, does not bind to the active site

Question 90

The ways of overcoming noncompetitive inhibitors

Answer 90

using heavy metals like mercury or use side groups

Question 91

Metabolic regulation

Answer 91

the conservation of energy and materials and the maintenance of metabolic balance despite changes in environment

Question 92

3 major mechanisms of metabolic regulation

Answer 92

metabolic channeling, direct stimulation, regulation of the synthesis of a particular enzyme

Question 93

Metabolic channeling

Answer 93

moving enzymes around to appropriate places within the cell depending on cell needs,

Question 94

Regulation of the synthesis of a particular enzyme

Answer 94

gene expression, whether this needs to be made or not

Question 95

Direct simulation

Answer 95

gene expression - turned on or off

Question 96

Allosteric regulation

Answer 96

most regulatory enzyme, binds non covalently to the regulatory site and changes the shape of the enzyme and laters the activity of the catalytic site, very specific and tightly controlled process

Question 97

Positive allosteric regulation

Answer 97

turns on so increases enzyme activity

Question 98

Negative allosteric regulation

Answer 98

turns off so inhibits enzyme activity

Question 99

Covalent modification

Answer 99

a reversible on and off switch which works by adding or removing functional groups to enzymes and turning it off or on by doing this and then the addition or removal of a chemical group, can respond to more stimuli in varied ways, regulation of enzymes that catalyze covalent modification adds a second level, there is a finer level of control compared to allosteric

Question 100

Feedback inhibition

Answer 100

the products can be used to turn it off, the ends product will bind to the metabolic pathway and turn off the feedback