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bio2200 > <3 microbio exam #2 > Flashcards

<3 microbio exam #2 Flashcards

1
Q

what are catabolic reactions?

A
  • the break down of complex molecules into smaller ones.
  • hydrolysis. add water!

*exergonic: release/produce energy.

  • involves the break down of lipids and proteins.
  • used to make ATP.
  • involves aerobic and anaerobic respiration, glycolysis, the kreb cycle, ETC, and fermentation.
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2
Q

what are anaebolic reactions?

A

*the building of complex molecules into simpler ones.

*involves dehydration to build a bond

ex. amino acids are the building blocks of proteins.

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3
Q

what is an apoenzyme?

A

an inactive enzyme.
needs to be activated with a cofactor or coenzyme.

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4
Q

what is the difference between a cofactor and a coenzyme?

A
  • a cofactor is inorganic! like Fe, Zn, and Mg.
  • a coenzyme is organic! like NAD and FAD!
    responsible for holding electrons, like from the kreb cycle to the ETC.
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5
Q

what is a holoenzyme?

A

an active enzyme!
cofactor/enzyme + an apoenzyme!

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6
Q

important coenzymes include:

A

catabolic: NAD and FAD.
anabolic: NADP.

NAD and NADP both include the vitamin niacin, which is present in energy drinks like celsius.

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7
Q

what influences enzyme activity?

A
  • pH
  • temperature
  • substrate concentration: once all enzyme active sites are filled, activity stops.
  • inhibitors:
    competitive - bind t the active site of an enzyme to prevent the subtrate from binding.
    noncompetitive - allosteric; interact with another part of the enzyme. can cause the active site to change shape etc.
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8
Q

what is a redox (oxidation-reduction) chemical reaction?

A

LEO goes GER.

  • oxidation: removal of electrons. dehydrogenation.
    NADH –> NAD
  • reduction: adding electrons.
    NAD –> NADH
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9
Q

what is a synthesis chemical reaction?

A
  • the build up of molecules; anabolic.
    involves dehydration.
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10
Q

what is a decomposition chemical reaction?

A
  • the breakdown of complex molecules to simpler ones; catabolic.
    involves hydrolysis.
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11
Q

what is an exchange (displacement) chemical reaction?

A
  • the adding and breaking of bonds at the same time; synthesis and decomposition.

ex. pull of the phosphate: ATP –> ADP. catabolic.
phosphate then forms a bond with glucose! anabolic.

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12
Q

what is involved in the catabolism of lipids?

A
  • lipids are broken down into a fatty acid, which then gives you acetyl coA which can feed in to the kreb cycle.
  • lipids can also be broken down into glycerol, which will also give us pyruvate acid, then acetyl coA to feed into the kreb cycle.
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13
Q

what is involved in the catabolism of proteins?

A
  • proteins are broken down into their building blocks, amino acids.
  • amino acids can be further synthesized/broken down into other substances that can enter the kreb cycle.
  • deamination
    decarboxylation
    desulfurization
  • the nitrogen component of the amino acid can be incorporated into other compounds or excreted
    or
  • the carbon skeleton of the amino acid can be synthesized/catabolized to create acetyl coA for the kreb cycle to feed into the ETC to create ATP.
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14
Q

what is a primary protein structure?

A

the basic polypeptide amino sequence

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15
Q

what is a secondary protein structure?

A

a helix and pleated sheet with 3 polypeptide strands.

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16
Q

what is a tertiary protein structure?

A

a helix and pleated sheet, with a 3D structure.

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17
Q

what is a quaternary protein structure?

A

the relationship of several polypeptide chains, forming a protein!

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18
Q

ATP (1)
what is substrate-level phosphorylation?

A
  • phosphate is removed from a substrate, then added to ADP to get ATP.
    this only occurs in GLYCOLYSIS and the KREB CYCLE. This is one way we get ATP.
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19
Q

ATP (2)
what is oxidation phosphorylation?

A
  • this occurs in the ELECTRON TRANSPORT CHAIN, in the plasma membrane of the microbe.
  • heavily relies on the OXIDATION of NADH and FADH.

summary: high energy electrons are used to create a hydrogen ion gradient- the generation of the gradient is called chemiosmosis. When NADH and FADH is oxidized, the electrons in the ATP synthase- place between the cell membrane and the cell wall- help get hydrogens across through the ATP synthase so that ADP can be converted into ATP.

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20
Q

catabolism (1)
what is glycolysis?

A
  • glycolysis occurs in the cytoplasm of ALL cells. every cell does this process since oxygen is NOT required. what process they do after is ultimately dependent on their DNA.

overview: glucose is oxidized to pyruvic acid! which then feeds in to the kreb cycle and ultimately cellular respiration as a whole or through the fermentation pathway.

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21
Q

what is the input in glycolysis?

A

1 glucose
2 NAD
2 ATP

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22
Q

what is the output in glycolysis?

A

2 pyruvic acid
2 NADH
2 ATP

*NAD is reduced to NADH!
*to break down glucose, you need 2 ATP, generated through substrate-level phosphorylation.

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23
Q

catabolism (2)
what is the transition step of the kreb cycle?

A

in the transition step of the kreb cycle/citric acid cycle, 2 NAD is reduced to NADH after 1 carbon is removed from each pyruvic acid molecule, gives us 2 acetic acid (coA) molecules!
* Coenzyme A attaches to both pyruvic acids to become acetyl coA; it removes the CO2.

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24
Q

what is the input of the transition step?

A

2 NAD
2 pyruvic acid

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25
Q

what is the output of the transition step?

A

2 NADH
2 acetyl coA
2 CO2

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26
Q

catabolism (2)
what is the kreb cycle?

A

in the kreb cycle, acetyl coA is what is being inputted, and then H20 is added to that, making it acetic acid (coA), a 2 carbon molecule. each coA molecule will then join with a 4 carbon molecule, oxaloacetic acid, forming citric acid which has 6 carbons!
citric acid is then OXIDIZED, NAD is reduced to NADH, while FAD is also reduced to FADH.
ATP in this cycle is generated through substrate level phosphorylation.

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27
Q

what is the input for the kreb cycle?

A

2 acetic acid
6 NAD
2 FAD
2 ADP

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28
Q

what is the output in the kreb cycle?

A

6 NADH
2 ATP
2 FADH
4 CO2

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29
Q

catabolism (3)
what is the electron transport chain?

A
  • occurs in the plasma membrane in prokaryotes.
  • occurs in the mitochondrial membrane in eukaryotes.
  • involves both aerobic and anaerobic respiration.
  • ATP synthase - place between the cell membrane and the cell wall.
  • plasma membrane - e- help move H+ to the other side.
  • cytoplasm: where ALL these processes occur + ATP production.
    NAD to NADH - reduction; KREB CYCLE AND GLYCOLYSIS
    NADH to NAD - oxidation; ETC.
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30
Q

what happens during the ETC?

A

the oxidation of NADH and FADH.
H+ gradient is formed across the cytoplasmic membrane.
the kinetic energy of H+ flowing through ATP synthase powers the SYNTHESIS of ATP to ADP + P, or oxidative phosphorylation.

aerobic: oxygen is REDUCED, joining with H+ to create H20.

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31
Q

what is the input in the ETC?

A

10 NADH
10 FADH

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32
Q

what is the output in the ETC?

A
  • aerobic: 38 ATP

4 from substrate-level phosphorylation: 2 from kreb cycle, 2 from glycolysis

34 from oxidative phosphorylation
NADH gets oxidized.
ADP is phosphorolated.

  • anaerobic: 5-37 ATP
    ETC produces less ATP without oxygen.
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33
Q

catabolism (4)
what is fermentation?

A
  • fermentation occurs when the microbe is not in the right environment or when there is no oxygen or an electron to use as the final electron acceptor for aerobic and anaerobic cellular respiration.
    NADH does not have a place for its e-, so it resorts to this, or due to genetic of a microbe not having the right enzymes to utilize the ETC.
  • organic molecules are the final electron acceptors.
  • generates ATP quickly, but produces a small amount.
  • electrons are transferred from REDUCED coenzymes (NADH and NADHP) to pyruvic acid or another derrivative.
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34
Q

what are the inputs of fermentation?

A

glycolysis! oxidated products.
2 NAD
2 ATP
glucose

35
Q

what are the outputs of fermentation?

A

2 NADH
2 ATP
2 pyruvic acid

reduced products.

36
Q

what is the lactic acid pathway of fermentation?

A

the end product of fermentation is lactic acid.

37
Q

what is the input of lactic acid fermentation?

A

2 pyruvic acid
2 NADH + 2H

38
Q

what is the output of lactic acid fermentation?

A

2 NAD (oxidized)
2 lactic acid (reduced, final e- acceptor)

39
Q

what is the alcohol pathway of fermentation?

A

the end product of fermentation is ethanol.

40
Q

what are the inputs for the alcohol pathway?

A

2 pyruvic acid

2 NADH + 2 H
C02 leaves with the oxidation of NADH, giving you 2 acetylaldeyde with the input of pyruvic acid.

41
Q

what are the outputs of the alcohol pathway?

A

2 NAD (oxidized)
2 ethanol (reduced)

42
Q

what is DNA?

A
  • DNA is part of the nucleic acid macromolecule group.
  • deoxyribose nucleic acid.
  • double stranded.
  • in the nucleoid in prokaryotes!
  • made out of nucleotides.
43
Q

what nucleotides make up the basis of the nucleic acids DNA and RNA?

A
  1. pentose (5 carbon sugar)
    deoxyribose in DNA.
  2. phosphate group
    gives the cell its negative charge.
  3. nitrogenous bases.
44
Q

what are the types of nitrogenous bases?

A
  1. purines
  2. pyrimidines
45
Q

what are purines?

A

double ringed with 9 members in their ring.
includes
ADENINE and GUANINE.

*AG = gold.

46
Q

what are pyrimidines?

A

single ringed with 6 members in their ring.
includes
CYTOSINE and THYMINE (DNA)
CYTOSINE and URACIL (RNA)

47
Q

how are nitrogenous bases paired?

A

car-garage: cytosine and guanine
apple-tree: adenine and thymine/uracil

always a purine and pyrimidine, never 2 of the same !!

48
Q

what is DNA replication?

A

cell replication is done through binary fission, which is vertical transmission!

  1. starts with the parent cell. DNA is pulled apart, breaking hydrogen bonds to form two separate strands, creating a replication fork.
  2. half daughter strand, half parent strand. this process is semi conservative.
  3. nitrogenous bases floating around in the cytoplasm attach to form that daughter strand.
49
Q

what is the lag phase?

A

preparation for replication.

50
Q

what is the log phase?

A

binary fission/replication!
replication outgrows cell death.

51
Q

what is the stationary phase?

A

death and growth are both equal.
equilibrium.

52
Q

what is the death phase?

A

death outnumbers growth; the cell must switch into a dormant metabolic state if it wants to survive.

53
Q

what is gene expression?

A

DNA to RNA is transcription.
RNA to protein is translation.

  • genotype: the genetic makeup of an organism. making the genes is the recipe.
  • phenotype: the expression of those genes. expressing those genes, as a protein, is the cake.

3 nitrogenous bases = a codon, which is 1 amino acid.

54
Q

what are mutations?

A

when DNA is messed up through the replication process; it may alter the protein function and permanent change can alter ALL cells. change the recipe, you change the cake.

VERTICAL TRANSMISSION

55
Q

what is a base substitution?

A

the most common type of mutation.
it involves single base pairs; sub 1 nitrogenous base for another.

56
Q

mutation (1)
what are the types of base substitutions?

A

1 silent mutation
2. missense mutation
3. nonsense mutation

57
Q

what is a silent mutation?

A

the change in the sequence of nucleotide bases that make up DNA, however, it does not change the amino acid or protein function!
this is called the wobble effect, the last letter is changed, however, you still get the same amino acid.

58
Q

what is a missense mutation?

A

the change in a nitrogenous base results in the change of the amino acid; the amino acid codon is altered.

59
Q

what is nonsense mutation?

A

this results in the STOP codon or a premature stop, which means RNA does not complete or make the protein needed.

60
Q

mutation (2)
what is a frameshift mutation?

A

a frameshift mutation is the insertion or deletion of one or more nucleotide pairs, shifting the translational reading frame. this could ultimately change the protein.

61
Q

what are the 3 types of horizontal transfer?

A
  1. conjugation
  2. transformation
  3. transduction
62
Q

what is conjugation?

A

it is mediated by a conjugative plasmid/an F factor.
requires cell to cell contact
need an F+ donor cell with a plasmid, and an F- recipient cell without a plasmid.

63
Q

what is transformation?

A

transformation refers to when genes are transferred from one microbe to another as “naked” DNA in a solution/outside the cell!

for example, during cell lysis! microbe can pick up DNA and integrate it into their DNA through recombination.

64
Q

what is transduction?

A

transduction refers to when bacterial DNA is transferred from a donor cell to a recipient cell by means of a VIRUS that infects bacteria; bacteriophage.
the virus hijacks the microbe.

65
Q

what are plasmids?

A

carry additional information that can enchance pathogenicity.
are optional.

66
Q

what are the 5 different types of plasmids?

A
  1. conjugative plasmids
  2. virulence plasmids
  3. dissimilation plasmids
  4. col plasmids
  5. resistance factors
67
Q

what are conjugative plasmids?

A

F factors!
carry the genes for sex pilli and for the transfer of plasmids to another cell.

68
Q

what are virulence plasmids?

A

code for toxin productions!
enchance pathogenicity.

69
Q

what are dissimilation plasmids?

A

cells have enzymes that trigger the catabolism of unusual sugars, which allows them to survive in extreme environments.

70
Q

what are col plasmids?

A

determines col protein production; these proteins have ABX activity that has toxic proteins that kill other bacteria; a mechanism.

71
Q

what are resistance factors?

A
  1. resistance transfer factor
    genes for plasmid replication
    pilli and conjugation proteins.
  2. r-determinant group
    resistance genes.
    code for the production of enzymes that inactivate certain drugs and toxic substances!
    can be dangerous since microbes can develop resistance against ABX.
72
Q

what are transposons?

A

jumping genes!
small segments of DNA that stay within its own bacteria moving from plasmid to chromosomes vice versa. only way it leaves the cell is if its on a plasmid.

can also carry ABX resistance genes.

73
Q

what are psychophiles?

A

cold loving microbes.

74
Q

what are psychotrophs?

A

more common than psychophiles
0-30°C, not over 40°C

75
Q

what are mesophiles?

A
  • moderate temperature loving microbes and are the largest/most common.
  • grow at 25°C to 40°C, which is the closest to human body temperature, which is 37°C or about 98.6°F.
  • include common food spoilage and disease causing microbes.
76
Q

what are thermophiles?

A

heat loving microbes
optimum growth is at 50°C to 60°C

in hot springs.

77
Q

what are hyperthermophiles?

A

over 80°C

78
Q

what are the 3 enzymes involved in dealing with the free radicals and hydrogen peroxide produced during AEROBIC respiration?

A
  1. superoxide dismutase
  2. catalase
  3. peroxidase
79
Q

what are obligate aerobes?

A
  • require oxygen to survive.
  • only aerobic/surface growth.
  • generate free radicals, hydrogen peroxide, and utilize the enzymes necessary to neutralize this.
80
Q

what are faculative anaerobes?

A
  • do both aerobic and anaerobic growth, but grow better with the presence of oxygen; utilize oxygen but can also have some growth without it.
  • best growth is at the surface where 02 is present, but it is seen everywhere.
  • generate free radicals, hydrogen peroxide, and utilize the enzymes necessary to neutralize this.
81
Q

what are obligate anaerobes?

A
  • only anaerobic growth.
  • growth is seen at the bottom, where there is NO OXYGEN.
  • no enzymes used to neutralize oxygen since it isnt utilized.
82
Q

what are aerotolerant anaerobes?

A
  • fermentative! do NOT use oxygen for growth, however, they can tolerate it if its present.
  • even growth all over.
  • the presence of ONLY superoxide dismutase since it can partially neutralize oxygen.
83
Q

what are microaerophiles?

A
  • only AEROBIC growth, but oxygen is required in very low concentrations.
  • growth occurs only in the middle.
  • limited tolerance to oxygen and will produce a lethal amount of oxygen if expose to normal/excess amount since it does NOT have the enzymes present to neutralize it.

bio2200 (14 decks)

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