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Microbiology Flashcards

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1
Q

membrane potential and what it means

A

K+ is -92V : so concentration gradient of K+ is + outside
Na+ is +67V: so concentration gradient of Na+ is +inside
when K+ out and membrane potential reach a plateau, balance each other out, that is membrane (equilibrium) potential

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2
Q

nuclear pore

A

allow passage of mRNA out, proteins w nuclear localization sequences in

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3
Q

nucleolus

A

site of ribosome production
DNA inside codes for rRNa (no mRNA), transcribed and assembled here. proteins that are a part of ribosome are brought into nucleus through nuclear pores
ribosomes (rRNA + protein) are sent out through nuclear pore

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4
Q

nuclear membrane is made up of

A

inner and outer membrane + nuclear pores

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5
Q

mitochondria outer membrane is permeable to

A

small molecules

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6
Q

folds in inner membrane of mitochondria are called, are permeable to?

A

cristae - not permeable

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7
Q

glycolysis molecules, where process happens

A

in cytoplasm: glucose (6C) +ADP + NAD-> pyruvate 2(3C) +2ATP + 2NADH

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8
Q

pyruvate dehydrogenase complex, molecules, where process happens

A

oxidatively decarboxylates pyruvate is attached by coenzyme A (CoA-SH)
pyruvate -> acetyl CoA
loses C, releases CO2, NAD+ to NADH 1 per pyruvate
in matrix

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9
Q

Krebs Cycle, where it happens

A

2 acetyl CoA (2Cs) + 2 oxaloacetate (4 Cs) -> 4CO2 + 6NADH, 2 FADH2 + 2GTP
in matrix

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10
Q

ETC, proteins involved, where it happens, steps

A 
inner mitochondria membrane
1. NADH reductase
NADH -> NAD+ + 2H+ + 2e-
(NADH gets oxidized, enzyme gets reduced)
2. cytochrome Q 
electrons passed here (gets reduced)
FADH2 -> FAD + 2H+ 
3. cytochrome reductase
electrons passed here (gets reduced)
4. cytochrome C 
electrons passed here (gets reduced)
5. cytochrome oxidase
2e- used to reduce oxygen and make water
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11
Q

how is the energy from e- jumping from enzyme to enzyme used by inner mitochondria membrane

A

used to pump H+ ions from matrix to intermembrane space, making it acidic and matrix basic

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12
Q

ATP synthase - what molecules involved across which areas of mitochondria

A

H+ come back to matrix from intermembrane space through ATP synthase
H+ causes enzyme to turn, bottom part of enzyme (in matrix) has ADPs and phosphates

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13
Q

chemiosmosis

A

process of H+ passing through special channels in ATP synthase

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14
Q

mitochondria & endosymbiosis

A

own genome, self replicating, unique system of transcription and translation (different from nucleus)

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15
Q

location of nucleus in relation to ER

A

space in nuclear envelope is contiguous with lumen of ER

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16
Q

smooth ER

A

site of steroid synthesis, toxin breakdown, metabolizes carbs
makes lipids that end up on cell membrane

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17
Q

rough ER’s role, where proteins go that are made here

A

has ribosomes - site of protein synthesis + post translational modifications
gets secreted, become integral proteins in membrane, remain in ER, golgi, lysosome

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18
Q

proteins made in free ribosomes end up

A

nucleus, mitochondria, peroxisome, or stay in cytoplasm

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19
Q

secretory pathway of secreted protein

A

made at RER, buds off in vesicle, merge with cis stack of golgi, medial, trans –> either lysosome or cell membrane

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20
Q

golgi apparatus

A

modifies proteins made in RER
sorts and sends protein to correct destination
synthesizes certain secreted molecules

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21
Q

2 ways lysosome digests molecules, and what happens to digested parts

A

autophagy: digests things made by cell (nonfunctioning organelles, macrophages that have eaten foreign things)
crinophagy: digests excess secretory products
released into cytoplasm after as building blocks

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22
Q

environment in lysosome/type of enzyme

A

acid hydrolase, pH of 5

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23
Q

role of peroxisome

A

lipid breakdown, help liver detoxify drugs/chemicals
make hydrogen peroxide from digestion (H2O2)
catalase enzyme in peroxisome breaks down H2O2

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24
Q

examples of protozoa (eukaryotes)

A

photosynthesizing (algae), non photosynthesizing (slime mold), protozoa (amoeba, feeds on organic matter)

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25
Q

kingdom that is prokaryote

A

archaea, bacteria

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26
Q

what make up the outside of a bacteria, potential attachments

A 
capsule (sometimes its a slime layer), cell membrane made of peptidoglycan (gram + or -), plasma membrane made of phospholipid
could have a prokaryotic flagella (made of flagellin not microtubules like eukaryote) for movement
sometimes pilli (all around)
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27
Q

how does bacteria get food

A

chemotaxis - sensing chemicals and moving towards it

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28
Q

components inside bacterium

A

nucleoid (chromsome area), ribosome, potential plasmids, inclusion bodies (Store stuff)

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29
Q

shapes of bacteria

A

cocci, bacilli, spirilla

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30
Q

potential extracellular traits of bacteria

A

capsule makes bacterial colony sticky, adhere, harder to kill, flagella, pilli

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31
Q

traits of Gram+ bacteria

A

stains

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32
Q

traits of Gram- bacteria

A

excretes endotoxin
periplasmic space in between peptidoglycan layers that degrades antibiotics
capsule, lipopolysaccharide layer, plasma membrane, peptidoglycan layer, plasma membrane

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33
Q

definition of virus

A

obligate intracellular parasite - only produces inside cell

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34
Q

viral genome

A

can be anything - DNA, RNA, single, double, linear, circular, but given type of virus can only have one type of nucleic acid

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35
Q

limiting factor of viral genome and how it makes up for it

A

space inside capsid head

make up for it with overlapping genes, proteins coded in same strand

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36
Q

parts of a virus

A

capsid made of protein virus identifier (head), collar, sheath, base plate, tail fibers

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37
Q

how viruses are specific

A

enveloped viruses only infect animal cells

only cells w corresponding receptors can be infected

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38
Q

steps of phage infection lytic, and its con

A 
attachment, penetration,
hydrolase transcribed to degrade host genome
phage genome copies made
lysozyme transcribed to break cell wall
con: destroys host cell
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39
Q

steps of phage infection lysogenic, and its con

A

attachment, penetration,

phage genome incorporated (now it is called a prophage and host is called a lysogen)

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40
Q

retrovirus

A

enveloped ssRNA

+RNA that integrates into genome, needs reverse transcriptase

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41
Q

how do enveloped viruses enter cell

A

tricking receptors, receptor mediated endocytosis, direct fusion

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42
Q

steps of retrovirus

A

uncoating
reverse transcriptase transcribes RNA gnome and makes cDNA, and then another cDNA (makes DNA)
integrase cuts of 3’ ends to make sticky, goes into host nucleus and integrates into DNA
viral RNA gets transcribed, viruses made, and bud off (taking host membrane with it)
protease also present to activate these proteins used and pack into each new virus

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43
Q

+RNA virus, type of genome, what it includes

A

single stranded RNA genome (mRNA)

must code RNA dependent RNA polymerase to replicate

44
Q

-RNA virus, type of genome, what it includes

A

complementary to mRNA

most carry RNA dependent RNA polymerase

45
Q

ds-DNA virus

A

needs to be able to code for dNTPs (since cells only make them during replication)
cells always have NTPs

46
Q

steps of animal virus infection and 2 pathway options

A 
use plasma membrane receptors to attach
endocytosis in
productive cycle (lytic but buds off and does not destroy host cell)
lysogenic cycle (prophage is called provirus, host is still a lysogen)
47
Q

subviral particle types, types of diseases triggered

A

prion:
self replicating protein, long incubation period (resistant to lysozymes)
disease - transmissible spongiform encephalopathies
viroid:
circular single stranded, self complimentary RNA
disease - mostly plants

48
Q

virion vs viroid

A

virion is complete virus
viroid is infectious entity affecting plants, smaller than a virus and consisting only of nucleic acid without a protein coat.

49
Q

cell theory 3 rules

A

all living things are made of cells
cell is monomer
cell comes from other cells

50
Q

enzymes used in glycolysis

A

hexokinase (uses ATP to phosphorylate glucose), phosphofructokinase (uses ATP to phosphorylate F6P), pyruvate kinase (2PEP to 2 pyruvate)

51
Q

committed step of glycolysis

A

phosphofructokinase
thermodynamically very favorable
conversion of F6P to F1,6P

52
Q

what would happen if anaerobic conditions without fermentation

A

NAD+ becomes entirely NADH - glycolysis would stop without NAD+

53
Q

how fermentation works, its limiting factor

A

pyruvate -> lactate
pyruvate –> ethanol
byproducts build up and acts as poison at high concentration

54
Q

what is a coenzyme, or a super tight coenzyme

A

non protein compound that make enzyme work

tight one is a prosthetic group

55
Q

Stage 1/3 of Krebs cycle

A

carbons of acetyl CoA and oxaloacetate are combined

oxaloacetate + acetyl- CoA +H2O -> citric acid + CoA-SH + H+

56
Q

Stage 2/3 of Krebs cycle (starts w citrate)

A

citrate oxidized to release CO2 and NADH

citrate (6C) -> isocitrate (6C) -> alpha ketoglutarate (5C) + CO2 + NADH -> succinyl CoA (4C) + CO2 + NADH

57
Q

Stage 3/3 of Krebs cycle (starts with succinyl CoA)

A

oxaloacetate is regenerated

succinyl CoA -> GTP + succinate -> FADH2 + fumarate -> malate -> NADH + oxaloacetate

58
Q

how do prokaryotes do oxidative phosphorylation without mitochondria, and what more do they get from it than euks

A

proton gradient created on cell membrane instead of inner mitochondrial membrane
get two more high energy phosphate bonds

59
Q

NADH converted to # of protons pumped across membrane

A

10 protons are pumped across membrane

60
Q

how many protons are needed to go through ATP synthase to make an ATP

A

4 protons = 1 ATP

61
Q

FADH2 converted to # of protons pumped across membrane

A

6 protons (because bypasses NADH reductase)

62
Q

total molecules formed by glycolysis

A

2ATP, 2 NADH, 2 pyruvate

63
Q

total molecules formed by PDC

A

2NADH

64
Q

total molecules formed by Krebs

A

6NADH
2FADH2
2GTP

65
Q

total ATP formed in cellular respiration

A

30 in euk, 32 in pro

66
Q

when does gluconeogenesis happen, where, what does it use

A

dietary glucose is unavailable and run out of glycogen/glucose stores
process occurs in liver
converts non carbohydrate precursor molecules into intermediates of cellular respiration pathway to become glucose

67
Q

examples of molecules used in gluconeogenesis

A

lactate, pyruvate, krebs cycle intermediates, carbon skeleton of amino acids —NOT ACETYLE COA, which is why fatty acids cannot be converted to glucose

68
Q

steps of gluconeogenesis (starting with pyruvate)

A

add CO2 to pyruvate to make oxaloacetate (by pyruvate carboxylase which uses ATP)
PEPCK turns it into PEP (PEP carboxykinase uses 2 GTP)
then uses same enzymes as glycolysis to turn PEP into fructose 1,6 bisphosphate
except fructose 1,6 to fructose 6 requires unique enzyme fructose 1,6 bisphosphatase to remove phosphate and make fru6p
glu6p needs to be dephosphorylated for it to be able to leave liver

69
Q

energy needed for gluconeogenesis

A

4ATP, 2 GTP, 2 NADH

70
Q

2 enzymes heavily regulated to keep glycolysis and gluconeogenesis regulated

A

PFK from glycolysis (F6P to F1,6bP)

F1,6BPase from gluconeogenesis (F1,6bP to F6P)

71
Q

other molecule controlled by insulin and glucagon that regulates glycolysis vs gluconeogenesis

A

F2,6BP
made by large protein regulated by insulin (promotes) and glucagon (inhibits)
stimulates PFK and inhibits F1,6BPase

72
Q

glycogenesis process, what it starts with

A

G6P -> G1P
G1P + UTP -> UDP glucose
UDP glucose added to growing glycogen polymer by glycogen synthase

73
Q

glycogenolysis, what molecule gets cut off

A

releases as G6P, needs to be dephosphorylated by glucose 6 phosphatase to release into bloodstream

74
Q

pentose phosphate pathway, what it uses, what it makes, function of what it makes

A

diverts glucose 6 phosphate from glycolysis to form 2 NADPH, ribose 5 phosphate, and glycolytic intermediates
NADPH: used as reducing agent in anabolic processes like fatty acid synthesis
ribose 5 phosphate: used to make nucleotides
glycolytic intermediates: can be sent back to glycolysis

75
Q

what enzyme regulates pentose phosphate pathway

A

first enzyme of PPP - glucose 6 phosphate dehydrogenase

it’s product NADPH acts via negative feedback

76
Q

what happens if glucose 6 phosphate is deficient

A

limits ability of red blood cells to eliminate reactive oxygen species (first enzyme of PPP)

77
Q

things that vary between people’s genome

A

SNPs, CNVs, tandem repeats

78
Q

DNA replication steps in human

A 
starts at origin of replication
helicase breaks H bonds
primase makes primer, DNA polymerase builds
SSBPs keep strands apart
topoisomerase unwraps helicase
DNA ligase replaces RNA w DNA
stops at termination signal
79
Q

prokaryotic dna polymerase types

A

3 - super fast, super accurate leading strand (has exonuclease ability)
1 - starts adding onto primer (slower, w exonuclease ability)
2,4,5

80
Q

how mutations can arise in DNA

A

physical (ionizing radiation)
reactive chemicals (oxygen species)
biological agents

81
Q

composite transposon, complex transposon, IS element

A

IS element - DNA sequence - IS element
transposase - gene A - gene B
transposase

82
Q

types of DNA repair

A
  1. direct reversal as soon as it happens- nucleotide excision repair
  2. homology dependent repair (when parent is methylated)
  3. excision repair (using endonuclease + DNA pol + ligase)
  4. DSB repair
  5. nonhomologous end joining (if cell is not replicating)
83
Q

1 mRNA becomes what in pro vs euk

A 
one protein (monocistronic)
multiple proteins (polycistronic)
84
Q

prokaryote mRNA order of things

A

non coding region, Shine Delgarno, NCR, AUG, stop, NCR

85
Q

how is prokaryotic transcription initiated

A

Core enzyme + alpha factor makes holoenzyme which binds to promoter making a closed complex.

86
Q

difference between pro and euk transcription

A

pro: transcription and translation at same time
no post transcriptional modification
has shine delgarno (ribosomal binding site)
f-met is first AA (this triggers our immune system)
euk: met is first AA, mRNA gets spliced and has 5’ cap and 3;’ poly A tail

87
Q

types of RNA polymerase

A

1: transcribes rRNA
2. transcribes hnRNA
3. transcribes tRNA

88
Q

prokaryotic elongation

A

binds at shine delgarno
amino acyl tRNA synthetase (specific per AA) requires 2ATP making peptide bond formation favorable
enters at A, moves to P, leaves at E
wobble location is last AA of mRNA, first of tRNA
ends at stop codon, release factor enters A site
4ATP used per amino acid n

89
Q

prokaryote ribosome composition

A

50S + 30S = 70S

90
Q

eukaryote ribosome composition

A

60S + 40S = 80S

91
Q

prokaryotic translation initiation

A

initiation: 30S + 1F1 + 1F3 binds to mRNA

amino acyl tRNA + 1F2 + GTP + 50S

92
Q

types of protein moodifications

A

acetylation (cotranslational), lipidation (forms an anchor), glycosylation (outer signal)

93
Q

eukaryotic translation initiation

A

40S +met-tRNA go to 5’ cap and find start codon, 60S recruited, e1F involved

94
Q

eukaryotic translation elongation

A

eEF1 (helps amino acyl tRNA into A site)

eEF2 (translocase)

95
Q

how to control gene expression at DNA level

A

gene dose, imprinting (one allele expressed), methylation/remodelling, X inactivation

96
Q

how to control gene expression at RNA transcript level

A

enhancers/activator proteins, gene

97
Q

how to control gene expression at mRNA level

A

RNA translocation (sent to other places), mRNA surveillance (only high quality mRNA make it)

98
Q

how to control gene expression at protein levell

A

chaperones help folding, processing (cleavage), covalent modifications

99
Q

how lac operon works with glucose & no lactose

A
  1. promoter for CRP working, producing CAP
  2. promoter for I working, producing lac repressor protein
  3. promoter for O blocked by lac repressor protein, RNA pol can’t bind
  4. glucose inhibits adenylyl cyclase which converts ATP to cAMP when there is no glucose — low cAMP
100
Q

how lac operon works with glucose + lactose

A
  1. promoter for CRP working, producing CAP
  2. promoter for I working, produces lac repressor protein that binds with lactose inhibit
  3. promoter for O works, RNA Pol binds, low levels of mRNA made coding for beta galactosidase, permease, transacetylase
  4. glucose inhibits adenylyl cyclase —- low cAMP
101
Q

how lac operon works without glucose + lactose

A
  1. promoter for CRP working, producing CAP
  2. promoter I works, lactose binds to lac repressor protein and inhibits
  3. promoter O is stimulated by cAMP which is an activator that is present when glucose is low, leading to high levels of mRNA and beta galactosidase, permease, transacetylase
  4. lack of glucose stimulated adenylyl cyclase + CAP + ATP to make cAMP and stimulate O
102
Q

organisms organized by temperature preference

A

thermophile, mesophile, psychrophile

103
Q

organisms organized by what they use for energy

A

phototroph (light), autotroph (simple inorganic substances like CO2), heterotroph (ingesting other organisms), chemotroph (chemicals)

104
Q

how is anaerobic respiration possible

A

everything is the same but the electron acceptor is something other than O2

105
Q

endospore, what type of bacteria it is, how it work

A

asexual spore when dormant even heat cant kill it - when germinates it comes back to life

106
Q

of cells vs time graph

A
  1. lag time while building machinery, growth, then stationary when resources are depleted
107
Q

F+/Hfr bacteria, how we use it for gene mapping

A

F+ is the male, conjugation bridge allows for transfer to female to make it F+
Hfr timed transformation allows for gene mapping
if gene makes it into next cell and it gets transformed, it is earlier on the genome

MCAT Biology (10 decks)

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