Microbiology Flashcards
(107 cards)
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
2
Q
nuclear pore
A
allow passage of mRNA out, proteins w nuclear localization sequences in
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
4
Q
nuclear membrane is made up of
A
inner and outer membrane + nuclear pores
5
Q
mitochondria outer membrane is permeable to
A
small molecules
6
Q
folds in inner membrane of mitochondria are called, are permeable to?
A
cristae - not permeable
7
Q
glycolysis molecules, where process happens
A
in cytoplasm: glucose (6C) +ADP + NAD-> pyruvate 2(3C) +2ATP + 2NADH
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
9
Q
Krebs Cycle, where it happens
A
2 acetyl CoA (2Cs) + 2 oxaloacetate (4 Cs) -> 4CO2 + 6NADH, 2 FADH2 + 2GTP
in matrix
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
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
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
13
Q
chemiosmosis
A
process of H+ passing through special channels in ATP synthase
14
Q
mitochondria & endosymbiosis
A
own genome, self replicating, unique system of transcription and translation (different from nucleus)
15
Q
location of nucleus in relation to ER
A
space in nuclear envelope is contiguous with lumen of ER
16
Q
smooth ER
A
site of steroid synthesis, toxin breakdown, metabolizes carbs
makes lipids that end up on cell membrane
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
18
Q
proteins made in free ribosomes end up
A
nucleus, mitochondria, peroxisome, or stay in cytoplasm
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
20
Q
golgi apparatus
A
modifies proteins made in RER
sorts and sends protein to correct destination
synthesizes certain secreted molecules
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
22
Q
environment in lysosome/type of enzyme
A
acid hydrolase, pH of 5
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
24
Q
examples of protozoa (eukaryotes)
A
photosynthesizing (algae), non photosynthesizing (slime mold), protozoa (amoeba, feeds on organic matter)
25
kingdom that is prokaryote
archaea, bacteria
26
what make up the outside of a bacteria, potential attachments
```
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)
```
27
how does bacteria get food
chemotaxis - sensing chemicals and moving towards it
28
components inside bacterium
nucleoid (chromsome area), ribosome, potential plasmids, inclusion bodies (Store stuff)
29
shapes of bacteria
cocci, bacilli, spirilla
30
potential extracellular traits of bacteria
capsule makes bacterial colony sticky, adhere, harder to kill, flagella, pilli
31
traits of Gram+ bacteria
stains
32
traits of Gram- bacteria
excretes endotoxin
periplasmic space in between peptidoglycan layers that degrades antibiotics
capsule, lipopolysaccharide layer, plasma membrane, peptidoglycan layer, plasma membrane
33
definition of virus
obligate intracellular parasite - only produces inside cell
34
viral genome
can be anything - DNA, RNA, single, double, linear, circular, but given type of virus can only have one type of nucleic acid
35
limiting factor of viral genome and how it makes up for it
space inside capsid head
| make up for it with overlapping genes, proteins coded in same strand
36
parts of a virus
capsid made of protein virus identifier (head), collar, sheath, base plate, tail fibers
37
how viruses are specific
enveloped viruses only infect animal cells
| only cells w corresponding receptors can be infected
38
steps of phage infection lytic, and its con
```
attachment, penetration,
hydrolase transcribed to degrade host genome
phage genome copies made
lysozyme transcribed to break cell wall
con: destroys host cell
```
39
steps of phage infection lysogenic, and its con
attachment, penetration,
| phage genome incorporated (now it is called a prophage and host is called a lysogen)
40
retrovirus
enveloped ssRNA
| +RNA that integrates into genome, needs reverse transcriptase
41
how do enveloped viruses enter cell
tricking receptors, receptor mediated endocytosis, direct fusion
42
steps of retrovirus
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
43
+RNA virus, type of genome, what it includes
single stranded RNA genome (mRNA)
| must code RNA dependent RNA polymerase to replicate
44
-RNA virus, type of genome, what it includes
complementary to mRNA
| most carry RNA dependent RNA polymerase
45
ds-DNA virus
needs to be able to code for dNTPs (since cells only make them during replication)
cells always have NTPs
46
steps of animal virus infection and 2 pathway options
```
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
subviral particle types, types of diseases triggered
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
virion vs viroid
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
cell theory 3 rules
all living things are made of cells
cell is monomer
cell comes from other cells
50
enzymes used in glycolysis
hexokinase (uses ATP to phosphorylate glucose), phosphofructokinase (uses ATP to phosphorylate F6P), pyruvate kinase (2PEP to 2 pyruvate)
51
committed step of glycolysis
phosphofructokinase
thermodynamically very favorable
conversion of F6P to F1,6P
52
what would happen if anaerobic conditions without fermentation
NAD+ becomes entirely NADH - glycolysis would stop without NAD+
53
how fermentation works, its limiting factor
pyruvate -> lactate
pyruvate --> ethanol
byproducts build up and acts as poison at high concentration
54
what is a coenzyme, or a super tight coenzyme
non protein compound that make enzyme work
| tight one is a prosthetic group
55
Stage 1/3 of Krebs cycle
carbons of acetyl CoA and oxaloacetate are combined
| oxaloacetate + acetyl- CoA +H2O -> citric acid + CoA-SH + H+
56
Stage 2/3 of Krebs cycle (starts w citrate)
citrate oxidized to release CO2 and NADH
| citrate (6C) -> isocitrate (6C) -> alpha ketoglutarate (5C) + CO2 + NADH -> succinyl CoA (4C) + CO2 + NADH
57
Stage 3/3 of Krebs cycle (starts with succinyl CoA)
oxaloacetate is regenerated
| succinyl CoA -> GTP + succinate -> FADH2 + fumarate -> malate -> NADH + oxaloacetate
58
how do prokaryotes do oxidative phosphorylation without mitochondria, and what more do they get from it than euks
proton gradient created on cell membrane instead of inner mitochondrial membrane
get two more high energy phosphate bonds
59
NADH converted to # of protons pumped across membrane
10 protons are pumped across membrane
60
how many protons are needed to go through ATP synthase to make an ATP
4 protons = 1 ATP
61
FADH2 converted to # of protons pumped across membrane
6 protons (because bypasses NADH reductase)
62
total molecules formed by glycolysis
2ATP, 2 NADH, 2 pyruvate
63
total molecules formed by PDC
2NADH
64
total molecules formed by Krebs
6NADH
2FADH2
2GTP
65
total ATP formed in cellular respiration
30 in euk, 32 in pro
66
when does gluconeogenesis happen, where, what does it use
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
examples of molecules used in gluconeogenesis
lactate, pyruvate, krebs cycle intermediates, carbon skeleton of amino acids ---NOT ACETYLE COA, which is why fatty acids cannot be converted to glucose
68
steps of gluconeogenesis (starting with pyruvate)
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
energy needed for gluconeogenesis
4ATP, 2 GTP, 2 NADH
70
2 enzymes heavily regulated to keep glycolysis and gluconeogenesis regulated
PFK from glycolysis (F6P to F1,6bP)
| F1,6BPase from gluconeogenesis (F1,6bP to F6P)
71
other molecule controlled by insulin and glucagon that regulates glycolysis vs gluconeogenesis
F2,6BP
made by large protein regulated by insulin (promotes) and glucagon (inhibits)
stimulates PFK and inhibits F1,6BPase
72
glycogenesis process, what it starts with
G6P -> G1P
G1P + UTP -> UDP glucose
UDP glucose added to growing glycogen polymer by glycogen synthase
73
glycogenolysis, what molecule gets cut off
releases as G6P, needs to be dephosphorylated by glucose 6 phosphatase to release into bloodstream
74
pentose phosphate pathway, what it uses, what it makes, function of what it makes
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
what enzyme regulates pentose phosphate pathway
first enzyme of PPP - glucose 6 phosphate dehydrogenase
| it's product NADPH acts via negative feedback
76
what happens if glucose 6 phosphate is deficient
limits ability of red blood cells to eliminate reactive oxygen species (first enzyme of PPP)
77
things that vary between people's genome
SNPs, CNVs, tandem repeats
78
DNA replication steps in human
```
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
prokaryotic dna polymerase types
3 - super fast, super accurate leading strand (has exonuclease ability)
1 - starts adding onto primer (slower, w exonuclease ability)
2,4,5
80
how mutations can arise in DNA
physical (ionizing radiation)
reactive chemicals (oxygen species)
biological agents
81
composite transposon, complex transposon, IS element
IS element - DNA sequence - IS element
transposase - gene A - gene B
transposase
82
types of DNA repair
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
1 mRNA becomes what in pro vs euk
```
one protein (monocistronic)
multiple proteins (polycistronic)
```
84
prokaryote mRNA order of things
non coding region, Shine Delgarno, NCR, AUG, stop, NCR
85
how is prokaryotic transcription initiated
Core enzyme + alpha factor makes holoenzyme which binds to promoter making a closed complex.
86
difference between pro and euk transcription
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
types of RNA polymerase
1: transcribes rRNA
2. transcribes hnRNA
3. transcribes tRNA
88
prokaryotic elongation
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
prokaryote ribosome composition
50S + 30S = 70S
90
eukaryote ribosome composition
60S + 40S = 80S
91
prokaryotic translation initiation
initiation: 30S + 1F1 + 1F3 binds to mRNA
| amino acyl tRNA + 1F2 + GTP + 50S
92
types of protein moodifications
acetylation (cotranslational), lipidation (forms an anchor), glycosylation (outer signal)
93
eukaryotic translation initiation
40S +met-tRNA go to 5' cap and find start codon, 60S recruited, e1F involved
94
eukaryotic translation elongation
eEF1 (helps amino acyl tRNA into A site)
| eEF2 (translocase)
95
how to control gene expression at DNA level
gene dose, imprinting (one allele expressed), methylation/remodelling, X inactivation
96
how to control gene expression at RNA transcript level
enhancers/activator proteins, gene
97
how to control gene expression at mRNA level
RNA translocation (sent to other places), mRNA surveillance (only high quality mRNA make it)
98
how to control gene expression at protein levell
chaperones help folding, processing (cleavage), covalent modifications
99
how lac operon works with glucose & no lactose
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
how lac operon works with glucose + lactose
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
how lac operon works without glucose + lactose
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
organisms organized by temperature preference
thermophile, mesophile, psychrophile
103
organisms organized by what they use for energy
phototroph (light), autotroph (simple inorganic substances like CO2), heterotroph (ingesting other organisms), chemotroph (chemicals)
104
how is anaerobic respiration possible
everything is the same but the electron acceptor is something other than O2
105
endospore, what type of bacteria it is, how it work
asexual spore when dormant even heat cant kill it - when germinates it comes back to life
106
of cells vs time graph
1. lag time while building machinery, growth, then stationary when resources are depleted
107
F+/Hfr bacteria, how we use it for gene mapping
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
