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MICRB 265 > Week 8 > Flashcards

Week 8 Flashcards

1
Q

Where are carbohydrates in bacteria?

A

-glycoproteins
-peptidoglycan
-(lipo)teichioc acid
-lipopolysaccharide
-capsule
-DNA/RNA

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2
Q

Bacteria have far greater _____ diversity than eukaryotes. All sugars can be made from ____

A

-monosaccharide
-glucose

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3
Q

______ is glycolysis in reverse

A

Gluconeogenesis

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4
Q

Gluconeogenesis makes glucose when there is _____;___ enzymes are shared, ___ are unique to gluconeogenesis;_____ are reversible

A

-no environmental source
-6
-4
-Enzymes

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5
Q

Pyruvate can come from _____ degradation and _____

A

-amino acid/peptide/protein
-beta-elimination

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6
Q

pentose phosphate pathway is offshot of _____; generates ______; key intermediate: _____

A

-glycolysis
-pentoses from other sugars for biosynthesis
-ribulose 5-phosphate

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7
Q

pentose phosphate pathway summary

A

-glucose 6-phosphate -> NADPH + 6-phosphogluconate -> NADPH +CO2, ribulose 5-phosphate
-MASSIVE SUGAR REARRANGEMENTS

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8
Q

ribulose 5-phosphate is used to produce _____

A

nucleotides (ATP, UTP, RNA, DNA)

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9
Q

special pathways are required to make ususual sugars that are unique to bacteria that make a _____

A

-specific polysaccharide

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10
Q

amino acid biosynthesis: glycolysis -> pyruvate -> ______

A

alanine family (valine, leucine)

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11
Q

amino acid biosynthesis: glycolysis -> 3-phosphoglycerate -> ______

A

serine family (glycine, cysteine)

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12
Q

amino acid biosynthesis: glycolysis + pentose phosphate -> ______

A

aromatic family (Phe, Tyr, Trp)

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13
Q

amino acid biosynthesis: citric acid cycle -> 3-a-ketoglutarate -> ______

A

glumate family (pro, glutamine, arg)

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14
Q

amino acid biosynthesis: citric acid cycle -> oxaloacetate-> ______

A

asparatate family (asparagine, lysine, methionine, threonine, isoleucine)

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15
Q

histidine biosynthesis involves ____

A

pentose phosphate pathway

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16
Q

all amino acids can be made from intermediates in _____; method: ______

A

-glycolysis or the citric acid cycle
-carbon skeleton is remodeled & amino groups and sometimes sulfur are added

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17
Q

amino acid biosynthesis: a single precursor metabolite can give rise to ______

A

several amino acids

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18
Q

purines (def.)

A

cyclic nitrogenous bases consisting of 2 joined rings (ex. adenine and guanine)

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19
Q

pyrimidines (def.)

A

cyclic nitrogenous bases consisting of single ring (ex. uracil, cytosine, and thymine)

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20
Q

Nucleoside = ______

A

nitrogenase base + pentose sugar

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21
Q

Nucleotide = _______

A

nucleoside + phosphate

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22
Q

purine biosynthesis requires _______

A
  • Aspartate
  • Glutamine
  • Glycine
  • Folic acid
  • CO2
  • Ribose
  • ATP
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23
Q

______ is the precursor of all purine nucleotides

A

inosinic acid (purine skeleton + ribose-5-P)

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24
Q

pyrimidine biosynthesis requires ______

A
  • Aspartate
  • NH3
  • CO2
  • Ribose
  • ATP
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25
______ is the precursor of all pyrimidine nucleotides
uridylate (pyrimidine (orotic acid) + ribose-5-P)
26
Deoxyribonucleotides are formed by reduction of ______ or ______
-nucleoside diphosphates -nucleoside triphosphates
27
Most ________ contain fatty acids. Fatty acids synthesized then added to other molecules to form other lipids such as _______
- bacterial and eukaryal lipids -triacylglycerols and phospholipids
28
Fatty acid biosynthesis: Synthesized from _______ by fatty acid synthase system + produces ______. During synthesis, the intermediates are attached to _______. Double bonds are formed by ______ of the intact fatty acid chain.
-acetyl-CoA, malonyl-CoA, and NADPH -CO2 -acyl carrier protein (ACP) -desaturation
29
Phospholipid biosynthesis: Synthesized from _____ by forming _____, then adding the head group
-phosphatidic acid (basis of phospholipids) -CDP-diacylglycerol
30
CDP-diacylglycerol + L-serine = _____ - CO2 = _____
-phosphatidylserine -phosphatidylethanolamine (most common phospholipids in E.coli)
31
DNA contains: ________ (4)
* genes (~88%) * structural RNAs (1%) * non-coding RNAs * regulatory sequences
32
Different types of RNA: _____ (4)
* mRNA (template for proteins) * tRNA (shuttle a.a to ribosome to make protein) * rRNA (structural component of ribosomes) * ncRNA (enzymes)
33
mRNAs make protein: _____ (3)
* Enzymes * Transporters * Structural proteins
34
DNA structure
-directional (5' -> 3') -nitrogen base @ 1' -nucleotides linked by phosphodiester bond (3' -> 5') -C & T = 3 HB -T/U (remove CH3) & A = 2 HB -chains are in opposite orientations (reverse complement); paired bases are inverted to each other -nucleotide flat rings stack on top of each other
35
major and minor grooves of DNA
-major: turns are farther apart & proteins bind here -minor: helix turns are closer together
36
DNA gyrase is a ______ that makes ______. requires energy from ____. in most bacteria DNA is _________. Back reaction releases ______
-topoisomerase -supercoiled DNA -ATP -negatively supercoiled (under-wound) -supercoils (requires no extra energy)
37
Replication: Each strand serves as a ______. Again, each strand is the _______ of the other.
-template for the new (daughter) strand (semiconservative replication) -reverse complement
38
______ catalyzes synthesis of complementary strand of DNA. DNA synthesis in 5’ to 3’ direction only forming _____
-DNA polymerase -phosphodiester bonds
39
DNA replication requires: _____ (3)
* a template – directs synthesis of complementary strand * a primer – DNA or RNA strand * dNTPs (dATP, dTTP, dCTP, dGTP) – deoxynucleotide triphosphates
40
Why does DNA polymerase need a primer?
It can elongate nucleic acid but not form it from nowhere
41
DNA in most Bacteria is ____ * ________ replication from a single origin; ___ strands produced @ the same time * replication fork is where _______
-circular -bidirectional -4 -DNA is unwound and strands are separated
42
Origin of replication: ______ terminus of replication: _______
-Oric -end of DNA replication/ter
43
____ proteins bind oriC (origin of replication) causing ______ of strands
-DnaA -bending and separation
44
DNA replication – step 1
-Helicases (like DnaB) separate strands (form the replication fork, requires ATP) -Single stranded binding proteins bind ssDNA to prevent strands from annealing (coming together)
45
______ synthesizes RNA primer; Lagging and leading strand is synthesized by _______. _______ are short pieces of DNA synthesized on lagging strand (needs a new primer each time)
-Primase -DNA polymerase III -Okazaki fragments
46
E. coli has ___ DNA polymerases with _______ playing the major role in ____
-5 -polymerase III -replication
47
Proofreading of DNA replication
* Carried out by DnaQ subunit of DNA polymerase III * Removal of mismatched base from 3’ end of growing strand by exonuclease activity of enzyme * This activity is not 100% efficient * Mutations rates are 10-8 to 10-11
48
Lagging strand
DNA polI removes RNA primers, fills gaps with DNA & okazaki fragments are joined by DNA ligase
49
DNA ligase forms a phosphodiester bond between ____ and the ______
- 3’-hydroxyl of the growing strand -5’-phosphate of an Okazaki fragment
50
Chromosome separation after DNA replication
* Tus protein binds ter sequence and prevents further replication * Chromosomes are wrapped around one another * Topoisomerases liberate chromosomes (cleave DNA, thread strand through, religate DNA)
51
mRNA structure? lifetime?
-unstructured -short lived (minutes)
52
rRNA structure? lifetime?
-highly structured but different -long lived
53
tRNA structure? lifetime?
-identical structures -long lived
54
tRNA structure
-1 strand (5' -> 3') that wraps around itself to form T-shape -3'OH amino acid attachment site -anticodon (to mRNA)
55
tRNA amino acylation
-amino acid + AMP (provides energy for 3-OH linkage) -enzyme: aminoacyl-tRNA synthetase 9specific with each a.a) -uncharged amino-acid specific tRNA + a.a-AMP = charged tRNA with a.a attached
56
rRNA structure (prokaryotes)
70S = 30S (16S) + 50S (23S + 5S) -S: sedimentation density gradient -has some basepairing + Mg 2+ (stabilization of phosphate esters)
57
Most bacterial RNA polymerases have core enzyme composed of _________
-5 chains which catalyzes RNA synthesis
58
Transcription: Sigma factors have no _____ but help the _______; has ______
-catalytic activity -core enzyme recognize the start of genes -specificity (binds to gene that needs to transcriped)
59
holoenzyme = ______. only the holoenzyme can begin _____
- core enzyme + sigma factor -transcription
60
Sigma factors help RNA polymerase bind to ______
-promoter (site where RNA polymerase binds to initiate transcription)
61
Promoters are not _____. have specific sequences before ______ and a ______ which contains consensus sequence
-transcribed -transcription starting point -Pribnow box
62
After binding, RNA polymerase _____Transcription bubble produced-> moves with the polymerase as it transcribes ________. Within the bubble a temporary _____ is formed. Complimentarity rule is the same except _____ is incorporated. RNA polymerase doesn't need _____
-unwinds the DNA -mRNA from template strand -RNA:DNA hybrid -U instead of T -primer
63
Transcription: Termination occurs when _____. DNA sequences mark the end of gene in the _____. Some terminators require the _____ for termination. Leaves you with _____ . In bacteria, there is ______. Also bacteria do not process their mRNAs.
-core RNA polymerase dissociates from template DNA. - trailer and the terminator -aid of the rho factor -free mRNA -no 5’ cap or long poly A tail

MICRB 265 (12 decks)

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