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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
Q

______ is the precursor of all pyrimidine nucleotides

A

uridylate (pyrimidine (orotic acid) + ribose-5-P)

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26
Q

Deoxyribonucleotides are formed by reduction of ______ or ______

A

-nucleoside diphosphates
-nucleoside triphosphates

27
Q

Most ________ contain fatty acids. Fatty acids synthesized then added to other molecules to form other lipids such as _______

A
  • bacterial and eukaryal lipids
    -triacylglycerols and phospholipids
28
Q

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.

A

-acetyl-CoA, malonyl-CoA, and NADPH
-CO2
-acyl carrier protein (ACP)
-desaturation

29
Q

Phospholipid biosynthesis: Synthesized from _____ by forming _____, then adding the head group

A

-phosphatidic acid (basis of phospholipids)
-CDP-diacylglycerol

30
Q

CDP-diacylglycerol + L-serine = _____ - CO2 = _____

A

-phosphatidylserine
-phosphatidylethanolamine
(most common phospholipids in E.coli)

31
Q

DNA contains: ________ (4)

A
  • genes (~88%)
  • structural RNAs (1%)
  • non-coding RNAs
  • regulatory sequences
32
Q

Different types of RNA: _____ (4)

A
  • mRNA (template for proteins)
  • tRNA (shuttle a.a to ribosome to make protein)
  • rRNA (structural component of ribosomes)
  • ncRNA (enzymes)
33
Q

mRNAs make protein: _____ (3)

A
  • Enzymes
  • Transporters
  • Structural proteins
34
Q

DNA structure

A

-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
Q

major and minor grooves of DNA

A

-major: turns are farther apart & proteins bind here
-minor: helix turns are closer together

36
Q

DNA gyrase is a ______ that makes ______. requires energy from ____. in most bacteria DNA is _________. Back reaction releases ______

A

-topoisomerase
-supercoiled DNA
-ATP
-negatively supercoiled (under-wound)
-supercoils (requires no extra energy)

37
Q

Replication: Each strand serves as a ______. Again, each strand is the _______ of the other.

A

-template for the new (daughter) strand (semiconservative replication)
-reverse complement

38
Q

______ catalyzes synthesis of complementary strand of DNA. DNA synthesis in 5’ to 3’ direction only forming _____

A

-DNA polymerase
-phosphodiester bonds

39
Q

DNA replication requires: _____ (3)

A
  • a template – directs synthesis of complementary strand
  • a primer – DNA or RNA strand
  • dNTPs (dATP, dTTP, dCTP, dGTP) – deoxynucleotide triphosphates
40
Q

Why does DNA polymerase need a primer?

A

It can elongate nucleic acid but not form it from nowhere

41
Q

DNA in most Bacteria is ____
* ________ replication from a single origin; ___ strands produced @ the same time
* replication fork is where _______

A

-circular
-bidirectional
-4
-DNA is unwound and strands are separated

42
Q

Origin of replication: ______
terminus of replication: _______

A

-Oric
-end of DNA replication/ter

43
Q

____ proteins bind oriC (origin of replication) causing ______ of strands

A

-DnaA
-bending and separation

44
Q

DNA replication – step 1

A

-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
Q

______ 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)

A

-Primase
-DNA polymerase III
-Okazaki fragments

46
Q

E. coli has ___ DNA polymerases with _______ playing the major role in ____

A

-5
-polymerase III
-replication

47
Q

Proofreading of DNA replication

A
  • 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
Q

Lagging strand

A

DNA polI removes RNA primers, fills gaps with DNA & okazaki fragments are joined by DNA ligase

49
Q

DNA ligase forms a phosphodiester bond between ____ and the ______

A
  • 3’-hydroxyl of the growing strand
    -5’-phosphate of an Okazaki fragment
50
Q

Chromosome separation after DNA replication

A
  • 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
Q

mRNA structure? lifetime?

A

-unstructured
-short lived (minutes)

52
Q

rRNA structure? lifetime?

A

-highly structured but different
-long lived

53
Q

tRNA structure? lifetime?

A

-identical structures
-long lived

54
Q

tRNA structure

A

-1 strand (5’ -> 3’) that wraps around itself to form T-shape
-3’OH amino acid attachment site
-anticodon (to mRNA)

55
Q

tRNA amino acylation

A

-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
Q

rRNA structure (prokaryotes)

A

70S = 30S (16S) + 50S (23S + 5S)
-S: sedimentation density gradient
-has some basepairing + Mg 2+ (stabilization of phosphate esters)

57
Q

Most bacterial RNA polymerases have core enzyme composed of _________

A

-5 chains which catalyzes RNA synthesis

58
Q

Transcription: Sigma factors have no _____ but help the _______; has ______

A

-catalytic activity
-core enzyme recognize the start of genes
-specificity (binds to gene that needs to transcriped)

59
Q

holoenzyme = ______. only the holoenzyme can begin _____

A
  • core enzyme + sigma factor
    -transcription
60
Q

Sigma factors help RNA polymerase bind to ______

A

-promoter (site where RNA polymerase binds to initiate transcription)

61
Q

Promoters are not _____. have specific sequences before ______ and
a ______ which contains consensus sequence

A

-transcribed
-transcription starting point
-Pribnow box

62
Q

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 _____

A

-unwinds the DNA
-mRNA from template strand
-RNA:DNA hybrid
-U instead of T
-primer

63
Q

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.

A

-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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