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Metabolism
Microbial Metabolism: sources, conditions, processes
157
Microbiology
Undergraduate 3
03/18/2013

Additional Microbiology Flashcards

 


 

Cards

Term
Phototroph
Definition
organism that uses light energy
Term
Chemotroph
Definition
organism that oxidizes reduced chemical compounds to obtain energy
Term
organotroph
Definition
organism that oxidizes organic compounds (chemotroph type 1)
Term
Lithotroph
Definition
organism that oxidizes inorganic compounds (chemotrophy type 2); only a few prokaryotic organisms fall under this category
Term
Ways to oxidize
Definition

1) addition of oxygen

2) removal of hydrogen/dehydrogenation (includes removal of 1 proton and 1 electron)

3) removal of electrons

 

Term
autotroph
Definition
obtain all of their C from CO2
Term
Heterotroph
Definition
require an organic carbon source
Term
chemoautotroph
Definition

obtain energy by oxidizing some reduced inorganic compound (e.g NH3 -> NO2-; "negativize") and their C from CO2

 

(only a few bacteria here)

Term
photoautotroph
Definition

obtain energy by photosynthesis and C from CO2

 

(eg. higher plants, eukaryotic algae, blue-green bacteria, etc.)

Term
photoheterotrophs
Definition

obtain energy from photosynthesis and C from organic compounds

 

(eg. photosynthetic bacteria, eukaryotic algae)

Term
chemoheterotrophs
Definition

obtain energy by oxidizing reduced organic compunds and C from the same compounds 

 

(eg. higher animals, protozoans, fungi, common bacteria)

Term
freeliving nitrogen fixers
Definition
blue-greens, Azotobacter spp, Clostridium spp,
Term
fix Nitrogen in symb relationship with higher plant
Definition
Rhizobium or Bradyrhizobium (infect roots of leguminous plants)
Term

Sulfur

1) needed in what structures?

2) obtained from?

Definition

1) 2 AA's and coenzymes

2) sulfates or S-containing AA's

Term

Phosphorus

1) needed to

2) obtained from 

Definition

1) make phosphate for nucleic acids, phospholipids, ATP, vitamins

2) as phosphate

Term
Organic growth factors
Definition
organic compound that an organism needs and cannot make for itself (eg. AA's, nitrogenous bases, and vitamins)
Term
Vitamins
Definition
organic compounds needed in small amounts for normal metabolism; function as organic cofactors/coenzymes
Term
Psychrophiles/Cryophiles
Definition

Optimum temp = 10C

Min = -10C

Max = 20C

Term
Mesophiles
Definition

Optimum = 20 - 40C

Min = 10C

Max = 50C

Term
Thermophiles
Definition

Optimum = 55-75C

Min = 45C

Max = 80C

Term
Hyperthermophiles
Definition
up to 110C
Term
Aerobe
Definition
use oxygen as final electron acceptor in metabolism
Term
Strict/obligate aerobe
Definition
cannot survive without oxygen
Term
Microaerophilic
Definition
need oxygen but cannot grow if the concentration of oxygen is to high
Term
Anaerobe
Definition
do not use oxygen in metabolism but use some other compound as final electron acceptor
Term
Strict/obligate anaerobe
Definition
cannnot grow in the presence of oxygen
Term
Aerotolerant
Definition
does not use oxygen but can survive in its presence
Term
Facultative anaerobe
Definition
can grow in the presence of oxygen or absence of oxygen
Term
Halophile
Definition

some archaebacteria which require high NaCl concentrations for growth

optimal = 25%

min  = 10%

max = 30-35% saturation

Term
Barophiles
Definition
organisms adapted for growth at extreme depths that can survive over 1000x normal atmospheric pressure and will burst if exposed to normal pressures
Term
Metabolism
Definition
all of the chemical reactions within a cell (most of which are enzyme catalyzed)
Term
Catabolism
Definition

break down, energy released

(energy released is trapped for storage in ATP by merging ADP with another Pi)

Term
Anabolism
Definition

synthesis, input of energy

(energy comes from hydrolysis of ATP by removing an Pi to form ADP)

Term
pyrophosphate
Definition
PPi, diphosphate
Term
Substrate level phosphorylation
Definition

chemically modify a molecule to a higher energy state (by oxidation or dehydration) and transfer the energy to ADP to form ATP

 

occurs during glycolysis and TCA

Term

Electron Transport phosphorylation

oxidative phosphorylation

Definition
ATP generated by passage of e-s through various intermediate e- carriers to final e- acceptor (which for aerobic organisms is O2, and for anaerobic organisms is some organic compound)
Term

OxPhos where?
1) proks 

2) euks

Definition

1) cell membrane

2) inner mitochondrial matrix

Term
Fermentation
Definition

anaerobes usually continue metabolism after glycolysis with this pathway that passes off electrons (and protons) to organic compounds to reduce them

 

Term
Photosynthetic Phosphorylation
Definition
high enery e- comes from excitation of chlorophyll molecule by visible light
Term

Photo Phosph where?

1) prok

2) euk

Definition

1) cell membrane

2) inner chloroplast membrane

Term
biological oxidations
Definition
the removal of hydrogens or electrons from reduced substrates
Term
dehydrogenase
Definition
enzyme that catalyzes reactions in which hydrogens are removed
Term
coenzymes
Definition

enzymes require them in their active site to carry electrons and protons

 

Term
niacin, riboflavin
Definition
vitamins used to make coenzymes that carry electrons and protons
Term
1) NAD+ and 2) NADP+
Definition

nicotinamide adenine dinucleotide (phosphate)

1) is used in oxidation rxns

2) is used as a source of reducing power in biosynthetic reactions

Term
1) FAD and 2) FMN
Definition

1) flavin adenine dinucleotide

2) flavin mononucleotide

both can accept 2 e-s and 2 protons

Term
flavoproteins
Definition
enzymes that contain either FAD or FMN (riboflavin derivatives) in their active sites
Term
Anaerobic Respiration
Definition

a few bacteria are capable of using their ETS even in the absence of oxygen by replacing O2 with some other inorganic compound as their final electron acceptor 

This only happens in the absence of oxygen

Term
NO3-, SO4-2, CO3-2
Definition

Other inorganic final electron acceptors;

allows organisms to use ETS in environments where others cannot (because O2 is not readily available as a final e- acceptor);

more efficient than no ETS, less efficient than with O2 as final e- acceptor -> because these compounds are not as far down the energy hill

Term

NAD+

 NADPH + H+

Definition
oxidized organic compounds
Term

NADH + H+

NADP+

Definition
reduced organic compounds
Term
Other name for glycolysis
Definition
Embden - Meyerhof Pathway
Term
glycolysis is the pathway for:
Definition
simple sugars (eg. glucose, fructose) and glycerol (backbone of fatty acids)
Term
most ubiquitous metabolic pathway
Definition

glycolysis, found in most proks and euks

can be used both aerobically and anaerobically

Term

glycolytic enzymes are 

1) located

2) questionable because

3) function in

Definition

1) on cell surfaces of bacteria and some euks (eg. protozoa and pathogenic fungi)

2) they lack sequences that typically are associated with transport across membranes or anchoring to cell walls or membranes, but are still transported/held there; maybe by charge or hydrophobic interactions 

3) production of ATP on the cell surfaces to support extracellular energy dependent activities

* also improve metabolic efficiency of RBC's

Term
anabolic significance of glycolysis
Definition
provides intermediates for synthesis of carbs, polysaccs, glycerol backbone of FA's, and pyruvate
Term
amphibolic
Definition
can be used both catabolically and anabolically
Term
overall rxn for glycolysis
Definition

Glucose + 2Pi + 2ADP + 2NAD+ -->

2Pyruvate + 2ATP + 2NADH + 2H+ + 2H2O

Term
Oxidative reactions reduce what?
Definition

coenzymes

NAD+= oxidizing agent

NADH = reducing agent

Term
ATPs produced in glycolysis
Definition
2 ATPs
Term
Tell me about NAD+
Definition

NAD+ is limited in living cells

NADH is reoxidized to NAD+ to continue generating ATP

Term

ATPs generated per

1) NADH

2) FADH2

Definition

1) 3 ATPs / NADH

2) 2 ATPs / FADH2

Term
Lactic Acid fermentation
Definition

pyruvate ----> lactate

|

v

2NADH +2H+ --->       2NAD+

Term
genera that use lactic acid fermentation
Definition

Lactobacillus, Lactococcus, and Streptococcus

ferment foods and beverages

Term
Alcoholic (ethanolic) fermentation
Definition

pyruvate  -->  acetaldehyde --> ethanol

|                        | 

v                        v

decarboxylation             NADH --> NAD+

Term

Genera that use alcoholic fermentation

uses

Definition
yeast (Saccharomyces - fruit juices, alcohol, bread) and bacteria (Zymomonas and Thermobacter - industrial ethanol/fuel)
Term
Propionic acid fermentation
Definition

members of genus Propionibacterium = facultative anaerobes that produce acid (prop, acetic, and CO2) as end products

used in Swiss cheese

Term
acetone-butanol fermentation
Definition

genus Clostridium produce mixture of acetone, butanol, isopropanol, butyric acid, CO2, etc. as fermentation products

produces acetone for gunpowder

butanol for rubber/tires

Term
Mixed acid fermentation
Definition

genera (Escherichia, Salmonella, Shigella) produce organic acids (-ates) plus ethanol, CO2, and H2

not commercially useful but analysis of this identifies enteric organisms in fecally contaminated foods

Term
2,3-butanediol fermentation
Definition
other G- rods (Enterobacter) difficult to distinguish from enterotoxins; their metabolism is MAF except they produce 2,3-butanediol as neutral end product; this substance can be detected with tests (eg. methyl red) to identify the presence of E. coli in foods
Term
Aerobic organisms do not ferment because they can...
Definition

reoxidize reduced coenzymes via ETS where oxygen acts as final e- acceptor

This frees the pyruvate made in glycolysis to be further catabolized in the TCA cycle

Term

TCA enzymes located in ___ in

1) proks

2) euks

Definition

1) cytoplasm

2) interior mitochondrial matrix

Term
TCA cycle catabolizes
Definition

1) pyruvate --> 3 CO2

2) fatty acid portion of fats

3) all 20 protein AA's

Term
TCA cycle rxn
Definition

2 pyruvate + 2 ADP + 2Pi + 8NAD+ + 2FAD

---> 6CO2 + 2ATP + 8NADH + 8H+ + 2FADH2

Term
Coenzyme A
Definition

functions as a carrier of short chain organic acids in metabolism

attaches to acetic acid via nucleophilic attack

fatty acids/many AA's enter pathway by way of acetyl-CoA

Term
ATP's produced in the TCA cycle
Definition

2 from substrate level phosphorylation

24 from ETS reox of 8 NADH

4 from ETS reox of 2 FADH2

 

30 TOTAL

 

(note recently NADH = 2.5 & FADH2 = 1.5)

Term
TOTAL ATP from aerobic prokaryotes
Definition

Glycolysis:  net 2 from SLP, 6 from ETS reox of 2 NADH

TCA Cycle:  30 (separate notecard)

 

38 TOTAL / glucose

Term
Why do some aerobic euks only generate 36 ATP/glucose
Definition
e-s on the NADH produces in glycolysis must be transferred to across the mito membranes by way of FADH2, which only generate 4 ATP via ETS reox
Term
Dehydrogenase
Definition

protein enzymes with niacin or riboflavin derivatives in their active sites to carry electrons and protons

either with NAD coenzymes or FAD/FMN coenzymes

Term
Cytochromes
Definition
small protein molecules with single iron atom in their active sites that can be alternatively oxidized or reduced (eg. Fe3+ can become Fe2+ by accepting only an e-)
Term
porphyrin
Definition
complex organic compound that forms a ring structure to hold iron atoms in the active site of certain enzymes
Term
heme group
Definition
porphyrin ring complexed with an iron atom
Term
iron-sulfur proteins
Definition

non heme iron proteins

proteins with 1,2,or4 iron atoms in active sites

also can accept only e-s, not protons

iron atom not complexed with a heme group but rather is held in place by interaction with sulfur residues

Term
Quinones
Definition

(Coenzyme Q or ubiquinone)

small, lipid-soluble organic compounds found in the membranes of organisms with ETS

can be reduced or oxidized by accepting/donating 2 protons and 2 e-s

Term
ATPase/ATP synthase
Definition
transmembrane proteins that can interconvert ATP  <---->  ADP + Pi
Term
Chemiosmotic theory
Definition

as e-s are passed to ETS components (coenzymes/e- carriers) and sent into the cytoplasm, the corresponding protons are dumped outside the membrane which establishes an H+ gradient that can be used to do work

 

Term
Proton Motive Force
Definition

H+/proton gradient established in the ETS that can be coupled to do work.  

 

Term
How do ATPases utilize the PMF
Definition

ATPases also can use this gradient to produce ATP from ADP and Pi 

OR

to hydrolyze ATP to ADP and Pi and pump protons back across the membrane and reestablish the gradient for further use

Term

Storage polymers

homo/hetero?

examples (3) with monomers

Definition

homopolymers

glycogen starch (polyglucoses)

volutin (polyphosphates)

poly-B-hydroxybutyrate

Term

1) UDP-sugar

2) ADP-sugar

which is used where?

Definition

1) eukaryotic glycogen synthesis

2) bacteria glycogen synthesis

Term
In polymer synthesis ADP acts as
Definition

a carrier and an activator

 

it carries the 1 side of the merge

 

and phosphorylates the other side of the merge/makes it available for nucleophilic attack

Term

structural polymers

homo/hetero?

examples (3) with monomers

Definition

USUALLY homopolymers

cellulose (polyglucose)

chitin (poly-N-acetylglucosamine)

 

peptidoglycan (heteropolymer of amino acids and amino sugars)

Term

Informational molecules

homo/hetero?

usage

examples with monomers

Definition

heteropolymers

storage/expression of genetic information

DNA (polymer of dNTPs=deoxyribonucleotide triphosphates)

RNA (polymer of NTPs)

Proteins (polypeptides; polymers of AA's)

Term
Flow of genetic information
Definition

DNA

DNA replication

Transcription

RNA

Translation

Protein

Term
gene
Definition
segment of DNA molecule that codes for the production of an RNA molecule
Term
structural genes
Definition
code for mRNAs, which in turn code for protein molecules via transcription/translation
Term

reverse transcription

enzyme?

originally found in?

Definition

RNA serves as a template for DNA synthesis

 

reverse transcriptase (RT)

 

retroviruses (eg. HIV)

Term

telomeres

enzyme?

 

Definition

protective repetitive DNA caps at the end of the 3' end of linear chromosomes in eukaryotes that protect the DNA molecule from shortening after replication

telomerase = a reverse transcriptase plus an RNA molecule to serve as a template for DNA synthesis)

Term
high telomerase activity occurs in
Definition

rapidly dividing cells

(eg. skin, embryos, cancer cells)

Term

Is DNA synthesis semi conservative

why?

Definition

YES

each strand of replicated DNA consists of one new strand and one old

Term
Needed for DNA replication (6 things)
Definition

1) dNTPs/activated subunits

2) DNA polymerases

3) DNA template

4) A primer (DNA or RNA); if RNA primer is used repair enzymes are required to replace RNA with DNA

5) Various replication proteins (helicase, single stranded DNA-binding proteins, RNA polymerase)

6) DNA ligase

Term
DNA polymerases
Definition

catalyze rxn

(dNTPs)n -----> DNA + nPPi

i.e. they add nitrogenous bases to the old strand of DNA removing 2 phosphates from the dNTP and forming a new strand of DNA corresponding to the template

Term
direction of DNA synthesis
Definition

5' ---> 3'  (on the new strand)

that it is it adds nucleotides to the OH present on the 3' end of the template strand

Term
possible active sites on DNA pol's
Definition

DNA polymerase III:

1) one on the front of the protein which forms the phosphodiester bonds between nucleotides of the old strand and the free standing ones to form a new strand; moves 5' to 3'

2) one beyond that site that breaks said bonds if mistakes present

works as a proof reader; moves 3' to 5' along new strand 

DNA polyerase I also has:

3) some have a 3rd active site ahead of site 1 (addition) that removes old DNA/RNA strnads to prepare for addition (removal of primers or mistakes); moves 5' to 3' behind poly #1

Term
exonuclease activity
Definition
enzymes that cleave phosphodiester bonds between nucleotides of a newly synthesized strand of DNA due to some mistake or to remove a primer
Term
DNA polymerase I
Definition

removes RNA primer and replaces it with DNA at the start of leading strand and on each Ogazaki fragment of the lagging strand;

repair enzyme that excises damaged DNA segments and replaces them with correct segments

Term
DNA polymerase III
Definition
synthesizes the vase majority of DNA during DNA replication
Term
DNA polymerase II
Definition

repair enzyme

only produced during stationary phase of growth and mutants lacking this enzyme show no defects

Term
DNA polymerase IV & V
Definition

do not proofread (no 3' to 5' exonuclease activity)

provide adaptive mutations thorugh SOS repair

produced in conditions of stress and fill gaps in the same regions of both strands of DNA

Term
origin of replication in E. coli
Definition
sequence of 245 bp
Term
Helicase/unwindase
Definition
breaks hydrogen bonding between two parent strands of DNA at the expense of hydrolysis of ATP (uses energy)
Term
single stranded DNA binding proteins (SSBPs)
Definition
attach to the separated strands of DNA in the replication fork and keep them from reforming H-bonds
Term
RNA primer
Definition
new DNA strands require this segment of about 5 nucleotides to begin replication by DNA pol III
Term
primase/RNA polymerase
Definition
builds RNA primer to begin replication
Term
topoisomerase
Definition
relieves tension built by unwinding of DNA strands by helicase
Term
Okazaki fragments
Definition
formed by DNA pol III in 1000-2000 nucleotides (in the 5' to 3' direction) on the discontinuous/lagging strand
Term
DNA ligase
Definition
connects the Ogazaki fragments on the lagging strand; i.e. forms bond between the Ogazaki fragment and the DNA that replaced the RNA primer (which was done by primase)
Term
replisome
Definition

multi protein complex at the replication fork that contains several proteins including 2 helicases, 2 primases, 2 DNA pol III molecules

 

hence why the lagging strand is looped through the complex

Term
transcription
Definition
RNA synthesis
Term
types of RNA
Definition

1) ribosomal

2) messenger

3) transfer

 

Term
ribosomal RNA
Definition
used, with ribosomal proteins, to make ribosomes, the factories for protein synthesis
Term
messenger RNA
Definition
carry information from structural genes that code for proteins to the ribosomes for translation into a protein molecule
Term
transfer RNA
Definition

used to activate amino acids for protein synthesis and to translate the information in mRNA molecules into a sequence of amino acids in a polypeptide chain 

73-95 nucleotides in loops/cloverleaf with one loop as anticodon loop 

Term
Transcription needs (3 things)
Definition

1) NTPs as activated subunits/monomers

2) RNA polymerase ie. DNA-dependent RNA polymerase

3) DNA template (only one strand of dsDNA)

*different strands are used as templates on different genes

Term
Steps in transcription
Definition

1) Initiation

2) Elongation

3) Termination

Term
Initiation of Transcription
Definition

RNA polymerase finds promoter sequence on a DNA molecule that 1) identifies gene and 2) tells RNA pol which strand to copy

 

RNA pol binds tighter to DNA and unwinds (about 17 bp = a transcription bubble) 

 

Initiates RNA synthesis at start of the gene

 

Term
Elongation of Transcription
Definition

RNA pol matches free living NTPs with those on the ssDNA template and attaches/polymerizes them via H-bonds

 

Term
Termination of Transcription
Definition

termination sequences (last base in coding region in transcribed before term seq) on DNA molecule signal RNA pol to stop RNA synthesis

 

nascent RNA molecule disjoins, DNA strands region bases of transcription bubble and RNA pol dissociates from DNA

Term

time takes to build mRNA molecule?

and # of AA's on it to build an average protein?

Definition

15 seconds

200-300 AA's

Term

1) base pair error occurs every ___ nucleotides in DNA replication of E coli

 

1) " " every ____ in RNA synthesis 

Definition

1) 108 - 10nucleotides

2) 104 nucleotides

Term

Prok vs. Euk Transcription

(5 comparisons/contrasts)

Definition

1) Prok = 1 RNA pol

Euk = 4-5 RNA pol

2) Prok = most have polycistronic mRNAs

Euk = VERY few have polycistronic

3) Prok = usually do not process mRNA

Euk = post transcriptional modifications

4) Both usually process tRNA and rRNA

5) Prok = transcription/translation closely coupled; proteins associate with mRNA before it is completely synthesized

Euk = this does not usually happen

 

Term

Types of Euk RNA pol

location and type of RNA it synthesizes?

Definition

1) nucleolus - rRNAs

2) nucleus - all mRNAs

3) nucleus (also) - all tRNAs and 1 type of rRNA

4) mitochondria - all mitochondrial RNAs

5) chloroplasts (plants and algae) - all chloroplast RNAs

Term
polycistronic mRNAs
Definition

ie. polygenic

encode several proteins via several open reading frames each of which can be translated into a polypeptide 

Term
operon
Definition
clustering together of 2 or more genes with common purpose that share same promoter which makes the copied mRNA polycistronic
Term
exons
Definition
coding regions of euk genes
Term
introns
Definition
noncoding regions of euk genes that must be spliced out of mRNA by splicosome
Term
Translation
Definition
protein synthesis that uses mRNA to code for specific AA monomers to form protein polymer
Term
First AA of protein chain in translation
Definition

N terminal

 

methionine (Eukarya and Archaebacteria)

 

N-formyl methionine (Bacteria, Mitochondria, Chloroplasts

 

Term
Last AA added to protein chain in translation
Definition
C terminal
Term

direction of translation

protein is built from which end to which end

Definition
N terminus to C terminus
Term
Needed for Translation (5 things)
Definition

1) free activated subunits that consists of an AA attached to carrier tRNA

2) mRNA as template 

(H-bonds form between nbs on mRNA and tRNA to transmit information)

3) ribosome - site of protein synthesis

4) ATP & GTP to provide required energy

5) various protein factors

 

Term
Ribosomes
Definition

site for protein synthesis

E coli/poor growth medium has as few as 2000

Rich growth medium 20,000-30,000

 

40% tRNA and 60% protein by weight

 

Term
Svedberg unit
Definition
measures sedimentation rate
Term
Bacterial Ribosomes' Svedberg units
Definition
70S
Term

1) Bacterial ribosomal subunits

2) how are they dissociated?

3) composed of how many proteins?

4) 3 types of rRNA?

 

Definition

1) 50S and 30S subunits

2) by reducing Mg2+ concentration

3) 55

4) 50S subunit has 5S and 23S

30S subunit has 16S

Term
Steps in Protein Synthesis
Definition

1) Activation of AA's

2) Formation of 70S initiation complex

3) Elongation (synthesis)

4) Termination

Term

Activation of AA's in Protein Synthesis

enzyme used

 

Definition

- carbonyl group on AA is activated by attachment to OH group of ribose at 3' end of specific tRNA molecule to form aminoacyl-tRNA

- catalyzed by aminoacyl-tRNA synthetases

- ATP hydrolyzed to AMP here

 

Term

Formation of 70S initiation complex

Elongation

Termination

Definition
Term
Proofreading mechanisms
Definition

1) abortive/premature termination of polypeptide synthesis and release of the polypeptide if an incorrect AA appears

2) slowing of the synthetic process to check codon-anticodon match at the A site of the ribosome

error rate = 1 in every 10-20k

Term

how long does it take to synthesize an average protein

molecular weight

ATPs used

Definition

15-30 seconds

30,000-40,000 MW

1000 ATPs

Term
Why do eukaryotes not couple transcription and translation
Definition

in euks, transcription takes place in the nucleus where there are no functional ribosomes

mRNAs must migrate out of the nucleus through pores in nuc membrane to get to ribosomes

Term
polysomes/polyribosomes
Definition

large complexes of many ribosomes associated with mRNAs

serve to increase the efficiency of protein synthesis

these complexes also prevent an mRNA molecule and its ribosomes from being degraded by intracellular RNases that turn over RNA molecules

Term
catalase
Definition
reverts toxic H2O2 back to water and oxygen
Term
superoxide dismutase
Definition
reverts toxic O2- back to H2O2 and O2 which can then be converted to water and more O2 by catalase
Term
aging --> death
Definition
cumulative damage from toxic forms of oxygen over time causes damage and death to cells
Term
toxic forms of oxygen
Definition

H2O2

O2-

OH+

Term

nonsense codons

stop codons

Definition

UAA

UAG

UGA

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