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Microorganisms > Exam 2 - Part 1 > Flashcards

Exam 2 - Part 1 Flashcards

1
Q

what is the combination of all reactions in the cell?

A

metabolism

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2
Q

what is catabolism?

A
  • fueling reactions
  • energy conserving reactions
  • provide ready source of reducing power (electrons)
  • generate precursors for biosynthesis
  • energy comes in, breaks it down, and is then used
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3
Q

anabolism

A
  • the synthesis of complex organic molecules from simpler ones
  • requires energy from fueling reactions
  • taking starch, turning it into glucose, and eventually using it to make ATP
  • energy from catabolism fuels this reaction
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4
Q

what is a fueling reaction?

A
  • catabolism

- reaction in which you break down molecules and extract energy from them

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5
Q

what is the energy currency of the cell?

A

ATP

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6
Q

where does the energy fueling the cell come from?

A

building blocks

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7
Q

what are precursors?

A

building blocks, like amino acids or lipids

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8
Q

chemical work

A

synthesis of complex molecules

- build polymers

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9
Q

transport work

A

take up nutrients, eliminate waste, and maintenance of ion balances
- pass through the cell membrane

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10
Q

mechanical work

A

cell motility and movement of structures within cells

- moving molecules within a cell, chromosomes during meiosis

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11
Q

what type of reaction is anabolism?

A

redox reaction

  • the source of energy is high reduced (more electrons and more energy)
  • electrons are extracted from this molecule making it oxidized (losses electrons)
  • example: NAD becomes NADH
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12
Q

thermodynamics

A
  • a science that analyzes energy changes in a collection of matter called a system (like a cell)
  • all other matter in the universe is called the surroundings
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13
Q

what is the first law of thermodynamics?

A
  • energy can be neither created nor destroyed
  • total energy in the universe remains constant
  • however energy may be redistributed either within a system or between the system and its surroundings
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14
Q

what is the second law of thermodynamics?

A

physical and chemical processes proceed in such a way that the disorder of the universe increases to the maximum possible

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15
Q

entropy

A

amount of randomness (disorder) in a system

- related to the second law of thermodynamics

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16
Q

free energy

A

amount of energy at standard conditions of concentration, pressure, temperature, and pH

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17
Q

what is the role of ATP in metabolism?

A

exergonic breakdown of ATP is coupled with endergonic reactions to make them more favorable

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18
Q

the more negative G (free energy) is, what happens to energy?

A

the more energy there is available outside

  • reaction can occur without outside energy
  • endergonic
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19
Q

the more positive G (free energy) is, what happens to energy?

A

the reaction is not favorable and requires energy

- endergonic reaction

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20
Q

what kind of a reaction is ATP?

A
  • ATP releases energy by releasing a high energy phosphate to become ADP
  • endergonic reaction, it has excess energy to give
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21
Q

where does ATP come from?

A
  • metabolic activity
  • fermentation, respiration, photosynthesis
  • extract from a source to make ATP, which turns into energy
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22
Q

Redox reactions

A
  • involved in many metabolic processes
  • electron carriers are often used to transfer electrons from an electron donor to an electron acceptor
  • types: ATP to ADP, PEP (intermediate in glycolysis) to 1,3-biphosphate, glycerite
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23
Q

what happens when electrons are transferred from a donor to an acceptor?

A
  • can result in energy release which can be conserved and used to form ATP
  • the more electrons a molecule has, the more energy rich it is
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24
Q

oxidizing reaction

A
  • one electron is donating
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25
Q

reducing reaction

A

one electron is accepting

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26
Q

an electron acceptor and donor are what?

A

a conjugate redox pair

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27
Q

what products are made from glucose?

A

glucose (C6H12O6) becomes CO2 and H2O

- makes 38 ATP

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28
Q

what is the standard reduction potential?

A
  • equilibrium constant for an oxidation reduction reaction

- a measure of the tendency of the reducing agent to lose electrons

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29
Q

the more negative the standard reduction potential is

A

the better the electron donor

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30
Q

the more positive the standard reduction potential is

A

the better the electron acceptor

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31
Q

the greater the distance between the standard reduction potential, and the donor and acceptor

A
  • the more negative G is
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32
Q

where are electron carriers in chemmoorganotrophs?

A
  • located in plasma membranes of bacteria and archaea

- located in mitochondria membranes in eukaryotic cells

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33
Q

what are some examples of electron carriers?

A

NAD, NADP, FAAD, Coenzyme Q (CoQ), and cytochromes

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34
Q

what is the first electron carrier in the ETC?

A

NAD

- most negative standard electron potential

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35
Q

what is the last electron carrier in the ETC?

A

cytochromes

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36
Q

what is the difference between an electron carrier and an electron acceptor?

A
  • an electron carrier has a temporary hold on the e-

- an electron acceptor will permanently accept the e-

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37
Q

electron transport chain

A
  • electron carriers are organized into the ETC
  • first electron carrier has the most negative standard electron potential
  • in mitochondria/chloroplast in euks
  • plasma membrane in pros
  • they are membrane bound
  • some only deal with e- others can pump out protons as well
  • FADH enters further into the system
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38
Q

what do enzymes do?

A
  • carry out reactions at physiological conditions
  • enzymes speed up the rate of a reaction to reach equilibrium quicker
  • enzymatic activity: when a protein becomes quaternary it is functional
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39
Q

how can enzymes act as protein catalysts?

A
  • high specificity for the reaction catalyzed and the molecules acted on
  • increases the rate of a reaction without being permanently altered
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40
Q

substrates

A

reacting molecules

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41
Q

products

A

substances formed by reaction

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42
Q

what are enzymes made of?

A

some can be made of solely one of more polypeptides

others can have nonprotein components

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43
Q

apoenzyme

A

protein component of an enzyme

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44
Q

cofactor

A

nonprotein component of an enzyme

  • prosthetic group: firmly attached
  • coenzyme: loosely attached, can act as carriers/shuttles
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45
Q

holoenzyme

A

apoenzyme and a cofactor

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46
Q

activation energy

A
  • energy required to form transition state complex

- enzyme speeds up reaction by lowering the standard potential energy

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47
Q

what impacts enzyme activity?

A
  • substrate concentration
  • pH
  • temperature
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48
Q

denaturation

A

loss of enzyme’s structure and activity when temperature and pH rise too much above the optima

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49
Q

competitive inhibitor

A
  • directly competes with binding of substrate to active site
  • control activity of the enzyme by substrate level
  • more substrate can be added to overcome the inhibitor
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50
Q

noncompetitive inhibitor

A
  • binds enzyme at site other than active site

- changes enzyme’s shape so that it becomes less active

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51
Q

examples of competitve inhibitor

A

PABA (substrate) is used to make nucleic acids in bacteria, if sulfa drug is added (inhibitor) it can inhibit PABA and prevent bacteria from replicating

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52
Q

regulation of metabolism

A
  • important for conservation of energy and materials

- maintenance for metabolic balance despite changes in the environment

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53
Q

what are the three major mechanisms for metabolism?

A
  • metabolic channeling
  • regulation of the synthesis of a particular enzyme (transcriptional and translational)
  • direct stimulation of inhibition of the activity of critical enzyme (post-translational)
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54
Q

metabolic channeling

A
  • differential localization of enzymes and metabolites
  • compartmentation (differential distribution of enzymes and metabolite among separate cell structures or organelles)
  • can generate marked variations in metabolite concentrations
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55
Q

what are two important reversible control measures in post-translational regulation of enzyme activity?

A
  • allosteric and covalent regulation
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56
Q

allosteric

A

add a molecule to a protein and change its function

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57
Q

covalent

A

permanent change to a protein, changes the shape

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58
Q

feedback inhibition

A
  • also called end-product inhibition

- inhibition of one or more critical enzymes in a pathway regulates entire pathway

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59
Q

aerobic respiration

A

final electron acceptor is oxygen

  • takes an energy source and electron source and goes through the central pathway of metabolism (glycolysis and krebs) applies to anaerobic too
  • exogenous reaction because the source must come from the outside, applies to anaerobic
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60
Q

anaerobic respiration

A
  • final electron acceptor is different exogenous acceptor such as NO3-, SO4 2-, CO2, Fe 3+, or SeO4 2-
  • in respiration, as electrons pass through the electron transport chain to the final electron acceptor, a proton motive force is generated to synthesize ATP
61
Q

fermentation

A
  • uses an endogenous electron acceptor - usually an intermediate of the pathway used to oxidize the organic energy source
  • does not involve the use of an ETC or PMF, by product is the e- acceptor
  • ATP synthesized by only a substrate level phosphorylation
  • only goes through glycolysis
  • absence of oxygen
  • minimal ATP made - 2
  • pyruvate makes lactic acid or alcohol
  • both prokaryotes and eukaryotes can ferment
62
Q

what are amphibolic pathways?

A
  • function both as catabolic and anabolic pathways

- important ones: embden-meyerhof, pentose, and TCA cycle

63
Q

pentose phosphate pathway

A

an amphibolic pathway that can operates aerobically/anaerobically oxidation steps produce NADPH, which is needed for biosynthesis

  • provides precursors for making nucleic acids for biosynthesis
  • not really used for ATP
64
Q

microbial fermentations

A
  • oxidation of NADH produced by glycolysis
  • pyruvate or derivative used as endogenous electron acceptor
  • substrate only partially oxidized
  • oxygen not needed
  • oxidative phosphorylation does not occur
65
Q

TCA cycle

A
  • citric/krebs
  • a key source of carbon skeletons for use in biosynthesis
  • after pyruvate is produced
  • amphibolic
  • 2 carbons enter from acetyl CoA
  • 2 carbons come off as CO2
  • synthetic process
  • broken down to extract energy
  • ATP made from GTP
66
Q

for each acetyl-CoA molecule oxidized, the TCA cycle generates:

A
  • two molecules of CO2
  • 3 molecules of NADH
  • one FADH
  • one GTP
67
Q

what is the chemiosmotic hypothesis?

A
  • most widly used hypothesis to explain oxidative phosphotylation
  • ETC organized so protons move outward from the mitochondrial matrix as electrons are transported down the chain
  • protonexpulsion during electron transport results in the formation of a concentration gradient of protons and a charge gradient
  • the combined chemical and electrical potential difference make up the proton motive force (PMF)
68
Q

oxidative phosphorylation

A
  • process by which ATP is synthesized as the result of electron transport driven by oxidation of a chemical energy source
  • only 2 ATP molecules synthesize directly from oxidation of glucose to CO2
  • most ATP made when NADH and FADH2 are oxidized in ETC
69
Q

electron transport chain

A
  • series of electron carriers that operate together to transfer electrons from NADH and FADH2 to a terminal electron acceptor
  • electrons flow from carriers with more negative standard potential to carriers with positive standard potential
  • as electrons transferred energy released
  • in eukaryotes the ETC carriers are within the inner mitochonidrial membrane
70
Q

what is the importance of the proton motive force?

A
  • PMF drives ATP synthesis
  • diffusion of protons back across the membrane (down gradient) drives formation of ATP
  • ATP synthase: enzyme that uses PMF down gradient to catalyze ATP synthesis
  • can also be used in flagella movement or to transport molecules across the membrane
71
Q

what is the theoretical maximum tield of ATP during aerobic respiration?

A

38 ATP molecules

72
Q

anaerobic respiration

A
  • uses electron carriers other than O2

- generally yields less energy less energy because E0 of electron acceptor is less positive than E0 of O2

73
Q

chemolithotrophy

A
  • electron released from energy source which is an inorganic molecule transferred to terminal electron acceptor by ETC make ATP via oxidative phosphorylation
  • have ecological importance
  • several bacteria and archaea oxidize hydrogen
  • they are metabolically flexible; use inorganics for energy or use organics for carbon
74
Q

what are the three major groups of chemolithotrophs?

A
  • hydrogen sulfide (H2S)
  • sulfur (S)
  • thiosulfate (SO2O3 2-)
  • nitrifying bacteria oxidize ammonia to nitrate
75
Q

dissimilatory nitrate reduction

A
  • use of nitrate as terminal electron acceptor

- the anaerobic reduction of nitrate makes it unavailable to cell for assimilation or uptake

76
Q

denitrification

A
  • reduction of nitrate to nitrogen gas

- in soil, causes loss of soil fertility

77
Q

nitryfing bacteria

A
  • oxidize ammonia to nitrate
78
Q

sulfur-oxidizing bacteria

A

ATP can be synthesized by both oxidative phosphorylation and substrate level phosphorylation

79
Q

photosynthesis

A

energy from light trapped and converted to chemical energy

80
Q

light reaction

A
  • photosynthesis

- light energy is trapped and converted to chemical energy

81
Q

dark reaction

A
  • photosynthesis

- energy produced in the light reactions is used to reduce CO2 and synthesize cell constituents

82
Q

oxygenic photosynthesis occurs in which organisms?

A
  • eukaryotes

- cyanobacteria

83
Q

anoxygenic photosynthesis occurs in which organisms?

A
  • all other bacteria besides cyanobacteria
84
Q

light reaction in anoxygenic photosynthesis

A
  • H2O not used as an electron source, therefore O2 is not produced
  • only one photosystem involved
  • uses different pigments and mechanisms to generate reducing power
  • carried out by phototrophic green bacteria, phototrophic purple bacteria, and heliobacteria
85
Q

bacteriohodopsin-based phototrophy

A
  • some archaea use a type of photography that involved bacteriorhodopsin a membrane protein which functions as alight driven proton pump
  • a proton motive force is generated
  • an ETC is not involved
86
Q

what are the components of anabolism?

A
  • energy from catabolism is used for biosynthetic pathways
  • using a carbon source and inorganic molecules, organisms synthesis new organelles and cells
  • antibiotics inhibit anabolic pathways
  • great deal of energy
  • metabolism is carefully regulated
87
Q

turnover

A

continual degradation and resynthesize of cellular constituents by nongrowing cells

88
Q

what do polysaccharides use for catabolism?

A
  • sugars
  • glycogen
  • starch
  • PHB
89
Q

what do proteins use for catabolism?

A
  • amino acids

- deamination

90
Q

what do lipids use for catabolism?

A
  • triglycerides

- beta oxidation

91
Q

transcription

A

yields a ribonucleic acid (RNA) copy of specific genes

92
Q

translation

A

uses information in messenger RNA (mRNA) to synthesize a polypeptide

93
Q

what is the nucleic acid structure?

A
  • polymer of nucleotides
  • contains the bases adenine, guanine, cytosine, and thymine
  • sugar is deoxyribose
  • molecule is usually double stranded
94
Q

what is the base pairing order?

A
  • A and T go together and are bonded by 2 hydrogen bonds

- G and C are bonded together by 3 hydrogen bonds

95
Q

what is the RNA structure?

A
  • polymer of nucleotides
  • contains bases adenine, guanine, cytosine, and uracil
  • sugar is ribose
  • most RNA are single stranded
  • three main different types: mRNA, tRNA, rRNA
96
Q

how is DNA configured in most archaea and bacteria?

A
  • supercoiled
  • DS
  • circular
97
Q

how is bacteria organized?

A

with the chromatin like protein

98
Q

what is the configuration of DNA in eukaryotes?

A
  • DNA is highly organized

- chromatin is associated with small basic proteins called histones

99
Q

what is the combination of DNA and proteins?

A

nucelosome

100
Q

what DNA organization is archaea most similar to?

A

eukaryotes

101
Q

DNA replication

A
  • complex process involving numerous proteins which help ensure accuracy
  • the 2 strands separate each serving as a template for synthesis of a complementary strand
  • synthesis is semiconservative, each daughter cell obtains one old and one new strand
102
Q

DNA replication in bacteria

A

bidirectional from a single origin replication

- archaea have more than one origin

103
Q

lagging strand

A

synthesized in short fragments call Okazaki fragments

- a new primer is needed for the synthesis of each okazaki fragments

104
Q

proofreading

A
  • carried out by DNA polymerase 3
  • removal of mismatched base from 3’ end of growing strand by exonuclease activity of enzyme
  • this activity is not 100% efficient
105
Q

termination of replication

A
  • replication stops when replisome reaches termination site on DNA
  • topoisomerases temporarily break the DNA molecules so the strands can separate
106
Q

what is a gene?

A
  • the basic unit of genetic information
  • defined as the nucleic acid sequence that codes for a polypeptide, tRNA or rRNA
  • linear sequence of nucleotides with a fixed start point and end point
  • codons are found in RNA and code for single amino acids
107
Q

reading frame

A

organization of codons such that they can be read to give rise to a gene product

108
Q

template strand

A
  • directs RNA synthesis

- is read in the 3’ to 5’ direction

109
Q

promoter

A
  • located at the start of the gene
  • is the recognition/binding site for RNA polymerase
  • functions to orient polymerase
110
Q

leader sequence

A

transcribed into mRNA but is not translated into amino acids

  • shine delgarno sequence
  • begins with AUG
111
Q

what are oxidation reactions?

A
  • source of energy is highly reduced
  • the more electrons, the more energy
  • this source is used to extract electrons
  • glucose is highly oxidized because it is a major source of electrons
112
Q

what are reduction reactions?

A
  • from the energy made in an oxidation reaction
  • another molecule will pick up the electrons from the molecule that was oxidized
  • for example, NAD becomes NADH
113
Q

what can reactions be?

A
  • cyclic, linear

- every reaction has an enzyme to catalyze it

114
Q

post-translational activity

A
  • protein is made and a group is added
  • allosteric and covalent
  • can change function or shape
  • can be reversible
115
Q

energy sources

A
  • chemical = organic or inorganic molecule

- photo = light source, photosynthetic

116
Q

carbon sources

A
  • auto = fixes CO2 from the air

- hetero = break down of organic molecules

117
Q

electron sources

A
  • organo = organic molecules

- litho = inorganic molecules

118
Q

substrate level phosphorylation

A
  • compound of a high energy molecule is used to make another high energy compound
  • the phosphorous combined with ADP to make ATP comes from the break of PEP, used in PTS in group translocation
119
Q

central pathway of metabolism

A
  • glycolysis (6 carbons)
  • pyruvate (3 carbons)
  • acetyl CoA, helps pyruvate enter the krebs (2 carbons)
  • krebs, 2 cycles, all carbon is gone
  • large molecule is broken down, purpose is to oxidized highly reduced polymers
120
Q

Embden-Meyerhof pathway

A
  • glycolysis
  • at the end of glycolysis, 2 ATP is made
  • has substrate level phosphorylation to make ADP into ATP
  • amphibolic
121
Q

Enter-Doudoff pathway

A
  • makes only 1 ATP
  • glucose to pyruvate
  • also makes NADH to NADPH
  • not amphibolic
122
Q

primary producers

A
  • uses CO2 from organic or inorganic sources to make electrons
123
Q

phototrophy

A

chemical energy from glucose

124
Q

what cycle do polysaccharides use?

A

glycolysis

125
Q

what cycle do nucleic acids use?

A

glycolysis

126
Q

what cycle do proteins use?

A

glycolysis and krebs

127
Q

what cycle do fatty acids use?

A

glycolysis

128
Q

what cycle do lipids use?

A

CoA

129
Q

what is the flow of genetic information?

A
  • central dogma: DNA is copied by RNA, RNA is used for protein synthesis
  • replication yields two copies
  • tRNA brings amino acids to make protein
130
Q

what molecules are linked together in DNA and how many hydrogen bonds are there?

A
  • G and C, 3 hydrogen bonds

- A and T, 2 hydrogen bonds

131
Q

purine

A

G and A

132
Q

pyridine

A

C and T

133
Q

major grooves

A

used to grab and unwind the DNA

134
Q

what are domains?

A
  • a region on DNA that proteins use to interact wit DNA
  • zinc finger and leucine zipper
  • identify proteins capable of binding with DNA
  • examples of these proteins are repressors, inducers, DNA and RNA synthesizers
135
Q

GC content

A
  • hard to break the bond

- there are more GC than AT

136
Q

mRNA

A

codon for amino acids

137
Q

tRNA

A

bring amino acids to ribosomes

- contain anticodon

138
Q

rRNA

A

ribosomal, interaction between ribosome and mRNA

139
Q

DNA replication

A
  • every cell gets a copy, going to a daughter cell
  • DNA is supercoiled and needs to be released
  • the ORI opens the DNA
  • DNA replication goes in the 5’ - 3’ direction, but can be synthesized the other way, just more steps involved
    directional with 2 replication forks
140
Q

DNA polymerase

A
  • synthesizes the DNA
  • has to start with a primer (made of RNA) for DNA pol to bind
  • 5’ - 3’ direction is continuous
141
Q

lagging strand

A
  • DNA that is synthesized in the 3’ -5’ direction
  • has to be added in pieces and synthesized with a new primer every time
  • has Okazaki fragments
142
Q

replisome

A
  • complex that opens DNA
  • places the primer
  • replicates DNA
143
Q

Shine-Delgarno sequence

A
  • where the ribosome recognizes and binds to rRNA

- codon always starts with TAC

144
Q

RNA polymerase

A
  • sigma factor recognizes the promoter

- binds to the -10 or -35 region to open DNA

145
Q

what is the process of transcription?

A
  • sigma factor binds to DNA, flags down RNA pol. the sigma factor recognizes a promoter, which is where RNA pol can bind and open the DNA
  • elongation occurs
  • termination occurs intrinsically or rho dependent
  • in prokaryotes, one mRNA can make multiple genes and make different polypeptides
146
Q

transcription in eukaryotes

A
  • similar process, expect there must be removal of introns
  • has to move out of the nucleus and into the cytoplasm
  • post-transcriptional = a guanine cap and poly A tail is added before moving into the cytoplasm
147
Q

genetic code

A
  • 3 base pairs makes one amino acid
  • 64 possibilities = 61 code for amino acids, but 3 are stop codons
  • AUG is always first
  • UGA, UAA, and UAG are stop codons
  • 1 amino acid can have multiple codons
148
Q

translation in bacteria

A
  • no post-transcriptional modification
  • as the RNA is made, ribosomes can jump onto the strand and make proteins.
  • multiple ribosomes can be replicating at the same time, making many polypeptides at a time, this is why bacteria grows so fast
  • transcription and translation are coupled in prokaryotes

Microorganisms (11 decks)

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