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exam 2 Flashcards

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Biology 101 flashcards
1
Q

thermodynamics

A

the branch of chemistry concerned with energy changes

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2
Q

definition of energy

A

the capacity to do work

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3
Q

what are the two states of energy

A
  1. kinetic

2. potential

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4
Q

what is kinetic energy

A

energy of motion

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5
Q

what is potential energy

A

stored energy

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6
Q

forms of energy

A

mechanical, light, sound, heat, electrical, radioactivity

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7
Q

most convenient way of measuring energy

A

heat

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8
Q

what is one calorie

A

the heat required to raise 1 gram of water by 1 degree celcius

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9
Q

where does energy flow from into the biological world?

A

the sun

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10
Q

what captures the sun’s energy

A

photosynthetic organisms

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11
Q

what is the energy from the sun stored as

A

stored as potential energy in chemical bonds

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12
Q

oxidation

A

atom/molecule loses an electron

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13
Q

reduction

A

atom/molecule gains and electron, higher level of energy than oxidized from

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14
Q

redox reactions done in what

A

pairs

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15
Q

first law of thermodynamics

A

energy cannot be created or destroyed

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16
Q

what is the total amt of energy in the universe?

A

remains constant

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17
Q

what happens to heat during each conversion

A

some energy is lost as heat

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18
Q

second law of thermodynamics

A

energy always converts from a more ordered/less stable form to a less ordered/ more stable form

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19
Q

entropy

A

disorder, continuously increasing

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20
Q

disorder happens

A

spontaneously

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21
Q

order requires

A

energy

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22
Q

free energy equation

A

G = H - TS

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23
Q

in G = H - TS, what does G stand for

A

energy available to do work

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24
Q

in G = H - TS, what does H stand for

A

enthalpy

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25
Q

G = H - TS, what does T stand for

A

absolute temp

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26
Q

in G = H - TS, what does S stand for

A

entropy

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27
Q

what is enthalpy

A

energy in a molecules bond

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28
Q

what is entropy

A

unavailable energy

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29
Q

where do our photosynthetic organism reside?

A

algae, bacteria, eukaryotes in ocean, trees, mostly in water

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30
Q

how do humans capture energy

A

from plants, convert it to glucose

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31
Q

how is sunlight stored as potential energy

A

take carbon to fix them together, Carbon-Hydrogen bond is stored energy

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32
Q

role of reducing sugar

A

reduce other molecules

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33
Q

what is oxidation

A

atom or molecule loses an electron

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34
Q

what is reduction

A

atom or molecule gains and electron, higher level of energy than oxidized from

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35
Q

redox is always..

A

paired, to reduce you must oxidize must always be done at the same time

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36
Q

what is a big cause of disease in cells?

A

oxidation

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37
Q

energy states always go from..

A

more ordered and less stable state to a less ordered and more stable form (easier to keep room messy)

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38
Q

change in free energy equation

A

change in free energy = change in enthalpy - temperature x energy lost/not able to use

DeltaG = deltaH - TS

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39
Q

positive delta G

A

products have more free energy than reactants, H is higher and S is lower, not spontaneous, requires energy input, endergonic

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40
Q

negative dela G

A

products have less free energy than reactants, H is lower or S is higher o both, spontaneous, but may not be instantaneous, exergonic

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41
Q

what is extra energy required to do

A

destabilize existing bonds and initiate a chemical reaction

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42
Q

exergonic reaction rate depends on

A

activation energy required

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43
Q

larger activation energy proceeds more

A

slowly

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44
Q

how can activation energy rate be increased

A
  1. increasing energy of reacting molecules (heating)

2. lowering activation energy (enzymes- catalysts)

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45
Q

what happens to activation energy without catalysts

A

its a lot longer

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46
Q

what are catalysts

A

substances that influence (destabilize) chemical bonds in a way that lowers activation energy

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47
Q

catalysts do not and cannot do what

A

cannot violate laws of thermodynamics, cannot make endergonic reaction spontaneous, do not alter the proportion of reactant turned into product

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48
Q

what is ATP

A

adenosine triphosphate, chief “currency” all cells use

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49
Q

what is ATP composed of

A

ribose - 5 carbon sugar, adenine, chain of 3 phosphates

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50
Q

ATP 3 chain phosphates, describe

A
  1. key to energy storage
  2. bonds are unstable
  3. ADP - 2 phosphates
  4. AMP - 1 phosphate (lowest energy form)
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51
Q

What happens in the ATP breakdown

A

ATP —> ADP (diphosphate) —> AMP (monophosphate) –> usually converts to —> cAMP

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52
Q

what is cAMP?

A

cyclic AMP(monophosphate), signal molecules that tells the cell its low in energy

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53
Q

fats or carbs store longer term energy

A

fats

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54
Q

how do animals store energy

A

store gylcogen in muscles, break down into glucose, which breaks down in ATP

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55
Q

what drives endergonic reactions

A

ATP hydrolosis, coupled reactions in net -delta G )exergonic and spontaneous

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56
Q

how long do cells store ATP

A

only a few seconds

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57
Q

what are enzymes

A

most are proteins, based on amino acid structures, helix and sheet folding, disulfide bond, ionic interaction, globular structure, enzymes change shape of bond and not destroyed or used up, not changed or consumed in reaction

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58
Q

what does the shape of an enzyme do

A

stabilizes a temporary association between substrates

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59
Q

carbonic anhydrase with and without enzymes

A

without - 200 molecules of carbonic acid per hour made

with - 600,000 molecules formed per second with enzyme

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60
Q

look at enzyme, substrate, active site diagram

A

ch. 6, page 8

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61
Q

what is the active site

A

pockets or clefts for substrate binding, forms enzyme- substrate complex, precise fit of substrate into the active site, applies stress to distort particular bond to lower energy

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62
Q

what is induced fit

A

enzyme can work on bonds and give a product

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63
Q

better the fit,

A

better the activation, the quicker the activation will take place

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64
Q

where would enzymes be found

A

suspended in the cytoplasm or attached to cell membranes and organelles

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65
Q

multienzyme complexes

A

subunits that work together to form a molecular machine, the product can be easily delievered to the next enzyme, unwanted side reactions are prevented, all reactions ar controlled as a unit

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66
Q

where are proteins found

A

in lipid bilayer, cytoplasm

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67
Q

rate of enzyme-catalyzed reactions depends on

A

concentration of substrate and enzyme

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68
Q

what conditions affect the enzymes 3D shape and change the rate

A

optimum temp and pH

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69
Q

taq polymerase

A

works at high temps and helps finding DNA

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70
Q

what is an inhibitor

A

substance that binds to enzyme and decreases its activity

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71
Q

what is a competitive inhibitor

A

competes with substrate for active site

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72
Q

what is a noncompetitive inhibitor

A

binds to enzymes at a site other than an active site, causes shape change that makes enzyme ubable to bind to substrate

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73
Q

what can inhibitors bind to?

A
  1. active site

2. allosteric site

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74
Q

what is an allosteric site

A

a site where an inhibitor binds to, other than active site

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75
Q

what happens when an inhibitor binds

A

causes a conformational change

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76
Q

allosteric enzymes

A

enzyme that have allosteric site, enzyme that exists in active and inactive forms

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77
Q

where do most noncompetitive inhibitors bind to

A

allosteric site - chemical on/off switch

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78
Q

what is an allosteric inhibitor

A

binds to allosteric site and reduces enzyme activity

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79
Q

what is an allosteric activator

A

binds to allosteric site and increases enzymes activity

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80
Q

what is a metabolism

A

total of all chemical reactions carred out by an organism

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81
Q

anabolic reactions/anabolism

A

expends energy to build up molecules

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82
Q

catabolic reactions/catabolism

A

harvest energy by breaking down molecules

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83
Q

what are biochemical pathways

A

reactions that occur in a sequence, product of one reaction is the substrate for the next, many steps take place in organelles, assembly line

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84
Q

what is a feedback inhibition

A

end-product of pathway binds to an allosteric site on enzyme that catalyses first reaction in pathway, shuts down pathway so raw materials and energy are not wasted

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85
Q

autotrophs

A

able to produce their own organic molecules thru photosynthesis

86
Q

heterotrophs

A

live on organic compounds produced by other organisms

87
Q

what do all organisms do to extract energy from organic molecules

A

cellular respiration

88
Q

dehydrogenations

A

lost electrons are accompanied by protons (a H atom is lost (1 e and 1 p))

89
Q

what is important in cellular respiration

A

redox

90
Q

what is NAD +

A

an electron carrier, accepts 2 electrons and 1 proton to become NADH, reaction is reversible

91
Q

in overall cellular energy harvest, what happens?

A

dozens of redox reacions take place, number of electron acceptors including NAD+, in end, high-energy electrons from initial chemical bonds have lost much of their energy, transferred to a final electron acceptor

92
Q

what is the final electron acceptor

A

oxygen

93
Q

why is this process of redox slow?

A

if it was released fast, energy would be lost as heat

94
Q

aerobic respiration final electron acceptor

A

O2

95
Q

anaerobic respiration final electron acceptor

A

is an inorganic molecule (not O2)

96
Q

fermentation final electron acceptor

A

organic molecule

97
Q

humans use anaerobic when

A

working out

98
Q

aerobic respiration equation

A

C6H12O6 + 6O2 = 6CO2 + 6H2O

99
Q

what are the carriers like?

A

soluable, membrane bound, move within the membrane

100
Q

carriers can be easily

A

oxidized and reduced

101
Q

what does NAD+ acquire to become NADH

A

2 electrons and a proton

102
Q

how is endergonic reactions driven

A

ATP

103
Q

2 mechanisms for ATP synthesis

A
  1. substrate level phosphorylation

2. oxidative phosphorylation

104
Q

what is substrate level phosphorylation

A

transfer phosphate group directly to ATP, during glycolysis, produces enzyme reactions

105
Q

what is oxidative phosphorylation

A

ATP synthase uses energy from a proton gradient, O2 and H2 gradient ends of steps

106
Q

what is a substrate

A

something that binds to an enzyme, enzyme converts it to speed up reaction

107
Q

what are the steps of the oxidation of glucose

A
  1. glycolosis
  2. pyruvate oxidation
  3. krebs cycle
  4. electron transport chain and chemiosmosis
108
Q

where does glycolosis happen

A

cytoplasm

109
Q

where does pyruvate oxidation, krebs cycle, electron transport chain and chemiosmosis happen

A

mitochondria

110
Q

why is glucose a carbon 6

A

each point is a carbon

111
Q

what is glycolosis

A

converts 1 glucose (6 carbon) to 2 pyruvate (3 carbon), 10-step biochemical pathway, occurs in cytoplasm, net production of 2 ATP molecules by substrate-level phosphorylation, 2 NADH produced by reduction of NAD+

112
Q

end of glycolosis has what

A

2 pyruvate molecules, 2 net ATP molecules, 2 molecules of NADH per one glucose

113
Q

how must glycolysis continue?

A

NADH must be recycled to NAD+ by either:

  1. aerobic respiration (produces significant amt of ATP)
  2. fermentation (occurs when O2 isnt avaliable)
114
Q

what is the fate of pyruvate after glycolysis

A

when O2 is present: oxidized to acetyl-CoA, which enters the Krebs cycle (aerobic respiration)
w/out O2: pyruvate reduced in order to oxidize NADH back to NAD+ (fermentation)

115
Q

what is pyruvate oxidation

A

occurs in mitochondria in eukaryotes, catalyzed by multienzyme complex called pyruvate dehydrogenase. occurs at plasma membrane in prokaryotes

116
Q

what does 3 carbon pyruvate do

A

removes CO2 and H2 and makes acetyl- CoA

117
Q

products of pyruvate oxidation

A

for each 3 carbon pryruvate molecule:
1 CO2 removed - decarboxylation by pyruvate dehydrogenase
generates 1 NADH
1 acetyl-CoA which consists of 2 carbons from pyruvate attached to coenzyme A (acetyl-CoA proceeds to Krebs cycle)

118
Q

what is pyruvate when it is oxidized

A

acetyl-CoA

119
Q

first molecule made in the krebs cycle

A

citric acid

120
Q

krebs cycle occurs and how

A

occurs in the matrix of the mitochondria, biochemical pathway of 9 steps in 3 segments

121
Q

3 segments of krebs cycle

A
  1. acetyl-CoA + oxaloacetate = citrate
  2. citrate rearrangement and decarboxylation
  3. regeneration of oxaloacetate
122
Q

what must be regenerated in the krebs cycle and why

A

oxaloacetate or cycle will not continue in krebs cycle

123
Q

for each acetyl - CoA entering krebs cycle, what is released and reduced, and produced

A
  1. release: 2 molecules of CO2
  2. reduce: 3 NAD+ to 3 NADH
  3. reduce: 1 FAD (electron carrier) to FADH2
  4. Produce 1 ATP
  5. regenerates oxoacetate
124
Q

what is electron transport chain

A

a series of membrane-bound electron carriers, embedded in the inner mitochondrial membrane, electrons from NADH and FADH2 are transferred to complexes of the ETC

125
Q

each complex in the ETC

A

a proton pump creating a proton gradient, transfers electrons to the next carrier.

126
Q

where does FADH and NADH accepted in ETC

A

NADH gives electrons an H, opening pump allowing 3 H to flow,1 FADH skips a pump, only creates 2 ATP while 1 NADH creates 3 ATP

127
Q

theoretical energy yield per glucose for bacteria

A

38 ATP

128
Q

theoretical energy yield per glucose for eukaryotes

A

36 ATP

129
Q

actual energy yield per glucose for eukaryotes

A

30 ATP

130
Q

why is the actual yield reduced?

A

leaky inner membrane, use of proton gradient for purposes other than ATP synthesis

131
Q

2 key control points of feedback inhibiton

A
  1. in glycolysis - phosphofructokinase is allosterically inhibited by ATP and/or citrate
  2. in pyruvate oxidation - pyruvate dehydrogenase inhibited by high levels of NADH, citrate sunthetase inhibited by high levels of ATP
132
Q

oxidation without O2

A
  1. anaerobic respiration - many prokaryotes use sulfur, nitrate, carbon dioxide or even inorganic metals as final electron acceptor
  2. fermentation - organic molecules final electron acceptor
133
Q

methanogen anaerobic respiration

A

CO2 is reduced to CH4 (methane), found in diverse organisms including cows

134
Q

sulfur bacteria anaerobic respiration

A

inorganic sulphate (SO4) is reduced to hydrogen sulfide (H2S), early sulfate reducers set the stage for evolution of photosynthesis

135
Q

fermentation reduces what

A

organic molecules in order to regenerate NAD+

136
Q

where does ethanol fermentation occur?

A

in yeast, CO2, ethanol, and NAD+ are produced

137
Q

lactic acid fermentation occurs where?

A

animal cells (especially muscles), electrons are transferred from NADH to pyruvate to produce lactic acid

138
Q

catabolism of protein - what do amino acids undergo

A

deamination to remove amino group, remainder of th amino acid is converted to a molecule that enters glycolysis or the Krebs cycle

139
Q

alanine (protein) is converted to what

A

pyruvate

140
Q

aspartate (protein) is converted to what

A

oxaloacetate

141
Q

catobolism of fat - fats are broken down

A

to fatty acids and glycerol, fatty acids are converted to acetyl groups by B-oxidation, oxygen-dependent process

142
Q

respiration of a 6-carbon fatty acid yields how much more energy than 6-carbon glucose

A

20% more energy

143
Q

evolution of metabolism

A
  1. ability to store energy in atp
  2. evolution of glycolysis
    3, anaerobic photosynthesis (using H2S)
  3. Use of H2O photosynthesis (not H2S)
  4. evolution of nitrogen fixation
  5. aerobic respiration evolved most recently
144
Q

how do we get energy from glucose

A

breaking down glucose slowly and producing ATP through chemiosmosis

145
Q

formula for photosynthesis

A

6CO2 + 12H2O = C6H12O6 + 6H2O + 6O2

146
Q

how is oxygenic photosynthesis carried out

A

cynobacteria, 7 groups of algae, all land plants-chloroplasts, more from water than land bc more water than land

147
Q

chloroplasts structure contains

A
  1. thylakoid membrane
  2. grana
  3. stroma lamella
  4. stroma
148
Q

what is the thylakoid membrane

A

interal choloroplasts membrane, contains chloryphyll and other photosynthetic pigments, pigments clustered into photosystems

149
Q

what is grana

A

stacks of flattened sacs of thylakoid membrane

150
Q

what is stroma lamella

A

connect grana

151
Q

what is stroma

A

semiliquid surrounding thylakoid membranes

152
Q

2 types of reactions of photosynthesis

A
  1. light-dependent reactions

2. light independent reactions

153
Q

who was Jan Baptista van Helmont

A

1550-1644, demonstrated that the substance of the plant was not produced only from the soil, 1st scientist to understand a plant was doing something, watched plant grow

154
Q

Joseph Priestly

A

1733-1804, living vegetation adds something to the air, candle in jar experiment

155
Q

CB van Niel

A

1897-1985, found purple bacteria do not release O2 but accumlate sulfur, proposed general formula for photosynthesis, later researchers found O2 produced comes from water

156
Q

what are pigments

A

molecules that abosorb light energy in the visible range

157
Q

what is a photon

A

particle of light

158
Q

what does photons do

A

acts as a discrete bundle of energy, energy content of a photon is inversely proportional to the wavelength of the light

159
Q

what is the photoelectric effect

A

removal of an electron from a molecule by light

160
Q

how is color shown?

A

visible light hits pigments and reflects color

161
Q

what happens when a photon strikes a molecule

A

energy is either lost as heat or absorbed by the electrons of the molecule (boosts electrons into higher energy levels)

162
Q

what is the absorption spectrum

A

range and efficency of photons molecule is capable of absorbing

163
Q

2 general types of pigments used in green plant photosynthesis

A

chlorophylls and carotenoids

164
Q

two types of chlorphyll

A

chlorophyll a and b

165
Q

what is chlorophyll a

A

main pigments in plants and cyanobacteria, only pigment that can act directly to convert light energy to chemical energy, absorbs violet-blue and red light

166
Q

what isn’t in chlorophyll

A

chloroplasts

167
Q

what is chlorophyll b

A

accessory pigment or secondary pigment absorbing light wavelength that chlorophyll a does not absorb

168
Q

what are pigments used for

A

dyes in clothing and photosynthesis in chloroplasts

169
Q

what is the structure of chlorophyll

A

porphyrin ring

170
Q

describe a porphyrin ring

A

complex ring structure with alternating double and single bonds, magnesium ion at the center of the ring in chlorophyll, has H-C tail and ring

171
Q

what also has a porphyrin ring

A

hemoglobin

172
Q

effect of photons on the clorophyll porphyrin ring

A

photons excite the electrons in the ring, electrons are shuttled away from the ring

173
Q

what is the action spectrum

A

relative effectiveness of different wavelengths of light in promoting photosynthesis, corresponds to the absorption spectrum for chlorophylls

174
Q

what are carotenoids

A

carbon rings linked to chains with alternating single and double bonds, can absorb photons with a wide range of energies, also scavenge free radicals (antioxidants-protective role)

175
Q

importance of phycobiloproteins

A

low-light in ocean areas

176
Q

what is the photosystem organization

A

-antenna complex and reaction center

177
Q

what is the antenna complex

A

hundreds of acessory pigment molecules, gather photons and feed the captured light energy to the reaction center, also called light-harvesting complex

178
Q

what do the antenna complexes do

A

capture photons from sunlight and channels them to the reaction center chlorophylls

179
Q

what do light-harvesting complexes do in chloroplasts

A

consist of web of chlorophyll molecules linked together and held tightly in the thylakoid membrane by a matrix of protiens

180
Q

what is the reaction center

A

transmembrane protein-pigment complex, when a chlorophyll in the reaction center absorbs a photon of light, and electron is excited to a higher energy level, light-energized electron can be transferred to the primary electron acceptor, reducing it, oxidized chlorophyll then fills its electron “hole” by oxodizing a donor molecule

181
Q

what happens in the reaction center

A

e- gets to a higher energy level, leaves a hole, water is e- donor, is split, donates e- to electron center to fill the hole that was left

182
Q

what are the steps in the light-dependent reactions

A
  1. primary photoevent
  2. charge separation
  3. electron transport
  4. chemiosmosis
183
Q

what happens during the primary photoevent

A

photon of light is captured by a pigment molecule, light excites a pigment

184
Q

what happens during charge separation

A

energy is transferred to the reaction center, an excited electron is transferred to an acceptor molecule, excited, passed onto another pigment (acceptor molecule)

185
Q

what happens during electron transport

A

electrons move thru carriers to reduce NADP+

186
Q

what happens during chemiosmosis during light dependent reactions

A

produces ATP

187
Q

what is cyclic photophosphorylation

A

in sulfur bacteria, only 1 photosystem used, generates ATP via electron transport, anoxygenic photosynthesis, excited electron passed to electron transport chain, generates a proton gradient for ATP synthesis

188
Q

where does The actual step that converts light energy into chemical energy takes place

A

in a multiprotein complex called the photosystem

189
Q

what happens in the photosystem one

A

bacteria, light excites pigment, passed onto enyzyme, electron lost to NADPH, moves onto something else, splitting H2O in PSII to keep passing electrons onto PSI

190
Q

what kind of photosystems do chloroplasts have

A

PSI (p700) and PSII (p680)

191
Q

oxygenic photosynthesis indicates

A

2 photosystems linked together

192
Q

what happens in photosystem two

A

can generate an oxidation potential high enough to oxidize water, creates higher energy potential

193
Q

what do the 2 photosystems do

A

they carry out a noncyclic transfer of electrons that is used to generate both ATP and NADPH

194
Q

where are 2 photosystems found

A

in chloroplasts and eukaryotic cells

195
Q

what does PSI makes

A

transfers electrons ultimately to NADP+ and produces NADPH

196
Q

what happens to the electrons lost from PSI

A

they are replaced by electrons from PSII

197
Q

what does PSII do to water

A

oxidizes it to replace electrons transferred to the PSI

198
Q

how are photosystems connected

A

by cytochrome/ b6-f complex

199
Q

what is noncyclic photophosphorylation

A

plants using PSI and PSII in series to produce ATP and NADPH, path of electrons is not a circle, photosystems replenished with electrons pbtained by splitting water. Z diagram!

200
Q

what type of photosystems do prokaryote use

A

they use only photo I, they recycles electrons

201
Q

what type of photosystems do eukaryotes use

A

undergo PSI and PSII (trees, grass, etc)

202
Q

what is PSII

A

resembles the reaction center of purple bacteria, core of 10 reansmembrane protein subunits with electron transfer components and 2 P680 chlorophyll, reactions center differs from purple bacteria in that it also contains four manganese atoms

203
Q

what is the purpose of four manganese atoms

A

essential for the oxidation of water in PSII

204
Q

what is the B6-f complex

A

proton pump embedded in thylakoid membrane

205
Q

describe reaction center of PSI

A

consists of a core transmembrane complex consisitng of 12 to 14 protein subunits with 2 bound p700 chlorophyll molecules

206
Q

how do humans make energy

A

take glucose from plants

207
Q

what do chloroplasts have

A

ATP synthase enzymes in the thylakoid membrane which allows protons into the stroma

208
Q

what does the stroma contains

A

enzymes that catalyze the reactions of carbon fixation - calvin cycle reactions

209
Q

what happens in the stroma

A

ATP, NADH, electron fixes CO2 and produces glucose

210
Q

what does noncyclic photophosphorylation generate

A

NADPH and ATP, but building organic molecules takes more than energy than that alone

211
Q

what is cyclic photophosphorylation used to do if not enough h2o around

A

used to produce additional ATP, short circuit PSI to make a larger proton gradient to make more ATP

212
Q

what happens in the calvin cycle

A

carbon fixation, takes CO2 and fix it to RUBP, rubisco is the enzyme used to form PGA

bio 111 (2 decks)

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