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BIO 93 midterm 2 > midterm 2 > Flashcards

midterm 2 Flashcards

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Biology 101 flashcards
1
Q

bioenergetics

A

the study of how energy flows through living

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2
Q

what state is a cell constantly in

A

constant activity preforming all sorts of work requiring energy

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3
Q

what are the types of work a cell needs to preform?

A

chemical, mechanical and transport

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4
Q

energy used by living things demonstrates ….

A

the first law of thermodynamics

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5
Q

what is the first law of thermodynamics

A

energy can be transferred and transformed but not created or destroyed

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6
Q

where does the energy come from to preform cellular work

A

chemical reactions

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7
Q

what is metabolism

A

the totality of an organism’s chemical reactions

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8
Q

what are the two options when it comes to chemical reactions

A

releases energy
needs energy

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9
Q

describe exergonic reactions

A

energy is releases and it is spontaneous

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10
Q

what does spontaneous mean

A

energetically favorable

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11
Q

what delta g is exergonic reactions

A

negative delta g

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12
Q

decribe what the exergonic graph looks like

A

the reactants free energy is much higher than that of the products

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13
Q

describe endergonic reactions

A

energy is required and it is nonspontaneous

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14
Q

what does non spontaneous mean

A

not energetically favorable

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15
Q

what is the delta g sign for an endergonic reaction

A

positive delta G

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16
Q

two words that describe exer - and ender reactions

A

exer- release
ender- consumption

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17
Q

describe the graph of an endergonic reaction

A

the reactants free energy is much lower than the products free energy

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18
Q

energy coupling? what mediates it most of the time?

A

ATP mediates most energy coupling in cells and provides an immediate source of energy to power cellular work

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19
Q

the cell does what in regards to endergonic and exergonic reactions

A

the cell couples endergonic and exergonic reactions

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20
Q

free energy is the

A

release or consumption of energy

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21
Q

Free energy defines whether

A

the reaction is exergonic or endergonic

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22
Q

hydrolysis of ATP

A

releases energy –> exergonic

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23
Q

what is ATP made of

A

an inorganic phosphate + ADP + energy

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24
Q

energy released by ATP hydrolysis can be

A

used to directly drive chemical/ mechanical reactions

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25
Q

enzyme function…

A

lower energy barrier to drive chemical reaction

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26
Q

LOOK AT ENERGY PROFILE of an exergonic reaction and try to draw with all labels

A

…

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27
Q

enzymes lower what?

A

THE ACTIVATION ENERGY

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28
Q

WHAT is the fancy name for enzymes

A

biological catalysts

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29
Q

what does the activation energy control

A

allows cells to control when chemical reactions occur

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30
Q

how many times can an enzyme be used?

A

UNLIMited- can be saturated but always reusable

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31
Q

describe the events of the enzyme substrate complex

A

1) substrates enter the active site
2) substrates are held in active site by weak interactions
3) the active site lowers Ea
4) substrates are converted to products
5) products are released
6) active site is available for new substrates
REPEAT

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32
Q

what is special abt enzymes

A

they have structural specificity for their substrates

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33
Q

how does temp affect enzymes

A

temperature- each enzyme has a different optimal temperature

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34
Q

how does ph affect enzymes

A

each enzyme has optimal ph

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35
Q

what environmental factors can effect enzyme function

A

temp and ph

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36
Q

competitive inhibition is

A

when a competitive inhibitor binds at the active site which blocks the substrate from binding

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37
Q

noncompetitive inhibition is

A

when a noncompetitive inhibitor binds to the enzymes allosteric site which changes the shape of the active site not allowing the substrate to fit anymore

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38
Q

what is induced fit

A

when the enzyme snuggles the substate when it binds

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39
Q

cellular respiration refers to

A

catabolic reaction used to generate ATP

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40
Q

what does catabolic mean

A

exergonic energy releasing process

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41
Q

how do organic molecules yield energy

A

through oxidation

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42
Q

what is chemiosmosis

A

energy coupling mechanism used to generate ATP

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43
Q

describe the energy cycle

A

the products of photosysnthesisi become the reactanst in cellular repiration while the reactants of cellular respiration become the reactants for photosynthesis

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44
Q

energy from catabolism helps what process

A

turn adp + P into ATP

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45
Q

aTP can be used for

A

cellular work

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46
Q

what does the mitochondria host

A

the site of cellular respiration in all eukaryotic cells

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47
Q

defects in mitochondrial function

A

are associated with degenerative disease, cancer, and aaging

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48
Q

what are symptoms of inherited genetic mitochondrial disease

A

muscle weakness, neurodegeneration, metabolic dysfunction

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49
Q

two components of redox reactions

A

oxidation and reduction

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50
Q

what happens in cellular respiration (think electrons)

A

relocation of electrons from food to oxygen –> relesed energy used to synthesize ATP

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51
Q

in celluar respiration, glucose is

A

oxidized

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52
Q

in cellular respiration, oxygen is

A

reduced

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53
Q

oxidized means

A

e- + H+ are removed

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54
Q

reduction means

A

e- and H+ are added

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55
Q

organic compounds like glucose posess

A

potential energy

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56
Q

why do organic compounds like glucose possess potential energy

A

as a result of the arrangement of electrons in the bond between their atoms

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57
Q

cellular respiration is a ________ explosion

A

controled

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58
Q

in cellular respiration what is the initial donor molecule

A

glucose

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59
Q

in cellular respiration what is the final acceptor molecule and through what

A

oxygen by an electron transport chain

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60
Q

how is cellular respiration a controlled explosion

A

controlled release of energy for synthesis of ATP through the transport of electrons from the initial donor molecule to the final acceptor molecule by ETC

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61
Q

what is NADH

A

an electron carrier

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62
Q

what is mediated by NADH

A

transfer of electrons from fuek to transport chain

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63
Q

dehydrogenase enzymes do what?

A

strip 2 H atoms (2H+ and 2 e-) from glucose

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64
Q

where do the 2H atoms that dehydrogenase strip go to

A

one H+ is release
pass one H+ and 2e- to NAD+ to form NADH

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65
Q

describe oxidation or reduction of NADH/NAD+

A

reduction of NAD+=> NADH
oxidation of NADH=> NAD+

NAD+ is oxidizing agent version of NADH

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66
Q

once NADH has electrons it

A

transfers the electrons from food to the electron transport chain where the energy os harnessed to generate ATP

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67
Q

NADH move ___ to ____

A

e- to ETC

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68
Q

1H=?

A

(`H+) + e-

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69
Q

what can be used as fuel for cellular respiration

A

proteins, carbohydrates, and fats

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70
Q

most basic description of cellular respiration

A

relocation of electrons from food to oxygen in which released energy is used to synthesize ATP

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71
Q

3 stages of cellular respiration

A

glycolysis, (pyruvate oxidation) + citric acid cycle, oxidative phosphorylation (aka electron transport chain and chemiosmosis)

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72
Q

what type of ATP is produced in glycolcysis

A

substrate level

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73
Q

what type of ATP is produces in citric acid cycle

A

substrate level

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74
Q

what type of ATP is produced in Electron transport chain & chemiosmosis

A

oxidative

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75
Q

glycolysis takes place in the

A

cytosol

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76
Q

what happens in glycolsysis

A

converts glucose to pyruvate

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77
Q

gylycolysis generates what?

A

substrates for citric acid cycle (pyruvate) and oxidative phosphorylation(NADH)

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78
Q

what are the products of glycolysis

A

2 pyruvate + 2 water + 2ATP + 2NADH + (2H+)

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79
Q

what is the investment phase

A

in glycolysis when 4 atps ate formed but 2 are used SO there is a total of 2 ATP genrated

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80
Q

what is substrate level phosphorylation

A

the phosphate is coming from a substrate rather than inorganic phosphate as in oxidative phosphorylation

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81
Q

what is the intermediate stage

A

pyruvate oxidation

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82
Q

where does pyruvate oxidation occur

A

Mitochondrial matrix

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83
Q

what happens in the intermediate stage

A

pyruvate is converted to acetyl CoA

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84
Q

what are the products of the intermediate stage

A

Co2, NADH, Acetyl CoA

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85
Q

what is added to pyrvate to create acetyl CoA

A

coenzyme A

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86
Q

how does pyruvate move into mitochondrial matrix

A

USING ACTIVE TRANSPORT MECHANISM

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87
Q

1 glucose=?

A

TWO pyruvates

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88
Q

the citric acid cycle takes place in

A

the mitochondrial matrix

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89
Q

the citric acid cycle is also known as the

A

krebs cycle or Tricarboxylic acid cycle

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90
Q

what enters the citric acid cycle

A

acetyl CoA

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91
Q

for each acetyl CoA that enters the citric cycle

A

2Co2
3NADH
1FADH2
1ATP or GTP

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92
Q

what could be different in some cells about the citric acid cycle

A

some cells generate GTP instead of ATP

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93
Q

oxidative phosphorylation creates what percentage of ATP in cellular respiration

A

90%

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94
Q

what is the third stage of cellular respiration

A

oxidative phosphorylation

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95
Q

where does oxidative phosphorylation occur

A

inner mitochondrial membrane

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96
Q

what are the two parts of oxidative phosphorylation

A

electron transport chain and chemiosmosis

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97
Q

what starts the ETC

A

the NADH and FADH2 donating electrons

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98
Q

all of the protein complex electron carries of the ETC

cellular respiration

A

power proton pumps that send protons to the intermembrane space generating high H+ concentration in the intermembrane space

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99
Q

the ETC uses energy from the donated electrons to

A

PUMP PROTONS TO THE INTERMEMBRANE SPACE

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100
Q

the chain of the ETC…

A

alternate between oxidized and reduced states as they pass the electrons form less to more electronegative compounds being oxygen the final acceptor producing water

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101
Q

the electrons in the ETC go from

A

less to more electronegative compounds

102
Q

where does chemiosmosis occur

A

the inner mitochondrial membrane

103
Q

ATP synthase allows…

A

passive transport of H+ back to the matrix

104
Q

the proton motive force of atp synthase has the ability to…

A

produce work

105
Q

the flow of H+ through synthase results in

A

joining of ADP + Pi to form ATP

106
Q

what mechanism is used to make ATP

A

energy coupling mechnaism –> proton motive force

107
Q

the flow of protons is like water…

A

in a stream moving waterwheel

108
Q

the force of the stream of protons moves…

A

THE ROTAR OF ATP synthase that catalyses the addition of Pi to ADP forming ATP

109
Q

how many atps does oxidative phosphorylation make

A

about 26 or 28

110
Q

for 1 glucose the citirc acid cycle produces how many atp

A

2 atp

111
Q

what is the maximum atp per glucose for cellular respiration

A

about 30 0r 32 atp

112
Q

what is special about pyruvate

A

is is a key juncture in cellular respirtation

113
Q

the continuation of cellular respiration after the intermediate stage requires

A

O2 present

114
Q

if O2 is not present after the intermediate stage

A

then fermentation will occur

115
Q

WHAT ARE THE TWO TYPES OF FERMENTATION

A

ethanol or lactate
alcohol fermentation or lactic acid fermentation

116
Q

high level overview of photosynthesis

A

converts solar energy into chemical energy

117
Q

photosynthesis is the source of

A

oxygen and reduced carbon for all other life forms

118
Q

what is reduced carbon

A

sugars, fats, proteins

119
Q

photosynthesis is the basis …

A

of life for all higher trophic levels on the planet

120
Q

the byproduct of photosyntheSIS AND its affect on planet

A

O2 is byproduct
has transformed the chemistry of the planet

121
Q

when the earth formed what was the atmosphere like?

A

reducing atmosphere, no O2

122
Q

what were the first cells like

A

anaerobic, simple enzymes and reaction

123
Q

what did the first photosynthetic cell look like

A

o2 production, c fix, chemiosmotic ATP synthesis

124
Q

what is the great oxidation event

A

O2 accumulation

125
Q

what happened 4.6 billion years ago

A

the earth formed

126
Q

what happened 3.7 billion years ago

A

the first cell appeared

127
Q

what happened 3.4 billion years ago

A

first photosynthetic cell appeared

128
Q

what happened 3.0 billion years ago

A

great oxidation event

129
Q

what happened 1.7 billion years ago

A

cellular respiration

130
Q

photosynthesis is what process

A

the process bywhich light is convereted to chemical energy stored in sugar and other molecules

131
Q

atp syntheis is driven

A

by an electrochemical gradient across a membrane

132
Q

NADPH and ATP produced by light reaction are used in..

A

the calvin cycle to produce sugar

133
Q

plants are….

A

PRIMARY species

134
Q

everything excluding plants are

A

secondary species

135
Q

Autotrophs

A

produce reduced carbon(sugar) using light or chemical energy

136
Q

examples of photoautotrophs

A

higher plants, protists, algae. cyanobacteria

137
Q

heterotrophs examples

A

animals, fungi, many bacteria

138
Q

what are heterotrophs

A

they obtain organic materical (energy) from other organisms

139
Q

who do heterotrophs rely on

A

they rely on photoautotrophs for food and O2

140
Q

Jan Baptist Van Helmont believed that

A

the biomass of plants came from water only

141
Q

in photosynthesis what is reduced and what is oxidized

A

co2 is reduced
water is oxidized

142
Q

in photosynthesis, co2…

A

gains e- to form sugar

143
Q

in photosynthesis water…

A

loses e- to form O2

144
Q

describe the electrons in photosynthesis

A

they increase in energy potential as they move from water to sugar

145
Q

photosynthesis takes place in

A

chloroplast

146
Q

most of the leafs chloroplasts are found in

A

MESOPHYLL cells

147
Q

why are plants green??

A

CHLOROPHYLL

148
Q

why is chlorophyll important

A

they absorb light used for photosynthesis

149
Q

on the absorption spectra..

A

chlorophyll and other leaf pigments absorb light

150
Q

action spectrum shows that

A

photosynthetic rate corresponds to light absorption

151
Q

what color light is best for photosynthesis

A

red and blue light

152
Q

how does chlorophyll absorb light

A

ELECTRONS IN THE PORPHYRIN RING ACCEOT ENERGY FROM PHOTONS

153
Q

how is light energy conserved

A

when electrons go to an excited state

154
Q

the porphyrin ring has a

A

magnesium at the center

155
Q

when chlorphyll absorbs a photon of light …

A

the energy is conserved by an electron going to a higher energy state

156
Q

how is energy from excited state lost as

A

heat or flueorescence with emission of a photon of red light

157
Q

chlorophyll under UV light shows up as

A

red light

158
Q

what are the 2 processes involved in photosynthesis

A

light reactions and the calvin cycle/ dark reactions

159
Q

where do light reactions take place

A

in the thylakoid membranes

160
Q

where do dark reactions take place

A

in the stroma

161
Q

IN the calvin cycle, atp provides

A

chemical energy

162
Q

in the calvin cycle , NADPH provides

A

reducing power

163
Q

the large trans-membrane complexes…

A

process energy in redox reactions

164
Q

what are tghe large trans-membrane complexes

A

photosystem 2, cytochrom complex, photosystem one

165
Q

what are the mobile electron carriers in the ETC of light reactions

A

Pq, Pc, Fd

166
Q

what are Pq. Pc, Fd and what are they capable off

A

they are small molecules or proteins that act as wires that move between the complexes
they are capable of redox rxn (accept or donate e-)

167
Q

what does the ETC of light reactions create

A

proton gradient

168
Q

the proton gradient created by the light reaction ETC …

A

drives ATP synthesis

169
Q

what are the inputs of the light reaction

A

h2o and light energy

170
Q

what are the outputs of the light reaction & chemiosmosis

A

NADPH, ATP and o2

171
Q

the thylakoid space has a …

A

high H+ concentration

172
Q

the stroma of the thylakoid has a

A

low H+ concentration

173
Q

what are the three steps of the calvin cycle

A

fixation, reduction, regeration

174
Q

what does the calvin cycel need as a reactant

A

co2 + ATP & NADPH ( from light reaction)

175
Q

what does the calvin cycle produce simplest

A

CH2O (sugar)

176
Q

whate does the calvin cycle create after multiple cycles

A

sucrose

177
Q

how many sugars from the calvin cycle to produce sucrose

A

3C sugars

178
Q

where is the sucrose then taken

A

export to roots, shoots, fruits

179
Q

what is the structure of DNA

A

double helix

180
Q

what is the base pairing rule

A

purine with a pyrimidine

181
Q

what words describe DNA replication

A

semi-conservative

182
Q

what is the key difference betwen fermentation and cellular resp.

A

oxygen isnt final electron acceptor but lactate is

183
Q

leber’s disease is caused by

A

a rare mitochondrial disorder

184
Q

leber’s diseases main effectt is

A

loss of vision

185
Q

the porohyrin ring of the chlorophyll has what type of bonds

A

double bonds

186
Q

in 1850s who discovered something and what was it

A

mendel- hereditary factors

187
Q

IN 1869 who discovered something and what was it

A

Friedrich Miescher discovers nucleins from pus

188
Q

In 1881 who discovered something and what was it

A

Albrecht Kossel discovers nucleins made of 5 distinct nucleotides and renames to DNA

189
Q

in 1875-1890s who discovered something and what was it

A

unknown- but meiosis and mitosis worked out via microscopy and cytology

190
Q

In 1902 who discovered something and what was it

A

Walter Sutton- chromosome theory of inheritance

191
Q

1930s who discovered something and what was it

A

Thomas Morgan- shows genes are located on chromosomes

192
Q

Why did so many people think that proteins were the genetic material

A

20 amino acids is greater than 4 nucleotides - aka longer alphabet

193
Q

Dr. Frederick Griffith did what experiment and what did the experiment find

A

he mixed heat killed pathogenic cells with living nonpathogenic r cells and found that the mouse died with living S cells (pathogenic)

this showed TRANSFORMATIOn, that bacteria can take up external instruction to change themselves

194
Q

Dr. Oswald Avery …

A

identified DNA as the transforming susbtance

195
Q

a virus is …

A

DNA sometimes RNA enclosed by a protective coat, often simply protein

196
Q

Hershey and Chase experiment + conclusion …

A

made radioactive sulfer and injected it in phage DNA and protein (two seperate experiments) –> only the radioactive DNA was found in the pellet

proof that DNA is the hereditary material

197
Q

Chargaff’s rules …

A

4 same nucleotides in every organism

A is always equal to amount of T
C is always equal to amount of G

198
Q

who made an incorrect structure of DNA

A

Pheobus Levene -1931

199
Q

who discovered the double helix

A

Rosalind Franklin

200
Q

how did ROsalind Fraklin and Maurice Wilkins picture the double helix

A

using x-ray crystallographic images

201
Q

the x-ray image of the double helix allowed…

A

Watson to deduce the width of the helix and the spacing of the nitrogenous bases

202
Q

what is the diameter of DNA

A

2nm

203
Q

how far are the bases apart

A

0.34 nm apart

204
Q

one full turn in dna happens

A

every 10 base pairs

205
Q

what is on the outside of DNA

A

the phosphate backbone

206
Q

the 5’ end has …

A

phosphate attached to the 5th carbon of the sugar

207
Q

the 3’ end has a …

A

hydroxyl attached to the 3rd carbon of the sugar

208
Q

purine + purine=

A

too wide

209
Q

pyrimidine + pyrimidine =

A

too narrow

210
Q

purine + pyrimidine=

A

width consistent with x-ray data

211
Q

A-T bond …

A

is a double bond

212
Q

c-g bond…

A

is a triple bond

213
Q

since the two strands or DNA are complementary…

A

each strand acts as a template for building a new strand in replication

214
Q

semiconservative means that

A

each copy contains one original strand and one newly synthesized strand

215
Q

how does the DNA unwind to start replication

A

the hydrogen bonds between the bases are broken

216
Q

DNA replication occurs in the …

A

5’ to 3’ direction

217
Q

what are telomeres…

A

sequences of DNA at the end of chromosomes

218
Q

where does replication happen

A

origins of replications

219
Q

what are origins of replication

A

site where the two DNA strands are seperated openig a replication bubble

220
Q

what is special abt eukaryotic chromosomes

A

they may have hundreds of even thousands of origins or replication

221
Q

in what direction does replication take place

A

replication proceeds in both directions from each origin, until the entire molecule is copies

222
Q

at the end of each replication bubble there is a

A

replication fork

223
Q

what is a replication fork

A

a y-shaped region where new DNA strands are elongating

224
Q

helicases…

A

are enzymes that untwist the double helix at the replication forks

225
Q

single-strand binding proteins…

A

binds to and stabilizes single stranded DNA until it can be used as a template also removes proteins from DNA

226
Q

topoisomerase…

A

corrects overwinding AHEAD of replication fork by breaking, swiviling and rejoining DNA strands

227
Q

why is topoisomerase important to doctors

A

it is a target of chemotherapy drugs + cipro bc inhibiting this will cause DNA to break down and cause apoptosis

228
Q

DNA polymerases 3 …

A

are enzymes that catalyze the elongation of new DNA at replication fork

229
Q

what do most DNA polymerase 3 require

A

a primer and a DNA template strand

230
Q

rate of elongation in bacteria

A

500 nucleotide per second

231
Q

rate of elongation in humans

A

50 per second in human cells

232
Q

the nucleus is full of…

A

nucleoside triposphates

233
Q

what are nucleoside triphosphates

A

dATP, dCTP, dGTP, dTTP

234
Q

where does the energy for the new phosphodiester bond come from (DNA replication)

A

comes from the 2 phosphates of the nucleoside tripphosphate ( 1 of the phosphate stays attached to the base)

235
Q

the initial nucleotide strand in DNA replication is

A

a short RNA primer

236
Q

primase…

A

is an enzyme that can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as templae

237
Q

what can DNA polymerase 3 not do

A

initiate synthesis of polynucleotide ; only adds nucleotides to 3’ end

238
Q

how long is the rna primer

A

5-10 nucleotides long

239
Q

the 3’ end of the RNA primer …

A

serves as the starting point for the new DNA strand

240
Q

leading strand=

A

continuous strand of newly snthesized DNA

241
Q

lagging strand=

A

short sequence of newly synthesized DNA

242
Q

okazaki fragments=

A

series of lagging strand

243
Q

how are the lagging strands joined

A

by DNA ligase t

244
Q

how are the lagging and leading strand different

A

the leading stand has one RNA primer per active origin of replication while the lagging strand receives several

245
Q

what does DNA polymerase 1 do

A

replaces RNA primer with DNA nucleotides

246
Q

what does DNA ligase do

A

join the two okazaki fragments replacing RNA primer with DNA

works after DNA polymerase 1 removes RNA

247
Q

DNA polymerase extra job is to

A

proofread newly made DNA, replacing any incorrect nucleotides

248
Q

what is a mismatch repair

A

repair enzymes correct errors in base pairing

249
Q

how can DNA be damaged

A

by exposure to harmful chemicals or physical agents such as cigarrets smoke and z-rays, can also undergo spontaneous change

250
Q

what happens in nucleotide excision repair

A

a nuclease cuts out and replaces a damaged stretches of DNA
the polymerase gomes and adds new bases
DNA ligase comes and joins them

251
Q

Xeroderma Pigmentosim

A

lacks the ability to repair DNA damages like thymine dimers and hence is extremely sensitive to sunlight

BIO 93 midterm 2 (1 decks)

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