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AOS2 Flashcards

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1
Q

what are biomechanical reactions

A

reactions occurring in cells that lead to the formation of a product from a reactant.

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2
Q

what are reactants

A

substances (molecules/elements) that are changed from a chemical reaction

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3
Q

what are products

A

a compound produced from the reactants reacting (from the chemical reaction)

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4
Q

what are biomechanical pathways

A

a series of linked biomechanical reactions

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5
Q

what is metabolism

A

The total activity of the reactions of all biochemical pathways in a living organism

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6
Q

what are substrates

A

a compound on which an enzyme acts

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7
Q

what are the types of biomechanical pathways

A
  • anabolic pathways
  • catabolic pathways
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8
Q

what are anabolic pathways (anabolism)

A

These pathways turn simple molecules into more complex ones

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9
Q

what happens to the energy levels in the anabolic pathways

A

anabolic pathways are energy-requiring or endergonic

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10
Q

what are catabolic pathways (catabolism)

A

These pathways break down complex molecules into more simple ones

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11
Q

what happens to the energy levels in catabolic pathways

A

Catabolic pathways are energy-releasing or exergonic

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12
Q

example of anabolic pathway

A

Photosynthesis, where glucose molecules are synthesised from carbon dioxide and water using radiant energy from the Sun

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13
Q

example of catabolic pathway

A

Aerobic cellular respiration, where glucose molecules are broken down into carbon dioxide and water molecules

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14
Q

are enzymes proteins

A

yes most enzymes are proteins

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15
Q

what are catalysts

A

factors that increase rate of reaction

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16
Q

are all catalysts enzymes?

A

no, enzymes are all catalysts but not all catalysts are enzymes

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17
Q

are enzymes specific to reaction?

A

yes, each different reaction will be catalysed by a specific enzyme

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18
Q

what is activation energy

A

minimum amount of energy required to initiate a chemical reaction

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19
Q

what is the active site

A

region of an enzyme that binds temporarily with the specific substrate of the enzyme

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20
Q

what do enzymes do to speed up a reaction

A

lower activation levels

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21
Q

how do enzymes lower activation levels (2)

A
  • Influence the stability of bonds in the reactants
  • Providing an alternative reaction pathway;
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22
Q

how do enzymes bind to substrates (2 steps)

A
  1. the enzyme and substrate with join to form the E-S complex (when it binds to the active site)
  2. the substrate forms weak bonds with particular amino acid residues (in the protein) at the active site.
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23
Q

what are the 3 types of enzyme activity (ways they can bind to substrates)

A
  • substrate specificity
  • bond specificity
  • group specificity
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24
Q

what is substrate specificity (enzyme activities)

A

they catalyse one particular substrate only

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25
Q

what is bond specificity (enzyme activities)

A

they act only on one kind of chemical bond (only peptide bonds)

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26
Q

what is group specificity (enzyme activities)

A

they act only on particular functional groups present as part of the substrate molecule (-COOH, or -OH)

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27
Q

what are coenzymes

A

an organic molecule that acts with an enzyme to alter the rate of a reaction

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28
Q

what are cofactors

A

a non-protein molecule or ion that is essential for the normal functioning of some enzymes

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29
Q

are cofactors and coenzymes the same

A

no, coenzymes are cofactors but not all cofactors and coenzymes

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30
Q

what are inorganic cofactors

A

cofactors that do not contain carbon and include metal ions such as magnesium or copper

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31
Q

what are organic cofactors

A

small non-protein organic molecules that are essential for the function of particular enzymes

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32
Q

what are the 2 types of organic cofactors

A
  • prosthetic groups
  • coenzymes
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33
Q

prosthetic groups are ……

A

cofactors that are tightly bound to an enzyme and are essential for it to function as a catalyst.

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34
Q

what is the difference between prosthetic groups and coenzymes

A

prosthetic groups are tightly bound to an enzyme, whereas, coenzymes are loosely bound

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35
Q

what are the 5 main coenzymes we focus on

A
  • NAD
  • NADP
  • FAD
  • ATP
  • CoA (coenzyme A)
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36
Q

what are the 2 roles of coenzymes to assist enzymes

A
  • transfers of atoms or groups of atoms, such as hydrogens, phosphate groups and acetyl groups
  • energy transfers
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37
Q

what are the 2 forms coenzymes can be in (interconvertible forms)

A
  • loaded and
  • unloaded
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38
Q

loaded coenzymes main info

A

they are high in energy and have a group that can be transferred. In simple they are electron donors

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39
Q

unloaded coenzymes main info

A

they have low energy, and accept groups. In simple they are electron acceptors

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40
Q

what are the 3 factors that impact enzyme activity

A
  • temperature
  • pH
  • substrate concentration
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41
Q

summary of what happens with varied temperatures for enzyme activity (rate of reaction)

A

when temperature first increases, the reaction rate also increases. This is because the reactants absorb heat energy and move faster, allowing them to collide and overcome the activation energy.
However, in enzyme-catalysed reactions, this increase only occurs up to the optimum temperature, after which the rate decreases, due to denaturation and the change in enzyme structure.

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42
Q

summary of what happen with varied pH for enzyme activity (rate of reaction)

A

As pH increases or decreases from optimum pH, the rate of reaction and the activity of an enzyme decreases.

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43
Q

do each enzyme have different optimum pH

A

yes, each with have different so different graphs with rate of reaction

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44
Q

summary of what happen with varied substrate concentration for enzyme activity (rate of reaction)

A

the rate of reaction increases with increasing substrate concentration — but only up to a point. Beyond this, any further increase in substrate concentration produces no significant change in reaction rate (active sites are all occupied)

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45
Q

what are enzyme inhibitors

A

substances that prevent the normal action of an enzyme and therefore slow the rate of enzymes-controlled reactions

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46
Q

what are the 2 types of inhibition

A

reversible inhibition
irreversible inhibition

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47
Q

what are the 2 types of reversible inhibition

A
  • competitive inhibition
  • non-competitive inhibition
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48
Q

what is competitive inhibition

A

inhibition in which a molecule binds to the active site of a molecule instead of the usual substrate

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49
Q

why does competitive inhibition slow down reaction rate

A

inhibitor molecules prevent the formation of the E–S complexes (as active site is partially occupied)

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50
Q

what is non-competitive inhibition

A

inhibition in which a molecule binds to the allosteric site of an enzyme causing a conformation change in the active site

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51
Q

is the active site and an allosteric site the same?

A

no, allosteric site is somewhere on the enzyme but not the active site itself

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52
Q

why does non-competitive inhibition slow down reaction rate

A

as the binding of the inhibitor to the allosteric site changes the shape of the enzyme’s active site the E-S complex cannot form

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53
Q

what is irreversible inhibition

A

occurs when a specific molecule can form a strong covalent bond with an enzyme at its active site, so that the normal substrate is permanently blocked from accessing the active site

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54
Q

what are common irreversible inhibitors?

A

Heavy metals

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55
Q

what are 3 things that the regulation of rates of reaction does

A
  • prevent waste, such as would occur if pathway products were made in excess of cell requirements
  • prevent the build-up in cells of products to potentially harmful levels
  • prevent depletion of substrates
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56
Q

what are the 2 types of regulation

A
  • allosteric regulation
  • feedback regulation
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57
Q

what is allosteric regulation

A

control of the reaction rate of enzymes through conformational changes in enzymes. This occurs when a regulator molecule binds to the allosteric site

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58
Q

what can the regulator molecules be (allosteric regulation)

A
  • allosteric inhibitors
  • allosteric activators
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59
Q

what does allosteric inhibitors do

A

their binding produces a change of shape in the enzyme that stops enzyme activity; they act like an OFF switch

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60
Q

what does allosteric activators do

A

the shape change resulting from the binding produces an increase in enzyme activity; they act like an ON switch

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61
Q

what is feedback regulation

A

the end product of a metabolic pathway acts as an inhibitor of the key enzyme that catalyses the first step in a pathway.

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62
Q

what is photosynthesis

A

the process by which plants use the radiant energy of sunlight trapped by chlorophyll to build carbohydrates (glucose) from carbon dioxide and water.

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63
Q

what is the photosynthesis equation

A

6 carbon dioxide + 6 water = glucose + 6 oxygen (gas)

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64
Q

what are the 2 stages of photosynthesis

A
  • light-dependent stage
  • light-independent stage
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65
Q

what is the function of the light dependent stage

A

to transform sunlight energy that is captured by chlorophyll into the chemical energy of loaded coenzymes

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66
Q

what is the function of the light independent stage

A

to assemble simple inorganic carbon dioxide molecules into more complex organic glucose molecules

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67
Q

what is another name for the light independent stage

A

Calvin cycle

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68
Q

where does photosynthesis occur

A

chloroplasts, in the chlorophyll pigment inside (in the cytosol of plants)

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69
Q

what does chloroplasts enable a plant to do

A

capture the radiant energy of sunlight, bringing it into cells as the starting point of photosynthesis

70
Q

what are the 3 main things inside the chloroplasts (not including chlorophyll)

A

thylakoids
grana
stroma

71
Q

what are thylakoids

A

flattened membranous sacs in chloroplasts that contain chlorophyll

72
Q

what is the grana

A

stacks of thylakoids are known as grana, where a singular stack is a granum

73
Q

what is stroma

A

fluid inside the chloroplasts, containing the enzymes that are involved in calvin cycle

74
Q

what does the light dependent stage involve

A

involved in the capture of sunlight and the transformation of its energy to the chemical energy of loaded coenzymes, NADPH and ATP.

75
Q

where is the light dependent stage occur (c3)

A

thylakoid (within the grana)

76
Q

what are the 3 inputs in the light dependent stage

A
  • water
  • ADP + Pi
  • NADP+
77
Q

what are the 3 outputs of the light dependent stage

A
  • oxygen
  • ATP
  • NADPH
78
Q

summary of what happens in light dependent stage

A

the energy caught by the chlorophylls make the electrons have high energy (excited) and the splitting of water molecules gives H+ ions (protons).
This then allows NADPH to form as well as ATP

79
Q

what do the chloroplasts have after the light dependent stage

A

a supply of high-energy loaded ATP molecules
a supply of high-energy loaded NADPH coenzymes that can act as donors of hydrogen ions and electrons

80
Q

light dependent equation

A

water + 18ADP + NADP into 6O2 + 18ATP + NADPH

81
Q

what happens in the light independent stage

A

inorganic carbon dioxide molecules (CO2) are built into energy-rich reduced organic molecules, such as glucose (C6H12O6).

82
Q

where does the light independent stage occur

A

the stroma

83
Q

what is required for the light independent stage

A

Rubisco, and the NADPH (donate H and e-) and ATP (energy source) from the previous stage

84
Q

what are the 3 inputs of the light independent stage

A
  • ATP
  • NADPH
  • CO2
85
Q

what are the 3 outputs of the light independent stage

A
  • ADP + Pi
  • NADP+
  • Glucose
86
Q

summary of what happens in light independent stage

A

inorganic carbon is converted in organic CO2 thru carbon fixation
NADPH donate hydrogens and electrons as molecules are reduced to higher energy levels
ATP supplies energy for anabolic steps

87
Q

what are the 3 types of plants

A

C3
C4
CAM

88
Q

why are there different types of plants

A

they are categorised into how they fix carbon into glucose

89
Q

how do C3 plants carry out the Calvin Cycle

A

These plants carry out the original Calvin Cycle, using Rubisco, and are prone to photorespiration

90
Q

what are optimal conditions for C3 plants

A

moist and cool conditions

91
Q

how do C3 plants use RuBisco

A

use the Rubisco enzyme to fix inorganic carbon dioxide from the air and it enters the Calvin cycle joined to a carrier molecule (RuBP)

92
Q

where does the Calvin Cycle take place in C3 plants

A

in the stroma of the leaf mesophyll cells

93
Q

Photorespiration definition

A

a process in which plants take up oxygen rather than carbon dioxide in the light, resulting in photosynthesis being less efficient. (Rubisco takes up O2 instead of CO2)

94
Q

what does rubisco normally do

A

the critical enzyme in C3 plants that brings carbon dioxide from the air into the Calvin cycle where the glucose is made

95
Q

when does photorespiration occur

A

rubisco binds oxygen rather than carbon dioxide

96
Q

does photorespiration make glucose

A

nooooo

97
Q

why will Rubisco bind to oxygen instead of carbon dioxide

A

the active site can readily accommodate the oxygen molecules as well as the carbon dioxide molecules, so the two different molecules are in competition for the active site of Rubisco.

98
Q

2 ways photorespiration arise in C3 plants (increase amount)

A
  • temperature increases
  • conditions dry out
99
Q

why does photorespiration increase as temperature increases

A

the ability of the Rubisco enzyme to distinguish between carbon dioxide and oxygen decreases and, as a result, Rubisco will increasingly bind oxygen.

100
Q

why does photorespiration increase as conditions dry out

A

C3 plants close their stomata to prevent water loss. This closure blocks the entry of carbon dioxide needed as input to the Calvin cycle and limits the exit of oxygen produced

creating a high oxygen low CO2 environment inside the mesophyll cells

101
Q

how do C4 plants carry out the Calvin Cycle

A

carry out an adapted Calvin cycle, in which carbon fixation and glucose production occur in different cells

102
Q

what are optimal conditions for C4 plants

A

These cells will thrive in warm and tropical regions

103
Q

what anatomy changes are present in C4 plants (compared to C3 and CAM)

A
  • bundle sheath cells have chloroplasts
  • mesophyll cells that are arranged in a close association around the bundle sheath cells
104
Q

where do the two processes occur in C4 plants

A

leaf mesophyll cells and bundle sheath cells

105
Q

what happens in the first process in C4 plants (light dependent stage)

A

Carbon dioxide is converted into malic acid, in the mesophyll cells
PEP carboxylase catalyses the binding of carbon dioxide to an acceptor molecule (malic acid) (this is called carbon fixation)

106
Q

what enzyme is used in the first step of C4 plants in photosynthesis

A

PEP carboxylase

107
Q

why is PEP carboxylase used instead of RuBisco (C4)

A

It cannot bind to oxygen so photorespiration cannot happen

108
Q

what happens in the second process of the C4 plants

A

Calvin cycle (glucose production) occurs in the bundle sheath cells

produce a steady supply of carbon dioxide from the breakdown of malic acid that raises the carbon dioxide concentration in their leaves. This allows the RuBisco in the bundle sheath cells to bind only to CO2

109
Q

how do CAM plants carry out the Calvin Cycle

A

two stages of the Calvin cycle occurring at different times

110
Q

what are optimal conditions for CAM plants

A

thrive in hot and arid environments, that are exposed to droughts

111
Q

when does carbon fixation happen in CAM plants

A

at night (stomata are open)

112
Q

when does the Calvin cycle happen in CAM plants

A

in the day (when the stomata are closed)

113
Q

where do photosynthesis processes occur in the CAM plants

A

mesophyll cells

113
Q

does CAM plants use PEP carboxylase or Rubisco initially

A

PEP carboxylase

114
Q

what happens to the malic acid produced in CAM plants when it is night time

A

it is stored in vacuoles waiting for the stomata to close (day time)

115
Q

what 3 things will make RuBisco work most efficiently

A
  • carbon dioxide levels in leaves are high
  • oxygen levels are low (as happens when water is freely available)
  • when temperatures are moderate.
116
Q

what are the 4 main factors that affect the rate of photosynthesis

A
  • the amount of light reaching their leaves
  • the temperature of the environment
  • the availability of water
  • the concentration of carbon dioxide
117
Q

what is a limiting factor

A

any environmental condition that restricts the rate of biochemical reactions in an organism.

118
Q

what happens to the rate of photosynthesis as light intensity increases

A

increases as light intensity increases, until it reaches a maximal point.

119
Q

what is the light saturation point

A

the point where further increases in light intensity have no effect and the rate of photosynthesis stays constant

120
Q

why does increased light intensity increase the rate of photosynthesis

A

more chlorophylls are energised

121
Q

what does too little or too much water do to the rate of photosynthesis

A

rate of photosynthesis declines and then stops because closed stomata prevent the uptake of carbon dioxide needed for the Calvin cycle

122
Q

what does waterlogging do to the rate of photosynthesis

A

the rate of photosynthesis will also decline and stop because the lack of oxygen for cellular respiration in root cells stops water uptake

123
Q

what happens to the rate of photosynthesis as temperature increases

A

As the ambient temperature is increased, the rate of photosynthesis also increases due to an increase in collisions between the reactants and the enzymes involved in photosynthesis. Eventually, as the heat passes a certain threshold, the enzymes start to denature, in which the tertiary structure of an enzyme is lost. This causes the rate to again decrease.

124
Q

what happens to the rate of photosynthesis as CO2 concentration increases

A

the rate of photosynthesis will increase until it levels off due to limiting factors

125
Q

does CO2 concentration impact the light dependent stage and why

A

no, because CO2 is not apart of the reaction

126
Q

what is cellular respiration

A

the process of converting chemical energy into a useable form by cells, typically ATP.

127
Q

what are the 2 types of cellular respiration

A

aerobic and anaerobic

128
Q

what is the equation for aerobic cellular respiration (without coenzymes)

A

glucose + oxygen arrow carbon dioxide + water + ATP

129
Q

how many ATP does aerobic respiration make

A

30-32, 36-38 in optimal conditions

130
Q

what are the 3 steps of aerobic cellular respiration

A
  1. glycolysis
  2. Krebs cycle
  3. electron transport chain
131
Q

what is the main (broad) thing that happens in glycolysis

A

glucose is broken down into pyruvate

132
Q

what is the main (broad) thing that happens in Krebs cycle

A

makes a supply of energy-rich loaded coenzymes

133
Q

what is the main (broad) thing that happens in the electron transport cycle

A

transfers energy from electrons supplied by loaded coenzymes to make ATP.

134
Q

where does glycolysis occur

A

cytosol

135
Q

how much ATP is produced from glycolysis

A

2

136
Q

what are the 3 inputs in glycolysis

A

glucose, 2x (ADP + Pi) and 2x (NAD+)

137
Q

what are the 4 outputs in glycolysis

A

2x (pyruvate), 2x ATP, 2x (NADH) and two hydrogen ions (protons)

138
Q

where does the Krebs cycle and electron transport chain occur

A

mitochondria

139
Q

where specifically does the Krebs cycle occur

A

the matrix

140
Q

what is the matrix of the mitochondria

A

gel like solution within their inner membrane

141
Q

where specifically does the electron transport chain happen

A

the cristae

142
Q

what does cristae do

A

It folds in the inner membrane of the mitochondria, it hold enzyme

143
Q

what happens in between glycolysis and Krebs cycle

A

pyruvate oxidation

143
Q

what in summary happens in pyruvate oxidation

A

pyruvate loses a C and an H atom, forming a 2C acetyl group that is delivered to the Krebs cycle by coenzyme A.

144
Q

what are the 2 coenzymes that are becoming high in energy in the Krebs cycle

A

FAD+ and NAD+

145
Q

what are the 4 inputs in Krebs cycle and pyruvate oxidation

A

2 x (acetyl CoA (acetyl groups)), 6 x (NAD+), 2 x (FAD) and 2 x (ADP + Pi)

146
Q

what are the 4 outputs in Krebs cycle and pyruvate oxidation

A

4 x (CO2), 6 x (NADH), 2 x (FADH2) and 2 x (ATP)

147
Q

detailed electron transport chain info

A

Electrons are transferred along enzyme complexes
The first input of high-energy electrons to the ETC comes from loaded NADH coenzymes.
FADH2 also donates its high-energy electrons to an acceptor, but further down the chain.
Oxygen accepts electrons and hydrogen ions, forming water

148
Q

how is so much ATP produced in the ETC

A

As electrons transfer from one enzyme complex to the next, the energy released is ultimately used to power the production of ATP from ADP and Pi.

149
Q

what are the 4 inputs of ETC

A

6 (oxygen)
26-28 (ADP + Pi)
10 (NADH)
2 (FADH2)

150
Q

what are the 4 outputs of ETC

A

6 (water)
26-28 (ATP)
10 (NAD+)
2 (FAD)

151
Q

which process of aerobic cellular respiration needs oxygen

A

electron transport chain

152
Q

what is anaerobic respiration/fermentation

A

processes that occur without the presence of oxygen, producing a net of 2 ATP molecules

153
Q

when does anaerobic fermentation occur in humans

A

occurs in human skeletal muscle cells when the supply of oxygen to the cells by aerobic cellular respiration cannot keep up with their demand for ATP.

154
Q

where does anaerobic fermentation take place

A

the cytosol

155
Q

is the rate of ATP production in anaerobic fermentation higher lower or similar to aerobic respiration

A

much faster, this is why it is able to produce enough ATP

156
Q

what are the 2 anaerobic fermentation pathways

A
  • alcohol (ethanol) fermentation
  • lactic acid fermentation
157
Q

what are the 2 processes that occur in both anaerobic fermentation pathways

A

glycolysis
short add on stage

158
Q

is glycolysis the same in aerobic and anaerobic cellular respiration

A

yes

159
Q

what happens in the add on stage for lactic acid fermentation

A

pyruvate, ADP and NADH is turned into ATP, lactic acid and NAD+

160
Q

what happens in the add on stage for alcohol fermentation

A

alcohol is created, NAH+ is regeneraed for glycolysis again

161
Q

what are the inputs and outputs of the alcohol fermentation

A

pyruvate, NADH, ADP

ethanol, CO2, NAD+ 2ATP

162
Q

what fermentation does yeast and animals use

A

animals use lactic acid
yeast uses alcohol

163
Q

what 3 factors affect the rate of cellular respiration

A

temp
oxygen concentration
glucose concentration

164
Q

glucose concentration affecting cellular respiration summary

A

an increase in glucose concentrations leads to an increase in the rate of cellular respiration. This rate eventually levels off from rate-limiting factors

165
Q

oxygen concentration affecting cellular respiration summary

A

As oxygen concentration increases, so does the rate of cellular respiration. This eventually levels off due to other factors limiting the rate.

166
Q

what is biomass

A

the organic material from plants and animals; it is a renewable source of energy.

167
Q

what is biofuel

A

Biofuels are any fuel source derived from biomass.

168
Q

what is food vs fuel (biofuel sustainability)

A

world’s population expected to increase, there needs to be a balance between increased production of biofuels and food availability

169
Q

what is land requirements (biofuel sustainability)

A

To meet the 2060 target for biofuel production it is estimated an additional 100 million hectares of land will be required

170
Q

what is energy efficiency (biofuel sustainability)

A

Creating biofuels from feedstocks is currently an inefficient process. The energy required to produce and then collect the raw materials required is far greater than the fuel produced

Biology 3&4 (7 decks)

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