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Metabolic processes Flashcards

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1
Q

First law of thermodynamics

A

Eng cannot be created or destroyed, only transfered

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2
Q

Examples of energy transformation how

A

Climbing a slide & sliding down- Converting kinetic energy to potential energy back to kinetic energy

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3
Q

Relate first law of thermodynamics to cell resp and photosynth

A

All of our energy comes from the food we it,
or from the sun in plants
its an examples of energy transformation

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4
Q

open vs closed system relate to bio

A

open - when eng can be lost to surroundings (oven)
closed - when eng stays in system
biological orgs are open systems

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5
Q

chemical potential eng

A

chem pot eng - the amount of chem eng that could be released
the greater the energy the more unstable to bond is
the more stable it is the more eng it take to break

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6
Q

exergonic vs endergonic processes

ex, spontaneity

A

exergonic - release eng,
change in eng - neg
spontaneous
becomes more stable
ex. cell resp
uses hydrolysis
endergoinic - absorbs eng
increase in eng
not spontaneous
less stable
ex. photosynth
uses synthesis

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7
Q

What is energy transformation by coupling

A

Exergonic reactions drive endergonic reaction
the energy outputted in exergonic is used in endergonic reactions

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8
Q

coupling and atp hydrolysis

A

atp hydrolysis when phosphate breaks off
phosphate from atp bonds to another molecule, makes it more reactive.

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9
Q

high eng bond on ATP and why it is weak

A

High eng bond on third phosphate
each phosphate has negative charge, constantly pushing away from one another
makes region unstable, easy to break

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10
Q

What are the 3 types of cellular work

A

Transport
ex. pumping things across barrier
Mech
ex. contraction of muscle cells
Chem
ex. synthesis of polymers from monomers

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11
Q

substrate lvl phosphorylation vs oxidative phosphorylation

A

sub lvl phos - direct way
phosphate is transferred directly from “food” to ADP -> ATP
uses Enzyme, found in kreb, glycolysis (Pep + ADP - > pyruvate +
ATP)
oxidative phos - indirect method
uses a redox reaction to transfer electrons to NADH or FADH2
before using it in making ATP (etc)

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12
Q

Principle of Redox reactions (defs)

A

Oxidation - loses electrons, is oxidized, is reducing agent
Reducing - gains electrons, is reduced, is oxidizing agent
When the reaction is reversed the one that gains and loses swap
can be seen as loss or gain of H

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13
Q

What is NAD+

A

oxidizing agent in metabolism
often gets reduced to make NADH
a coenzyme

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14
Q

What is NADH

A

reducing agent in metabolism
can get oxidized to make NAD+
stores energy that can make ATP

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15
Q

How can cell resp just be described as oxidation of glucose

A

what comes out of cell resp is H2O, CO2 and Eng
the glucose gets oxidized into CO2, it loses energy
the O2 gets reduced into H2O
C6H12O6+ 6O2 -> 6CO2+ 6H2O + Energy

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16
Q

Second law of thermodynamics

A

Energy transformation make the universe more disordered
entropy increases overtiem
it takes energy to have order

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17
Q

Heat and its relation to the second law of thermodynamics

A

organisms make give off heat
most random state of energy
increased entropy of the universe is caused mainly by heat

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18
Q

equilibrium meaning in chem reaction and life

A

means its at max stability
delta G = 0, equilibrium convert easily
reaction in closes system reach equilibrium and then do no work
if delta G = 0 in orgs they are dead (living things must not be equilibrium, disequilibrium causes work)

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19
Q

Diff sources of eng in human and uses

A

glycogen
- primary source of eng, only changes when it runs out
fats
- becomes main source when glucose is depleted
muscle tissue (protein)
- final resort, cells are breaking down (bad)

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20
Q

Equation of cellular respiration and goal

A

C6H12O6 + 6 O2 →6 CO2 + 6 H2O
to break glucose down and make 6 CO2
to collect eng in the form of atp
to move glucose electrons to O2, make 6 H2O

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21
Q

What are the 4 major stages of cell resp

A

glycolysis
oxidative decarboxylation(pyruvate oxidation)
krebs cycle
electron transport chain

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22
Q

what are the 7 enzymes used in cell resp

name, function, class

A

dehydrogenase - redox,1
kinase - phosphorylation, 2
lyase - cleavage, 4
decarboxylase - decarboxylation, 4
hydrase - hydration, 4
isomerase / mutase - isomerization, 5
synthase - synthesis, 6

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23
Q

What are the major steps of glycolysis

A
  1. atp-> adp
  2. isomeration
  3. atp->adp
  4. split into DHAP, G3P
  5. isomerization between G3P, DHAP
    equilibrium
  6. 2NaDH is made, dehydrogenase + phospho (p added)
  7. 2 Atp made, kinase, released
  8. isomerization
  9. water leaves (make PEP) lyase, released
  10. 2ATP made, kinase (puryvate)
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24
Q

energy investment phase vs energy payoff phase

A

energy investment phase - first 5
2 atp are put into glycolysis, invested
energy payoff phase - last 5
4 Atp are made from glycolysis, payoff

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25
Q

Why are all reaction in eng payoff phase doubled

A

the glucose breaks into 2 parts, the 2 parts each do the payoff phase

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26
Q

Which steps make or use energy in glycolysis

A

1.ATP - adp
3.ATP -> ADP
6.2 NADH is made
7.2 ATP is made
10.2 ATP is made
makes 4 atp
2 NADH

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27
Q

Purpose of fermentation

A

When there is no oxygen present, the cell can still make NAD+ for glycolysis to make ATP without O2
(usually made in ETC)

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28
Q

Process of lactic acid fermentation

A

2pyruvate
takes 2NADH, turns it into 2NAD+
becomes 2lactate
NAD+ goes to glycolysis

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29
Q

Process of Alcoholic fermentation

A

2pyruvate
CO2 leaves
becomes 2 acetaldehyde
gets 2NADH into 2NAD+
becomes 2Ethenol
NAD+ goes to glycolysis

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30
Q

Lactic vs alcohol fermentation

A

alcohol fermentation not in humans, yeast, makes CO2, has middle step.
Ethanol will not be converted back to pyruvate ever
Lactate can be converted back
both regen 2NAD+

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31
Q

impact of lactic acid fermentation on the body

A

builds up in muscles, transported to liver
used to be thought to cause soreness actually just swelling
allows you to make eng without O2
gets tiring because less eng is made

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32
Q

Why does anaerobic respiration cause fatigue

A

no CO2 is released or H2O
The NADH made from glycolysis has to be used up. less energy is made

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33
Q

Energy molecules made at the end of anaerobic respiraiton

A

just 2 ATP
usually glycolysis makes 2 NADH also

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34
Q

Process of oxidative decarboxylation (steps, reaction type, enzyme )

A

Pyruvate
release CO2, decarboxylation, decarboxylase
NAD+ -> NADH, redox, dehydrogenase
add coenzyme A, synthesis, synthase

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35
Q

Major steps in kreb cycle

A
  1. Coa leaves, join c4 - c2 makes citrate, synthesis
  2. isomerization
  3. NADH made, CO2 release, redox,decarbox
  4. NADH made, CO2 release, COA added, redox, decarbox, synth
  5. ATP made, COA leaves, sub lvl phose(kinase), lyase
  6. FADH2 made, redox
  7. hydration, rearrange molec, makes malate
  8. NADH release, recreate molec to restart, redox, makes OAA
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36
Q

How much energy from Krebs and pyruvate oxidation (what step )

A

per 1 glucose
Py oX - 2 NADH (2)
Krebs - 6NADH (3.4.8), 2ATP(5), 2FADH(6)

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37
Q

Purpose of electron shuttle

A

bring NADH into mitochondria
indirect
needs to get to etc

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38
Q

Glycerol phosphate vs malate aspartate shuttle

A

gly phos - converts to FADH2, less efficient, molecs don’t go into matrix
malate aspartate - stays as NADH, uses glutamate and other things to change back, more molec involved
humans do both

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39
Q

What are the main steps in Malate aspartate shuttle

A
  1. dehydrogenase in cytoplasm, takes electrons from NADH to OAA, makes Malate
  2. Malate enters mitochondria
  3. Dehydrogenase in matrix removes electrons, adds to NAD+ makes NADH
  4. OAA becomes Aspartate with glutamate help
  5. Aspartate leaves
  6. Aspartate becomes OAA with aKG
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40
Q

WHat are the main steps in glycerol phosphate shuttle

A

DHAP takes H from NADH
becomes glycerol 3 phosphate
glycerol 3p goes into inner mito space
H attaches to FAD making FADH2
Glycerol becomes DHAP, leaves

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41
Q

What are the 2 methods of ATP synthesis

A

Substrate lvl phosphorylation - Direct, uses phosphate transfer, in glycolysis, krebs
oxidative phosphorylation - indirect ATP formation through redox reactions involving O2 as a final electron acceptor, driven by ETC, phos starts off free

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42
Q

Proteins in electron transport chain

A

Complex 1 - takes 2e- from NADH, pumps protons out
Complex II only for FADH2, not a pump
ubiquinone (Q) - in bilayer, transfer e from Cl to CIII
CIII - pumps protons
cytochrome C - peripheral in IMM
CIV - pumps protons, leads electrons to O2, makes H2O

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43
Q

Which way is the ATP synthase facing

A

cell resp - Bulb always in matrix of mitochondria
Photosynth - bulb in stroma

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44
Q

What is the driving force behind the energy transformation in ETC

A

Oxygen

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45
Q

How is each step in ETC a redox reaction

A

Movement of electrons
redox is transfer of electrons
each step electrons are transferred to another complex one thing gets oxidized and another gets reduced

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46
Q

describe Chemiosmosis

A

high conct of protons outside
passive transport
high to low cont, gradient is electrochemical

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47
Q

explain how NADH and FADH2 produce diff amt of ATP

A

NADH powers 3 pumps
FADH powrs 2 pumps

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48
Q

Define proton motive force

A

Movement of protons causes conformational change in ATP synthase, makes ATP

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49
Q

What are the components of ATP synthase

A

rotar
Stator
Knob
Rod

50
Q

What does the stator do in ATP synthase

A

anchored in the membrane holds rod stationary

51
Q

What does the rotar do in ATP synthase

A

protein channel, transmembrane
rotate clockwise when protons pass down gradient

52
Q

What does the knob do in ATP synthase

A

peripheral, catalytic site that phosphorylates ATP
has 2 types of subunits alpha, beta
beta has active site for ATP, 3 beta
Rotational catalysis

53
Q

What does the rod do in ATP synthasee

A

spins, causes conformational change in Knob which creates ATP

54
Q

What is rotational catlysis

A

when rod spins it causes conformational change in Knob.
interactions with rod dictates step in ATP synthesis
some int - loosly binds ATP
close int - strongly binds ATP
little int - ATP released

55
Q

Give ex of energy transformation from kinetic to mech to chem pot eng

A

kinetic energy - > movement of H+/Protons through rotor
Mech - protons causes rotor and rod to spin
chem - mech eng causes conformational change in Knob, makes ATP
ATP has chem pot eng in phosphate bonds

56
Q

photosynthesis vs cellular resp

A

cell resp - does not require light
photosynth - inorganic source of CO2
equation is reversed

57
Q

What is the purpose of photosynth

A

use light eng to convert inorganic compounds into organic fuels that can store potential eng in carbon bonds

58
Q

WHat aren’t cell resp and photosynth considered opposites

A

equation is reversed but the order of events and processes are not reversed

59
Q

What is the overall equation for photosynth

A

CO2+ water - > glucose + O2

60
Q

What is autotroph

A

orgs that get eng without eating others
uses inorganic resources

61
Q

what - troph are plants

A

photoautotrophs
they can make eng without eating (light)
require input from inorganic substances from env

62
Q

What troph are humans

A

chemoherterotroph
needs other orgs for eng

63
Q

Name parts of leaf (7)

A

Cuticle - bottom and top layer
Epidermis - bottom and top under cuticle
Palisade mesophyll - longer cells on top
Spongy mesophyll - middle portion
Guard cells - gates at bottom
Stoma / stomata - space in between guard cells
Vascular bundle - lines

64
Q

WHich part of leaf prevents water loss and gas exhcange

A

cuticle

65
Q

WHat does do the guard cells do, location why

A

regulation gas exchange
found on the underside of the leaf so water cant evaporate out

66
Q

what does the vascular bundle do

A

Transports water and nutrients

67
Q

what does palisade mesophyll do and why shape

A

mainly photosynthesis, contains the most chloroplast
shaped as longer oval cells to more could fit in smaller area and get more sun

68
Q

What are the parts of the chloroplast and function (6)

A

outer membrane
inner membrane
stroma - like mitochondrial matrix
thylakoid - disk thing
granum - stack of thylacoids
thylakoid space/ lumen

69
Q

Stroma vs stoma

A

stroma - found in chloroplast, like mitochondrial matrix
stoma - part of leaf structure, in between guard cells, helps gas exchange

70
Q

What type of light is used in photosynthesis

A

visible light

71
Q

how to read absorbtion spectrum

A

Low parts are reflected light
colour on bottom is light being talked about
peaks are more absorbed (colour would not be seen)

72
Q

How wavelengths correlate to colour

A

diff colors have diff wavelengths and energy
the shorter the wavelength the higher the eng
purple is high eng
red is low

73
Q

WHat is a pigment

A

pigment - group of light absorbing molecs
ex chlorophyll, carotenoid

74
Q

role of pigments in how we see colour

A

the colour of pigment is due to wavelength of light reflected back into eyes
pigments reflects certain wavelength

75
Q

absorption vs reflection of light

A

you cannot see what it absorbs
the colour of the object is what it reflects
ex chlorophyll reflects green

76
Q

Carotenoids colour vs chlorophyll colour

A

Carotenoid - reflect red orange, absorb blue green
chlorophyll - absorbs mainly red blue, reflects green

77
Q

Main purpose of light reactions

A

takes in water and light
makes ATP NADH
O2 is byproduct

78
Q

What are the 4 stages of light reaction

A

photoexcitation -light is absorbed and excites electrons
photolysis - energy from light is used to split water
electron transport - harnessing energy in elect to make gradient photophosphorylation - atp synthesis due to electrochem grad and Proton mot force

79
Q

What is photoexcitation

A

happens in chlorophyll in thylakoid
when atoms absorb eng from the sun and electrons get excited

excited electrons go to primary electron acceptor before it gets unexcited

80
Q

What is a photosystem structure and function

A

cluster of hundreds pigments (chlorophyll, carotenoid)
embedded in transmembrane proteins of thylakoid membrane
(found in chloroplasts found in palisade mesophyll cell)
has reaction center chlorophyll and primary electron acceptor

81
Q

How Photosystem captures eng

A

photon hits antennae pigment molecs
energy bounces around
eventually get to reaction centre chlorophyll
RC chlorophyll electron causes primary electron acceptor to trap electron and preserve eng

82
Q

What is photosystem I and II

what is the P number

A

Diff types of photosystems

have diff optimal wavelengths to absorb
PI - has P700 reaction centre chlorophylll
PII - has P680, takes in electrons, is first

83
Q

Parts of the light reaction ETC

A

Photosystem II
Plastoquinone (PQ)
Cytochrome complex (NOT Cyt C)
PC
PSI
FD
NADP+ reductase

84
Q

What does the photosystem II do

A

First part in light ETC
Takes in light
takes in electrons
Excited eng in P680 gets captured by primary electron acceptor
P680 gets oxidized
does photolysis

85
Q

What does PQ do

location, name

A

Plastoquinone
second step of light ETC
transfers electrons to cytochrome complex
found in thylakoid memb
also gets protons from stroma
lipid soluble

86
Q

What does the cytochrome complex do

A

Third step
Part of light ETC
does not take in light
gets electrons from PQ
get protons from PQ pumps against gradient into lumen
Passes electrons to plastocyanin

87
Q

What does plastocyanin do

location

A

Fourth step in light ETC
movable component on lumen side of thylakoid membrane
peripheral
transfers electrons to PI

88
Q

What does Photosystem I do

A

step five in light ETC
electrons in P700 excited and captured by primary electron acceptor
P700 is oxidized
electrons from PC replace those lost

89
Q

What does FD do

A

step six in light ETC
ferredoxin
mobile component on stromal side of thylakoid memb
transfers electrons from photosystem I to NADP+ reductase

IN CYCLIC ELECTRON FLOW
transfers electrons back to cytochrome complex

90
Q

What does NADP+ reductase do

A

last step of light ETC
gets electrons from ferredoxin
attaches them to NADP+ final acceptor of electrons
NADP+ reduced to NADPH

91
Q

What does NADPH do

A

provides eng for Calvin cycle
in reduction phase

92
Q

Why must electrons be replaced in photosystem I

A

electrons lose energy by the time they get to PI.
electrons from photolysis in PII are used to replace them

93
Q

What does ATP Synthase do in Light ETC

A

protons are pumped into lumen, makes high concentration
ATP synthase passive transports them out
ATP is produced in the stroma

93
Q

What is photolysis

A

SOmething only photosystem II does
splits water into electron, H+ and 1/2(O2)
used to replace electrons lost in PI

94
Q

How much eng does Light ETC make

A

1 ATP
1 NADPH
both go to calvin cycle
NADPH in reduction
ATP in regenertion

95
Q

What is photophosphorylation

A

Making of ATP from ADP using the energy from light
done in ATP synthase in photosynth

96
Q

Differences between light ETC and animal ETC (pump, names of Pumps, lipid sol, peri mob molec,source of elec, final acceptor, conc, ATP synth loc )

A

Proton pumps
2-3
Names of Pumps
Cytochrome comp - Complex 1,3,4
Lipid soluble mobile molecule
PQ - quinone
peri mobile molec
Plastocyanin, Ferredoxin - Cyt C
Source of elec
H2O, Photosystem II, I - NADH, FADH2
Final electron accepton
NADPH - O2 in H2O
high conct
in lumen - in inner mitochondrial space
where ATP synthase
thylakoid memb- IMM

97
Q

What is cyclic ETC in photosynth, function and causes

A

when ferredoxin sends the electrons back to Cytochrome C
so that it can pump more protons
makes more ATP
No NADPH is made
ATP is used up faster than NADPH
WHen NADPH accumulates it triggers cyclic

98
Q

Why is cyclic ETC needed in plants

A

linear ETC makes roughly same amt of ATP and NADPH
plant uses more ATP than NADH
cyclic increases ATP more efficiently
Rise in NADH will cause change to cyclic

99
Q

Where does calvin cycle take place

A

for C3/CAM plants - in chloroplast stroma
For C4 plants - in bundle sheath

100
Q

What are the 3 phases of calvin cycle

A

Carbon fixation: takes in CO2
Reduction: uses eng to make organic comp
Renegeration: regenerates molec to go again

101
Q

What happens in carbon fixation phase of calvin cycle

A

take in CO2 and starts with RuBP
uses Rubisco to join CO2 and RuBP to make 3x 6C
C3 plants - breaks into 2 groups of 3x3C
ends up as 6 x 3C
Synthesis, eng is absorbed

102
Q

what is rubisco and its properties

A

synthase found in first step of calvin cycle in carbon fixation
very slow
most abundant protein on earth
leaves need a lot of it

103
Q

What happens in the reduction phase of calvin cycle

A
  1. ATP sends P into each 3C molec (theres 6)
    phosphorylation, kinase , absorbed
  2. NADPH sends H to make G3P (uses 6 NADPH)
    redox, dehydrogenase, absorbed
  3. 1/6 of the G3P leave to become glucose (in similar way backwards glycolysis)
104
Q

What happens in regeneration phase in calvin cycle

A

Other 5G3P continue on
1. G3P (3C) turns back into RuBP (3 x 5C) uses 3 ATP
synthesis, synthase, absorbed

105
Q

What are C3 plants

A

first product of carbon fixation is 3C
more common than C4
not good in hot weather

106
Q

limitations of C3 plants

A

not good in hot weather
close of stomata and cant do gas exchange
drop in CO2
increase in O2
no change to light reaction
no calvin cycle needs CO2 so no glucose made
Rubisco binds do O2 instead of CO2 causes problems

107
Q

How can rubisco cause issues for C3 plants in hot weather

A

hot weather, close guard cell to protect water
No CO2
rubisco binds to O2 instead and makes PGA and PG instead of 2 PGA
PG is hard to use, too energy intensive to convert

108
Q

What is photorespiration

A

when rubisco binds with O2 instead of CO2
makes no organic fuel (no calvin cycle)
no atp
wastes energy
makes H2O2 - bad
baggage from earlier time when much more CO2 and ability didnt matter
now its issue

109
Q

What 2 other plant types have adapted to dry arid places

A

C4 plants
CAM plants

110
Q

Describe C4 plants difference from C3

A

hardier
Corn, sugar cane
starts Calvin cycle witn a 4C instead of 3C
has bundle sheath cells
LIght and Calvin reaction happen at diff places

111
Q

What are bundle sheath cells

A

found in C4 plants
surrounds vascular bundle with palisade mesophyll

112
Q

What is the C4 adaptation

A

LIght reactions with O2 (in palisade) kept separate from Calvin cycle with CO2 (in bundle sheath)
Has PEP carboxylase to stop O2 from getting to bundle sheath

113
Q

How do C4 plants stop O2 from getting to bundle sheath (6 steps)

A
  1. Palisade takes in CO2 and adds to PEP carboxylase
  2. Makes OAA
  3. turns into malate
  4. malate goes into bundle sheath
  5. malate releases CO2 and pyruvate
  6. CO2 is used, pyruvate goes back to palisade to become PEP carbox
114
Q

describe CAM plants

A

crassulacean acid metabolism
succulents, cacti, pineapples
has Pep carboxylase
does light reaction in day calvin at night

115
Q

How does the CAM plant overcome arid conditions

A

Works at night
CO2 Is stored at night to be used in the day
Day :Stomata closed, Conserve water, no CO2 uptake, Light reactions make ATP and NADPH and O2, Calvin cycle runs,
Night: takes in CO2, does PEP carboxylase, stores CO2 in malic acid vacuole

116
Q

How does the CAM overcome the RUbisco problem

A

CO2 is stored at nightj
when calvin and light reactions take place in the day the stored CO2 are in high conct so RUbisco binds to them instead

117
Q

factors that affect photosynth

A

Light intensity
Carbon dioxide concentration
Temperature

118
Q

How to read light intensity graphs

A

measure of carbon fixation
in beginning light limits the production rate
graph increases until it plateaus, that is optimal
graph decreases because then the O2 concentration is too high causing photorespiration

119
Q

What is light compensation point

A

minimum light intensity needed for plant to make carbon

120
Q
A

Biology 12 (6 decks)

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