Midterm Flashcards
1
Q
what is the energy of life
A
modules of metabolism, ATP
2
Q
what type of energy to we focus on
A
chemical
3
Q
what does energy refer to
A
chemical, food, location, climate, time
4
Q
location energy
A
where is something relative to something else
5
Q
climate energy
A
too hot - too much energy
too cold - not enough energy
6
Q
time energy
A
enourmous amounts of energy in a tenth of a second - an explosion
enourmous amounts of energy in millions of years - biology
7
Q
metabolism
A
metabolism is the totality of an organism’s chemical reactions
metabolism is an emergent properry of life that arises from interactions between molecules within the cell
8
Q
organisaiton of the chemisty of life into metabolic pathways
A
a metabolic pathway begins with a specific molecule and end siwth a product
each step os catalysed by a specific enzyme
metabolic pathways are clearly denifed steps
9
Q
two types of pathways
A
catabolic
anabolic
10
Q
catabolic pathways
A
releases energy by breaking down complex moleucles into simpler compounds
includes cellular respiration
11
Q
cellular respiration
A
in a catabolic pathway
the breakdown of glucose in the presence of oxygen
12
Q
anabolic pathway
A
small to large molecuels
consume energy to build complex molecules from simpler ones
anabolic steroids
the synthesis of preoteins from amino acids is an example
13
Q
bioenergetics
A
the study of how organisms manage theyir energy resources
14
Q
what is energy
A
the capacity to cause change
can exist in various forms, some of which can perform work
15
Q
4 types of energy
A
kinetic
heat
potential
chemical
16
Q
kinetic energy
A
motion
17
Q
heat
A
thermal energy
random movement of atoms or molecules
18
Q
potential energy
A
related to location or structure
19
Q
chemical energy
A
potential anergy available for release in a chemcial reaction
20
Q
binding site
A
if a protein uses ATP, it has a binding site that recognises ATP
21
Q
charge of ATP
A
negative
22
Q
charge of rpotein at the catalytic ATP binding site
A
positive - since ATP is negative
23
Q
what is thermodynamics the study of
A
energy transformations
24
Q
what is a closed system
A
isolated form its surroudnigns
25
what is an open system
energy can be transferred between the system and its surroundings
26
are all living things open systems
yes
27
is earth an open system
yes
28
first law of thermodynamics
the energy of the universe is constant
energy can be transferred and transformed, but it cannot be created or destroyed
29
second law of thermodynamics
during every energy transfer or transformation, some energy is unusable, and is often lost as heat
disoder is a representation of energy
30
does a polypeptide have more energy than loose amino acids
yes
31
do cells convert organised forms of energy to heat
yes
32
how do spontaneous processes occur
without energy input
they can happen slowly or quickly
33
what happens when a process occurs without energy input
the entropy of the universe increases
34
do cells create ordered structure form less ordred materials
yes
35
do organisms replace ordered froms of matter and energy with less ordred forms
yes
36
simple low of energy thorugh the ecosystem
enters as light, exists as heat
37
how to know whether a reaction will occur spontaneously or not
free-energy change
need to determnie the energy changes that occur in teh chemical reactions
38
free energy change - ∆G
a living system's free energy is the energy that cna do work when temperature and pressure are uniform, as in a living cell
the change in energy during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy (∆S) and temperature in Kelvin
only processes with a negative ∆G are spontaneous
spontaneous processes can be harnessed to perfom work
39
change in free energy equation
∆G = ∆H - Tx∆S
40
DNA polymerisation
DNA is a polymer of individual nucleotides contianing a base, a sugar, and three phosphate groups
energy from breaking of the phosphoanhydride bond of an incoming nucleotide is used to form a new phosphodiester bond
reactions is catalysed by DNA polymerase
41
what is the Ea barrier
activation energy barrier
42
how do enzymes lower the Ea barrier
they catalyse reactions
they do not affect the change in free energy (∆G); instead they hasten the reaction that would eventually occur
43
Gibbs free energy
in endergonic reactions, net change in gibbs free energy is positive, and energy must be added to the system
44
gibbs free energy def
a thermodynamic quantity equal to the enthalpy (of a system or process) minus the product of the entropy and the absolute temperature
45
exergonic reaction
releases energy
46
endergonic reaction
costs energy
47
cellular respiration
includes both aerobic and anerobic respiration but it often used to refer to aerobic respiration
although carbs, fats, proteins, are all consumed as fuel, it is helful to trace cellular respiration with the sugar
48
glucose synthesis
C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + energy (ATP + heat)
49
substrate
the reactant that an enzyme acts on the the enzymes substrate
50
enzyme-substrate complex
when the enzyme binds into its substrate the enzyme substrate complex is formed
51
active site
the region on the enzyme where teh substrate binds
52
induced fit of a substrate
brings chemical groups of the active sire into postions that enhace their ability to catalyse the reactions
53
functional groups
give rise to molecuels with diverse charge and shape
54
ATP
the molecules that is used to transfer energy in cells
drives endergonic reactions by phosphorylation, trasnferring a phosphate group to some other molecule, such as a reactant
the recipeitn molecule is now phophorylated
55
redox reactions
oxidation and reduction
the transfter of electrons during chmeical reactions releases energy stores in organic moleuces
this released energy is untimately used to syntehsise ATP
56
osixation-reduction reactions/redox reactions
chemical reactions that transfer electrons between reactants
57
oxidation
susbtance loses electrons
it is oxidised
58
reduction
substance gains electrons
it is reduced
59
stepwise energy harvest
in cellular respiration, glucose and other organic molecules are broken down in a series of step
electrons form organic compounds are usually transferred to NAD+, a coenzyme
each NADH (reduced form of NAD+) represented stored energy that is tapped to syntehsis ATP
60
what is released when wood is burned
glucose
61
what will happen when phosphates move around
will give an input of energy
62
glycolysis
breaks down glucose into pyruvate
there is an organic molecule that comes out of this process - pyruvate
63
how mayn carbons in pyruvate
3
64
how many carbons in glucose
6
65
how many pryruvates are made in teh glycolysis of 1 glucose molecuels
2
66
how many times does teh krebs cycle run with 1 glucose molecule
2
67
stages of cellular respiration
glycolysis
pyravate oxidation
citric acid cycle
oxidative phosphorylation
68
cristae
the folding of the organelle
found in mitochondria
69
matrix
innermost compartment
70
intermembrane space
narrow region between the inner and outer membranes
71
the citric acid cycle
aka the krebs cycle
takes place within the mitochondrial matrix
the cycle oxidises organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH2 per turn
it is an open cycle
72
the FADH2 is closest to which class of molecule subunit
nucleotide
73
does CO2 have energy
yes
74
can the energy from CO2 be used in a biological setting
no, and thus is tends to stay pretty stable
75
is ⍺-keto-glutarate an acid or a base
acid
76
is FAD a battery
yes
77
what type of molecule subunit is GTP
nucleotide
78
the stages of cellular respiration
glycolysis
citric acid cycle
oxidative phosphorylation
79
glycolysis simple def
breaks down glucose into two molecules of pyruvate
80
the citic acid cycle
completes teh breakdown of glucose
81
oxidative phosphorylation
accounts form most of the ATP syntehsis
82
where is the electron transport chain
in teh cristae of the mitocondria
83
what are the main compenets of the ETC
proteins
they exists in multiprotein complexes
84
what happens to the carriers in eh ETC
they are alternately reduced and oxidised as they accept and doante electrons
85
what happens to electrons as they go down teh ETC
they drop in free energy and are finnaly passed to O2, forming H2O
86
are electrons transferred from NADH or FADH2 to the electron trasnprot chain
yes
87
what is one type of protein in teh ETC
cytochrome
they ahve an iron atom
electrons are passed through this
88
does teh ETC generate ATP
no
89
function of the ETC
to break large free-energy drop ffrom food to O2 into smaller steps that release energy in manageable amounts
loos of one erngy is represented by antoher type of energy, usually heat
90
which stores more energy - NADH or FADH2
NADH
91
the energy coupling mechanism
chemiosomsis
92
chemiosmosis
electron transfer in teh ETC causes proteins to pump H+ form the mitochondrial matrix to the intermembrane space
H+ then moves back across the membrane, passing through channels in ATP synthase
ATP synthase uses the exergonic flow of H+ to drive phosphorylationr in ATP
93
where is the lowest pH in teh mitochondrial structure
intermembrane space
94
why do our bodies form water
water is a byproduct of respiration
95
how does a dam create energy
as it flows from high concetration to low, energy is produced
96
proton motive force
the energy stored in a H+ gradient across a membrane couples teh redox reactions of teh ETC chain to ATP syntehsis
97
oxidative phosphoryalation
accounts for almost 90% of the ATP generated by cellular respiration
a smaller amoutn of ATP is formed in glycolysis and the citric acid by substrate-level phosprylation
98
accounting of ATP production in cellular respiration
energy flows:
gluse -> NADH -> ECT -> proton-motive force -> ATP
99
% of energy in a glucose moleues that is transferred to ATP during cellular respiration
40%, making about 32 ATP
100
wehre is the majority of energy lost
in heat and CO2
about 60% of the energy
101
how to get the max number of H+ ions across
start at the highest possible spot on teh ETC
102
does cellular respiration include aerobic and anaerobic respiration
yes, but is often used to revefer to aerobic respiration
103
aerobic respiration
it is about pathways and biomolecules
it was a great scientific achievement to understand energy flow in the living
if you can understand this pathway, you will be able to understand all ptahways in courses, jobs, ect
104
fermentation and anerboic repsiariton
enable cells to produce ATP wihtout the use of oxygen
most cellular respiration requires O2 to produce ATP
glycolysis can produce ATP with ot without O2 (in aerobic and anaerobic conditions)
in teh absence of O2, glycolysis couples iwth fermentation or anerobic respiration to produce ATP
oxidative phosphorylation does not occur without oxygen - NAD -> NADH H+ is a reduction reactions - the reverse of this is oxidative phosphyrlation
aerobic respiration uses an ETC with an electron acceptor other than O2
fermentation sues phosphroylation instead of an ETC to generate ATP
105
types of fermentation
alcohol fermentation
lactic acid fermentation
106
fermentation
consists of flycolysis plus reactions that regerneate NAD+ which can be resued in glycolysis
107
alcohol fermentation
2 carbons, 5 hydrogens, OH group
pyructe (3 carbon) is converted to ethanol in two steps
108
1st step of alcohol fermenaiton
release CO2 converting pyruvate to acetaldehyde
109
2nd step of alcohol fermenation
acetaldehyde is reduced to ethanol by NADH
this regenerates teh supply of NAH+ needed for the continuation of glycolysis
110
lactic acdi fermentaion
eg. yogurt (yogurt is acidic)
3 carbons, 6 hydrogens, 3 O
pyruvate is reduced directly by NADH to form lactate
no CO2 is produced - we know this by looking at the structure - something is still serving the 3 carbons
lactate is the ionised form on lactic acid
lactic acid fermentation by certain fungi and bacteria is used in the dairy industry to make cheese and yogurt
111
fermentation vs aerobic respiration
fermentation and aerobic cellular respiration are anaerobic and aerobic alternatives for producing ATP by harvesting the chimcal energy of food
both processes use glycolysis to oxidise glucose and other organic fuels to pyruvate
cellular respuration produces 32-34 ATP per glucose molecule, fermentaiton produces 2 ATP per glucose molecule
humans cannot do fermentaiton
112
what are major intersections to various catabolic pathways
glycolisys and the citric acid cycle
113
does glucose or ethanol contian more chemical energy
glucose
it has more carbon hydrogen bonds
114
photosyntehsis
the dynamics of an ecosystem incldue two major processes
cycling of nutrient, in which materials acquired by plants eventually return to the soil
the flow of energy from sunlight to producers to consumers
light from the sun is eventually turned to heat that is lost form the ecosystem
115
autotrophs
sustain themselves without eating anthing derived from other organisms
autotrophs are the producers of the biosphere, producing organic molecules form CO2 and other inorganic molecules
almost all plants are photoautrotrophs, using the energy of sunlight to make organic moelcules form H2O and CO2
you need autorthrophs before heterothrophs
116
hterothrophs
obtain their organic matter from other organisms
117
what type of energy is light
electromagnetic energy, aka electromagnetic radiation
it travels in rythmic waves
118
what is wavelength
the distance between crests of waves
119
what does wavelength determine
the type of electromagnetic energy
120
what is the electromagnetic spectrum
the entire range of electromagnetic energy or radiation
121
what is visible light
consists of wavelengths (including those that drive photosynthesis) that produce colours that we can see
122
visible light wavelength
380-750nm
the larger teh wavelength, the lower the enegery
123
what do microwaves absorb
water
124
where are radiowaves
everywhere
125
two stages of photodsyntehsis
light reactions (the photo part) and the calvin cycle (the syntehsis part)
126
what is the goal of photosyntehsis
takes energy that is out there and trasnforms it into usable energy
chemical energy is more reliable than photon energy
127
what is the main photosynthetic pigment on the planet
chlrophyll a
128
what are accessory pigments + 2 examples
broaden the spectrum used for photosynteheis
chlrophyll b, carotenoids
129
carotenoids
absorbs excessive light that would damage chlorophyll
they don't absorb red, yellow, orange, and some green
this is why carrots and tomatoes are red
130
where do light reactions occur
in teh thykaloids
131
light reaction in teh thykaloid
splits H2O
releases O2
reduces NADP+ to NADPH
generates ATP from ADP by photophosphorylation
132
photosyntehtic pigments - the light receptors
pigments are moelcules that absorb visible light
differne tpigments absorb different wavlengths
leaves appear green because chlorophyll reflects and transmits green light
not beacuse it absorbs green light, but beacsue it reflects that wavelength of light
133
photosynthesis quation
6CO2 + 12H2O + Light energy -> C6H1206 + 6O2 + 6H20
134
moelcuels that carry energy in cells
molecules with the phosphate group carry more energy
plants have both, but more this the phosphate group
135
hydrocabron tail
allows the molecules to be anchaored in a particular spot in the cell
this allows the energy to be trasnmitted to something close to it
permits compoartmentalisaiton
136
what is a photosystem
a reaction-centre complex (a type of protein complex) associated iwth light-harvesting complexes
137
what do light-harvesting complexes do
they are pigment molecuels bound to proteins and they funnel the enery of the photons to the reactions centre
138
what are the two types of photosystems in teh thykaloid membrane
photosystem I
photosystem II
139
PS II
functions first
best at absorbing a wavelengths of 680 nm
the reactions centre chlorophyl is called P680
140
PS I
best at absorbing a wavelength of 700 nm
the reactions center chlrorophyll of PS I is called P700
141
which of teh two photosystems captures photons of the highest energy
PS II
142
how many possible routes for electron flow during a light reactions
two - linear and cyclic
143
linear electron flow
the primary pathway
involved both photosystems and produces ATP and NADPH using light energy
those are chemicals that biological organisms will use to do work
144
linear electron flow steps
a photon hits a pigment and its energy is passed among pigment molecuels until it excites P680
an excited electron from P680 is transferred to teh primary electron acceptor
P680+ (P680 that is missing an electron) is a very strong oxidising agent
H20 is split by enzymes and the electrons are transferred from the hydrogen atoms to P680+. thus reducing it to P680
O2 is released as a byproduct of this reaction
energy released by teh fall drives the creation of a proton gradient across the thykaloid membrane
diffusion of H+ protons across the membrane drives ATP synthesis
in PSI (like PSII) transferred light energy excits P700, which loses an electron to an electron acceptor
each electron "falls" down an electron transport chain from the primary electron acceptor of PSI to the protein ferredoxin (Fr)
hydrogen ions are moved across a membrane
the electrons of NADPH are available for teh tractions of the calvin cycle
145
cyclic electron flow
cyclic electron flow uses only photosysm I and produces ATP, but not NADPH
cyclic electron flow generatees additional ATP, satisfying the higher demand for ATP ion the calvin cycle
146
chemiosmosis in chloroplasts
transform light energy into chemical energy
portons are pumped into the thykaloid space and drive ATP synthesis as they diffuse back into stroma
ATP and NADH are produced on teh side facing the stroma, where the calvin cycle takes place
147
chemiosmosis in mitochindria
transfer chemical energy from food to ATP
protons are pumped to the intermembrane space adn drive ATP syntehsis as they diffuse back into the mitochondrial matrix
148
calvin cycle uses ATP and NADPH to convert CO2 to sugar
carbon enters the cycle as CO2 and leaves as a sugar named glyceraldehyde-3-phosphate (G3P) - 3 carbons
for net syntehsis of 1 G3P, the cycle must take place 3 times, fixing 3 molecuels of CO2
the calvin cycle has 3 phases
149
rubisco
most abundant protein on the planet
all plants use it to capture CO2 from the atmosphere
150
what do plants produce from solar energy
ATP, NADPH, carbs
151
alternative mechnisms of carbon fixation
have evolved in hot, arid climates
dehydration is a problem for plants, sometimes requiring trade-offs with other metabolic processes, especially photosynthesis
on hot, dry days, plants close stomata, which conserves H2O but limits photosynthesis
the closing of stomata reduces access to Co2 and causes O2 build up
these conditions favour a seemingly wasteful rpocess called photorespiration
152
photorespiraiton
in most plants (c3 plants) initial fixation of CO2, via rubisco, forms a 3 carbon compound
in photorespiration, rubisco adds O2 instead of CO2 in the calvin cycle
photorespiration consumes O2 and organic fuel and releases CO2 without producing ATP or sugar
153
C4 plants
C4 plants minimise the cost of photorespiration by incorporationg CO2 into 4 carbon compounds in mesophyll cells
this step requires the enzyme PEP carboxylsase (phosphoenolpyruvate)
PEP caboxylase has a higher affinity for CO2 than rubisco does - it can fix CO2 even when CO2 concentrations are low
these 4 carbon compounds are exported to bundle-sheath cells, where they release CO2 that is then used in teh calvin cycle
154
does purple sulfur bacteria (and some other organisms) have PSI and not PSII
yes
155
did cyclic electron flow or linear electron flow evovel first
cyclic
156
waht might cyclic electron flow protect cells form
light-induces damage
157
exceptions to standard photosyntehsis
envirnomental resistance
carbon storage
158
celli division
a mechanical and mapping part, done by biomolecuels and requires a lot of energy
159
the key roles of cell division
the ocntinuity of life is based on the reproduction of cells, or cell division
in multicellular organisms, cell division is balanced by cell death (apoptosis)
cell growth is the outcome of proliferation adn cell death
160
apoptosis
when cell division is balanced by cell death
cell death =/ apoptosis
a series of molecular steps lead to its death - a specific kind of cell death
161
what happens when there is cell growht without apoptosis
can be cancer, ect
162
what happens when there is apoptosis without cell growth
can be dementia, alzheimers, ect
163
what do multicellular organisms depend on cell division for
development from a ferlised cell
growth
repaid
cell division is an integral part of the cell cycle, the life of a cell
164
the cell cycle steps
cell doubling
DNA doubling
biochemically
165
cell organisation of the genetic material
all the DNA in a cell constitutes the cell's genome
DNA molecules are packaged into crhomosomes
every eukaryotic species has a characteristic number of chromosomes in each cell nucleus
166
genome
can consist of one DNA molecule (common in prokaryotic cells) or a number of DNA molecules (common in eukaryotic cells)
167
somatic cells
non reproductiv ecells
two sets of chromosomes
168
gametes
reproductive cells
sperm and eggs
half as many chromosomes are somatic cells
169
human chromosoms #
46
in each somatic cell, each strand has 46 chromososms
170
deer - munjac # of chromosomes
4
171
fruit fly # of chromosomes
4
172
does chromosome number represent the complexity of a species
no
173
minum number of genes for being aliave
420
174
is DNA a good example of an emergent property
yes
through its associaton with other molecules and its strucure other attributes will emerge
175
teh cell cycle gaols
not cell division
about the copying and preparation for distrubution
176
4 phases of the cell cycle
G1
G2
S1
mitosis
177
what does the G in g1 and g2 mean
gap
getting ready for DNA syntehsis and for mitosis
178
what does the s in s pahse mean
DNA syntehsis
179
cytokinesis
is the sum of the cell division
180
interphase
in between teh phases of mitosis
G1, G2, S phase
181
intermediate filamanets
holding hte nucleus together
182
centrosome
composed of tubulin microtubules
point of attachment
kinetochore on it
183
chromosomes
always present, but in prophase they become mitotic chromosomes
184
DNA molecule width
2nm
185
DNA molecule length
2m, broken up into 23 pieces (the chromosomes)
186
chromosome shape
folded so that they don't break
187
metaphase anaphase transition arrow
leads into anaphase
188
claspin
protein that holds the sister chromatids together
189
when is claspin released
the cell has the biochemical capacity to count and measure 46, then when all are accounted for the claspin is told to release
190
is the distribution of chromosomes a random event
no
191
does the nuclear envelope disassemble or degrade
it disassembles
if it degraded, ribosomes would have to rebuild the nuclear envelope which would be too much time
192
what object "measures" the greatest diameter of the cell
microtubule
the longest microtubules in the cell will mark positional information
the actin gets deposited at hte palce of greatest diameter
193
mitotic spindle
apparatus of microtubules that controls chromosome movememnt during mitosis
during prophsase, assembly of spindle microtubles begins in teh centrosome, the microtubules organsiing centre
during prometaphsae, some spindle microtubules attach to the kinetochoes of chromosomes and begin to move the chromosomes
at metaphase, the chromosomes are all lined up at the metaphse plate, the midway point between the spindle's two poles
194
kinetochores
positioned on the centromere
the centromere is a place on a chromosome that incldues dna sequences that will attract kinetochore proteins
the sequence that the DNA contains says that it is a binding sire for other proteins
195
soliditity of the plasma membrane
somewhat fluid
196
anaphase
sister chromatids seperate and move along the kinetochore microtubules towards opposite ends of teh cell
the microbulues shroten by depolymerising at their kinetochore ends
nonkinetochore microtubules from opposite poles overlap and push agaisnt each other, elongating the cell
197
telophase
genetically identical daughter nuclei form at opposite ends of the cell
198
cytokinesis
in animal cells, cytokinesis occurs by cleavage, forming a cleavage furrow
on plant cells, a cell plate forms during cutokinesis
199
binary fission
proaryotes (bacteria and archaea) reproduce by a type of cell division called binary fission
in binary fission, the chromosomes replicate (beginning at the origion of replication) and the two daughter chromosomes actively move apart
200
ORC
origin of replication
there is a position on the chromosome that says start replication here
DNA thus starts there
201
