Test 3 Flashcards
1
Q
Large bacteria picture
What did scientists initially think this organism?
Why?
How does this species overcome the challenges
of large cells?
A
Turns out it is a bacteria not a eukaryote. It was large.
the copy number increased as the cells grew. they produce thousands of copies of the chromosome ensuring that transcription and translation can occur at sufficient levels.
2
Q
Viruses are diverse in form. What are the two
structures that all viruses share? What do only
some viruses have? Define them.
Where does the virus get the membrane
envelope from?
A
They all share protein coat (capisd) and some type of genetic material. Only some viruses have. some of them have membrane envelopes with enzymes such as reverse transcriptase.
capsids are from capsomeres.
viral membrane envelope is a phospholipid bilayer that the virus steals from a host.
2
Q
protein encoding genes v genome size graph. What pattern does this figure highlight? What
makes it difficult to separate a free-living cell vs.
a symbiont vs an organelle?
A
symbionts and parasites are smaller. however, some free living bacteria can be smaller. once symbionts and organelles become acclimated to living inside of a cell, they become redundant.
3
Q
Graph about bacteria with lines. Approximately how much distance would there be between two molecules if there were 100
inside E. coli?
A
200 nm, since that means the
concentration is ~10^2.5
4
Q
pink cell engulfing another cell. What does this figure show? What is secondary endosymbiosis (see lecture)? How can you tell if a chloroplast came from secondary or primary endosymbiosis?
A
It shows the origin of diatoms, which are photosynthetic unicellular eukaryotes.
A non-photosynthetic eukaryote ate a photosynthetic algae. The algae eventually became the cholorplasts .
5
Q
Why are cells so small? Explain the relationship
of surface area to volume. Also explain how
diffusion constrains the size of cells
A
Cells are small so that they can have a high surface area to volume ratio so that it can easily exchange material in itself and the environment. As the cell grows, the volume increases at a higher rate than the surface area.
High protein concentration reduce distance between two molecules, but the proteins diffuse slower because of the increased viscosity.
.
6
Q
As the size of a cell increases, what happens to
the surface area to volume ratio?
How would this affect traffic into and out of the
cell?
A
If a cell grows, the surface area to volume ratio will decrease. The SA will grow proportionately slower than the volume. It would decrease traffic in and out of the cell.
7
Q
What are the different types of viral genomes?
A
they can be linear or circular. They can have double DNA, single DNA, double RNA, or singel RNA.
8
Q
What are prions? How are they
transmitted? What do they do?
A
prions are infectious proteins that cause degenerative brain diseases in animals. they are most likely transmitted through food. they cause proteins to misfold. leads to brain damage and death.
9
Q
What are alarming characteristics of prions?
A
their incubation period is like 10 years. they do not get destroyed by heat.
they convert normal host proteins into misfolded prion protiens. lack nucleic acids.
10
Q
Which virus is the only one we have eradicated
globally due to vaccinations?
A
smallpox
11
Q
Expalin cell theory
A
all cells come from other cells
12
Q
dendrites
A
receive signals from other neurons
13
Q
axon
A
carries nerve impulses away from cell body towards target cells
14
Q
synapse
A
the junction where a neruon communicates with another cell across a narrow gap via neurotransmitter or electric coupling
15
Q
synaptic terminal
A
part of each axon branch that releases neurotransmitters
16
Q
neurotransmitter
A
chemical messenger that passes information from transmitting neuron to receiving cell across synaptic cleft
17
Q
cell body
A
part of the neuron that houses the nucleus and most other organelles
18
Q
myelin sheath
A
composed of many lipid membranes. poor electrical conductors. good insulator.
19
Q
nodes of ranvier
A
gaps in sheath where voltage gated channels occur.h
20
Q
threshold of action potential
A
-50
21
Q
resting voltage of neuron
A
-70
22
Q
What does this figure highlight about voltage gated
ion channels?
A
they do not open and close in sync.
23
Q
Figure with neuron with light specturm that turns red
What does this figure show? What were they
measuring and how does this relate to neuron
function?
A
When action potential reaches axon terminal, it becomes flooded with calcium ions because voltage gated calcium channels open in reaction to action potential, and the Ca ions rushed down their gradients. this triggers exocytosis of neurotransmitters to communicate with muscle or neuron.
24
Explain how an action potential is transmitted from
one cell to another across a synapse by summarizing
what is shown above in four steps. Use the example
of neuromusclar junction and acetylcholine.
1. an action potential arrives and depolarizes membrane.
2. depolarization opens Ca channels triggering an influx of Ca ions.
3. The elevated Ca2+ concentration
causes synaptic vesicles to fuse
with the presynaptic membrane,
releasing neurotransmitter into
the synaptic cleft (exocytosis)
4. The neurotransmitter diffuses
across cleft and binds to ligandgated ion channels in the
postsynaptic membrane.
5.In muscles, acetylcholine is
release and binds to chemicallygated sodium channels. The
allows sodium to flow into the
muscle cells and triggers an
action potential to eventually
release Calcium ions to cause
muscle contraction.
25
Label the neuromuscular junction.
Here is a jumbled summary of steps involved in
muscle contraction. Put them into correct order in
the following chart, and then place the number for
each step in the correct location on the preceding
diagram.
1. nerve impulse arrives at neuromuscular junction
2.acetylcholine is released from synaptic vesicles
3.acetylcholine binds to receptors on muscle fibers this allows Na ions to rush, causing depolarization.
4. depolarizaton
5. Ca++ is released from cisterns of SR
6. Ca binds to troponin on thin filaments.
7. The troponin/tropomyosin is moved so that myosin binding site of actin is exposed.
8. in presence of ca++ myosin acts as an enzyme. it catalyzes breakdown of ATP. energy is transferred from ATP to myosin head myosin is activated.
26
How does myosin use ATP to cause muscles to
contract? Describe why rigor mortis happens to
muscles after death?
In the presence of Ca++, myosin acts as an enzyme. it catalyzes the brreakdown of ATP. it goes and activates the myosin heads. myosin binds to the actin and pulls the actin fibers toward center of sarcomere. atp is necessary to release myosin from actin. when a cell is dead, it cannot produce atp, so myosin cannot release, and is stuck as contracted.
27
Use this figure to explain how Calcium ions modify
the thin filament
Ca++ is relased from cisterns in the SR. Ca++ binds to troponin, and causes the troponin and tropomyson to move so the active site is open for the myosin to bind.
28
Describe the function of the sarcoplasmic reticulum
and transvers (T) tubules in muscle cells
the t-tubles allow for the action potential to continue throughout the interior of a skeletal muscle.
the SR stores calcium and has voltage gated ca++ channels that allow Ca to flow into cytoplasm to trigger action potential once action potential reaches them.
29
Use this figure to explain two things
Why do action potentials only travel in one direction
down and axon?
What does myelenation do to the speed of an action
potential travelling down and axon?
action potentials only travel one way down the axon because there is a recovery phase where another action potential could not occur. (refractory period).
Action potentials can only be generated in the nodes of ranvier. The inward current produced during the rising phase of the action potential at a node
travels to the next node, where
it depolarizes the membrane and
regenerates the action potential.
This saves the time of opening
and closing many ion channels,
instead limiting it to a certain
number of positions along the
axon, a mechanism called
saltatory conduction which is
faster.
30
Why is an action potential an example of positive
feedback mechanism?
Once the threshold is reached, more Na channels open which leads to more depolarization which continues to open more channels etc. the system enhances the original stimulus.
initial depolarization oepns Na channels.
Na+influx leads to more depolarizaton.
More depolarization opens more Na channels and the loop repeats,
31
How does the sodium potassium pump work? What
is its function? Is is a part of the action potential?
it reestablishes a resting membrane potential. it uses one ATP to move 3 Na+ out of cell and 2 K+ into cell. Maintains a more negative charge inside cell.
32
Describe the distribution of ions (Na⁺, K⁺) across the
cell membrane at resting membrane potential. How
do these distributions contribute to the resting
membrane potential?
There is more Na+ outside the cell.
There is more K+ inside the cell.
33
What is the definition of depolarization?
Hyperpolarization?
depolarization is when Na+ channels open and the insdide of the cell becomes less negative because the Na+ go into the cell.
Hyperpolarization is when K+ channels open and K+ flows out of the cell and makes the cell more negative. cl- can also enter.
34
Figure with a bunch of acid molecules Describe this experiment and what important
discovery for how our body breaks down lipids to get
energy from them. What is this process called? What is
the end product of the process that we use to extract
energy from.
Beta oxidation breaks down lipids two carbons at a time. It produces acetyl to eventually attach to coA
35
Explain this experiment and what did they conclude
was needed for beta oxidation of lipids to occur?
ATP is required for beta oxidation and octonoic acid.
36
What are enzymes that break down proteins called?
Why do we have so many different kinds of enzymes
that break down proteins? How does the bottom
figure support having multiple proteins that break
down proteins?
Which enzyme breaks down proteins in your stomach?
What is the optimal pH for that enzyme?
Protease is the enzyme that breaks down proteins.
There are so many different ones for the different kids of proteins and the environments they are found in per the different pHs. Pepsin is found in the stomach 1-2 pH.
Some ezymes are simply justn better at breaking down proteins than others.
37
What is the process of breaking down proteins called?
What are the products of this process? Are there any
toxic products that must be excreted from the body?
What are inhibitors of deamination?
Deamination. They must go through this before cellular respiration. This means their amino groups are removed. This makes pyruvate. it can also produce ammonia which is toxic and NADH. ATP and GTP inhibit deamination. GTP is a stronger inhibitor.
38
What does it mean to be lactose intolerant? Is lactose
intolerance as an adult the wild-type allele, or mutant
allele?
it means you don't have lactase and can't break down lactose. It is wild-type to be lactose intolerant.
39
What is the meaning of glycolysis? What occurs in this
step of cellular respiration? Is oxygen required?
The starting product of glycolysis is the six-carbon
sugar and the ending products are
two -carbon molecules of .
For one glucose molecule, in glycolysis, how many
ATPs are used and how many are produced? What is
the net gain of ATP? What are the other high energy
molecules are produced by glycolysis?
After glycolysis, you have pyruvate oxidation (see
figure). What are the products of this process and
where does it occur?
Gylcolysis is breaking apart glucose. It splits it into pyruvate. Oxygen is not required. 2 ATPs are used and 4 ATPs are produed.
Pyruvate oxidation turns pyruvate into acytl coA
Per one glucose (2 pyruvates) it produces 2 CO2, 2NADH, 2 Acetyl CoA.
Glycolysis occurs in the cytoplasm and pyruvate oxidation occurs in the mitochondria.
40
Based on this figure, Which enzyme is the limiting
reaction that regulate glycolysis rates?
PFK is the slowest enzyme because substrate has accumulated behind it. PFK regulates the rate of glycolysis.
41
Based on the figure above, which molecules act to
inhibit PFK activity in glycolysis? Which molecules
speed up the rate of PFK activity?
Why do cancer cells have a selective advantage over
normal cells for creating energy?
PFK is inhibited by citrate and high leves of ATP.
AMP speeds up PFK to produce more ATP.
Cancer cells continue to undergo glycolysis even when citrate is high. Therefore, they will continue to grow and divide even when the cell has enough ATP and stuff.
42
Where does the citric acid cycle take place in cells?
Following glycolysis and pyruvate oxidation, which
molecule enters into the citric acid cycle?
For one molecule of Glucose (6C) (which means two
Acetyl-CoA molecules) how many of the following
products are produced?
CO2
NADH
FADH2
GTP
Where has most of the energy been stored? Where is
that energy taken? What will that stored energy be
used for?
It takes place in the mitochondrial matrix.
Acetyl CoA enters the citric acid cycle. This 2C is bound to a 4C to become citirc acid.
to complete the oxidation of glucose, you must complete the cycle twice. So after 2 cycles you get
4 CO2
6NADH,
2 FADH2
2 GTP
the energy has been stored in NADH and FADH2
43
Through glycolysis, beta oxidation, deamination,
pyruvate oxidation, and the citric acid cycle, no oxygen
has been used. Based on this table where is oxygen
actually consumed in cellular respiration?
Oxygen consumption occurs in the mitochondria. It is used as the final electron acceptor in the ETC.
44
What is the function of the electron transport chain in
cellular respiration? Where are proton concentrations
higher, outside mitochondria (intermembrane space)
or mitochondrial matrix? What provides the energy to
pump protons against their gradient?
In the experiment with carbon monoxide, which of the
ETC protein complexes is inhibited by CO?
The ETc nprovides e- that pump ATP to intermembrane space to create a proton gradient which is used to make ATP.
More protons are in the intermembrane space. NADH and FADH2 donate electrons for the energy.
Oxygen is the final acceptor and is reduced to H2O.
CO binds and inhibits the 4th ETC complex.
45
Explain how ATP synthase uses energy from a proton
gradient to power ATP production from ADP and
inorganic phosphate. What is the final process of
making ATP called?
How does the movement of protons drive the
synthesis of ATP?
ATP synthase used the proton gradient and H+ions travel donw their concentration and power the production of ATP. Thi9s entire process is called oxidative phosphorylation. Cjhemisomosis is producing the ATP through ATP synthase.
46
Based on this figure, which molecules inhibit and
which molecules promote Cellular respiration? Think
general.
Why would calcium act to promote cellular
respiration?
ATP, NADH, and citric acid inhibit metabolic enzymes. (energy rich products)
energy poor mnolecules of CR (ADP, AMP, CoA, NAD+ promote)
muscles require Ca+ and ATP to contract.
When there is more Ca+, muscles contract more, so more cellular respiration happens to produce more ATP.
47
According to the first law of thermodynamics, what
can and cannot happen to energy?
energy cannot be created or destroyed.
48
What is free energy? What is its symbol?
It is the energy that can perform work. G.
49
Chemical reactions change the free energy available in
molecules. Once we know the value of ΔG for a
reaction we can use it to predict whether it will require
energy or release energy. For a reaction that releases
energy, is ΔG negative or positive?
Releasing energy has a -∆G.
50
Here is a molecule of ATP. Label it. Use an arrow to show
which bond is likely to break.
The bonds between the phospahtes aqre most likely to break because they are all negative and pushing against each other.
51
How is ATP used in your body? What is energy
coupling?
When ATP -> ADP, it releases energy. we use that energy to power reactions.
energy coupling is use of energy released from a reaction to drive a reaction that needs energy
52
Both cellular respiration and photosynthesis are redox
reactions. In redox reactions, pay attention to the flow
of electrons. What is the difference between oxidation
and reduction? (OIL RIG)
Oxidation is the loss of electrons.
Reduction is the gaining of electrons.
53
When compounds lose electrons, they energy;
when compounds gain electrons, they energy.
When they lose electrons, they lose energy, and wehen they gain elecgtrons, they gain energy.
54
It is essential for you to understand the concept of
oxidation/reduction and energy transfer. For the
following pair, which molecule is the oxidized form,
and which is reduced? Which molecule holds higher
potential energy? Which is lower in potential energy?
NAD+
Oxidized or Reduced?Higher Energy/Lower Energy
NADH
Oxidized or Reduced? Higher Energy/Lower Energy
NAD+ is oxidized, has lower energy and
NADH is reduced, has higher energy
55
Where does each stage of cellular respiration occur?
Glycolysis
Pyruvate oxidation
Citric Acid Cycle
Oxidative phosphorylation
glycolyssi occurs in the cytoplams
rest are in mitochonrial matrix
56
Explain what has happened to the six carbons found in
the original glucose molecule.
a total of 6 CO2s are released, accounting for the 6 glucose carbons. (2 from pyruvate oxidation) 4 from krebs cycle.
57
What is the primary role of oxygen in cellular
respiration?
Explain why oxygen is considered the ultimate electron
acceptor.
Oxygen stabilizes the electrons by combining with two
hydrogen ions to form what compound?
What would happen to the ETC if oxygen were not
around or if a toxin, like cyanide, stops ETC from
functioning?
Oxygen is used as the final electron acceptor.
It removes electrons to allow the chain to continue.
It is electronegative and attracts electrons.
Oxygen is reduced to water.
If oxygen is not present, the e- will have nowhere to go and the ETC will stop. less ATP produciton.
58
Paraquat is a herbicide. However, it also harms
humans that are exposed to it. Which is why it is illegal
in the EU. How does it work to harm humans?
How does paraquat kill plants?
paraquat steals e- from the ETC. they produced hihgly reactive oxygen ions that destroy nucleic acids, lipids, and proteins. death in humans.
it aborbs e- in plants. stops proton pumping. ATP and NADPH are not produced.
59
The figure above describes the classic experiment of
Theodor W. Englemann. Describe how he determined
an action spectrum long before the invention of a
spectrophotometer.
algea to different wavelengths. blue and red light (anything besdies green) produced the most oxygen.
60
Which wavelengths do plants generally absorb? Which
do they reflect? Why are plants green?
They absorb all colors besides green.
61
Use these figures to explain how plants harvest energy
from the sun?
pigments in the cholorplast absorb all colors besides green. Light goes to the chlorophyll and excites e- within. the e- are rleased and pump protons. light energy was turned into chmeinal energy in ATP and NADPH.
62
What did this experiment highlight about these three important steps of photosynthesis? Which step
seemed to be more inhibited by the enzymatic
inhibitor?
they are all inhibted differently. splitting water, [producing atp, and fixing carbons are performed by 3 distinct pathways.
carbon fixation was inhibited the most.
63
Use these figures to explain how light is used to create
a proton gradient.
Which part of the chloroplast has greater proton
concentration? When chloroplasts are exposed to light
what happens to proton concentration? Where do
they move?
What will that proton gradient be used for?
Where do the light reactions take place chloroplasts?
The Calvin Cycle?
Thylakoid space has more H+.
with light, protons are pumped to Thylakoid.
proton gradient is energy to produced ATP
light reactons are in the thylakoid membrane. calvin cylce in the stroma.
64
The chlorophyll a at the reaction center of PS II is P680.
P680+ may be the strongest biological oxidizing agent.
Why is this necessary? What molecule is it oxidizing?
In linear electron flow, As electrons fall from
photosystem II to photosystem I, the cytochrome
complex uses the energy to pump ions. This builds a
proton gradient that is used to produce what
molecule?
Photophosphorylation is most similar to what process
in cellular respiration?
What is the source of energy that excites the electron
in photosystem II?
Where do the electrons come from that replace the
excited electrons in photosystem II?
Where do the electrons come from that replace the
excited electrons in photosystem II?
Where do electrons have the highest potential energy?
P680 pulls electrons from oxygen in water.
proton gradient produces ATP.
photophosphorylation is similar to oxidative phosphorylation.
light energy excigtes the elecftrons.
water is split to provide the e-.
e- have highest potential energy at end of PSI,
65
What does this figure highlight about a plants ability to
make ATP? What does it need?
it needs light to generate a proton gradient.
66
What is the source of O2 in the atmosphere? Is water
always split to form water in plants?
it is the splitting of water.
water is only split durong linear. wnen light is dim.
67
Based on these figures what is apparent about CO2
concentrations in the atmosphere?
Have concnetrations varied naturally in the past?
Based on more recent CO2 data, what is the trend in
CO2 concentrations?
co2 is rising. heat up because humans. be liBEral.
68
When CO2 concentrations in the atmosphere are high,
what does that mean about global temperatures?
Why does CO2 concentrations vary within a year? How
is this related to photosynthesis and cellular
respiration?
HigH co2 is high temp;. less co2 in summer cuz photosynthesis. moer in winter cuz less pjotosuntheedsis. `
69
Sometimes the Calvin cycle is call the “dark reactions”
of photosynthesis. What does the figure on the left
suggest about an environmental factor that signficant
impacts the rate of carbon fixation in photosynthsis?
light is needed, even for carbon fixation. for production of atp nadph so it can change co2 into organic sugwr. no power in darkness.
70
What is the most abundant enzyme (protein) in the
world?
What is its role in photosynthesis?
Building sugars takes energy. What molecules provide
the energy to build sugars in the calvin cycle? Where
did they come from?
The net production of one G3P
requires molecules of ATP and molecules
of NADPH.
How many CO2 molecules are fixed to make one G3P
and how many turns of the calvin cycle to make one
G3P? Why?
rubisco is most abundant enZYme.
responsible for carbon fixation.
atp and nadph made in ld rxns power calvin cycle.
The net production of one
G3P requires 9 molecules
of ATP and 6 molecules
of NADPH.
Each turn of the Calvin
cycle fixes one molecule of
CO2; therefore, it will take
3 turns of the Calvin cycle
to net one G3P.
71
Where does the Calvin cycle (rubisco) take place in a
chloroplast? How does this graph support that rubisco
is in the optimial pH? What do these graphs suggest
about impacts of pH and Mg on rubsico activity?
calvin cycle in stroma w higher ph.\
rubisco better in basic.
sensitive to ph and mg2+ conc.
72
Do microbes live at every depth sampled in the Figure?
Do you see any trends in the data with regards to
depth or type of metabolism?
yes at every depth, no pattern.
73
All of these figures are related to one another. Sunlight
does not reach deep sea thermal vents and yet this is
evidence that light might exist. What is that evidence
and where is the light coming from?
from tnermal vents and bioluminescense.
74
What is chemosynthsis? Do all organisms need light to
survive? Do they need oxgen as their final electron
acceptor in cellular respiration?
when organisms produce food by using chemical energy rather than light energy like Hydrogen sulfide or methane.
bacxteria does not need oxygen they can use other ,molecules.
75
What is a halophile?
Compared to E. coli, does H. cutirubrum have more
positive charges or negative charges in its proteins?
Why?
like salt.
more acidic (negative charge) than E coli. negaticve charge offset NA+. have to deal with osmotic stress of extracellualr salt.
76
What is the relationship between the light reaction
and Calvin cycle? What does the light reaction provide
to the Calvin Cycle? What does the Calvin cycle provide
to the light reactions?
light reactions turn lgiht energy into chemical energy in form of ATP and NADPH. These are used in Calvin Cycle to build sugar moelcules. NADP+ and ADP can be resued.
77
Use the following figures to explain the differences
between cyclic and non-cyclic electron flow in
photosynthsis.
The following set of questions deals with linear
electron flow
What is the source of energy that excites the electron
in photosystem II?
What compound is the source of electrons for linear
electron flow?
What is the source of O2 in the atmosphere?
As electrons fall from photosystem II to photosystem I,
the cytochrome complex uses the energy to
pump ions. This builds a proton gradient
that is used in chemiosmosis to produce what
molecule?
In photosystem I, NADP+ is reduced by the excited
electron and H+ to form .
The following set of questions deals with non-linear
electron (cyclic) flow
What is the source of energy that excites the electron
in photosystem I?
What compound is the source of electrons for linear
electron flow?
Is water split in non-linear electron flow?
light excites e-
water is source of e-.
splitting water is source of O2
in cyclic, e- circlue continuously.
78
Does Cyclic electron flow within PSI converts high
energy electrons into an H+ ion gradient?
In photosystem I, is NADP+ reduced to NADPH in cyclic
electron flow?
What are light conditions that favor cyclic electron
flow in plants?
What are light conditions that favor non-cyclic (linear)
electron flow in plants?
water is not splic in cyclical.
aTp is still made.
nadph is not made.
bright light is favored for cylcic flow to make ATp and conserve water.
for non cyclic dim lgiht is favored rto made NADPH and ATP and split water wqhne its not too hot.
79
Examine the Figure while we tally carbons.
This figure is designed to show the production of one
net G3P.
That means the Calvin cycle must be turned three
times.
Each turn will require a starting molecule of ribulose
bisphosphate (RuBP), a five-carbon compound.
This means we start with ______ carbons distributed
in three RuBPs.
After fixing three molecules of CO2 using the enzyme
__________, the Calvin cycle forms six G3Ps with a
total of ___________carbons.
At this point there is a net gain of ________ carbons,
or one net G3P molecule.
How many times would the calvin cycle have to turn to
produce one glucose molecule?
How many ATP and NADPH for one glucose molecule?
in calvin cycle start iwth 15 C.
after fixing 3 molcues of CO2 with rubisco, calivn cycle produces 6 G3Ps with a total of 18 carbons.
net gain 3 carbons or one G3p molecule.
3 turns for 1 G3P.
6 turns for 1 glucose.
used per one glucose molecule: 18 ATP and 12 NADPH
