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Biology 2 > Unit 2 > Flashcards

Unit 2 Flashcards

Cell Communication and Homeostasis (Ch 40,41,7,11)

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1
Q

What are peripheral proteins

A

peripheral proteins = outer side of the plasma membrane (phospholipids head)
they need to be able to interact with ions (charges)

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2
Q

How can flip-flopping across the membrane increase?

A

if you destroy / poke a hole through the phospholipids bilayer itself.

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3
Q

What is permeability of the cell?

A

moving in or out of the cell
the permeability of the cell (how good it lets stuff cross through) is based on the polarity and size of the substance.

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4
Q

What can cross through the membrane with high permeability?

A

gases (CO2, N2, O2)
Lipids/fats (ie: hormones)
small uncharged molecules (ethanol)

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5
Q

What can cross through the membrane with moderate permeability?

A

water
urea

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6
Q

What can cross the membrane with low permeability?

A

polar organic molecules (sugars)

very very low permeability:
ions
charged polar molecules (amino acids, ATP, proteins, DNA/RNA)

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7
Q

What cannot cross through the membrane?

A

-> large amount of substances (ie: lots of water won’t be able to cross on its own)

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8
Q

what is the relationship between solute concentration and osmotic pressure? (proportional or inversely proportional)

A

proportional correlation
high solute concentration = high osmotic pressure
small solute concentration = low osmotic pressure

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9
Q

What are the 3 types of passive transport?

A
  1. diffusion
    -> happens in-out and out-in, as long as their one side with less concentration
    ex: glucose will go through facilitated protein
  2. osmosis
  3. facilitated diffusion (need the help of an integral membrane)
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10
Q

Explain passive transport : diffusion

A

does not need energy to happen (spontaneous)
substance move from high concentration to low concentration area

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11
Q

what is the direction of the net movement of molecules ?

A

in direction of the concentration gradient (high to low concentration)

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12
Q

what is the net movement of molecules at equilibrium?

A

zero
but exchanges still occur

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13
Q

Explain passive transport: osmosis

A

= diffusion of water across a membrane

from area of low solute concentration (lot of water) to an area of high solute concentration (few water)

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14
Q

what does free water mean in osmosis?

A

molecules that are free to use (bc they aren’t interacting with solute)

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15
Q

Passive transport

A

diffusion
- does not require energy
- will continue to diffuse until equilibirum
- in a biological pov, our body are never actually in equilibrium. bc your fat cells want as much fat inside the cell, not outside, it will diffuse in the direction that it needs for your body to work.
- movement from high to low concentration

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16
Q

Why is the flow of concentration not really in a biological equilibrium

A

in a biological pov, our body are never actually in equilibrium. bc your fat cells want as much fat inside the cell, not outside, it will diffuse in the direction that it needs for your body to work.

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17
Q

osmosis is limited to what substance?

A

water

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18
Q

osmotic pressure

A

ability that a molecule has to pull water towards it.
or
the amount of pressure you need to apply to stop water flow across a membrane

a side has more solute = a higher capacity to pull water towards it = higher osmotic pressure
minimum amount of force that you can apply

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19
Q

Tonicity

A

tonicity = ability of a solution to gain/lose water = measure of the osmotic pressure gradient

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20
Q

what is an isotonic solution ?

A

you want the concentration in and out of the cell to be the same, so that there is no net movement of water across the plasma membrane
= isotonic solution

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21
Q

what does an isotonic solution in plants look like?

A

plants are looking good, but no pressure from the vacuole to help them stay upright

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22
Q

what is an hypertonic solution?

A

hypertonic solution
more solute in solutions that in the cell, so osmotic pressure will be larger outside and pull the water outside = shrivelled cells

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23
Q

what does an hypertonic solution in plants look like?

A

plants are dying/dried out

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24
Q

what does an hypotonic solution in plants look like?

A

plants have a water vacuole = no bursting, the extra water just goes inside the vacuole
filled water vacuole = vacuole helps the plant stay rigid = cell is “turgid”

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25
Q

what is an hypotonic solution?

A

hypotonic solution
more solute in the cell than in the solution, so osmotic pressure is larger inside the cell and pull the water inside = lysed/burst

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26
Q

What is osmolarity

A

= what is the concentration of your solution?
=the total concentration of all solutes

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27
Q

iso-osmotic

A

of solutes outside = # of solutes inside the membrane

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28
Q

hyper-osmotic

A

of solutes outside is higher than # of solutes inside the membrane

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29
Q

hypo-osmotic

A

of solutes outside is lower # of solutes inside the membrane

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30
Q

Is ethanol hypotonic or isotonic?

A

hypotonic
regardless of the concentration of ethanol, it will end up being hypotonic and lead (log-term) to bursting of cells

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31
Q

what does plasmolyze mean in plants?

A

hypertonic solutions with shrivelled cells in plants

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32
Q

what does flaccid mean?

A

isotonic solutions with normal cells in plants

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33
Q

what does turgid mean?

A

hypotonic solution with lysed cells in plants

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34
Q

What does glycerol do

A

alcohol will enter the cell and cause hypertonicity and eventually cause the cell to burst

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35
Q

what is osmoregulation?

A

the control of water balance

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36
Q

Give 3 biological examples of osmoregulation.

A
  1. paramecium
    it is hypertonic to the water in which it lives (water rushes inside the paramecium)
    to avoid bursting, the paramecium’s cells have a contractile vacuole that pumps water out of the cell
    = Paramecium’s cells never burst
  2. ethyl alcohol has the same osmolarity as the cytoplasm of mammals, yet it is hypotonic to mammals (it enters the cell)
  3. cell walls of plant cells help maintain water balance
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37
Q

Explain passive transport: facilitated diffusion

A

use of transport proteins to speed up the movement of molecules across the plasma membrane

  • no energy required
    -high to low concentration (“down its concentration gradient”)

can occur with channel proteins or carrier proteins

  1. channel proteins
    no change to the channel ever
  2. carrier protein
    change the channel depending on what it is transporting

some channels stay open, some open/close and act as regulators

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38
Q

Explain facilitated diffusion: channel proteins

A
  • channel proteins act as hydrophilic corridors
  • allows specific molecules to cross.
  • usually gated, which gives the cell a regulation of what comes in/out

2 types of channel proteins:
1. Aquaporins (facilitate the diffusion of water)
2. Ion channels (open/close in response of stimulus)

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39
Q

Give 2 examples of a gated channel protein.

A
  1. voltage-gated channels in neurons
    = ion channels that only let ions pass through the membrane
  2. aquaporins
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40
Q

what does GLUT4 mean?

A

glucose transporter (a type of carrier protein)

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41
Q

Explain facilitated diffusion: carrier proteins

A
  • change their shape when binding to a solute
  • they can be:
    uniporter (ONE solute moves in one direction)
    symporter (2 solutes move in one direction)
    antiporter (2 solute move in opposite direction)
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42
Q

which protein is faster between channel and carrier? why

A

carrier is slower than channel because they change shape first

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43
Q

what does the speed of carrier proteins depend on?

A

the rate of carrier proteins depends on the number of carriers in the membrane

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44
Q

What are the 2 types of active transport?

A
  1. transporter pumps
    - requires energy
    - see ATP = active transport
    - moves from low to high concentration
    - requires protein channel
  2. bulk transport:
    - you package what youre transporting in molecules to release them outside of the cell
    -requires energy
    -endocytosis and exocytosis
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45
Q

What are the 2 types of transporter pumps?

A

Primary active transport
Secondary active transport

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46
Q

What is active transport?

A

moving of substances against their concentration gradient

with the help of specific integral proteins and an input of energy (ATP)

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47
Q

What are the 2 characteristics of primary active transport?

A
  1. carrier-mediated
  2. transport with energy from ATP
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48
Q

What are the 3 characteristics of secondary active transport?

A
  1. transport with co-transport
  2. transport with ATP
  3. ion gradient as a mean of transport
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49
Q

Explain primary active transport

A

requires ATP
1st: ATP gives a phosphate group to a carrier protein
2nd: the carrier protein changes conformation
3rd: the substance passes through the membrane against the gradient

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50
Q

How does NA+/K+ ATPase work?

A
  1. Downward shape of a pump = high affinity for Na+ from the cytoplasm
  2. phosphorylation of ATP occurs (ATP gives a phosphate group to the pump) & the pump changes conformation (flips upward)
  3. new conformation =
    low affinity for Na+ -> Na+ is released
    high affinity for 2 K+ from the extracellular matrix side
  4. the binding of 2 K+ triggers the release of the phosphate group, which restores the conformation of the pump (low affinity for K+)
  5. K+ is released into the cytoplasm

cycle repeats

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51
Q

What is an example of a primary active transport ion pump?

A

NA+/K+ ATPase

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52
Q

What are ion pump’s role in primary active transport?

A

generate a membrane potential

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53
Q

What is another name for ion pump?

A

electrogenic pump

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54
Q

What is the specific type of gradient that active transportation creates?

A

electrochemical gradient
electrical gradient (net charge inside vs outside)
concentration gradient (net concentration of Na+ higher outside the cell)

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55
Q

What processes do the electrochemical gradient drive?

A

cellular respiration
transmission of nerve impulse
muscle contraction

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56
Q

What is a membrane potential?

A

a voltage difference across a membrane
ex: cytoplasmic membrane = negative charge
extracellular matrix side = positive charge

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57
Q

What is the membrane potential generated by Na+/K+ ATPase?

A

pumps sends 3 Na+ out and brings 2 K+ in
= positive exterior
= negative interior

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58
Q

What are the differences between passive and active transport?

A

passive is in the direction of the gradient, so no energy input

active is always against the gradient, so energy input is needed. also, active needs a carrier/transporter protein

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59
Q

what happens first, primary active or secondary active transport?

A

Primary active transport must first happen to create concentration gradient
then secondary active transport can happen with the use of concentration gradient

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60
Q

Explain secondary active transport

A

using an existing gradient (which stored energy) to drive the active transport of a solute

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61
Q

What is an example of a secondary active transport in plants?

A

plants
First step:
they use ATP to pump H+ against the gradient (out of the cell) through a proton pump
= high [H+] outside the cell

Second step:
Now, as the H+ naturally diffuse back inside the cell into its gradient , the sucrose will “sneak in” and go inside the cell

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62
Q

What type of pump is the sucrose-H+ transporter pump? (active/passive transport protein, uniporter/symporter/antiporter protein)

A

active transporter protein
(as soon as you hear “pump” you know its active transport)
and symporter bc it transports H+ and sucrose inside the cell (one direction)

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63
Q

What is an example of secondary active transport that happens with the help of the Na+/K+ ATPase pump

A

Na+/K+ ATPase created a sodium gradient (low [Na+] inside the cell)

Na+ outside the cell will thus naturally diffuse through its gradient (inside the cell)

a 2 Na+/glucose symporter will take the opportunity and provide a pathway for Na+ to diffuse into the cell.

glucose will sneak in and diffuse into the cell using the same pump

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64
Q

Why does glucose need a sodium gradient to happen (in the human intestine)?

A

we want glucose to go inside the intestine, which is a net movement against its gradient

against gradient = need a transport protein, can’t happen spontaneously

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65
Q

What happens if a drug inhibits sodium deposit in the intestine?

A

no sodium = no sodium gradient = no 2Na+/glucose symporter = glucose will deposit elsewhere = death

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66
Q

Explain active transport: bulk transport

A

primary/secondary active transport & passive transport are not efficient enough to let large molecules, viruses and bacteria cross the membrane.

= Bulk transport comes in handy
-> large molecules enter the cell by endocytosis
-> exit by exocytosis
-> both processes requires ATP

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67
Q

Explain endocytosis

A
  1. large molecule = trapped on the surface of the outside membrane
  2. membrane folds in on itself and forms a vesicle around the large molecules
  3. the vesicle buds off the membrane and enters the cell
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68
Q

explain exocytosis

A
  1. materials too large to diffuse out the cell accumulate on the surface of the inside membrane
  2. a vesicle forms around them and buds to the membrane
  3. the vesicle opens and empties itself into the extracellular environment
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69
Q

What is exocytosis useful for?

A

membrane proteins and phospholipids are incorporated into the membrane by exocytosis

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70
Q

What are the 2 types of exocytosis?

A
  1. regulated
    only occurs in response to a signal
    ie: insulin release by pancreatic cells & neurotransmitter release by neurons
  2. constitutive
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71
Q

What are the 3 types of endocytosis?

A
  1. phagocytosis
    LARGE molecules/bacteria
    use of a lysosome
  2. pinocytosis
    “cell-drinking”
    FLUID gets surrounded by a vesicle
  3. receptor-mediated endocytosis
    specific mechanism
    specific molecules bind to their respective receptors on the outside surface of the membrane -> vesicle forms -> endocytosis
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72
Q

What is an example of receptor-mediated endocytosis?

A

lipoproteins that transport cholesterol

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73
Q

Can you name examples of each of the two classes of membrane proteins?

A
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74
Q

Can you explain the assymetrical distribution of the cytoplasmic and extracellular faces (leaflets)
of the plasma membrane?

A
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75
Q

Can you explain the six major functional classes of membrane proteins?

A
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76
Q

Describe how the plasma membrane (phospholipid bilayer, proteins, ect.) is made within a
eukaryotic cell. If a glycoprotein or glycolipid is being made for the plasma membrane, where would you expect to see the carbohydrate part of a glycoprotein or glycolipid in a transport vesicle (inside? outside?) and where does this end up once the vesicle fuses with the plasma membrane?

A
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77
Q

Does diffusion typically reach equilibrium in cells? Explain.

A
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78
Q

Can you list factors that can affect the rate of diffusion of a substance? What effect do they have on the rate? Why do they have this effect?

A
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79
Q

Compare the kinetics of simple and facilitated diffusion using a graph that illustrates the
diffusion rate vs. the concentration of diffusing substance (on one side of the membrane) for
each mechanism. Explain why this relationship is observed for each.

A
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80
Q

Does osmosis typically reach equilibrium in cells? Explain.

A
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81
Q

Does the mechanism of a pump more closely
resembles a channel or a carrier?

A

carriers
bc they undergo conformational changes, like pumps

carriers can transport molecules against their gradient (active transport, using ATP) or into its gradient (passive). pumps are always against

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82
Q

What is the main function of membranes?

A

give structure, which allows metabolic order
ex: enzymes are kept in a specific metabolic pathway by the membrane

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83
Q

what are the 2 functions of the plasma membrane?

A

separate living cells from their surroundings

selective permeability (passive transport and active transport)

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84
Q

what is the plasma membrane composed of?

A

phospholipid bilayer
protein
stereoid lipids

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85
Q

what is the structure of the phospholipid bilayer?

A

amphipathic
hydrophilic head = phosphate group
hydrophobic tails = fatty acid chains

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86
Q

is a membrane fluid? what experiment proved whether it was fluid or not fluid?

A

fluid
1 mouse cell and a human cell were fused
each membrane was labelled
after fusion, we observed that the labelled plasma membrane moved = fluid membranes
conclusion : plasma membrane proteins must be able to move around the phospholipid bilayer

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87
Q

what does the membrane fluidity depend on?

A

on the lipid components

hot temperature
-> membrane is too fluid and doesn’t hold shape

cold temperature
-> membrane is rigid, not flexible
-> it might break

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88
Q

what happens to the membrane when it reaches a critical point?

A

critical point = very low temperature
the membrane becomes solid gel
transport across the membrane stops

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89
Q

how do organisms maintain optimal fluidity?

A

they change the fatty acid content of their membrane lipids (change # of unsaturated fatty acids)

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90
Q

what is homeoviscous adaptation?

A

temperature goes down (cold)
increase the proportion of unsaturated fatty acids
membrane stays fluid

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91
Q

how can fatty acid chain length affect membrane fluidity?

A

the longer the chain, the less fluid the membrane
bc longer chain = more van der Waals forces between chains = strong attraction = less fluid

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92
Q

what happens to the membrane fluidity if the # of double bonds in fatty acids is increased?

A

more double bonds = more unsaturated = more fluid

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93
Q

What is a fluidity buffer? give an example

A

cholesterol

at high temperature
it stabilizes the membrane
OH- group of cholesterol binds to a nonpolar head
this adds stability = less fluid

at low temperature
cholesterol gets in between fatty acid chains
this reduces van der Waals interaction = less attraction between chains = more fluid

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94
Q

what are the 2 types of membrane proteins?

A

integral (inside)
peripheral (outside)

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95
Q

what are the characteristics of integral proteins?

A

bound to the membrane (in the middle of the lipid bilayer)
amphiphatic:
- hydrophilic region qui depasse le lipid bilayer et touche le cytoplasm/l’extérieur of the cell
- hydrophobic region in the middle of the bilayer that interacts with fatty tails

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96
Q

what is the difference between transmembrane integral proteins and integral proteins?

A

transmembrane = extend all the way through the membrane = dépasse à l’extérieur de la cellule et dans le cytoplasm

normal integral = embedded inside the bilayer, mais ne dépasse pas

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97
Q

what is the most common transmembrane structure?

A

alpha helix

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98
Q

in the alpha-helix structure of a transmembrane protein, where is the C-terminus and the N-terminus oriented towards?

A

C-terminus on the cytoplasmic side (inside the cell)
N-terminus on the extracellular side (outside the cell)

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99
Q

what are 2 examples of integral proteins?

A

aquaporins
transport water in/out the cell by osmosis

glycoproteins
its sugar is oriented towards the extracellular matrix

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100
Q

what are the characteristics of peripheral proteins?

A

located on the surface of the membrane (outer/inner surface)

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101
Q

what is th asymmetry of the bilayer due to?

A

proteins are inserted into different sides (p-face / e-face) of the membrane in an asymmetric orientation

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102
Q

What differs from one side of the bilayer to another?

A

one side has more proteins embedded to it
different proteins on it = membrane with different characteristics

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103
Q

What is the P-face vs E-face of a bilayer?

A

e-face = towards extracellular matrix
p-face = towards cytoplasm

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104
Q

which organelle makes the peripheral proteins on the inner surface of the membrane?

A

free ribosomes in the cytoplasm

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105
Q

which organelle makes the peripheral proteins on the outer surface of the membrane?

A

ribosomes in the rough ER

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106
Q

which organelle makes integral proteins?

A

ribosomes in the rough er

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107
Q

why are cell-cell recognition proteins important ?

A

1- give identification tags to cells for them to be recognized by other cells

2- the immune system can recognize and reject foreign

3- cells can sort themselves into tissues and organs

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108
Q

how do cell-cell recognition work?

A

outer portion of plasma membrane contains glycoproteins and glycolipids that vary from:
species to species
individual to individual of the same species
from cell to cell of the same individual

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109
Q

how do autoimmune disease occur?

A

immune system have antibodies.
the antibodies thinks its own healthy tissue is a foreign cell and attacks it.

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110
Q

gives an example of autoimmune disease

A

rheumatoid arthritis
antibodies attack the synovial membrane of joints

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111
Q

what is intercellular joining?

A

membrane proteins of 2 different cells hook together via different junctions
long-lasting binding

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112
Q

how is plant cell junctions in intercellular joining called?

A

plasmodesmata

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113
Q

what are plasmodesmata?

A

channels where 2 plant cells can communicate rapidly
water and small molecules can pass through plasmodesmata

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114
Q

how are the animal cell junctions in intercellular joining called? (name 3)

A
  1. demosomes
  2. tight junctions
  3. gap junctions
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115
Q

what are desmosomes?

A

junction that allows intercellular joining
1. attach animal cell to another animal or
attach animal cell to the extra cellular matrix
2. very strong junctions
3. explain more structure***

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116
Q

what are tight junctions?

A

junction that allows intercellular joining
so tight that substances cannot leak between them
hold the cell together in physical contact, forming a sheet of tissue

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117
Q

what are biological examples of tight junctions?

A

stomach uses tight junctions to prevent its very acidic secretions to leak on organs/tissues near it

brain uses tight junctions to prevent substances in the blood to enter the brain

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118
Q

what are gap junctions?

A

form a sort of bridge between animal cells where substances can pass through rapidly

similar to desmosomes, but they cover a narrower space

allows rapid chemical/electrical communication

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119
Q

what are examples of gap junctions?

A

cells in pancreas are linked by gap junctions
one cell receives a signal to secrete insulin = signal is passed to other pancreatic cells

gap junctions of heart muscle cells allow flow of ions & help synchronize contractions of the heart

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120
Q

what are proteins that do not move freely within the plasma membrane good for?

A

they help keep the membrane in place

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121
Q

what are proteins that do not move freely within the plasma membrane linked to?

A

they are covalently liked to the cyto-skeleteon and to fibers of the extracellular matrix

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122
Q

what is the structure of the extracellular matrix?

A

ECM is made of :
carbohydrates (fibronectins, a type of glycoprotein)
fibrous proteins (collagen)

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123
Q

What do fibronectins in the ECM bind to?

A

they bind to proteins called integrins

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124
Q

What are integrins?

A

integral transmembrane proteins

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125
Q

what are the 4 functions of integrins?

A
  1. membrane receptors for the ECM
    - activate pathways that allows information to travel from the ECM to the cell
  2. help cell movement
  3. organize the cytoskeleton
  4. anchor the ECM to the microfilaments of the internal cysto-skeleton
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126
Q

what is an example of a dysfunctional ECM?

A

cancer cells that cannot anchor properly to the ECM spread through the body

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127
Q

 Describe the activity of signal receptors. Compare intracellular and extracellular receptors. What
physical characteristics (polar/non-polar amino acids/-helices or not) would you expect for
signaling molecules for each type? Why?
 List and describe the activity of the two main types of membrane receptors discussed in class.
How do GPCRs and TKRs differ from each other? What do G-proteins do? What do they
hydrolyze? What does dimerization mean?
 Can you define a second messenger and discuss how these are involved in cell signaling? List the
2 second messengers discussed in class and describe how their concentrations in the cytosol can
build up during cell signaling.
 What is a phosphorylation cascade and how are these are involved in cell signaling? What is the
term used for enzymes that can phosphorylate other proteins?
 What is signal amplification and why it is possible during signal transduction?
 List the main molecular mechanisms for how a cell changes its activity in response to a signal.
Which of these would be considered a nuclear response? Cytoplasmic response? Which one
takes longer?
 Describe signal deactivation and its importance in cell signaling. Describe how a signaling
pathway can be deactivated at its various steps.
 Describe how signaling pathways form signaling webs. Describe pathway branching and
pathway crosstalk.
 Explain how one signaling molecule can have different effects on different cell types and lead to
different effects in different organs.
 Can you name specific examples of when cell-signaling is abnormal?

A
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128
Q

What is the purpose of cell-cell signalling in unicellular organisms?

A

to make sure cells can coordinate with one another and work as a team to accomplish a task

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129
Q

Explain how cell-cell signalling in unicellular organism work.

A

when the concentration of autoinducer made by a bacteria reaches a high level, the population coordinate a response

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130
Q

What are the different types of responses in a cell-cell signalling (unicellular)?

A
  • sporulation
  • exchange of plasmid DNA
  • bioluminescence
  • virulence
  • production of biofilms
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131
Q

What are 2 examples of molecules used in cell signalling in multicellular organisms?

A
  1. pheromones
    - chemicals released by organisms
    - used for sexual reproduction/mark territory
    - ie: male luna moth detects pheromone released by a female
  2. plants
    - release volatile compounds when attacked by herbivores
    - = a way to ask their “friends” for help
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132
Q

What are different types of local cell-signalling?

A
  1. though cell junctions
  2. cell surface molecules
  3. paracrine signalling
  4. synaptic signalling (neurotransmitters)
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133
Q

Explain local cell-signalling: cell junction

A

adjacent cells communicate by transferring signalling molecules through cell junctions
= using gap junctions (animals) or plasmodesmata (plants)

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134
Q

Explain local cell-signalling: cell-to-cell recognition

A

the surface marker of one cell binds to the receptor of another
= alters cell activity

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135
Q

what is cell-to-cell recognition important for?

A

embryonic development
immune response

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136
Q

Explain local cell-signalling: paracrine signalling

A

a cell secretes local regulator molecules that travel through the ECM and reaches another cell

= the local regulator molecule affects the second cell

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137
Q

what is an example of paracrine signalling?

A

the release of growth factor by a secretory cell

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138
Q

Explain local cell-signalling: synaptic signalling

A
  1. neurotransmitters are released
  2. they act as chemical messenger:
  3. the neurotransmitter is released into the synapse
  4. the neurotransmitter binds to the receptors of the target cell
    = allows neurons to communicate with other cells.
139
Q

What is the type of signalling involved in long-distance cell-signalling?

A

endocrine signalling (hormones)

140
Q

Explain long distance cell-signalling: endocrine signalling

A

hormones are specific
= they only affect cell with specific receptors for them to bind to (called target cells)
= lock&key principle

different cells = different target cells, but 1 hormone can bind to receptors in different target cell
= 1 hormone will = different response depending on the kind of cell

141
Q

name a hormone with a wide range of targets? what does that mean

A

sex hormones
many different cells in the body have receptors that are compatible with testosterone
but each cell’s receptor will respond differently to the binding of testosterone

142
Q

name a hormone with a narrow range of targets? what does that mean

A

gastrin in the stomach
pretty much only one type of cell that has the receptors that are compatible to gastrin
= only one response possible

143
Q

Can you list the four main stages in cell-signalling?

A
  1. Reception
    signalling molecule binds to receptor of target cell
  2. Transduction
    message is transmitted & amplified into the cell
    involves multistep pathway
  3. Response
    target cell alters its activity
  4. Signal deactivation
    signalling is turned off
144
Q

Explain the first stage of cell-signalling (Reception)

A
  • a signalling molecule (ie: hormone) approches its target cell
  • it binds to the receptor protein the target’s cell surface or its inside
  • binding leads to a change in the shape of the receptor protein = active shape
  • = can interact with the inside of the cell
145
Q

Explain the second stage of cell-signalling (transduction)

A
146
Q

Explain the third stage of cell-signalling (Response)

A
147
Q

Explain the fourth stage of cell-signalling (Signal deactivation)

A
148
Q

What types of signalling molecules would have
their receptors on the surface and those within?

A

surface
= hydrophilic signalling molecule (ie: GASTRIN, neurotransmitters, insulin/glucagon)
= bc they can’t cross the membrane (polar)

within
= hydrophobic (ie: STEROIDS\THYROID, TESTOSTERON, ESTROGEN)
= can cross the membrane (bc non polar)

149
Q

What type of signalling molecules is directly involved in gene expression? How?

A

intracellular signalling
they activate transcription factors:
up-regulation of genes = more proteins made
down-regulation of genes = less proteins made

150
Q

how is signalling molecule with receptors on the surface called?

A

cell surface signalling

151
Q

how is signalling molecule with receptors on the inside called?

A

intracellular signalling

152
Q

what are the 2 major types of cell-surface signalling?

A

G protein-coupled receptors (GPCRs)
receptor tyrosine kinase (RTKs)

153
Q

how does a G protein gets activated?

A

a signalling molecule binds to the receptor of a GPCRS, which turns it into its activated shape on the extracellular side.

this change allows the GPCRs to interact with a G protein from the cytoplasmic side

the G protein is previously bound to a GDP. once it binds to the GPCRs, the GPCRs replace the GDP for a GTP (GTP = abundant molecule in the cytoplasm).

154
Q

Once the G protein has been activated, what is the next step in transduction signalling

A

the activated G protein detaches from
the GPCRs
->diffuse along the membrane
-> attach to an enzyme
-> the enzyme becomes activated and can trigger the next step in signal transduction

155
Q

What happens to the G protein after a cellular response has been emitted?

A

the G protein hydrolyzes their GTP back into GDP
= inactivates itself

156
Q

what is a way to regulate the activity of enzymes?

A

G proteins are GTPase enzymes
= they hydrolyze their GTP to GDP
= inactivate theirselves

157
Q

what are the characteristics of G protein-coupled receptors (GPCRs) ?

A
  • present in every type of cell in our body
  • composed of 7 transmembrane alpha-helices joined by intracellular and extracellular loops
  • each type of GPCRs
    = specific active site conformation & specific cytoplasm conformation
    = bind to a different ligand
158
Q

what are functions of GPCRs in the body?

A

embryonic development
sensory reception
autonomic nervous system transmission
mood regulation

159
Q

are GPCRs peripheral proteins or integral proteins?

A

peripheral

160
Q

if a G protein is bound to a GDP, is it active or inactive?

A

inactive

161
Q

if a G protein is bound to a GTP, is it active or inactive?

A

active

162
Q

Receptor tyrosine kinases are kinase enzymes. But what are kinase enzymes?

A

enzyme that catalyze the transfer of a phosphate group

163
Q

what is the key difference between GCPRs and RTKs?

A

RTKs have the ability to initiate multiple signalling cascades from a single ligand-binding event

164
Q

What is the structure or RTKs?

A
  • the tyrosine amino acid end is in the cytoplasmic region
  • the alpha helix domain is in the plasma membrane
  • the ligand-binding site is in the extracellular end
165
Q

what is the difference in configuration of the active RTKs vs inactive RTKs?

A

inactive = monomer
active = dimer

166
Q

how to dimerization of RTKs occur?

A

a signalling molecule bind to the receptors of the RTKs
one monomer RTKs now has high affinity for the other monomer RTKs = they dimerize

167
Q

how are dimerized RTKs able to trigger a cellular response?

A
  1. dimerization activates the tyrosine end of the RTKs
  2. each tyrosine bind to a phosphate group (from an ATP)
  3. specific proteins bind to the phosphorylated tyrosine end, which turns the proteins in its active form
  4. each protein is now able to emit a cellular response
168
Q

How are the molecules in a transduction pathway called?

A

relay (effector) molecules

169
Q

Why is transduction said to amplify the response? How many molecules in each step of the signalling process?

A

reception = 1 molecule

transduction = cascade of reactions where more molecules are activated in each step
(1 step = 10^2 molecules
last step = 10^6 molecules)

response = 10^8 molecules

total = 1 molecule -> 10^8 molecules

170
Q

What is the first step of transduction?

A

activation of a G protein
= 1 molecule (from reception) into 10^2 molecules

171
Q

What is the second step of transduction?

A

activation of adenylyl cyclase
= 10^2 molecules

172
Q

What is the third step of transduction?

A

ATP into cyclic AMP
= 10^4 molecules

173
Q

What is the fourth step of transduction?

A

activation of protein kinase A
= 10^4 molecules

174
Q

What is the fifth step of transduction?

A

activation of phosphorylase kinase
= 10^5 molecules

175
Q

What is the sixth step of transduction?

A

activation of glycogen phosphorylase
= 10^6 molecules

176
Q

What is the step of reception?

A

epinephrine binds to GPCRs
= 1 molecule

177
Q

What is the step of response?

A

Glycogen -> glucose-1-phosphate

178
Q

how is cAMP made in transduction pathways?

A

removing 2 phosphate groups from ATP

179
Q

how does cAMP differ from the other steps of a transduction pathway?

A

it is not a protein; it is a water-soluble molecule

180
Q

how can cAMP be deactivated? why is this important?

A

an enzyme called phosphodiesterase converts cAMP to AMP = it deactivates cAMP once enough enzymes have been made

bc otherwise way too much enzymes will be produced

181
Q

apart from cAMP, what is another type of second messenger? where is it found?

A

CA2+
higher [Ca2+] in the smooth ER & mitochondria than in the cytosol

182
Q

explain the link between phosphorylation and how it creates this cascade event in transduction

A

the transduction cascade is a series of phosphorylation: the signalling molecule attaches to the receptor, and an activated relay molecule activates the first kinase protein. then the activated kinase 1 transfers an phosphate group from ATP to a inactivate kinase protein and ainsi de suite.

183
Q

how do Ca2+ build up in the cytosol?

A

neurotransmitter lead to the release of Ca2+ into the cytosol, which creates a cell response

184
Q

What types of response can a cell produce?

A

catalysis by an enzyme
rearrangement of cytoskeleton
activation of specific genes in nucleus

185
Q

what are the 2 categories of response in a cell?

A
  1. nuclear
    change in which genes are expressed = slow
  2. cytoplasmic
    activation/deactivation of target protein that are in the cytoplasm = fast
    ie: glycogen into glucose-1-phosphate
186
Q

how can the same signalling molecule create different response? what does the response depend on? give an example

A

depend on the type of receptor and type of molecule involved

epinephrine = different effects throughout the body:
liver = increase blood glucose level
muscle cell = increase/decrease flow of blood to different part of the body

187
Q

what is the 4th step in cell signalling ?

A

signalling deactivation
= turn cell signals off

188
Q

What is apoptosis?

A

programmed cell suicide
protects the animal from abnormal/infected cells

189
Q

what are the 2 possible pathways in abnormal cell signalling in cell division?

A

positive regulators (kinase) are over-activated and become oncogenic

negative regulators called tumor suppressors are inactivated

190
Q

Can you name specific examples of when cell-signaling is abnormal?

A

cancer

191
Q

What are 3 ways cells generate atp (energy)?

A

glycolysis with fermentation
aerobic cellular respiration
anaerobic cellular respiration

192
Q

what are 2 types of fermentation?

A

alcohol fermentation
= produce ethanol + organic acids
= happens in bacteria (anaerobic conditions)

lactic acid fermentation
= produce lactacte
= happens in fungi, bacteria and animals (anaerobic)

193
Q

define glycolysis with fermentation

A

organic compounds (ie: monosaccharide) are incompletely broken down to produce few ATP

194
Q

is glycolysis with fermentation aerobic or anaerobic?

A

anaerobic

195
Q

what does aerobic & anaerobic mean

A

aerobic = requires of oxygen
anaerobic = no use of oxygen

196
Q

define aerobic cellular respiration

A

breakdown of glucose to produce many ATP
- in eukaryotes
- some prokaryotes

197
Q

how many ATP per glucose in aerobic cellular respiration?

A

32

198
Q

how many ATP per glucose in anaerobic cellular respiration?

A
199
Q

what is the most efficient catabolic pathway?

A

aerobic cellular respiration

200
Q

define anaerobic cellular respiration?

A
  • breakdown of glucose to produce many ATP by using nitrate or sulfate instead of oxygen
  • some prokaryotes
201
Q

what is the formula of aerobic cellular respiration?

A

C6H12O6 + 6 O2 + ADP + Pi -> 6 CO2 + 6 H2O + Energy

*glucose here can be replaced by any carbohydrates, fats and protein

202
Q

why doesn’t aerobic cellular respiration (breakdown of glucose) happen in one simple step?

A
  • the body temperature is not high enough to start the instantaneous process (of combining H with O)
  • if energy is released at once, it cannot be used efficiently for constructive work
203
Q

what powers the cellular work in cellular respiration? where is the energy coming from?

A

phosphorylation
transfers of electrons

204
Q

what are the 3 electron carrier molecules ? What are they used for?

A

NAD+
FAD
dehydrogenases

electrons are removed from glucose. each electron travel with a H+. the electron & H+ combo does not directly transfer to oxygen -> it needs an electron carrier

205
Q

what is the most versatile electron acceptor?

A

NAD+

206
Q

NAD+ is a coenzyme to enzymes called ____________

A

dehydrogenases

207
Q

What are the 2 forms in which NAD+ can cycle between? the oxidized and reduced forms

A

NAD+ = oxidized form
NADH = reduced form

208
Q

What are the 2 forms in which FAD can cycle between? the oxidized and reduced forms

A

FAD = oxidized form
FADH2 = reduced form

209
Q

FAD & NAD+ can temporarily store free energy in their oxidized or reduced form?

A

reduced
FADH2 and NADH

210
Q

how do the electron carriers dehydrogenases work?

A

by oxidizing the glucose molecule
in other words:
by removing a pair of hydrogen (H2, which = 2 electrons and 2 protons) from the glucose molecule

the enzyme dehydrogenase then delivers the 2 electrons and 1 proton to its coenzyme NAD+.
NAD+ + 2H -> NADH + H+

the extra proton is released into the surroundings

211
Q

as NADH transfers electrons to molecules, what else gets transferred?

A

energy

212
Q

what happens when you bring H2 and O2 together?

A

cellular respiration: goal = bring H2 and O2 together
in nature:
electrons from hydrogen are pulled to the electronegative oxygen = creates “explosive” energy

213
Q

why is electron transport chain crucial in cellular respiration?

A

if NADH brought the electrons directly to oxygen, the cell would not be able to harness the explosive energy
= too much for the cell = uncontrolled

ETC “breaks” the explosiveness of the bringing of electrons to oxygen into several steps
= controlled

214
Q

define the structure of ETC

A

proteins built in the inner membrane of the mitochondria (animals) or the plasma membrane (prokaryotes)

215
Q

how does the ETC work?

A

dehydrogenase enzyme transport electrons removed from glucose to NADH at the top (high energy) end of the chain.

O2 captures the electrons & the H+ from NADH + H+ at the bottom (lower energy end)

every electron transfer = electrons energy level decreases = release of energy = make ATP

216
Q

how can electron travel downhill, from one carrier protein to the other in ETC?

A

each carrier protein is more electronegative than the previous
= pulls the electrons towards it

217
Q

a carrier protein is said to ______ its previous “uphill” neighbour

A

a carrier protein is said to oxidize its previous “uphill” neighbour by pulling its electrons

218
Q

what are the different components of the mitochondria? start from the outside and work your way to the inside

A

porin (on the outer membrane)
outer membrane
inter-membrane space
cristae
inner membrane
atp synthase (on inner membrane)
ETC (on inner membrane)
matrix (liquid inside the inner membrane)
ribosome
circular DNA

219
Q

what are the components surrounding the ETC?

A

ETC = in the inner membrane
inter-membrane space = outside of the inner membrane
matrix = inside of the inner membrane

220
Q

in which step of the cellular respiration multiple cycle is ETC found?

A

oxidative phosphorylation

221
Q

what is substrate-level phosphorylation?

A

when a small amount of atp is formed directly in the process of glycolysis and in the citric acid cycle

222
Q

what is the difference between oxidative phosphorylation and susbtrate-level phosphorylation?

A

in oxidative phosphorylation:
an enzyme transfers an inorganic phosphate group to ADP

but in susbtrate-level phosphorylation:
an enzyme transfers a phosphate group from a substrate molecule to ADP
= ATP

223
Q

how much of atp is generated by substrate-level phosphorylation?

A

10%
the remaining 90% comes from oxidative phosphorylation

224
Q

how does oxidative phosphorylation occur?

A

ETC oxidizes NADH & FADH2
= H+ gradient (a lot of H+ in the inter membrane space)
= lots of free energy
= lower activation energy needed to for ATP synthase
= 32 ATP molecules!!

225
Q

what are the 4 stages of the aerobic cellular respiration?

A
  1. glycolysis
  2. pyruvate oxidation
  3. citric acid cycle
  4. oxidative phosphorylation
226
Q

what is the only stage that happen outside the mitochondria? where is it located exactly?

A

glycolysis
in the cytoplasm

227
Q

define the process of glycolysis

A

the cutting of the big glucose molecule (6 carbons) into 2 smaller molecules (3 carbons)
glucose -> 2 pyruvate + 2 atp + 2 NADH

228
Q

glycolysis if O2 vs if no O2 , what happens?

A

O2
glycolysis produces pyruvate and nadh, 2 molecules with chemical energy stored.
that energy is taken into the mitochondria and aerobic cellular respiration takes place
= 32 atp

no O2
pyruvate and nadh stay in the cytoplasm to make fermentation
= 2 atp

229
Q

what are the 2 phases of glycolysis?

A

energy investment phase
energy payoff phase

230
Q

explain the energy investment phase of glycolysis

A

6-carbon glucose is broken down into 2 3-carbon sugars (“G3P”)

you need energy to breakdown glucose, so you need to invest atp molecules in the rxn

231
Q

what does the energy payoff phase yield?

A

substrate level phosphorylation successfully made 4 molecules of atp
2 molecules of NADH are formed
2 molecules of pyruvate are formed

232
Q

what does the energy investment phase of glycolysis yield?

A

1 molecule of glucose
+
2 molecules of atp
= 2 ADP + 2 G3P

233
Q

what are 2 important regulatory enzymes in glycolysis?

A

hexokinase

PFK (phosphofructokinase)

234
Q

how does glucose enter the cell?

A

through a carrier protein called GLUT4

235
Q

what is the first step in glycolysis in which atp is CONSUMED?

A

Glucose + ATP -> G6P+ ADP

as soon as glucose enters the cell, hexokinase takes a phosphate group from an atp and adds it to glucose
= glucose is now very charged = can’t escape, it must proceed forwards
= this also maintains the glucose concentration gradient

236
Q

what are the intermediate step in the energy investment phase, from a glucose until right before the energy pay-off phase?

A

glucose
atp + hexokinase
G6P (glucose-6-phosphate)
F6P (fructose-6-phosphate)
atp + PFK
G3P (glucose-3-phosphate)

237
Q

explain the energy pay-off phase of glycolysis

A

before it starts, we have 2 G3P
each G3P rearrange & form a pyruvate
all whilst reducing 1 NAD+ into 1 NADH
all whilst producing 2 ATP from 2 ADP

238
Q

what is the net yield of the energy pay off phase?

A

2 G3P become:
2 NADH
4 ATP

239
Q

what are the intermediate step in the energy pay-off phase, from a G3P until right before the pyruvate oxidation cycle?

A

G3P
2 NADH
2 ATP
pyruvate kinase forms pyruvate (and releases 2 ATP)

240
Q

in the energy pay-off phase, the $ of each molecule is ______?

A

doubled

241
Q

how does PFK regulation work?

A

AMP is a molecule that activates PFK
citrate inhibits PFK

when [citrate] or [atp] are too high, PFK is allosterically inhibited = stops the process of cellular respiration

when [citrate] or [atp] drop, [amp] increases, which activates PFK, which starts cellular respiration again

242
Q

in which organisms is glycolysis enough source of energy?

A

yeast
bacteria
(glycolysis by fermentation)

243
Q

What is the next step after glycolysis and right before pyruvate oxidation?

A

each pyruvate formed must enter the mitochondrion’s inner membrane

244
Q

Where does each of the 4 steps of cellular respiration occur?

A

glycolysis = cytoplasm
pyruvate oxidation = matrix
citric cycle = matrix
oxidative phosphorylation = inner membrane of mitochondrion

245
Q

How does the pyruvate pass through the outer membrane of the mitochondrion?

A

by facilitated diffusion

246
Q

How does the pyruvate pass through the inner membrane of the mitochondrion?

A

via pyruvate/H+ symporter carrier protein (secondary active transport)
high [H+] in the inter-membrane space and low [H+] in the matrix
= concentration gradient
= pyruvate “sneaks in” and profits from the natural movement of H+ down its gradient

247
Q

what happens if there is no O2 to accept electrons at the end of the ETC?

A

no H+ gradient, so pyruvate won’t be able to cross the inner membrane and get to the matrix;
it will stay in the inter membrane space

248
Q

what is the 1st stage of pyruvate oxidation?

A

the pyruvate enters the mitochondrion
- carboxyl group of pyruvate has very few chemical energy and is thus easily removed
- carboxyl group then diffuses out of the cell into blood

249
Q

what is the 2nd stage of pyruvate oxidation?

A
  • what’s left of pyruvate molecule is oxidized into acetate
  • an enzyme transfers 2 e- & 1 H+ to NAD+ -> NADH
250
Q

what is the 3rd stage of pyruvate oxidation?

A

co-enzyme A (coA) attaches to acetate and turns it into acetyl coA

acetyl coA = now very high potential energy

251
Q

What is the total yield of pyruvate oxidation ?

A

2 pyruvate (3C) -> 2 acetyl-coA (2C)
Pyruvate + coA + NAD+ -> acetyl-coA + CO2 + NADH + H+

yield for 1 glucose:
2 CO2
2 NADH

252
Q

what are the inputs vs outputs of the Krebs cycle?

A

inputs
2 acetyl-coA (from 2 pyruvate)

outputs
2 atp & 6 NADH
4 CO2 & 2 FADH2

253
Q

what happens to acetyl-coA once the pyruvate oxidation stage is done?

A

2 options:
1. enter the Krebs cycle
2. enter different metabolic pathways to make fatty acids and cholesterol (when acetyl-coA is in excess)

254
Q

in each step of the Krebs cycle, which carbon is the one that leaves (to form CO2)?

A

the COO- that is attached to a tertiary carbon
= carbon from the oxaloacetate end

NOT the COO- that is at the top of the molecule (this one is attached to a secondary carbon)
= carbon from the acetyl coA end

255
Q

the Krebs cycle is the regeneration of which molecule?

A

oxaloacetate

256
Q

what are the 3 goals of the Krebs cycle?

A
  1. complete the breakdown of glucose
  2. store electron energy (by oxidizing NAD+ and FAD into NADH and FADH2)
  3. create atp by substrate-level phosphorylation
257
Q

what is the first step of the Krebs cycle?

A

acetyl-coA (2C) binds its acetyl end to oxaloacetate (4C)
= forms citrate (6C)

258
Q

what enzyme is used in the first step of the Krebs cycle?

A

citrate synthase

259
Q

What is the relationship between citrate and citric acid?

A

citrate is the ionized form of citric acid

260
Q

Describe the 6 steps of the Krebs cycle

A
  1. formation of citrate using the enzyme citrate synthase
    = 6 Carbons
  2. 1 CO2 is released & 1 NADH is formed
    = 5 Carbons
  3. 1 CO2 is released & 1 NADH is formed
    = 4 Carbons
  4. ADP is made by substrate-level phosphorylation
  5. FADH2 is formed
  6. NADH is formed

oxaloacetate is left

261
Q

what is the net yield of the Krebs cycle?

A

for 1 glucose molecule:
2 atp
6 NADH
2 FADH2
4 CO2

262
Q

how many CO2 molecules are produced in each stage of the glucose catabolism? for 1 glucose molecule

A

for 1 glucose molecule :

glycolysis = 0
pyruvate oxidation = 2
Krebs cycle = 4

263
Q

how many atp are produced from glycolysis and Krebs cycle together?

A

4 atp only (per glucose molecule)

264
Q

what are the 2 processes involved in oxidative phosphorylation

A

electron transport chain
oxidizes NADH and FADH2
creates a H+ gradient across the inner membrane

chemiosmosis
phosphorylation of ADP by ATP synthase

265
Q

what molecule(s) link the Krebs cycle to oxidative phosphyrlaton?

A

NADH and FADH2

266
Q

what is the [H+] across the mitochondrion? where is the concentration gradient ?

A

outer membrane
inter-membrane space = high [H+]
inner mitochondrial membrane (concentration gradient)
mitochondrial matrix = low [H+]

267
Q

what is the first step of the ETC?

A

NADH (from the Krebs cycle) comes near the inner membrane.
NADH is oxidized into NAD+

268
Q

what is the second step of the ETC?

A

1 e- and 1 H+ from NADH oxidation goes inside the first protein complex of electron carriers

269
Q

what is the third step of the ETC?

A

the electron travels to the Q complex

270
Q

is electron transfer endergonic or exergonic ?

A

exergonic; each complex is more electronegative than the previous one

271
Q

what accounts for the very high number of ETC in a single mitochondrion? how many chains/ mitochondrion?

A

the folding of the inner membrane into cristae
= increases surface area
= very “long” inner membrane
= 1000 ETC

272
Q

what component does the ETC need for its electrons to move from 1 complex to another?

A

the prosthetic group

273
Q

when is a component of the ETC said to be reduced vs oxidized ?

A

reduced
= accepts electrons
= becomes more negative
= when a component accepts e- from its “uphill” neighbour

oxidized
= donates electrons
= becomes more positive
= when a component donates e- to its “downhill” neighbour

274
Q

in the ETC, are NADH and FADH2 reduced or oxidized?

A

oxidized (donates electrons = more positive charge)

275
Q

what is the order of the 6 complexes in the ETC?

A

complex I
CoQ
complex II
complex III
CoCyt C
complex IV

276
Q

what happens in the complex I of the ETC

A
  • NADH from the Krebs cycle & glycolysis enters the Complex I
  • NADH is oxidized into NAD+ and H+
  • FMN accepts the electron from the previous oxidation
  • 4 H+ are pumped into the inner membrane
  • FMN transfers the electrons to coQ, which leaves the complex I and reaches the complex III
277
Q

what happens in the complex II of the ETC

A
  • FADH2 from the Krebs cycle & glycolysis enters the Complex II
  • FADH2 is oxidized into FAD and 2H
  • FE-S centers accepts the electrons from the previous oxidation
  • no H+ are pumped here
  • Fe-S centers transfers the electrons to coQ, which leaves the complex I and reaches the complex III
278
Q

the coQ transfers e- from where to where ?

A

takes e- from the complex I and from the complex II
transfers it all to the complex III

279
Q

the enzyme Cyt c transfers e- from where to where?

A

from the complex III to the complex IV

280
Q

how many H+ are pumped into the inner mitochondrial membrane in each complex of the ETC?

A

complex I = 4H+
complex II = none
complex III = 4 H+
complex IV = 2 H+

total: 1 NADH ends up pumping 10 H+ in total

281
Q

why is oxygen important in the ETC stage in terms of the inter-membrane space content?

A

O2 is the final acceptor in the ETC

if no O2:
ETC is blocked
= H+ can’t be pumped into the inner membrane

282
Q

why is oxygen important in the ETC stage in terms of the mitochondrial matrix content?

A

O2 takes H+ from the matrix to form H2O and then create an electronegative O that can accept the e- from the ETC

if no O2:
matrix will not have a low [H+]
= no concentration gradient

283
Q

why does FADH2 pump 1/3 less H+ than NADH

A

bc FADH doesn’t go through the complex I, which pumps 4 H+

FADH = 6 H+
NADH = 10 H+

284
Q

what is a poison that inhibits ETC? how does it work and what is the consequence?

A

cyanide
it binds to Cyt a3 of the complex IV
= prevents the release of e- to oxygen
= stops the whole ETC process
= no H+ gradient
= no chemiosmosis
= no atp
= cell dies

285
Q

how does chemiosmosis start?

A

by using the H+ gradient formed by the ETC to power the synthesis of ATP by atp synthase

286
Q

atp synthase can work one way or both ways?

A

both ways
it can hydrolyze atp or synthesize it
depends on the delta G of the rxn (exergonic or endergonic)

287
Q

describe the 4 main parts of the ATP synthase’s structure.

A

rotor
on the plasma membrane
spins when H+ transfers through it

stator
on the plasma membrane (anchored=fix)
holds the knob in stationary position
keeps the enzyme in the plasma membrane

rod
spins, which activates the knob’s active sites
top end = linked to rotor
bottom end = knob

knob
stationary
has 3 active sites that allows ADP -> ATP

288
Q

how much atp do NADH give

A

1 NADH = 3 ATP

289
Q

how much atp do FADH2 give

A

1 FADH2 = 2 ATP

290
Q

what are the 2 mechanisms that provide ATP to cells without oxygen O2?

A

anaerobic respiration
fermentation

291
Q

which organisms form atp without oxygen?

A

obligate anaerobes
organisms that can only live in anaerobic conditions
fermentation or anaerobic respiration

facultative anaerobes
organisms that can live in both conditions
if O2: aerobic cellular respiration
if no O2: fermentation

292
Q

are yeasts (fungi) obligate anaerobes or facultative anaerobes?

A

facultative anaerobes

293
Q

what is the difference between aerobic and anaerobic respiration?

A

less atp made in anaerobic
bc the final electron acceptor of the ETC is not as electronegative as oxygen = less efficient

294
Q

what can be used in anaerobic respiration instead of O2?

A

the final electron acceptor can be:
NO2, NO3, CO2, metal ions, SO4

295
Q

what is the difference between fermentation and anaerobic respiration?

A

anaerobic = you go through all the cycles of respiration, just replace the O2 in the ETC by another electronegative molecule

fermentation only uses glycolysis

296
Q

how is NAD+ recycled in fermentation? why is it crucial?

A

NAD+ is recycled by substrate-level phosphorylation
= important to amorce the next glycolysis cycle, otherwise glycolysis will stop

297
Q

what are the 2 types of fermentation? explain them

A

alcohol fermentation
1. glucose -> pyruvate
2. pyruvate -> acetaldehyde
3. this release 1 CO2
4. acetaldehyde is reduced into ethanol by NADH
acetaldehyde + NADH -> ethanol + NAD+

lactic acid fermentation
1. glucose -> pyruvate
2. pyruvate -> lactate (no CO2 release)
3. NAD+ is regenerated

298
Q

what are applications in our life of fermentation? (lactic and alcohol)

A

lactic acid fermentation
- the making of cheese & yogourt by fungi & bacteria
- our muscle cells in anaerobic conditions

alcohol fermentation
- yeast in bread

299
Q

how does lactic acid build up in muscle occur?

A

during a hard/long gym sesh
= when our body need to make atp faster than the blood can supply oxygen
= when our body’s glucose metabolism is higher than the rate of oxygen intake from the blood

300
Q

compare lactic acid fermentation and aerobic, which is faster?

A

lactic acid fermentation is 2.5x faster
but makes much less ATP

301
Q

what is a consequence of lactic acid build up in muscle?

A

cause muscle fatigue and pain

302
Q

what happens to lactate in muscle cell after fermentation happened?

A

lactate is transported to the liver via the blood
lactate is converted into pyruvate
it then enters mitochondria in liver cells and complete cellular respiration

303
Q

compare the where the electrons of NADH goes in
aerobic, anaerobic and fermentation

A

aerobic / anaerobic
to the ETC complex I

fermentation
to an organic molecule (pyruvate or acetaldehyde)

304
Q

what other groups apart from carbohydrates can be broken down to feed cellular respiration? rank them in order of usage

A
  1. carbohydrates
  2. fats (lipids)
  3. proteins
305
Q

what is the breakdown of glycogen called? what is the product?

A

glycogenolysis
glycogen -> Glucose-6-phosphate

306
Q

what is glycogen synthesis called ? what is the reactant?

A

glycogenesis
glucose-6-phosphate - glycogen

307
Q

excess amino acids from protein we eat are converted to what? before doing so, what is one important step?

A

to intermediates of cellular respiration
before entering cellular respiration, amino acid deamination must occur
= amino groups are removed by deamination

308
Q

how do organisms get rid of the amino groups from amino acid deamination?

A

amino acid deamination:
amino acid -> amino group + carboxyl group
amino group -> ammonia -> ammonium -> urea
urea is then excreted in urine

309
Q

when do proteins come into play in the cellular respiration?

A

at the end of glycolysis, or after glycolysis

after deamination, the carboxyl groups of an amino acids enters different pathways:
carboxyl end -> pyruvate & enters Krebs cycle
carboxyl end -> acetyl coA & enters Krebs cycle

310
Q

when do lipids come into play in the cellular respiration?

A

lipids -> glycerol + fatty acids
glycerol -> G3P -> glycolysis
fatty acids -> beta oxidation -> acetyl coA

311
Q

how does beta oxidation work

A

fats are broken down into 1 glycerol + fatty acids
beta oxidation breaks down each fatty acid chain into smaller chains of 2-carbon length called acetyl-coA

312
Q

why does lipid metabolism creates more ATP

A

bc apart from yielding acetate units , beta oxidation also generates NADH and FADH2 thus increasing the efficiency of the ETC.
each “cut” into an acetate unit releases 1 FADH2 and 1 NADH

313
Q

what is the difference in atp yield with lipids vs carbohydrate cellular respiration?

A

lipids = more than twice the amount of ATP

314
Q

a fatty acid is a 16-carbon chain, how many rounds of beta-oxidation does it have to go through?
how many acetate units will be yielded?
how many FADH2/NADH will be yielded?

A

7 cuts necessary
= 7 rounds of beta-oxidation
= 8 units of acetate
= 8 FADH2 and 8 NADH

315
Q

why is bruning fats by exercising very hard?

A

bc fats yields so much atp, so fats holds so much energy, it is difficult to release that energy

316
Q

is the atp yield obtained from glycerol high?

A

no, what you get from 1 glycerol is half of what you get from 1 glucose
but fatty acids compensate for that

317
Q

how is the synthesis (building) of glucose named?

A

gluconeogenesis

318
Q

how is the synthesis (building) of fats named?

A

lipogenesis

319
Q

show that the pathways of cellular respiration are reversible

A

the compounds formed in the Krebs cycle can be modified into amino acids

pyruvate can form glucose

acetyl coA can form fatty acids

DHP -> G3P

= all endergonic rxn = require ATP

320
Q

what is the difference between autotrophs and heterotrophs?

A

autotrophs
=producers
= “self”-feeders; produce their own food

heterotrophs
= consumers
= consume food made by other organisms

321
Q

what are photoautotrophs?

A

organisms that use:
- light as source of energy to make the organic substances they need
- CO2 from atmosphere as their source of carbon

convert light energy into chemical energy through photosynthesis

322
Q

give 4 examples of photoautotrophs

A

plants
algae (protist)
cyanobacteria
purple and green sulfur bacteria

323
Q

what trophic levels are the primary producers? what is their role

A

chemoautotrophs
photoautotrophs

= they are the base of all food chain & provide energy to all other organisms

324
Q

in photosynthesis, where does O2 in the product comes from?

A

from water
CO2 gets reduced to sugar, and water gets reduced to oxygen

325
Q

what is the equation for oxygenic vs anoxygenic photosynthesis

A

oxygenic
light + 6 CO2 + 6 H2O = C6H12O6 + 6 O2
= uses water and produces 6 O2

anoxygenic
light + 6 CO2 + 6 H2S = C6H12O6 + 6 S
= uses H2S and produces 6 S

326
Q

which of the 4 organisms that are photoautotrophs undergo oxygenic photosynthesis?

A

plants
algae
cyanobacteria

327
Q

which of the 4 organisms that are photoautotrophs undergo anoxygenic photosynthesis?

A

green and purple sulfur bacteria

328
Q

between plants and animals, what is the main difference regarding the cellular respiration process?

A

plants make their own glucose through photosynthesis
and then go through the same stages of respiration

329
Q

what is the structure of a leaf? 4 components of its structure

A

cuticle
palisade mesophyll
vascular bundle
spongy mesophyll
stoma

330
Q

how does the stomata help in photosynthesis?

A

gas exchanges, which are crucial in photosynthesis happen through the stomata
= pores in the lower epidermis

331
Q

the stomata has 2 components, which are they?

A

the hole where gas goes through
and guar cell that controls it (close1open)

332
Q

how does the vascular tissue help in photosynthesis?

A

by distributing substances throughout the plant
= crucial for survival of all plant cells

333
Q

how does the mesophyll help in photosynthesis?

A

mesophyll cells contain an extremely large amount of chloroplasts for photosynthesis

334
Q

what is the structure of a chloroplast? start from the outer membrane and work your way to the middle

A

outer membrane
inter membrane space
inner membrane
stroma (liquid inside the inner membrane; equivalent of matrix)
thylakoid (disk shape)
stroma lamellae (bar that connects 2 thylakoid)
lumen (inside of a thylakoid)

335
Q

where are pigments that capture light found in a chloroplast

A

on the membrane of a thylakoid

336
Q

what are the 3 pigments of chloroplast?

A

chlorophyll a
chlorophyll b
carotenoids

337
Q

what is the difference between chlorophyll a and b?

A

one different functional group
a = CH3
b = CHO
so b is more polar than a

338
Q

what is the job of caratenoids?

A

photo protection
= absorb and dissipate excess light
(to prevent damage to the chlorophyll pigments)

339
Q

what is the absorption spectrum of each pigment of chloroplasts?

A

Chlorophyll a:
absorbs
blue-violet = 430-450 nm
red 660-680 nm
It reflects blue-green light

Chlorophyll b:
absorbs
blue 450-500 nm
orange-red 640-660 nm
It reflects yellow-green

Carotenoids:
absorbs
blue 400-500 nm
reflect yellow, orange, and red

340
Q

why do see orange leaves only in autumn?

A

We see carotenoid pigments only in autumn because chlorophyll breaks down as temperatures drop and daylight decreases.

In summer: orange pigments are masked by strong green pigments.

341
Q

what accounts for the specificity of certain pigment molecules for certain wavelengths?

A

many photons can be emitted, but
only the photons that are exactly equal in energy to the energy difference between the ground and the excited states are absorbed

342
Q

what happens when one photons hits one pigment molecule?

A

electrons are excited, which creates vibration
the vibration is transferred from one pigment to the next by inductive resonance until it reaches the reaction center.

343
Q

in photosynthesis, what is reduced and what is oxidized?

A

Energy + 6CO2 + 6 H2O -> C6H12O6 + 6O2

the LION says GRR
loss of e- = oxidized / gain of e- = reduced

H2O loses electrons
= becomes more negative
= H2O is oxidized into 6 O2
= oxidation

CO2 gains electrons
= becomes more negative
= 6CO2 is reduced into C6H12O6
= reduction

344
Q

in cellular respiration, what is reduced and what is oxidized?

A

C6H12O6 + 6O2 -> Energy + 6CO2 + 6 H2O

the LION says GRR
loss of e- = oxidized / gain of e- = reduced

O2
= reduced into H2O
= reduction

C6H12O6
= oxidized into 6CO2
= oxidation

Biology 2 (6 decks)

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