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BIOL 260 > Energy and Nutrient Acquisition (Unit 1) > Flashcards

Energy and Nutrient Acquisition (Unit 1) Flashcards

1
Q

why do organisms need nutrients?

A

nutrients provide the building blocks needed for growth, development and repair.
- nucleic acids, amino acids, hydrocarbons, proteins, etc.

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2
Q

Four major organic biomolecules

A

carbohydrates - CHO
lipids - CHO
proteins - CHON
nucleic acids - CHONP

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3
Q

what are the main types of nutrients?

A

inorganic - calcium, iron, phosphorus, nitrogen, CO2, water
organic - carbohydrates, lipids, proteins, vitamins

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4
Q

where do organisms get nutrients?

A

organisms get nutrients and energy by eating other organisms
they burn some nutrients as fuel, and recycle some of them to use as building blocks

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5
Q

what are the 3 main fates of nutrients?

A
  1. oxidized and energy captured as ATP
  2. oxidized and energy released as heat
  3. used as building blocks for new molecules
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6
Q

what are the two main components of the mitochondria?

A
  • Krebs (citric acid) cycle
  • electron transport system
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7
Q

Krebs (citric acid) cycle

A
  • oxidizes organic (like sugars) molecules
  • breaks them down into CO2
  • transfers protons to the electron carriers NADH and FADH2
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8
Q

Electron transport chain

A
  • electron carriers transfer electrons to the ETC
  • results in protons pumped into the inter-membrane space, creating electrochemical gradient for ATP production
  • oxygen is the terminal electron acceptor, released as H2O
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9
Q

aerobic respiration equation

A

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

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10
Q

how does ATP synthase work

A
  • protons flow down the concentration gradient, back into the matrix, through ATP synthase
  • this powers the rotation of ATP synthase which causes the phosphorylation of ADP to ATP
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11
Q

catabolism vs. anabolism

A

catabolism - uses energy to break down molecules i.e. energy is converted from potential energy to kinetic energy
anabolism - uses energy to synthesize molecules i.e. energy is converted from kinetic energy to potential energy

  • catabolism supplies the energy for anabolism *
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12
Q

how is energy extracted from nutrients?

A
  • nutrients are broken down through oxidation
  • energy from oxidation is transferred to ATP through the addition of P to ADP)
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13
Q

thermogenesis pathway

A

in the tissues of thermogenic species, mitochondria have a type of pore called Uncoupling Protein.
- protons “leak” through this pore, and biochemical work occurs which produces heat, and no ATP.

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14
Q

what are thermogenic species?

A

thermogenic species have specialized pathways for generating heat, which help to maintain body temperature.
- mammals, birds, certain types of fish, etc.

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15
Q

where does metabolic heat come from?

A

metabolic processes are inefficient, so some energy transferred during any chemical reaction is lost as heat

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16
Q

how do we get the building blocks for growth and development?

A

there are certain essential nutrients organisms need like certain amino acids, fatty acids, vitamins, minerals, water, etc. these are typically obtained through diet.
these essential nutrients vary among species

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17
Q

endotherms

A

thermogenic animals that generate substantial amounts of heat internally which allows them to maintain relatively constant body temperature.

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18
Q

ectotherms

A

animals that are not thermogenic and cannot maintain their internal body temperature even with environmental changes.

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19
Q

what role does the mouth play in the digestion of foods?

A
  • ingestion
  • mechanical digestion (chewing)
  • enzymatic digestion (salivary ezymes)
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20
Q

how does saliva begin enzymatic digestion?

A

saliva contains salivary amylase, which is an enzyme that breaks down carbohydrates into disaccharides (simpler sugar molecules)
- amount of salivary amylase changes with diet habits & consumption of starch diets

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21
Q

what kind of animals have salivary amylase gene?

A

omnivores, especially those which are adapted to living amongst humans
- rats, pigs, dogs, etc.

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22
Q

parasympathetic nervous system

A

system of nerves that relaxes your body after periods of stress or danger.

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23
Q

sympathetic nervous system

A

fight or flight system
- kicks into action when feeling like you’re in some sort of danger

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24
Q

how does the stomach digest food?

A

mechanical digestion - muscles constrict and physically break down food
chemical - hydrochloric acid (HCl) aids in breakdown of proteins
enzymatic - pepsin breaks down amino acids (pepsinogen is a protein that HCl breaks down into pepsin)

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25
Q

goblet cells (in stomach)

A

produce mucus that contains bicarbonate, which helps protect stomach lining and neutralize the stomach acids

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26
Q

parietal cells (in stomach)

A

produce HCl
- pump protons into the stomach lumen to lower the pH
- Cl- is moved from the bloodstream, through the parietal cell, into the stomach lumen, where it combines with H+ to form HCl.
- Cl- in moved with a CL-/bicarbonate exchanger b/w the blood vessel & parietal cell

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27
Q

carbonic anhydrase

A

an enzyme that assists rapid inter-conversion of carbon dioxide and water into carbonic acid, protons and bicarbonate ions.
- bicarbonate gets exchanged into the blood stream
- protons pumped into stomach lumen

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28
Q

what happens in carbonic anhydrase is inhibited?

A
  • blood may become acidic due to lack of bicarbonate being added
  • stomach lumen becomes more basic due to lack of H+ additions
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29
Q

chief cells (in stomach)

A

produce pepsinogen (pepsin precursor)
- low pH causes pepsinogen to change conformation into pepsin for protein digestion

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30
Q

3 main chemicals that stimulate stomach acid secretion

A
  1. Acetylcholine
  2. Histamine
  3. Gastrin
    - these bind to receptors on the parietal cell and cause it to release Cl- and H+ to form HCl in the stomach.
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31
Q

what turns off stomach acid secretion?

A
  1. Somatostatin - when pH is low, somatostatin is released which decreases the release of gastrin and histamine, reducing stomach acid secretion
  2. Presence of food in the intestine - sends a signal to the brain which decreases activity of neurons leading to the stomach, reducing stomach acid production
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32
Q

what is the role of the small intestine in digestion?

A
  • performs enzymatic and chemical digestion
  • secretions from the pancreas and gall bladder are critically important
  • majority of nutrient absorption occurs in the small intestine
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33
Q

role of the pancreas

A

secretes enzymes (lipase, amylase, protease) and bicarbonate into the small intestine which help neutralize stomach acid and protect lining of the small intestine

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34
Q

function of protease

A
  • secreted by the pancreas
  • aids in break down of proteins into amino acids
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35
Q

function of lipase

A
  • secreted by the pancreas and gallbladder
  • aids in digestion of fats into glycerol and fatty acids
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36
Q

role of the gall bladder

A

secretes bile into the small intestine which aids in digestion of fats

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37
Q

what is the role of the large intestine in digestion?

A

primary role is water re-absorption, with some absorption of remaining nutrients.
- contains many colonies of bacteria which aid in repressing growth of pathogenic microbe and digest nutrients into absorbable forms.

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38
Q

how is cellulose digested?

A
  • no animal produces the enzymes needed to break down cellulose
  • commensal bacteria found in the gut are able to digest cellulose (in the appendix in humans)
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39
Q

what are hind-gut fermenters?

A

term for herbivores that have very large cecum that forms an out-pocketing of the large intestine, specifically for cellulose digestion
- small animals will have large cecum, small colon
- large animals will have large cecum, very large colon.

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40
Q

what are foregut fermenters (ruminant animals)?

A

herbivores that have a specialized pocket of the stomach that houses bacteria for cellulose digestion.
- long small intestine for nutrient absorption, usually smaller colon.

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41
Q

how is glucose absorbed?

A

Secondary active transport (ATP isn’t directly used to move glucose across membranes)
- glucose is transporter from the lumen of small intestine into intestinal cells via a symporter with Na+.
- antiporter uses ATP to transport K+ into intestinal cell from the bloodstream and Na+ from the intestinal cell into the bloodstream (against their conc. gradients)

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42
Q

how are amino acids absorbed?

A
  • similar to glucose transport
  • symporter carries amino acid + Na+ into intestinal cell.
  • facilitated transporter transports amino acids to bloodstream for transport around the body.
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43
Q

water movement in the body

A

water movement is passive, occurs through aquaporins and through spaces between cells.
- net movement of water is driven by relative concentration gradients of solutes.
- water moves TOWARD high concentrations of Na+ (and high solutes in general)

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44
Q

how does the digestive system regulate water?

A
  • water will be absorbed by the body when the colon has lower solute concentration that the cells lining it.
  • if you eat something that has a lot of remaining solutes that do not get absorbed, water will be drawn out of your cells into the colon/remain in the colon because of its higher solute concentration.
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45
Q

what is lactase persistence?

A

lactose can only be broken down by the enzyme lactase.
- lactase persistence means your body continues to produce the enzyme, lactase, which allows you to digest lactose-containing products like dairy.
- common in herding cultures where dairy is a commonly consumed product (like northern Europe)

46
Q

photosynthesis equation

A

6CO2 + 12H2O + Light -> C6H12O6 + 6O2 + 6H2O

47
Q

where did chloroplasts evolve from?

A

endosymbiotic event of a cyanobacteria being “absorbed” by a eukaryote, evolved to be a chloroplast capable of photosynthesis.

48
Q

what was the Great Oxidation mass extinction?

A

~2.5 million years ago
photosynthesizing bacteria began to produce so much oxygen, it killed most anaerobic organisms on earth because they weren’t adapted to having an oxygenated atmosphere.

49
Q

most important aspect of photosynthesis?

A

it is the only biological process that transforms carbon from an inorganic to organic form
it releases O2 from water! (which led to so much life evolving on earth)

50
Q

where does most of the photosynthetic activity happen on earth?

A

phytoplankton account for ~50% of all carbon fixation on the planet.
they are arguably the most important food source on the planet due to their role in primary productivity of the oceans.

51
Q

how much of plant biomass is derived from atmospheric CO2?

A

96% of all plant biomass comes from CO2 taken from the atmosphere

52
Q

light dependent reaction

A

light hits pigments and reaction centres in the thylakoid membrane, setting off the ETC and producing electron/energy carries that will be used for the Calvin Cycle
- water is a substrate & is split into O2, 2 e- and 2H+.

53
Q

light-independent reaction
(dark reaction)

A

Calvin cycle, happening in the stroma of the chloroplast, utilizes CO2, ATP, NADPH and RuBP to generate triose phosphates for glucose production.
- this is the cycle that fixes CO2 into organic carbon molecules.

54
Q

when are light-independent reactions most active?

A

high activity in the day, stops in the night. this is because it requires the products of light reactions to run.

55
Q

how are light-dependent and dark reactions linked?

A

light-reactions provide the ATP and NADPH needed to power the Calvin cycle (dark reaction) which fixes CO2 into carbohydrates

56
Q

what are stomata?

A

stomata are pores, typically located on the underside of leaves, in the lower epidermis which open and close to control gas (CO2 and O2) and water exchange with the air

57
Q

what controls stomatal opening and closure?

A

stomata are controlled by guard cells which open when they are filled with water (high turgor pressure) and close when they are not saturated with water (low turgor pressure)

58
Q

high energy wavelengths

A

shorter wavelength >400 nm
violet/blue light

59
Q

low energy wavelengths

A

longer wavelength <710 nm
red/orange light

60
Q

what makes plants green?

A

plants contain pigments (chlorophylls) that absorb wavelengths that correspond to blue and red parts of the light spectrum
i.e. they reflect green back so they appear green

61
Q

chlorophyll pigments

A

absorb red and blue light
transmit green light

62
Q

carotenoid pigments

A

absorb blue and green light
transmit yellow, orange or red light

63
Q

how is energy captured by pigments in the chloroplast?

A

photons are captured by pigments and the energy is either
1. re-emitted as heat or fluorescence
2. transferred to adjacent pigments
3. transferred to acceptor molecules/reaction centre

64
Q

what is the antenna complex?

A

a complex of molecules that capture and direct energy from photons towards the reaction centre.
1. peripheral antenna - containing Chl a, Chl b, carotenoids, and accessory pigments
2. core antenna - exclusively Chl a
3. reaction centre - modified Chl a dimer that transfers one excited electron to an acceptor

65
Q

fluorescence emission

A

photons emitted as fluorescence has lower energy and longer wavelength than the photon originally absorbed

66
Q

what is pheophytin?

A

carries electrons from PSII to plastoquinone

67
Q

what ferredoxin?

A

accepts electrons from PSI and delivers them to the terminal electron acceptor - NADPH

68
Q

what is the Z-scheme?

A

PSII and PSI work together to move electrons from water to form NADPH while producing ATP

69
Q

steps of the Z-scheme?

A

680 nm light hits PSII which takes e- from H2O and boosts them to pheophytin (high energy), then they are sent to PQ (which simultaneously sends H+ across the membrane) -> Cyt b6f -> PC -> PSI (hit with 700 nm light), this sends e- to even higher energy level to be accepted by Ferredoxin and sent to NADP+

70
Q

how do protons accumulate in the lumen?

A
  • from splitting of H2O
  • from PQ sending H+ across the membrane
71
Q

what happens to ATP synthesis if translocation of PQ from stroma to lumen is inhibited?

A

synthesis of ATP is reduced due to only water contributing to the H+ gradient

72
Q

what happens to NADPH synthesis if translocation of PQ from stroma to lumen is inhibited?

A

it is stopped quickly because PSI is no longer receiving electrons to send to Fe to NADP+

73
Q

how does cyclic electron flow work?

A

excited e- at PSI flow back to Plastoquinone (PQ) by Ferredoxin where they return to the ETC cycle
- this occurs when the cell requires additional ATP but no NADPH, because it stops production of NADPH.

74
Q

3 stages of the Calvin cycle

A
  1. Carbon fixation
  2. Reduction
  3. Substrate Regeneration
75
Q

Step 1 of Calvin Cycle

A
  1. Carbon Fixation
    - Rubisco binds CO2 and RuBP and produces PGA
    - 1 turn of the cycle fixes 1CO2, 3 turns are required to produce 1G3P molecule
    - 3PGA molecules produced have 3 carbons, known as C3 photosynthesis.
76
Q

Step 2 of Calvin Cycle

A
  1. Reduction
    - 3PGA are produced using ATP and NADPH, and generate 1 G3P after 3 turns of the cycle.
    - 20% of G3P go to make glucose
    - 80% of G3P go to regeneration of RuBP substrate
77
Q

Step 3 of Calvin Cycle

A
  1. Regeneration
    - G3P use ATP to regenerate RuBP to start the cycle again
78
Q

what is Photorespiration?

A

when O2 levels become high inside the leaf and CO2 levels drop, Rubisco utilizes O2 as a substrate instead of CO2, however this process does not contribute to completion of the Calvin cycle AND uses up ATP and NADPH molecules.

79
Q

why is Rubisco inefficient?

A

it is a very slow enzyme, and has low CO2 binding affinity.
- it evolved ~3 billion years ago in a CO2 rich environment, and didn’t evolve to adapt to the comparatively reduced CO2 levels of the current atmosphere.

80
Q

how do C3 and C4 plants differ in CO2 uptake?

A

C3 - have no way to store CO2, so they uptake it through opening their stomata regularly
C4 - open stomata less often and fix CO2 into malate (organic acids) and store in vacuole, so there’s more steady fixation of carbon.

81
Q

structure of C4 vasculature

A

C4 plants have radial vasculature, so the outer layer is mesophyll cells (where CO2 is stored as malate), then there’s a layer of bundle sheath cells (where malate is shuttled for actual carbon fixation), and then there’s the xylem/phloem vein.

82
Q

how do CAM plants differ from C3 and C4?

A

CAM plants trap CO2 and store it as malate during the night, when they open their stomates. These are stored until daytime when they are utilized to power the Calvin cycle.

83
Q

what are the main products of photosynthesis?

A

carbohydrates (sugars) with O2 as a byproduct

84
Q

define essential nutrient

A
  • an element that is absolutely required for normal plant growth and reproduction
  • cannot be replaced by any other element
  • directly/indirectly involves in metabolism
  • if deficient in this element, plant will exhibit symptoms but would recover if supplied with the element again.
85
Q

what % of plant biomass comes from the soil?

A

~4% comes from soil
96% is from H2O and CO2

86
Q

plant essential macronutrients

A

Nitrogen
Potassium
Calcium
Magnesium
Phosphorus
Sulfur

87
Q

plant essential micronutrients

A

Chlorine
Iron
Manganese
Zinc
Boron
Copper
Nickel
Molybdenum

88
Q

Properties of soil that support plant growth?

A

texture and charge
- % of gravel/sand/silt/clay
organic and inorganic content
- minerals (S, P, K, Fe)
- organic soils have more air spaces and water retention

89
Q

negative soil ions …

A
  • don’t bind clay particles (they are also negatively charged)
  • are readily available for plant uptake
  • can be easily washed away (leaching)
90
Q

positive soil ions …

A
  • adhere to clay
  • not easily available for plant uptake
  • better retained in soils/won’t wash away
91
Q

why is soil pH important?

A

soil pH impacts ion availability in soils

92
Q

what is a limiting nutrient?

A

the limiting nutrient is whichever nutrient will run out first (not necessarily the least abundant)

93
Q

primary function of roots?

A
  • they anchor the plant
  • they search for water and minerals in the soil so the plant can grow
94
Q

function of root hairs

A
  • root hairs increase surface area of the root for maximum nutrient absorption
  • they regulate mineral and water uptake
  • contain multiple ion channels and high affinity ion-transporters
95
Q

Apoplastic route

A

water uptake by roots flows through the extracellular spaces and bypasses the plasma membrane
- ends at the Casparian strip (endodermis)

96
Q

Symplastic route

A

water uptake by roots crosses the plasma membrane once and then moves from cell to cell via plasmodesmata.
- ends at the Vasculature

97
Q

Transmembrane route

A

water uptake by the roots flows from cell to cell crossing the plasma membrane multiple times through aquaporins
- ends at the Vasculature

98
Q

what is the Casparian strip?

A

a hydrophobic barrier on the cell walls of the endodermal cells that stop water passage through the apoplastic route.
- it forces water to pass THROUGH cells instead of flowing around them.

99
Q

components of an electrochemical gradient

A
  • differences in concentration with movement from high to low concentration
  • differences in electrical charge with opposite charges attracting each other
100
Q

what is voltage?

A

voltage is reported as the charge inside relative to the charge outside
- in both plants and animal cells, the intracellular side of the membrane is more negative than the extracellular side

101
Q

why is it difficult for plants to acquire nutrients in the roots?

A

because plants must acquire nutrients against a concentration gradient. Plant material usually has much higher nutrient concentration than soil.
- moving ions against electrochemical gradient requires energy (ATP)!

102
Q

2 ways ions cross biological membranes

A
  1. Channels - passive transport, driven by electrochemical gradients
  2. Transporters - active transport, typically moves against the electrochemical gradient
103
Q

how do cations enter the cell?

A

cations enter the cell with a favourable electrical gradient and against a concentration gradient

104
Q

how to anions enter the cell?

A

anions must enter the cell against concentration and electrical gradients

105
Q

what is passive exclusion?

A

Passive exclusion results from a lack of membrane transporters/channels
- prevents toxins from entering roots through the symplastic and transmembrane pathways

106
Q

what is active exclusion & sequestration into vacuoles?

A

Active exclusion eliminates toxic ions from the cytosol.
- they store harmful ions in the central vacuole or transport them to the extracellular media.

107
Q

what is binding/detoxification?

A

toxic metals can be detoxified using Metallothioneins (cysteine-based proteins w/ high affinity for metals)
- metals get trapped in the protein which is then exported out of the cell

108
Q

mutualistic interactions

A

when two species in a mutual interaction where goods/services are exchanged. Each species involves must receive a benefit from the interaction

109
Q

relationship between plants and Mycorrhizae

A

symbiotic relationship
- fungus delivers inorganic nutrients to the plant
- plant delivers fixed organic carbons (sugars) to fungus

110
Q

relationship between plants and Rhizobia (N-fixing bacteria)

A

symbiotic relationships
- bacteria form root nodules on the plant roots where it fixes N2 into NH4+ to make it available for the plant to use
- plant delivers organic carbons to bacteria

BIOL 260 (3 decks)

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