Unit #2: Chapters 6-9 Flashcards Preview

Principles of Biology I > Unit #2: Chapters 6-9 > Flashcards

Flashcards in Unit #2: Chapters 6-9 Deck (108):
1

oxidation

* loss of electrons
* results in positive charge

2

reduction

* gain of electrons
* results in negative charge

3

reduced carbon

stores energy in chemical bonds of organic molecules

4

enzyme

* globular protein with one or more active sites ("pockets")
* determines the course of metabolism by facilitating particular chemical reactions
* almost every reaction has a corresponding enzyme to facilitate it
* may also have inhibitors (competitive or non-competitive)

5

photosynthesis (defn and formula)

* Formula: 6CO2 + 6H2O -> C6H12O6 + 6H2O + 6O2
* Uses light energy to convert carbon dioxide and water to sugars and oxygen
* occurs in the chloroplast

6

photon

* a particle of light
* acts as a discrete bundle of energy
* energy content of a photon is inversely proportional to the wavelength of the light

7

proton

Positively-charged particle of an atom - H+

8

light-dependent reactions

* capture energy from photons to make ATP and reduce NADP+ to NADPH

9

light-independent reactions

* also called Calvin Cycle and carbon fixation reactions
* If O2 is available, uses ATP and NADPH to synthesize organic molecules from CO2
* If O2 is not available, side reactions store (?) as oxyloacetate when plant stomata are closed (C4 plants)

10

chlorophyll

* green-colored pigment; absorbs red/blue light wavelengths, reflects green
* chlorophyll a – primary pigment in plants and cyanobacteria that absorbs violet-blue and red light
* chlorophyll b – secondary pigment absorbing light wavelengths that chlorophyll a does not absorb

11

absorption

atoms can only absorb photons with energy levels that correspond to the atom's available energy levels. so each molecule has a specific range of photons it can absorb.

12

stroma

semiliquid substance surrounding thylakoid membranes

13

thylakoid

* In the chloroplast
* internal membrane arranged in flattened sacs
* contains chlorophyll and other pigments

14

grana

* stacks of thylakoid membranes
* includes a thylakoid space

15

chloroplast

An organelle in plant cells where photosynthesis takes place.

16

ATP (definition, function, structure)

* adenosine triphosphate
* the energy “currency” of cells - energy is released when PO4 is removed
* portable and on-demand source of energy for endergonic reactions
* ATP structure:
-ribose, a 5-carbon sugar
-adenine
-three phosphates

17

NAD+

* nicotinamide adenosine dinucleotide
* one of the most important electron (e-) acceptor/carriers
* a low-energy cofactor that accepts a pair of e- and a proton (H) to create NADH
* composed of two nucleotides bound together by the phosphates

18

NADH

* Reduced form of NAD+, that has accepted 2 e- and one proton
* Reaction is reversible: can release 2 e- and 1 proton to become NAD+ again
* Used in the mitochondrion in the e- transport chain

19

NADPH

* Reduced NADP
* synthesized in the chloroplast by light-dependent reactions
* Used directly by the Calvin Cycle to synthesize organic molecules from CO2

20

FADH2

* Reduced e- carrier (FAD that has accepted 2 e-)
* Bound to its enzyme in the inner mitochondrial membrane, so only releases e- to the electron transport chain.
* Worth 2 ATP

21

Calvin Cycle (defn and location)

* biochemical pathway in photosynthesis that allows for carbon fixation
* occurs in the stroma of chloroplast
* uses ATP and NADPH as energy sources
* incorporates CO2 into organic molecules
* output is 2 molecules of G3P for every 6 molecules of CO2 (glucose is synthesized in a separate reaction)

22

ribulose biphosphate carboxylase

enzyme that carries out Phase 1 of the Calvin Cycle (the carbon fixation reaction), reacting RuBP (ribulose 1,5-biphosphate) with CO2 to produce 2 molecules of PGA

23

rubisco

* nickname for ribulose biphosphate carboxylase
* the most prevalent enzyme in nature

24

CAM

* alternative CO2 source for photosynthesis for tropical plants (like pineapple)
* like C4 photosynthesis, fixes CO2 to PEP instead of PGA to form a C-4 molecule that stores CO2 until released to the Calvin Cycle
* unlike C4 photosynthesis, these plants capture CO2 at night and decarboxylate (do the Calvin Cycle) during the day

25

C3

* most plants use this form of photosynthesis
* called C3 because the first intermediate of the Calvin Cycle is phosphoglycerate (PGA), with 3 C atoms

26

C4

* alternative photosynthesis plants (like grasses, corn)
* fixes CO2 to PEP instead of PGA to form a 4-C molecule which stores the CO2 until it is released to the Calvin Cycle
* reduces photorespiration (which reduces the yield of carbohydrates)

27

Krebs Cycle (summary description and location)

* 9-step process to reduce the acetyl group from Pyruvate Oxidation
* Occurs in the matrix of the mitochondria
* Otherwise known as the citric acid cycle or TCA cycle
* When the cell's ATP concentration is high, the process shuts down and acetyl-CoA is channeled into fat synthesis.

28

Glycolysis (definition/description)

* The break-down of glucose in a cell for metabolism
* E- of C-H bonds are stripped off in a series of reactions
* Occurs in the cytoplasm
* Results in net gain of 2 ATP

29

cytoplasm

Material inside a cell, not including the nucleus.

30

oxyloacetate

* "Feeder" molecule (4-carbon) that reacts with acetyl-CoA to start the Krebs Cycle
* Also the Step 9 product of the Krebs Cycle

31

carbon dioxide

CO2 - feeds photosynthesis and is an output of respiration

32

cis-aconitate

an intermediate in the isomerization of citrate to isocitrate in the citric acid cycle

33

alpha-ketoglutarate

Step 4 product of the Krebs Cycle, a 5-carbon molecule

34

acetyl-CoA

* The end product of Pyruvate Oxidation
* Feeds the Krebs Cycle
* consists of 2 carbons from pyruvate attached to coenzyme A

35

citric acid

* Step 1 product of the Krebs Cycle, a 6-carbon molecule

36

isocitrate

in isomer of citrate where on OH group is repositioned

37

fermentation

* Occurs when oxygen is not available
* ATP must be produced by glycolysis
* Final electron acceptor is an organic molecule
* ex: yeast grows in O2, then runs out and ferments pyruvate to alcohol

38

lactate

Ionized form of lactic acid

39

alcohol

A reduced organic compound through fermentation.

40

electron transport system

* Series of e- carriers to store energy from oxidation reactions
* Located in the inner membrane of the mitochondrion.
* Electrons from NADH and FADH2 are transferred from complex to complex, with some e- energy lost at each transfer, used to pump H+ out of matrix to inter-membrane space.

41

catabolism

* chemical reactions that harvest energy when bonds are broken (respiration)

42

anabolism

* chemical reactions that expend energy to make new chemical bonds (photosynthesis)

43

metabolism

all chemical reactions occurring in an organism (anabolism + catabolism)

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fumarate

Step 7 product of the Krebs Cycle, a 4-carbon molecule

45

malate

Step 8 product of the Krebs Cycle, a 4-carbon molecule

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succinate

Step 6 product of the Krebs Cycle, a 4-carbon molecule

47

succinyl-CoA

Step 5 product of the Krebs Cycle, a 4-carbon molecule

48

isocitrate

Step 2/3 product of the Krebs Cycle, a 6-carbon molecule

49

matrix

The inner-mitochondrial space, inside the inner membrane.

50

cristae

The folds of the inner membrane layer of the mitochondrion, creating many layers to pack lots of e- transfer enzymes

51

aerobic

involving oxygen (final electron acceptor is O)

52

anaerobic

* not involving oxygen (final electron acceptor is an inorganic molecule other than O)
* in respiration, won't go to Pyruvate Oxidation, only glycolysis

53

autotroph

organism that makes its own food (plants that photosynthesize sugars)

54

heterotroph

organisms that do not make their own food and so eat autotrophs or other heterotrophs

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potential energy

stored energy (put into chemical bonds)

56

kinetic energy

energy of motion, much wasted as heat

57

pyruvate

* Step 10 product of glycolysis.
* The further fate of pyruvate depends on oxygen availability:
- When oxygen is present, pyruvate is oxidized in Pyruvate Oxidation to acetyl-CoA, which enters the Krebs cycle
- Without oxygen, pyruvate is reduced in order to oxidize NADH back to NAD+

58

glucose-6-phosphate

* Step 1 product of glycolysis
(glucose has gained a phosphate from ATP)

59

fructose-6-phosphate

* Step 2 product of glycolysis
(glucose 6-phosphate has been reorganized)

60

cyanide

a poison that stops the e- transport system, and consequently ATP generation

61

cyclic photophosphorylation

bacterial cycles, with one photosystem

62

non-cyclic photophosphorylation

e- are boosted from photosystem II to photosystem I and absorbed by NADP to NADPH which is used in Calvin Cycle (not cycled back)

63

citric acid cycle

Also known as the Krebs Cycle, or TCA cycle

64

TCA cycle

Also known as the Krebs Cycle, or citric acid cycle

65

fructose-1,6-biphosphate

* Step 3 product of glycolysis

66

substrate level phosphorylation

* The creation of ATP from ADP by transferring a phosphate group from another molecule
(Endergonic, enzyme-facilitated reaction where PEP and ADP bind to an enzyme's active sites and a phosphate group is transferred from PEP to ADP.)

67

ATP synthase

* An enzyme that facilitates the synthesis of ATP through oxidative phosphorylation (a second method to substrate-level - energy to transfer the phosphate comes from a proton gradient).
* A membrane-bound enzyme that uses the energy of the proton gradient to synthesize ATP from ADP + Pi
* 1 proton results in 1 ATP
* process is called chemiosmosis

68

proton motive force

the proton gradient that drives oxidative phosphorylation via the ATP synthase enzyme

69

phospho-gluco isomerase

the enzyme that turns glucose-6-phosphate into fructose-6-phosphate

70

PEP carboxylase

enzyme used in C4 metabolism

71

G protein

* cell surface (membrane) receptor
* a go-between for the receptor and the enzyme the signal is intended for
* causes signal to 2nd messenger, etc. on signal transduction system

72

photosystem 1

* protein-bound bundle on the thylakoid membrane with pigments
* collects energy output from photosystem II

73

photosystem 2

* protein-bound bundle on the thylakoid membrane with pigments
* collects energy from protons and outputs an e-

74

end product inhibition

* competitive & non-competitive
* final product of a reaction feeds back and shuts it down

75

ligand

* signaling molecule
* when signal reaches a receptor protein, this initiates signal transduction which converts the signaled information into a cellular response

76

desmosome

* junctions between cells
* glycoproteins that paste cells together

77

hemidesmosome

* half a desmosome
* faces a basal lamina

78

gap junction

* connects cytoplasms of cells
* facilitates diffusion between them

79

tight junction

* water-proof seal that attaches cells together

80

adherens junction

will stick cells together

81

cAMP

* cyclic adenosine monophosphate
* reacts with own hydroxyl end to form a circle
* a 2nd messenger
* primitive signal molecule (used by slime molds)

82

kinase

anything that attaches PO4 to something else

83

chemiosmosis

the proton pump/ATP synthase process to produce ATP

84

proton pump

see ATP synthase

85

NADH dehydrogenase

* the first membrane-embedded enzyme to receive e- in the e- transport chain
* oxidizes NADH to NAD+ and releases a proton (H+) to the intermembrane space

86

cytochrome b-c complex

* bc complex is the second enzyme in the e- transport chain which uses energy from e- to pump a proton to the intermembrane space
* cytochrome oxidase complex does the same thing, pumping another proton

87

Calvin Cycle (steps)

* Phase I - carbon fixation
* Phase 2 - reduction
* Phase 3 - regeneration of RuBP

88

carbon fixation

the conversion of inorganic carbon as CO2 into organic carbon in the form of carbohydrates

89

glyceraldehyde-3-phosphate (G-3-P)

* 3-carbon sugar
* can link together to form glucose
* Step 4/5 product in glycolysis.

90

endocrine

* hormonal cell signalling
* sent throughout system; target cells have receptors

91

paracrine

* signals nearby cells by releasing its signal into the extracellular fluid between cells and sent by diffusion
* concentration of signal is dependent on the distance from the signalling cell

92

autocrine

* signals itself
* secretes signals that bind to specific receptors on a cell's own plasma membrane

93

exocrine

* sends molecules outside self, or even the organism (such as sweat or digestive stuff)

94

steroid hormones

* binds to an intracellular receptor, usually in the nucleus
* have a nonpolar, lipid-soluble structure
* can cross the plasma membrane to a steroid receptor
* usually act as regulators of gene expression
* An inhibitor blocks the receptor from binding to DNA until the hormone is present.

95

1st law of thermodynamics

energy is neither created nor destroyed by natural processes, just converted between kinetic and potential

96

2nd law of thermodynamics

disorder is always increasing in the universe - energy used to create order in one place creates disorder elsewhere (releases heat in the process)

97

action spectrum

plant growth vs. wavelengths of light

98

absorption spectrum

wavelengths absorbed where plants grow best

99

evolution

* chloroplasts and mitochondria evolved by endosymbiosis (double membranes, DNA)
* photosynthesis likely developed first
* metabolism may have developed to remove toxic O2

100

Glycolysis Steps

* Step 1: Phosphate group added to glucose by ATP (to ADP). Produces Glucose 6-phosphate
* Step 2: Rearrange Glucose 6-phosphate into Fructose 6-phosphate. Produces Fructose 6-phosphate
* Step 3: Phosphate group added to Fructose 6-phosphate by ATP (to ADP). Produces Fructose 1,6-biphosphate
* Step 4/5: Fructose 1,6-biphosphate is split into two 3-carbon molecules. Produces one G3P and one that is converted into G3P in a second reaction.
* Step 6: Two G3P molecules are each oxidized by NAD+ and a P-group added. Produces 2 NADH and 2 BPG.
* Step 7: One phosphate group removed from each BPG by ADP. Produces two ATP and two 3PG.
* Step 8: Two 3PG molecules rearranged into two 2PG.
* Step 9: Dehydration reaction on two molecules of 2PG. Produces 2 molecules of water and two PEP.
* Step 10: One phosphate group removed from each of two molecules of PEP by ADP. Produces two ATP and two Pyruvate.

101

Glycolysis: summary of 1st 5 reactions and 2nd 5 reations

* 1st 5: Convert a molecule of glucose into two molecules of G3P.
* 2nd 5: Convert two molecules of G3P into two molecules of pyruvate.

102

Krebs Cycle steps

* Step 1: (Condensation) Oxaloacetate reacts with acetyl-CoA to produce citrate.
* Steps 2/3: (Isomerization) 2-step process to rearrange citrate into an isomer isocitrate.
* Step 4: (1st Oxidation) Isocitrate is oxidized, producing alpha-ketoglutarate, one CO2, and one NADH.
* Step 5: (2nd Oxidation) alpha-ketoglutarate is oxidized, producing succinyl-CoA, one CO2, and one NADH.
* Step 6: (Substrate-level Phosphorylation) Succinyl-CoA is cleaved into two molecules and the energy released bonds a phosphate to GDP, which releases it to ADP, producing succinate and one ATP.
* Step 7 (3rd Oxidation) Succinate is oxidized, producing fumarate and one FADH2.
* Step 8/9 (Regeneration of Oxaloacetate) Fumarate accepts a water molecule, turning into malate, which is then oxidized, producing oxaloacetate one NADH.

103

Krebs Cycle output

* 2 CO2
* 1 ATP
* 3 NADH (3 pairs of e-)
* 1 FADH2 (1 pair of e-)

104

photosynthesis (steps)

* pigment molecules capture photons, passing the energy through the photosystem
* the energy is passed as an excited e- to a protein and down an e- transport chain, producing ATP and NADPH
* NADPH and ATP are then used in the Calvin Cycle to build organic molecules (carbohydrates)

105

competitive inhibitors

a molecule that binds to the same active site as an enzyme's substrate, competing with the substrate

106

non-competitive inhibitors

a molecule that binds to a location other than the active site of an enzyme, changing the enzyme's shape so that it cannot bind to its substrate

107

respiration ATP generation

36 for eukaryotes

108

ATP usage to make one glucose

54