IB Bio HL Unit 5

ATP

The molecule that serves as the energy currency of the cell

ATP monomer

a modified nucleotide

Production of ATP

mitochondria, aerobic cellular respiration

Processes where ATP is used

active transport, anabolic reactions, muscle contractions, cellular movement

ATP structure

1 adenine, 1 ribose sugar, 3 negatively charged phosphate groups

ATP Hydrolysis

energy is released when the 3rd phosphate is broken off due to the bonds between the 2nd and 3rd phosphate bonds breaking

ADP

Adenosine diphosphate

ADP phosphorylation

adding a phosphate group to ADP, requires energy from the breakdown of food molecules (like glucose) through cellular respiration

Diagram of ATP-ADP cycle

ATP loses a phosphate due to hydrolysis (exergonic) and turns into ADP. ADP gains a phosphate from phosphorylation (endergonic) and turns back into ATP.

Photosynthesis

transforming light energy from the sun into chemical energy (organic molecules)

Photosynthesis equation

6CO₂ + 12H₂O —> C₆H₁₂O₆ +6O₂ + 6H₂O

autotroph

organisms that can produce their own chemical energy (organic compounds). also called producers

phototroph

autotrophs that use light to produce organic compounds (aka photosynthesis)

Producers (autotrophs)

source of energy in ecosystems

3 examples of photosynthetic organisms

Plants, algae, cyanobacteria

location of photosynthesis in plants

mesophyll cells in leaves

endosymbiosis

why chloroplasts have two membranes, organelle was engulfed by eukaryotic cell

thykaloid

flattened, membrane bound sacs (high sa:v ratio)

thykaloid membrane

outer part of thykaloid

thykaloid space

inner region of thykaloid

function of thykaloids

light-reaction, contains chlorophyll embedded in membrane

granum (pl: grana)

stack-like arrangement of thykaloids in chloroplast to maximize light absorption

stroma

fluid filled space between inner membrane and thykaloid membrane

stroma function

contain enzymes and materials for Calvin cycle, also location of Calvin cycle

3 spaces in a chloroplast

intermembrane space (between inner and outer membrane), stroma(between inner membrane and thykaloid membrane, thykaloid space (within thykaloid membrane)

lamellae

bridge-like structure that connects grana

diagram of chloroplast

[image]

wavelength-color of light relation

visible light is a part of the electromagnetic spectrum

pigment

molecules that absorb light

pigment vs wavelength

pigments ABSORB light, wavelengths REFLECT light

3 pigments in plants

Chlorophyll, xanthophyll, carotenoids.

major photosynthetic pigment

chlorophyll

chlorophyll and chloroplasts

chlorophyll reflects green light and absorbs all other colors. this makes chloroplasts green.

absorption spectrum

a graph measuring the different wavelengths of light absorbed by a particular substance or pigment. each line represents one pigment

light absorption and photosynthesis

plants have several different types of pigments, so overall rate of photosynthesis is a result of a combination of ALL pigments absorbing light

action graph

a graph that represents the effectiveness of different wavelengths of light on photosynthesis

difference between action and absorption graphs

absorption spectrum measures 1 pigment, action spectrum measures all pigments

paper chromatography

a lab technique used to separate mixtures of substances as they move up the paper

how pigments are separated during paper chromeotography

pigments dissolve in the solvent and will separate based on solubility. the more soluble the pigment is, the further it travels

Retention factor R_f

ratio of distance moved by a pigment to the distance moved by the solvent, in mm.

formula for R_f

distance of pigment/distance of solvent (in mm)

Calvin Cycle location

Occurs in the stroma

Calvin Cycle desc.

uses ATP and NADPH from light reaction

Calvin Cycle input/output

input is CO₂, output is sugar (glucose)

light reaction location

occurs in thylakoids

light reaction desc.

utilizes photosynthetic pigments to absorb light

light reaction input/output

splits H2O and produces O2 as a byproduct, creates ATP and NAPDH for CC. CC gives light reaction ADP and NADP+

light reaction/CC relation

light reaction creates ATP and NAPDH for CC. CC gives light reaction ADP and NADP+

reduction reaction

gaining electrons/negative charges (Reduction Is Gain)

oxidation reaction

losing electrons (Oxidation Is Loss)

photosystems

integral proteins complexes within the phospholipid bilayer

photosystem location

thylakoid if eukaryotic, cyanobacteria if prokaryotic

process of photoactivation in photosystems

photons strike pigment molecules, which excites electrons. the electrons are transferred between an array of pigments before they reach a reaction centre, where they are emitted from the photosystem. OXIDATION REACTION

difference between photosynthesis I and II

PS II comes before PS I. PS II is attracted to a lower wavelength than PS I.

electron transfer chain (ETC)

where electrons go after leaving the reaction centre, part of PS II

photolysis

the process of using light energy to break water molecules in order to replace missing electrons in PS II

equation for photolysis

2H₂O →4H⁺ + O₂ +4e^-

photolysis location

thylakoid space by PS II

what happens to protons (H⁺ ) in photolysis

remain in thylakoid space and begin to build concentration gradient

what happens to O₂ in photolysis?

diffuses out of the chloroplast and into the atmosphere

what happens to electrons (e^-) in photolysis?

transferred from water to PS II

structure of first ETC

a series of integral protein complexes within a thylakoid membrane

functions of 1st ETC

transfers electrons from PS II to PS I, harnesses extra energy from electrons to pump protons into thylakoid space. establishes a high concentration gradient (active transport)

3 ways protons are concentrated inside a thylakoid

1) protons produced in thylakoid during photosynthesis, 2) protons are pumped into thylakoid by ETC proton pump, 3)thylakoids are small spaces so protons accumulate quickly. ALL of this allows for facilitated diffusion of protons OUT of thylakoid.

proton gradient function

allows for passive transport of protons OUT of thylakoid (down concentration gradient). MUST be used for facilitated diffusion

chemiosmosis

the diffusion of H⁺ down its concentration gradient through ATP synthase (facilitated diffusion)

ATP synthase

a transmembrane integral proteins that performs ADP phosphorylation to create/synthesize ATP

ATP synthesis through chemiosmosis

As the H+ diffuses through ATP synthase, it causes the enzyme to turn providing energy needed to phosphorylate ADP into ATP

photophosphorylation

using photosynthesis to turn ADP into ATP

destination for ATP in light reaction

ATP will go to power the Calvin cycle

process in photosystem I

photoactivation occurs in PS I

destination of excited electrons after leaving PS I

protons go to reaction centre, then transferred to NADP⁺ Reductase

replacement of missing electrons in PS I

electrons from PS II via first ETC will replace missing electrons from PS I

NADPH function

electron carrier enzyme, reduced form

NADP⁺

electron carrier enzyme, oxidized form

NADP⁺ reduction process

electrons leave PS I and transferred to NADP⁺ Reductase, where they will combine electrons to form NADPH. occurs on stroma side of thylakoid membrane

destination of NADPH in light reaction

NADPH (full of electrons) will go to the Calvin Cycle to drop off electrons

flow of electrons in non-cyclic photophosphorylation

electrons flow from water →PS II →1st ETC →PS I →NADPH

flow of electrons during cyclic photophosphorylation

sometimes electrons from PS I go back to 1st ETC by accident, but ATP is still made normally in ETC

3 phases of Calvin Cycle

carbon fixation, reduction, regeneration

carbon fixation

attacing a CO2 to a Ribulose biphosphate (RuBP)

RuBisCO

enzyme that performs the carbon fixation process

rubisco characteristics

slow enzyme, non-efficient, high energy requirement for CC

photorespiration

adding an O₂ instead of CO₂, making rubisco less efficient b/c molecule cannot continue through CC

rubisco CO₂ concentration

rubisco works best at a high CO₂ concentration to reduce the chance O₂ is accidentally added to RuBP

event after initial carbon fixation

each of the resulting 6-carbon compounds breaks into 2×3 carbon compounds called glycerate 3-phosphate (GP)

reduction phase

GP molecules converted into trioses phosphate (aka glyceraldehyde 3-phosphate G3P)

inputs of reduction phase

6 GP, 6 ATP, 6 NADPH

outputs of reduction phase

6 TP/G3P, 6 ADP, 6 NADP⁺

reduced molecule in reduction phase

GP gains electrons to become TP

molecules exiting CC after reduction phase

1 TP exits cycle (5 remain)

regeneration

5 TPs remaining in cycle (15 carbon atoms) are rearranged into 3 RuBP. requires energy from 3 ATP (creates ADP)

inputs of regeneration

5xG3P/TP, 3xATP

outputs of regeneration

3xRuBP

“regeneration” in regenerating phase

CO₂ receptor is recreated, allowing for CC to continue

glucose formation in Calvin cycle

TP is turned into glucose 5 G3P

molecules made from CC outputs

carbs, amino acids, nucleotides

light dependent reaction

alternate name for light reaction b/c it is dependent on light, but light is not the only thing needed

light independent reaction

alternate name for CC, but CC relies on ATP/NADPH from light reaction

cellular/aerobic respiration

utilizing oxygen when breaking down organic molecules, occurs in mitochondria