8.1-8.3: Metabolism IB Biology

Enzyme

proteins that are catalysts to speed up chemical reactions

How enzymes work

lower reaction activation energy, break and form chemical bonds

Active site

region on enzyme that protein binds to substrate

Factors that affect enzyme activity

pH, temperature, substrate concentration

Denaturation

modifying molecular structure of a protein caused by extreme temperatures

Immobilized enzymes

enzymes that are attached to a material, used commercially (biofuels, medicine, food production)

Metabolism

sum total of all reactions that occur in cells

Metabolic pathway

series of steps toward a final product, each step is catalyzed by a different enzyme

Linear pathway

glycolosis

Cycle pathway

Krebs cycle, Calvin cycle

Enzyme inhibitor

substrate that binds to enzymes and reduces enzyme activity, keeps substrate from binding

non-competitive inhibitor

binds to the enzyme at a location other than the active site, but changes the shape of the active site so substrate can't bind

Allosteric site

A site on an enzyme other than the active site, to which a specific substance binds, thereby changing the shape and activity of the enzyme.

End product inhibition

enzymes can be regulated by substances that bind to sites away from the active site

purpose of end product inhibition

cells save energy when there is excess product in the reaction steps

Activation energy chart

Paradigm shifts

chemiosmotic theory

Cell respiration

the controlled release of energy from glucose to produce ATP

CO2 is changed from gas to solid in photosynthesis

carbon fixation

Source of oxygen (O2) released into the air as a product of photosynthesis

water

Type of light that is least useful for photosynthesis in plants

white

Factors that influence the rate of oxygen production in photosynthesis

temperature, light intensity

Product of light reactions and consumed by the Calvin cycle

ATP

When chloroplast pigments absorb light

their electrons become excited

Why is light important in photosynthesis?

To produce ATP and split water molecules

The energy used to produce ATP in light reactions of photosynthesis comes from

the movement of hydrogen ions through a membrane

Reason for cellular respiration

to convert nutrient/macromolecules into usable energy (ATP) to fuel cellular functions

Glycolysis summary

rearrange and convert glucose into pyruvate

Link reaction summary

convert pyruvate to acetyl group

Krebs Cycle (Citric Acid Cycle) summary

harvest acetyl group energy

Electron transport chain summary

transfer energy stored in high energy electrons to produce ATP

Oxidation

loss of electrons

Reduction

gain of electrons

Electron carrier

accept and give up electrons, when reduced, they carry the electrons to the electron transport chain

Glycolysis

splitting the sugar

Glycolysis location

cytoplasm

Stages of glycolysis

phosphorylation, lysis, oxidation, ATP formation

Phosphorylation

2 ATP used to add phosphates to the glucose

Lysis

splits into two 3 carbon sugars

Oxidation

hydrogen atoms removed from each triose phosphate to reduce NAD+ to NADH

ATP formation

energy released from sugar intermediates is used to synthesize ATP

Inputs of glycolysis

1 glucose, 2 ATP

Outputs of glycolysis

4 ATP (net gain of 2), 2 NADH, 2 pyruvate

Outer membrane

boundary between inside and outside of the mitochondria

Inner membrane

contains electron transport chain and ATP synthase

Cristae

infoldings of the inner membrane that increase surface area

Inner membrane space

small spaces that allow proton build up to create a concentration gradient for oxidative phosphorylation

Matrix

contains enzymes for Krebs cycle and Link reaction

Location of the link reaction and the Krebs cycle

matrix

When is pyruvate decarboxylated

when it enters the matrix

Decarboylated

carboxyl group removed

What happens to the carbon when pyruvate is decarboxylated

leaves as CO2

What forms acetyl CoA

Coenzyme A joins with the acetyl group

Inputs of link reaction

2 pyruvate

Outputs of link reaction

2 CO2 (waste), 2 NADH, 2 acetyl CoA

How is 6 C (citric acid) formed

acetyl CoA transfers acetyl group (2 C) to a 4 C molecule already in the Krebs cycle

Oxaloaetate

4 C carbon molecule

How is NAD+ reduced to NADH

Citric acid is decarboxylated and oxidized

When NAD+ is reduced, what is released

CO2

NADH

5 carbon molecule

When the 5 C molecule is further decarboxylated and oxidized, what is formed

4 C molecule

When the 4 C molecule is further decarboxylated and oxidized, what is formed

oxaloacetate (4 C), NADH, FADH2, ATP

Where are the carbons from the original glucose molecule at the end of the Krebs cycle

gone

Inputs of Krebs cycle

2 Acetyl CoA

Outputs of Krebs cycle

2 ATP, 6 NADH, 2FADH2, 4CO2

2 stages of oxidative phosphorylation

electron transport chain and chemiosmosis

Electron transport chain cell respiration

series of proteins embedded in the inner membrane of the mitochondria

What happens to NADH and FADH2 in the ETC

give up their electrons (oxidized) to the electron carrier proteins (reduced) of the ETC

Where is the energy from that is used to pump H+ ions to create proton gradient

the passing of the electrons from protein to protein to release energy

Concentration/proton gradient

created my the accumulation of hydrogen in the intermembrane space

Chemiosmosis

once accumulated, H+ ions flow back to the matrix through ATP synthase (special protein channel)

ATP synthase

Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP

Amount of ATP produced by chemiosmosis

32 ATP

Final electron acceptor of the ETC

oxygen

Water produced in the ETC

oxygen collects spent electrons as the foll out of the ETC and H+ ions

If there is no O2 in the ETC

electron flow stops and NADH cannot be re-converted to NAD+ (NAD+ runs out which stops link reaction and krebs cycle)

cellular respiration equation

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

What is the goal of aerobic respiration

break down glucose to produce energy

2 stages of photosynthesis

light dependent reactions and light independent reactions (Calvin cycle)

photosynthesis equation

6CO2 + 6H2O + e (light) --\> C6H12O6 + 6O2

Thylakoid membrane

large surface area for light dependant reactions

Stroma

area outside the thylakoids, contains enzymes for the Calvin cycle

Thylakoid space

small space inside the thylakoid

Light dependant reactions

light energy converted into chemical energy (NADPH and ATP) to be used in Calvin cycle

Photosystems

groups of chlorophyll molecules that absorb sunlight in the thylakoid membrane

Stages of light dependant reactions

photoactivation, photolysis, electron transport chain, chemiosmosis & ATP synthesis, NADP reduction

Photoactivation

Chlorophyll in photosystem II absorbs light which excites its electrons to a higher energy state

Order of photosystems

photosystem II then photosystem I

Photolysis

water is split by light to replace the lost electrons from PSII

By-product of photolysis

oxygen

Electron transport chain photosynthesis

excited electrons passed along a series of electron carriers through a series of redox reactions from photosystem II to photosystem I

Chemiosmosis & ATP synthesis

as electrons move down ETC, they release energy which is used to pump hydrogen ions into the thylakoid space which creates a proton gradient

When proton gradient accumulates in photosynthesis

protons diffuse across the membrane to the stroma through ATP synthase which allows ATP synthase to make ATP

Photophosphorylation

The production of ATP by chemiosmosis during the light reactions of photosynthesis.

NADP reduction

light strikes PSI, which re-excites electrons to higher energy state, forms NADPH to be used in Calvin cycle

Final electron carrier in photosynthesis

NADH+

Photophosphorylation types

non-cyclic and cyclic

non-cyclic photophosphorylation

NADPH produced at the end

cyclic photophosphorylation

doesn't produce NADPH, the electrons move through the electron transport chain releasing energy to pump H+ ions to thylakoid space by NADP isn't available to be reduced, so the electrons return to PSI

Input of light dependent reactions

light, water