metabolic processes

Substrate level phosphorylation

The direct addition of a phosphate to an ADP from something else to make ATP or the removal of a phosphate

Oxidation phosphorylation

The synthesis of ATP through the transfer of elections in a series of chemical reactions

Ex.

Redox reactions

A chemical reaction involving the transfer of one or more electrons from one reactant to nether

Oil Rig

Oxidation is loss

Reduction is gain

Example of redox reactions

Combustion

Cellular respiration

A series of redox reaction to create energy in the form of ATP

What is NADH

Nicotinamide Adenosine dinuelectide + hydrogen

FADH2

Flavin Adenosine Dinucleotide + 2 hydrogen

The structure of the mitochondria

• Inner membrane (Cristae)

  folded in on itself

• Matrix - liquid inside the cristae

• outer membrane

Mitochondria function

Site for cellular respiration and photosynthesis

Two phases of cell respiration

• Anaerobic - in the absence of oxygen - glycolysis taking place in the cytoplasm

• Aerobic - in the presence of oxygen - all the other steps

4 main steps of cell respiration

• Glycolysis

• Pyruvate Oxidation

• Kreb cycle

• Electron Transport Chain

Glycolysis

• Glucose is broke down to release 2 pyruvate and energy in the form of ATP

• takes places in the cytoplasm

Step 1 of glycolysis

Hexose kinase converts glucose into glucose-6- phosphate by removing a phosphate from ATP to form ADP

Step 2 of glycolysis

The enzyme phosphogincoisomerase reacts with glucose-6- phosphate to make its isomer fructose-6-phosphate

Step 3 of glycolysis

Phosphofructokinase converts fructose-6-phosphate into fructose 1,6 bisphosphate by removing a phosphate from ATP

Step of glycolysis

Aldolase cuts fructose 1,6 bisphosphate in half to form Glyceraldehyde 3 phosphate (G3P) and dihydroxyacetone phosphate.

Step 5 of glycolysis

The enzyme aldolase quickly turns dihydroxyacetone into GP3

Step 6 of glycolysis

Triode phosphate dehydrogenase oxidizes G3P into bisphosphocglycerate (BPG) by removing electrons/H+ from NAD+ to form NADH (x2)

Step 7 of glycolysis

Phosphoglycerkinase removes a phosphate from BPG to form 3-phosphoglycerate and puts the phosphate on ADP to for ATP (x2)

Step 8 of glycolysis

Phosphoglyceromutase relocates the phosphate on 3-phosphoglycerste to form 2-phosphoglycerste (x2)

Step 9 of glycolysis

A water molecule is removed from each 2-phosphoglycerate by enolase to form phosphoenol pyruvate (x2)

Step 10 of glycolysis

The last phosphate is removed from each phosphoenol pyruvate and added to ADP to form ATP by pyruvate Kinase. Resulting in 2 by pyruvates (x2)

At the end of glycolysis there is?

• 2 pyruvate

• 2 ATP

• 2 NADH

• 2 water molecules

Pyruvate oxidation

At the end of glycolysis, the two pyruvate molecules move into the mitochondria. There, one carbon is removed from each pyruvate and released as carbon dioxide. The hydrogen from that carbon is used to turn NAD⁺ into NADH with the help of an enzyme called pyruvate dehydrogenase. The remaining two-carbon part joins with Coenzyme A (CoA) to form Acetyl-CoA

Result of pyruvate oxidation

2 NADH

On the Carpet In the Kitchen Sally C Saw Five Mice

• Oxaloacetate

• Citrate Synthase

• Isocitrate

• a-Ketoglutarate

• Succinyl - CoA

• Succinate

• Fumarate

• Malate

Step 1 of the kreb cycle

• Acetyl-CoA is binded to oxaloacetate by citrate synthase to create citrate

• Citrate in converted to isocitrate by aconitase

Step 2 kreb cycle

Isocitrate is oxidized removing cabon dioxide and a H+ to reduce NAD+ to NADH due to isocitrate dehydrogenase resulting in a-ketogluterate

Step 3 of kreb cycle

A-ketogluterate is oxidized by removing carbon dioxide, NAD+ is reduced to NADH and CoA is bonded to form succinyl -CoA due ketoglutate dehydrogenase

Step 4 of kreb cycle

Water and succinyl-CoA reacts to produce CoA ATP and succinate due to succinyl CoA synthase

Step 5 of kreb cycle

Succincte reacts with FAD to produce FADH2 and fumerate due to succinate dehydrogenase

Step 6 of kreb cycle

Fumerate produces water and malate due to fumerase

Step 7 of the kreb cycle

Malate is oxidized by NAD to form oxaloacetate and NADH+ due to malate dehydrogenase

Result of kreb cycle

• 6 NADH

• 2 ATP

• 2 FADH

Sugar metabolism

• Penrose and hexose is modified into glucose or fructose to enter glycolysis

• Triose is converted to G3P or dehydroxyaetone phosphate to enter glycolysis

Metabolism of starch and glycogen

• Hydrolysis (addition of water) breaks alpha 1-4 and 1-6 bonds to leave the sugars to enter glycolysis

Metabolism of fats

• Triglycerides split into fatty acids and glycerol

• Glycerol - converted to glucose due to “glucogenisis” or G3P to enter glycolysis

• Fatty acids - are brought to the matrix where it undergoes B- oxidation

B-oxidation

The process splitting a molecule into 2 carbon acetyl groups starting with the carboxyl end

• Turning into acetyl-CoA breaking down 1 ATP and tuning the resulting NADH and FADH into ATP

Metabolism of proteins

• Undergoes deamination removing the amp group and turns it into ammonia

• Other reactions converts the different side chains into different products in glycolysis and krebs cycle

Examples of protein metabolism

Leucine → acetyl-CoA

Alanine → pyruvate

Proline→ a-ketogluterate

Anaerobic respiration

• Oxygen is only made at the end of the ETC and it receives the electrons from NADH and FADH2

• without oxygen the electrons can't go anywhere resulting in NADH and FADH2 to not get oxidized

Results of a lack of oxygen

• Kreb need NAD+ and FAD not NADH and FADH+ so this will stop the whole kreb cycle (shuts down mitochandria)

• glycolysis keeps going producing 2 ATP and 2 NADH because its anaerobic but a pathway needs to be made

Fermentation

The process when NADH is oxidized by breaking pyruvate into another product

Types of fermentation

• Alcohol fermentation

• lactic acid fermentation

Alcohol fermentation

• Done by yeast and bacteria

• Pyruvate loses a CO2 and turns into acetaldehyde

• NADH gives an H+ to reduce acetaldehyde into ethanol

Latin acid fermentation

• Done in all living organisms that anaerobically respire

• pyruvate is converted to lactic acid by removing H+ from pyruvate.

Electron transport chain

A series of proteins that are found in the cristae. Each protien accepts electrons . and pumps protons into the intermentrane space

Etc process

NADH and Fadh2 release their electrons in the protiens to move across the chain. As the electrons move from protein to protien protons into the intermembrane space.

What causes pH drop?

The increase of H+ cause the pH to drop making the the intermembrane space more acidic

Electrochemical gradient

The gradient that forms form the intermenbrane space and the matrix this remains consistent as the charge of the protons make them unable to diffuse

Final electron acceptor

Oxygen accepts the electrons from complex 4 resulting in water

What pumps H+?

The energy evenly released during the oxidation of each protein is enough to pump the H+ from the matrix to the intermembrane space

ATP synthase function

To synthesize ATP

Pumps H+ back into the matrix and uses that energy to fuse an inorganic phosphate to ADP (H+ serves as a battery)

How much ATP is made per FADH2 and NADH

NADH →3 ATP

FADH2 → 2 ATP

How much ATP is made at the end of aerobic respiration?

36 ATP is made (theoretical yield)

Why is it not exactly 36?

• H + is not completely impermeable to the membrane so some are lost

• NADH from glycolysis need to be actively transport into the mitochondria losing 1 ATP per NADH

Types of glucose formation

Photosynthesis → use light

Chemosynthesis → uses hydrogen sulfide and extreme temperature

Photosynthesis equation

Sunlight + 6CO2 + H2O → C6HI2 + 6O2

Where does photosynthesis the place?

The thylokids in the mitochondrial matrix

Pigments

The molecules just absorb light energy efficiently

Photons

Tiny bundles of light energy

Chlorophyll a

• Is a long hydrocarbon chain attended to an 8 ring structure (Porphyrin) and a methyl group

• Essential for photosynthesiS

Chlorophyll B

• Is a long hydrocarbon chain attended to an 8 ring structure (Porphyrin) and an aldehyde

Electromagnetic radiation

• Light is a form of electromagnetic radiation

• it has particle duality - sometime its a wave and others it can be a particle

How do we see color?

• Each color has its own type of photon wavelength. When light strikes pigment molecules the color that is seen is reflected while what's not is absorbed

Have are the main stages of photosynthesis

• Light dependant reaction

• light independent reaction

Light dependent reaction

• Absorbs light energy and converts it into chemical

• occurs in the thylakoids

photosynthetic reaction centres (PRCs)

• The series of protiers on the thylakoids membrane

• made of photosystems (1 and 2) that absorb light

Light independent reaction intro

• ATP and NADPH are now found in the stroma of chloroplast are used to power this reaction

Stage #1 of the light independent reaction

3 CO2 + 3 ribulose bisphosphate (3RuBP) = 6 Phosphoglycerate (PGA)

• Using the enzyme ribulose bisphosphate carboxylase

Stage #2 of light independent reaction

6 ATP +6 phosphoglycerate →6 bisphosphoglycerate (BPG)

6 NADPH + 6 BPG → glyceraldehyde 3 phosphate + NADP+

Stage #3 of the light independent reaction

2G3P → glucose (most do 2 cycles to get 2 G3P)

5 G3P → 3 ribulose-5 - phosphate molecules

3ATP + 3 ribulose －5-phosphate → ribulose bisphosphate

The restarts

C3 cycle

The Calvin cycle because the first stable molecule is 3 carbons long (RuBP)

C4 Cylce

C4 photosynthesis or CAM when the first stable molecule is 4 carbons long (RuBP+CO2)

Alternate mechanisms of carbon fixation

• The Calvin cycle thrives in cooler climate so hotter/dryer cause water loss when the stomata opens to get CO2

Photorespiration

Photosynthesis continue to consume CO2 and H2O and producing O2 causing an increase in O2 stoping stage 1 of the Calvin cycle

Reaction: O2 + RuBP + phosphoglycerate + phosphglycate

• Bad takes a lot of energy

C4 photosynthesis

Co2 is bonded to a phospheonol pyruvate to make oxaloacetate

And is transported into a bundle sheath (made of wax). The CO2 is put into the Calvin cycle where C4 and C3 happen of the same time in different placeses

Crassulacean acid metabolism (CAM)

Co2 is stored as crassulalean acid before it's brought into the bundle sheath. CAM or a form of C4 happen at night and the CO2 is entered into the stomata. During the day the Calvin cycle happens