Notes 

Chapter 7 (Cellular respiration, Fermentation, and secondary metabolism.)

Cellular respiration –

Refers to the metabolic reactions that a cell uses to get energy from food and release waste.

-Training for endurance, small blood vessels become more extensive and muscle cells produce more mitochondria

-The “burning” of calories is very controlled while burning of wood is NOT

Aerobic respiration – When oxygen (O2) is used in ATP.

-CO2 is formed in the process of oxidation of organic molecules

-Equation for respiration of glucose:

C6H12O6 + 6 O2 à 6 CO2 + 6 H2O + Energy intermediates + Heat

ΔG=-686 kcal/mole

*Large amounts of energy are stored in covalent bonds of glucose.

*The three intermediates are ATP, NADH, and FADH2

Four pathways in Aerobic respiration:

1) Glycolysis

2)Pyruvate breakdown

3)Citric Acid Cycle 

 4)Oxidative phosphorylation

1Glycololysis

Glucose-6carbon molecule is broken down into 2 pyruvates(3-carbon) molecules and 2ATP and 2NADH molecules are produced.  *Occurs in the cytosol*

2)Breakdown of pyruvate to an acetyl group.

2 Pyruvate molecules enter the mitochondrial matrix and each pyruvate is broken into 1 CO2, 1 acetyl group(2-carbon) and 1 NADH is formed.

3)Citric Acid Cycle

Each acetyl group is incorporated into an organic molecule, and later oxidized to liberate 2-CO2 molecules.

Each acetyl group forms 1-ATP, 3-NADH, and 1 FADH2.

4)Oxidative phosphorylation:

The energy from the Hydrogen bond in NADH and FADH2 is converted into ATP.

Substrate-level phosphorylation – When an enzyme directly transfers a phosphate from an organic molecule to ADP.

Chemiosmosis – A process for making ATP in which energy stored in an ion electrochemical gradient is used to make ATP from ADP and Pi.

Glycolysis – A metabolic pathway that breaks down glucose to pyruvate. It involves the breakdown of glucose, a simple sugar

*German Biochemists Gustav Emden, Otto Meyerhof, and Jacob Parnas determined glycolysis involved 10 steps with an enzyme at each step.

*This process of glycolysis is virtually identical in all living species.

Three phases of glycolysis

1)Energy investment phase

2) Cleavage phase 

3) Energy liberation phase

*Glycolysis is controlled by feedback inhibition of ATP.

ATP binds to an allosteric site of phosphofructokinase that renders the enzyme ineffective.

Biochemistry – The study of the chemistry of living organisms

Metabolic cycle – A biochemical cycle in which particular molecules enter while others leave; the process is cyclical it involves a series of organic molecules that are regenerated with each turn of the cycle.

Citric acid cycle (Krebs cycle)– A cycle that results in the breakdown of carbohydrates to carbon dioxide; also known as the Krebs cycle.

*Discovered by Hans Krebs in the 1930s, but wasn’t awarded the Nobel Prize until 1953.

*One turn in the Krebs cycle produces 2 molecules of CO2, 3-NADH, 1-FADH2 and 1 ATP via GTP.

Oxidative phosphorylation – NADH and FADH2 have had electron recovered and have thus become oxidized and ATP is made by phosphorylation of ADP.

Respiratory chain – The electron transport chain because the Oxygne we breathe is used in this process.

*Redox reactions occur at each step*   p. 144-145

H+ electrochemical gradient – A transmembrane gradient for H+ composed of both a membrane potential and a concentration difference for H+ across T cells.

Proton-motive force – The H+ electrochemical gradient (because hydrogen ions consists of protons)

*NADH dehydrogenase, cytochrome b-c, and cytochrome oxidase are H+ pumps.

*The energy to pump the H+ ions into the intermembrane is from the free electron.

** Look where the NADH and the FADH2 enter.**

ATP synthase – Second event of oxidative phosphorylation, it is the synthesis of ATP by an enzyme.

*the H+ flow back through the prtein embedded ATP synthase that harness the energy to synthesize ATP from ADP.

*1978 Peter Mitchell was awarded a Nobel Prize in chemistry for this.

Maximum ATP is rarely reached due to:

1)Some of the 10 NADH and 2 FADH2 may be used for anabolic pathways in the cell.

Ex. Synthesis of glycerol and lactate(muscle cells with no O2)

2)The mitochondria may use the H+ gradient for another purpose.

Ex. Uptake of pyruvate via a H+/pyruvate symporter.  Fig 7.4 p. 141

*Read the Racker and Soekenius experiment on p. 146 and feature investigation p. 147.*

ATP synthase figure 7.10 p.146.

·         ATP synthase makes ATP by using the H+ electrochemical gradient as energy.

·         It is made of subunits a, b, and c.

Each time a H+ passes through a c unit, a conformational change causes the γ subunit to turn clockwise 120o.

Conformation 1-ADP and Pi bind with good affinity.

Conformation 2-ADP and Pi bind so tighly ATP is formed.

Conformation 3-ATP is released.

1970’s Paul Boyer proposed the concept of the rotary machine.

1994 John Walker and colleagues determined the 3-D structure.

Genomes and Protenomes connection

1931 German physiologist Otto Warburg discovered cancer cell use glycolysis for ATP

*p. 149 Fig. 7.12

Glycolytic enzymes are overexpressed in cancer cells.

*Both genetic and physiological factors increase production of glycolytic enzymes.

Changes in DNA cause the formation of tumors.

Tumors exhibit hypoxia- Oxygen deficiency.

*Cancer cells grow quickly because of hypoxia.

Figure 7.13 p. 150 Show the connection of proteins, carbohydrates and fats to energy.

Proteins break down into Amino Acids.

*Because Amino Acids have a defferent R group on the A.A., they enter at different levels.

Fat is broken down into glycerol and fatty acids.

*Glycerol can be modified to glyceraldehyde-3phsophate and enter glycolysis at step 5.

*Fatty acid tails can be modified and bind with Acetyl CoA then enter the Citric Acid Cycle.

Carbohydrates are broken into sugar.

***Using the same pathways make metabolism more efficient.

Carbohydrates can be used to manufacture parts of amino acids, fats and nucleotides.

Ex. Glucose-6phosphate of glycolysis is used to construct sugar and phosphates portion of the nucleotide.

Oxaloacetate of the citric acid cycle is used as a precursor for purines and pyramidines.

Portions of Amino Acids can be made from pyruvate and oxaloacetate.

7.2 Anaerobic Respiration and Fermentation

Anaerobic – Environment that lacks oxygen

(Microbes in the intestines, bacteria deep in soil, muscle cells during strenuous exercise.)

*Many bacteria, archaea and some fungi in anerobic conditions still oxidize organic molecules to get sufficient energy.

Anaerobic respiration – The use a substance other than O2 as the final electron acceptor of an electron transport chain.

Ex. Escherichia Coli-Bacteria in the intestines that uses Nitrate(NO3-) as the final e- acceptor.

*fig. 7.14 p. 151-Look at the red line

*Chemiosmosis is achieved in three ways:

1)NADH dehydrogenase pumps H+ out of the cytoplasm.

2)Ubiquinone picks up H+ in the cytoplasm and carries it to the other side of the membrane.

3)Reduction of Nitrate(No3-1) to Nitrite(NO2-1)

*Many animals and yeast can only use O2 as the final e- acceptor.

*Under anaerobic conditions, cells do NOT use the citric acid cycle or electron transport chain, but make ATP only via glycolysis.

Anaerobic conditions cause an increase in NADH and a decrease in NAD+.

*This is bad because NADH haphazardly donates electrons which causes formation of free radicals.

*Free radicals damage DNA and proteins.

*NAD+ is needed to keep glycolysis running and produce ATP via substrate-level phosphorylation.

*Muscle cells avoid this NADH to NAD+ by producing lactate.

*Yeast cells avoid this NADH to NAD+ by producing ethanol.

Fermentation – The breakdown of organic molecules to harness energy without any net oxidation.

**(No electron removal.)

A)     Lactate-Equation on p.152.

B)     Ethanol-Equation on p.152.

*Electrons are removed from glucose, but they are donated back to an organic molecule.

*Fermentation is far less efficient than Oxidative Phosphorylation. (34-38 ATP vs. 2 ATP)

Reasons why fermentation is less efficient:

A)     Glucose is NOT completely Oxidized to CO2 and H2O.

B)     NADH mad during glycolysis in fermentation is NOT made into ATP.

Primary metabolism – The synthesis and breakdown of molecules and macromolecules that are found in all forms of life and are essential for cell structure and function. (Chapter 6)

Secondary metabolism – Involves the synthesis of molecules

Secondary metabolites – Synthesized molecules that are NOT essential for cell structure and growth

-Generally unique to one species or a group of species

-These metabolites enhance the chance of survival and reproduction

Examples:

1)      Insects that taste bad to prevent animals form eating them

2)      Plants or bacteria release chemicals that prevent growth of other plants/bacteria

3)      Strong smells or colors attract or repel other organisms

*These are very common in plants, bacteria, and fungi

*Animals tend to produce relatively few

*Humans use these metabolites for cooking to antibiotics

Secondary metabolites are divided into four groups

I)Phenolic- compounds containing a benzene ring with a hydroxyl group

*Phenol is not common, but amino acids such as phenylalanine and tyrosine are common

Divisions of phenolics

1)      Flavonoids – molecules that produce a lot of flavor or smells

*remarkable antioxidants

*scientists think plants use these to protect against UV damage

Ex. Blueberries, broccoli, spinach, and dark chocolate

2)      Tannins – large polymeric molecules composed of many phenolic units

*typically deter animals because the bitter taste or toxic effects by inhibiting digestive enzymes

*Used to make leather by combining with protein in the skin

*This process is called tanning, because the skins turn a tan color

Abundant in grape skins, but break down as wines age.

3)      Liguins – Large polymers found in plant cell walls

*These strengthen plant cells and the make up about 1/3 weight of dry wood

*To make paper, lignius needs to be removed from the wood (more pliable)

II)Alkaloids – A group of secondary metabolites that contain nitrogen and usually have a cyclic, ring-like structure. Examples include caffeine, nicotine, atropine, morphine (depressant), ergot, quinine, and capsaicin

-Common in plants and sometimes fungi, and shellfish

-Animals can taste these bitter molecules, but birds can NOT (this helps disperse seeds)

-Capsaicin is the hot in peppers and atropine is the deadly toxin in night shade – causes the heart to beat extremely fast

III)Terpenoids – A group of secondary metabolites synthesized from five-carbonisoprene units. (called isoprenoids)

-Volatile – become gases as a result produce strong odors

-may be used to attract pollinators or repel animals

Ex. Mint, cinnamon, fennel, cloves, cumin, caraway, and tarragon

IV)Polyketides – A group of secondary metabolites produced by diverse organisms. Examples include streptomycin, erythromycin, and tetracycline

-Produce by bacteria, fungi, plants, insects, dinoflagellates, mollusks, and sponges

-these are generally highly toxic to other organisms

-these toxic effects are very specific, which makes them valuable medical tools

-strong colors such as carotenoids (give carrots, salmon, goldfish, and flamingos color)