Chapter 5: Metabolism, synthesis and degradation of biological molecules

What are metabolic pathways?

Result of energy stored in chemical bonds that is released and transformed. Series of biochemical reactions that turn molecules to different molecules.

Series of enzyme catalyzed reactions

The product of one reactions is the substrate of the next

Metabolic pathways characteristics

Series of separate, intermediate reactions

Each reaction catalyzed by specific enzyme

Similar in all organisms

Compartmentalized

Each controlled by key enzymes that can be inhibited/activated

ATP

Adenosine Triphosphate. Main energy currency in cells.

ATP function

Exergonic: energy released is stored in ATP bonds

Endergonic: When ATP is hydrolyzed, free energy is used to drive this reactions.

Exergonic reactions

Cell respiration and catabolism. ATP synthesis form ADP/Pi

Endergonic reactions

Active transport

Cell movement

Anabolism

Hydrolysis of ATP to ADP/Pi

Redox reactions

Energy transferred by transfer of electrons.

Reduction: gain electrons

Oxidation: lose electrons

More reduced, more energy stored in molecules’s bonds

Redox in terms of water

Thought of as loss or gain of hydrogen atoms. Transfer of hydrogen atoms involve transfers of electrons.

Redox reactions carriers

Cells use coenzyme nicotinamide adenine dinucleotide NAD as electron carriers. NAD+ oxidized NADH reduced

Catabolism

Produces NADH but most energy consuming reactions require ATP. Oxidation of NADH must be coupled to synthesis of ATP from ADP/Pi by OXIDATIVE PHOSPHOLYRATION

Cellular respiration

Metabolic reactions used by cells to harvest energy from food. Energy is released when organic molecules oxidize to CO2

Aerobic respiration

Oxidation of glucose in the presence of oxygen

Glycolysis

Ten reactions

Takes place in cytosol

2 molecules of pyruvate, ATP and NADH

Redox reactions (repeated MP)

6: glyceralhyde 3 phosphate is oxidized and energy is trapped via reduction of NAD to NADH

Substrate level phosphorylation

7: energy released transfer a phosphate from 1, 3 bisphosphoglycerate to ADP, forming ATP.

Pyruvate oxidation

In mitochondria, links glycolysis to citric acid cycle.

Products: CO2 and acetate, bound to coenzyme A to form Acetyl CoA. NAD reduced to NADH

Citric Acid Cycle/ Krebs cycle

8 reactions to form NADH, FADH2, GTP.

In mitochondria

Operates twice for every glucose molecule

Acetyl CoA, Acetyl oxidize to 2 CO2

Oxaloacetate is regenerated at las step

Oxidative phosphorylation

Cells transfer energy from NADH and FADH2 to phosphoanhydride bonds of ATP.

Electron transport

Chemiosmosis

Electron transport

NADH oxidation is used to transport protons across inner mitochondrial membrane = proton gradient.

Chemiosmosis

Diffusion of proton back across the membrane then drives synthesis of ATP

Electron transport characteristics

Electrons from NADH and FADH2 oxidation pass from one carrier to next in respiratory chains. Reaction is Exergonic, released energy used to transport H ions across membrane

Oxidation and reduction coupling

When NADH oxidizes into NAD, the reduction is the formation of water from O2. O2 acts as an electron acceptor and becomes reduced in cells

ATP synthases

H gradient to drive synthesis of ATP by Chemiosmosis - Ion movement across semipermeable barrier from higher concentration to lower region

ATP synthases characteristics

Converts potential energy of proton gradient tinto chemical in ATP

Structure/function of enzyme is shred by living organisms.

Relies on proton gradient across membranes

ATP synthase in eukaryote

Chemiosmosis occurs in mitochondria and chloroplasts

ATP synthase in prokaryotes

Gradient set up across the cell membrane

How are metabolic pathways controlled?

Via the control of enzyme abundance and activity

Feedback inhibition

Product of a pathway binds and inhibits and enzyme that catalyzes an early step of the pathway.

Fermentation

Break down of glucose in absence of oxygen. Its overall yield of ATP is only 2, made at glycolysis. Occurs in cytoplasm

Lactic acid fermentation

Animals and bacteria: end product is lactate

Alcoholic fermentation

Plants and yeast: end product is ethyl alcohol (ethanol)

What is catabolism?

Breakdown products that eventually enter aerobic respiration pathways

Carbohydrate catabolism

Polysaccharides hydrolyze to monosaccharides which enter GLYCOLYSIS

Lipids catabolism

Triglycerides hydrolyze to GLYCEROL, fatty acids are converted into Acetyl CoA that enter CITRIC ACID CYCLE

Protein catabolism

Proteolysis hydrolyze to amino acids which convert to molecules that enter GLYCOLYSIS or CITRIC ACID CYCLE

Nucleic acids catabolism

Hydrolyzed to nucleotides which then break down into phosphates, bases that enter CITRIC ACID CYCLE and sugars that enter GLYCOLYSIS

Anabolic pathways

Macromolecules are synthesized in a series of condensation reactions which requiere energy, most often supplied by hydrolysis of ATP. Subunits that can’t be synthesized become essential nutrients. Often reversals of catabolic

Gluconeogenesis

Citric acid cycle and glycolysis intermediates are reduced to form glucose. Some steps are exact reversals of glycolysis and use same enzymes. Others differ because the energy required at that step is too large

Acetyl CoA vs Citric acid cycle

Fatty acids vs Nucleic acids

System of catabolism & anabolism

Quantity of different molecules are at constant levels in metabolic pools - cells regulate synthesis and breakdown of macromolecules and subunits

What is photosynthesis?

Reverse of aerobic respiration; an anabolic process in which sunlight energy is used to convert CO2 and H2O into carbohydrates and oxygen

Pathways of photosynthesis (Chloroplasts)

Light reaction: light to chemical energy ( ATP & NADPH)

Carbon fixation: ATP and NADPH to produce carbohydrates

Light reactions

Form of electromagnetic radiation, propagated as wave and behaved as photons.

The amount of of energy is inversely proportional to wavelength

Photons are absorbed by specific receptor molecules that are raised to excited state.

Pigments

Molecules that absorb wavelengths in visible spectrum. In plants chlorophyll a & b absorb light energy.

Plant light absorption

Chlorophyll: blue and red light. The rest is mostly green

Accessory pigments ( b carotene)

Light harvesting complexes

Arrangement of pigments that a are bound to membrane proteins

What is a photosystem?

Multiple antenna systems surrounding a reaction center. Span the thylakoid membrane in the chloroplast

Photosystem process

Chlorophyll absorbs light, enter excited state then returns to ground state releasing an excited electron. Is given to acceptor and becomes oxidized to CHL+. Acceptor molecule is reduced. Reaction center has converted light to chemical energy

1st vs last acceptor

Electron acceptor becomes 1st carrier in electron transport system in thylakoid membrane. Final acceptor is NADP that reduces to NADPH

Photophosphorylation

ATP is produced chemiosmotically during electron transport

Photosystem in photosynthesis

1: 700nm absorption of light energy; excited electron to NADP+ reducing it to NADPH

2: light energy at 680nm, oxidizes water, initiates ATP production

Calvin cycle

Energy in ATP & NADPH is used in carbon fixation to produce carbohydrates from CO2. Occurs in storm, each reaction catalyzed by specific enzyme, carbon is reduced.

Calvin cycle processes

Fixation of CO2: CO2 added to RuBP catalyzed by enzyme rubisco

Reduction/sugar production: 3PG reduced to form G3P

CO2 acceptor RuBP is regenerated

Calvin cycle importance

Its products are crucial to earth’s biosphere, since the c-h bonds provide almost all energy for life on earth

Autotrophs vs heterotrophs

Use energy to support own growth/reproduction vs cannot photosynthesize and depend on autotrophs for energy

Photorespiration

Rubisco uses O2 as substrate, but one carbon is oxidized to CO2 instead of becoming fixed.

Increase affinity of rubisco for O2

Higher relative concentration of O2 to CO2 and higher temperatures

Plants in hot environments

Have different photosynthetic systems to reduce photorespiration

C3 plants

First product of CO2 fixation has 3 carbons. Rubisco can fix O2

C4 plants

First product has 4 carbons, reaction is catalyzed by enzyme that does not react with O2. It releases CO2, producing locally high concentration around rubisco. CO2 is fixed in CC and photorespiration is kept at minimum.

CAM plants

Initial and second fixation of CO2 are separated in time not space

Initial occurs at night and CO2 release near rubisco occurs in the day