UNIT 8. Bioenergetics and oxidative metabolism: Mitochondria and peroxisomes.

1. Mitochondria

1.1. Organization and function of mitochondria

1.1.1. A double-membrane system: **Inner** and **outer** **membranes** separated by an intermembrane space

1.1.1.1. The matrix and inner membrane rrepresent the major working compartments of mitochondria

1.1.1.2. The **outer **membrane

1.1.1.2.1. permeable to small molecules through Porins (free diffusion channels for molecules < 1000 daltons)

1.1.1.3. The **inner** membrane:

1.1.1.3.1. increase its surface with cristae

1.1.1.3.2. contains high percentage of proteins (70%): Oxidative phosphorylation related proteins and proteins for metabolite transport between the cytosol and the mitochondria

1.1.1.4. The **intermediate space**

1.1.1.4.1. High proton (H+) concentration

1.1.1.5. Mitochondria are constantly fusing with one and other and dividing: In most cells mitochondria exist as part of a large interconnected network

1.1.2. The Mitochondrial lumen: **Matrix**

1.1.2.1. contains

1.1.2.1.1. The mitochondrial genetic system

1.1.2.1.2. The enzymes responsible for the central reactions of oxidative metabolism

1.1.3. The inner membrane folds into the matrix: The cristae

1.2. Electron transport and Oxidative phosphorylation

1.2.1. **Glucose,** is a major source of cellular energy. Its complete oxidative breakdown to CO2 and H20 releases a large amount of energy in a three step process, each step is coupled to the synthesis of ATP as the energy-storage form

1.2.1.1. 1: Glycolysis (in the cytosol)

1.2.1.1.1. 1 y 2: 4 ATP + 10 NADH + 2 FADH

1.2.1.2. 2: Krebs cycle or acid citric cycle (in the mitochondria matrix)

1.2.1.2.1. 1 y 2 : 4 ATP + 10 NADH + 2 FADH2

1.2.1.3. 3:Electron transport and oxidative phosphorylation (in the inner membrane of mitochondria)

1.2.1.3.1. 32/34 ATP

1.2.2. Four complexes in the inner mitochondrial membrane - Complexes I, III and IV pump protons from the matrix to the intermembrane space

1.3. The genetic system of mitochondria

1.3.1. Mitochondria contain their own genetic system, separate and distinct from the nuclear genome of the cell

1.3.1.1. Are circular DNA molecules (like in bacteria) and are present in multiple copies per organelle

1.3.1.2. They vary considerably in size between different species

1.3.1.3. They encode 13 proteins in mammals

1.3.1.4. Some codons specify different amino acids in mitochondria than in the universal code

1.3.1.5. Mutations in mitochondrial DNA are transmitted to the next generation by the mother

1.4. Protein import and lipid incorporation into mitochondria

1.4.1. Protein final destination in Mitochondria are mainly the inner membrane and the matrix – Tom and Tim family proteins

1.4.1.1. 1- N terminal pre-sequences of 15-55 amino-acids with multiple positively charged amino acid residues usually in an alpha helix that direct the protein import to the mitochondrial matrix or the inner membrane.

1.4.1.2. 2- Internal mitochondrial import signals are transmembrane sequences recognized by mobile chaperones (Tim9-Tim10) in the intermembrane space that escort the unfolded protein to the Tim 22 complex

1.4.1.3. 3- Transmembrane proteins encoded by the mitochondrial genome aresynthesized on mithocondrial ribosomes and targeted to the Oxa1 translocase

1.4.2. Mitochondria lipids come from the smooth ER and Golgi

1.4.2.1. Mitochondria only synthesize cardiolipin and phosphatidyethanolamine from phosphatidylserine

1.4.2.1.1. With four fatty acid chains

1.4.2.1.2. Localize in the inner membrane

1.4.2.1.3. Improves the efficiency of oxidative phosphorylation restricting proton flow across the membrane

1.4.2.2. Lipids transfer between the ER and mitochondria takes place at sites of close contact between the ER and mitochondrial membranes

1.4.3. The phospholipid transfer proteins transport single lipids between ER-Mitochondrial membranes

1.5. Transport of metabolites across the inner membrane

1.5.1. Transport is

1.5.1.1. mediated by membrane-spanning proteins (small molecule transporters)

1.5.1.2. driven by the electrochemical gradient

1.5.2. **ATP/ADP transport** The Adenine Nucleotide Translocator transports one molecule of ADP into the mitochondrion inexchange for one molecule of ATP transferred from the mitochondrion to the cytosol

1.5.3. This exchange is driven by the voltage component of the electrochemical gradient -> ATP/ADP exchange is energetically favorable.

1.5.4. Phosphate ions (Pi) transport The Phosphate Translocator exports hydroxyl ions (OH-) which are higher concentrated in the matrix, and imports phosphate

1.5.4.1. The exchange is driven by the proton concentration gradient: Higher pH –> higher OH

1.5.4.2. The import of pyruvate from the cytosol (a glycolysis product) is mediated by a transport protein that exchanges pyruvate for hydroxyl ions

2. Peroxisomes

2.1. Functions

2.1.1. Small, single membrane-enclosed organelles

2.1.2. Contain at least 50 different enzymes involved in a variety of metabolic reactions -> energy metabolism (different cells / different enzymes)

2.1.3. Their proteins are synthesized on free ribosomes and then imported into peroxisomes. -> Only certain proteins come from the ER (Peroxins)

2.1.4. They can replicate by division and can be rapidly regenerated even if entirely lost to the cell

2.1.5. Most human cells contain between 100-1000 peroxisomes depending on their metabolic activity

2.1.6. Peroxisomes carry out oxidation reactions leading to the production of H2O2 Uric acid, amino acids, purines, methanol, and fatty acids are broken down by such oxidative reactions in peroxisomes

2.1.6.1. the enzyme Catalase decomposes H2O2 either by converting it to water or by using it to oxidize another organic compound.

2.1.7. Mammalian peroxisomes are involved particularly in the catabolism of very long chain and branched fatty acids.

2.2. Biogenesis

2.2.1. The enzyme content, and therefore the metabolic activities of peroxisomes may change depending on the biogenesis pathway followed, so, they can adjust themselves to the metabolic needs of the cell

3. Chloroplasts

3.1. Structure

3.1.1. Chloroplasts, the organelles responsible for photosynthesis

3.1.1.1. Similar to mitochondria

3.1.1.1.1. Generate metabolic energy

3.1.1.1.2. Have evolved by endosymbiosis

3.1.1.1.3. Contain their own genetic system

3.1.1.1.4. Replicate by division

3.1.1.2. Different to mitochondria

3.1.1.2.1. Structurally more complex

3.1.1.2.2. Convert CO2 to carbohydrates

3.1.1.2.3. Synthesize amino acids, fatty acids, and the lipid components of their own membranes

3.1.1.2.4. Reduce nitrite (NO2–) to ammonia (NH3)

3.1.2. Double membrane -> chloroplast envelope: the inner and outer membranes

3.1.3. Third internal membrane system - the thylakoid membrane system

3.1.4. Three distinct internal compartments:

3.1.4.1. **The intermembrane space** between the two membranes of the chloroplast envelope

3.1.4.2. **The stroma,** which lies inside the envelope but outside the thylakoid membrane

3.1.4.3. **The thylakoid lumen**

3.1.4.4. **The thylakoid membrane** - electron transport chain and ATP generation - Protons are pumped across this membrane from the stroma to the thylakoid lumen.

3.1.4.5. **Outer membrane** - contains porins and is freely permeable to small molecules

3.2. Photosynthesis

3.2.1. Sunlight is used by plants and photosynthetic bacteria to drive the synthesis of carbohydrates in chloroplasts.

3.2.1.1. It takes places in two stages

3.2.1.1.1. **First stage** - the light reactions -> Energy absorbed from sunlight drives the synthesis of ATP and NADPH (similar to NADH) coupled to the oxidation of H2O to O2.

3.2.1.1.2. **Second stage** - the dark reactions -> The ATP and NADPH generated drive the synthesis of carbohydrates from CO2 and H2O. These reactions do not require sunlight.

3.2.2. The light reactions

3.2.2.1. The electron acceptor molecules are localized on two different multiprotein complexes on thylakoid membranes – the Photosystem I and the photosystem II (PSI and PSII complexes)

3.2.2.2. The proton gradient generated by these two complexes drives the chemiosmotic synthesis of ATP by the ATP synthase

3.2.3. The dark reactions

3.2.3.1. Take place in the chloroplast stroma

3.2.3.2. The ATP and NADPH produced from the light reactions drive the synthesis of carbohydrates from CO2 and H2O. One molecule of CO2 at a time is added to a cycle of reactions— the Calvin cycle —that leads to the formation of carbohydrates

3.3. The chloroplast genome

3.3.1. Circular DNA molecules present in multiple copies per organelle

3.3.2. Chloroplast genomes are larger and more complex than mitochondria genomes, ranging from 100–200 kb and containing approximately 150 genes

3.3.3. There is considerable variability between the chloroplast genomes of different species