OVERVIEW OF METABOLISM
Define the terms: metabolism, catabolism, anabolism
Metabolism includes all the chemical processes that occur within an individual in order to keep it alive. There are basically two types of metabolism: catabolism, which is the breaking down of molecules into smaller ones (generate ATP and NADH+H+ and FADH2, mostly in mitochondrion), and anabolism which is the building of molecules from smaller ones (using ATP, GTP and UTP, mostly in cytosol).
Draw a diagrammatic scheme that relates the main energy conserving metabolic pathways (glycolysis, TCA cycle, beta-oxidation, oxidative phosphorylation) to each other.
Glycolysis happens in the cytoplasm of every cell. During this processes glucose is converted into two molecules of pyruvate with the net production of 4ATP molecules. Therefore, glycolysis depends on the presence of glucose within the cell. It happens in both aerobic and non-aerobic conditions. The rate-limiting step for glycolysis is the one involving the enzyme Phosphofructokinase-1.
The TCA cycle involves the full oxidation of acetyl CoA (which is produced by pyruvate in the mitochondrial matrix) into carbon dioxide and water. This involves the production of 6NADH+H+, 2FADH2 and 2ATP molecules (and 2CO2 molecules). The rate limiting step in the TCA cycle is the one involving isocitrate dehydrogenase (IDH), the first step of the cycle. The TCA cycle is carried out in most cells of the body (except erythrocytes which do not have a mitochondrion and therefore depend solely on glycolysis for energy, therefore, only on ATP for energy), it is carried out when oxygen is present. It does not depend only on glucose, as other things can also be converted into acetylCoA, such as triglycerides and amino acid chains and glycerol and ethanol.
Beta oxidation is the breakdown of fatty acids for energy. This is done by the removal of 2 acetic acid molecules at a time from the fatty acid chain, converting them into acetylCoA, and then using them in the TCA cycle to produce energy. This is done either in times of low glucose availability, or in the heart, which relies only on fatty acid metabolism as its source of energy.
Oxidative phosphorylation is the production of ATP from the oxidation of the reduced NADH+H+ and FADH2, reducing and oxidising Fe3+ to Fe2+ on electron carrier proteins on the inner mitochondrial membrane, which produce the energy for pumping H+ ions from the inner mitochondrial matrix into the inter-membranous space between the two mitochondrial membranes. These protons can move down their concentration gradient through ATP synthase proteins on the inner mitochondrial membrane, forming ATP in the process.
Indicate the subcellular locations of each of these pathways
TCA cycle: mitochondrial matrix
Beta-oxidation: mitochondrial matrix (or peroxisomes when they are too long for the matrix) (note: acetylCoA themselves are synthesised into fatty acids in the cytosol)
Oxidative phosphorylation: inside the mitochondrion, the enzymes are on the inner mitochondrial membrane, the FADH2 and NADH+H+ are in the matrix, the H+ flow into the inter-membranous space and then back into the matrix
Revise the mechanisms by which fuel molecules such as glucose and fatty acids enter cells
Glucose uptake is done via glucose transporters, and different cells have different types of glucose transporters on their surface: this ensures that glucose goes to the major tissues that need it (brain and erythrocytes) and also allows total body glucose level control through pancreatic glucose uptake and allows the liver to maintain glucose homeostasis by allowing glucose to both freely enter and leave it.
GLUT1 and GLUT3 transporters are expressed on plasma membranes throughout the body and are responsible for a basal rate of glucose uptake. They have a high affinity for glucose and maintain constant uptake from the bloodstream (blood glucose is approximately 5mM and their Km value is 1mM)
GLUT2 in contrast has a high Km of 15-20mM, so a low affinity for glucose, allowing for glucose sensing: in hepatocytes.
GLUT4 transporters are insulin sensitive, so are found in muscle and adipose tissue: this is because these are principle storage sites for glucose (muscle) and triglycerides (adipose tissue) so they are important for the uptake of excess glucose from the bloodstream.
When it comes to the entry of amino acids into the cell, this is a bit more complicated since amino acids have different electrical and chemical properties. What the cell needs to do is
to establish a favourable cytoplasmic environment for the entry of amino acids (in terms of electrochemical gradients) and
express proteins on its surface that can use this gradient for the entry of amino acids into the cell through:
symports of Na+ and amino acids
antiports of Na+ and amino acids
As in many other cells, the sodium potassium pump establishes this gradient through the sodium potassium pump 2K+ in and 3Na+ out. This is primary active transport.
Then, secondary active transporters couple this established electrical chemical gradient and either
cotransport amino acids with Na+ (uncharged aa)
cotransport amino acids with Na+ while simultaneously exchanging K+ for H+ (negatively charged aa)
cotransport amino acids with Na+ while removing H+ (uncharged aa)
or simply allowing amino acids to enter through channels (positively charged aa)
There are also anti-ports for the entry of amino acids into the cell, used when the cell wants to exchange its amino acids with those of the blood
both Na+ and aa enter and leave the cell simultaneously (positively charged aa)
both Na+ and aa enter the cell but only aa exit it (positively charged aa)
uncharged amino acids exchange for each other
Important basic concepts
The structure of ATP: the adenosine and the ribose are not involved in the release of Pi from ATP to release energy, they are there for recognition only. There are also UTP (synthesis of complex sugars), GTP(synthesis of proteins) and CTP(lipid synthesis) (no TTP because life evolved from RNA using organisms first).
Why we phosphorylate glucose: this adds a charge to it and now “traps” it within the cell, it cannot leak anymore
Enzymatic control: there can be many different enzymes in a pathway, the first enzyme is of great importance because by phosphorylating or dephosphorylating it (so activating and unactivating it) you can control whether the pathway will continue or not.
Reversibility: where ATP is used, pathways are generally irreversible: this means that either there needs to be a mechanism to pass that step or if we do not have such an enzyme, then it is completely irreversible (acetylCoA to pyruvate for example)
Covalent modifications of enzymes: phosphorylation, phosphorylation, PHOSPHORYLATION controls whether an enzyme is active or inactive (depends on the enzyme in which state it will be active). Kinases are responsible for phosphorylation.
Allosteric control: many enzymes in the beginning of a pathway are allosteric (back to the point of those being very important to control), but there are activating and inhibiting sites on many enzymes to which other enzymes/substrates/allosteric inhibitors or promoters can attach and control the activity or the enzymes.
Cofactors: can be ions Mg2+, Zn2+ or Cl- or coenzymes/prosthetic groups. ATP can also act as a high-energy cofactor for kinase enzymes, pumps, transporters, contractile events and movement.