Lipids have two steps in their digestion. The first is emulsification and the second is hydrolysis.
Emulsification is necessary because lipids are not water soluble. When they travel through the digestive tract from food, they maintain rather large aggregates of themselves. Emulsification is carried out by bile salts (in bile, produced by the liver and stored and concentrated in the gall bladder) which are amphipathic as they have both hydrophobic and hydrophilic parts.
This enables them to sequestrate lipids into smaller droplets.
Pancreatic lipase then hydrolyses these in further digestion into monoglycerides and free fatty acids. The smaller, emulsified droplets provide a much greater surface area for the enzyme to work, and hence the first step is necessary in the digestion of lipids.
Smaller yet droplets called micelles of both the lipid products as well as the bile salts still hanging onto them come into contact with the brush border. They are then absorbed in the intestine by simple diffusion into the epithelial cell, however there are also specific fatty acid transporters to help them cross the membrane.
Fatty acids convert into acetyl coenzyme A following beta-oxidation reactions and enter respiration at the Krebs cycle step. Glycerol is converted into one of the glycolysis intermediates, thus entering the respiration pathway.
Proteins, too, need to be broken down in multiple steps. The first involves enzymes like endopeptidases and exopeptidases secreted by the pancreas. They break down long amino acid chains, polypeptides, into smaller ones like dipeptides. Endopeptidases break peptide bonds between amino acids, while exopeptidases break the peptide bonds of amino acids with terminal amino or carboxy groups either end of a polypeptide.
The second step is similar to that of carbohydrates. Membrane-bound enzymes on the brush border break down the small polypeptides left into free amino acids or short polypeptide chains of no more than 4 amino acids. The former can then be absorbed in the same way as carbohydrates via co-transport with sodium ions, while the short polypeptides can be absorbed via co-transport with hydrogen ions (H+).
Amino acids enter the Krebs cycle either through transamination or deamination. These reactions can transfer amino groups from one amino acid to another, or altogether remove it.