Pepsin

• Primary enzyme for protein degradation in stomach
• Optimal pH: 1.5-2.0 (acidic)
• Secreted as inactive pepsinogen
• Cleaves proteins into smaller peptides

Histone

• Protein rich in basic amino acids (lysine and arginine)
• Packages DNA in chromosomes
• Forms nucleosomes with DNA
• Types: H1, H2A, H2B, H3, H4

Casein

• Example of phosphoprotein
• Major protein in milk
• Contains phosphate groups attached to serine residues
• Forms micelles in milk

Antibodies (Immunoglobulins)

• Structure composed of 2 long (heavy) & 2 short (light) peptide chains
• Y-shaped structure
• Connected by disulfide bonds
• Variable regions bind to antigens
• Constant regions determine antibody class

Insulin Receptors

• Tetrameric glycoprotein
• Consists of 2 α and 2 β subunits
• α subunits: Extracellular, insulin-binding
• β subunits: Transmembrane, tyrosine kinase activity
• Essential for glucose homeostasis

Collagen

• Contains triple helix structure
• Most abundant protein in mammals
• Composed of three polypeptide chains (tropocollagen)
• Amino acid sequence: Gly-X-Y (where X is often proline, Y is often hydroxyproline)
• Provides structural support to tissues

Step 1.  Acyl-CoA Dehydrogenase catalyzes oxidation of the fatty acid moiety of acyl-CoA, to produce a double bond between carbon atoms 2 and 3.

There are different Acyl-CoA Dehydrogenases for short (4-6 C), medium (6-10 C), long and very long (12-18 C) chain fatty acids. Very Long Chain Acyl-CoA Dehydrogenase is bound to the inner mitochondrial membrane. The others are soluble enzymes located in the mitochondrial matrix.

FAD is the prosthetic group that functions as electron acceptor for Acyl-CoA Dehydrogenase. 

A glutamate side-chain carboxyl extracts a proton from the a-carbon of the substrate, facilitating transfer of 2 e^- with H⁺ (a hydride) from the b position to FAD. The reduced FAD accepts a second H⁺, yielding FADH₂

The carbonyl oxygen of the thioester substrate is hydrogen bonded to the 2'-OH of the ribityl moiety of FAD, giving this part of FAD a role in positioning the substrate and increasing acidity of the substrate a-proton

The reactive glutamate and FAD are on opposite sides of the substrate at the active site. Thus the reaction is stereospecific, yielding a trans double bond in enoyl-CoA.

FADH₂ of Acyl CoA Dehydrogenase is reoxidized by transfer of 2 electrons to an Electron Transfer Flavoprotein (ETF), which in turn passes the electrons to coenzyme Q of the respiratory chain.

Step 2. Enoyl-CoA Hydratase catalyzes stereospecific hydration of the trans double bond produced in the 1st step of the pathway, yielding L-hydroxyacyl-Coenzyme A

Step 3. Hydroxyacyl-CoA Dehydrogenase catalyzes oxidation of the  hydroxyl in the b position (C3) to a ketone. NAD⁺ is the electron acceptor.

Step 4. b-Ketothiolase (b-Ketoacyl-CoA Thiolase) catalyzes thiolytic cleavage.

A cysteine S attacks the b-keto C. Acetyl-CoA is released, leaving the fatty acyl moiety in thioester linkage to the cysteine thiol. The thiol of HSCoA displaces the cysteine thiol, yielding fatty acyl-CoA (2 C shorter).

A membrane-bound trifunctional protein complex with two subunit types expresses the enzyme activities for steps 2-4 of the b-oxidation pathway for long chain fatty acids. Equivalent enzymes for shorter chain fatty acids are soluble proteins of the mitochondrial matrix.

Summary of one round of the b-oxidation pathway:

fatty acyl-CoA + FAD + NAD⁺ + HS-CoA → 
            fatty acyl-CoA (2 C shorter) + FADH₂ + NADH + H⁺ + acetyl-CoA

The b-oxidation pathway is cyclic. The product, 2 carbons shorter, is the input to another round of the pathway. If, as is usually the case, the fatty acid contains an even number of C atoms, in the final reaction cycle butyryl-CoA is converted to 2 copies of acetyl-CoA

ATP production:

• FADH₂ of Acyl CoA Dehydrogenase is reoxidized by transfer of 2 e^- via ETF to coenzyme Q of the respiratory chain. H⁺ ejection from the mitochondrial matrix that accompanies transfer of 2 e^- from CoQ to oxygen, leads via chemiosmotic coupling to production of approximately 1.5 ATP. (Approx. 4 H⁺ enter the mitochondrial matrix per ATP synthesized.)
• NADH is reoxidized by transfer of 2 e^- to the respiratory chain complex I. Transfer of 2 e^- from complex I to oxygen yields approximately 2.5 ATP.
• Acetyl-CoA can enter Krebs cycle, where the acetate is oxidized to CO₂, yielding additional NADH, FADH₂, and ATP. 
• Fatty acid oxidation is a major source of cellular ATP

b-Oxidation of very long chain fatty acids also occurs within peroxisomes

FAD is electron acceptor for peroxisomal Acyl-CoA Oxidase, which catalyzes the first oxidative step of the pathway. The resulting FADH₂ is reoxidized in the peroxisome producing hydrogen peroxide FADH₂ + O₂ à FAD + H₂O₂

The peroxisomal enzyme Catalase degrades H₂O₂ by the reaction:
2 H₂O₂ → 2 H₂O + O₂
These reactions produce no ATP

Once fatty acids are reduced in length within the peroxisomes they may shift to the mitochondria to be catabolized all the way to CO₂. Carnitine is also involved in transfer of fatty acids into and out of peroxisomes

Cholesterol synthesis:

Hydroxymethylglutaryl-coenzyme A (HMG-CoA) is the precursor for cholesterol synthesis. 

HMG-CoA is also an intermediate on the pathway for synthesis of ketone bodies from acetyl-CoA. The enzymes for ketone body production are located in the mitochondrial matrix. HMG-CoA destined for cholesterol synthesis is made by equivalent, but different, enzymes in the cytosol.

HMG-CoA is formed by condensation of acetyl-CoA and acetoacetyl-CoA, catalyzed by HMG-CoA Synthase.

HMG-CoA Reductase, the rate-determining step on the pathway for synthesis of cholesterol.

Niacin: Vitamin B3, Nicotinamide, Nicotinic Acid Niacin, or vitamin B3,

 is involved in energy production, normal enzyme function, digestion, promoting normal appetite, healthy skin, and nerves.

RDA Males: 16 mg/day; Females: 14 mg/day

Niacin Deficiency : Pellagra is the disease state that occurs as a result of severe niacin deficiency. Symptoms include cramps, nausea, mental confusion, and skin problems.

3-D Structure of proteins

Proteins are the main players in the life of a cell. Each protein is a unique sequence of amino acid residues, each of which folds into a unique, stable, three dimentional structure that is biologically functional.

Conformation = spatial arrangement of atoms that depends on rotation of bonds. Can change without breaking covalent bonds.

• Since each residue has a number of possible conformations, and there are many residues in a protein, the number of possible conformations for a protein is enormous.

Native conformation = single, stable shape a protein assumes under physiological conditions.

• In native conformation, rotation around covalent bonds in polypeptide is constrained by a number of factors ( H-bonding, weak interactions, steric interference)
• Biological function of proteins depends completely on its conformation. In biology, shape is everything.
• Proteins can be classified as globular or fibrous.

There are 4 levels of protein structure

• Primary structure
  • linear sequence of amino acids
  • held by covalent forces
  • primary structure determines all oversall shape of folded polypeptides (i.e primary structure determines secondary , tertiary, and quaternary structures)
• Secondary structure
  • regions of regularly repeating conformations of the peptide chain (α helices, β sheets)
  • maintained by H-bonds between amide hydrogens and carbonyl oxygens of peptide backbone.
• Tertiary structure
  • completely folded and compacted polypeptide chain.
  • stabilized by interactions of sidechains of non-neighboring amino acid residues (fibrous proteins lack tertiary structure)
• Quaternary structure
  • association of two or more polypeptide chains into a multisubunit protein.

Role of Coenzymes

The functional role of coenzymes is to act as transporters of chemical groups from one reactant to another.

Ex. The hydride ion (H+ + 2e-) carried by NAD or the mole of hydrogen carried by FAD;

The amine (-NH2) carried by pyridoxal phosphate