LC 02: Proteins

• Proteins are composed of amino acids, with the primary structure being the amino acid sequence
• Secondary structure examples include the alpha Helix and beta sheet
• The secondary structure affects the tertiary structure, which is the long-range folding and the 3D structure of the protein
• The definition of a protein varies depending on the example, and not all proteins have a quaternary structure or form multi-protein complexes
• Amino acids consist of the alpha carbon, amino group (NH2 or NH3), carboxy group (C double bonded to O), hydrogen attached to the alpha carbon, and the R Group
• The R Group, or amino acid side chain, is variable and determines the type of amino acid
• Major categories of amino acids include acidic, basic, uncharged polar, and non-polar
• Amino acids are classified into three-letter codes, but memorization of specific amino acids and their categories is not required
• The genetic code links three nucleotides in RNA to specific amino acids, grouped based on properties like non-polar, polar, charged, and uncharged
• Cysteine is a unique amino acid with an R Group of CH2SH, forming disulfide bonds under oxidation conditions to stabilize protein structures
• Proteins play a crucial role in maintaining the structure of cells, with disulfide bonds bracing the shape of proteins like hair
• In a reducing condition, disulfide bonds in hair are broken by adding chemicals, reshaping the hair, and then reforming the bonds with oxidation chemicals
• The process of forming a peptide bond between two amino acids occurs in the ribosome, involving a condensation reaction where an H2O molecule is removed
• The ribosome removes the O from the carboxy group of one amino acid and the H from the amino group of another, forming a bond between the carboxy carbon and the amino nitrogen to create a peptide bond
• After the formation of a peptide bond, amino acids are referred to as residues, and a chain of amino acids stitched together forms a polypeptide chain
• The end of a polypeptide chain with an amino group is called the amino end, while the end with a carboxyl group is called the C terminus
• Differences in the primary amino acid sequence are crucial for the structure and function of proteins
• Vasopressin and oxytocin, both nine amino acid peptides, have distinct structures and functions in the body
• Both vasopressin and oxytocin are nine amino acid long neuropeptide hormones
• The amino acid sequence of vasopressin and oxytocin is almost identical, differing only at two positions
• Vasopressin controls urine production rates, while oxytocin is involved in birth, lactation, and pair bonding
• The difference in amino acid sequence between vasopressin and oxytocin, specifically at two positions, leads to completely different functions
• The N to C orientation of a peptide is essential for its function
• The order of amino acids in a peptide is crucial for its function, as shown by the example of two pentapeptides with the same amino acids but in reverse order
• The alpha helix in protein structure can be a small part or the whole polypeptide chain, depending on the protein
• In an alpha helix, the first residue forms a hydrogen bond with the fifth residue, the second residue with the sixth, and so on
• The hydrogen bonds in an alpha helix are formed between the carbonyl oxygen and amide hydrogen of the peptide bonds, not involving the R groups
• In an alpha Helix, the hydrogen bonds are formed by the carbonyl oxygen and amide hydrogen
• R groups do not form the hydrogen bonds in an alpha Helix
• In a beta sheet, typically containing four to five beta strands but can have 10 or more, the hydrogen bonds are formed between different polypeptide chains
• The colors used to represent atoms in a beta sheet are: red for oxygen, gray for the carbonyl carbon, blue for nitrogen, white for hydrogen, and the alpha carbon with the R Group sticking out
• Alpha Helix and Beta Sheets are secondary structures in proteins
• In Alpha Helix, hydrogen bonds form between the carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid, four amino acids apart within the same segment of the polypeptide chain
• Some Alpha Helices can form a coiled coil structure if they are amphipathic, with hydrophobic and hydrophilic amino acids on different sides
• Coiled coils are found in proteins like alpha keratin of skin and hair, and myosin motor proteins
• Tertiary structures in proteins are the 3D overall structures held together by hydrophobic interactions, non-covalent bonds, and disulfide bonds
• Tertiary structures include interactions among residue backbones and R groups, and between many helices and beta sheets
• Chaperone proteins assist in protein folding to ensure proper folding dictated by the amino acid sequence
• Proteins have a primary structure, secondary structure (Alpha helices, Beta sheets), and tertiary structure (multiple Alpha helices, multiple beta sheets, dulfide bonds)
• Protein domains are specialized for different functions, representing portions of a protein with their own tertiary structure, often functioning semi-independently