Lecture 4 Summary - Protein Structure & Function PDF

**Lecture 4 Summary (Page 1 of 2)** - Proteins carry out the vast majority of functions in cells, ranging from catalysis of biochemical reaction, providing structural frameworks, transporting small molecules across membranes, etc. - Proteins all function through specific interactions w...

**Lecture 4 Summary (Page 1 of 2)** - Proteins carry out the vast majority of functions in cells, ranging from catalysis of biochemical reaction, providing structural frameworks, transporting small molecules across membranes, etc. - Proteins all function through specific interactions with other proteins and/or small molecules. - Proteins are made up of a sequence of amino acids. As the name implies, each amino acid has an amino group, linked to the a-carbon with attached R-group, linked to the carbonyl group. - There are 20 different amino acids, each with a different R-group. - R-groups can be acidic (- charge, e.g. aspartic acid) or basic (+ charge, e.g. lysine), uncharged but polar (i.e. having uneven charge due to differences in electronegativity, e.g. serine), or nonpolar (e.g. leucine). There is a three and one letter code for amino acids. - Amino acids are linked through peptide bonds, a condensation reaction that eliminates H~2~0. As a result, proteins have amino (or N-) and a carboxyl (or C-) terminal ends. - The nucleotide sequence of a mRNA is translated into the amino acid sequence of a protein. - A 3-base code (a 'codon') specifies amino acids. Since there are 64 possible variations in a 3-base code, most amino acids are encoded by multiple codons. - An mRNA sequence must be read in the correct reading 'frame'. This is specified by the start codon AUG, which encodes for methionine. - Three codons do not specify an amino acid and are called 'stop' codons, because they signal termination of the polypeptide sequence. - For every codon that specifies an amino acid, there is a tRNA adaptor that can recognize that codon through base-pairing as it has a complementary 'anticodon' sequence in it. - Enzymes called amino acyl-tRNA synthetases attach the correct amino acid to the appropriate tRNA. For example, the codon UGG specifies the amino acid tryptophan. Tryptophan becomes linked to a tRNA with a CCA anticodon. - mRNA is decoded, or translated, on ribosomes. These are large macromolecular machines formed by 4 large rRNA molecules and 82 proteins. - Ribosomes have three sites for tRNAs: the E-site (exit site), P-site (for peptidyl-tRNA) and A-site (aminoacyl-tRNA). - Translation occurs in four steps on the ribosome. [Step 1]: With the growing peptide in the P-site, the appropriate amino acyl-tRNA finds the A site. [Step 2]: A peptide bond is formed by elimination of H~2~0 catalyzed by the rRNA in the large ribosome subunit. [Step 3]: The large ribosomal subunit translocates down the mRNA. [Step 4]: the small ribosomal subunit translocates moving the free tRNA into the E-site and the tRNA with the newly attached amino acid into the P site. The unattached tRNA can now leave and the cycle starts over. - Specific protein factors are important for translation initiation and termination ("release"). - Proteins come in all sizes and shapes. The sequence of the polypeptide chain in each protein has evolved to fold in a unique way to serve a specific function. - Structure nomenclature: [Primary] structure is amino acid sequence; [secondary] structure is the a-carbon chain backbone and reveals elements like α-helices and β-sheets; [tertiary] structure is the structure with all the side-chains in place, and [quaternary] structure relates to the structure of proteins with more than one subunit. - The structure of a protein is determined by its amino acid sequence. - Proteins fold into the conformation with the lowest energy state. - Many proteins require chaperones, which themselves are proteins, to allow a protein to fold into its lowest energy state. - Four types of non-covalent interactions help proteins fold: electrostatic interactions, van der Waals forces, hydrogen bonds, and hydrophobic interactions. - Hydrophobic groups associate with each other as this lowers their disrupting effect on water. Thus, hydrophobic forces help proteins fold and hydrophobic regions are often found on the interior of proteins. **Lecture 4 Summary (Page 2 of 2)** - Two types of folding patterns are common in proteins: the α-helix and the β-sheet. - An α helix is right-handed helix with a complete turn every 3.6 amino acids. - In the α helix the C=O group of every amino acid hydrogen bonds with the N-H group of the amino acid four residues down the chain. - Side chain residues extend outward from an α helix. They are not involved in helix formation.\ Therefore, an α helix can be formed from any amino acid sequence - β-sheets form when hydrogen bonds form between C=O and N-H is adjacent polypeptide chains. - Protein secondary, tertiary and quaternary structures can be visualized in many ways, e.g. simple carbon backbone, ribbon format, wire format and space-filling format.