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Lecture 11

Biochemistry 2280A Lecture 11: Biochem Notes for midterm

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Department
Biochemistry
Course Code
Biochemistry 2280A
Professor
Eric Ball

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Biochem Notes Proteins are the largest and most varied class of biological molecules Many have intricate three-dimensional folding patterns that result in a compact form, but others do not fold up at all Still others fold into elongated shapes that give rise to fibrous proteins The function of proteins depends on their structure To make a protein, amino acids are connected together by a type of amide bond called a "peptide bond" This bond is formed between the alpha amino group of one amino acid and the carboxyl group of another in a condensation reaction Multiple amino acids result in a polypeptide, with shorter (< 50 amino acid) ones often referred to as "peptides" Because water is lost in the course of creating the peptide bond, individual amino acids are referred to as "amino acid residues" once they are incorporated Another property of peptides is polarity: the two ends are different  One end has a free amino group (called the "N-terminus") and the other has a free carboxyl group ("C- terminus") polypeptides are elongated by the addition of amino acids to the C-terminal end of the growing chain peptides are written N-terminal first; therefore, Gly-Ser is not the same as Ser-Gly or GS is not the same as SG  the connection gives rise to a repeating pattern of "NCC-NCC- NCC..." atoms along the length of the molecule If stretched out, the side chains of the individual residues project outwards from this backbone The peptide bond is written as a single bond, but it actually has some characteristics of a double bond because of the resonance between the C-O and C-N bonds  six atoms involved are coplanar, and that there is not free rotation around the C–N axis  This constrains the flexibility of the chain and prevents some folding patterns Primary structure is simply the sequence of residues making up the protein  Thus primary structure involves only the covalent bonds linking residues together Secondary structure describes the local folding pattern of the polypeptide backbone and is stabilized by hydrogen bonds between N-H and C=O groups  by far the most common are the orderly repeating forms known as the α-helix and the β-sheet An α-helix, as the name implies, is a helical arrangement of a single polypeptide chain, like a coil spring The backbone carbonyl and N-H groups are oriented parallel to the axis  Each carbonyl is linked by a hydrogen bond to the N-H of a residue located 4 residues further on in the sequence within the same chain All C=O and N-H groups are involved in hydrogen bonds, making a fairly rigid cylinder  3.6 residues per turn, 0.54 nm per turn In a β-sheet, the polypeptide chain folds back on itself so that polypeptide strands lie side by side, and are held together by hydrogen bonds the polypeptide backbone N-H and C=O groups form hydrogen bonds to stabilize the structure, but unlike the α-helix, these bonds are formed between neighboring polypeptide (β) strands the primary structure folds back on itself in either a parallel or antiparallel arrangement, producing a parallel or an antiparallel β-sheet  In this arrangement, side chains project alternately upward and downward from the sheet A single polypeptide chain may have different regions that take on different secondary structures  many proteins have a mixture of α-helices, β- sheets, and other types of folding patterns to form various overall shapes Several factors come into play: steric hindrance between nearby large side chains, charge repulsion between nearby similarly-charged side chains, and the presence of proline and glycine  Proline contains a ring that constrains bond angles so that it will not fit exactly into an α-helix or β-sheet there is no H on
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