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o Proteins are __ formed by linking the __ of one amino acid to the __ of another amino acid, called a __. __is also lost
§ The equilibrium of this reaction lies to the side of __. Therefore, making peptide bonds requires __
- linear polymers
- alpha-carboxyl group
- alpha-amino group
- peptide bond or an amide bond
- Water
- hydrolysis rather than synthesis
- free energy
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· They are still quite stable kinetically because the __
§ Several amino acids joined by peptide bondsà __chain (each amino acid unit in a polypeptide is called a __)
o A polypeptide chain has polarity due to the __ at one end and the __ at the other end
§ The amino end= __
- rate of hydrolysis is really slow
- polypeptide
- residue
- amino group
- carboxyl group
- beginning
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o A polypeptide chain consists of a regularly repeating part, called the __, and a __, comprising the distinctive side chains
§ Rich in __
§ Each residue contains a __, which is a good hydrogen bond acceptor, and, with the exception of proline, an __, which is a good H-bond donor
· These groups interact to stabilize structures
- main chain or backbone
- variable part
- hydrogen bonding potential
- carbonyl group
- NH group
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o Most natural polypeptide chains have between 50 and 2000 amino acid residues and are referred to as __, __being the largest (27k amino acids)
§ Peptides with small numbers of amino acids are __
- proteins
- titin
- oligopeptides (peptides)
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o In some proteins, the linear polypeptide chain is __, the most common being __, formed by the oxidation of a pair of __. The resulting unit of two linked __ is called __
§ Extracellular proteins often have several __bonds, whereas intracellular proteins usually lack them. Rarely are __ present in proteins
- cross-linked
- disulfide bonds
- cysteine residues
- cysteines is called cystines
- disulfide
- nondisulfide cross-links derived from other side chains
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Frederick Sanger
- Sequences are determined by __
- determined the sequence of amino acids of insulin
- o
only L amino acids linked by peptide bonds- nucleotide sequences of genes
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o Knowing amino acids sequences is important:
- § Knowledge of the sequence of a protein is essential to elucidating its mechanism of action
- § Amino acid sequences determine the 3D structure of proteins (from DNAà 3D structure)
- § Sequence determination is a component of molecular pathology; alterations in the sequenceà abnormal function and disease
- § The sequence of a protein reveals much about its evolutionary history
- · Molecular events in evolution can be traced from amino acid sequences
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o Polypeptide chains are __ yet __, revealing important features in the backbone
§ The peptide bond is essentially planar: explain this
- flexible yet conformationally restricted
- for a pair of amino acids linked by a peptide bond, six atoms lie in the same plane—the two alpha carbons and the CO group of the first amino acid and the NH of the second
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§ The nature of the chemical bonding within a peptide accounts for the bond’s __. The bond resonates between a single bond and a double bond giving it __ and thus __
o The peptide bond is __, allowing polymers of amino acids linked by peptide bonds to do what?
- planarity
- double-bond character and thus restricting rotation
- uncharged
- form tightly packed globular structures
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o Two configurations: __(alpha carbons on opposite sides of peptide bond) and __(same side). Almost all peptide bonds in proteins are __due to __
§ The most common cis peptide bonds are __, which show less preference for the trans configuration because what?
- trans
- cis
- trans
- elimination of steric clashes between groups
- X—Pro linkages
- the nitrogen of proline is bonded to two tetrahedral carbon atoms, limiting the steric differences between the trans and cis forms
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o The bonds between the amino group and the alpha carbon and between the alpha carbon and the carbonyl group are pure __ and can rotate, taking on various orientations, as well as allowing proteins to fold in different ways
§ The rotation about these bonds can be specified by __
- single bonds
- torsion angles
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§ The angle of rotation about the bond between the nitrogen and the alpha carbon atom is called __and the angle of rotation about the bond between the alpha carbon and the carbonyl carbon atoms is called __.
§ Clockwise rotation as viewed from the N atoms or the carbonyl group towards the alpha carbon = __ value. The phi and the psi also determine the __
- phi (Φ)
- psi (Ψ)
- positive
- paths of the polypeptide chain
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Gopalasamudram Ramachandran
- o recognized several rotations are forbidden due to steric collisions and can be plotted on a Ramachandran diagram
- § Steric exclusion is a powerful organizing principle
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o An unfolded protein can exists as a __; each copy of an unfolded polymer will have a different __, yielding a mix of possible forms
§ The favorable entropy associated with a mixture of many possible conformations opposes __ and must be __
- random coil
- conformation
- folding and must be overcome by interactions favoring the folded form
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§ The __ and the __ limits the number of structures accessible to the unfolded form sufficiently to allow __ to take place
- rigidity of the peptide unit
- restricted set of allowed Ψ and Φ angles
- protein folding
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