Proteins Flashcards
Peptide Bonds
•___ reaction – release of ____ during bond formation
- Peptide unit is ___ and ____
- Assumes a ____ configuration. (Which bond)
- Free rotation occurs around the ____ & _____bonds adjacent to the peptide bond.
_____ character for ____ bond
There is resonance with ____ double bond
Peptide bond is hardser to break then regular single bond
•Condensation reaction – release of water during bond formation
- Peptide unit is rigid and planar.
- Assumes a trans configuration. (C=O and NH)
- Free rotation occurs around the C-Ca1 and Ca2-N bonds adjacent to the peptide bond.
Double bond character for CN bond
There is resonance with C=O double bond
Peptide bond is hardser to break then regular single bond
Properties of Peptide Bonds
Peptide bonds are ____
___ form is favored (CO and NH). Less ___ ____ (bw ____ ____) occurs in the ___ than in the ____ form
Peptide bond is ____, however, bonds between the a-carbon and the ____ ____ (___) and ____ atom (___) are able to rotate.
Rotation about these bonds can be defined by the___ ____.
The rotation about these bonds allow proteins to ____in different ways.
Peptide bonds are planar
Trans form is favored (CO and NH). Less steric collisions (bw side groups)occurs in the Trans than in the cis form
Peptide bond is rigid, however, bonds between the a-carbon and the carbonyl carbon (Psi) and nitrogen atom (Phi) are able to rotate. Rotation about these bonds can be defined by the dihedral angles. The rotation about these bonds allow proteins to fold in different ways.
Levels of Structure with in a Protein
The structure of a protein is determined by the
The structure of a protein is determined by the amino acid sequence.
Primary Structure of a Protein
•The linear sequence of amino acids of a polypeptide chain.
Assess the Charge on a Small Peptide at a given pH
•The charge of an amino acid at given ____ is a function of the ____ of the dissociation of protons by the ___ ____ and ____ groups.
•The isoelectric point is the
•The charge of a polypeptide chain can be determine by considering the _________of amino acids,
- The charge of an amino acid at given pH is a function of the pKa of the dissociation of protons by the carboxyl, amino and the side chain groups.
- The isoelectric point is the pH at which the net charge of the molecule is zero.
- The charge of a polypeptide chain can be determine by considering the pKa of the side groups of amino acids, the amino and carboxy groups at the N and C termini.
pKa Values of Amino Acid Side Chains
Remember the amino group and the carboxyl group at the N and C termini of the polypeptide chain have pKa values of ~ 9 and ~2 respectively.
Asp (D)
Glu (E)
His (H)
Cys (C)
Tyr (Y)
Lys (K)
Arg (R)
Calculate the charge on the polypeptide chain at pH=7.4
At low pH all the groups (Acidic and basic groups) are protonated.
As the pH increases the side groups will dissociate in order of their increasing pKas.
Negative charges will be contributed by the carboxyl groups of Glu, the two Asp and the carboxyl group of the C terminus. (Total negative charge will be -4)
The positive charge will be contributed by the amino groups of Lys and N-terminal amino group. (Total positive charge will be +2)
Ala, Phe and Pro do not contribute any charge to the peptide (non-polar and hydrophobic groups)
Hence total charge on the peptide will be -2 (-4 + +2)
pH< pka Protonated
pH > pka Deprotonated
Secondary Structures of Proteins
•Form ___ ____ structures within regions of the polypeptide chain.
•Two common regular secondary structures
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•Irregular structures are ___ ___ and ____
•Form recurring localized structures within regions of the polypeptide chain.
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•Two common regular secondary structures
–a-Helix
–b-sheet
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•Irregular structures are loops, turns and coils.
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The a-Helix
- a-Helices are ___ handed structures.
- Peptide backbone of the helix is formed by ____ between each ______ and the _______atom ___ residues apart. (Occurs within the ____)
- Found in____,___ ____and ___ ____proteins.
- _____is absent in helical region, since it doesn’t _____ and ____
- a-Helices are right handed structures.
- Peptide backbone of the helix is formed by H-bonds between each carbonyl oxygen atom and the amide hydrogen atom 4 residues apart. (Occurs within the same strand)
- Found in globular, membrane spanning and DNA binding proteins.
- Proline is absent in helical region, since it doesn’t posses an amide nitrogen for H-bonding and the appropriate bond angles to fit within the helix.
b-Sheet
•b-sheets are composed of ____/____
•The strands/chains are held together by _______. Optimal H-bonding occurs when the strands are _____(____)
•These strands can run in ___ or ____
•Anti-parallel arrangement is composed of the ____ that _____
•In anti-parallel strands the atoms involved in H-bonding are_______
While the atoms in involved in H-bonding in the parallel arrangement are _____, one amino acid is H-bonded to ____ amino acids in the opposite strand.
•b-sheets are composed of strands/chains.
•The strands/chains are held together by H-bonding. Optimal H-bonding occurs when the strands are pleated (bent)
•These strands can run in the opposite (anti parallel) or in the same direction (parallel).
•Anti-parallel arrangement is composed of the same strand that folds back on it’s self.
•In anti-parallel strands the atoms involved in H-bonding are directly opposite to each other. While the atoms in involved in H-bonding in the parallel arrangement are skewed, one amino acid is H-bonded to two amino acids in the opposite strand.
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Irregular Secondary Structures of Proteins
- b-turns consist of _______that connect ____ in ______ arrangement.
- In turns, the _____ residue is always ____, while the _____ is ____
- Loops are generally _____ residues long.
- Both loops and turns are found on the _____ of proteins which are involved in _____
- b-turns consist of 4 successive residues that connect b-strands in anti-parallel arrangement.
- In turns, the second residue is always proline, while the 3rd is glycine.
- Loops are generally 6 - 16 residues long.
- Both loops and turns are found on the surfaces of proteins which are involved in interaction with other molecules.
Motifs
•Within a polypeptide chain there are _________________________known as structural motifs.
Similar structural motifs can be seen in ______.
•Example: _______ motif found in ___________. The ________structural motif is found within a domain of the enzyme _________
•Within a polypeptide chain there are arrangement of secondary structure that form a pattern known as structural motifs.
Similar structural motifs can be seen in different proteins.•
Example: Helix turn helix motif found in DNA binding proteins.
The ba ba b structural motif is found within a domain of the enzyme lactate dehydrogenase.
Tertiary Structure of a Protein
- ______ of the secondary structures.
- Specifies the locations of______ in a protein.
- The structural elements fold into a___________
- The structures are not ___. They are_____ and _____. (bonds continually______)
- Types of bonding that holds the 3-D structure are ______, _____, ______ and _______.
- Folding of the secondary structures.
- Specifies the locations of each atom in a protein.
- The structural elements fold into a three dimensional structure.
- The structures are not rigid. They are dynamic and flexible.
- Types of bonding that holds the 3-D structure are Ionic interactions, H-bonds, disulfide bonds and hydrophobic interactions.
Dynamic bc bonds continually make and break
Interactions that Stabilize Protein Structures
- Ionic interaction occurs between amino acid whose side chains are___
- Disulfide bridges are formed between______within and between polypeptide chains.
_____ of the sulfhydryl groups of the free cysteine residues results in the formation covalent disulfide bridges.
•Ionic interaction occurs between amino acid whose side chains are charged (Acidic and Basic amino acids).
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•Disulfide bridges are formed between two cysteine residues within and between polypeptide chains. Oxidation of the sulfhydryl groups of the free cysteine residues results in the formation covalent disulfide bridges.
Insulin Contains Two Polypeptide Chains Connected By Disulfide Bonds
Chain _ and _ are connected by __ disulfide bridge (_____), _____ disulfide bridge exist within chain __ (____)
Chain A and B are connected by two disulfide bridge (intermolecular), a single disulfide bridge exist within chain A (intramolecular)