module 4 Flashcards
what are the general facts about peptide bonds?
-are covalent linkages between amino acids
-form by condensation reactions involving the loss of a water molecule
-formation eliminates the a-carboxyl and a-amino charged groups, which will be important for protein folding
-peptide bonds are the same, independent of the amino acids being joined
what is the polypeptide main chains of peptide bonds?
-as a result of the conserved nature of peptides bond, there is a repeating pattern within the main chain
-the main chain is the constant portion of the polypeptide, the side chains are variable
-within the main-chain there is a repeating pattern of NCCNCC
what is the partial double bond characteristic of peptide bonds?
-rotation around C-N peptide bond is restricted due to its partial double-bond characteristic
-as a consequence of the partial double bond characteristic the six atoms of the peptide group are rigid and planar
why are trans configuration favored?
-the cis configuration is more likely to cause steric interference between side chain groups
-steric exclusion means that two groups can’t occupy the same place at the same time
what is the configuration of peptide bonds?
-the partial double bond of the peptide bond creates cis-trans isomers
-the oxygen of the carbonyl group and the hydrogen of the amide nitrogen are usually trans to each other
what are the four levels of protein structure?
-primary: the linear sequence of amino acids
-secondary: localized interactions within the polypeptide
-tertiary: the final folding pattern of a single polypeptide (highest in most proteins)
-quaternary: the folding pattern when multiple polypeptides are involved
what is the primary structure of proteins?
-presented from the N (amino) terminus to the C (carboxyl) terminus
-the info specifying correct folding is contained within
-defines the linear arrangement of amino acids in a polypeptide
-ex: YGGFL
can we predict 3D structure based on primary structure?
-it is not yet possible to reliably predict 3D structure based on primary structure
-primary structure is often determined through investigation of the corresponding gene
what is the secondary structure of proteins?
-represents localized patterns of folding in a polypeptide
-maintained by hydrogen bonds between main-chain amide and carbonyl groups
-examples include a-Helicies and B-sheets
what are secondary structure conserved across proteins?
-elements of secondary structure are found in different proteins
-they retain the same overall characteristics independent of protein context
what are the two key rules of secondary structures? (viable forms must:)
-optimize the hydrogen bonding potential of main-chain carbonyl and amide groups
-represent a favored conformation of the polypeptide chain
what are the main chain hydrogen bonding groups in secondary structure?
-each peptide bond has a hydrogen bond donor and acceptor group
-equal number of hydrogen bond donors and acceptors within the polypeptide main-chain
-important for optimizing hydrogen bonds
who discovery the a-helix?
-in 1948, Linus Pauling spent a day sick in bed reading detective stories
-be began to doodle
-for this he received the nobel prize in chemistry in 1954
what are alpha helix (hydrogen bonds)?
-right-handed helix with 3.6 turns
-stabilized by hydrogen bonds which run parallel to the axis of the helix
-carbonyl group point toward the C-terminus; amide groups to the N-terminus
-each carbonyl of residue n hydrogen bonds with amide groups of residue n+4
what can form an alpha helix?
-most sequences can theoretically but there are some guidelines and trends
what are the guidelines and trends of what can form an alpha helix of proline and glycine?
-proline because of its rigidity
-glycine because of its flexibility
what are the guidelines and trends of what can form an alpha helix of amino acids and charged residues?
-AA with side chain branches (Val, Thr, Ile) are less common due to steric interference
-AA with H bonds groups near the main-chain (Ser, Asp, Asn) are also less common
-charged residues tend to be positioned to form favorable ion pairs (residues of opposite charge separated by 3-4 position)
what are the basic facts about tertiary structures?
-the final folding pattern of a single polypeptide
-residues separated by great distance in primary struc may be close in proximity in tert structure
-the biological active folding pattern is the native conformation
-AA determines
-describes the long range aspects of sequence interactions within a polypeptide
what are the differences in tertiary structures in different proteins?
-vary in their content of alpha helicies and beta sheets
-diff proteins have different tertiary structures which relates to their unique functions
what is the stability of a protein?
-proteins are only marginally stable (stability is defined as the tendency to maintain a native conformation)
-weak interactions predominate in stabilizing protein structure
-the protein conformation with the lowest free energy (the most stable) is usually the one with the maximum number of weak interactions
-the stability of a protein reflects the difference in the free energies of the folded and unfolded states
what is protein folding?
-folded proteins occupy a low-energy state of great stability
-is a rapid process, indicating proteins don’t sample all possible folding patterns
-some proteins spontaneously fold to their native conformations, other require the help of chaperones
what can proteins folding be imagined as?
-a funnel where a large number of unstable conformations collapse to a single, stable folding pattern
what is denaturation?
-the disruption of native conformation with loss of biological activity
-energy required for denaturation is often small, perhaps only a few hydrogen bonds
-protein folding and denaturation is a cooperative process
-for many proteins denaturation is reversible
what is the secondary structure of keratin?
-forms and alpha helix
-residues from positions a and d end up on the same face of the helix resulting in a hydrophobic strip along the length of the helix
how does keratin form a coiled-coil?
-two amphipathic helicies of keratin interact to bury their hydrophobic faces together
-involved two right-handed helicies wrapping around each other in a left-handed fashion
where does the strength of keratin arise from? (post translational stabilization)
-from covalent linkages of individual units into higher-order structures
-individual units are linked together through disulfide bonds
-the extent of disulfide bonding will determine the strength of the overall structures
what is the primary structure of collagen?
-contains repeating Gly-X-Y where X is often proline
what is the secondary structure of collagen?
-forms a left-handed helix of three residues per turn
what are the post-translational modifications of collagen?
-strength arise from covalent linkages between the individual units into higher order structures
-rather than disulfides, these linkages occur from residues that undergo post-translational modification (hydroxyproline)
-more of these cross links occur with age, accounting for the increasing brittle characteristics of aging connective tissue and tougher meat
what does collagen require in post-translational modifications?
-the covalent crosslinks of collagen involve post-translationally modified residues (hydroxyproline, hydroxylysine)
-the enzymes performing these modification require Vitamin C
-without these modified residues, collagen cannot form the stabilizing crosslinks
what is the strength and flexibility of silk?
to appreciate molecular basis, need to consider its structure in each dimension:
-fully extended polypeptide chains (strength)
-association of strands by hydrogen bonding (flexible)
-association of sheets by van der waals and hydrophobic interactions (flexible)
