Week 2: 3D Structure of Proteins Flashcards
(35 cards)
What are protein chains?
Linear polyamides
What is the rotation of the backbone constrained by?
a) partial double bond nature of peptide bond (omega) b) steric clash for the psi and phi
What is secondary structure maintained by?
Hydrogen bonding
Where are polar vs. nonpolar residues found on protein?
Polar residues tend to be found on outside, nonpolar on inside.
What is the orientation of side chains in alpha helix?
adiate away from axis and point downward
What is the orientation of side chains in beta sheets?
Alternating up and down
What bonds to polar residues form with water on surface?
can form hydrogen bonds with each other and with water, van der Waals interactions occur, charged residues can also interact favorably with water
What interactions occur among nonpolar residues shielded from water?
van der Waals interactions occur among closely-packed atoms
What are the amino acids with aliphatic side chains?
G, A, V, L, I
What are the amino acids with polar uncharged side chains?
S, T, N, Q, C
What are the 3 consequences of hydrogen bonding?
- Gives water high melting and boiling point 2. Means water can H-bond to polar molecules dissolved in it 3. Can influence how nonpolar molecules interact with it.
What is heat capacity?
energy that must be added to raise or lower temp of substance by 1C, Liquid water has large heat capacity - is a temperature buffer. Are 15% fewer hydrogen bonds in liquid water than in ice. Water has high viscosity and high surface tension
What is hydration? Hydration shells?
Water is a great ion solvent. The interactions of negative ends of water dipoles with cations and positive ends with anions in aqueous solution cause ions to become hydrated - surrounded by shells of oriented water molecules - hydration shells.
What is a clathrate? What is hydrophobic effect?
When hydrophobic molecules do dissolve, the water lattice forms ice-like clathrate structures - cages - about nonpolar molecules - decreases entropy which is unfavourable thermodynamically. Therefore, water molecules tend to aggregate - releasing some molecules from clathrates, increasing entropy of solvent - hydrophobic effect - important to protein folding.
What are fibrous proteins? Name 3
distinguished from globular proteins by long extended structure. Tend to be composed of single secondary structure type and have repeat sequences of residues that gives them their repeat structures and use just a few types of residues. Most play structural rolls.
Keratin, fibroin, collagen
What are the two forms of keratin?
Alpha and Beta
What are alpha keratins? Describe their structure
major proteins of hair and fingernails + major fraction of animal skin - members of broad group of intermediate filament proteins - important structural roles in cells - predominantly alpha-helical in structure. Have long sequences - over 300 residues that are alpha helical. Pairs of them twist about one another in left-handed coiled-coil structure. In every 3rd or 4th amino acid has a nonpolar, hydrophobic side chain. There is a strip of contiguous hydrophobic surface area along one face of helix - makes a shallow spiral. To maximize contact between hydrophobic surfaces, the two alpha- keratin helices entwine. The alpha-keratin molecule has small globular region covalently attached to coiled-coil. In intermediate filaments, pairs of the coils associate into flexible fibrils. alpha-keratin is hardened in some tissues because of introduction of disulfide cross-links.
What can cysteine form?
Disulfide bonds
Describe beta-keratin
The beta-keratins contain much more beta-sheet structure. found mostly in birds and reptiles in feathers and scales.
Describe fibroin
beta-sheet structure used in silkworm and spider fibroin (spin fibres). Silkworm fibroin has long regions of stacked antiparallel beta sheets with polypeptide chains parallel to fiber axis. The stacked sheets are held together by noncovalent interactions between side chains. (Gly, Ala, Ser) - small amino acids. This allows sheets to fit together and pack on top of each other - strong and inextensible fiber but are very flexible because bonding between sheets involves only van der Waals interactions. There are compact folded regions that periodically interrupt the beta segments.
Describe collagen
Collagen - most abundant protein in vertebrates - material in bond, tendons and skin. Basic unit is tropocollagen molecule - triple helix of 3 polypeptide chains - each 1000 residues long. The individual chains are left-handed helices - 3.3 residues/turn,. Three of the chains wrap in right handed sense with hydrogen bonds extending between them. Every third residue must be glycine - any other would be too bulky. The conformation of left-handed collagen helix is favored by presence of proline or hydroxyproline in tropocollagen molecule. Sequence: Gly-Proline-Proline or hydroxyproline and alanine. Proline favors an extended structure because of limited conformational flexibility. -OH groups in hydroxyproline stabilize the fiber. Hydroxylation of lysine residues also occurs in collagen - serving to form attachment for polysaccharides. The enzymes that catalyze hydroxylation’s require vitamin C, L-ascorbic acid. Scurvy is due to weakening of collagen fibers because of failure to hydroxylate side chains.
What can proline not do? What does it favor?
Cannot make backbone peptide bonding. Cannot form alpha helixes or beta sheets. Favors extended rather than compact helixes
How do tropocollagen molecules pack in collagen?
Individual tropocollagen molecules pack in collagen fibre in specific way. Each molecules is 300 nm long and overlaps neighbor by 640 amperes. Part of collagens toughness is due to cross-linking of tropocollagen molecules to each other via reaction involving lysine - some are oxidized to aldehyde derivatives (allysine) which can react with a lysine residue or with another one. The accumulating cross-links throughout life make collagen less elastic and more brittle.
What are the common residues of keratin?
S, C, Q, E
