Proteins (Alpha and Beta helixes) (Week 3-4) Flashcards
(28 cards)
What are the properties of the alpha-helix?
-forms when amino acids all have same orientation and alpha carbon bonds turn in the same direction they will rotate at every other carbon
-Pauling’s models showed a very stable structure with 3.6 amino acids per turn of Helix
-#1C=O lines up with H-N #5 to form hydrogen bonds that make alpha Helix stable
-distance between each turn of Helix is 5.4 A
-5.4 / 3.6 = 1.5 A and that is the distance along the Helix per amino acid
-the r groups look like ornaments
When does the extended beta strand and beta sheet occur?
-strands in opposite directions make antiparallel beta sheet where the terminus changes sides (switch which side N and C are on)
- hydrogen bonds align better in antiparallel mode
strands in the same direction to make a parallel beta sheet
How do the dimensions of Beta sheet match B-Keratin patterns?
-max space available for bulky or awkward shaped side chains
Which amino acids that prefer to form beta structures?
-Trp Tyr (Phe) are big
-Val, Ile, Thr have a branch on B-C
-Cys has large S atom on B-C
-they need room
Which amino acids tend to form alpha helix?
-Ala Arg Gln Glu His Leu Lys Met (Phe)
-they have a default behaviour of amino acids
Which amino acids have secondary structure H-Bonds?
-Gly, Pro, Asn, Asp, Ser
-disrupt secondary structure 2 breakers in a group of
4 amino acids interrupts the secondary structure
-forms a turn or flexible allows the polypeptide main chain to change direction
What is the native state?
Most proteins are folded into a unique 3D tertiary structure which is required for their function
What is denaturation ?
-unfold proteins unfolded form may be unstructured or aggregated and often irreversible
What are the ways to denature a protein?
Heat disruptive solvents or harsh detergents like MSDS -when purifying proteins to study them we usually try to avoid denaturation
Which structure is the overall pattern of folding of the whole polypeptide chain?
-teritary
-alpha keratin is totally alpha helix
-Fibroin a B-keratin is totally anti-paralell beta sheet
-collagen has a unique triple helix structure
-requires -Gly-Pro-X
What allows folding?
-flexible loops and turns
-breaks in secondary structure which is rigid
Which effect is a major force driving protein folding?
-The hydrophobic effect
-Fold in the protein encloses most of the nonpolar amino acids in the core
-Nonpolar AAs group together to minimize contact with water hydrophobic effect
-Polar AAS form outer layer interact well with surrounding water good hydrogen bonding or with ions in solution
How do amino acids pack together?
-side chains interlock to maximize the number of close atom-to-atom contacts
-close contacts attract by weak van der waals forces
-good fit makes hundreds of close contacts in macromolecule and helps hold structure together
Which groups fold into alpha-helix bundle?
-mostly groups of alp AAs
-small clusters of breakers set the limits of each helix
-non-polar AAs every 3 or 4 places in the helix make a non-polar patch or strips which fold inside of bundle
-AAs that prefer beta sheet are present but scattered
-Myoglobin is a bundle of 8 alpha helix sections
-must be in certain sequence to make
Which groups fold into antiparallel beta sheet?
-groups of beta sheet forming amino acids
-anti parallel sheet is more stable because H-bonds are arranged in straight line
-side chains project out of the sheet odd on one side even on the other
-sheet can be non-polar on one side, polar on the other side
-breakers are flexible and allows chains to change direction
-fold opposite ways
-stronger due to hydrogen bonds
-long loop connects to the first
-arrows are pointed both up and down
What happens when a beta sheet is polar on one side and non-polar on the other?
-wrap to enclose the non-polar face inside
-a small sheet (3-5 strands) makes an open fold
-a larger sheet (8 strands) wraps all the way around to form an antiparallel B-barrel
-this is an example of a green fluorescent protein
Which sequences from a parallel beta-sheet?
-B-a-B-a
-helical sections connect the strands which all run in the same direction
-helix lies above or below the lane of the sheet
-parallel b-sheets are less stable so must be sequestered away from water
-usually buried in center of protein thus made up of mostly non-polar amino acids
What are the differences in a parallel sheet vs anti-parallel sheet?
-hydrogen bonds are strong for anti-parallel water cant break the bonds
-direction which amino acids point
-hydrogen bonds in parallel sheet can be broken by water so have to protect beta sheet
How does a parallel aB-barrel form?
-if all the helices lie on one side of the sheet the sheet wraps around
-the b-sheet forms he central barrel surrounded by the connecting alpha-helices
-the enzyme triose phosphate isomerase is an example
How does the ab-sandwich structure occur?
-when there is helices on both sides of the sheet
-sandwich filling is the non-polar beta sheet between two layers of a-helix
-the b-sheet if often twisted for better packing
-an example of this is the enzyme lactate dehyrdogenase
-twisted but still in a sheet
-a-helices lie on top of the beta sheet causing an alpha-beta sandwich but does not have to fold
What is a domain?
-larger proteins which fold up into different sections
-fold up in 10-20 kDa sections -a protein of 50 kDa may have 3 or 4 domains
-each domain may adopt a different folding pattern
-the larger proteins are often modular in nature
-example is lactate dehydrogenase with two aB-sandwich domains
What bonds and effects contribute to protein stability and function?
-covalent bonding links amino acids in a chain in a specific sequence
-difficult to break bonds in primary structure
-non-covalent interactions dictate folding pattern and stability
-hydrophobic effect and van der Waals effect are the most important in non-covalent interactions
-hydrophobic effect locates non-polar amino acids in core of folded protein avoiding unfavourable interaction with water (biggest)
-Van der waals interaction-dipole dipole interactions between atoms that are not close but not covalently bonded to each other (london dispersion)
What does polar interactions contribute to?
-help stabilize the correct folding of a protein
-H-bonds: may form between donors and acceptors that line up in the folded protein (bond to H2O)
-contributes most to the formation of secondary structure
-Ion bonds: strong electrostatic interaction of negative side chains which pair up with positive side chains that are nearby in the folded protein (salt bridge)
-found on the outside of the protein and polar groups face the exterior
Which bonds help hold together the tertiary structure of some proteins?
-disulfide bonds
-form when pairs of Cys-SH groups react with O2 releasing water
-makes a strong covalent bond (difficult to denature protein) to help hold the folded protein together
-a few have these mostly those that function outside cells since O2 is needed
