Secondary Structure of Proteins

00:14:15
https://www.youtube.com/watch?v=4YbwjjZWGPA

概要

TLDRPolypeptides, as chains of amino acids with a specific sequence, form what is initially known as the primary structure. This linear arrangement quickly evolves into more complex structures through the formation of secondary structures, which include Alpha helices, beta pleated sheets, beta turns, and omega loops. The ability to form these structures is attributed to the rotation around single bonds in the chain, while peptide bonds, due to their double-bond nature, do not rotate. Hydrogen bonds play a crucial role in stabilizing these secondary arrangements. For instance, the Alpha helix features a helical arrangement, stabilized by hydrogen bonds between every fourth amino acid. Right-handed helices are more prevalent due to lower steric hindrance compared to left-handed ones. Beta sheets can form either parallel or anti-parallel arrangements, with specific interactions corresponding to the orientation of the strands. Beta turns contribute to the compactness of proteins by allowing tight turns and are stabilized by similar hydrogen bonds. These diverse structures enable proteins to perform their versatile functions in biological systems.

収穫

  • 🔬 Polypeptides begin as linear polymers forming a primary structure.
  • 🔄 Secondary structures include Alpha helices, beta pleated sheets, beta turns, and omega loops.
  • 🔗 Single bonds in polypeptide chains enable twisting and folding for secondary structures.
  • 💡 Peptide bonds don't rotate due to double-bond character.
  • 🤝 Hydrogen bonds stabilize secondary structures of proteins.
  • 🏛️ Alpha helices have right- and left-handed forms, with right-handed being more stable.
  • 🔀 Beta sheets can be parallel or anti-parallel with different interaction patterns.
  • 🔄 Beta turns allow compact folding and are usually at the polypeptide surface.
  • 🧬 Right-handed alpha helices are predominant due to lower steric hindrance.
  • 🪢 Beta turns are crucial for three-dimensional protein structures due to tight folding.

タイムライン

  • 00:00:00 - 00:05:00

    The primary structure of a polypeptide is a linear sequence of amino acids, which can twist and turn into four types of regular patterns: alpha helices, beta pleated sheets, beta turns, and omega loops. These patterns form the secondary structure of a polypeptide. The polypeptide twists are due to single bonds within the chain that rotate, while peptide bonds remain stable and don't rotate due to their double bond character. Hydrogen bonds between amino acids help stabilize these secondary structures. An alpha helix is a rodlike structure where the backbone is inside, and side chains project outward. Alpha helices can be right-handed (more stable due to less steric hindrance) or left-handed. The structure is stabilized by hydrogen bonds between the NH group of one amino acid and the CO group of another, four residues ahead.

  • 00:05:00 - 00:14:15

    Beta pleated sheets are structures where polypeptide chains align in either an antiparallel or parallel orientation. In antiparallel beta sheets, strands run in opposite directions, allowing the NH and CO groups of amino acids to line up for hydrogen bonding. In parallel beta sheets, strands run in the same direction, causing an amino acid to interact with two amino acids on the opposing strand because the NH and CO groups do not align perfectly. Beta turns allow polypeptides to make sharp turns, creating a compact three-dimensional structure. These turns are stabilized by hydrogen bonds, specifically between the CO group of one amino acid and the NH group of another three residues away. Beta turns are often on the protein's surface, interacting with solvent and other molecules.

マインドマップ

ビデオQ&A

  • What forms the primary structure of a polypeptide?

    The primary structure of a polypeptide is a linear polymer of specific amino acids sequence.

  • What are the four types of secondary structures in polypeptides?

    The four types are Alpha helixes, beta pleated sheets, beta turns, and omega loops.

  • How do polypeptides twist to form secondary structures?

    Polypeptides twist due to the rotation of single bonds, not the double-bonded peptide bonds.

  • What stabilizes the secondary structures in polypeptides?

    Hydrogen bonds between amino acids stabilize the secondary structures.

  • What is the difference between right-handed and left-handed Alpha Helix?

    The right-handed Alpha Helix is more stable due to less steric hindrance compared to the left-handed.

  • What are beta turns?

    Beta turns are abrupt turns in polypeptides that help in forming compact structures.

  • What is the role of hydrogen bonds in beta turns?

    Hydrogen bonds stabilize beta turns by bonding between certain amino acid groups.

  • How do beta pleated sheets differ in parallel and anti-parallel arrangements?

    In parallel sheets, strands run in the same direction, while in anti-parallel, they run in opposite directions.

  • What are the common interactions in anti-parallel beta sheets?

    In anti-parallel beta sheets, NH and CO groups align and interact linearly.

  • Where are beta turns usually found in polypeptides?

    Beta turns are typically found on the surface of polypeptides.

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    the primary structure of a polypeptide
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    describes that polypeptide as being a
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    linear polymer of a specific sequence of
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    amino acids now once the polypeptide
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    forms its primary structure what happens
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    next well next that primary polypeptide
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    begins to twist and begins to turn via
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    these regular patterns and there are
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    four different types of regular patterns
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    we have Alpha helixes we have we have
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    beta plated sheets we have beta turns
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    and we have omega loops and these four
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    different types of regular patterns
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    compose the secondary structure of our
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    protein of our
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    polypeptide now the question is how
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    exactly does the PO polypeptide begin to
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    twist to form these four different types
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    of structures well inside the
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    polypeptide we have different bonds now
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    the peptide bonds the bonds holding the
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    amino acids inside the polypeptide
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    together and these peptide bonds have a
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    double bond character what that means is
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    they don't actually rotate but all the
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    other single bonds inside the
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    polypeptide chain do rotate and it's the
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    rotation of these other single bonds
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    inside the polypeptide chain that allows
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    the linear polypeptide to eventually
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    fold into the Beta plated sheet into the
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    Alpha Helix into the Beta turn and our
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    Omega Loop now once we form these
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    regular patterns the question is what
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    exactly stabilizes these structures and
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    allows them to exist in the first place
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    well it's the hydrogen bonds that exist
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    between the amino acids in that
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    polypeptide chain as we'll see in just a
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    moment that allows each one of these
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    secondary structures to actually exist
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    in the first place so let's begin with
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    the alpha Helix so what exactly is an
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    alpha Helix well an alpha Helix is
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    formed when we have our polypeptide
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    chain and that polypeptide chain begins
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    to twist to form a rodlike structure and
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    inside that rodlike structure we have
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    the backbone and on the outside we have
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    those archain groups that are pointing
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    outside of that Alpha Helix so the alpha
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    Helix is a rodlike structure as shown on
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    the board that contains the backbone
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    being in the inside of that Helix and
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    the side chain groups on the outer
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    portion of that Helix now let's suppose
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    that this is our axis of rotation so the
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    axis of rotation along which that Alpha
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    Helix actually forms runs runs along the
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    xaxis in this direction so this is the
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    beginning of our polypeptide and this is
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    the end so we see that in this case we
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    go into the board then we come out of
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    the board we go into the board out of
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    the board we go into the board out of
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    the board we go into the board out of
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    the board and so forth so the screw
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    sense of our Alpha Helix basically
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    describes the directionality of rotation
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    about the axis of rotation for that
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    particular Alpha Helix now what do we
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    mean by that well if this is the axis of
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    rotation so and if we look at the axis
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    of R ation and we examine the
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    directionality of that rotating Alpha
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    Helix the rotating polypeptide chain in
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    this case it will point in the clockwise
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    Direction so going this way is clockwise
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    and in this particular case the screw
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    sense of this Alpha Helix is clockwise
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    and this is known as the rightand Helix
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    now we can also have a leftand helix in
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    which the directionality is reversed it
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    would be counterclockwise wi now the
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    left hand the left-handed Helix is much
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    less stable because there's more sterak
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    hindering there is a greater number of
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    collisions between the r chains of our
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    polypeptide and so because of that the
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    energy level of the left-handed Helix is
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    higher than the energy level of the
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    right-handed Helix and what that means
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    is for the majority of the proteins that
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    contain the alpha Helix it will be the
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    right right-handed Helix and not the
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    left-handed Helix that will exist within
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    that protein so the right-handed Alpha
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    Helix predominates because there is less
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    steric hindrance between the side chains
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    on our Alpha Helix now the final thing
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    I'd like to mention about the alpha
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    Helix is the actual hydrogen bonding
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    that exists between our Amino groups so
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    let's suppose that this is our uh this
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    is our amino acid that we actually
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    examining so this is our amino acid and
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    this green bond is the peptide bond that
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    does not rotate that connects this amino
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    acid to the next amino acid then we have
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    this peptide bond that connects this
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    amino acid and so forth so remember
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    these green bonds are peptide bonds and
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    because those peptide bonds are resonant
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    stabilized they have a double bond
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    character and they will not rotate but
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    these other bonds are single bonds and
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    they do rotate and it's their rotation
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    that allows this Helix and the other
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    structures of the secondary structure to
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    actually form in the first place now
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    once we form them it's the hydrogen
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    bonds that exist between the NH group of
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    one amino acid and the co group of
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    another amino acid that stabilizes these
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    structures and allows them to exist for
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    an extended period of time now let's
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    focus on this amino acid here so we see
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    that we have this NH group of this amino
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    acid here that interacts with the COO
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    group of this amino acid here the
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    question is what is the numerical
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    relationship between this group here and
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    this group here so let's count so we
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    have this peptide bond here so let's
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    call this amino acid number one then we
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    have this peptide here we have amino
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    acid number two we have this peptide
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    here amino acid number three and finally
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    we have this peptide here and amino acid
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    number four and so what we see is if
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    this is our amino acid that contains the
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    NH group then it will interact with the
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    co group with the uh the C group of the
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    amino acid that is found four units
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    ahead of that particular amino acid and
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    this is always true for the alpha Helix
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    so it's the NH group of one amino acid
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    that interacts with the co group of the
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    amino acid that is found four units
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    ahead of that amino acid and the reason
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    this takes place is because these are
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    the groups that are found in closest
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    proximity and are able to interact
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    strongly now let's move on to the beta
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    pleated sheets we see that in the alpha
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    Helix we have we we we have this helical
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    directionality of our polypeptide but in
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    the the beta plated sheets these
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    polymers are linear so the polypeptide
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    is linear and they're basically stacked
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    on top of one another now just like in
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    the helical case where we have two
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    different types of alpha helixes we have
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    the right-handed and the left-handed we
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    also have two types of beta pleated
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    sheets so we can have these two linear
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    peptides or polypeptide chains uh
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    basically point in the opposite
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    directions or they can point in the same
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    direction so anti-parallel
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    directionality basically means they are
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    stacked on top of one another but they
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    point in opposite directions and the
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    parallel beta sheet basically means
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    they're stacked on top of one another
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    and they point in the same direction so
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    let's begin with the anti- parallel case
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    and let's discuss how the bonding
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    actually takes place within the
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    anti-parallel beta pleaded sheets now
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    because we essentially have one of these
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    chains running in this direction and the
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    other one is reversed we see that these
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    groups actually line up with one another
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    perfectly and what that means is if we
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    examine this amino acid here and this
  • 00:08:47
    amino acid here they're groups that are
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    able to interact line up perfectly so we
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    have this hydrogen accepting group that
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    interacts with this hydrogen donating
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    group on the other amino acid and here
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    we have this hydrogen donating group
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    that interacts with this hydrogen
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    accepting group of the other opposing
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    amino acids so in the anti-parallel beta
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    sheets we see that the NH and the co
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    groups of an amino acid on one strand
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    interact with the co and NH groups of
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    the opposing amino acid on the other
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    strand so we have a one toone perfect
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    interaction between our were groups on
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    opposing amino acids now how exactly can
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    this actually exist well let's imagine
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    we have our polypeptide that runs in the
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    following Direction and somewhere here
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    we have a turn that will take place and
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    that turn can be a beta turn that we're
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    going to discuss in just a moment and
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    once that turn takes place it extends
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    and moves in the opposite direction and
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    so we have the anti-parallel arrangement
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    of two strands of polypeptide now in
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    this particular case the only difference
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    is there's still a parallel with respect
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    to one another but now they run in the
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    same direction and what that will do is
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    it will change the type of interaction
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    that exists between our amino acids in
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    this case we have a one toone
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    interaction so one amino acid interacts
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    with the opposing amino acid but here we
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    have one amino acid in interacts with
  • 00:10:30
    two different amino acids on the
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    opposing strand so let's call this amino
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    acid number one this let's call amino
  • 00:10:39
    acid number two and this amino acid
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    number three so we have the NH Bond of
  • 00:10:45
    amino acid number one interacts with the
  • 00:10:47
    co Bond of amino acid 2 on the opposing
  • 00:10:50
    Strand and the co Bond of this amino
  • 00:10:54
    acid number one interacts with the NH a
  • 00:10:58
    group of a different amino acid on that
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    opposing strand we call that amino acid
  • 00:11:04
    3 so in the parallel beta sheet the
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    Jason strands run in the same direction
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    and an amino acid on one strand connects
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    to two amino acids on the opposing
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    strand via the hydrogen bond so we see
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    that not only do we have these opposing
  • 00:11:22
    directions but because in this case we
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    have the opposing directions they line
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    up perfectly but in this case because
  • 00:11:30
    they run in the same Direction They
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    Don't line up perfectly and so we have
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    this type of one to two interaction as
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    opposed to one: one in this case now the
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    final type of secondary structure that
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    I'd like to discuss are the beta turns
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    so what do we mean by Beta turn and why
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    do our polypeptides need to create these
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    beta turns in the first place well if we
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    examine the three dimensional structure
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    of poly peptides we'll see that the
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    structure is very very Compact and the
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    compactness of that polypeptide is
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    because the polypeptide is able to make
  • 00:12:09
    many sharp turns as it conforms into
  • 00:12:12
    that threedimensional structure and this
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    ability to form these turns is known as
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    beta turning and these turns themselves
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    are known as beta turns or reverse turn
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    so the compact nature of proteins is in
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    part due to the polypeptide's ability to
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    make these sudden turns known as the
  • 00:12:34
    beta turns now in the same way that the
  • 00:12:38
    alpha Helix and the beta pleated sheet
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    are stabilized by hydrogen bonds these
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    abrupt turns are also stabilized by H
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    bonds and to see what we mean let's take
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    a look at the following diagram so let's
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    suppose we have polypop polypeptide that
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    runs eventually turns in the following
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    Direction so this is let's say the nth
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    amino acid in our sequence this is the
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    n+1 amino acid this is the n plus2 amino
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    acid this is the n+3 amino acid and so
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    forth now to actually stabilize the beta
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    turn and to make sure that it is
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    stabilized and exists for an extended
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    period of time we have to have a bond
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    that forms between the co group
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    so wow this is an H not an N so so if we
  • 00:13:29
    examine the nth amino acid the co group
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    of the nth amino acid interacts with the
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    NH group of the N plus3 amino acid and
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    this is the hyrogen bond that stabilizes
  • 00:13:42
    our beta turns and these beta turns are
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    usually found on the surface of that
  • 00:13:48
    Amino of that polypeptide and what that
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    means is these R chains found on the
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    beta turns are the one that interact
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    with the polar nature the polar solvents
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    found outside our protein as well as
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    with the molecules the macro molecules
  • 00:14:04
    that interact with our protein in
  • 00:14:07
    general so these are the different types
  • 00:14:10
    of secondary structure that exists that
  • 00:14:13
    make up our polypeptide
タグ
  • polypeptide structure
  • secondary structures
  • hydrogen bonds
  • alpha helix
  • beta pleated sheet
  • beta turns
  • omega loops
  • primary structure
  • bond rotation
  • protein stability