Week 3 Flashcards
Primary structure of protein
Sequence of amino acids, N-terminal to C-terminal
Secondary structure of protein
The folding of parts of the primary structure sequence into particular structures, usually involving several amino acids that are contiguous or from different parts.
Usually form either: a helix or b pleated sheet
Alpha helix 1
Very stable
Usually formed from stretches of 5-40 amino acids
Main chain N-H and C=O groups are hydrogen bonded to one another along the axis of the helix
Alpha helix 2
3.6 amino acids per turn, each turns the structure 100°
Vertical distance from one amino acid to the next is 0.15nm so pitch is 0.54nm
C=O group of amino acid n is hydrogen bonded to N-H group of amino acid n+4
Alpha helix 3
Amino acid side chains project out from the edge of the helix
Sequence of amino acids in an alpha helix can be plotted on a helical wheel diagram. Each is plotted 100° around a circle or spiral
Beta pleated sheet formed from…
Non-continuous regions of the polypeptide chain. (Beta strands)
These line up and form H bonds between C=O groups of one strand and the N-H groups of another
If strand all run in same direction = parallel
If strands run in opposite direction = anti-parallel
Parallel B sheet
Hydrogen bonds evenly spaced within the sheet
B strands are in an almost fully extended conformation
B strands run in the same direction
Anti-parallel B sheet
Has narrowly spaced H bond pairs separated by a larger gap
The B strands are in an almost fully extended conformation
The B strands run in opposite directions
Why the pleated structure of B sheet
The Carbon alpha carbons lie successively above and below the plane of the sheet
The variable side regions point alternately above and below the sheet
Loop regions 1
Secondary structures are linked by loop regions
Loops vary in length, long loops are called random coils and are highly flexible
Short loops connect anti-parallel B strands are called hairpin loops or B turns
Loop regions 2 (examples)
Proline: often found in loop regions as it’s locked ring structure introduces a ‘kink’ into the polypeptide chain
Glycine: often found in loops as it’s small side chain enables it to form turns when other amino acids couldn’t
Both examples tend to be hairpin loops
Beta-alpha-beta motif
Although anti-parallel B strands are usually connected by hairpin loops, parallel B strands are usually connected by an A helix
The helix crossed the B sheet from one edge to another,
This is called B-a-B motif
Tertiary structure of a protein
For most proteins, it’s the final three-dimensional structure of a protein. Produced by association of the secondary structure into compact domains
What non-covalent bonds are important for correct tertiary structure
Ionic
Hydrogen
Van der Waals forces
What covalent bond is important for correct tertiary structure
Disulphide Bridge - make proteins more resistant to degradation and denaturation
(The side chain of one cysteine can form a cross link with the side chain of another which is near to it in space)
How are tertiary structures usually represented in a drawing?
A helix = spiral or cylinder
B sheet = arrows (pointing from N-C terminal)
Quaternary structure of a protein
Many proteins are formed from more than one polypeptide chains
The chains, subunits, associate into a multimeric complex which is held together by electrostatic, hydrogen and van der Waals bonds (sometimes disulphide bridges)
Homodimers and Heterodimers
(Quaternary protein structure)
Homodimer are 2 of the same polypeptides interacting (eg superoxide dismutase)
Heterodimers are 2 different polypeptides interacting (eg CDK4 and Cyclin A)
What are the two major classes of proteins
Globular: protein chains arranged in compact domains (usually active components of cellular machinery)
Fibrous: protein chains arranged into fibres (have structural roles)
Three main groups of fibrous protein defined by secondary structure
Coiled-coil (eg keratin and myosin)
B-sheets (eg amyloid fibres and silks)
Triple helix (eg the collagens)
Example of fibrous proteins: a-keratin 1
Mechanically durable proteins found in hair, nails, feathers, etc
Primary structure has a 7 amino acid repeat which forms an a-helix
The first and fourth amino acid in sequence are hydrophobic and lie on same side of the alpha helix. The others can be any amino acid (forms alpha helix structure)
Two keratin helices twist around eachother, associating via hydrophobic faces of the helices - forms a coiled-coil
Example of fibrous proteins: a-keratin 2
Coiled-cool dimer lines up with another to form a staggered antiparallel tetramer
Tetramers are building blocks of protofilaments which form protofibrils which form microfibrils
Example of fibrous proteins: fibroin
Produced by silkworms
Long stretches contain a 6 amino acid repeat which forms an antiparallel B-sheet
Extremely strong as any stretching requires breaking covalent bonds, but is flexible as the B-sheets are interacting via weak van der Waals bonds
They can stack into an array with layers of contacting Gly side chains altering with layers of Ser/Ala side chains
Example of fibrous proteins: collagen
Most abundant vertebrate protein, forming strong fibres present in skin, bone, teeth, cartilage, etc
Nearly 1/3 of amino acids are glycine, 15-30% are proline or hydroxyproline
Primary amino acid sequence consists of repeating tripeptide of Gly-X-Y
It cannot form an a-helix as the Pro and Hyp residues (restricted nature) - forms a loose helix with around three residues per chain instead
