Chapter 6: Proteins: Three-Dimensional Structure Flashcards
What is the order of the 4 structures of a protein?
Primary, Secondary, Tertiary, Quaternary
What is the primary structure?
the linear sequence of amino acids in the protein/amino acid sequence in a polypeptide chain
What is the secondary structure?
The secondary structure arises from the hydrogen bonds formed between atoms of the polypeptide backbone that form into 3 main structures: a helixes b sheets b turns
when the sequence of amino acids are linked by hydrogen bonds
side chains not included
What is the tertiary structure?
the three-dimensional structure of an entire polypeptide, including its side chains/one complete protein chain (β chain of hemoglobin)
What is the quaternary structure?
the spatial arrangement of its subunits./ the four separate chains of hemoglobin assembled into an oligomeric protein
A The Planar Peptide Group Limits What and Why?
Polypeptide Conformations because of its rigid planar structure and it has a partial double bond character due to resonance
Which conformations do peptide groups assume?
Trans Conformation- successive C atoms are on opposite sides of the peptide bond joining them
Cis Conformation- successive C αatoms are on the same side of the peptide bond
Which conformation is more stable and why?
Trans because of the steric interference between neighboring side chains in cis
when is steric interference reduced
this steric interference is reduced in peptide bonds to Pro residues, so ∼10% of the Pro residues in proteins follow a cis peptide bond.
Torsion Angles/dihedral angles/rotation angles between Peptide Groups Describe? and where
Polypeptide Chain Conformations. around the CαN bond ( ϕ ) and the CαC bond ( ψ ) of each residue
Another name for backbone
main chain
what is a backbone
The backbone just refers to the polypeptide chain apart from the R groups
The backbone or main chain of a protein refers to the atoms that participate in peptide bonds, ignoring the side chains of the amino acid residues. The backbone can be drawn as a linked sequence of rigid planar peptide groups
conformations degrees
trans, ω ≈ 180°, and cis, ω ≈ 0°.
Which Diagram Indicates Allowed Conformations of Polypeptides?
The Ramachandran
how does a peptide bond form
When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed.
the most common regular secondary structures?
𝛂 Helix and the 𝛃 Sheet
structure of an α helix? each turn contains how many amino acids?
In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they avoid steric interference with the backbone and each other.
structure of a β sheet?
two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet,
2 types of a β pleated sheet ?
The strands of a β pleated sheet may be Parallel, pointing in the same direction (meaning that their N- and C-termini match up),
Or Antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other).
which strand of β sheet is more stable?
Antiparallel
parallel β sheets are less stable than antiparallel β sheets,possibly because the hydrogen bonds of parallel sheets are distorted compared to those of the antiparallel sheets (Fig. 6-9).
not related but β Sheets containing mixtures of parallel and antiparallel strands frequently occur.
compare and contract α helix and the β sheet
Like the α helix, the β sheet uses the full hydrogen-bonding capacity of the polypeptide backbone. In β sheets, however, hydrogen bonding occurs between neighboring polypeptide chains rather than within one, as in an α helix.
what are the reverse turns or β bends
β-Turns are one of the most common structural motifs in proteins and change the direction of the peptide backbone by nearly 180°, allowing the peptide chain to fold back onto itself.
what are the reverse turns or β bends
β-Turns are one of the most common structural motifs in proteins and change the direction of the peptide backbone by nearly 180°, allowing the peptide chain to fold back onto itself.
what are the two kinds of proteins based on their morphology?
Fibrous
Globular
2 Fibrous proteins discussed?
Keratin and Collagen
2 Fibrous proteins discussed?
Keratin and Collagen
Describe 𝛂 Keratin, what are the two types?
Keratin is a coiled coil.is a mechanically durable and relatively unreactive protein that occurs in all higher vertebrates. It is the principal component of their outer epidermal (skin) layer and its related appendages, such as hair, horn, nails, and feathers.
Keratins have been classified as either α keratins, which occur in mammals, or β keratins, which occur in birds and reptiles. Humans have more than 50 keratin genes that are expressed in a tissue-specific manner.
difference between fibrous and globular
Fibrous proteins are generally composed of long and narrow strands and have a structural role (they are something)
Globular proteins generally have a more compact and rounded shape and have functional roles (they do something)
fibrous has little to no tertiary structure.
collagen structure
the collagen polypeptide assumes a left-handed helical conformation with about three residues per turn. Three parallel chains wind around each other with a gentle, right-handed, ropelike twist to form the triple-helical structure of a collagen molecule
amino acid composition of collagen
Nearly one-third of its residues are Gly; another 15 to 30% of its residues are Pro and 4-hydroxyprolyl (Hyp). 3-Hydroxyprolyl and 5-hydroxylysyl (Hyl) residues also occur in collagen, but in smaller amounts.
Gly-X-Y over a segment of ∼1000 residues, where X is often Pro and Y is often Hyp
what is collagen
occurs in all multicellular animals, is the most abundant vertebrate protein. Its strong, insoluble fibers are the major stress-bearing components of connective tissues such as bone, teeth, cartilage, tendon, and the fibrous matrices of skin and blood vessels. A single collagen molecule consists of three polypeptide chains.
well-packed, rigid, triple-helical structure is responsible for its characteristic tensile strength.
Keratin forms what kind of bonds that collagen doesn’t
disulfide bonds contains Cys so it cross links to adjacent polypeptide chains unlike collagen resulting in collages poor solubility.
most proteins are ?
globular
Which Proteins Have Repeating Secondary Structures
Fibrous
Which Proteins Have Nonrepetitive Structures
Globular
What BEST distinguishes irregular secondary structure from regular secondary structure?
Unlike regular secondary structure, successive residues in irregular secondary structure do not have the same backbone configuration.
what happens in the tertiary structure?
The tertiary structure of a protein describes the folding of its secondary structural elements and specifies the positions of each atom in the protein, including those of its side chains.
What are the 3 methods used to determine the positions of atoms in proteins? *******
X-Ray crystallography, NMR spectroscopy, and cryo-electron microscopy
What are the 3 methods used to determine the positions of atoms in proteins?
X-Ray crystallography, NMR spectroscopy, and cryo-electron microscopy
What does X-Ray crystallography do?
a technique that directly images molecules
a crystal of the molecule to be imaged (e.g., Fig. 6-20) is exposed to a collimated beam of X-rays and the resulting diffraction pattern, which arises from the regularly repeating positions of atoms in the crystal, is recorded by a radiation detector or, now infrequently, on photographic film
what do X-rays specifically image and why
X-Rays interact almost exclusively with the electrons in matter, not the nuclei.
An X-ray structure is therefore an image of the electron density of the object under study.
Most Crystalline Proteins Maintain Their what kind of Conformations.
native
why do Most Protein Crystal Structures Exhibit Less than Atomic Resolution.
it is highly hydrated 40-60% water,necessary for the structural integrity of the protein crystals, because water is required for the structural integrity of native proteins themselves
a crystal structure analysis depends on?
the crystal’s resolution limit. a crystal structure analysis depends on the crystal’s resolution limit. Indeed, the inability to obtain crystals of sufficiently high resolution is a major limiting factor in determining the X-ray crystal structure of a protein or other macromolecule.
Most protein crystal structures are too poorly resolved for their electron density maps to reveal clearly the positions of individual atoms (e.g., Fig. 6-23). Nevertheless, what can be obtained?
the distinctive shape of the polypeptide backbone usually permits it to be traced, which, in turn, allows the positions and orientations of its side chains to be deduced
Most Crystalline Proteins Maintain what kind of conformations
native ,crystalline proteins assume very nearly the same structures that they have in solution: