Chapter 4: Protein Three-Dimensional Structure.
heme
Capacity of myoglobin to bind oxygen depends on the presence of _____
Unit of mass very nearly equal to that of hydrogen atom. ( Therefore: 5500 g mol-1 = 5500 daltons)
Dalton.
Most common cross-links, formed by the oxidation of a pair of cystine residues, resulting in a residue called Cystine.
Di-sulfide bonds
* Primary. * Secondary. * Tertiary. * Quaternary. *
Different structures of a protein.
secondary structure
Either an alpha helix or beta pleated sheet.
Peptides made of small numbers of amino acids
Oligopeptides.
beta pleated sheet
One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.
Formed by linking the α-carboxyl group of one amino acid to the α-amino of another amino acid.
Linear Polymers.
Regular repeating part, Rich in hydrogen-bonding. Each Residue contains carbonyl group (C=O), which is a good Hyfrogen-bond donor
Main Chain or Backbone.
110 daltons
Mean Molecular weight of an amino acid residue.
Bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O).
Peptide Bond.
A series of amino acids joined by peptide bonds. It has directionality. (Its ends are different: in one side α-amino, and a α-carboxyl on the other. For Convenience α-amino is taken to be the beginning. SEE PAGE 46)
Polypeptide Chain.
Another name for the sequence of amino acids. It determines the final 3 dimensional structure of a protein.
Primary Structure.
A large group of nitrogenous compounds of high molecular weight that are essential constituents of all living organisms. They consist of one or more chains of amino acids linked by peptide bonds and are folded into a specific three-dimensional shape maintained by further chemical bonding
Protein
metamorphic protein
Proteins that exist in an ensemble of structures of approximately equal energy that are in equilibrium
When many proteins require more than one chain to function.
Quaternary Structure.
Each amino acid in a Polypeptide.
Residue.
Freedom of rotation created by the bonds between the amono group and the α-carbon and between the α-carbon and the carbonyl group.
Rotation that allows proteins to fold in many different ways.
The 3 dimensional Structure of Proteins. Result from a regular pattern of hydrogen bonds between the Nitrogen-Hydrogen (NH) and Carbon-Oxygen (CO) of the amino acids.
Secondary Structure.
folding funnel
Shows 3D version of 2D energy states. Lowest energy is stable protein. Rough funnel is less cooperative.
Ramachandran plot
Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.
supersecondary structures/motifs
Specific combination of alpha helices and B sheets Tell structural information
disulfide bond
Strong chemical side bond that joins the sulfur atoms of two neighboring cysteine amino acids to create one cystine, which joins together two polypeptide strands like rungs on a ladder.
* The peptide Structure is essentially planar. (trans and Cis only.Almost all peptide bonds in proteins are trans due to sterics ) * Peptide bond has considerable double-bond character. * Peptide bond is unchanged.
Structure characteristics of Polypeptides.
Highest level of structure that an individual polypeptide can attain. It happens when the 3 dimensional structure becomes more complex when the R group of amino acids far apart in the primary structure.
Tertiary Structure.
primary structure
The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.
quaternary structure
The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.
tertiary structure
The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.
proline glycine
___ in position 2 or ___ in position 3 are common in beta turns
ferritin
___, an iron storage protein is built from a bundle of alpha helices
backbone and variable side chains
a polypeptide chain consists of 2 things:
directionality
a polypeptide chain has
glycine
acts as a helix breaker because the tiny R group supports other conformations.
trans
almost all peptide bonds in proteins are ___
direction
amino acid sequences have ___
peptide bonds
amino acids are linked by ___ ___
myoglobin
an extremely compact molecule
phi angle
angle around the alpha carbon-amide nitrogen bond
psi angle
angle around the alpha carbon-carbonyl carbon bond
beta turn
another common type of secondary structure is
domain
compact globular units
two cysteine
disulfide bonds form by the oxidation of
no
do all polypeptide sequences adopt alpha helices
right-handed
essentially all alpa helices found in proteins are
structural support
fibrous proteins provide what for cells and tissues
beta sheets
formed by adjacent beta strands
3
how many bonds separate sequential alpha carbons in a polypeptide chain
steric repulsion
hydrogen bonds within each peptide chain are absent of helices, instead the helices are stabilized by ___ ___ of the pyrrolidine ring of the proline residues
6
in a pair of linked amino acids, ___ atoms lie in a plane
opposite
in antiparallel beta sheets, the H-bonded strands run in the ___ direction
four
in beta turns, The 180° turn is accomplished over ___ amino acids
fully extended
in contrast to alpha helices, the polypeptide in a beta strand if ___ ___
same
in parallel beta sheets, the H-bonded strands run in the ___ direction
disulfide bonding
in some proteins, the polypeptide chain can be cross-linked by disulfide bonds
uncharged
is the peptide bond charged or uncharged?
beta turns
occur frequently whenever strands in b sheets change the direction
amide bond
peptide bond
reverse turns and loops
polypeptide chains can change direction by making
prion
protein particles that cause disease
genes
proteins have unique amino acid sequences specified by
intrinsically unstructured protein
proteins that in whole or in part lack discrete three-dimensional structure under physiological conditions
alanine leucine
small hydrophobic residues such as ___ and ___ are strong helix formers
beta pleated sheets
stabilized by hydrogen bonds between adjacent segments that may not be nearby
alpha helix
stabilized by hydrogen bonds between nearby residues
molten globule
structure characterized by dynamic hydrophobic interactions
3D structure
the amino acid sequence of a protein determines its
intermediates
the essence of protein folding is the tendency to retain partly correct ___
steric exclusion
the fact that two atoms cannot be in the same place at the same time, restricts the number of possible peptide conformations and is thus a powerful organizing principle
dehydration synthesis
the forming of two molecules while water is being removed as well
many different ways
the freedom of rotation about two bonds of each amino acid allows proteins to fold in
thermodynamically
the native structure for 3D structure is the ____ most stable structure
glycine
the only residue that can fit in an interior position is
canonical structures
the peptide bond is a resonance hybrid of 2 ___ ___
planar
the peptide bond is essentially ___
double-bond
the peptide bond of the primary structure has a partial ___-___ character
buried surface
the polypeptide chain folds so that its hydrophobic side chains are ___ and it polar, charged chains are on the ___
alpha carbons
the polypeptide is made up of a series of planes linked to
amino carboxyl
the primary structure is always written from the ___ terminal to the ___ terminal, left to right
Aino acid residues
the primary structure is the
fibroin
the protein of silk, is produced by insects and spiders. It consists of layers of antiparallel beta-sheets
assembled subunits are
the quaternary structure
rigid planar prohibited
the resonance causes the peptide bond to be quite ___ and nearly ___; rotation about the bond is ___
cystine
the resulting unit of two linked cysteines is called
hydrogen bonds
the secondary structure arises from the ___ bonds formed between atoms of the backbone.
alpha helix
the secondary structure is the
subunit
the section of a DNA molecule that contains a sugar, phosphate, and a base
polypeptide chain
the tertiary structure is
steric
there are ___ clashes between R groups in the cis configuration
C---N
what bond cannot rotate
N---C(alpha) C(alpha)---C
what two bonds can rotate
trans cis
what two configurations are possible for a planar peptide bond
regular local
when the secondary structure arises it is called a ___ ___ spatial arrangement of the polypeptide backbone
proline
•acts as a helix breaker because the rotation around the N-Ca (φ-angle) bond is impossible
beta strand
A polypeptide chain that is almost fully extended rather than being tightly coiled as in the alpha helix
Most natural polypeptide chains containing between 50 and 2000 amino acids residues.
A protein.
alpha helix
A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.
Range from 50 to 300.
Amino acids in a protein.
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Largest Protein Known, with almost 27000 amono acids.
Titin.
alpha helix beta pleated sheet
What are the two most common types of secondary protein structure?
