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147 Cards in this Set
- Front
- Back
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Primary structure
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complete description of all the covalent bonding in a polypeptide chain or protein
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In some proteins, the linear polypeptide chain is cross-linked
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disulfide bonds
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However, the primary structure does not indicate the position of
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amino acids in space
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It is the ordered arrangement or conformation of amino acids in localized regions of a polypeptide or protein molecule
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Ssecobndary structure
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plays an important role in stabilizing these folding patterns
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HYdrogen bonding
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The two main secondary structures are the
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Alpha and beta helix
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It is the combination of all of the secondary structures adopted by the different local regions of the protein.
It is the 3D arrangement of the atoms within a single polypeptide chain |
Tertiary protein
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It is used to describe proteins composed of multiple subunits (multiple polypeptide molecules each called a monomer);
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Quad protein
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Quad protein subunits can be
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identical or different
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Most proteins with a molecular weight greater than 50 000 Da consist of ?
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two or more noncovalently-linked monomers;
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The arrangement of the monomers in the 3D protein is the
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Quadary stucture
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A protein usually adopts a single tertiary structure: this is also called the
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Native confirmation of a protein
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For proper folding..
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weak non-covalent forces are required
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Primary type of bonds determine primary protein structure?
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covalent
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secondary type of bonds determine protein structure?
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backbone H-bonds
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tertiary type of bonds determine protein structure?
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Side chain H-bonds, ionic, van der waals interactions and hydrophobic interactions
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The clarity/elucification of the secondary structures of proteins was possible only after understanding the __________ of the peptide bond
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Geometry
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The peptide bond is_______ in space
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Planar
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lie in the same plane (peptide bond)
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the two atoms involved in the peptide bond four substituents carbonyl oxygen atom, the amide hydrogen atom, and the two adjacent α-carbon atoms
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Which atoms are involved in the amino acid resonance structure?
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electrons are delocalized over the carbonyl oxygen, the carbonyl carbon and the amide nitrogen
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The peptide bond is non-polar
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False
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Cis and trans conformations are both equally possible at the Alpha carbon
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false- to much steric hinderence between side chains
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Nearly all peptide groups are in this confirmation
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Trans
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What percentage of cis exist in X-PRO linkages
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10%
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These bonds show less preference for the trans conformation(prolinelink) because
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the nitrogen of proline is bonded to two tetrahedral carbon atoms limiting the steric differences between trans and cis forms
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The rotation around N-Cα bond of the peptide group is designated?
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Φ (phi)
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bond around Cα-C is designated?
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Ψ (psi)
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look at diagram
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know diagram
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The Alphac helix was proposed in 1950 by ______ and______
They considered the dimensions of peptide groups, possible steric constraints and opportunities for stabilization by formation of _____________ |
Linus Pauling and Robert Corey
Hydrogen bonds |
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Their model accounted for the major repeat observed in the structure of the fibrous protein called______
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α-keratin
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The α-helices found in proteins are almost always found _____ direction screw
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right handed
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The pitch of the helix is?
the rise is______ and the number of amino acid residues for |
0.54nm
0.15nm |
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one complete turn for a alpha helix is
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3.6
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The carbonyl oxygen has a partial____ charge and can serve as a _____ acceptor in ___bonds;
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negative
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The nitrogen has a partial______ charge and the NH group can serve as a _____ donor in____bonds
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postive
hydrogen hydrogen |
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Within an α-helix, each carbonyl oxygen (residue n) of the polypeptide backbone is _________ to the backbone _____________ of the ________ residue further toward the C-terminus (residue n + 4);
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hydrogen bonded
amide hydrogen fourth |
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These ________ tend to “lock in” rotation around the _____ and the_______ bonds restricting the _____ and _____ angles to a narrow range
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H-bonds
N-Cα Cα-C bonds Φ Ψ |
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The Φ and Ψ angles of each residue in an α-helix are similar. They cluster in the Ramachandran plot at a____ value of -57° and a _____ value of -47°.
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Φ and Ψ
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The similar bond values of the psi and phi bonds give alpha helixes there___________ stucture
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regular, repeating structure
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H-bonds between amino acid residues are especially stable in the hydrophobic or hydrophilic interior?
Explain your choice |
hydrophobic
Water molecules do not enter and therefore compete for h-bonding. |
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In an α-helix, all the carbonyl groups point toward the________
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C-terminus
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Since each peptide group is polar/nonpolar and all the Hhydrogen/covalent bonds point in ___ direction, the entire helix is a _____ with a_____ ___-terminus and a _____ ______-terminus
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polar
h-bond Same dipole positive N negative C |
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The side chains of the amino acids in an α-helix point _________ from the cylinder of the helix
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Outword
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The stability of the α-helix is affected by the identity of the side chains. Name the three factors that effect its stability and why they do so.
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Electrostatic repulsion - between amino acids having same charged R groups separated by 4 residues (destabilizes)
Steric hindrance - between adjacent R groups (destabilizes) i.e. aromatic amino acids Interactions (electrostatic or hydrophobic) between R groups situated 3 to 4 amino acid residues away (stabilizes) i.e. positively charged amino acid situated 3 to 4 amino acids away from a negatively charged amino acid |
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Some amino acids are found/absent in α-helical conformation due to stability.
Would alanine,prolineTyrosine,asparagine, glycine fit well explain? |
alanine: Small, uncharged R group and fits well into the α-helical conformation;
Proline: least common residue in α-helix because of its rigid cyclic side chain disrupts the helical structure by occupying space that a neighboring residue of the helix would otherwise occupy Tyr/Asn: bulky R groups so they are less common Glycine: R group is a single H atom and destabilizes the structure since rotation around the Cα is unconstrained For this reason, many α-helices begin or end with Gly |
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Many α-helices have ____________ amino acids on one face of the helix cylinder and _______ amino acids on the opposite face (amphipathic nature);
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hydrophobic
hydrophilic |
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Amphipathic helices are often located on the ______ of a protein, with the _______ side chains facing outward (toward the aqueous solvent) and the______side chains facing inward (toward the ________ interior);
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surface
hydrophilic hydrophobic hydrophobic |
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Two ________ α-helices can interact to produce an extended coiled coil structure where two helices wrap around each other with their __________faces in contact and their _________ faces exposed to the solvent
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amphipathic
hydrophobic hydrophilic |
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A common structure in DNA-binding proteins is called a__________
Two helices are “zippered” together by the ___________interactions |
a leucine zipper
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_______________ is found in hair and nails;
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α-keratin
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Two molecules of ________ will form a coiled coil _______ bonds
The coiled coil will pair up with other coiled coils forming _________ and ___________ |
α-keratin
disulfide bonds protofilaments protofibrils |
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Four __________ will form a keratin ______ _________
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protofibrils
intermediate filament |
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The other common secondary structure is called the _______ ____________which includes _________ and __________
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β structure
β strands and β sheets |
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___________are portions of the polypeptide chain that are almost fully extended having a “__________” shape
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β strands
zig-zag |
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When multiple__________ are arranged side-by-side, they form ______
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β strands
β sheets |
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Why do proteins rarely contain isolated B-strands?
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The structure by itself is not significantly more stable than other conformations
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β sheets are stabilized by ________between _____ ________and _____ _____on adjacent β strands.
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hydrogen bonds
carbonyl oxygens amide hydrogens β strands. |
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The _____ ______β strands can be on separate ____ ______ or on different segments of the ____ _______
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hydrogen bonded
polypeptide chains same chain |
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The___ ______in a sheet can be either ________ or ________ direction. Distance per residue is ____ in length
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β strands
parallel antiparallel 0.35 nm |
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The hydrogen bonds are nearly ___________ to the extended polypeptide chains
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perpendicular
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The carbonyl oxygen and the amide hydrogen atoms of one residue form _________ bonds with the amide hydrogen and carbonyl oxygen of a single residue in the other strand
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hydrogen
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In the________arrangement, the _______ bonds are not ___________ to the extended chains, and each residue forms ___________bonds with the carbonyl and amide groups of two different residues on the adjacent strand
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parallel
hydrogen perpendicular hydrogen |
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Many strands, typically ____or______ but as many as ____or more, can come together in _______. Such sheets can be purely ____,______, or ______
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4 or 5
10 β sheets antiparallel, purely parallel, or mixed |
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The R groups from the amino acids _____ _______above and below the plane of the sheet
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point alternatively
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In certain proteins adopting a β conformation, _______ from amino acids such as ___ ___ ___ allow the β sheets to stack ____ _____
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small R groups
Ala, Gly and Ser closely together |
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This β conformation is responsible for the ______characteristic of the _____ ____.
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flexible
silk filaments |
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Structure of fibroin give example
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the protein component of silk and spider webs
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In an ____ or a ________, consecutive residues have a __________ that is _________throughout the structure
Most of these regions of _________ structures can be characterized as___ and ____ since they cause ______changes in the _______ |
beta strand
alpha helix similar conformation repeated loops turns directional polypeptide backbone |
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____ and____ connect ______and ______and allow the _____ _____to fold back on itself, producing the compact ______ shape seen in ____ ______;
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Loops
turns α-helices β strands polypeptide chain 3D native structures |
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Loops often contain ______ _________ and are usually found on the ______ of ________where they are exposed to ______ and form ______with______
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hydrophilic residues
surfaces proteins solvent H-bonds water |
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Loops containing only a _______ residues are referred to as _____ if they cause an _______ change in the ______ of a .
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few (up to 5)
turns abrupt direction polypeptide chain |
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The most common types of tight turns are called ________ or ______ because they usually connect different ________ _________
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reverse turns
β turns antiparallel β strands |
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β turns contain ____ _____ ______ _____and are stabilized by ______bonding between the ______ ______ of the first residue and the ______ _____ of the ___ _____
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4 amino acid residues
hydrogen Carbonyl oxygen amide hydrogen fourth residue |
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____ ____ produce an abrupt (usually about ___°) change in the direction of the polypeptide chain
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β turns
180 |
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______and _____ are often part of the ____ ___
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Gly
Pro β turns |
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_____ is capable of forming a _____ _____ ___conformation which is highly susceptible in forming ____ ____
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Pro
cis peptide bond β turns |
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______has a small ___ _____ which is capable of generating unique ____ AND _____ ______permitting a high degree of flexibility
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Glycine
R group psi and phi angles |
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Family of over 20 rod-like proteins;
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collagen
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________ is an Important part of connective tissue ( __ of all proteins in mammals);
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collagen
1/3 |
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________ is Classified into ___ different types, according their ________ ___ _____ , their ____ _______and their ____ _____.
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collagen
5 amino acid content primary structure sugar content |
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What are the five types of collagen? Which is found in small quantities?
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Type 1 - bone, tendon, fibrocartilage, dermis, cornea
Type 2 - nucleus pulposus, hyaline cartilage Type 3 - intestinal and uterine wall Type 4 - endothelial, epithelial membranes Type 5 - cornea, placenta, bone, heart valve |
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_______Consists in a ____ ______: 3 polypeptide chains (___ ____) are intertwined together to form a _____ ______
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Collagen
triple helix each left handed right-handed superhelix |
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For each left-handed helix:_______
Pitch: _______ Rise: _______ _______ __________ |
0.94 nm
0.31 nm per residue 3 residues per turn 1000 residues per chain |
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So: the collagen helix is more _______ than the ____ ____
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a-helix
extended |
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The collagen polypeptides have a very specific amino acid composition:
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1/3 Gly
1/4 Pro 1/4 Hypro (hydroxyproline) and 5-Hylys (hydroxylysine) |
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These residues follow a strict sequence where Gly is always repeated every third position – WHY??;
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causes its gangsta
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The presence of ____ at every _____ ____allows each ____ _____ to form a_____ _____ ______that can accommodate ___/___ (which are otherwise rarely included in helices);
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Gly
third residue collagen chains tightly wound helix Pro/Hypro |
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Since the _____ has _____ ____ _____, having ___ at every ____ _____means that _____ is always on the same side of the helix;
It just so happens that_____is always positioned at the ______ of the _____ _____; This allows ____ _____ of the ____ ____, which can interact and yield a very strong, _____ ______ _______. |
helix
3 a.a. per turn Gly third residue Gly Gly center triple helix close packing three helices rope-like structure |
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________ bonds stabilize the _____ ______ ________
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Hydrogen
collagen triple helix |
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Formation of collagen fibers
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.
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Tertiary structure:
Involves the folding, in space, of the whole _________ __________ |
polypeptide chain
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(Tertiary)
Involves several elements of _____ ______, which interact together through different interaction forces/bonds. List the 5 interactions/forces: |
secondary structures
H bonds Electrostatic interactions Van der Waals interactions Hydrophobic interactions Disulfide-bonds |
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Absolutely _______ for a protein to be________.
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required
active |
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Two main types of tertiary structures exist:
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Fibrous (e.g. collagen)
Globular (e.g. myoglobin) |
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For proteins in an________ environment:
__________ amino acids are buried in the interior of the structure; __________amino acids are exposed to the _______ Conversely, ______ _______ proteins are exposed to an _______ environment: __________ amino acids are exposed; __________amino acids are buried inside |
aqueous
Hydrophobic Hydrophilic solvent; membrane-bound hydrophobic Hydrophobic Hydrophilic |
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Protein folding occurs in specific steps:
Some individual elements of ____ ______are first formed; A few elements of _____ _______ cluster together to form ____ ____ ____ These bundles of ___ ______ then form_____, which fold _________ of the rest of the protein; Finally, several _______interact to form the final, ____ _____ _____ of the protein. Any given protein will always adopt the same ___ ______ ____ |
secondary structure
secondary structure conserved folding motifs; secondary structure domains independently domains functional 3-D structure functional 3-D structure. |
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What are the dfferent tertiary motifs?
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Protein domains
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Label
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Kinase domain:
Adds ________ groups from ATP to _____ residues of other proteins. SH2 domain: Allows______ to bind to _________ of other proteins; SH3 domain: Allows _____ to bind to _______ ______ sequences of other proteins |
phosphate
tyrosine SRC Phospho-Tyr SRC PROLINE RICH |
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SH2 and ______ domains are found in many proteins
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sh3
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Myoglobin
Found in _________ Binds the ______required for ______ metabolism; Associated with a ____ ____, which is actually responsible for binding _______; |
muscles
oxygen aerobic heme group oxygen |
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know picture
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Porin – a _____ -____ ______
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membrane-bound protein
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For some proteins, folding requires the help of other proteins called _____________;
________ generally work by binding to exposed ________patches on the unfolded protein, preventing __________and _______ ________. |
chaperones
Chaperones hydrophobic aggregation irreversible inactivation |
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Proteins can be _______ by treatments that destroy the _____ _______required for the adoption of the proper_______ _________:
Heat pH Solvent Urea/guadinium: breaks up H-bonds b-ME |
denatured
interaction forces 3-D structure |
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The fact that __________ can be reversibly _________ and __________in _______ shows that the information required for the proper folding of a protein resides in its _______ ________
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ribonuclease
denatured renatured vitro primary structure |
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Green flouresence
Protein found in the____ _____; Has the unique property to emit a_____ ____ ; Different variants were produced by ________ _______to produce red, yellow, cyan, blue light. Extremely useful in _____ _________: one can tag it to her/his protein of interest and follow the protein in the cell using ____________ __________. |
jelly fish
green light genetic engineering cell biology fluorescence microscopy |
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prions
Normal form = ______ Toxic form = ______ |
PrP _c
PrP_nc |
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Glycine puts _____ in alpha helix thus is only found in the start and beginning of helixes
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kinks
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Beta strands can be stretched because they are not fully extended.
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false
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Anti-parallel forms easier _____ bonds than paralell.
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hydrogen
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Turns can be strictly ____ aswell
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glycine
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Tyrosinase mutation and Siamese cat coat color
Tyrosinase: Essential for ______ _________ Other breeds: ____ at position ____ Siamese cats: _____ at position ____ This mutation turns _______ into a ______-_______enzyme: _____ _____ in colder body areas _____ warmer body areas. |
melanin synthesis
gly 302 302 Arg tyrosinase temperature-sensitive Native structure Denatured |
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Quaternary structure involves several _______;
These subunits interact with each other through the usual weak interaction forces ____,_____,________ and _______ For ____ _____, frequently, but not always, the interface between two subunits is made of _____ ______. |
polypeptides
H bonds, Van der Waals, ionic interactions, hydrophobic interactions aquous proteins hydrophobic amino acids. |
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Hemoglobin
Made up of _______ ______ _____: 2 copies of _______ _______yellow and blue; 2 copies of______ _____red and pink Each subunit binds its own ____ ____: so each subunit can bind ______ Each_____is highly similar in structure to ________; Both hemoglobin and myoglobin bind O2 in a very ____ ____ |
4 polypeptide chains
a-subunit (or HbA): b-subunit (or HbB): heme group O2 subunit myoglobin similar fashion |
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Oxygen binding by Hb and myoglobin
4 major residues surround the heme group: ______ ______ ______ ________ These ____ ____ create a _________ environment which help _____ the ____ ______ in place; Also: ___ ___ binds the ___ atom; |
Phe 43
His 64 Val 68 His 93 amino acids hydrophobic hold heme group His 93 Fe2+ |
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O2 binds the ____ atom of the ____ _____, and is held in place with ___ ___;
____-_____ myoglobin/Hb is called _____/_______ _____ _____ myoglobin/Hb is called _______/________ Now, if both ____ and ____ can bind ___, why is it that ___is a ___ _____, while ______ is ______??? WHY???? |
Fe2+
heme group His 64 Oxygen-bound oxymyoglobin/oxyHb Oxygen-free deoxymyoglobin/deoxyHb Myo Hb O2 Hb multimeric protein myoglobin monomeric |
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Oxygen binding by Hb and myoHb
___ binding to ____ shows a simple ________where the amount of____ ____ _____ directly depends on the concentration of ____ present; However, O2 binding to Hb is more complex: At low O2 concentration, very little Hb binds O2 even as the concentration of O2 increases (part A of the Hb curve); However, at a certain threshold of ___ concentration, ___becomes rapidly saturated with ____ (part B of the Hb curve); |
O2
myoglobin equilibrium O2 bound-myoglobin (y) O2 o2 Hb o2 |
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Oxygen binding by Hb and myoHb
At high ___concentrations, both ____ and ____ are ______, meaning there are no more ____ ____ ____ available. Interestingly: the ______ of ______and ____ ___ ____varies by a factor of ___: Only __ ___are required to get _____of _______ saturated; However, ___ ____are required to -___ ____ ____ |
O2
myoglobin and Hb saturated O2-binding spot affinity myoglobin Hb for oxygen 10 2.8 Torr 50% myoglobin 26 Torr half-saturate Hb. |
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O2 binding changes the 3-D shape of Hb
In the _______ form, _____ is bonded to___ _____: __ ___and __ ____from the ____ ____; When __ _____of ____ binds ___, the ____ atom moves foward the ______of the ____ _____, pulling with it the ___ ___and the____ _____; This causes a slight but significant ______ in the_____structure of all the other____ ____ , even if they are in the _____ ______; |
deoxyHb
Fe2+ 5 ligands His 93 4 amines heme group one subunit Hb O2 Fe2+ plane heme group His 93 a-helix change tertiary Hb subunits deoxyHb form |
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O2 binding changes the _____ ____ of ____
The consequence of this slight change in conformation is an ________ in the ______ of these other _______ ______ for O2; This phenomenon, where a change in the shape in one subunit trigger similar changes in other subunits of the same molecule, is called_________; Molecules exhibiting cooperativity are also called ______ ________; Hb is an ____ ______ This phenomenon explains very well the behaviour of ___ in the presence of O2: At low _____ all of the _____ _____ in the molecule are in the _____ form with _______ ______for O2: they bind O2 very poorly; At higher ____, one of the _____ ____ binds O2, changes its conformation to the one with_____ _____, and transmits this change in ____ ____ to the other ____ _____; The other 3 subunits, now having ____ ___ for O2, readily bind the molecule and rapidly become _______ |
3-D shape
Hb increase affinity Hb subunits cooperativity allosteric molecules; allosteric protein Hb pO2, Hb subunits deoxy low affinity pO2 4 subunits high affinity 3D structure 3 subunits high affinity saturated |
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Why Hb is ______, while ______ is not?
If Hb behaved like Myoglobin, then most of the Hb molecules would remained______ bound to ____ and would not ____ ______in tissues; Conversely, if ______ behaved like Hb, it would readily let go of its ______, drastically limiting our_____ ______ to perform _______ _________; |
allosteric
Myoglobin tightly O2 unload O2 myoglobin O2 muscles ability aerobic work |
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The ___ ______ concerns the observed _____in ____ binding by __________ when the ____ is lowered;
This effect explains why _______binds O2 in the ______, and releases it in the ________; |
Bohr effect
decrease O2 hemoglobin pH hemoglobin lungs tissues |
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Gas exchange In the tissues
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Gas exchange In the lungs
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...
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Enzymes can be ___ or ______
Catalysts: Fully active enzyme is regenerated at the end of the reaction Speed-up chemical reactions in cells by placing the ____ in an environment that facilitates the reaction So:____ ___ ____(tertiary and, when applicable, quaternary) is _____ ____for the function of enzymes; |
Proteins
RNA Substrate proper 3D structure ABSOLUTELY ESSENTIAL |
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Enzymes
Very powerful catalysts; Very specific for their ______; Can distinguish between ______ Some enzymes require additional _____ or _____to function: 5 of them |
substrate
enantiomers chemicals , groups Metal ions Prosthetic groups: Heme Co-factors ATP |
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Classes of enzymes
Only__ types of chemical reactions are catalyzed by enzymes: Enzymes are classified according to the type of reaction they catalyse: each enzyme is given a systematic name and a IUBMB number (EC XXXX) IUMBM = International Union of Biochemistry and Molecular Biology |
6
1. oxido-reduction: oxidoreductases 2. Transfer of chemical groups: transferases 3. Hydrolysis: hydrolases 4. Removal of chemical groups: lyases 5. Isomerisation: isomerases 6.Linking two groups together: ligases |
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IUBMB enzyme nomenclature
Example: ATP: D-glucose-6 phosphotransferase (aka hexokinase) EC 2.7.1.1 2 = transferase 7 = phosphotransferase 1 = acceptor group is OH 1 = glucose binds the phosphate group |
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know the comp of enzymes
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Collegen fibers are several _____ _____
______ from the two helixes come together and form ____ bond Lycines are converted into ____ There are ___ between adjacent collegen fibers Chemicals turn ____ black on electron microscope |
collegen helixes
lycines covalent aldehydes gaps gaps |
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________ is the "concrete" in our bones. they are crystals which reinforce collegen fibers
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Hydroxylapatite
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Without Vitamen C _____ is absent which is involved with the production of ____ ____
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Fe2+
hydroxl prolines |
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What are doman characteristics?
-can _____on its own and has its own function - can link to other proteins -made from multiple motifs |
fold
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C-src is known to be involved with ______
SH3 and____ found alot in body |
Cancer
SH2 |
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____ asked what are the requirements for a protein to fold into its ___ _________
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anfinsen
3d structure |
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Urea and G break the ____ bonds
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hydrogen
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Chaperones fold proteins?
Chaperones find ________ parts that shoulded be exposed. |
False - they unfold proteins to let them refold by themselves
hydrophobic |
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Disulfide bonds need to be bonded specifically to other disulfide bonds in order to be ____
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NATIVE
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Enzymatic reactions take place in multiple steps involving reaction: _________
Note that, while in theory these reactions are ______, in practice, the low levels of the one of the reactants (S or P) usually pushes the equilibrium in ______ ______; Enzymes increase the rate of chemical reactions, but do NOT alter the _________ of the equilibrium. |
intermediates
reversible one direction direction |
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In chemical reactions, _____ conditions must be met for a reaction to take place:
1. the molecules must collide to react. If two molecules simply collide, however, they will not always react; therefore, the occurrence of a ______ is not enough 2. there must be enough energy (____ ___ ____) for the two molecules to react. If two slow molecules collide, they might bounce off one another because they do not contain enough energy to reach the energy of activation and overcome the transition state (the highest energy point). 3. the molecules must be _______ with respect to each other correctly. |
three
collision energy of activation orientated |
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The _________ _______is not a reaction intermediate: it is a _______ molecular structure that is no longer the substrate, but not yet the product.
G = Gibbs free energy the ability of the molecule to react The greater the _____ ____, the more unstable the molecule is. DG = Gproduct – Gsubstrate: If DG > 0 = reaction does not occur spontaneously (because S is more stable that P) If DG < 0 = reaction occurs spontaneously (because P is more stable than S) In other words: the more negative the DG, the more likely the reaction will take place; |
transition state
transitory free energy |
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In the presence of an enzyme, the reaction is facilitated because the enzyme provides a better environment for the reaction to occur:
______ _____of substrate and chemical groups of the enzyme _____ ______ of the chemical groups with respect to the substrate The formation of the transition state is favoured; |
Close proximity
Proper orientation |
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The « lock and key » thing is a______:
If the enzyme and substrate were perfectly complementary, like a lock and key, the interaction between E and S would be so _______ that the reaction would not occur! Instead, the 3D shape of the enzyme is complementary to the transition state; by doing so, the enzymes favours the formation of the ______ _____, lowers the energy of activation, and accelerates the reaction…COOL! |
MYTH
stable transition state |
