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92 Cards in this Set
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- Back
- 3rd side (hint)
Define:
Primary Structure |
Linear sequence of amino acids
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Define:
Secondary Structure |
Made up of α-helices and β-sheets.
How polypeptide backbone is folded locally. Held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone. |
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Define:
Tertiary Structure |
3d shape of the entire protein.
The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is. |
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What are the 3 types of bonds that bond Tertiary Structures together?
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Hydrogen Bonds - which are weak.
Ionic Bonds - between R-groups with positive or negative charges, which are quite strong. Disulfide Bonds - covalent S-S bonds between two cysteine amino acids, which are strong. |
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Define:
Quaternary Structure |
Spatial arrangement of more than 2 polypeptide chains together.
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Peptide bonds are formed through _____ reactions.
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...condensation...
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How many atoms participate in a peptide group?
Which ones are they? |
6 atoms.
2 alpha-carbon atoms on either side of the peptide bond (C-N). 1 Double bonded oxygen coming off of C of C-N 1 Hydrogen coming off of N of C-N 2 - The C-N peptide bond itself. |
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A peptide group lies in a _____ _____.
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...single plane.
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Peptide groups are usually found in _____ (cis/trans) conformation.
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...trans...
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Relative orientation around the peptide groups is specified by what?
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Φ (phi) and Ψ (psi) angles.
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Which way does a torsion angle (psi or phi) rotate to increase its angle?
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Looking down the alpha Carbon toward either N or C, the angle increases by rotating *clockwise*
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Why are most Φ and Ψ angles not possible?
How can this be represented with a picture? |
Because of steric hindrance.
This can be represented with a Ramachandran Plot; a plot showing which Φ and Ψ angles are sterically possible. |
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Which amino acid is the most restricted in terms of the Φ and Ψ angles it can take on?
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Proline.
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Φ (phi) refers to rotation around which bond?
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Cα - N
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Ψ (psi) refers to rotation around which bond?
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Cα - C
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Φ and Ψ are called...
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...torsion angles or dihedral angles.
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What three things (single letter variables) are helices characterized by?
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p, n, and d
p ≡ Pitch distance. The distance the helix rises along its axis per turn. n ≡ # of repeating units per turn. d ≡ helical rise per repeating unit (p/n) |
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What are 4 characteristics of α-helices?
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• Stabilized by H-bonding within
helix/strand • right-handed • 3.6 residues per turns • Pitch is 5.4 Å |
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How do you distinguish between a right-handed and a left handed helix?
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Looking down the middle (axis) of the helix...
...if the helix turns clockwise, it is right-handed. ...if the helix turns counterclockwise, it is left handed. |
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Define:
Helix capping |
The last 3-4 residues at the end of a helix are not completely hydrogen bonded, so the polypeptide folds back to provide hydrogen donors or acceptors.
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Define:
β - Sheets |
Hydrogen bonding occurs between neighboring polypeptide chains.
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What are the two ways β-Sheets can be oriented?
Describe each setup. |
Parallel:
Neighboring polypeptides run in the same direction. Antiparallel: Neighboring hydrogen bonded polypeptide chains run in opposite directions. |
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4 points that summarize β-Sheets:
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1. parallel
2. antiparallel 3. most are mixed 4. sheets are pleated and twisted |
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Define:
β-Bilges |
Amino acid that is not h-bonded to the neighboring strand. Results in a bulge.
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2 points that summarize the polypeptide backbone:
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1) Peptide group is planar
2) Conformation of two amine planes around alpha-carbon can be described in phi (Φ) and psi (Ψ) angles. |
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Define:
Regular Secondary Structures |
Composed of sequences of residues with repeating Φ and Ψ values.
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Describe the structure of fibrous proteins.
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Dominated by a single type of secondary structure.
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What are the 3 types of fibrous proteins we talked about?
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1) Keratin
2) Fibroin 3) Collagen |
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What role do fibrous proteins play in the body?
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Protective
Connective Supportive |
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What are some examples structures with α-keratin in them?
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Skin, hair horns, feathers
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Name 7 physical characteristics of:
α-keratin |
• Two α-helices (right-handed)
• Parallel • Left handed coiled-coil ( for both helices together) • The pitch is 5.1 Å (instead of 5.4 Å) • Stabilized by van der Waals forces • 7 residues pseudo-repeat (a-b-c-d-e-f-g) • a and d are hydrophobic |
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Where are hydrophobic and hydrophilic residues located in α-keratin?
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Hydrophobic residues are on the inside of the coil.
Hydrophilic residues are on the outside |
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Name the 4 structures of α-keratin, from smallest to largest.
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α-helix --->
Dimer ---> Protofilament ---> Microfibril |
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In α-keratin, dimers are able to cross-link to each other via...
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...disulfide bonds.
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The two helices in dimers in α-keratin are kept together via...
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...hydrophobic interactions.
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Name the 3 forces that help stabilize α-keratin.
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1) Individual α-helices are stabilized by hydrogen bonds between backbone residues
2) vdW forces between monomers 7 residue pseudo repeat H-phobic strip along the side of the monomers 3) disulfide bonds between dimers |
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Define:
Fibroin |
A stack of β-Sheets
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What is the most abundant vertebrate protein?
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Collagen
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What bodily structures does collagen help provide strength to?
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Bone
Cartilage Tendons Skin Blood vessels |
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How many α-helix coils make up collagen?
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3
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What 3 amino acids largely make up the structure of collagen?
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Glycine (35%)
Proline (20%) Alanine (10%) |
GPA
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What are the 5 characteristics of the Quaternary structure of Collagen?
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1. 3 helices run parallel
2. Wind around each other (right handed helix) 3. Glycine in the center, 4. Proline on the outside 5. Molecule is stabilized by H-bonds Gly N-H to Pro C=O |
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Collagen:
Prolyl is converted to _____ by what enzyme? When does this reaction take place? What molecule does the enzyme require to maintain its activity? |
...hydroxyprolyl..., by prolyl hydroxylase
Reaction takes place after proline is incorporated into the growing polypeptide. Vitamin C |
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Vitamin C deficiency could lead to what disease in humans?
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Scurrrveee (arr!)
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Collagen:
Lysyl is converted to... What do these residues function as attachment sites for? |
...hydroxylysyl
Sugars |
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Describe the first 2 steps in the process of cross-linking allysine residues.
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pg. 139
(1) Lysyl oxidase deanimates (gets rid of amine) Lysine to form Allysine. *Step (1) happens to two Lysine AA's. The two Allysine react together via. an aldol condensation reaction (releases water) to form allysine aldol. This reaction creates a double bond between the two allysine molecules. |
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True or False:
In native (folded) proteins, non-repetitive structures are less ordered than helices and β-Sheets. |
False.
They are simply irregular and hence more difficult to describe. |
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What are 2 methods that can be used to determine protein structure?
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1) X-Ray Crystallography (XRC)
2) Nuclear Magnetic Resonance (NMR) |
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What are the 5 steps to viewing a protein via. X-Ray Crystallography?
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1) *Purify* protein
2) Produce a *crystal* 3) Expose crystal to a beam of x-rays to get a *diffraction pattern* 4) Translate diffraction pattern data into an *electron density map*. 5) Fit polypeptide sequence to the map. |
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Crystals are made up primarily of what?
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40-60% water
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What are 3 characteristics of NMR?
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1) Protein is in solution
2) Relatively small proteins ( < 40 kDa) 3) NMR gives information about the *distance between atoms*. |
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What are the 5 stages of NMR?
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1. Get nuclei with magnetic moment (^1H, ^13C, ^15N)
2. Align in a magnetic field 3. Excite with radio frequency pulses 4. Reversion to low energy state and emission of radio frequency signal 5. Frequency gives information about the molecular environment |
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When constructing a picture of the protein, NMR is limited by what kind of restraint?
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Distance restraint (between the two nuclei)
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What are the 3 main differences for X-Ray Crystallography and NMR?
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XRC:
1) Crystal 2) Electron density map 3) No size limitation NMR 1) In solution 2) Distance restraints 3) 40 kDa size limit |
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What 3 models/methods are used to structurally visualize proteins?
What are some of their advantages/disadvantages? (This is not X-Ray Cryst. and NMR) |
1) Ball and Stick - Gives details, but is cluttered.
2) Space fitting - Only shows the outside 3) Artistic rendition - Gives overview, but is imprecise. |
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What 3 main things have we learned from the 60,000 protein structures we've solved?
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1) Side chain location varies with polarity
2) Helices and β-strands/sheets combine in a variety of ways 3) Large proteins contain domains. |
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AA Side chain location in globular proteins varies with _____.
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...polarity.
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AA Side chain location in globular proteins:
Which 5 AA's are mainly found in the center? What type of polarity do they possess? |
{M, I, L, F, V}
Methionine Isoleucine Leucine Phenylalanine Valine **NON-POLAR RESIDUES** |
IV MLP
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AA Side chain location in globular proteins:
Which 5 AA's are mainly found on the surface? What type of polarity do they possess? |
{R, H, K, D, E}
Arginine Histidine Lysine Aspartic Acid Glutamic Acid **CHARGED POLAR RESIDUES** |
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AA Side chain location in globular proteins:
Which 5 AA's are mainly found on the outside? What polarity do they possess? |
{S, T, N, Q, Y}
Serine Threonine Asparagine Glutamine Tyrosine **UNCHARGED POLAR RESIDUES** |
3 of the 5 are AA's with -OH groups
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Globular proteins are built from...
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...combinations of secondary structural elements
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Define:
Supersecondary structures (motifs) |
Groupings of secondary structural elements in globular proteins.
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What are the 4 types of supersecondary structures (motifs) we looked at?
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βαβ motif - alpha helix connects two beta sheets
β hairpins - antiparallel strands connected by relatively tight turns αα motif - two successive antiparallel alpha helices pack against each other with their axes inclined. β barrels - β-sheets rolled up. |
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Define:
Domains |
The separate globular clusters of large proteins.
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What are 5 characteristics of Domains?
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1) Two or more layers of secondary structures.
2) Function independently 3) Fold independently 4) Connected by a single polypeptide strand 5) Binding sites for small molecules at the interface between two domains |
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Define:
Kinase |
An enzyme that transfers a phosphoryl group between ATP and another molecule.
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Domains assume their normal 3d structure when...
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...isolated from the rest of the protein.
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What has the greatest influence on protein stability?
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The Hydrophobic Effect
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Define:
Hydrophobic Effect Leads to what? |
Tendency of water to minimize its contacts with nonpolar substances.
Induces substances to aggregate. |
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Define:
Ion Pairs (i.e. Salt Bridges) |
Association of two ionic protein groups of opposite charge.
EXA: Lysine (+'ve) and Glutamate (-'ve) |
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Ion pairs are located mostly on the _____ of proteins
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...surface...
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How can metal ions influence protein structure?
What is an example? |
Metal ions may function internally to cross-link proteins.
EXA = Zinc finger |
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True or False:
The aggregate of all the forces that hold proteins together makes them rigid structures. |
False.
Proteins are very dynamic structures. |
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Define:
Breathing (in terms of proteins) |
Conformational flexibility
Allows for structural displacement of up to 2 angstroms, and for small molecules to diffuse in and out of the interior of some proteins. |
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What are 4 things that can lead to protein denaturization?
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1) Increase in temperature
2) pH charge distribution 3) Detergens Interact with non-polar side chains 4) Chaotropic agents Increase the solubility of nonpolar sidechains |
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How do the functions of Detergens and Chaotropic agents lead to protein denaturization?
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They interfere with hydrophobic interactions (i.e. the main force that maintains protein stability)
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What are two examples of chaotropic agents?
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Guanidinium
Urea |
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What are 2 reasons that protein folding in-vivo is different than in-vitro?
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1) Proteins start folding during synthesis in-vivo.
2) Proteins are present in-vivo that help with folding |
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What are the 3 steps in the protein folding pathway?
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1) Elements of secondary structure fold. (5 ms)
2) Molten globule (collapsed state from step (1)) (5 - 1000 ms) - Further stabalization of secondary structures. - Formation of super-secondary (motifs) structures or subdomains. 3) Protein 'wobbles' into its final position over the next few seconds. |
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What does the trough on a "Folding Funnel" graph represent?
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The native structure of the protein.
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What 2 functions does PDI (Protein Disulfide Isomerase) perform?
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1 - Rearranges disulfide bonds
2 - Catalyzes initial disulfide bond formation |
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Why is PDI needed to rearrange disulfide bonds?
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Because improperly folded proteins expose non-polar regions on their surfaces. This would promote aggregation of proteins due to the hydrophobic effect.
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Define:
Chaperones |
Help proteins fold properly
Detailed (pg. 165) Essential proteins that bind to unfolded and partially folded polypeptide chains to prevent the improper association of exposed hydrophobic segments that might lead to non-native folding as well as polypeptide aggregation and precipitation. |
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Describe the GroES/GroEL reaction cycle
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pg. 166 - 168
Improperly folded protein = * Big barrel binds * via. it's hydrophobic parts. 1 - GroES caps off GroEL, resulting in a conformational change. In this change, the upper chamber expands, hydrophobic portions turn into hydrophilic (allowing release of *) while helping to pull * apart allowing for it to fold back into its native shape. 2 - Hydrolysis of 7 ATP's releases 7 phosphates. This weakens GroES/GroEL connection. 3 - 7 ATP bind to bottom of barrel, along with another *. 4 - Binding from (3) releases GroES, 7 ADP, and the now properly folded protein. GroEL turns 180 degrees and the process can start over. |
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What are 4 reasons for proteins to make multiple subunits?
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1 - There can be different sites for subunit and end-product assembly.
2 - Defective subunits can be replaced. 3 - Less genetic information. 4 - Additional properties for protein (cooperation) |
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Define:
Oligomer |
A protein containing multiple subunits
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Define:
Protomer |
The identical (repeating) subunits of a protein.
EXA: In hemoglobin, there are 2 α parts and 2 β parts. 1 protomer is one αβ complex. *Note: Protomer is not the two repeated α's or β's as a group. |
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What are 3 properties of multi-subunit proteins?
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1 - The have identical or non-identical subunits
2 - They're usually non-covalently associated 3 - Interfaces often contain tightly packed non-polar residues. |
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Proteins only have _____ symmetry.
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...rotational...
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Define:
Cyclic symmetry |
Protomers are related by a single rotational axis.
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In Dihedral symmetry, how do you find 'n' in:
D_n |
(total # of subunits) / 2
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Which dihedral symmetry is the most common?
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D_2
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