Term
| What are the four arrangement of secondary structures of globular proteins? |
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Definition
1) anti-parallel alpha-helix
2) parallel or mixed beta-sheet proteins
3) anti-parallel beta-sheet
4) metal- and disulfide-rich bonds |
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Term
| Which structure is is more likely to occur: anti-parallel or parallel |
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Definition
| anti-parallel, due to folding back and forth to create the smallest space |
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Term
| What forces are most important in setting up initial structure of globular protein? |
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Definition
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Term
| What shape do beta-strands tend to be in in a globular protein and why? |
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Definition
| They are curved instead of straight because there is higher stability due to increased hydrogen bonding. |
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Term
| If the adjacent arrows of a globular protein are pointing in the same direction the structure is ___. |
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Definition
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Term
| Define protein domain (or protein module). |
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Definition
| A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. They generally don't have the same function in different proteins, and contain between 40 to 100 amino acids. |
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Term
| What do all beta-domains contain? |
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Definition
| A core comprising of antiparallel β-sheets, usually two sheets packed against each other. |
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Term
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Definition
1) a polypeptide forms segments of secondary structure (alpha-helix and beta-sheet)
2) these unite into a globular structure, primarily through hydrophobic interactions
3) The final tertiary structure is generated by small adjustments to the folded structure
4) In the cell, protein folding may require the assistance of molecular chaperones |
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Term
| Define quaternary structure |
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Definition
| The arrangement of multiple folded protein molecules in a multi-subunit complex |
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Term
| Are covalent bonds necessary to hold quaternary structures together? |
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Definition
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Term
| Name the forces involved in producing quaternary structures. |
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Definition
| Hydrophobic interactions, hydrogen bonding, ionic interactions and disulfide bonds |
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Term
| What are the structural and functional advantages to quaternary structure? |
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Definition
1) Stability
2) Genetic economy and efficiency
3) Bringing catalytic sites together
4) Cooperativity (e.g., with hemoglobin, the first molecule to bind makes the next molecules easier to bind)
5) The interaction between subunits allows for the subunits to influence each other's behaviors. |
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Term
| What is the structure of DNA polymerase and hemoglobin? |
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Definition
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Term
| Because hemoglobic has two alpha and two beta units, it can be considered a ______ of _____. |
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Definition
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Term
| Give 5 examples of protein domains or modules. |
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Definition
a) complement control
b) immunoglobin
c) fibronectin
d) growth factor
e) kringle |
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Term
| What are the shortest domains (i.e. zinc fingers) stabilized by? |
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Definition
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Term
| How are protein domains produced? |
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Definition
| By the duplication of DNA segments within a gene or by the movement of DNA from one gene to another |
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Term
| What are some advantages for domains to fold individually? |
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Definition
a) accelerates folding process
b) reduces large combination of residue interactions
c) allows a large protein to bury its hydrophobic residues and keep hydrophilic residues at surface |
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Term
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Definition
| the place buried in the mass of globular protein where proteins bind |
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Term
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Definition
| cytoskeletal fibers built from small globular protein subunits: rigid & thick, constructed as a hollow tube |
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Term
| Components of microtubule: |
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Definition
beta-tubulin + alpha-tubulin= dimer (each contains ~ 450 amino acids)
end to end dimers = protofilaments
protofilaments wrap into a hollow tube to create a microtubule |
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Term
| Intermediate filaments are exclusively what kind of protein? |
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Definition
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Term
| Basic structure of intermediate filaments: |
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Definition
a dimer of alpha-helices that wind into a coil of a 7-residue repeating unit wth hydrophobic residues in contact
Intermediate filament may consist of 16 to 32 polypeptides in cross section
*Crosslinked thru disulfide bonds |
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Term
| 3 main amino acids of collagen |
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Definition
| Glycine (every 3rd), proline and hydroxyproline |
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Term
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Definition
| three polypeptides wind around each other to form a right-handed triple helix |
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Term
| How is collagen stabilized |
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Definition
| hydrogen bonding (N-H group of each Gly is linked to a backbone C=O group) |
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Term
| Collagen cross-links are ___ bonds |
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Definition
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Term
| Define tertiary structure |
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Definition
| the folding of a single polypeptide chain in 3-D |
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Term
| Provide examples of Type I, II and III collagen |
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Definition
I: bones, skin and tendons
II: cartilage
III: blood vessels |
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Term
| Provide conformation of alpha-helices and give examples |
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Definition
| coiled coil of two alpha-helices, which are twisted w/ additional coils into a rigid filament: examples include hair and fingernails |
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Term
| Provide examples of fibroin and beta-keratin |
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Definition
fibroin: silk fibers
beta-keratin: bird feathers |
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Term
| 4 classifications of globular proteins |
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Definition
1) Antiparallel alpha-helix proteins
2) Parallel or Mixed Beta-Sheet Proteins
3) Antiparallel Beta-Sheet proteins
4) Metal & Disulfide-Rich Proteins |
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Term
| Define quarternary structure |
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Definition
| the association of monomeric protein subunits to form multi-subunit complexes |
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Term
| Define isologous interactions |
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Definition
| the interacting surfaces are identical and the resulting structure is dimeric (quarternary structure) |
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Term
| Define heterologous associations |
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Definition
| involve nonidentical interfaces with complementary surfaces (quarternary structure) |
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Term
| Forces involved with quarternary structure |
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Definition
| hydrophobic, hydrogen bonding & ionic interactions |
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Term
| Advantages of Quarternary Association |
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Definition
1) Stability: reduces the protein's surface-to-volume ratio
2) Genetic Economy & Efficiency: less DNA is required to code monomer
3) Bringing catalytic sites together
4) Cooperativity: binding at one site increases binding at other sites |
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Term
| Most common type of protein |
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Definition
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Term
| Describe metal and disulfide-rich proteins |
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Definition
| Have unusual amounts of methyl ions bound to disulfide bonds--highly stable structure |
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Term
| Most important force behind initial globular protein structure |
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Definition
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Term
| Describe beta-strands in globular protein |
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Definition
| Tend to curve & there are pairs of them rather than a straight line...more stability due to Hydrogen bonding |
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Term
| Which ends of globular protein have greatest freedom of movement? |
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Definition
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Term
| How to tell anti-parallel from a parallel globular protein: |
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Definition
*Adjacent arrows pointing in same direction: parallel
*Adjacent arrows pointing in opposite directions: anti-parallel |
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Term
| Define protein domain or module |
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Definition
| Amino acid sequences used repeatedly in the same protein or found in different proteins. |
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Term
| How many amino acids are typically found in a protein domain/module? |
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Definition
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Term
| How are protein domains or modules produced? |
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Definition
| by the duplication of DNA segments w/in a gene or by the movement of DNA from one gene to another |
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Term
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Definition
| Proteins that increase the rate of chemical reactions; catalysts |
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Term
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Definition
| Create pathways that break down nutrient molecules, release energy, synthesize precursors, and link them together to form new molecules |
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Term
| 3 Distinctive features of enzymes |
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Definition
1) Catalytic Power--can speed reaction up to 10^6 times
2) Specificity--selectively act upon a substrate to create a particular reaction
3) Regulation--inhibitors + synthesized enzymes control levels of active enzymes in cell |
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Term
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Definition
| molecules at the beginning of process |
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Term
| Substrates converted into different molecules are called ___ |
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Definition
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Term
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Definition
a) the rate of disappearance of the substrate
b) the rate of appearance of the product |
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Term
| Relationship between catalyst and reaction speed |
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Definition
| The more catalyst present, the faster the reaction |
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Term
| Name 6 classifications of enzymes |
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Definition
1) Oxioreductases (oxidation & reduction reactions)
2) Transferases (transfer of functional groups)
3) Isomerases (isomerization reactions)
4) Hydrolases (hydrolysis reactions)
5) Lysases (addition to double bonds)
6) Ligases (formation of bonds with ATP cleavage) |
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Term
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Definition
| metal ions or organic molecules that bind to enzymes & are required for enzyme activity |
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Term
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Definition
| Organic molecules (particularly water-soluble vitamin derivatives) that act as enzyme cofactors |
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Term
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Definition
| tightly bound cofactors or coenzymes that are crucial to the enzyme's function |
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Term
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Definition
| Catalytically active complex of protein and coenzyme |
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Term
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Definition
| Protein without the prosthetic group |
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Term
| Enzyme-Substrate Complex in Practice: |
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Definition
1) @ high substrate conc., enzyme activity levels off as it approaches max. value
2) @ low substrate conc., the enzyme quickly converts all the substate to product, but...
3) as more substrate is added, the enzyme is saturated with substrate and so not all substrate can be converted |
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Term
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Definition
v = k[A]
velocity = rate constant [A]
*reaction velocity is directly proportional to concentration of A |
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Term
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Definition
A + B = C
v = k[A][B]
*velocity of 2nd order is proportional to the product of the two reactant concentrations |
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Term
| Enzyme-catalyzed reaction |
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Definition
v = k2 [ES]
*when [S] is very high, virtually all the enzyme is in its ES form (saturated with substrate) |
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Term
| Michaelis-Menten equation (rate equation that describes the hyperbolic curve) |
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Definition
| vo (initial velocity) = vmax[S]/km + [S] |
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Term
| Relationship between Michaelis-Menten equation and variables |
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Definition
| it describes the reaction if all other variables are constant |
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Term
| Equation for Vmax (maximum reaction velocity) |
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Definition
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Term
| How can Km and Vmax be determined graphically? |
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Definition
| From a straight-line plot derived from the Michaelis-Menten equation |
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Term
| Explain what happens in Michaelis-Merten equation when [S]>>Km |
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Definition
| v = Vmax...v is no longer dependent on [S] and the reaction is zero-order |
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Term
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Definition
| the substrate concentration @ which the reaction velocity is half-maximal |
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Term
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Definition
| how efficiently an enzyme selects its substrate and converts it to product |
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Term
| Relationship between a low Km and effectiveness |
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Definition
The lower the Km, the more effective enzyme is at low substrate conc.
The higher the Km, the less effective enzyme is at high substrate conc. |
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Term
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Definition
It is unique for each enzyme-substrate pair:
1) comparing activities of two enzymes that act on the same substance
2) assessing the ability of different substrates to be recognized by a single enzyme |
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Term
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Definition
| enzyme's affinity for a substrate |
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Term
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Definition
Km ~ [E][S]/ [ES]
This is only true when the ES--> E + P is slower than the rate of ES --> E + S reaction |
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