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167 Cards in this Set
- Front
- Back
Hydrophobic |
Alanine, Proline, Glycine, Valine, Isoleucine, Leucine, Cysteine |
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Hydrophilic |
Arginine, Glutamine, Asparagine, Histidine, Aspartic acid, Serine, Cysteine, Threonine, Glutamic acid |
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Amphipathic |
Lysine, Methionine, Tryptophan, Tyrosine |
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isolated system |
cannot exchange matter or energy with itssurroundings
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closed system |
may exchange energy, but not matter, with the surroundings
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open system |
may exchange matter, energy, or both with the surroundings
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Living things are typically ___________ system. |
open |
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first law of thermodynamics
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states that thetotal energy of an isolated system is conserved |
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internal energy
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commonly designatedE or U, and it includes all the energies that might be exchanged in physical orchemical processes, including rotational, vibrational, and translational energies of moleculesand also the energy stored in covalent and noncovalent bonds |
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state function
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depends only on the present state of a system |
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independent of path |
does not depend on how the system got there |
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internal energy depends only on ________ and not on _________. |
present state of the system, how the system got there |
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Internal Energy (E) will not change if _____ is returned to its original state. |
the system |
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Mechanical work |
movementthrough some distance caused by the application of a force |
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Both ______ and _______ are required for work to have occurred. |
movement, force |
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enthalpy |
H, a function that is especially suitable forconstant pressure processes |
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van’t Hoff plot |
A plot of R(ln Keq) versus1/T |
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second law of thermodynamics |
1. Systems tend to proceed from ordered (low-entropy or low-probability) states to disordered(high-entropy or high-probability) states.2. The entropy of the system plus surroundings is unchanged by reversible processes;the entropy of the system plus surroundings increases for irreversible processes.3. All naturally occurring processes proceed toward equilibrium, that is, to a state ofminimum potential energy. Energy flows spontaneously so as to become diffused ordispersed or spread out. Energy dispersal results in entropy increase |
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entropy
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ameasure of disorder and randomness in the system
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energy dispersion
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the dispersion of energy amonga large number of molecular motions relatable to quantized states (microstates)
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For solutes in a solution, the standard state is ____________. |
normallyunit activity (often simplified to 1 M concentration) |
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Consensus value of Delta G° of ATP in biological systems |
-30.5kJ/mol |
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Why does the G° of ATP hydrolysis depend so strongly on Mg 2+ concentration? |
The answer lies in the strong binding of Mg 2+ by the triphosphate oxygens of ATP. The binding of Mg21 to ATP is dependent on Mg 2+ ion concentrationand also on pH. At pH 7 and 1 mM [Mg2 +], approximately one Mg 2+ ion is boundto each ATP. The decrease in binding of Mg 2+ at low pH is the result of competition byH+and Mg 2+ for the negatively charged oxygen atoms of ATP. |
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thermodynamic potential |
in the direction of positive Delta G |
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Many of the reactions necessary to keep cells and organisms alive must run against their __________. |
thermodynamic potential |
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The anti-thermodynamic potential reactions are driven in the unfavorable direction by _______. |
coupling |
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Important anti-thermodynamic potential reactions |
intermediarymetabolism, oxidative phosphorylation, and membrane transport |
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Human consumption of ATP |
11,700 kJ |
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standard reduction potential |
Eo, quantitates the tendency of chemical species to be reduced oroxidized |
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reaction half-cells |
A half-cell consists of a solution containing 1 M concentrationsof both the oxidized and reduced forms of the substance whose reductionpotential is being measured and a simple electrode |
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redox couple |
the oxidized and reducedforms of the substance |
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Energy represents _____________. |
energy dispersion. |
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free energy |
a thermodynamic quantity equivalent to the capacity of a system to do work |
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Free energy depends on __________ and __________ concentrations |
reactant, product |
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Free energy is pH-dependent if protons are __________________ ina reaction. |
produced or consumed |
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ATP |
is an intermediate energy-shuttle molecule |
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zwitterion |
carboxyl group exists as OCOO2 and the amino group as ONH31, amino acid contains one positive and one negative charge |
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peptide bond |
eliminating a water molecule and forminga covalent amide linkage |
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The repetition of a reaction forming a peptide bond creates ________ and _______. |
polypeptides, proteins
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peptide bond |
remove H2O form CO-NH bond |
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y-Aminobutyric acid/GABA
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amino acid produced by the decarboxylation ofglutamic acid and is a potent neurotransmitter |
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Histamine |
synthesized by decarboxylationof histidine |
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serotonin
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derived from tryptophan, similarlyfunction as neurotransmitters and regulators |
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Epinephrine/adrenaline |
derived from tyrosine, is an important hormone |
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glycine hydrochloride |
glycine, at low pH, boththe amino and carboxyl groups are protonated and the molecule has a net positive charge.If the counterion in solution is a chloride ion. |
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glycinate |
increase in pH eventually results in dissociationof the amino group to yield the negatively charged |
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Edman reagent |
A number of reactions of amino acids are noteworthy because they are essential to thedegradation, sequencing, and chemical synthesis of peptides and proteins. The reaction with phenylisothiocyanate, |
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glycine |
only achiral amino acid |
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Serine, Threonine, and Tyrosine |
they can become phosphorylated/ acetylated because of the (-OH) |
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Proline |
only secondary amine |
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Histidine |
will form in both positive and negative forms |
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Methionine and Cysteine |
two with sulfur in them |
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Methionine and Cysteine can created and __________ bond. |
disulfide |
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Phenylalanine, Tyrosine, Tryptophan, and Histidine |
4 are aromatic |
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aromatic amino acids can: |
1.) absorb light in the UV range 2.) Tryptophan will fluorescence |
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Seleno Cysteine/ Pyrrolysine |
-C-Se-H
-Not in higher organisms |
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hydroxylysine & hydroxyproline |
-in collagen -the hydroxylation only occurs post translation -turns into the protein of each |
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Pyroglutamic Acid/Bacterorhodopsin |
-converts to glutamate |
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Gamma-aminobutyric acid (GABA) |
-neurotransmitter -neuromuscular junction involved in muscular tension -CNS- inhibitor |
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histamine |
r-antagonist-anti-histamines |
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Serotonin |
-derivative of Tryptophan -CNS neurotransmitter -causes feeling of well being and relaxation |
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epinephrine/adrenaline |
-released from the adrenal grands -flight or fight response -derivative of Tyrosine -a techolamine |
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IR is looking at the _______ vibrations. |
bond |
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NMR is observing Nuclear magnetic residence which looks for ____________________. |
H+, C13, N15, P31 |
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NMR |
-will not observe a diamagnetic ion -D20 will cause a large signal -alaphatic protons lower than 4.84 -aramatics at 6 & 8 |
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Negative charge near an amino acid causes________. |
the amino acid to not let go of the proton, even 3 times as many. |
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Wobble Hypothesis |
position three doesn't matter you'll get the right nucleic acid |
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dimeric enzyme |
-homo dimer = two copies of the same chain |
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homoglobin heterotetramer |
4 copies of the gene |
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primary structure |
backbone & sequence of side chains held by covalent bonds |
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How to break a primary structure? Why? |
hydrolyze it- 6M HNO3, no air, cook it because they are really stable |
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secondary structure |
regular repeated patterns in the structure of the backbone are held by hydrogen bonds from amide H-----carbonyl O |
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Why was x-rays used with secondary bonds? |
-used to map the molecules within the structure
- found to map all the molecules in the structure but H |
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tertiary structure/domain structure |
-held by intramolecular EaH (H-bonds, H0, e-statics) btwn side chains -noncovalent except cys-s-s-cys = everything is in equilibrium nothing can change that |
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Quaternary structure |
- just like tert but between different chains -conformational change vs configuartional change |
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conformational change |
moving |
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configurational change |
breaking and forming of covalent bonding |
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Isoelectro Point |
pI= pH of protein at no net charge |
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N-term |
amino |
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C-term |
carboxyl |
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enz |
ase |
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trypsin & chymotrypsin |
serine proteases, breaking the peptide the amine bond |
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Serine invariant residue |
cannot be replaced w/out destroying the function |
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silent mutation |
no change |
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innoculous |
not much effect |
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deleterious |
causes the whole thing to unravel |
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post translation modifications |
PO4-ylated, acetylated, fatty acid esterification |
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golgi apparatus |
puts sugars on the proteins called glycosylation |
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prosteketic groups |
cofactors (inorganics) Zn 2+, Mg 2+, Mn 2+, PO4 2- |
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coenzyme |
(organic) rhodopsin, NAD+, |
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Amino acids link to form_______. |
polypeptide chains |
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The polypeptide backbone is __________. |
relatively polar |
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dipeptide |
two amino acids |
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tripeptide |
three amino acids |
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tetrapeptide |
four amino acids |
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oligopeptides |
12 - 20 amino acids |
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polypeptide |
several dozen amino acids |
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protein |
broadly defines molecules composed of one or morepolypeptide chains |
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monomeric proteins |
Proteins with one polypeptide chain |
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multimeric proteins |
Proteinscomposed of more than one polypeptide chain |
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homomultimeric |
Multimericproteins may contain only one kind of polypeptide |
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heteromultimeric |
Multimeric proteins composed of several different kinds of polypeptide chains |
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homodimer |
an alpha-type protein is adimer of identical polypeptide subunits |
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The peptide bond has partial _______________ character. |
double bond |
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The amide plane of the peptide backbone includes all the atoms EXCEPT:
a. Cα-carbon. b. amide nitrogen. c. side chain carbons. d. carbonyl carbon. e. none, all are included. |
c. side chain carbons |
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Hemoglobin is an α2, β2 _______ whereas, glutamine synthatase from E. coli is an α12 _______________. |
heteromultimer, homomultimer |
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Collagen serves as what roll in the cell? |
structural |
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Globular proteins are usually all EXCEPT: a. Insoluble in water. b. Roughly spherical. c. Folded so that the hydrophobic amino acids are in the interior of the molecule. d. Hydrophobic side chains are exposed to the water. |
a. insoluable in water |
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10. Molecules of a given protein have all EXCEPT: a. a fixed amino acid composition. b. a defined amino acid sequence. c. a sequence read from C-terminal end to N-terminal end. d. an invariant molecular weight. e. a nucleotide sequence from which they are encoded. |
c. a sequence read from c-terminal end to n-terminal end. |
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Disulfide bond is formed in which levels of protein structure? |
tertiary, quaternary |
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Which of the following levels of protein structure is correctly defined? a. primary: interaction between subunits of a protein b. secondary: hydrogen bond arrangement of polar R-groups c. tertiary: three dimensional arrangement of all atoms in a single peptide d. quaternary: order of amino acid residues in the peptide chain e. none of the above are correct |
c. tertiary: three dimensional arrangement of all atoms in a single peptide |
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22. The amino acid sequence is NOT: a. a distinctive characteristic of a polypeptide. b. encoded by the nucleotide sequence of DNA. c. a form of genetic information. d. read from N-terminal end to C-terminal end. e. constant for proteins with the same function from different organisms. |
e. constant for proteins with the same function from different organisms. |
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Edman degration |
will determine the N-terminal amino acid |
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What is the product formed from the acid hydrolysis of a simple amide? |
acid & amine |
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The C-terminal residue of a polypeptide can be determined by first cleaving the polypeptide with:
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carboxypeptidase
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Proteins that do NOT perform any obvious chemical transformation, but control the ability of other proteins to carry out their physiological functions are: |
regulatory proteins. |
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Heparin |
a naturalanticoagulant substance |
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Proline acts as a _______. |
helix breaker |
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beta form |
stretched helical structure that are uncoiled and extended |
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alpha form |
protein structure in unstretched fibers was a helix
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denaturation |
loss of protein structure and function |
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helixcapping
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providing H-bond partners for the otherwise bare NOH and CPO groupsand folding other parts of the protein to foster hydrophobic contacts with exposed nonpolarresidues at the helix termini
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polyamino acids
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polymers in which all the amino acids areidentical
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Beta-pleated sheet
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structure commonly observed in proteins also forms because of local,cooperative formation of hydrogen bonds
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parallel beta-pleated sheet
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adjacent chains run in the same direction
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antiparallel beta-pleated sheet
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adjacent strands run in opposite directions
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Each single strand of the beta-sheet structure can be pictured as a twofold helix, that is,a helix with ________________.
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two residues per turn
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beta-turn |
which the peptide chain forms a tight loop withthe carbonyl oxygen of one residue hydrogen bonded with the amide proton of theresidue three positions down the chain. Is a relatively stable structure. |
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Type I beta-turns are __________ than type II. |
more common |
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Type 1 beta turn has _________ in position 3 while Type 2 has ________ in position 2 and _________ in position 3. |
proline, proline, glycine |
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chaperones
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proteins that assistin the process of protein folding in the cell |
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______________ are not needed in diluted solutions, proteins can fold and unfold themselves without their assistance. |
Chaperones |
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Proteins are typically a mixture of _________ and _________ amino acids. |
hydrophilic, hydrophobic |
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Why do proteins fold? |
Because its made of both hydrophilic and hydrophobic amino acids |
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hydrophobic effect
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inducesformation of a compact structure—the folded protein
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Keratin |
claws, fingernails, hair,and horns in mammals. structure is dominated by alpha-helical segments of polypeptide |
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Globular proteins |
so named fortheir approximately spherical shape |
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amphiphilic helix
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consists mainly of polar andcharged residues, whereas the inward face contains mostly nonpolar, hydrophobic residues
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domains or modules
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larger globular proteins are usually made up of two or more recognizable and distinctstructures, compact, folded protein structuresthat are usually stable by themselves in aqueous solution
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hydrophobiccollapse
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Nonpolar residues may aggregate or coalesce in a process termed
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flexibility and motion
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All chemical bonds undergo a variety of motions, includingvibrations and (for single bonds) rotations. This propensity to move, together with themarginal stability of protein structures, means that the many noncovalent interactionswithin a protein can be interrupted, broken, and rearranged rapidly.
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Atomic fluctuations
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such as vibrations typically are random, are very fast, and usually occur oversmall distances
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Conformational changes
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involve motions of groups of atoms (individual side chains,for example) or even whole sections of proteins
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metamorphic protein
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exists naturally in an equilibriumbetween two diffferent three-dimensional structures under physiologicalconditions (Keq ~1). Example (chemokine* protein lymphotactin)
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Hairpins |
connect adjacent antiparallel beta-strands |
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Cross-overs |
necessary to connect adjacent (or nearly adjacent) parallel beta-strands |
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betaalphabeta-loop |
In many cross-over structures, the cross-over connectionitself contains an alpha-helical segment |
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alpha/beta proteins |
in which helices and sheets are intermingled |
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alpha+beta proteins |
in which a-helical and b-sheet domains are separated forthe most part |
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all alpha proteins and all beta proteins |
in which the structures are dominated bya-helices and b-sheets, respectively |
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molecular chaperones |
are essential for the correct folding of certainpolypeptide chains in vivo; for their assembly into oligomers; and for preventing inappropriate liaisons with other proteins during their synthesis, folding, and transport |
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natively unfolded proteins |
do not possess uniform structural properties butare nonetheless essential for basic cellular functions |
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heat shock proteins |
which are induced incells by elevated temperature or other stress |
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oligomers |
complexes composed of (often symmetric)noncovalent assemblies of two or more monomer subunits |
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Orthologous proteins
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are proteins that perform the same functionin different cells
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Paralogous proteins
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are proteins found within the same speciesthat have homologous amino acid sequences; paralogous proteinsarise through gene duplication
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Related proteins shared a ________ evolutionary origin.
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common |
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A __________ protein is a protein with a slightly different amino acidsequence. |
mutant |
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Coupled processes
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Enzymatic coupling of a thermodynamically unfavorable reaction with athermodynamically favorable reaction to drive the unfavorable reaction. Thermodynamically favorable reactionis often hydrolysis of high-energy molecule
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High-energy molecules
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Phosphoric anhydrides (ATP, ADP, GTP, UTP, etc.)
Enol phosphates (phosphoenolpyruvate a.k.a. PEP) Phosphoric-carboxylic anhydrides (1,3-bisphosphoglycerate) Guanidino phosphates (creatine phosphate) |
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Transfer of proton reaction equation:
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pKa= ∆G/2.303RT |
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Why is hydrolysis of high-energy bonds favorable?
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Destabilization of reactant due to electrostatic repulsion
Product isomerization and resonance stabilization Entropy factors |
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Thermodynamics of ATP hydrolysis influenced by:
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pH, cation concentration, reactant and productconcentrations
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Anion exchangers |
Matrix is positively charged so anions bind
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Cation exchangers
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Matrix is negatively charged so cations bind
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Carboxyl group + amino group – water =
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peptide bond |
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Sulfur containing amino acids
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cysteine, methionine
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