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96 Cards in this Set
- Front
- Back
What is the range of the number of amino acids a polypeptide can contain? |
50 to 2000
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What is the mean molecular weight of an amino acid? |
110 gm/mol |
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What mass unit is used for amino acids? |
Dalton (Da) |
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1 dalton = how many gm/mol? |
1 |
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What is the protein structural hierarchy? |
Primary, secondary, tertiary, quaternary |
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The ___ (primary/secondary/tertiary/quaternary) structure is the ordered sequence of amino acids in that protein |
Primary |
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A ___ (hydrogen/peptide) bond arises from the carboxyl group of one amino acid and the amino group of another |
Peptide |
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Water is liberated in the formation of peptide bonds in a process called what? Hint: 2 names |
Condensation reaction or dehydration process |
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Is there rotation around peptide bonds? |
No |
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Peptide bonds are ___ (rigid/flexible) and have partial ___ (single/double/triple) bond characteristics |
Rigid, double |
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Why do peptide bonds have partial double bond characteristics? |
They have resonance |
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Peptide bonds are ___ (shorter/longer) than a single bond, but ___ (shorter/longer) than a double bond |
Shorter than a single bond, longer than a double bond |
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How many atoms lie within the same plane in a peptide bond? |
6 |
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What are the 6 atoms that lie within the same plane in a peptide bond? |
Alpha carbons, carbonyl carbon, oxygen, amide nitrogen, amide hydrogen |
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Cis and trans configurations in a peptide bond refer to the positions of what carbons? |
Alpha carbons |
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What configuration, cis or trans, is favored in peptide bonds? |
Trans |
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The trans position is favored in peptide bonds because there is ___ (more/less) steric interference between ___ (alpha carbons/R groups) |
Less, R groups |
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What amino acid is an exception to the trans favorability rule and both the trans and cis configuration is seen? |
Proline |
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In the case of proline, cis configurations are seen as relatively ___ (more/equal/less) than trans configurations in terms of steric clash |
Equal |
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The amino acid that is ___ (N/C)-terminal to the proline can be cis or trans configuration |
N-terminal |
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Peptide bonds are rigid and ___ (triangular/planar) |
Planar |
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What must be able to occur for proteins to be able to fold into their 3D shapes? |
Rotation |
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Rotation occurs between the alpha amino nitrogen and the ___ (alpha carbon/alpha carbonyl carbon) |
Alpha carbon |
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Rotation occurs between the alpha carbonyl carbon and the ___ (alpha carbon/alpha carbonyl carbon) |
Alpha carbon |
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Bond angles made between the alpha amino nitrogen and the alpha carbon are called ___ (psy/phi) angles |
Phi
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Bond angles made between the alpha carbonyl carbon and the alpha carbon are called ___ (psy/phi) angles |
Psy |
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What are the two major secondary structural elements of proteins? |
Alpha helices and beta sheets |
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For an alpha helix, the path is ___ (compact/loose) and winds around a central ___ (peptide bond/axis) of rotation |
Compact, axis |
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Alpha helices are stabilized by ___ (hydrogen/peptide) bonds that are ___ (parallel/perpendicular) to the central axis of rotation |
Hydrogen, parallel |
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Alpha helix hydrogen bonds arise between what 2 groups in the peptide backbone? |
Amino groups and carboxyl groups |
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Alpha helix hydrogen bonds arise between amino acids that are how many residues apart in the peptide chain? |
3-4 |
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How many amino acids are there per 360 degree turn in an alpha helix? |
3.6 |
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R groups of an alpha helix point ___ (toward/away) from the central axis of rotation, ___ (outward/inward) from the helix |
Away, outward |
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What is the center of an alpha helix filled with? |
Atoms of the peptide backbone |
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___ (Right/Left)-handed alpha helices are the most common type of helices |
Right |
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What amino acid is an alpha helix breaker? |
Proline |
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A series of ___ (charged/uncharged) amino acids is an alpha helix breaker |
Charged |
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Amino acids with ___ (small/large) side chains are helix breakers |
Large |
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Amino acids that branch at the ___ (alpha/beta) carbon are helix breakers |
Beta |
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What are beta sheets made up of? |
Individual beta strands |
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Beta strands have a directionality that ___ (corresponds to/is opposite to) the direction of the peptide backbone |
Corresponds to |
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Beta strands run from the ___ (amino/carboxyl) group to the ___ (amino/carboxyl) group |
Amino group to the carboxyl group |
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Beta strands run ___ (C/N) to ___ (C/N) |
N to C |
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In beta sheets, adjacent R groups are on the ___ (same/opposite) side of the backbone, and are ___ (above/inward) and ___ (below/outward) strands |
Opposite, above, below |
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In beta sheets, the hydrogen bonds extend between the beta strands from the carbonyl ___ (hydrogen/oxygen) of one strand to the amino ___ (hydrogen/oxygen) of another strand |
Carbonyl oxygen, amino hydrogen |
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Beta sheets are stabilized by ___ (hydrogen/peptide) bonds that are ___ (parallel/perpendicular) to the direction in which the peptide backbone is going |
Hydrogen, perpendicular |
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___ (Parallel/Antiparallel) beta strands have stronger hydrogen bonding between the beta strands |
Antiparallel |
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Antiparallel beta strands have stronger hydrogen bonding between the beta strands because there is greater ___ (circularity/linearity) in these bonds than in parallel strands |
Linearity |
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What is the more stable configuration of beta strands: parallel or antiparallel? |
Antiparallel |
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What type of repetitive secondary structure is located in a place where the peptide backbone is making a sharp turn? |
Beta turn |
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Beta turns allow for compact conformation of what type of proteins? |
Globular |
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Where on a protein are beta turns usually located? |
Protein surface |
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What amino acid is often found in beta turns? |
Glycine |
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What is the start of a beta turn referred to as? |
i |
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What is the end of a beta turn referred to as? |
i+3 |
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In beta turns, i corresponds to what terminus? |
N |
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In beta turns, i+3 corresponds to what terminus? |
C |
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In an alpha helix, each right-handed turn is how many amino acids? |
3.6 |
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In alpha helices, each main chain N-H (amino group) is hydrogen bonded to the ___ (alpha carbon/oxygen) (carbonyl group) 3-4 amino acids away |
Oxygen |
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On a ramachandran diagram, what quadrant are beta sheets located in? |
Upper left |
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On a ramachandran diagram, what quadrant are alpha helices located in? |
Lower left |
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On a ramachandran diagram, what quadrant are right-handed alpha helices located in? |
Lower left |
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On a ramachandran diagram, what quadrant are left-handed alpha helices located in? |
Upper right |
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On a ramachandran diagram, ___ (light/dark) green represents psy and phi angles that are seen most often |
Dark |
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What are 2 types of non-repetative structures? |
Loops and coils |
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Loops and coils are ___ (more/less) ordered than alpha helices and beta sheets, and ___ (are/are not) random |
Less ordered, not random |
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What is another name for super-secondary structures? |
Motifs |
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Motifs are in between what 2 structures? |
Secondary and tertiary |
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What 3 characteristics do motifs have? |
Sequential, recurrent, similar functions |
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Angiostatin, topoisomerase, and myoglobin are all examples of ___ (primary/secondary/tertiary) structures |
Tertiary |
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The ___ (primary/secondary/tertiary) structure is the overall 3D structure that the peptide chain adopts |
Tertiary |
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What is the name of the unit of organization that makes up the tertiary structure? |
Protein domain |
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True or false: Protein domains are functional units within the protein |
True |
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Motifs are ___ (smaller/bigger) than protein domains |
Smaller |
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What effect is the largest driving force in tertiary and quaternary protein folding? |
Hydrophobic effect |
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With proteins in aqueous solution, hydrophilic amino acid side chains will seek to be ___ (buried within the protein/facing the solution) |
Facing the solution |
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With proteins in aqueous solution, hydrophobic amino acid side chains will seek to be ___ (buried within the protein/facing the solution) |
Buried within the protein |
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With proteins in lipid environment, hydrophobic amino acid side chains will seek to be ___ (buried within the protein/facing out) |
Facing out |
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With proteins in lipid environment, hydrophilic amino acid side chains will seek to be ___ (buried within the protein/facing out) |
Buried within the protein |
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What property of secondary structural elements promotes formation of higher order structures? |
Amphipathic property |
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What effect of water drives the formation of higher order structures? |
Entropic |
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When proteins fold, there is a ___ (increase/decrease) in entropy |
Decrease |
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The amino acids found in a peptide chain in unfolded protein have ___ (more/less) of a chance for randomness in their position than they would in a folded protein |
More |
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As proteins fold and entropy decreases, what also decreases in order to counteract this? |
Enthalpy |
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What are 4 interactions that must be formed to help stabilize proteins? |
Hydrogen bonds, hydrophobic interactions, disulfide bonds, and ionic interactions |
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Disulfide bonds are ___ (covalent/noncovalent) linkages between two S-H groups of two ___ (prolines/cysteines) in ___ (reducing/nonreducing) environments |
Covalent, cysteines, non-reducing |
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What are 2 examples of non-reducing environments that disulfide bonds can form in? |
Endoplasmic reticulum, extracellular space |
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Ionic interactions can form between two ___ (charged/uncharged) R groups and in ___ (acidic/basic) conditions |
Charged, acidic |
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Ionic interactions between R groups and termini are also called what? |
Salt bridges |
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___ (Primary/Secondary/Tertiary/Quaternary) structure is only found in those proteins that are made up of more than one peptide chain |
Quaternary |
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In quaternary structures, each peptide chain folds into what? |
A monomer |
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Quaternary structure is made up of two or more ___ (monomers/dimers/trimers) that come together to make up the whole protein |
Monomers |
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What are the subunits of quaternary structure? |
Monomers |
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True or false: Monomers may be identical or different |
True |
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Subunits (monomers) of quaternary structure add to what 2 characteristics of a protein? |
Stability and function |
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What 3 options may subunits (monomers) have in terms of effect on the activity of other subunits? |
May activate, inhibit, or have no effect |