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76 Cards in this Set
- Front
- Back
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Is oxygen electron withdrawing or donating?
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withdrawing causing it to hold a slightly negative charge in a water molecule
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what happens to a neutral molecule in water
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water tend to weaken the interaction between the ions and thus promotes dissocation of the molecule into ions
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T or F H bonds are covalent
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FALSE
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are H bonds considered strong or weak?
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weak, but with a large amount of H bonds, pretty stable
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_____ interactions are the dominant noncovalent forces encountered in most if not all biological systems
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hydrophobic
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If [H+] = 10e-4 what is the ph?
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4
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If [OH-] = 10e-4 what is the pH?
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10, because [H+] would be 10e-10, so pH is 10
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a change by one number in pH is actually a change by a factor of ____
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10
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[H+]x[OH-] =
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10e-14
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Keq =
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[B-][H+]/[HB]
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pH =
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pK + log[HB]/[B-]
or pK + log[B-]/[HB] |
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how do you define pK'
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the pH at which an acid is 50% ionized
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keq =
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[B-][H3O+]/[HB]
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what makes up a buffer
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a weak acid AND it's conj base
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what is the rule of thumb for when a buffer is a good buffer
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when it is within one pH of it's pK value
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what are the four major components of any amino acid
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alpha amino group, R group, alpha carbon, alpha carbonyl
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what is the three letter abbrev for asparagine
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Asn
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Three letter abbrev for glutamine
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gln
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Name the nonpolar aa
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GAVIL P FWM
gly ala val ile leu pro phe trp met |
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name the polar aa
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STNQCY
ser thr Asn Gln cys tyr |
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Name the acidic aa
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asp glu
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Name the basic aa
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lys arg his
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The solubility of an amino acid is strongly influenced by what two things
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size and polarity of the R group
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are human proteins L or D
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L
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which are the two strongly basic aa
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arg and lys.. his is very sensitive to pH around neutral pH
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pK of alpha carboxyl
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3
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pK of beta carboxyl like asp and glu
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4
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What is an example of an imidazole? what is the pK?
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His
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Which sufhydryl aa has a pK of 8?
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Cys
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what is the pka of an 1 primary alpha amino free
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8 N terminal only
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what is pK of lys and tyr
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10
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what is the pK of 2 alpha amino like proline
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9
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which aa is an example of a guanido? what is the pK?
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arg
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what is another name for peptide bond?
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series of amide linkages
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is a peptide bond a covalent bond?
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yes
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T or F
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when alpha amino and alpha carboxyl groups are joined to make peptide bonds they become amides and no longer have appreciable acid base properties
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what do you call a protein less than 5000 daltons or less than 50 aa?
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peptides
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what do you call a protein with two amino acids
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dipeptide
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are peptides named C to N or N to C
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N to C
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the ______ of the aa is critical for the structure and activity of a protein
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sequence
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describe primary structure
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sequence of aa
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describe secondary structure
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local folding
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describe tertiary structure
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global folding
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describe quaternary structure
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oligomerization state
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how can you tell between a secondary and tertiary structure
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secondary structure is primarily a result of the chemical nature of the peptide bond whereas tertiary structure is more influenced by interactions between R groups
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why do peptide bonds in a secondary structure tend to be all in the same plane
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the CN single bond has considerable double bond character which puts restraint and leads to a tran formation which is also planar
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in an alpha helix, the oxygen atom of one residue interacts with the hydrogen on the amide of the aa ___ residues away
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4-- this allows it to complete an almost full turn
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A H bond is weak, so how is an alpha helix so stable?
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many h bonds make it stable
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each aa can participate in how many h bonds
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2
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segments of proteins that cross membranes often form long sections of ______ (alpha or beta) composed of hydrophobic aa residues
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alpha helix
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T or F. polypeptide chains in a beta sheet can be parallel or antiparallel
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true
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definition. particular sequences of aa that are evolutionarily conserved among proteins
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motifs
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supersecondary structures (motifs) are frequently orgnanized into compact regions of tertiary structure called _____
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domains
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what makes up tertiary structures? aka what characteristics
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3D folding and domains
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what is the general format of an aa?
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see photo
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what is the henderson hasselbach equation?
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pH = pK - log(prot)/(unprot)
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what does the HH equation tell you
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calculate ratio of weak acid and conj base at any pH
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aa are strung together by what kind of bond
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peptide
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If [HB]/[B-} = 100. what do you know?
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that there is more HB in solution by 100 fold
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can a peptide chain be formed by R groups between aa?
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No, peptide bonds are formed using alpha carbon or alpha aa never the R group
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why is a peptide bond planar?
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due to resonance structure that restricts the number of conformations of a protein to si and phi
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definiton. cluster of conserved residues
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motif
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what is the difference between conserved and variant
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conserved is generally similar
invariant is always the same |
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t or f. conserved parts of a protein tend to cluster
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true. probably due to a very important function
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definition. local foldings of residues into regular patterns
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secondary structure
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t or false a beta sheet cannot be twisted
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false, beta sheets can be twisted -- beta turns!
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are secondary structures limited to interprotein reactions?
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no may be intra protein reactions too
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what secondary structures do pro and gly tend to have
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NO alpha helix and lots of beta turns
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why doesn't glycine like to be an alpha helix?
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thermodynamically disfavored. gly is small however and easily makes tight beta turns
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why doesn't pro like to be alpha helix?
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sterically disfavored. Small, kinked, easily makes tight turns.
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definiton. global folding of protein chain
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tertiary structure
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definiton. higher order assembly of proteins
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quaternary structure
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what are three ways we can classify proteins?
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functions definition
structural definition cellular localization definition |
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what are four types of function definition proteins
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enzymes
structural transport defense |
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what are two types of structural definition proteins
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globular
fibrous |
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what are two examples of the cellular localization definition
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membrane and soluble
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