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bich 410 > Quiz 5 > Flashcards

Quiz 5 Flashcards

1
Q

the primary structure of a protein

A

provides information about its function

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2
Q

in cells, this potential variety

A

is limited by the efficiency of protein synthesis and by the ability of the polypeptide to fold into a functional structure

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3
Q

the peptide backbone

A

-N-Ca-Co

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4
Q

N

A

the amide nitrogen of the amino acid

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5
Q

Ca

A

is the alpha carbon of the amino acid

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6
Q

Co

A

is the carbonyl carbon of the amino acid

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7
Q

peptide formation is the creation of an

A

amide bond between the carboxyl group of the first amino acid and the amino group of the next amino acid

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8
Q

condensation reaction

A

results in a low of water

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9
Q

the peptide bond

A
  • adopts a trans conformation
  • due to the partial double bond character of the peptide bond, the six atoms of the peptide-bond group define a plane the AMIDE PLANE
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10
Q

environmental conditions that affect a proteins stability during purification

A
  • pH
  • temperature
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11
Q

an assay based on a proteins chemical or binding properties

A

may be used to quantify a protein during purification

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12
Q

fractionation procedures

A

take advantage of a proteins unique structure and chemistry in order to separate it from other molecules

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13
Q

” salting out”

A
  • increasing the salt concentration causes selective salting out [precipitation ] of proteins with different solubilities
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14
Q

what influences a proteins chromatographic behavior

A
  • charge
  • polarity size
  • ligand-binding
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15
Q

ultracentrifugation

A

what the overall size and shape of macromolecules and larger assemblies can be assessed through.

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16
Q

salting out [1]

A

separates based on protein solubility in high ammonium acetate concentration

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17
Q

chromatography [1]

A

separates based on a proteins ionic charge, polarity, size or ligand binding ability.

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18
Q

gel electrophoresis [1]

A

and its variations can separate proteins according to charge, size, and isoelectric point

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19
Q

ultracentrifugation [1]

A

separates based on the overall size and shape of macromolecules and larger assemblies

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20
Q

below the isoelectric point or PI

A

[the pH at which there is a net charge of 0] the protein will carry a net positive charge

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21
Q

above the pl

A

a net negative charge

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22
Q

positively charged proteins

A

bind cation exchange columns

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23
Q

negatively charged proteins

A

bind anion exchange columns

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24
Q

proteins are eluted [released] by

A

high salt concentration

25
Q

dialysis

A

semipermeable membrane bag is immersed in beaker of solution, diffusible solutes in the dialysis bag equilibrate across the membrane, while your protein stays inside

26
Q

small proteins are impeded

A

by access to the inside of the gel beads, delaying travel through the column

27
Q

large proteins

A

have no access to the matrix of the gel beads and flow easily around gel beads

28
Q

proteins are eluted in the order

A

largest to smallest

29
Q

small-molecule targets (ligands, black)

A

are immobilized through covalent attached to a solid matrix (tan) column

30
Q

absorbance

A

dated the presence of proteins, but it does not distinguish between different proteins

31
Q

proteins in a small sample can be separated by

A

electrophoresis, based on their size, using a semi-solid phase gel.

32
Q

after separation, proteins are detected by staining with

A

coomassie brilliant blue for visualization of “bands” representing the proteins of different sizes

33
Q

SDS page

A

sodium dodecyl sulfate poly acrylamide gel electrophoresis.
small samples are taken from fraction tubes, SDS is added, samples are boiled to denature and coat all of the amino acids with negative charges and separated by electrophoresis on a gel

34
Q

260 nm is problematic, why?

A

at 280nm there is a strong absorbance by Tyr and Top but not Phe

35
Q

A reducing agent, such as DTT or BMe

A

is needed to disrupt structure but does not break disulfide bonds

36
Q

a proteins mobility in the gel

A

is inversely proportional to the molecular weight

37
Q

separation is based on

A

size, without irreversibly denaturing the protein

38
Q

to be sequenced

A

a protein must be separated into individual polypeptides that can be cleaved into sets of overlapping fragments

39
Q

the amino acid sequence can be determined by

A

Edman degradation, a procedure for removing N-terminal residues at one time

40
Q

mass spectromy

A

can identify amino acid sequences from the mass-to-charge ration of gas-phase protein fragments

41
Q

proteins can be sequenced in two ways

A
  1. direct amino acid sequencing
  2. sequencing the corresponding dna of the gene
    today, gene databases provide these deduced protein sequences
42
Q

acid hydrolysis

A

liberates the amino acids of a protein
- some amino acids are partially or completely destroyed by acid hydrolysis especially, trp

43
Q

chromatography is used

A

to separate amino acids

44
Q

the amino acid compositions

A

of different proteins are different

45
Q

the sequence of amino acids in a protein is

A

distinctive but composition is not

46
Q

subunit interactions depend on weak forces, which can

A
  • be denatured
47
Q

denaturation can be achieved with

A
  • extremes of pH
  • high urea concentration
  • high guanidine HCL concentration
  • high salt concentration
48
Q

disulfide reducing agents

A

-2-mercaptoethanol, B-me
- dithiothreitol, DTT

49
Q

to prevent disulfide bridges from reforming, follow with

A

an irreversible alkylating agent, like iodoacetate, IOAc

50
Q

n terminal analysis, uses

A

edmans reagent
- derivatives are PTH

51
Q

c-terminal analysis is enzymatic with carboxypeptidases

A
  • carboxypeptidase A cleaves any residue except PRO, ARG, AND LYS
  • carboxypeptidase B cleaved only works on arg and lys
52
Q

enzymatic fragmentation

A
  • trypsin
  • chymotrypsin
  • staphylococcal protease
53
Q

chemical fragmentation

A

cyanogen bromide

54
Q

trypsin

A

cleavage on the C side of Lys, Arg [basic]

55
Q

chymotrypsin

A

C side of Phe , Tyr, Trp, less so Leu [large nonpolar]

56
Q

staphylococcal protease

A
  • c side of glu, asp[acidic] in phosphate buffer pH7
  • specific for glu, in acetate [pH 5] and bicarbonate. buffer [pH 10]
57
Q

cyanogen bromide

A
  • CNBr acts only on methionine residues
  • CNBr useful because proteins usually have only a few Met residues
  • a peptide with a C-terminal homoserine lactone
58
Q

compare and align overlapping peptide sequences

A

to learn the sequence of the original polypeptide chain

59
Q

mass spec [MS]

A

mass spectrometry separates particles on the basis of mass-to-charge ratio

bich 410 (13 decks)

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