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Biochemistry > Chapter 5 > Flashcards

Chapter 5 Flashcards

1
Q

What type of reaction forms amino acid chains?

A

Condensation Reaction

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2
Q

What type of bond holds together amino acids?

A

Peptide Bond

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3
Q

How are peptides read?

A

N-terminus to C-terminus

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4
Q

How are amino acid chains named?

A

Drop “-ine” from amino acid and add “-yl”

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5
Q

What was the first protein to be sequenced?

A

Insulin

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6
Q

What are the units for Daltons?

A

g/mol (atomic mass unit)

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7
Q

What holds amino acid chains together?

A

Disulfide Bridges

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8
Q

What is an isopeptide bond?

A

Amide bond that includes carboxylic acid or amine that isn’t from the backbone (comes from the side chain)

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9
Q

What is the issue with trying to determine protein sequence from corresponding DNA?

A

Not all DNA is translated into amino acids

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10
Q

What technique separates all amino acids?

A

Acid hydrolysis

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11
Q

Are protein subunits held together with strong or weak forces?

A

Weak

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12
Q

What are the four ways to separate protein subunits?

A
  1. extreme pH
  2. 8M urea
  3. 6M guanidine HCl
  4. High Salt Concentration
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13
Q

How do 6M guanidine HCl and 8M urea cause protein separation?

A

Associate with protein and replace hydrogen bonds

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14
Q

What is used to reduce disulfide cross-bridges?

A

2-Mercaptoethanol

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15
Q

How does 2-mercaptoethanol reduce disulfide bonds?

A

Reduces disulfide bridge to thiols

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16
Q

What do you need to be careful of when using 2-mercaptoethanol to reduce disulfide bridges?

A

Deprotonating the resulting thiols

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17
Q

What amino acid is the most common to form disulfide bridges?

A

Cystine

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18
Q

What is used to prevent (block) the reformation of disulfide bridges?

A

Iodoacetate

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19
Q

What side of the peptide bond does trypsin cut on?

A

Right (C-terminus side)

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20
Q

What side of the peptide bond does chymotrypsin cut on?

A

RIght (C-terminus side)

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21
Q

What side of the peptide bond does elastase cut on?

A

Right (C-terminus side)

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22
Q

What side of the peptide bond does thermolysin cut on?

A

Left (N-terminus side)

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23
Q

What side of the peptide bond does pepsin cut on?

A

Left (N-terminus side)

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24
Q

What side of the peptide bond does endopeptidase V8 cut on?

A

Right (C-terminus side)

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25
Q

What is the specificity of trypsin?

A

R(n-1) = Arg, Lys
Except: R(n) = Pro

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26
Q

What is the specificity of chymotrypsin?

A

R(n-1) = Phe, Trp, Tyr
Except: R(n) = Pro

27
Q

What is the specificity of elastase?

A

R(n-1) = Ala, Gly, Ser, Val
Except: R(n) = Pro

28
Q

What is the specificity of thermolysin?

A

R(n) = Ile, Met, Phe, Trp, Tyr, Val
Except: R(n) = Pro

29
Q

What is the specificity of pepsin?

A

R(n) = Leu, Phe, Trp, Tyr
Except: R(n) = Pro

30
Q

What is the specificity of endopeptidase V8?

A

R(n-1) = Glu

31
Q

What hydrolyzes on the C-terminal side of a methionine?

A

Cyanogen Bromide Hydrolysis

32
Q

What does carboxypeptidase function for in the sequencing of polypeptides?

A

Hydrolysis of the C-terminal amino acid

33
Q

What does dansyl chloride do in the sequencing of polypeptides?

A

Determines the N-terminal amino acid, but destroys the rest of the polypeptide in the process

34
Q

What does the Edman reagent do in the sequencing of polypeptides?

A

Determines the N-terminal amino acid, while leaving the rest of the polypeptide intact

35
Q

What is the primary means of protein identification?

A

Mass Spectrometry

36
Q

How does mass spectrometry separate proteins?

A

Based on the mass-to-charge ratio

37
Q

What is a protein domain?

A

Highly conserved amino acid sequence often with a conserved function between proteins

38
Q

What is the difference between a polymorphism and a mutation?

A

Polymorphism - relatively common natural variation, usually conservative and benign
Mutation - uncommon change, usually non-conservative, and may be detrimental

39
Q

What is a homolog?

A

Proteins that are evolutionarily related

40
Q

What is an ortholog?

A

Homologous proteins with the same function in different species

41
Q

What is a paralog?

A

Homologous proteins created from a gene duplication

42
Q

What does SDS do?

A

Binds to hydrophobic interactions in proteins and prevents refolding

43
Q

What is the function of beta-mercaptoethanol?

A

Reduces disulfide bridges

44
Q

What chemicals disrupt hydrogen bonding?

A

Urea and Guanidinium

45
Q

What is homogenization?

A

The process of breaking open cells

46
Q

What chemical is used to target cell walls?

A

Lysozyme

47
Q

What is used to disrupt the lipid bilayer?

A

Detergents (ex. SDS)

48
Q

What are the three ways of quantifying protein in solution?

A

UV
Bradford
BCA Assay

49
Q

What UV do proteins absorb light at? Which amino acids do this?

A

280nm
Amino Acids with rings (Tyr, Trp, Phe)

50
Q

How does a Bradford assay work?

A

Binding of a dye to hydrophobic areas of protein to create blue color change

51
Q

What absorbance is a Bradford assay read at?

A

595nm

52
Q

What limits Bradford assays?

A

Detergents

53
Q

How does a BCA assay work?

A

Reduction of Cu(2+) to Cu(+) by protein backbone. BCA turns purple with Cu(+) but not Cu(2+)

54
Q

What absorbance is a BCA assay read at?

A

562nm

55
Q

What limits a BCA assay?

A

Reducing agents

56
Q

What protein purification technique is used to sort by solubility?

A

Salting Out

57
Q

What is the eluent of chromatographic purification?

A

Molecules released from the column during separation

58
Q

How does ion exchange chromatography separate molecules?

A

Based on charge
Cation/Anion in the stationary phase that binds to the opposite

59
Q

What is the difference between a strong and weak resin?

A

Strong resin will always have its charge; weak resin will change its charge based on pH

60
Q

How does gel filtration chromatography separate molecules?

A

Based on size
Larger molecules then smaller molecules

61
Q

How does affinity chromatography work?

A

Small ligands are attached to the matrix that binds to the protein of interest. Protein is then eluted with a high concentration of the free ligand.

62
Q

How does SDS-PAGE separate proteins?

A

Based on size

63
Q

How does two-dimensional gel electrophoresis separate molecules?

A

First separated by isoelectric focusing (x-axis), then separated by size (y-axis)

Biochemistry (17 decks)

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