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BCH451 > Chapter 3: Amino Acids, Peptides, & Proteins > Flashcards

Chapter 3: Amino Acids, Peptides, & Proteins Flashcards

1
Q

What are proteins?

A

polymers of amino acids

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2
Q

What are the three components of an amino acid?

A

acidic carbonyl, basic amino, a-hydrogen

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3
Q

What form are amino acids commonly in?

A

L form

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4
Q

What amino acid is the ONLY one that is not chiral?

A

glycine

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5
Q

What absorbance range to aromatic amino groups usually react in?

A

270-280 nm

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6
Q

Why is cysteine an important amino acid?

A

can form disulfide bonds

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7
Q

What amino acids are positively charged?

A

lysine, arginine, histdine

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8
Q

What amino acids are negatively charged?

A

aspartate and glutamate

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9
Q

What is pK1?

A

pK value that deprotonates -COOH

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10
Q

What is pK2?

A

pK value that deprotonates -NH3+

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11
Q

What is pKr?

A

pK value that deprotonates the R group

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12
Q

What is pI?

A

the isoelectric point, pH value at which a particular molecule has no NET electric charge

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13
Q

Are amino acids positive or negative at a low pH?

A

positive

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14
Q

Are amino acids positive or negative and a high pH?

A

negative

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15
Q

What is the name for a peptide that has a net charge of zero?

A

a zwitterion

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16
Q

What type of reaction is a protein synthesis reaction?

A

dehydration reaction

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17
Q

Why is peptide hydrolysis favorable?

A

water is very abundant, there is a high activation energy for dehydration

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18
Q

What is a residue?

A

the name for an amino acid in a protein

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19
Q

What pK values do you pay attention to when determining pI?

A

first pK2, last pK1, all pKr values

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20
Q

What are the four general functions of amino acids?

A

hormones, neuropeptides, antibodies, protection

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21
Q

What is a cofactor?

A

functional components added to a protein

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22
Q

What is a coenzyme? What’s an example?

A

an organic cofactors such as NAD+

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23
Q

What is a prosthetic group? What are 3 examples)

A

covalently attached cofactors such as heme, lipids, and sugars

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24
Q

What are other names for separation by size (2)?

A

gel filtration chromatography; size exclusion

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25
Q

In gel filtration chromatography, which type of protein elutes first?

A

larger proteins

26
Q

What is another word for separation by charge?

A

ion exchange chromoatography

27
Q

What are the two types of ion exchange chromatography?

A

anion exchange and cation exchange

28
Q

Which type of ion exchange uses positively charged beads?

A

anion exchange

29
Q

Which type of ion exchange purifies positively-charged proteins?

A

cation exchange

30
Q

How can you elute proteins trapped on an ion exchange chromatography?

A

with different salt concentration solutions

31
Q

What is another word for separation by affinity?

A

affinity chromatography

32
Q

What is usually the very first purification step?

A

affinity chromatography

33
Q

What are the four steps to affinity chromatography?

A

1) add solution of ligand to column
2) add protein mixture to column
3) wash unwanted protein through the column
4) elute protein of interest with ligand solution

34
Q

How can we still do affinity chromatography is a native ligand is unavailable?

A

recombination DNA technology!

35
Q

What are two recombinant protein chromatographys?

A

GST/GSH and Ni-NTA

36
Q

How does GST/GSH work?

A
  • bind GST tag to protein
  • GSH is anchored to the column
  • protein (with GST) binds to GSH
  • protein is eluted out with a high glutathione (GSH) solution
37
Q

How does Ni-NTA work?

A
  • NTA tag is coupled to an Ni ion and binds to the column
  • protein (with His6) binds to the Ni ion
  • elute protein out with imidazole
38
Q

How is separation for analytical measurement done?

A

electrophoresis

39
Q

How does an SDS page work?

A
  • SDS binds to and unfolds all proteins, adding a negative charge to all proteins
  • electric field (- to +) pulls smaller proteins farther through the gel
40
Q

Why would you use DTT in an SDS PAGE?

A

DTT breaks disulfide bonds and makes everything a monomer

41
Q

What are the two uses of an SDS PAGE?

A

1) to check the purity of a sample
2) to estimate molecular weight

42
Q

If I know how many amino acids are in a protein, how can I determine molecular weight?

A

(aa x 110)/1000 = weight in kDA

43
Q

If I know the molecular weight of an amino acid, how can I determine the number of amino acids?

A

weight x 9 = number of amino acids

44
Q

What is the use of a nonreducing SDS PAGE?

A

indicates the presence of disulfide bonds

45
Q

What is the use of a native PAGE?

A

can see protein-protein interaction

46
Q

What is the use of an Isoelectric Focusing PAGE?

A

can determine the isoelectric point of a protein in its native conformation

47
Q

How does isoelectric focusing work?

A

proteins stop traveling where their net charge is zero

48
Q

What is 2D electrophoresis?

A

the combination of isoelectric focusing with 2D electrophoresis?

49
Q

How can you quantify how many proteins are in a sample?

A

by using a spectrophotometer

50
Q

How does western-blotting work?

A

1) sorts all proteins by size using SDS page gel
2) sandwich this gel with a membrane coated in buffer
3) soak the membrane in a primary antibody that binds to only our protein
4) add a secondary antibody that binds with the first antibody for visualizaiton

51
Q

What biochemistry technology is the basis for COVID-19 tests and pregnancy tests?

A

ELISA

52
Q

What are the two ways to do protein sequencing?

A

edman degradation and mass spectrometry

53
Q

What are the constraints of the edgman degradation?

A

can only do 50 amino acids, can only identify protein with known sequence

54
Q

How does mass spectrometry work (very generally)?

A

identifies the mass of a peptide (and thus the aa sequence)

55
Q

Why is mass spectrometry wildly used over the edman degradation?

A

can sequence all amino acids, can be used to determine post-translational modifications

56
Q

How can you identity a protein using mass spec? Explain.

A

using electron ionization! utailizes the mass to charge ration for protein identification

57
Q

What are paralogs?

A

homologous proteins found within the same species

58
Q

What are orthologs?

A

homologous proteins found in different species

59
Q

What is a consensus sequence? What does it indicate?

A

a sequence that has not changed over the course of evolution, indicates that that protein is extremely important

60
Q

What is a signature sequence?

A

a small set of amino acids that accurately identifies a specific set of proteins

BCH451 (3 decks)

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