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Biochem > Amino Acids and Protein Structure > Flashcards

Amino Acids and Protein Structure Flashcards

1
Q

L-alpha-AA is a ___ acid with an amino group on carbon ___

A

carboxylic; 2 (the alpha carbon)

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2
Q

What is the role of the Hydrogen on an AA

A

prevents bulkiness and allows side chains to fit

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3
Q

Almost all AAs are ___ AAs

A

L-alpha

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4
Q

How many AAs are coded for by DNA?

A

20

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5
Q

What are the non polar AAs?

A

glycine, alanine, proline, valine, leucine, isoleucine

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6
Q

What are the aromatic AAs?

A

phenylalanine, tyrosine, tryptophan

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7
Q

What are the polar, uncharged AAs?

A

asparagine, glutamine, serine, threonine

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8
Q

What are the sulfur-containing AAs?

A

Methionine, Cysteine

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9
Q

What are the negatively charged AAs?

A

aspartate, glutamate

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10
Q

What are the positively charged AAs?

A

arginine, lysine, histidine

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11
Q

Aspartate has a pKa of 3.9. Give the ratio of COOH to COO- at a pKa of 2.9, 1.9, and 4.9

A

pKa 2.9: 10 times more COOH
pKa 1.9: 100 times more COOH
pKa 4.9: 10 times more COO- or 10 times less COOH

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12
Q

What is the isoelectric point?

A

at a certain pH, there will be an equal number of postive and negative charges

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13
Q

In regards to protein structure, what is unique about the isoelectric point

A

proteins are least stable at pI

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14
Q

This AA forms disulfides

A

cysteine, between 2 cysteine molecules

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15
Q

disulfide bridges have what affect on protein structure?

A

stability

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16
Q

This is found in only a few enzymes and is incorporated via a specialized tRNA which is then incorporated into a protein

A

Selenocysteine

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17
Q

At any given pH, a peptide will have a characteristic charge. Changes in a pH will do what?

A

change the charge on the peptide

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18
Q

Which AAs are involved in carbohydrate addition, specifically O-glycosylation?

A

serine, tyrosine, and threonine

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19
Q

Which AAs are involved in carbohydrate addition, specifically N-glycosylation?

A

asparagine

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20
Q

Which AAs are involved in lipid addition, specifically palmitoylation?

A

cysteine

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21
Q

Which AAs are involved in lipid addition, specifically prenylation?

A

cysteine

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22
Q

Which AAs are involved in lipid addition, specifically myristoylation?

A

glycine

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23
Q

Which AAs are involved in regulation, specifically phosphorylation?

A

Serine, Threonine, and Tyrosine

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24
Q

Which AAs are involved in regulation, specifically ADP-ribosylation?

A

arginine, glutamine, cysteine

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25
Q

Which AAs are involved in regulation, specifically Acetylation?

A

lysine

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26
Q

Which AAs are involved in modification, specifically oxidation?

A

proline, lysine

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27
Q

Which AAs are involved in modification, specifically carboxylation?

A

glutamate

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28
Q

This is the bond between the alpha-carboxyl group of one amino acid and the alpha-amino group of another amino acid

A

peptide bond

29
Q

The peptide bond is ___, with the alpha-carbon, the carbonyl carbon, the carbonyl oxygen, the nitrogen, the nitrogen-hydrogen and the second alpha-carbon all in the same plane

30
Q

Adjacent R groups of two amino acyl residues are almost always in the ___ configuration

31
Q

What is primary structure of a protein

A

sequence of AAs

32
Q

Residue #1 is the amino terminal or ___-terminal; The last residue is the carboxyl terminal or ___-terminal

A

N-terminal; C-terminal

33
Q

Different protein isoforms or isozymes may be expressed at different developmental stages. true or false?

A

true, ex: HbF, HbA

34
Q

Give an example of different protein isoforms or isozymes expressed simultaneously but restricted to different tissue

A

creatine kinase isoenzymes and lactate dehydrogenase isozymes

35
Q

In regards to primary structure, give an example of species variation

36
Q

What is secondary protein structure

A

recurring, localized structures found within regions of a polypeptide chain - primarily alpha helix and beta sheets

37
Q

The alpha helix is stabilized by ___ bonds between the amide hydrogen of an amino acyl residue and the carbonyl oxygen atom of a second amino acyl residue located four amino acyl residues down the chain

38
Q

Which AA can’t be part of an alpha helix

39
Q

True or false? beta sheets form a planar surface

40
Q

The surfaces formed by B-pleated sheets are often ___

41
Q

What are some other secondary structures that are less repetitive and uniform than alpha helices and beta sheets?

A

bends, loops, and turns

42
Q

patterns of secondary structures are frequently found in several different proteins. These repeating patterns often function similarly to each other and represent what?

A

motifs and domains

ex: nucleotide binding domains are found in many proteins which bind and hydrolyze ATP

43
Q

What is tertiary protein structure?

A

the folding pattern of the secondary structural elements into a 3D conformation

44
Q

What five forces are involved in tertiary protein structure?

A
  1. hydrogen bonds
  2. salt bridges
  3. hydrophobic interactions
  4. van der waals forces
  5. disulfide bridges
45
Q

Globular proteins soluble in aqueous environment are part of tertiary structure. The “core” of a soluble globular protein usually contains a high proportion of ____ amino acyl residues and ____ ____ amino acyl residues are usually concentrated on the surface of soluble globular proteins

A

hydrophobic; charged polar

46
Q

Globular proteins in tertiary structure interact with a polar aqueous environment to form ___ ___ to stabilize structure

A

salt bridges

47
Q

In regards to tertiary structure, transmembrane proteins are membrane spanning domains made up of what?

A

alpha helices and hydrophobic residues that are exposed to the lipid environment

48
Q

In transmembrane proteins, extracellular and intracellular domains may be more characteristic of ___ interactions

A

hydrophillic

49
Q

What is quaternary protein structure?

A

association of individual polypeptide chain subunits into one functional protein

50
Q

In regards to quaternary structure, what are the four forces involved in globular proteins

A
  1. hydrogen bonding
  2. hydrophobic interactions
  3. salt bridges
  4. rarely disulfide bonds
51
Q

In regards to quaternary structure, in fibrous (connective tissue) and other structural proteins, there may be extensive ___ linkages to other proteins

52
Q

What is an example of cooperativity between subunits?

A

hemoglobin-O2 binding

53
Q

The ___ structure of a protein specifies the folding of the mature protein

54
Q

What do heat shock proteins do?

A

prevent improper folding of proteins

55
Q

Other heat shock proteins that require energy do what?

A

promote proper folding

56
Q

The following describes a technique used in protein purification and analysis:
separations of compounds based on the relative affinity of the compounds for a given stationary phase and for the mobile phase

A

chromatography

57
Q

This chromatography medium is porous beads. The protein mixture flows through a column. Smaller proteins can enter the pores of the beads, and therefore take longer to flow through the column. Larger proteins elute first.

A

size exclusion chromatography

58
Q

In ion exchange chromatography, the medium is resin beads with covalently bound chemicals which bear a charged group. Explain the difference between cation exchange and anion exchange

A

cation exchange

  1. the bound chemicals have a negative charge
  2. positively charged compounds (cations) will adhere to the column

anion exchange

  1. chemicals have a positive charge
  2. negatively charged compounds (anions) will adhere to the column
59
Q

Describe hydrophobic interaction chromatography

A

medium contains hydrophobic groups; proteins with exposed hydrophobic surfaces will adhere to column; adhering proteins are eluted by decreasing polarity of the eleuent

60
Q

The following describes what type of chromatography?
medium contains a bound ligand; proteins which bind ligand will adhere to column; adhering proteins may be eluted by adding excess ligand

61
Q

In this type of chromatography, eluent is pumped under high pressure - separation is faster and at a higher resolution and usually uses hydrophobic interaction.

A

high-pressure liquid chromatography

62
Q

Separation based on migration of charged molecules in an applied electrical field is called what?

A

electrophoresis

ex: hemoglobin isoforms

63
Q

Describe what happens in an SDS-PAGE

A

large number of SDS (detergent) molecules interact with each protein molecule, producing proteins of approximately equal charge-to-mass ratios, also disrupting quaternary structure and separation into monomers - then migration through the PA gel is based on sized, smaller proteins migrating faster

64
Q

Special, proprietary buffers are used to generate a pH gradient within a PA gel. proteins will migrate to the pH which is equal to the protein’s pI. Once at the pH which equals the pI, the protein will no longer migrate. What technique is this?

A

Iso-electric focusing

65
Q

Give the first and second dimension of two-dimensional electrophoresis

A
  1. IEF

2. SDS-PAGE

66
Q

Describe a western blot

A
  1. proteins separated by electrophoresis (usually SDS-PAGE) are transferred to synthetic membrane
  2. membrane is incubated with antibody (primary antibody) to a specific protein
  3. a second antibody (to the primary antibody) conjugated with a reporter molecule is added to visualize the specific protein
67
Q

The following description is of what technique:

  1. penylisothiocyanate reacts with N-terminal
  2. derivative can be removed, analyzed, and AA identified
  3. a new N-terminal is produced which is subjected to a 2nd round of the reaction
  4. process may be repeated multiple times to determine the AA sequence of a peptide
A

edman sequencing

68
Q

Mass spec separates molecules based on what?

A

their mass

69
Q

When would you use mass spec?

A

to identify protein through determination of masses of peptides produce from tryptic digestion of protein; to detect covalent modifications of a protein

Biochem (38 decks)

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