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Biological and Biochemical Foundations > Amino Acids & Proteins > Flashcards

Amino Acids & Proteins Flashcards

1
Q

Transmembrane proteins

A

Cross the phospholipid bilayer of cellular membranes; the surface consists mostly of hydrophobic amino acid residues

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2
Q

Post-translational modifications

A

Covalent additions of non-amino acid groups to a protein; catalyzed by enzymes and generally only occur at specific amino acid residues

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3
Q

Phosphorylation

A

Common post-translational modification that is facilitated by protein kinase enzymes; occurs at serine, threonine, and tyrosine, each of which contain a hydroxyl group in its side chain

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4
Q

Asparagine and glutamine

A

Amide groups

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5
Q

Cysteine

A

Thiol group

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6
Q

Aspartate and glutamate

A

Carboxylic acids

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7
Q

Proteases

A

(i.e., trypsin, pepsin) degrade proteins into smaller fragments by hydrolysis the peptide bonds that link amino acids in the polypeptide chain

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8
Q

G proteins

A

Common signaling proteins in cells that are switched “on” when they bind GTP. After the G protein hydrolyzes GTP into GDP, the G protein switches “off” until the GDP is exchanged for a new GTP

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9
Q

GTPase-activating proteins (GAPs)

A

Inhibit G protein signaling activity by enhancing their intrinsic hydrolase activity

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10
Q

Guanine nucleotide exchange factors (GEFs)

A

Job is to catalyze G proteins and therefore stimulate G protein signaling activity

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11
Q

Four substituents the α-carbon is bonded to, in order of stereochemical priority are:

A
  1. An N atom, in the form of either an amine group or an amide group
  2. A carbonyl carbon, in the form of either a carboxylic acid or an amide group
  3. A variable R group that constitutes the amino acid’s side chain
  4. A hydrogen atom
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12
Q

L/S Configuration

A

Natural amino acids are typically L
Given priority rankings of N atom > carbonyl carbon > side chain > α-hydrogen, the absolute stereochemistry of amino acids is typically S
Two exceptions: glycine and cysteine

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13
Q

Chiral amino acids, including cysteine

A

L configuration

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14
Q

Achiral residue (glycine)

A

No D or L designation

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15
Q

Tryptophan

A

An aromatic amino acid with extensive conjugation that allows for fluorescence (has pi orbitals)

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16
Q

Ligand-binding

A

pH-independent

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17
Q

Covalent attack

A

pH-dependent

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18
Q

Positive charged amino acids

A

Lys and Arg, His is partially positive

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19
Q

Aromatic amino acids

A

Try, Phe, and Trp

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20
Q

Non-polar amino acids

A

Val, Ala, and Gly

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21
Q

Negatively charged amino acids

A

Asp and Glu

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22
Q

α-tubulin

A

Acts as a control to confirm that the same amount of cell lysates have been loaded into the cells during gel electrophoresis

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23
Q

Contain hydroxyl groups and are able to hydrogen bond:

A

Serine, threonine, and tyrosine

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24
Q

Approximate mass of one amino acid

A

110 daltons

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25
Q

37 kDa = ? Da

A

37,000 Da

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26
Q

Calculate amino acids

A

(37,000 Da) x (1 amino acid/100) = slightly fewer than 370 amino acids

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27
Q

18 Carbons, how much NADH is produced? (Beta-oxidation)

A

The eighth oxidation of a C4 acid produces two molecules of acetyl-CoA. Thus, eight rounds of beta-oxidation are needed, and so only 8 molecules of NADH will be produced

28
Q

Five-membered cyclic amino acid, proline, prevents the alpha-amine nitrogen from participating in hydrogen bonding, what is true?

A

Proline decreases the stability of beta-pleated sheets

29
Q

pI = pH

A

AA is neutral and will not bind to the negatively charged beads

30
Q

pI

A

ALWAYS higher than pKa1
pI lies between pKa1 and pKa2

31
Q

pI > pH

A

AA is positive and will be attracted to the negatively charged beads, inhibiting elution

32
Q

pI < pH

A

Elution is best, as it is the only type of AA that will be repelled to the beads due to the AA’s negative charge

33
Q

Gel electrophoresis

A

Anode (+) larger
Cathode (-) smaller

34
Q

Histidine

A

Basic and heterocyclic

35
Q

Heterocyclic

A

Ring is composed of different elements

36
Q

Homocyclic

A

Composed of rings made of the same element

37
Q

Misfolding of proteins

A

Protein folding is most likely to be disrupted at the level of tertiary structure (forming globules or fibers)

38
Q

Secondary or primary structure problems

A

Tend to result from translation errors or mutations of the gene encoding the protein

39
Q

Quaternary structure problems

A

Only impacted when there is more than one subunit

40
Q

Non-polar hydrophobic AA

A

Glycine

41
Q

Basic and hydrophilic AA

A

Histidine, Lysine, and Arginine

42
Q

Pyranoses

A

Sugar composed of six-membered rings

43
Q

Furanoses

A

Composed of 5-membered rings

44
Q

Glucogenic AA

A

Converted into glucose
Arginine

45
Q

Ketogenic

A

Can be converted into acetyl-CoA or ketone bodies
Lysine

46
Q

Both Keto and Gluco

A

Tyrosine and phenylalanine

47
Q

Isoelectric points of AA

A

Glycine and Lysine are 6.0 and 9.6, respectively, so they can be separated by gel electrophoresis at a pH of 6.0 and 9.6

48
Q

Myosin

A

Acts primarily as a protein motor, but also has secondary activity as an ATPase
- Myosin binds to actin, which as motor activity, but does not hydrolyze ATP

49
Q

Troponin

A

A chaperone of actin, its activity is modulated by calcium, not ATP

50
Q

Kilocalories

A

Lipids = 9 kcal/g
Carbs = 4 kcal/g
Ethanol = 7 kcal/g
Fats provide the most energy per gram of any fuel source used by mammals

51
Q

pI is calculated by averaging:

A

The pKa values for: the main chain carboxyl group and the side chain

52
Q

Metabolic difference between glucose and lactose

A

Lactose is a disaccharide, so it must be cleaved before it can be metabolized, while glucose does not

53
Q

Most of the lipids found in the two leaflets of the cell membrane of euk. are synthesized in the

A

Endoplasmic reticulum

54
Q

α-carbon

A

Each amino acid residue, except Gly, has a chiral α carbon

55
Q

β-carbon

A

With the exception of Ile and Thr, the β carbon in AA residues is achiral; CD spectra arise from the massively greater presence of α carbon chirality

56
Q

Indole

A

Trp

57
Q

Imidazole

A

Two AA residues blocking access to W15 are histidines, each with an imidazole ring-containing side chain

58
Q

Denaturation of proteins

A

Means that the protein is unfolded and exposed

59
Q

Tyr

A

Can form a π-stacking interaction

60
Q

Asp

A

Has a negatively charged side chain that will repel

61
Q

Ser

A

Not capable of π-stacking interactions

62
Q

Arg

A

Positively charged side chain, which can make a salt bridge

63
Q

Glycoprotein

A

Cannot cross the membrane and must bind to receptors on the cell surface; it is likely it would be located on the surface of the plasma membrane

64
Q

Glycoprotein

A

Cannot cross the membrane and must bind to receptors on the cell surface; it is likely it would be located on the surface of the plasma membrane

65
Q

GTP

A

Guanosine tri-phosphate, which is a nucleotide

66
Q

Transport affinity for substrates

A

Is an inherent property of transport proteins, and this transport affinity is independent of the concentration of transport protein

Biological and Biochemical Foundations (14 decks)

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