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MCAT Biochem > Chapter 1: Amino Acids, Peptides and Proteins > Flashcards

Chapter 1: Amino Acids, Peptides and Proteins Flashcards

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MCAT flashcards
1
Q

What are the two functional groups within an amino acid?

A

amino group (NH2) and carboxyl group (COOH)

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2
Q

What are the four components of an amino acid?

A

amino group, carboxyl group, hydrogen atoms and a side chain

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3
Q

What helps amino acids be specific in determing their function?

A

R group/side chain

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4
Q

If the amino group and carboxyl group are bonded to the same carbon this is called

A

the alpha amino acid

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5
Q

what is the name for the 20 amino acids encoded by the human genetic code?

A

proteionogenic amino acids

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6
Q

Is the alpha carbon for most amino acids chiral or achiral?

A

chiral

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7
Q

what amino acid is the exception to chirality?

A

glycine is achiral

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8
Q

Are all chiral amino acids L or D configuration? S and R?

A

L and S configuration

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9
Q

What kind of amino acids are in the interior of a protein?

A

hydrophobic

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10
Q

What kinds of amino acids are on the exterior of the protein?

A

hydrophilic

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11
Q

Ala (A)

A

Alanine

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12
Q

Arg (R)

A

Arginine

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13
Q

Asn (N)

A

Asparagine

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14
Q

Asp (D)

A

Aspartic acid

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15
Q

Cys(C)

A

Cysteine

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16
Q

Glu(E)

A

glutamic acid

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17
Q

Gln (Q)

A

glutamine

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18
Q

Gly (G)

A

glycine

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19
Q

His (H)

A

histidine

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20
Q

Ile (I)

A

Isoleucine

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21
Q

Leu (L)

A

leuicine

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22
Q

Lys (K)

A

Lysine

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23
Q

Met (M)

A

Methionine

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24
Q

Phe (F)

A

Phenylalanine

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25
Q

Pro (P)

A

proline

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26
Q

Ser (S)

A

serine

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27
Q

Thr (T)

A

threonine

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28
Q

Trp (W)

A

tryptophan

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29
Q

Tyr (Y)

A

tyrosine

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30
Q

Val (V)

A

valine

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31
Q

amino acids have both an BLANK carboxylic group and a BLANK amino group? (Acidic or basic). What is the name of this?

A

acidic carboxylic group and basic amino group, amphoteric species

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32
Q

An amino acid will either accept a proton or donate a proton depending on?

A

the pH of their environment

33
Q

Ionizable groups tend to BLANK protons under acidic conditions and BLANK them under basic conditions (Lose or gain)?

A

gain protons under acidic conditions and lose them under basic conditions

34
Q

Will a low pH be protonated or deprotonated?

A

protonated

35
Q

Will a high pH be protonated or deprotonated?

A

deprotonated

36
Q

pH<pKA Will it be protonated or deprotonated

A

species will be protonated

37
Q

pH> pKa Will it be protonated or deprotonated?

A

species will be deprotonated

38
Q

How many groups do amino acids have that can be deprotonated and how many pKa values must they have?

A

must have at least two groups that can be deprotonated, meaning they have at least two pKa values

39
Q

What is the approximate pKa for the carboxyl group?

A

around 2

40
Q

What is the approximate pKa value for the amino group?

A

between 9-10

41
Q
  • at pH 1 (acidic): far below the pKa of the amino acid group, the amino group will be full protonated (NH3+) and BLANK charged, the carboxylic acid group will be protonated and BLANK (positive, negative or neutral)
A

the amino group will be positively charges and the carboxylic acid group will be neutral

42
Q

What is it called when the molecule has both a positive and negative charge but will be electrically neutral?

A

zwitterions

43
Q

Where do zwitterions exist?

A

in water as internal salts

44
Q
  • pH of 10.5-> carboxylate group is deprotonated and amino group is deprotonated, the entire molecule is BLANK charged
A

negatively

45
Q

Define isoelectrical point

A

pH at which the molecule is electrically neutral

46
Q

How is the isoelectric point calculated?

A

averaging the two pKa values for the amino and carboxyl groups

47
Q
  • amino acids with acidic side chains have BLANK isoelectric points while those with basic side chains have relatively BLANK ones.
A

acidic is low and basic is high

48
Q

Define polypeptide

A

composed of amino acid subunits called residues

49
Q

Define oligopeptide

A

classify small peptides of up to 20 residues

50
Q

How are residues in peptides joined together?

A

peptide bonds

51
Q

Define petide bonds

A

specialized form of amide bond which forms between the -COO- group of one amino acid and the NH#+ of another

52
Q

Peptide bond formation is an example of what type of reaction?

A

Condensation or dehydration reaction

53
Q

Define condensation/dehydration reaction

A

removal of a water molecule and also can be seen as acyl substitution reaction which can occur with all carboxylic acid derivatives

54
Q

The Steps of Polypeptide formation

A

1.) The electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid
2.) the hydroxyl group of the carboxylic acid is kicked off and the result is the formation of a peptide bond

55
Q

When a peptide bond forms, the free amino end is known as?

A

N terminus

56
Q

When a peptide bond forms the free carboxyl end is the?

A

C terminus

57
Q

Peptides are draw in what configuration?

A

N terminus on the left and C on the right

58
Q

For enzymes to carry out their functions do peptides need to be unstable or stable in a solution?

A

stable

59
Q

What are the two acid/base catalysts that can hydrolyze amides in living organisms?

A

trypsin and chymotrypsin

60
Q

Define proteins

A

polypeptide chains that function as enzymes, hormones, membrane pores and receptors and elements of cell structure, they are the main actors–> the genetic code is a recipe for making thousand of proteins

61
Q
  • Primary structure
A

linear arrangement of amino acids coded in an organisms DNA, it is stabilized by the formation of covalent peptide bonds between adjacent amino acids
* the primary structure alone encodes all the info needed for folding at all the higher structural levels

62
Q
  • sequencing
A

how primary structure of a protein can be determined using the DNA that coded for the protein

63
Q
  • Secondary structure
A

local structure of neighboring amino acids and the result of hydrogen bonding between nearby amino acids. The two most common secondary structures are alpha and beta pleated sheets
* the key to stability of both structures is the formation of intra-molecular hydrogen bonds

64
Q
  • alpha helix
A

a rodlike structure in which the polypeptide chain coils clockwise around a central axis
* the helix is stabilized by intramolecular hydrogen bonds between the carbonyl group and the amide hydrogen atoms four residues down the chain
* the side chains of the amino acids in the alpha helical conformation point away from the helix core. The alpha helix is an important component in the structure of keratin

65
Q
  • beta sheets
A

can be parallel or antiparallel, the peptide chains lie alongside one another forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen and the amide hydrogen atoms
* to accommodate as many hydrogen bonds as possible, the beta sheets are plated or rippled shaped
* the r groups of the amino residues point above and below the plane of the beta sheet.
* Fibroin, primary protein component of silk fibers is composed of beta sheets

66
Q

What are the two categories proteins can be divided into?

A

fibrous and globular

67
Q
  • Tertiary structure
A

the result of moving hydrophobic amino acid side chains into the interior of the protein

68
Q
  • disulfide bonds:
A

when two cysteine molecules become oxidized to form cystine and create loops in the protein chain. They also determine how wavy or curly human hair is (more disulfide=more curly)

69
Q

is protein folding fast or slow?

A

fast

70
Q

what is it called if a protein loses its tertiary structure

A

denaturation and loses its function

71
Q

A hydrophobic interior, hydrophilic exterior is due to what chemical property?

A

entropy

72
Q
  • solvation layer
A

whenever a solute dissolves in a solvent

73
Q
  • quaternary structure:
A

not all proteins have this structure, only exist for proteins that contain more than one polypeptide chain.
* an aggregate of smaller globular peptides or subunits and represents the functional form of the protein
* examples include hemoglobin, immunoglobulins
* formation of quaternary structures can be to: be more stable by reducing the surface area of the protein complex, reduce the amount of DNA needed to encode the protein complex, bring catalytic sites close together allowing intermediates from one reaction to be directly shuttle to a second reaction, and can induce cooperativity (allosteric effects) –> one subunit can undergo conformational or structural changes which either reduce or enhance the activity in other subunits

74
Q
  • conjugated proteins:
A

function from covalently attached molecules (prosthetic groups)

75
Q
  • Prosthetic groups:
A

can be organic molecules, vitamins, ions, * prosthetic groups role is determining the function of their respective proteins

76
Q
  • Lipoproteins, Glycoproteins, and Nucleoproteins
A

are proteins with lipid, carbohydrate and nucleic acid prosthetic groups

77
Q

Is denaturation reversible?

A

most oftentimes no

78
Q

Can unfolded proteins catalyze reactions

A

no

79
Q

what are the two main causes of denaturation

A

heat and solutes

MCAT Biochem (1 decks)

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