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MABS Biochemistry > lecture 6 > Flashcards

lecture 6 Flashcards

Amino Acids and intro to protein structure

1
Q

what are the features of an amino acid?

A

a carboxylic acid, an amino group attached to the alpha carbon, a hydrogen atom, a chemical group called a side chain

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2
Q

what is a zwitterion?

A

the amino acid form at physiological pH with a net zero charge, so that we see the amino portion fully protonated and the carboxylic acid deprotonated

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3
Q

what are the non polar aliphatic side chains?

A

glycine, alanine, proline, valine, leucine, isoleucine

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4
Q

typically, where would we find glycine?

A

found in bends or in the tightly packed chains of fibrous proteins

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5
Q

what are the amino acids with aromatic side chains?

A

phenylalanine, tyrosine, and tryptophan. Tyr (-OH) and Trp (-NH) have groups that can participate in H-bonds

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6
Q

what are the polar uncharged amino acids?

A

asparagine, glutamine, serine, and threonine. Note that Ser and Thr can serve as the site of attachment for structures such as phosphate groups

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7
Q

what are the sulfur containing amino acids?

A

methionine and cysteine

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8
Q

what is the pKa of cysteine?Why is this important?

A

8.4; because it is predominantly undissociated and uncharged at the physiologic pH of 7.4

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9
Q

what are the charged negative (acidic) side chains?

A

aspartate and glutamate

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10
Q

what are the charged positive (basic) side chains?

A

Histidine, Lysine, and Arginine

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11
Q

which amino acid has the side chain that can only ionize within the physiologic pH?

A

Histidine because when it is incorporated into a protein, its R group can only be wither positively charged or neutral and we see this in its buffering role with hemoglobin

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12
Q

which amino acids are obtained from nutrition?

A

leucine, isoleucine, valine, histidine*, lysine, methioine, phenylalanine, threonine, and tryptophan

*conditionally essential

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13
Q

which amino acids are synthesized by the body?

A

alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine

*conditionally essential

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14
Q

what is an essential amino acid?

A

these are amino acids that cannot be synthesized de novo by the organism and so it must be supplied

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15
Q

how many essential amino acids are their for the human?

A

9

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16
Q

what are the structures and abbreviations ( 1 and 3 letter abbreviations)

A

refer to amino acid deck

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17
Q

what do proteins consist of?

A

1 or more linear polypeptide chains containing hundreds of amino acids

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18
Q

how are amino acids joined?

A

through peptide bonds between the carboxylic acid of 1 aa and the amino group of the adjacent aa

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19
Q

why are the types of interactions that the side groups form important?

A

these interactions dictated the folding pattern of the molecule

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20
Q

are disulfide bonds primary structure?

A

no, because the primary structure of a protein is defined as the linear sequence of amino acids linked by amide bonds, neither secondary or tertiary

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21
Q

why are disulfide bonds important?

A

bring together elements of secondary structure into its tertiary configuration or an intermediate structure on the way to being the final form

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22
Q

what is a disulfide bond?

A

side chain of cysteine containing a sulfhydryl group and 2 of these linked together causes the cysteines to be oxidized to form a covalent cross link and can be referred to as a cystine

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23
Q

what is the idea of aromatic staking?

A

driven by the hydrophobic effect in which nonpolar side chains will gather together in the protein interior whenever possible and also, aromatic side chains are rarely exposed to polar/aqueous environments

24
Q

where do we see H-bonding occur?

A

Peptide backbone and side chains

25
Q

why are ionic bonds important in structure and function of amino acids?

A

because amino acids can have formal positive and negative charges and so attraction occurs where we see electrostatic interaction

26
Q

what can we note about basic and acidic amino acids?

A

they act as proton donors and acceptors; also note that amino acids in solution also contain a weakly acidic alpha carbonyl carbon and a weakly basic alpha amino group and can act as buffers

27
Q

when the pH is more than one unit lower than the pKa, the molecule will be deprotonated, T/F?

A

F, protonated

28
Q

When the pH is more than one unit higher than the pKa, the molecule will be deprotonated? T/F

A

T

29
Q

When the pH = pKa, the molecule will be what percent ionized.

A

50%

30
Q

what is pKa again?

A

The pKa is the pH at which half the molecules of an amino acid in solution have side chains that are charged, half are uncharged

31
Q

For some side chains, the pK values are several units different than physiological pH. So it is safe to say that for aspartate, for example, has a pka value of 3.9. How much of the side chains will be deprotonated at pH 7.4.

A

100%

32
Q

Likewise, what percentage of tyrosine, for example, would be protonated at a pH of 7.4, if its pKa value is 10.5?

A

100%

33
Q

why are weak forces important in our understanding of amino acids?

A

because its important for structure and function and is responsible for bimolecular recognition

34
Q

what are the environmental conditions that affect weak forces?

A

temperature, pH, ionic strength, and solvent medium

35
Q

what are the four examples of weak forces?

A

van der waals, H-bonds, ionic bonds, hydrophobic interactions

36
Q

why are weak forces important for say macromolecules?name other examples?

A

because there are many sites for weak forces to interact and so they help to stabilize the macromolecules; folding of polypeptides, binding of an antigen, binding of a hormone

37
Q

what are van der waals forces?

A

a subset of electrostatic interactions involving permanent or induced dipoles and depends strongly on the distance between interacting atoms, in short they are weak interatomic attractions.

38
Q

name the different van der waal interactions?

A

permanent or induced dipoles (or multipoles) permanent dipole-dipole interactions (Keesom force)dipole-induced dipole interactions (Debye force)induced dipole-induced dipole interactions (London dispersion force)

39
Q

how much energy does each van der waals interaction produce?

A

0.4 to 4 kj/mol of energy

40
Q

what is a Hydrogen bond?

A

Form between a hydrogen atom that is covalently bonded to an electronegative atom (O, N), and a second electronegative atom that serves as the hydrogen bond acceptor.

41
Q

how much energy does each H bond contribute?

A

10-12 kj/mol

42
Q

H bonds are covalent bonds? T/F

A

F

43
Q

what is the electrostatic interaction between an H-bond?

A

between an electronegative atom and electropositive H atom

44
Q

what are ionic interactions?

A

Electrostatic attractive forces between oppositely charged ions (cations and anions)

45
Q

describe the ionic bond? and the role water plays? and how much energy the ionic bond contributes?

A

non-directional, and strength in solution depends on the magnitude of charges, the distance between the charged groups, and dielectric constant; water is effective in screening the electrostatic interactions; 20 kj/mol

46
Q

what are hydrophobic interactions? examples?

A

Hydrophobic interactions are weak forces that hold nonpolar regions of molecules together; formation of lipid bilayers and stabilization of 3-D structure of proteins

47
Q

what is formed as a result of hydrophobic interactions when The nonpolar regions of an amphipathic molecule cluster together to present the smallest hydrophobic area, and the polar regions are arranged to maximize interaction with water?

A

micelle

48
Q

when are Hydrogen Bonds strongest?

A

when the bonded molecules are oriented to maximize electrostatic interaction like a straight line

49
Q

what effect do H-bonds have on proteins since they are highly directional and capable of holding 2 H-bonded molecules or groups in specific arrangement?

A

it confers a very precise 3-D structure on protein and nucleic acid molecules

50
Q

What are hydrophobic interactions the result of?

A

the systems achieving the greatest thermodynamic stability by minimizing the number of ordered water molecules required to surround hydrophobic portions

51
Q

are non polar compounds able to undergo energetically favorable interactions with H-bonding among water molecules?

A

no, because the water molecules are constrained in their possible orientations as they form a highly ordered cage shell around each solute, resulting in a decrease in entropy

52
Q

what is the magnitude of entropy decrease proportional to?

A

the surface area of hydrophobic solute, so how can we increase the entropy?

53
Q

How is the system of entropy increased with respect to an amphipathic molecule and its aqueous environment?

A

The nonpolar regions of an amphipathic molecule cluster together to present the smallest hydrophobic area, and the polar regions are arranged to maximize interaction with water, this is called a micelle

54
Q

why is arginine important?

A

because children and pregnant women have a high rate of protein synthesis to support growth and require this

55
Q

when a patient has phenylketonuria, what has happened?

A

the patient cannot synthesize tyrosine from phenylalanine, possibly due to enzyme deficiency

56
Q

how is cysteine synthesized?

A

by using the sulfur from methionine and may be required in the diet under conditions of low methionine intake or malabsorption disorders

MABS Biochemistry (54 decks)

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