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biochemistry 2065 > Lecture 7: The Amino Acids > Flashcards

Lecture 7: The Amino Acids Flashcards

1
Q

__ are the most versatile biomolecules

A

proteins

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2
Q

proteins tend to function as __ (enzymes)

A

catalysts

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3
Q

besides catalysts, provide 3 more functions of proteins

A
  1. mechanical support
  2. generate movement
  3. control growth
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4
Q

DNA is a relatively __ carrier of information, mostly for genes that code for __

A

inert; proteins

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5
Q

proteins are __ polymers made of monomers

A

linear

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6
Q

what are the monomers of proteins?

A

amino acids

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7
Q

what determines the 3-D shape of proteins?

A

amino acid sequence

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8
Q

the function of the protein relies on the __ of the protein

A

shape

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9
Q

aside from shape, what accounts for the wide array of protein functions?

A

functional groups

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10
Q

proteins can interact with each other to form __

A

complex assemblies

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11
Q

what is a possible benefit of forming a complex assembly rather than remaining as a single protein?

A

typically more or different capabilities

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12
Q

what characteristic of proteins makes them good structural elements?

A

they are rigid

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13
Q

proteins with some flexibility can act as __ , __ or __ involved in protein function or assembly of protein complexes

A

hinges, springs, levers

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14
Q

the primary structure of proteins

A

amino acid sequence

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15
Q

the secondary structure of proteins

A

discrete regions of higher order structure (alpha helix, beta sheets)

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16
Q

the tertiary structure of proteins

A

higher order folding of secondary structures

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17
Q

the quaternary structure of proteins

A

multi-protein (subunit) assemblies

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18
Q

why is the chemistry of amino acids relevant (3)

A
  1. determines structure, which determines function
  2. mediate interactions between proteins and molecules
  3. help catalyze chemical reactions in the active site of enzymes
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19
Q

all amino acids contain an alpha carbon attached to __ (4)

A
  1. amino group
  2. carboxylic acid group
  3. hydrogen
  4. side chain
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20
Q

the amino and carboxyl group can be __ depending on the surrounding pH

A

ionized

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21
Q

at physiological pH: the amino group will be __ and the carboxyl will be __

A

protonated; deprotonated

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22
Q

amino acids at physiological pH exist mostly in the __ form

A

zwitterionic

23
Q

what is a chiral molecule?

A

not superimpossable on its mirror image and has at least one chiral centre

24
Q

which chiral isomer is the only one used for making proteins? (R/L)

A

L

25
Q

the CORN rule can be used to determine ___ in amino acids

A

R/L consiguration

26
Q

using the corn rule, the cw direction is the ___ isomer

A

D

27
Q

using the corn rule, the ccw direction is the __ isomer

A

L

28
Q

the hydrophobic amino acids have __ R groups

A

nonpolar

29
Q

the polar amino acids have __ R groups where the charge is ___ distributed

A

neutral; unevenly

30
Q

positively charged amino acids have ___ R groups at pH 7

A

positively charged (ionic)

31
Q

negatively charged amino acids have __ R groups at pH 7

A

negatively charged (ionic)

32
Q

what three factors are important to consider with side chains?

A
  1. are there polar groups
  2. are they ionizable
  3. size
33
Q

what is an ampiphatic molecule?

A

has both hydrophillic and hydrophobic parts

34
Q

the larger the hydrocarbon, the ___ hydrophobic

A

more

35
Q

hydrophobic R groups are hydrophobic, but Phe, Trp, and Tyr can form ___ interactions

A

van der waals

36
Q

protein folding patterns are driven by ___

A

the hydrophobic effect

37
Q

the polar neutral side chains contain a ___ that hoards electrons

A

heteroatom (O,N,S)

38
Q

most neutral polar side chains are typically ___

A

unreactive

39
Q

which neutral polar amino acid has an ionizable OH group?

A

tyrosine

40
Q

negatively charged amino acids are also called __ amino acids

A

acidic

41
Q

negatively charged amino acids have what type of side chain at pH 7?

A

deprotonated carboxyl group

42
Q

positively charged amino acids are also called __ amino acids

A

basic

43
Q

histidine has an imidazole group with pka =6, making both forms abundant at pH 7, therefore it is chemically ___

A

versatile

44
Q

histidine is often found in the active sites of enzymes where the imidazole ring can bind and ___

A

release H ions in enzymatic reactions

45
Q

the 7 amino acids with ionizable side chains play important roles in the active sites of

A

active sites of enzymes

46
Q

amino acids which have a direct role in catalysis are called ___ amino acids

A

catalytic

47
Q

amino acids that have an accessory role in catalysis are called __ amino acids

A

active site

48
Q

when the pH > pka

A

unprotonated (basic)

49
Q

when the pH

A

protonated (acidic)

50
Q

the hydrophobic side chains are neither ___ nor ___, therefore water molecules cannot interact with them

A

charged; polar

51
Q

hydrophobic side chains typically do not take part in __ or __

A

interactions; chemical reactions

52
Q

amino acids mediate the interactions between what three pairs?

A
  1. protein–protein
  2. protein–nucleic acid
  3. Substrate–enzymes
53
Q

what 4 interaction types are used by amino acids?

A

van der waals, dipole-dipole, charge-charge, stacking

54
Q

what are essential amino acids?

A

amino acids which cannot be made and must be obtained from the diet

biochemistry 2065 (19 decks)

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