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Biochemistry > Chapter 4 > Flashcards

Chapter 4 Flashcards

1
Q

what biological macromolecules perform most biochemical functions and catalyze most biochemical reactions?

A

proteins

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2
Q

what are proteins made of? how linked?

A

amino acids linked by peptide bonds (aka polypeptides)

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3
Q

what size range are most proteins?

A

100-1000 amino acids long

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4
Q

what determines the structure of a protein?

A

the amino acid sequence

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5
Q

what determines the function of a protein?

A

the structure, determined by the amino acid sequence

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6
Q

what are residues?

A

amino acids within a polypeptide chain that are linked together

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7
Q

what are amino acids called by themselves?

A

amino acids (versus residues when they are linked together)

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8
Q

how many common amino acids are there?

A

20

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9
Q

how do amino acids differ?

A

by side chain (R group)

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10
Q

how many amino acid side chains are ionizable?

A

7

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11
Q

what are 3 ways that the side chain can contribute dofferences to an amino acid?

A
  1. polarity
  2. charge
  3. size
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12
Q

are amino acids chiral or achiral? what does this mean?

A

they are chiral; means alpha carbon is attached to 4 unique groups

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13
Q

what are the 4 unique groups that the chiral alpha carbon of an amino acid is attached to?

A
  1. amino grouo
  2. carboxyl group
  3. hydrogen
  4. side chain
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14
Q

what amino acid is the exception to the chiral rule and why?

A

glycine has a hydrogen side chain, so its alpha carbon is connected to 2 hydrogens, making it achiral

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15
Q

what are the 2 possible configurations of an amino acid? which one are natural amino acids always in?

A

L and D; natural amino acids are always in L form

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16
Q

Know the 3 letter and 1 letter names of all 20 amino acids

A

see flashcards!

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17
Q

what is a special property of aromatic amino acids? name property and the 3 aromatic amino acids

A

they can absorb and emit radiation
1. phenylalanine
2. tyrosine
3. tryptophan

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18
Q

what is a unique property of cysteine?

A

in can form disulfide bonds, which helps form tertiary and quarternary protein structures

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19
Q

what is a unique property of proline?

A

its backbone is fused to its sidechain, makes for kinky polypeptide chains ;)

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20
Q

what is a unique property of glycine?

A

its alpha carbon is NOT chiral!! (hydrogen is side chain)

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21
Q

give the levels of protein structure from smallest to largest (4)

A
  1. primary
  2. secondary
  3. tertiary
  4. quarternary
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22
Q

describe primary protein structure

A

the amino acid sequence; governs all subsequent structure levels

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23
Q

describe secondary protein structure

A

3D arrangement of polypeptide backbone into a few common structures

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24
Q

describe tertiary protein structure

A

folding and arrangement of secondary structures

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25
Q

describe quarternary protein structure

A

3D arrangement of separate polypeptide chains; the only structure level that involves multiple chains

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26
Q

what kind of reaction forms peptide bonds? give the 2 names

A

amino-carboxylate condensation aka dehydration synthesis

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27
Q

where does peptide bond formation take place?

A

in the ribosome

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28
Q

how can peptide bonds be broken? give general process then 2 examples

A

peptide bond hydrolysis
1. proteases
2. peptidases

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29
Q

what kinds of amino acids are used in acid/base catalysis?

A

ionizable amino acids

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30
Q

list the 7 ionizable amino acids

A
  1. aspartate (aspartic acid)
  2. glutamate (glutamic acid)
  3. tyrosine
  4. cysteine
  5. histidine
  6. lysine
  7. arginine
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31
Q

how many pKas do ALL amino acids have and why?

A

2; 2 for N terminus and 1 for C terminus

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32
Q

why does the N terminus have a higher pKa than the C terminus?

A

it has a more basic group than the carboxylic acid end

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33
Q

what is the net charge of an amino acid? what does it depend on?

A

the overall charge of a molecule; the sum of all charges; depends on pH

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34
Q

what is the isoelectric point?(pI)

A

the average pH at which a molecule has no net electrical charge

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35
Q

what is the pI governed by?

A

two pKas that create the neutral species

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36
Q

what does the pI form?

A

a zwitterion

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37
Q

what is a zwitterion?

A

electroneutral molecule that contains both positive and negative charges

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38
Q

what are the 3 steps for calculating the net charge of a peptide?

A
  1. find the ionizable groups
  2. determine the charge of each ionizable group at the given pH
  3. sum charges of all ionizable groups
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39
Q

give the 5 steps for calculating pI?

A
  1. find all ionizable groups
  2. sort pKa’s from lowest to highest
  3. determine net charges as pH increases (pH=0)
  4. once the net charge = 0, take pKa above and below current pH
  5. average the 2 pKas
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40
Q

what is the x axis value for the 1st pKa in a titration curve? how do all other pKas increase?

A

always 0.5, increase by 1.0 on x axis from there

41
Q

what are the 3 major types of secondary protein structures?

A
  1. alpha helix
  2. beta sheet
    3 beta turn
42
Q

what is protein folding caused by?

A

mostly due to noncovalent interactions

43
Q

are proteins still?

A

no! proteins are dynamic; always in motion

44
Q

describe the concept of local versus global conformational changes in proteins

A

local changes in residues lead to global changes in the whole protein

45
Q

what causes the secondary structures of proteins?

A

arrangements of local backbone regions

46
Q

what is key to the secondary structure of proteins?

A

hydrogen bonds of the backbone groups

47
Q

what way do alpha helices turn?

A

right handed

48
Q

how many residues are there per turn in an alpha helix (on average)?

A

3.6

49
Q

describe the bonds in an alpha helix

A

n to n+4h; backbone carbonyl oxygen hydrogen bonds with the backbone N-H 4 residues away

50
Q

give an example of an alpha helix bond

A

residue 237 and 241

51
Q

describe the side chain in an alpha helix

A

extend outward to reduce steric strain

52
Q

descibe the effects of charged side chains on alpha helices

A

can help or hurt
1. mix of positive and negative side chains attract and help maintain the helix
2. if all negative or all positive side chains will repel and break the helix

53
Q

describe the effects of bulky side chains on alpha helices

A

steric hindrance breaks the helix

54
Q

describe the effect of proline on an alpha helix and why

A

helix breaker (side chain fused to backbone)

55
Q

is glycine a good or bad helix maker? why?

A

bad helix maker because it has no side chain to interact in any way with other peptides

56
Q

why does the alpha helix have a dipole moment?

A

the resonance in the peptide bonds gives them a double bond character and rotation around the double peptide bond is impossible so the peptide backbone has a dipole moment (partial positive on Nterm and partial negative on Cterm), so the alpha helix has an overall dipole moment

57
Q

what is an amphipathic helix?

A

an alpha helix with one hydrophobic face and one hydrophilic face

58
Q

what are amphipathic helices good for? (2)

A
  1. gating (keeping the binding site inside and protectec)
  2. fat hydrolysis
59
Q

describe the beta strand secondary protein structure

A

extended polypeptide chains where the side chains extend above and below the backbone

60
Q

how are beta strand depicted

A

as an arrow where the point of the arrow points toward the c terminus

61
Q

describe the beta sheet secondary protein structure

A

beta strands arranged side-by-side

62
Q

how are beta sheets joined together?

A

hydrogen bonding occurs between strands, between the backbone N-H and the carbonyl O

63
Q

what are the 2 types of beta sheets? describe

A
  1. parallel: both strands run same direction
  2. antiparallel: strands run in opposite directions
64
Q

what is the beta turn secondary protein structure needed for?

A

anti-parallel beta sheets only

65
Q

describe the beta turn secondary protein structure (2)

A
  1. connects 2 adjacent segments of antiparallel beta sheets
  2. 4 residues long
66
Q

how are beta turns joined together?

A

residues 1 and 4 interact via hydrogen bonds (between C=O of residue 1 and N-H of residue 4)

67
Q

where do beta turns occur? what happens to residues 2 and 3?

A

occur in solvent-exposed regions, residues 2 and 3 hydrogen bond with water (the solvent)

68
Q

what makes secondary protein structures possible?

A

phi and psi dihedral angles

69
Q

what 4 atoms make the phi dihedral angle

A

amino nitrogen and alpha carbon, then the 2 carbons of each carbonyl

70
Q

what 4 atoms make the psi dihedral angle?

A

alpha carbon with carbonyl carbon, then the two amino nitrogens

71
Q

what 3 factors affect dihedral angles?

A
  1. steric interference has to be minimized (larger side chains may clash)
  2. H-bonding is maximized, as the carbonyl O is H-bond acceptor and amide N-H is H-bond donor
  3. the side chains present: proline’s phi angle is blocked
72
Q

what are ramachandran plots?

A

a plot of all phi and psi angles in a protein

73
Q

what shade do lower energy regions appear in a ramachandran plot?

A

darker

74
Q

what is the importance of a ramachandran plot?

A

different secondary structures exhibit the same phi and psi angles, so you can plot them to see what secondary structures exist in a peptide

75
Q

what do you have to know about ramachandran plots?

A

the general locations of secondary structures, go draw them NOW!!

76
Q

what is the tertiary structure of a protein?

A

the 3D shape of a protein including the backbone and side chains (folding); how the secondary structure is arranged

77
Q

what is the tertiary structure of a protein driven by?

A

hydrophobic effects

78
Q

what are the two main shapes of tertiary protein structures?

A

globular and fibrous

79
Q

describe globular protein shape

A

spherical

80
Q

describe globular protein solubility

A

soluble in water

81
Q

describe the core and exterior of globular proteins

A

hydrophobic core, hydrophilic exterior

82
Q

what kind of secondary structure types can globular proteins have?

A

several types

83
Q

give two common protein types that are often globular

A

enzymes and regulatory proteins

84
Q

describe the shape of fibrous proteins

A

rod shaped

85
Q

describe fibrous protein solubility

A

insoluble in water

86
Q

describe the secondaary structures found in fibrous proteins

A

usually one repeating element of secondary structure (house of many of the same brick)

87
Q

give a protein class that is often fibrous

A

structural proteins

88
Q

when referring to tertiary protein structures, what does domain mean?

A

separate structural unit of a protein

89
Q

when referring to tertiary protein structures, what does denaturation mean? how is this accomplished?

A

unfolding of a protein; through chaotropic agents and detergents

90
Q

when referring to tertiary protein structures, what does renaturation mean?

A

refolding of a protein to native state

91
Q

describe the beta barrel domain tertiary protein structure

A

a bunch of beta sheets combined

92
Q

describe the leucine zipper domain tertiary protein structure

A

leucines in between alpha helices

93
Q

describe the alpha/beta domain tertiary protein structure

A

alpha helices mixed with beta sheets

94
Q

how are domains held together?

A

cross-linking

95
Q

how is cross-linking accomploshed to hold together domains in tertiary protein structures? give 3 ways and describe

A
  1. ion pairs (salt bridges) such as acidic/basic side chains
  2. disulfides: two cysteine residues that interact after oxidation
  3. coordination around metals: zinc fingers (metal ion in betwene proteins)
96
Q

what is quarternary proetin structure?

A

the 3D assembly of all polypeptide chains

97
Q

what are the 2 prefixes to describe quarternary protein structure? describe

A
  1. homo: identical subunits
  2. hetero: different subunits
98
Q

how aare quarternary protein structures held together?

A

the same forces as tertiary (H-bonds, disulfides, ionic)

99
Q

what do quarternary protein structures allow for?

A

allow large proteins to be expressed separately

Biochemistry (20 decks)

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