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BIOCHEM 200 > 3 - Protein Structure And Function > Flashcards

3 - Protein Structure And Function Flashcards

1
Q

Function of a protein is determined by

A

Structure

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2
Q

Components of an amino acid

A
  • amino group (H3N+)
  • carbonyl group (—COO-)
  • H atom
  • R group (side chain)
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3
Q

Titration curve for weak acid

A

—COOH ——-> (—COO-) + H+

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4
Q

PKa =

A

PH at which the group is 50%:50% weak acid and conjugate base.

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5
Q

If pH is > 1 above or below the titration curve for weak acids, it means that

A
  • If its above, it mostly conjugate base

- if its below, it mostly weak acid

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6
Q

At what pH will half the solution be of something, and the other half be of another form?

A

Ph= ~7

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7
Q

The ionization state of amino acids is altered by a change in

A

pH

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8
Q

At physiological pH, what form will carbonyl and amino be in?

A

Carbonyl = —COO-

Amino - —H3N+

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9
Q

Are amino acids achiral?

A

NO they are chiral

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10
Q

What kind of stereoisomer are amino acids? What properties

A

They are enantiomers,

  • mirror images
  • non superimposable
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11
Q

What does chiral mean

A

4 diff substituents

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12
Q

What are the three categories of amino acids

A

1) non polar/hydrophobic 8#
2) polar (H-bonding possible) 8#
3) charged (ionizable) 4#

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13
Q

What does it mean for an amino acid to be charged

A

It’s ionized

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14
Q

Are all the amino acids chiral

A

NO, glycine’s is the only one that isnt

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15
Q

What are the hydrophobic side chains properties

A
  • Hydrophobic (C,H)
  • aromatic
  • non polar
  • aliphatic And/or cyclic
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16
Q

What are the hydrophobic/non polar amino acid side chains?

A

1) alanine, Ala
2) valine, Val
3) phenylalanine, Phe
4) thyrophan, Trp
5) leucine, Lue
6) isoleucine, Ile
7) methionine, Met
8) Proline, Pro

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17
Q

Alanine

A

Ala,

  • aliphatic
  • non polar / hydrophobic
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18
Q

Valine

A

Val,

  • highly hydrophobic
  • aliphatic hydrocarbon
  • impacted by hydrophobic effect and therefore hydrophobic
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19
Q

Leucine

A

Leu,

  • 4 C atoms (large bulky)
  • aliphatic
  • non polar
  • highly hydrophobic
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20
Q

Isoleucine

A

Ile,

  • 4 C atoms
  • aliphatic
  • highly bulky and large
  • highly hydrophobic
  • 2 chiral carbons
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21
Q

Phenylalanine

A

Phe,

  • very badly rigid
  • aromatic, NOT aliphatic
  • absorbs UV light at 260nm
  • highly hydrophobic
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22
Q

Tryptophan

A

Trp,

  • bulky, rigid
  • aromatic
  • absorbs U.V at 260nm
  • hihgly hydrophobic
  • the HN in the aromatic 5 membered ring can potentially be a H bond donor
  • 5 membered ring + 6 membered ring
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23
Q

Methionine

A

Met,

  • aliphatic, non polar
  • hydrophobic
  • contains thioether. (C-S-C)
  • S could potential be a H bond acceptor
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24
Q

Proline

A

Pro,

  • aliphatic, cyclic
  • distorted geometry around alpha carbon
  • non polar, hydrophobic
  • internally cyclized
  • amino is H2N and NOT H3N+.
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25
Q

What are all the polar side chains

A

1) serine, Ser
2) Theonine, Thr
3) tyrosine, tyr
4) cysteine, Cys
5) asparagine, Asn
6) glutamine, Gln
7) histidine, His
8) glycine, gly

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26
Q

Glycine

A

Gly,

  • only amino acid that isnt chiral = its achiral
  • smallest side chain
  • good for small spaces for polar folding
  • weakly polar - can be surface of protein (in contact with H2O)
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27
Q

Serine

A

Ser,

  • polar
  • H-bond donor
  • contains primary alcohol
  • OH can carry phosphate group sometimes
  • not ionizable (can’t be —O-)
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28
Q

Threonine

A

Thy,

  • polar
  • H-bond donor
  • secondary alcohol
  • can have phosphate attached sometimes
  • non ionizable (—O-)
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29
Q

Tyrosine

A

Tyr,

  • primary alcohol on 6 membered ring (polar)
  • the alcohol can be potential H bond donor
  • absorbs light at 280nm
  • highly hydrophobic (ring)
  • can have phosphate group attached sometimes
  • ionizable —> (—O-)
  • PKa = 10,
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30
Q

What’s the pKa of tyrosine and what does it mean

A

PKa = 10

  • therfore midpoint is 10 where 50% is ionized and the other 50% isnt ionized
  • ionization more likely when buried in hydrophobic environment with no H2O
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31
Q

Cysteine

A

Cys,

  • contains sulfur
  • reactive cuz its ionizable
  • thiolate ion
  • pKa =8.5
  • reactivity = formation of cystine
  • HS— cna be both H bond donor and ecceptor
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32
Q

Cystine

A

Cysteine — S—S—cysteine

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33
Q

What kind of bonds does cystine held by

A

Disulphides bridge

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34
Q

Disulphides bridges are

A
  • highly non polar

- entire side chain is now non polar when turns cystine

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35
Q

What happens to polarity when cysteine turns into cystine?

A

Becomes entirely non polar

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36
Q

What kind of bond binds S-S in cystine?

A

Strong covalent bond that formed between 2 ionizable cystines

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37
Q

Asparagine

A

Asn,

  • amide
  • hihgly polar
  • non ionizable
  • H-bond acceptor (carbonyl) and donor (amino)
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38
Q

Glutamine

A

Gln

  • amide
  • highly polar
  • forms H-bonds
  • non ionizable
  • carbonyl (acceptor)
  • amino (donor)
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39
Q

Histidine

A

His,

  • aromatic
  • absorbs UV at 280nm
  • polar
  • ionizable
  • pKa = 6
  • highly reversible ionization as charged/uncharged equilibrium
  • can act as acid or base
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40
Q

Whihc polar amino acids contains alcohols?

A

Serine, threonine, and tyrosine

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41
Q

Whihc polar amino acids are ionizable?

A

Tyrosine, cysteine, histidine

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42
Q

Whihc polar amino acids contains amide group (H2N)

A

Asparagine, glutamine, histidine

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43
Q

What are the pKa values for the polar amino acids?

A

Tyrosine - pKa = 10
Cysteine - pKa = 8.5
Histidine - pKa= 6.5

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44
Q

Which amino acids contains sulfur atom?

A

Cysteine

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45
Q

What are the charged side chains

A

Acidic structure:

  • aspartate, Asp
  • Glutamate, glu

Basic structure:

  • lysine, lys
  • arginine, arg
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46
Q

Aspartate

A

Asp,

  • salt bridge
  • forms H-bonds
  • hihgly polar
  • charged (-)
  • formation of conjugate base favoured at ph7
  • pKa = 4
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47
Q

At ph = 1, aspartate will be in what form?

A

Weak acid form

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48
Q

Glutamate

A

Glu,

  • very polar
  • salt bridge
  • charged (-)
  • ## formation of conjugate base formed at ph=7
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49
Q

What form will glutamate be in ph=1

A

Weak acid form

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50
Q

Lysine

A

Lys,

  • primary amide
  • polar
  • Hbonds
  • salt bridge
  • charged (+)
  • pKa = 10.5
  • formation of weak acid formed at ph = 7
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51
Q

Arginine

A

Arg,

  • aliphatic, non polar region
  • very polar
  • H-bonds
  • always (-) charged
  • pKa = 12.5
  • bulky
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52
Q

Is arginine ever not charged?

A

No its always charged (-)

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53
Q

What is primary structure?

A

The sequence of amino acids joined by peptide bonds and phosphodiester bonds

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54
Q

What kind of bonds are peptide bonds

A

Covalent bonds

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55
Q

Formation of peptide bonds occurs via

A

Nucleophilic attack between 2 amino acids to form peptide bond to bind them together,

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56
Q

Each amino acid in a dupe-tide is referred to as?

A

Residue

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57
Q

What is the sequence for a peptide bond?

A

O=C-N-H

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58
Q

A peptide bond is also an

A

Amide bond

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59
Q

Dipeptide, tropeptide, tetrapeptide

A

2,3,4 amino acid residues joined together via peptide bonds

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60
Q

N-terminus is always ____ and on the _____

C-terminus is always ____ and on the _____

A

N-terminus is always (+) and on the left

C-terminus is always (-) and on the right

61
Q

( amide ) joines the

A

alpha carboxyl group of one amino acid to the alpha amino group of another amino acid.

62
Q

• this sequence of amino acids is unique to each

A

gene product / polypeptide —-> unique function.

63
Q

Peptide bonds have distinct chemical characteristics

A
  • partial double bond character
64
Q

Partial double bond character

A

Not a true double bond but has double bond character in that it cannot rotate.

  • polar
  • H Bonding
65
Q

The amino group is always the H bond _____

The carbonyl group is always the H bond ____

A

The amino group is always the H bond donor

The carbonyl group is always the H bond acceptor

66
Q

Peptide bonds are flexible or rigid

A

rigid and planar

67
Q

Polypeptide backbone strucure sequence

A

N-Ca(R)-C(=O)-N

68
Q

Whihc bonds in the polypeptide backbone can and cannot rotate

A

N-Ca = can rotate

Ca-Cc = can rotate

Cc-N = polypeptide bond and had partial double bond character so CANNOT ROTATE

69
Q

In the polypeptide backbone, whihc bond is the peptide bond?

A

Cc-N

70
Q

Why is the rotation of polypeptide backbone limited?

A

Because of the steric hindredness and O atoms.

71
Q

What is Secondary structure

A

Folding of polypeptide backbone

72
Q

Regular patterns of secondary structure

A

Alpha-helixes

Beta-sheets

73
Q

Within each peptide bond there is a

A

H bond Acceptor (O=C) and donor (N-H)

74
Q

What bond connects two peptides together

A

H bond between H form (N-H) and O form (O=C)

75
Q

Secondary structure is all about folding of the

A

backbone and putting the peptide bonds in positions so that they can form H-bonds with one another.

76
Q

Alpha - helixes

A
  • right handed
  • H-bonding between peptide bonds
  • H-bond between carbonyl atom of C1 and H of amino of N5.
  • H-bond between carbonyl atom of C2 and H of amino of N6.
  • H-bond between carbonyl atom of C3 and H of amino of N7.
  • first 4 amino groups and last 4 carbonyl groups are excluded from H-bonding. Because peptide has limited length.
77
Q

Side chains of alpha helix

A
  • sidechains outside
  • ## backbone polypeptide (right handed)
78
Q

Why are side chains in alpha helix outside?

A

Because they of the right handed polypeptide backbone

79
Q

Alpha helix secondary structure is stabilized by

A

H-bonding of the polypeptide backbone and not in the side chains

80
Q

Proline is

A

Cyclic

81
Q

Why is proline alpha helix different

A
  • cuz of distorted backbone geometry = doesnt allow for regular structure to form in alpha helix
82
Q

Because proline has distorted backbone structure its known as a

A

Helix disrupter = backbone turns

83
Q

Polypeptide chains have a sense of

A

direction

N————> C
Right —-> left

84
Q

What are the two different ways of aligning polypeptide backbone?

A

Parallel and anti parallel

85
Q

Antiparallel

A

N—->C
CC
C

86
Q

Parallel

A

N—> C
N—> C
N—> C
N—> C

  • long irregular loops connecting C to N going all the way around
87
Q

Parallel B-sheets

A
  • donor and acceptors alternate throughout sequence
  • held together by H-bonds between peptide bonds
  • very long irregular loops
  • stabilized by H-bonding b/w peptide bonds
  • H-bonds in parallel B-sheet are at an angle.
88
Q

Antiparallel B-sheets

A
  • Have 180 degree irregular loops

- perpindicular H-bonds (upright, no angle)

89
Q

Between the polypeptide backbones going in opposite directions for B-sheets, what bonds are between them?

A

H-bonds

90
Q

Irregular secondary structure

A

loops
- not flexible, have specific position
-

91
Q

In alpha helix and B-sheets, where are the H-bonds located

A
  • alpha helix: it’s between groups IN THE SAME HELIX.

* beta-sheets: it’s between backbone groups of neighbouring strands.

92
Q

Both alpha helixes and b-sheets have conformations that require specific

A

angles of rotation around the peptide bond.

93
Q

Both a-helices and B-sheets form only from sequential

A

amino acid residues in the polypeptide.

94
Q

What is tertiary structure?

A

3D, space filling arrangement of all the atoms in space

95
Q

Tertiary structures feature what?

A
  • 3d arrangement of ALL atoms to all other atoms
  • arrangement of secondary structure
  • arrangement of sidechains
  • prosthetic groups arrangement
96
Q

Proteins can be either

A

Fibrous or globular

97
Q

Fibrous proteins

A

“Filaments”
- connective tissue, tendon, muscle, bond

  • B-sheets layered on top of each other
  • alpha helixes
98
Q

Globular proteins

A

Spherical

  • functional proteins
  • enzymes
  • transporters
  • receptors
99
Q

Secondary structure within globular proteins is

A

varied.

Meaning they could have helixes only or B-sheets only or both, with or without irregular loops.

100
Q

Hydrophobic residues are generally located

A

“inside” soluble-globular proteins

101
Q

In proteins, where are hydrophilic R groups located, and where are hydrophilic R groups located

A
  • Hydrophobic R groups (aliphatic, aromatic) located inside structure
  • hydrophilic R groups (polar, charged) located on surface
102
Q

a-helix and B-sheet secondary structure is generally located in the

A

interior of folded proteins

103
Q

Where are irregular loops located and why

A

The H bonding capacity of the polypeptide backbone in irregular loops is not fully satisfied, and so these sequences interact with water at the surface.

104
Q

In the polypeptide, whihc groups aren’t involved in H-bonding

A

The first 4 amino and last 4 carbonyl

105
Q

Regular secondary structure is generally found in the

A

interior of folded proteins

106
Q

Are a-helixes amphipathic or aliphatic?

A

Amphipathic

107
Q

The polar and non polar sidechains in the a-helix are where in the secondary structure?

A

Non polar sidechains stay inside, and polar sidechains stay outside

108
Q

Why is it important for non polar side chains to remain inside protein structure and polar to remain outside?

A

To keep hydrophobic interaction inside protein to keep it stabilized

109
Q

What drives protein folding?

A

Hydrophobic effect

110
Q

How does the hydrophobic effect drive protein folding?

A

It causes the hydrophobic side chain to cluster so they dont interact with H2O. Causing the structure to fold keeping the non polar regions inside.

111
Q

Sometimes during protein folding, what is put sindie besides non polar sidechains

A

Polar side chains

112
Q

Salt bridge occurs between

A

O(-) and N(+) of the O-O(-) and H3N(+)

  • between charged amino acids
113
Q

Disulphides bridges are

A

Covalent

114
Q

Disulphide bridges enhance the stability of

A

3D tertiary structures in extracellular proteins ONLY (NOT cytosolic)

115
Q

Disulphide bridge occurs between what amino acids ?

A

Cys-84 and Cys-26

CH2-S-S-CH2 (cystine) has Disulphide bridges

116
Q

Polar amino acids in the hydrophobic core of a globular protein are usually involved in either

A

H-bonding or ion pairs.

117
Q

H-bonding and formation of salt bridges are enhanced when

A

Amino acids are buried in hydrophobic environment so that no H2O gets in.

118
Q

Having polar regions inside the protein sometimes is good or bad? Why?

A

GOOD

Because it magnifies the ionization of certain amino acids

119
Q

Which Amino acids are ionized when polar regions are inside the hydrophobic core?

A

Cys and thr, both becomes (-) charged

120
Q

Tertiary structure may include

A
  • domains
  • motifs
  • prosthetic groups
121
Q

Domain:

A

an independent folded 3D structure within a single polypeptide

122
Q

Each domain has its own

A

Hydrophobic core

123
Q

What kind of bonds are between Domains?

A

Covalent bonds

124
Q

What stabilized domains ?

A

Hydrophobic effect

125
Q

Pyruvate kinase

A

Has 3 domains within its tertiary structure

  • 3 hydrophobic cores.
126
Q

A domain is entirely dependant on the

A

unique amino acid sequence of any given protein.

127
Q

Prosthetic group:

A

a non protein, organic molecule,
• Permenant part of the 3D structure tertiary structure.
• Absolutely required for function.
• Provide additional chemical reactivity.

128
Q

MOTIF:

A

A short region that is a recognizable, common pattern or arrangement of secondary structure elements and/or specific amino acid side chains within a domain

129
Q

Example of a motif ?

A

Zn finger

130
Q

Zinc finger

A
  • Common transcription factor for binding
  • contains a-helix and antiparallel b-sheets with 180 irregular loops
  • central cavity with Zn2+ ion held tightly in with coordination bonds
131
Q

Example of prosthetic group

A

Heme in hb and Mb

132
Q

What drives tertiary structure

A

Hydrophobic effect?

133
Q 
Which of the following do you think affects the stability of protein tertiary structure the most?
A. salt concentration 
B. pH 
C. temperature 
D. detergent
A

D. detergent

134
Q

Why does detergent have the most impact on the stability of tertiary structure?

A

Because it solubilized the hydrophobic groups and sit-ups the hydrophobic effect.

135
Q

How does salt concetration effect tertiary structure

A

effecting the formation of salt bridges

136
Q

How does temperature effect tertiary structure

A

Effects the possibility of forming hydrophobic interactions (van der waal), H-bonds, and salt bridges

137
Q

How does ph effect tertiary structure

A

Effects the possibility of forming H-bonds and salt bridges.

138
Q

What determines the tertiary structure?

A

Sequence of amino acids (primary structure)

139
Q

Prion Folding & Misfolding

A

Prion is infectious protein that induces misoflding

140
Q

Prion effects

A
  • increases B-sheets
  • decreases a-helixes
  • loops change
  • flips into infectious state
  • causes mad cow disease
141
Q

A NORMAL prion protein has mostly what’s

A

A-helixes and irregular loops

142
Q

Disulphide bonds are covalent and it requires a _______ to break them

A

reduction reaction

143
Q

WHAT KIND OF REACTION FORMS DISULPHIDE BRIDGES?

A

OXIDATION

144
Q

What is Quartenary structure

A

Required more then 1 polypeptide subunit

145
Q

What is quartenary strcure stabilized by?

A

Non covalent bonds

146
Q

Heterodimer and homodimer

A

Heterodimer: has two different kinds of polypeptide units, therfore 2 different genes

Homodimer: single kind of polypeptide unit, so identical gene

147
Q

Which of the following statements about quaternary structure is TRUE?

A. Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four subunits.

B. Quaternary structure exists where a protein contains more than one domain.

C. Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.

D. Quaternary structure requires covalent interactions such as disulphide bridges between polypeptide chains

A

C. Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.

148
Q

In the quartenary effect, what drives the association of the subunits?

A

Hydrophobic effect.

BIOCHEM 200 (4 decks)

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