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BMSC 200 > Chapter 4 > Flashcards

Chapter 4 Flashcards

1
Q

what are peptide bonds

A

covalent linkages between amino acids

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2
Q

peptide bonds form by condensation reactions involve…

A

the loss of a water molecule

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3
Q

what does the formation of peptide bonds eliminate

A

the alpha carboxyl and alpha amino charged groups which will be important for protein folding

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4
Q

peptide bonds are the same, independent of…

A

the amino acids being joined

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5
Q

how does the carboxyl and amine groups change when peptide bonds join

A

the carboxyl turns into a carbonyl
the CH3 looses 2 Hs

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6
Q

the main chain is the _____ portion of the polypeptide, the side chains are the ____

A

constant, variable

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7
Q

what is the main chain pattern

A

there is a repeating pattern of NCCNCC

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8
Q

why is rotation of C-N peptide bonds restricted

A

due to its partial double-bond characteristic

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9
Q

what is a consequence of the partial double bond characteristic

A

the six atoms of the peptide group are ridged and plainar

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10
Q

what is a partial double bond

A

Partial double bond characters have the bond order between 1 and 2

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11
Q

what does the partial double bond create

A

cis-trans isomers

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12
Q

what configuration are amino acids usally

A

the oxygen of the carbonyl group and the hydrogen of the amide nitrogen are usually trans to each other

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13
Q

why is trans configuration favored over cis

A

cis is more likely to cause steric strain interference between side chain groups

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14
Q

what does steric exclusion mean

A

that two groups cant occupy the sam space at the same time

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15
Q

what is a primary protein structure

A

-its the linear sequence of amino acids
-defines linear arangement of amino acids in polypeptides
-primary structure is presented from the N terminus to the C terminus

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16
Q

what is a secondary protein structure

A

its localized interactions within a polypeptide

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17
Q

what is a tertiary protein structure

A

its the final folding pattern of a single polypeptide

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18
Q

what is a quaternary protein structure

A

it is the the folding pattern when multiple polypeptides are involved

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19
Q

do all proteins need to be quantinary structures

A

no in many proteins the tertiary structure is the highest structure

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20
Q

if something has a more complex structure what would this indicate

A

a more complex biological function

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21
Q

what structure is the information specifying correct folding contained

A

within the primary structure

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22
Q

is it possible to reliable predict 3D structure based on primary structure

A

no, not yet

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23
Q

how is primary structure often determined

A

through investigation of the corresponding gene

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24
Q

what kind of bonds are secondary structures maintained by

A

hydrogen bonds between main chain amide and carbonyl groups

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25
Q

what are the kinds of structures that secondary structures can form

A

alpha helicies and and beta sheets

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26
Q

what are the characteristics of secondary structures in-context of the protein

A

they retain the same overall characteristics independent of the protein context

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27
Q

what are the two key rules of viable forms of secondary structures

A

they must:
-optimize the hydrogen bonding potental of main chain carbonyl and amide groups
-represent a favored conformation of the polypetide chain

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28
Q

what does each peptide bond have regarding secondary structure main chain H bonding groups

A

-a hydrogen bond doner and acceptor group
-equal number of hydrogen bond donors and acceptors within chin

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29
Q

in the main chain of amino acids what species acts as the hydrogen bond donor/acceptor

A

amine=donors
carboxyl=acceptors

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30
Q

each alpha carbon is held within the main chain through single bonds what are they defined as

A

Phi Ca-N and Psi Ca-C

(a means alpha a)

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31
Q

what bond hold the alpha c to the carbonyl

A

Psi Ca-C

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32
Q

what bond hold the alpha c to the NH

A

Phi Ca-N

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33
Q

how much can Phi and Psi bonds rotate

A

180 degrees

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34
Q

what interference prevents formation of most conformations

A

steric

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35
Q

what does ramachadran plots illustrate

A

-the possible combinatioins of phi and psi
-combinations of phi and psi that are actually observed in proteins are highlighted

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36
Q

what does the favored conformations of phi and psi correspond to

A

the common elements of secondary structures

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37
Q

who discovered alpha helix and how

A

linus pauling and he spent a day sick in bed reading detective stories and bored he began to doodle. he realized if you fold it the bonds line up

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38
Q

how many amino acids does it take a right handed helix to make a turn

A

3.6 turns

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39
Q

what bonds stabilizes the alpha helix

A

hydrogen bonds

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40
Q

what way to the hydrogen bonds run to the axis of the helix

A

they run parallel

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41
Q

in a alpha helix carbonyl groups run towards the ____; amide groups to the _____

A

C-terminus, N-terminus

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42
Q

what is the H bonding pattern in a a-helix

A

n+4

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43
Q

in a alpha helix what way do alpha bond donors and acceptors point

A

h bond doners point up
h bond acceptors point down

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44
Q

what amino acids are you less likely to see in a a-helix

A

amino acids that have side chains that branch close to a carbon
i.g. valine, leucine, isolucine

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45
Q

what kind of amino acids do you not see in a-helix

A

ones that have side chains that have H bonding groups near a carbon
i.g. serine, threonine

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46
Q

what amino acids are you less likely to see in a a-helix and why

A

-proline, because of rigidity, usually not found
-glycine, because of flexibility, uncommon
-amino acids with side chain branches (val, thr, lle) less common due to steric interference
-amino acids with H bonding groups near main chain (asp, asn, ser) less common
-charged residues tends to be positioned from favorable ion pairs (residue of opposite charged separated by 3-4 position)

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47
Q

where can small electrical dipoles be found on a-helixes

A

the c terminus is slightly more negative dipole charge (carboxyl terminus)
the n terminus has partial positive dipole charge (amino terminus)

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48
Q

how are dipoles stabilized in a helixes

A

by residues at each termini whose charge opposes the helix dipole

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49
Q

what are some examples of amino acids that would be found at the N terminus

A

neg charges residues Asp, Glu, found at N terminus

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50
Q

what are some examples of amino acids that would be found at the C terminus

A

pos charges residues (Lys, Arg, His) at the C terminus

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51
Q

how many amino acids positions will separate residues on that same side of the a helix

A

three or four residues in the primary structure

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52
Q

how many residues need to separate amino acids for them to be on the opposite side of the a helix

A

two residues in the primary structure

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53
Q

what does the positioning of hydro phobic and philic residues within a primary structure do to a a-helix

A

it generates a amphipathic helix with polar and non polar faces

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54
Q

what would 2 amphipathic a helix do when they interact with each other

A

they will want to have both non polar regions against eachother

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55
Q

what does the properties of a a-helix determine

A

how they will want to behave with in context of a protein

56
Q

how are b-sheets contructed

A

-they involve multiple B strands arranged side by side
-they are made up of B strands
-B sheets often involve 4 or 5 strands (can get longer)

57
Q

what is the conformation of B strands

A

they are fully extended polly peptide chains

58
Q

what is the H bonding pattern of Beta sheets

A

the are stabilized by hydrogen bonds between C double bond O and -NH on adjacent strands

59
Q

what are the two forms that beta sheets can come in

A

they can come in parallel or anti parallel and they can be mixed

60
Q

what is the construction of a parallel B sheet

A

the strands run in the same direction

61
Q

what is the construction of the anti-parallel B sheet

A

the strands run in the opposite direction

62
Q

what is more stable anti-parallel or parallel? and why

A

the anti parallel B sheet are more stable due to better geometry of H bonding

63
Q

what is H bond straight dependent on

A

the geometery

64
Q

does stronger always mean better when it comes to B sheets

A

no, stronger doesn’t mean better.
just depends on the biological functions being preformed.
parallel will have greater flexability

65
Q

how do side chains tend to connect on the polypeptide chain of a B sheet

A

they tend to alternate above and below the polypeptide chain

66
Q

what does the alternating of polar and non polar residues within the primary structure in beta sheets result in

A

and amphipathic beta sheet

67
Q

what determines the tertiary structure

A

the animo acid structure (primary structure)

68
Q

how can a peptide chain of 250 amino acids have number 17 and 213 right beside eachother

A

because primary structures are far away but when folded into final tertiary conformation 17 and 213 can be right beside eachother

69
Q

what does the stability of a protein reflect

A

the difference in the free energies of the folded and unfolded state

70
Q

what interactions predominate in stabilizing protein structure

A

weak interactions

71
Q

the protein with the lowest free energy (most stable) is usually the one with the max number of…

A

weak interactions

72
Q

because protein folding is a rapid process what does this indicate

A

that proteins dont sample all possible folding patterns

73
Q

what can protein folding be imagined as

A

a funnel where a large number of unstable conformations collapse to a single, stable folding pattern

74
Q

some proteins spontaneously fold into their native conformations others require help from

A

chaperones

75
Q

how do chaperones work

A

they bind to protein as its being produced until whole polypeptide has been produced then they let go. its away to delay the process until whole polypeptide has been produced

76
Q

what kinds of molecules often require chaperones

A

larger, more complex molecules

77
Q

why are chaperones also called heat shock proteins

A

they are induced by shock

78
Q

how were chaperones descovered

A

from bacteria. they realized that if they slowly tuned heat of for bacterias environment they could adapt. because the proteins could but if done to fast they died

79
Q

what is denaturing of protein

A

it is the disruption of native conformation with loss of biological activity

80
Q

how much energy is required for denaturalization

A

it is often small, perhaps only a few h bonds

81
Q

what kind of a process is denatuization

A

a cooperative process

82
Q

is denaturation permanent

A

no for many proteins it its reversible

83
Q

why wouldn’t you find a protein 35% unfolded

A

because once they fall apart they fall apart really fast

84
Q

who are quaternary structures constructed

A

-the are made of multiple subunits in which each subunit is a separate polypeptide
-many involve multiple subunits of the same polypeptides

85
Q

what bonds are quaternary protein structures associated through

A

non covalent interactions

86
Q

what kind of biological function do quaternary structures have

A

more complex

87
Q

how many polypeptide chains need to be involved with quaternary structures

A

2 or more (dont need to be 4)

88
Q

what are some biological roles proteins play

A

-enzymes
-storage/transport
-physical cell support and shape
-mechanical movement (actin+myoglobin)
-decoding cell info (transcription factors)
-hormones and/or hormone receptors
-+more

89
Q

do all organisms have the same amount of proteins

A

no, they all have different

90
Q

how many protein does bacteria have

A

5000 (min # additional isoforms age generated through post translational modifications)

91
Q

how many proteins do fruit flies have

A

16,000 (min # additional isoforms age generated through post translational modifications)

92
Q

how many proteins do humans have

A

25,000 (min # additional isoforms age generated through post translational modifications)
humans may have up to a million different protein isoforms

93
Q

how big are proteins typically

A

100 to 1000 amino acids long
200-600 is the norm

94
Q

what is the smallest protein

A

51 amino acids is the smallest which is how many make up insulin

95
Q

what is the largest protein that has been discovered

A

titin with an isoform containing 34,350 amino acids

96
Q

how would you estimate the amount of amino acids in a protein

A

dividing the molecular weight of the protein by 110 (average weight of an AA)

i.g. horse myoglobin molecular weight: 16,890
16,890/110=153.55 (actual residues=153)

97
Q

what are the 5 important facts of amino acids

A

-the function of a protein depends on structure
-the 3D structure is determined by its amino acid sequence
-non covalent forces are the most important forces stabilizing protein structures
-within a huge number of unique protein structures there are common structural patterns
-an isolated protein usually exists in one or a small number if structural forms

98
Q

what are some fibrous proteins

A

keritan
collagen
silk

99
Q

what does keratin make

A

its the principal component of hair, wool, horns, and nails

100
Q

what is keratin like at a level of primary structure

A

it cantains a pseudo-seven repeat where positions a and d are hydrophobic residues

101
Q

what secondary structure does keratin form

A

a alpha helix

102
Q

what side of the a helix does the a and d end up on for keratin

A

the same face of the a helix resulting is a hydrophobic strip along the length of the helix

103
Q

how would two helicies of karatin interact

A

by burring there hydrophobic faces together

104
Q

what are coiled-coils

A

they are formed when two or more helicies entwine to form a stable structure

105
Q

how does the coiled-coil of a keratin interact

A

it involves two right handed helicies wrapping around each other in a left handed fashion

106
Q

what does the strength of keratin arise from

A

covalent likages of individual units into higher order structures

107
Q

how are individual units of keratin linked together

A

through disulphide bonds

108
Q

what is the difference between keratin in hair and in ryno horns

A

the amount of sufide bonds

109
Q

how much protein of vertebrates is collagen

A

25% of total protein

110
Q

what is the pattern of collagen at a primary level

A

it contains repeats of Gly-X-Y where X is offten proline

111
Q

what does collagen do at a level of secondary structure

A

it forms a left handed helix of 3 residues per turn (as opposed to 3.6 residues/turn of a a-helix

112
Q

what do the 3 left handed helices of collagen come together to form

A

a coiled-coil
the three left handed helicied wrap around eachother in a right handed fashion

113
Q

where are the prolines on the coiled-coil of collogen

A

they are on the out side of the coiled-coil

114
Q

what does the strangth of collogen arise from

A

the covalent linkages between the individual units into higher order structures

115
Q

what covalent linkages does collagen use

A

these linkages occur form residues that undergo post translational modifacation (hydroxyproline, hydroxylysine)

116
Q

how does more and more cross linkages occur in collagen

A

it occurs with age, accounting for the increasing brittle character of aging connectivity tissue and tougher meat

117
Q

the covalent crosslinks of collagen involve…

A

post-translationally modified residues (hydroxyproline, hydroxylysine)

118
Q

what do enzymes preforming post translational modified residues require

A

vitamin C

119
Q

what if collagen does not have modified residues

A

it cant form the stabilizing crosslinks

120
Q

what happens if you have a vitman C deficency

A

scurvy will lead to weakened structures of collagen which manifests in skin lesions, fragile blood vessels, bleeding gums, etc

121
Q

how much of magellans crew was last to scurvy

A

around 80%

122
Q

what are severe and mild symptoms of scurvy

A

mild cases cause fatigue, irritability, and susceptibility to illness

severe cases are numerous bruses, tooth loss, poor wound healing, bone pain and eventually even heart failure

123
Q

how many uni students dont get enough vitaman C

A

10%

124
Q

linus pauling proclamed that hight levels could… and what was the outcome

A

help avoid colds, cure cancer, and prolong life

trails showed no tharaputic value. instead individuals who took mega doses of vitamin C were more likely to develop cancer

125
Q

what can genetic disorders involving collagen and related connective tissue be associated with

A

they can be associated with brittle and abnormal bone structure, weakened cardiovascular capabilities, loose skin and joints, and hyper-flexability

126
Q

who is niccolo paganini

A

the greatest violinist to ever live
he was really good at playing because its belived he had marfans syndrom resulting in hyper extendable joints allowing him to play music beyond range of “normal individuals”

127
Q

how is silk produced and what is it used for

A

its produed by insects and spiders for formation of webs and cocoons

128
Q

what is most silks primary structure like

A

has six residue repeat (GSGAGA)(GSGAGA)…

129
Q

what is silk like at the level of secondary structure

A

its composed primarily from beta sheets

130
Q

what does the silk have off Beta and what do they offer

A

fully extended polypeptides and they offer considerable strangth

131
Q

what is on of the strongest known material on a cross section basis

A

silk

132
Q

what things give silk its strength and flexibility

A

-fully extended polypeptide chains (strength)
-association of strands by hydrogen bonding (flexibility)
-association of sheets by van der waals and hydrophobic interactions (flexability)

133
Q

why does spider silk have potential for medical applications

A

due to its enticing properties.
bu the exciting properties of silk are matched by challenges of its availability

134
Q

what are some potential things that spider silk could be used for in medical applecation

A

sutures
nerve repair
bone repair
brain implants
artificial skin
knee replacement

135
Q

what are prion diseases

A

a novel paradigm of infectious disease based on the misfolding of a self protein into a pathological, infectious protein

BMSC 200 (10 decks)

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