Chapter 4 Flashcards
1
Q
what are peptide bonds
A
covalent linkages between amino acids
2
Q
peptide bonds form by condensation reactions involve…
A
the loss of a water molecule
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
4
Q
peptide bonds are the same, independent of…
A
the amino acids being joined
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
6
Q
the main chain is the _____ portion of the polypeptide, the side chains are the ____
A
constant, variable
7
Q
what is the main chain pattern
A
there is a repeating pattern of NCCNCC
8
Q
why is rotation of C-N peptide bonds restricted
A
due to its partial double-bond characteristic
9
Q
what is a consequence of the partial double bond characteristic
A
the six atoms of the peptide group are ridged and plainar
10
Q
what is a partial double bond
A
Partial double bond characters have the bond order between 1 and 2
11
Q
what does the partial double bond create
A
cis-trans isomers
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
13
Q
why is trans configuration favored over cis
A
cis is more likely to cause steric strain interference between side chain groups
14
Q
what does steric exclusion mean
A
that two groups cant occupy the sam space at the same time
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
16
Q
what is a secondary protein structure
A
its localized interactions within a polypeptide
17
Q
what is a tertiary protein structure
A
its the final folding pattern of a single polypeptide
18
Q
what is a quaternary protein structure
A
it is the the folding pattern when multiple polypeptides are involved
19
Q
do all proteins need to be quantinary structures
A
no in many proteins the tertiary structure is the highest structure
20
Q
if something has a more complex structure what would this indicate
A
a more complex biological function
21
Q
what structure is the information specifying correct folding contained
A
within the primary structure
22
Q
is it possible to reliable predict 3D structure based on primary structure
A
no, not yet
23
Q
how is primary structure often determined
A
through investigation of the corresponding gene
24
Q
what kind of bonds are secondary structures maintained by
A
hydrogen bonds between main chain amide and carbonyl groups
25
what are the kinds of structures that secondary structures can form
alpha helicies and and beta sheets
26
what are the characteristics of secondary structures in-context of the protein
they retain the same overall characteristics independent of the protein context
27
what are the two key rules of viable forms of secondary structures
they must:
-optimize the hydrogen bonding potental of main chain carbonyl and amide groups
-represent a favored conformation of the polypetide chain
28
what does each peptide bond have regarding secondary structure main chain H bonding groups
-a hydrogen bond doner and acceptor group
-equal number of hydrogen bond donors and acceptors within chin
29
in the main chain of amino acids what species acts as the hydrogen bond donor/acceptor
amine=donors
carboxyl=acceptors
30
each alpha carbon is held within the main chain through single bonds what are they defined as
Phi Ca-N and Psi Ca-C
(a means alpha a)
31
what bond hold the alpha c to the carbonyl
Psi Ca-C
32
what bond hold the alpha c to the NH
Phi Ca-N
33
how much can Phi and Psi bonds rotate
180 degrees
34
what interference prevents formation of most conformations
steric
35
what does ramachadran plots illustrate
-the possible combinatioins of phi and psi
-combinations of phi and psi that are actually observed in proteins are highlighted
36
what does the favored conformations of phi and psi correspond to
the common elements of secondary structures
37
who discovered alpha helix and how
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
38
how many amino acids does it take a right handed helix to make a turn
3.6 turns
39
what bonds stabilizes the alpha helix
hydrogen bonds
40
what way to the hydrogen bonds run to the axis of the helix
they run parallel
41
in a alpha helix carbonyl groups run towards the ____; amide groups to the _____
C-terminus, N-terminus
42
what is the H bonding pattern in a a-helix
n+4
43
in a alpha helix what way do alpha bond donors and acceptors point
h bond doners point up
h bond acceptors point down
44
what amino acids are you less likely to see in a a-helix
amino acids that have side chains that branch close to a carbon
i.g. valine, leucine, isolucine
45
what kind of amino acids do you not see in a-helix
ones that have side chains that have H bonding groups near a carbon
i.g. serine, threonine
46
what amino acids are you less likely to see in a a-helix and why
-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)
47
where can small electrical dipoles be found on a-helixes
the c terminus is slightly more negative dipole charge (carboxyl terminus)
the n terminus has partial positive dipole charge (amino terminus)
48
how are dipoles stabilized in a helixes
by residues at each termini whose charge opposes the helix dipole
49
what are some examples of amino acids that would be found at the N terminus
neg charges residues Asp, Glu, found at N terminus
50
what are some examples of amino acids that would be found at the C terminus
pos charges residues (Lys, Arg, His) at the C terminus
51
how many amino acids positions will separate residues on that same side of the a helix
three or four residues in the primary structure
52
how many residues need to separate amino acids for them to be on the opposite side of the a helix
two residues in the primary structure
53
what does the positioning of hydro phobic and philic residues within a primary structure do to a a-helix
it generates a amphipathic helix with polar and non polar faces
54
what would 2 amphipathic a helix do when they interact with each other
they will want to have both non polar regions against eachother
55
what does the properties of a a-helix determine
how they will want to behave with in context of a protein
56
how are b-sheets contructed
-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
what is the conformation of B strands
they are fully extended polly peptide chains
58
what is the H bonding pattern of Beta sheets
the are stabilized by hydrogen bonds between C double bond O and -NH on adjacent strands
59
what are the two forms that beta sheets can come in
they can come in parallel or anti parallel and they can be mixed
60
what is the construction of a parallel B sheet
the strands run in the same direction
61
what is the construction of the anti-parallel B sheet
the strands run in the opposite direction
62
what is more stable anti-parallel or parallel? and why
the anti parallel B sheet are more stable due to better geometry of H bonding
63
what is H bond straight dependent on
the geometery
64
does stronger always mean better when it comes to B sheets
no, stronger doesn't mean better.
just depends on the biological functions being preformed.
parallel will have greater flexability
65
how do side chains tend to connect on the polypeptide chain of a B sheet
they tend to alternate above and below the polypeptide chain
66
what does the alternating of polar and non polar residues within the primary structure in beta sheets result in
and amphipathic beta sheet
67
what determines the tertiary structure
the animo acid structure (primary structure)
68
how can a peptide chain of 250 amino acids have number 17 and 213 right beside eachother
because primary structures are far away but when folded into final tertiary conformation 17 and 213 can be right beside eachother
69
what does the stability of a protein reflect
the difference in the free energies of the folded and unfolded state
70
what interactions predominate in stabilizing protein structure
weak interactions
71
the protein with the lowest free energy (most stable) is usually the one with the max number of...
weak interactions
72
because protein folding is a rapid process what does this indicate
that proteins dont sample all possible folding patterns
73
what can protein folding be imagined as
a funnel where a large number of unstable conformations collapse to a single, stable folding pattern
74
some proteins spontaneously fold into their native conformations others require help from
chaperones
75
how do chaperones work
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
what kinds of molecules often require chaperones
larger, more complex molecules
77
why are chaperones also called heat shock proteins
they are induced by shock
78
how were chaperones descovered
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
what is denaturing of protein
it is the disruption of native conformation with loss of biological activity
80
how much energy is required for denaturalization
it is often small, perhaps only a few h bonds
81
what kind of a process is denatuization
a cooperative process
82
is denaturation permanent
no for many proteins it its reversible
83
why wouldn't you find a protein 35% unfolded
because once they fall apart they fall apart really fast
84
who are quaternary structures constructed
-the are made of multiple subunits in which each subunit is a separate polypeptide
-many involve multiple subunits of the same polypeptides
85
what bonds are quaternary protein structures associated through
non covalent interactions
86
what kind of biological function do quaternary structures have
more complex
87
how many polypeptide chains need to be involved with quaternary structures
2 or more (dont need to be 4)
88
what are some biological roles proteins play
-enzymes
-storage/transport
-physical cell support and shape
-mechanical movement (actin+myoglobin)
-decoding cell info (transcription factors)
-hormones and/or hormone receptors
-+more
89
do all organisms have the same amount of proteins
no, they all have different
90
how many protein does bacteria have
5000 (min # additional isoforms age generated through post translational modifications)
91
how many proteins do fruit flies have
16,000 (min # additional isoforms age generated through post translational modifications)
92
how many proteins do humans have
25,000 (min # additional isoforms age generated through post translational modifications)
humans may have up to a million different protein isoforms
93
how big are proteins typically
100 to 1000 amino acids long
200-600 is the norm
94
what is the smallest protein
51 amino acids is the smallest which is how many make up insulin
95
what is the largest protein that has been discovered
titin with an isoform containing 34,350 amino acids
96
how would you estimate the amount of amino acids in a protein
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
what are the 5 important facts of amino acids
-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
what are some fibrous proteins
keritan
collagen
silk
99
what does keratin make
its the principal component of hair, wool, horns, and nails
100
what is keratin like at a level of primary structure
it cantains a pseudo-seven repeat where positions a and d are hydrophobic residues
101
what secondary structure does keratin form
a alpha helix
102
what side of the a helix does the a and d end up on for keratin
the same face of the a helix resulting is a hydrophobic strip along the length of the helix
103
how would two helicies of karatin interact
by burring there hydrophobic faces together
104
what are coiled-coils
they are formed when two or more helicies entwine to form a stable structure
105
how does the coiled-coil of a keratin interact
it involves two right handed helicies wrapping around each other in a left handed fashion
106
what does the strength of keratin arise from
covalent likages of individual units into higher order structures
107
how are individual units of keratin linked together
through disulphide bonds
108
what is the difference between keratin in hair and in ryno horns
the amount of sufide bonds
109
how much protein of vertebrates is collagen
25% of total protein
110
what is the pattern of collagen at a primary level
it contains repeats of Gly-X-Y where X is offten proline
111
what does collagen do at a level of secondary structure
it forms a left handed helix of 3 residues per turn (as opposed to 3.6 residues/turn of a a-helix
112
what do the 3 left handed helices of collagen come together to form
a coiled-coil
the three left handed helicied wrap around eachother in a right handed fashion
113
where are the prolines on the coiled-coil of collogen
they are on the out side of the coiled-coil
114
what does the strangth of collogen arise from
the covalent linkages between the individual units into higher order structures
115
what covalent linkages does collagen use
these linkages occur form residues that undergo post translational modifacation (hydroxyproline, hydroxylysine)
116
how does more and more cross linkages occur in collagen
it occurs with age, accounting for the increasing brittle character of aging connectivity tissue and tougher meat
117
the covalent crosslinks of collagen involve...
post-translationally modified residues (hydroxyproline, hydroxylysine)
118
what do enzymes preforming post translational modified residues require
vitamin C
119
what if collagen does not have modified residues
it cant form the stabilizing crosslinks
120
what happens if you have a vitman C deficency
scurvy will lead to weakened structures of collagen which manifests in skin lesions, fragile blood vessels, bleeding gums, etc
121
how much of magellans crew was last to scurvy
around 80%
122
what are severe and mild symptoms of scurvy
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
how many uni students dont get enough vitaman C
10%
124
linus pauling proclamed that hight levels could... and what was the outcome
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
what can genetic disorders involving collagen and related connective tissue be associated with
they can be associated with brittle and abnormal bone structure, weakened cardiovascular capabilities, loose skin and joints, and hyper-flexability
126
who is niccolo paganini
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
how is silk produced and what is it used for
its produed by insects and spiders for formation of webs and cocoons
128
what is most silks primary structure like
has six residue repeat (GSGAGA)(GSGAGA)...
129
what is silk like at the level of secondary structure
its composed primarily from beta sheets
130
what does the silk have off Beta and what do they offer
fully extended polypeptides and they offer considerable strangth
131
what is on of the strongest known material on a cross section basis
silk
132
what things give silk its strength and flexibility
-fully extended polypeptide chains (strength)
-association of strands by hydrogen bonding (flexibility)
-association of sheets by van der waals and hydrophobic interactions (flexability)
133
why does spider silk have potential for medical applications
due to its enticing properties.
bu the exciting properties of silk are matched by challenges of its availability
134
what are some potential things that spider silk could be used for in medical applecation
sutures
nerve repair
bone repair
brain implants
artificial skin
knee replacement
135
what are prion diseases
a novel paradigm of infectious disease based on the misfolding of a self protein into a pathological, infectious protein
