BMSC 200 > Module 4: The Three Dimensional Structure of Proteins > Flashcards

Module 4: The Three Dimensional Structure of Proteins Flashcards

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1
Q

how are peptide bonds linked

A

covalent linkages between alpha carbon carboxyl and alpha carbon groups of two amino acids

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2
Q

what type of reactions form peptide bonds

A

condensation reactions

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3
Q

what is generated by condensation reactions

A

water

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4
Q

will different residue cause different peptide bonds

A

no, peptide bonds are the same independent of the residues being joined

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5
Q

what is eliminated during peptide bonds

A

the charged a-carboxyl and a-amino groups

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6
Q

what is the repeating pattern of the main chain in peptide bonds

A

NCCNCC

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7
Q

what restricts the rotation C-N peptide bonds

A

due to partial double bond characteristics
cis-trans isomers

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8
Q

what is the characteristics of the 6 atom peptide group

A

rigid and planar

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9
Q

what does the partial double bond of the peptide bond create

A

cis-trans isomers

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10
Q

what atoms are usually trans to each other in peptide bonds

A

the oxygen of the carbonyl group and the hydrogen of the amide group

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11
Q

what does the cis conformation of peptide bonds more likely to cause

A

steric interference between side chains

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12
Q

steric exclusion

A

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

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13
Q

primary structure

A

the linear sequence of amino acids

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14
Q

secondary structure

A

the localized interactions within a polypeptide

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15
Q

tertiary structure

A

the final folding pattern of a single polypeptide

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16
Q

quaternary structure

A

the folding pattern when multiple polypeptides are involved

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17
Q

how are primary structure presented

A

from N terminus to C terminus

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18
Q

where is the information specifying correct folding located

A

in the primary strcuture

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19
Q

is it possible to predict the three dimensional structure based on primary structure

A

yes theoretically, but very difficult

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20
Q

how is primary structure determined

A

through investigation of the corresponding gene
codon- amino acid relationship

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21
Q

how are secondary structures maintained

A

by hydrogen bonds between amide and carbonyl groups of the main chain

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22
Q

two key rules of secondary structures

A

optimize the hydrogen bonding potential of main-chai carbonyl and amide groups
represent a favored conformation of the polypeptide chain

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23
Q

2 points of main chain hydrogen bonding groups in secondary structure

A
  • each peptide bond has a hydrogen bond donor and acceptor group
    -equal numbers of h-bond donors and acceptors in the main chain
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24
Q

how are alpha carbon held to the main-chain

A

through single bonds which have complete freedom of rotation

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25
what is the range for phi and psi
-180 - 180 but steric interference prevents the formation of many conformations
26
phi and psi
define the single bonds of alpha carbons in the main chainr
27
how are combinations of phi and psi visualized
Ramachadran plots
28
how do hydrogen bonds run in alpha helix
parallel
29
what stabilizes the alpha helix
hydrogen bonds
30
alpha helix
right handed helix with 3.6 residues/turn
31
where do carbonyl and amide groups point in alpha helixs
carbonyl toward C terminus and amide groups toward N terminus
32
what will carbonyl group of residue n bond with
amide group of residue n + 4
33
what two amino acids are very uncommon in alpha helixs and why
proline because of its rigidity glycine because of its flexibility
34
what amino acids are less common in alpha helixes do to steric interference
Val, Thr, Ile
35
what amino acids are less common in alpha structures due to hydrogen bonding groups near the main chain
Ser, Asp, Asn
36
how are charged residues tend to be positioned
to form favorable ion pair residues of opposite charge are separated by 3-4 positions
37
what is the helix dipole
every peptide has a small electrical dipole each dipole communicated through helix has a net dipole
38
partial charges on N and C terminus
N terminus has a partial positive C terminus has a partial negative
39
how are helix dipoles stabilized at each termini
by residues whose charge oppose the helix dipole
40
how is the N terminus stabilized
negative residues Asp, Glu
41
how is the C terminus stabilized
positively charged residues Lys, Arg, His
42
how will residues seperated by 3 or 4 positions in the primary sequence be positioned in alpha helix
on the same side
43
how will residues separated by 2 residues in the primary structure be located in the alpha helix
will be on opposite sides
44
how are amphipathic helicies made
positioning of hydrophobic and hydrophilic residues within the primary structure generates an amphipathic helix with polar and non polar faces
45
how many beta strands are beta sheets made out of
often 4 or 5 strands
46
what is the conformation of beta sheets
fully extended polypeptide chains
47
how are beta sheets stabilized
by hydrogen bonds between C=O and -NH on adjacent strands
48
are parallel of anti-parallel beta sheets more stable
anti-parallel beta sheets are more stable due to better geometry of hydrogen bonding
49
mixed beta sheets
contain parallel and antiparallel beta strands
50
amphipathic beta sheets
side chains tend to alternate above and below the polypeptide chain -alternating polar and non-polar residues within the primary structure of a beta sheet will result in an amphipathic beta sheet
51
tertiary structure
final folding pattern of a polypeptide -different proteins have different tertiary structures which relates to different functions -describe the long-range aspects of sequence interaction within a polypeptide
52
what determines tertiary structure
primary structure
53
native conformation
biological active folding pattern
54
what is stability defined as in tertiary structures
tendency to maintain a native conformation
55
what mostly stabilizes proteins
weak interactions
56
what does the stability of a protein reflect
the difference in the free energies of the folded and unfolded states
57
what does the rapid folding of proteins indicate
proteins don't sample all possible folding patterns
58
what can protein folding be imagined as
a funnel -many unstable conformations collapse to a single, stable folding pattern
59
denaturation of proteins
the disruption of native conformation with loss of biological activity cooperative low energy required reversible
60
quaternary structure
involves multiple polypeptide -may be the same or different polypeptides -subunits formed by each polypeptide usually associate through non-covalent interactions - usually reserved for proteins of more complex biological function
61
biological advantages of quaternary structures
-may help stabilize subunits and prolong life of protein -unique active sites produced at the interface between subunits -help facilitate unique and dynamic combinations of structure/function through physiological changes in tertiary structure and quaternary structure -conservation of functional subunits more efficient than selection for new protein with ideal function
62
size of proteins
100-100 amino acids smallest is insulin with 51 amino acids largest id Titin with 34 35o amino acids
63
how to find number of amino acids
divide protein molecular weight by 110
64
five important facts about proteins
-the function of a protein depends on structure -the three dimensional structure of a protein is determined by its amino acid sequence - non-covalent forces are the most important forces stabilizing protein structure -within the huge number of unique proteins structures, there are common structural patterns -an isolated protein usually exist in one, or in a small number, of structural forms
65
fibrous proteins
keratin, collagen, silk
66
globular proteins
myoglobin and hemoglobin
67
primary structure of keratin
pseudo seven repeat where position a and d are hydrophobic residues
68
secondary structure of keratin
alpha helix -residues a and d end up on the same face of the helix resulting in a hydrophobic strip along the length of the helix
69
coiled coil in keratin
two amphipathic helices of keratin interact to bury their hydrophobic faces together - two right handed helices wrapping around each other in a left handed fashion
70
how are coiled coils formed
when two or more helices entwine to form a stable structure
71
strength of keratin
arises from covalent linkages of individual units into higher order structures -linked together through disulfide bonds -amount of disulfide bonds determine strength
72
primary structure of collagen
contains repeat of gly-x-y where x is often proline
73
secondary structure of collagen
forms a left handed helix of three residues per turn
74
coiled coils of collagen
three left handed helices of collagen form a coiled coil -form a right handed coiled coil -bulky side chains of proline on the outside -small side chains of glycine are tightly packed in the core
75
strength of collagen
arise from covalent linkages between the individual units -occur from residues that have undergone post translational modification -more cross links occur with age, accounting for the increasing brittle character of aging connective tissue
76
what happens and causes when modified residues cannot form stabilizing cross links
Vitamin C is needed for enzymes to perform these modification -leads to weakened structure of collagen which manifests in skin lesions, fragile blood vessels, bleeding gums
77
primary structure of silk
six residue repeat GSGAGA
78
secondary structure of silk
composed from sheets
79
silk strength and flexibility
association of strands by hydrogen bonding (flexibility) association of sheets by van der Waals and hydrophobic interactions (flexible) fully extended polypeptide chains (strength)
80
which amino acid are you most likely to find at the N terminal end of alpha helix
D
81
which functional groups involved in the formation of a peptide bond
carboxyl and amino
82
the secondary structure of a protein reflects:
elements of localized folding within the polypeptide chain
83
the strength of silk arises as a consequences:
fully extended polypeptide chains
84
the final folding pattern of single polypeptide chain represents
tertiary structure
85
localized patterns of folding within a polypeptide are described at the level of ___ structure
secondary
86
proteins that contain coiled coils
keratin and collagen
87
the final folded structure an individual polypeptide is described at the level of ____ structure
tertiary
BMSC 200
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