Flashcards in peptide formation + structure Deck (100):
1
stereochemistry of peptide bond
trans
2
true structure of peptide bond
resonance hybrid
3
which is stronger, peptide or single bond
peptide
4
which is longer, peptide or single bond
single
5
protein function
proteins accelerate thousands of biochemical reactions in the cell
catalysis
6
examples of proteins involved in catalysis
rubisco (photosynthesis)
hexokinase (first enzyme in glycolysis)
7
most abundant protein in earth
rubisco
8
first enzyme in glycolysis
hexokinase
9
protein function
some proteins provide protection and support
structure
10
ex of proteins for structure
collagen (connective tissue), elastin (elastic fibers), keratin (hair)
11
protein function
proteins are involved in all cell movements and muscle contraction
movement
12
– movement of sperm and protozoa
*dynein
13
protein function
various proteins have protective functions
Defense -
14
ex proteins for defense
keratin
immunoglobulins
15
protein function
various proteins regulate cellular processes
5. Regulation –
16
ex proteins for transport
glucose transporter
hemoglobin
LDL and HDL
transferrin
17
storage proteins containing 20 AA
Casein and ovalbumin
18
example of proteins for toxin
plant lectins, venom of snake
19
protein structure
the order or sequence of amino acids in the polypeptide chains
*Peptide bond is a covalent bond
primary
20
protein structure
conformation of the polypeptide backbone
2ndary
21
protein structure
arrangement in space of all atoms in the polypeptide chain
tertiary
22
protein structure
describes the interaction of the subunits in an oligomeric protein
*stabilized by both covalent & non-covalent forces
quaternary
23
levels of protein structure stabilized by covalent and non-covalent forces
quaternary and tertiary
24
has *intersubunit interaction
quaternary
25
has intrasubunit interaction
tertiary
26
what proteins have quaternary structure
only oligomericproteinswith ≥ 2 subunits
e.g. dimer
27
stabilizing force of secondary structure
H-bonding between the amide proton and carboxyl oxygen
28
the sequence of amino acids linked by peptide bonds.
▪ The backbone of a peptide chain or protein.
primary structure
29
Proteins are composed of ___ only
L-amino acids
30
conformation of the polypeptide backbone (stabilized by H-bonding) without side chains
secondary
31
which is stronger? H bond or peptide
Peptide bonds
32
– combination of α-helix & β-pleated sheet
random coil
33
The backbone can change direction by making __
reverse turn and loops.
34
type of secondary structure
Backbone coils into a periodic/repeating, compact structure (rigid)
alpha-helix
35
H-bonds of alpha helix are typically ____ (olarity)
amphiphilic
36
is alpha helix left-handed or right handed
right handed
37
is a “helix-breaker”
- no more H in Nitrogen of _____; no more H-bonding
- cannot rotate freely at ф
proline
38
a helix breaker
due to too much flexibility of H atom in _ H atom is too small
glycine
39
- Polypeptide backbone is almost fully extended.
β-pleated sheet (Zigzag)
40
≥ 2 backbones aligned for H-bonding
β-pleated sheet (Zigzag)
41
Backbones are aligned side by side leading to formation of H-bonds between carbonyl O of one chain & -NH group of the adjacent chain
β-pleated sheet (Zigzag)
42
maybe parallel or antiparallel orientation
- more stable than α-helix
β-pleated sheet (Zigzag)
43
these AA make reverse turns
Proline & glycine
44
this type of 2 structure is typical of fibrous proteins such as silk
β-pleated sheet (Zigzag)
45
– combination of coils; higher form of secondary structure
SUPERSECONDARY STRUCTURE
46
bonding with the side chain creates a specific overall shape (3-D structure) of the protein
“arrangement of all the atoms”
tertiary structure
47
type of conformation wherein Polypeptides fold into its 3-D structure
(native conformation)
48
Covalent & Non-covalent Interactions in the 30 Structure
H-bonding
- hydrophobic interaction
- π- π complexation reaction (specifically for aromatic rings)
- salt bridge/ionic/electrostatic
- metal-ion coordination bond (hemoglobin, myoglobin) for transition metal (Fe)
- oxidation of two cysteine to form cystine
49
- combination of large number of βαβ motifs
*β-barrelor superbarrel
50
– composed of 4 amino acids; due to glycine & proline
bends
51
– they do not have regular, periodic structures
loop
52
– denaturation of proteins
unfolding
53
types of tertiary structure
globular
disordered
fibrous
54
type of tertiary structure
interacts well with water and takes a random config
disordered
55
type of tertiary structure
many insoluble amino acids
proteins tend to minimize surface to volume ratio
globular
56
type of tertiary structure
strong secondary structure allows protein to retain a nonspherical shape
fibrous
57
type of protein structure
aggregates of two or more protein chains connected by weak non-covalent interactions
quaternary
58
examples of tetramers
alcohol dehydrogenase
hemoglobin
59
example of dodecamer
glutamine synthetase
60
– has only 10, 20 & 30 structures
*MONOMERIC PROTEINS
61
– has 10, 20, 30 & 40 structures
*OLIGOMERIC PROTEINS
62
▪ rod-like forming fibers; elongated
▪ insoluble in H2O (because they are structural proteins)
▪ usually has structural functions
▪ e.g. keratin, collagen, elastin
Fibrous Proteins
63
▪ spherical shaped
▪ soluble in H2O
▪ mostly functions as enzymes; for catalysis (non-structural functions)
▪ the interior is highly hydrophobic; amino acids are nonpolar inside
▪ the surface of the globular protein has polar amino acids
▪ e.g. casein, albumin, hormones
Globular Proteins
64
approximately spherical in shape; consist of several different lobes called domains
◦ hydrophobic core; hydrophilic external surface that reacts with water
◦ highest level maybe 30 or 40
Globular Proteins`
65
◦ elongated molecules in which the 20 structure (either α-helices or β-pleated sheets) is the dominant structure.
◦ muscle movement and cilliary proteins
◦ insoluble in water; structural functions
◦ often have repeating structures
◦ generally have 10 and 20 structures only
FIBROUS PROTEINS
66
amide linkages between the α-carboxyl group of one amino acid and the α-amino group of another
-not broken by conditions that denature proteins, such as heating or high concentrations of urea
peptide bonds
67
each component amino acid in a polypeptide
-named as such because it is the portion of the amino acid remaining after the atoms of water are lost in the formation of peptide bond.
Residue –
68
Bonds between ___ can be freely rotated (which allows the polypeptide chain to assume a variety of configurations
α-carbons and the α-amino or α-carboxyl groups
69
_____ of the peptide bond are uncharged, polar, and involved in hydrogen bonds
-C=O and –NH groups
70
– sequence of amino acids
-order in which amino acids are covalently linked by peptide bonds; one dimensional
-important to understand because many genetic diseases result in proteins with abnormal amino acid sequences
-dictates the secondary structure
primary structue
71
-folding of the backbone
-regular folding
-have repetitive interactions resulting from hydrogen bonding
-conformations of the side chain are not part of ----- structure
SECONDARY STRUCTURE
72
-spatial arrangement of the atoms in a polypeptide chain
-interaction: H-bond between the amide proton and carbonyl oxygen
SECONDARY STRUCTURE
73
• spiral structure consisting of a tightly packed, coiled polypeptide backbone core
• side chains extend outward to avoid steric interference
alpha helix
74
• stabilized by extensive hydrogen bonding between peptide-bond carboxyl oxygens and amide hydrogens
-hydrogen bonds extend up and are parallel to the spiral
-intramolecular H-bonds
alpha helix
75
disrupts the helix because its secondary amino group is not geometrically compatible with the right-handed spiral of the helix
-inserts a kink in the chain
Proline –
76
disrupt the helix by forming ionic bonds or by repelling each other
Charged amino acids
77
all of the peptide bond components are involved In the hydrogen bonding
-surfaces appear pleated
β-sheet
78
have hydrogen bonds perpendicular to the polypeptide backbone, instead of parallel.
β-sheet
79
– when hydrogen bonds are formed between the polypeptide backbones of separate polypeptide chains
Interchain bonds
80
when a β-sheet is formed by a single polypeptide chain folding back on itself
Intrachain bonds
81
– usually produced by packing side chains from adjacent secondary structural elements close to each other
-combinations of alpha and beta strands
Supersecondary Structures
82
– repetitive supersecondary structure
Motif
83
Other secondary structures (3)
• Other helix structures
• Random coils
• Reverse turns or β-bends
84
– almost similar with β-pleated sheet but there are bends
-glycine and proline are frequently encountered in reverse turns
Reverse turns or β-bends
85
– refers to both folding of domains and final arrangement of domains in the polypeptide
-three-dimensional arrangement
-important aspect: arrangement of side chains as AA residues
Tertiary
86
– covalent linkage formed from the sulfhydryl group of each of two cysteine residues
Disulfide bond
87
-spatial arrangement of polypeptide subunits
-interactions: same with tertiary structure
quaternary
88
-unfolding of a protein
-loss of high-level of structural organization of protein except for primary structure
DENATURATION
89
-denaturing agents (6)
1. Heat – increase in temp
2. Change in Ph – high or low extremes of ph
3. Organic solvents (alcohol, urea) – urea may form stronger H-bonds and can disrupt hydrophobic interactions
4. Detergents (SDS) – disrupt hydrophobic interactions
5. Salts of heavy metals
6. Performic acid and 2-mercaptoethanol
Β-mercaptoethanol – reduce disulfide bridges to two sulfhydrryl groups
90
-may be acid, base, neutral hydrolysis
-breakdown of peptide bond or the primary structure
HYDROLYSIS
91
leads to unfolding of protein and subsequent loss of biological function
denaturation
92
remains of hydrolysis
individual aa
93
remains of denaturation
group of aa
94
physical agents of protein denaturation
Heat or temperature
Mechanical agitation or stress
95
by applying __, bubbles will form (foam) which signifies denaturation
e.g. Bradford assay
stress
96
a chemical agent which targets the salt bridges in the protein.
Strong acid
97
Chemical agents
target ionic interactions with protein
Strong acids and bases
98
Most common reducing agents are for breaking ____ bonds
disulfide
99
reducing agents
1. β-mercaptoethanol
2. Dithiothreitol (DTT)
100