amino acids Flashcards
(158 cards)
1
Q
what are proteins
A
complex group of macromolecules (enzymes,proteins,hormones)
2
Q
proteins are polymers
A
of 20 diff a.a
3
Q
they an be distinguished by
A
number, composition, sequence of a.a
4
Q
A.A
A
polymer of 50> peptides
50< proteins or polypeptides
5
Q
how many standard A.A
A
20
6
Q
nonstandard A.A
A
they are standard but have been chemically modified after being incorporated into protein
7
Q
19 have same structure
A
central c, amino group, H, R group
8
Q
exception (proline)
A
has secondary amine
9
Q
R group
A
gives the A>A its unique properties
10
Q
what are zwitterions
A
molecules that have -ve and +ve charges
11
Q
A.A have four classes
A
nonpolar
polar
acidic
basic
(in ppt)
12
Q
nonpolar
A
contain hydrocarbon groups w no charges makes it hydrophobic
13
Q
polar
A
functional groups can interact w water thru h-bonds (hydroxyl and amide)
14
Q
acidic
A
has carboxylate group
15
Q
basic
A
amino group
16
Q
some a.a have their derivatives
A
as neurotransmitters and hormones
17
Q
thyroxine
A
tyrosine derivatives produced by thyroid gland (regulates metabolism)
18
Q
melatonin
A
regulates night/day and sleep/wake cycle
19
Q
GABA
A
neurotransmitter
20
Q
serotonin
A
neurotransmitter and stabilizes mood and feeling
21
Q
A.A are precursors of nitrogen containing molecules such as
A
the nitrogenous base components of nucleotides and nucleic acids
22
Q
standard and nonstandard act at metabolic intermediates
A
arginine, citrulline and ornithine (urea cycle)
23
Q
some proteins have a.a modified after synthesis
A
- y-carboxyglutamate
- 4-hydroxyproline 5-hydroxylysine (collagen)
- serine, threonine, tyrosine (phosphorylated)
24
Q
structural isomers
A
same molecular formula diff structure (aldehyde, ketone)
25
stereoisomers
same molecular formula and structural diff arrangement
26
geometric stereoisomers
mol. having c/c double bond w 2 diff groups attached to each carbon if attached to opp charges (cis) all other type (trans)
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optical stereoisomers
having chiral c are optically active (D+,L-)
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enantiomers
mirror image
29
diastereioisomers
non-mirror image
30
epimers
diastereoisomers that are diff in one chiral c
31
alpha carbon is attached to 4 diff groups
exist as stereoisomers
32
enentiomers
mol. are mirror images of one another
33
optical isomers
cannot be superimposed over 1 another and rotate polarized light in opposite direction
34
D or L
to indicate similarity of arrangement of atoms around mol. asymmetric c
35
L-a.a
found in proteins
36
free a.a contain ionizable groups which are
carboxyl, amino groups
37
ionic form depends on
PH
38
a.a have no charge due to ionization of both groups
isoelectric point (used to separate and purify proteins)
39
a.a w ionizable side chains have
complex titration
40
glutamic acid
carboxyl side chain, low PH loses protons to final net charge -2
41
a.a can undergo many chemical reactions
peptide and disulfide bridge they affect polypeptide structure
42
dehydration (forming peptide bond)
amide linkage (dipeptide)
43
dehyrogenation
formation of disulfide bond
44
schiff base
formation
45
peptide bond formation
polypeptides are linear polymers of a.a by peptide bonds
46
peptide bonds are
amide linkage formed by nucleophilic acyl substitution
47
2 a.a
dipeptide
48
a.a w free amino group
N-terminal
49
a.a w free carboxyl group
C-terminal
50
peptide bond formation
a-carboxyl of one a.a and a-amino of next a.a
51
a.a sequence leads to
protein native conformation
52
linus pauling
first to characterize peptide bonds as rigid and flat
53
C-N bonds
btw 2 a.a are shorter than others
54
because of the rigidity
1/3 of the bond backbone cannot rotate freely (limiting # of conformational possibilities)
55
disulfide bond formation
cystein oxidation -> reversible bond
56
disulfide bridge forms
when 2 cysteine residues forms bond
57
oxidation of r-group
2 cysteine leads to reversible bond
58
disulfide
strong covalent bond helps stabilize structure
59
schiff base formation
imine product of primary amine groups interacting reversibly w carbonyl groups (a.a biosynthesis)
60
schiff base referred to as
aldimines (intermediates) formed by a reaction of an amino group and aldehyde group
61
peptides
less complex than large proteins
62
glutathione
tripeptide in all organisms (protein and DNA synthesis, toxic subs. metabolism, a.a transport)
63
vasopressin
nonapeptide, antidiuretic regulates water balance, appetite and body temp
64
oxytocin
nonapeptide hormone aids uterine contraction and lactation
65
proteins
most diverse
66
catalysis
enzymes
67
structure
call and organismal
68
movement
amoeboid movement
69
defense
antibodies
70
regulation
insulin is a peptide hormone
71
transport
membrane transporter
72
storage
ovalbumin in bird eggs
73
stress response
heat shock proteins
74
proteins are categorized into
families on sequence of 3D shapes
75
superfamilies
more distantly related proteins
76
proteins classified by
shape : globular, fibrous
composition: simple, conjugated(protein and non protein components)
77
protein structure
complex: primary, secondary, tertiary, quaternary
78
primary
sequence of a.a help by peptide bonds
79
homologous proteins
share similar sequence arose from same ancestor gene
80
a.a sequence of proteins
can change due to alteration in DNA called mutations
81
mutation
alteration in DNA sequence leads to change in primary structure (not function)
some are conservative(changes to a similar a.a)
82
mutations can be
deleterious leading to diseases
83
how is sickle anemia caused
substitution of valine for glutamic acid
84
subs for valine hbs
molecules move and for sickle shaped cells
85
secondary structure
polypeptide variety of repeating structures (a-helix, b-pleated sheets)
86
how are both structured stabalized
by h-bond btw carbonyl (C=O) and amine (N-H)
87
a-helix
h-bond within the same chain
88
B-helix
h-bond btw one chain and another
89
a-helix
rigid, rod-like, right handed, stabilized by N-H bond (glycine and proline do not foster)
90
B-pleated sheets
2 or more polypeptide chains line up (parallel or antiparallel) fully extended and stabilized by N-H (parallel less stable than antiparallel)
91
supersecondary structure
patterns of a-helix and b-sheets (5 types)
92
tertiary structure
3D structures and have prosthetic groups
93
protein folding
a nascent molecule acquires a highly organized structure (info from a.a sequence)
94
what stabilizes interaction of side chains
electrostatic forces
95
Tertiary structure imp feature 1
polypeptides fold in way to bring distant a.a into close proximity
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Tertiary structure imp feature 2
globular proteins are compact cuz of efficient packing (a.a side chains associate w lipid bilayer)
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Tertiary structure imp feature 3
globular protein contain domains
98
what are domains
structurally independent segments that have specific functions (core is called fold)
99
EF hand
helix loop binds to ca2+
100
leucine zipper
DNA binding domain
101
human retinol
B-barrel domain
102
aBzinc-binding motif
core feature of numerous DNA binding domains
103
Tertiary structure imp feature 1Tertiary structure imp feature 1
#of proteins called mosaic or modular consists of repeated domains
104
fibronectin
3 repeated domains (F1,F2, and F3)
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domain modules
coded by genetic sequence created by gene duplication
106
interactions that stabilize tertiary structure
hydrophobic interaction, electrostatic interaction, h-bond, covalent bond, hydration
107
covalent disulfide bond
btw 2 non-adjacent cysteine, protects protein structure from changes in ph or salt concentration
108
why do intracellular proteins not contain disulfide bridges
ciz of high cytoplasmic conc of reducing agent
109
ionic interactions
btw opp charged R-groups
110
H-bonds
btw a.a r-groups or btw carbonyl o2 and hydroxyl groups or amine
111
hydrophobic interactions
btw non-polar a.a r-groups
112
hydration
free the polypeptide from some of its internal interactions
113
quaternary structure
protein composed of several polypeptide chains
114
identical subunits are referred to as
oligomers
115
what are polypeptide subunit held by
noncovalent subunits
116
covalent (disulfide)
less common
117
why are multisubunit common
synthesis more efficient, replacement of worn-out components can be more effective, function may be regulated by complex interactions of many subunits
118
how is the interaction btw subunits more affected
by ligand binding,, triggering a conformational change which alters its affinity for other ligands
119
what is allostery
controls protein function by ligand binding
120
allosteric transition
change in protein conformation and function
121
ligands triggers
effectors and modulators
122
unstructured proteins
proteins that are partially or completely unstructured referred to as (IUPs)
123
protein denaturation
disruption of the structure (not primary) it causes loss of activity and precipitate becomes insoluble
124
proteins denaturation
there are 8 conditions
125
1. strong acid or base
change in PH affects ionic and H interactions
126
2.change in temp
disrupts hydrophobic and h interactions
127
3. organic solvent
polar and non-polar
128
4.reducing agent
disrupts disulfide bonds and hydrophobic interactions
129
5. detergents
amphipathic distrupt hydrophobic interactions
130
6.salt conc
disrupts ionic ineractions
131
7. heavy metal ions
bind and disrupt ionic interaction and disulfide bond
132
8.mechanical stress
stirring, grinding, whipping
133
small polypeptides (<100a.a)
form with no intermediates
134
large polypeptides
several intermediates
135
why do proteins use molecular chaperons
to help correct folding and targeting
136
what are molecular chaperons
network of proteins play a main role in cellular protein quality control by improving the folding
137
molecular chaperons
assist protein folding by protecting them from inappropriate protein-protein folding
138
Hsp70
chaperons that bind and stabilize proteins in early stages of folding
139
chaperonins
increase speed and efficiency of folding
140
hsp70 and chaperonins
both use ATP hydrolysis and facilitate folding
141
misfolded proteins lead to
alzheimers and huntington
142
fibrous proteins
high amount of a-helices and b-pleated it imp for str
143
keratin
double a-helix hair
144
fibroin
b-sheets forming silk
145
collagen
part of ct synthesized by ct secreted into extracellular triple a-helix held together by h-bond
146
globular proteins
hemoglobin, myoglobin, emzymes, peptide, immunoglobeulins
147
myoglobin
high conc in cardiac and skeletal muscle 8a-helices for storing o2
148
hemoglobin
spherical protein has 4 subunits binds to1 o2 (transport o2) 2a-chains and 2b-chains (ab dimers)
149
oxygenation of hemoglobin
causes the dimers to slide by each other relaxed state
150
deoxygenated hemoglobin
taut state
151
cooperative binding
causes a sigmoidal o2 dissociation cure for the hemoglobin
152
myoglobin dissociation curve is
hyperbolic
153
ph decreases
enhances o2 release from hemoglobin
154
waste of CO2
emhances o2 releasede by increasing H conc
155
decrease in ph
increase in h conc forming carbonic acid
156
binding h to many ionixable groups
shifts it to t state
157
increase in temp
decrease o2 binding affinity
158
