Chapter 3: Protein Structure and Function Flashcards
1
Q
building blocks of proteins in living organisms
A
amino acids
2
Q
how many amino acids can be found in nature
A
500 amino acids
3
Q
number of amino acids the human genetic code directly encodes
A
20 amino acids
4
Q
must be obtained from the diet
A
essential amino acids
5
Q
can be synthesized in the body
A
non-essential amino acids
6
Q
aliphatic amino acids
A
- alanine
- glycine
- isoleucine
- leucine
- proline
- valine
7
Q
aromatic amino acids
A
- phenylalanine
- tryptophan
- tyrosine
8
Q
acidic amino acids
A
- aspartic acid
- glutamic acid
9
Q
basic amino acids
A
- arginine
- histidine
- lysine
10
Q
hydroxylic amino acids
A
- serine
- threonine
11
Q
suflur-containing amino acids
A
- cysteine
- methionine
12
Q
amidic amino acids
A
- asparagine
- glutamine
13
Q
What are the nine (9) essential amino acids? (PriVaTe ThIM HiLL)
A
- Phenylalanine
- Valine
- Tryptophan
- Threonine
- Isoleucine
- Methionine
- Histidine
- Lysine
- Leucine
14
Q
What are the 11 non-essential amino acids?
(Almost All Girls Go Crazy After Going To A Pretty Shop)
A
- Alanine
- Arginine
- Glycine
- Glutamine
- Cysteine
- Asparagine
- Glutamic Acid
- Tyrosine
- Aspartic Acid
- Proline
- Serine
15
Q
often referred to as the 21st amino acid
A
Selenocysteine
16
Q
glycine
A
gly
17
Q
alanine
A
ala
18
Q
valine
A
val
19
Q
leucine
A
leu
20
Q
isoleucine
A
Ile
21
Q
methionine
A
met
22
Q
tryptophan
A
trp
23
Q
phenylalanine
A
phe
24
Q
proline
A
pro
25
serine
ser
26
threonine
thr
27
cysteine
cys
28
tyrosine
tyr
29
asparagine
asn
30
glutamine
gln
31
aspartic acid
asp
32
glutamic acid
glu
33
lysine
lys
34
arginine
arg
35
histidine
his
36
where is the word protein derived from
Greek, proteios
37
proteios
first
38
What are proteins
- large molecules made up of chains of amino acids
- found in every cell in the body
- involved in most of body's functions and life processes
- sequence of amino acids is determined by DNA
39
Different classes of proteins
1. structural
2. contractile
3. transport
4. storage
5. hormone
6. enzyme
7. protection
40
provide structural components
structural protein
41
examples of structural protein
1. collagen
2. keratin
42
collagen examples
- tendons
- cartilage
43
keratin examples
- hair
- skin
- wool
- nails
44
make muscles move
contractile protein
45
examples of contractile protein
1. myosin
2. actin
46
myosin and actin
contract muscle fibers
47
carry essential substances throughout the body
transport protein
48
examples of transport proteins
1. hemoglobin
2. lipoproteins
49
hemoglobin
transports oxygen
50
lipoproteins
transports lipids
51
store nutrients
storage proteins
52
examples of storage proteins
1. casein
2. ferritin
53
casein
stores protein in milk
54
ferritin
stores iron in spleen and liver
55
regulate body metabolism and the nervous system
hormone
56
examples of hormone
1. insulin
2. growth hormone
57
insulin
regulates blood glucose level
58
growth hormone
regulates body growth
59
catalyze biochemical reactions in the cells
enzymes
60
example of enzymes
1. sucrase
2. trypsin
61
sucrase
catalyzes hydrolysis of sucrose
62
trypsin function
catalyzes hydrolysis proteins
63
recognize and destroy foreign substances
protection proteins
64
example of protection protein
immunoglobulins
65
immunoglobulins
stimulate immune responses
66
structure, characteristic, and classes of amino acids differ in
R groups
67
amino acids vary in
1. size
2. shape
3. charge
4. polarity
5. solubility in water
68
attached to four different substituents
α-Carbon
69
Four substiuents of amino acids
1. hydrogen atom
2. carboxyl group
3. amino group
4. R group
70
nonionic form:
amino group
NH2
71
nonionic form:
carboxyl group
COOH
72
Zwitterionic form:
amino group
NH3+
73
Zwitterionic form:
carboxyl group
COO-
74
two forms of amino acid
1. nonionic form
2. Zwitterionic form
75
compounds that form amino acids
- amine
- acid
76
α-amino acids
amine is adjacent to the carboxylate group
77
19 out of the 20 amino acids are __
stereoisomers
78
amino acid that is not a stereoisomer
Glycine
79
compounds that have the same constitution but differ in the spatial arrangement of their atoms
stereoisomers
80
α-carbon of amino acids is __
chiral
81
chiral molecules
nonsuperimposable on their mirror images
82
achiral molecules
superimposable on their mirror images
83
have the hydroxy group attached to the left side of the asymmetric carbon furthest from the carbonyl
L isomers
84
have the hydroxy group on the right side
D isomers
85
where do the differences of amino acids depend upon
side-chain R groups
86
Amino acids form classes based on what?
polarity of side chains
87
Nonpolar
hydrophobic R groups
88
Polar neutral
- high affinity for water
- not ionic at pH
89
Polar acidic
- ionized carboxyl groups
- negatively charged
90
Polar basic
- basic as side chain reacts with water to release hydroxide ion
- positively charged
91
What are the polar uncharged amino acids
1. serine
2. threonine
3. asparagine
4. glutamine
5. tyrosine
6. cysteine
92
R groups of polar uncharged amino acids
- OH
- amide group
- sulfhydryl/ thiol groups
- H-bond with water
93
where are polar uncharged amino acids found
surface of globular proteins
94
polar uncharged amino acids are __ in aqueous solutions
soluble
95
bears hydroxylic R group
- serine
- threonine
96
has amide-bearing side chain
- asparagine
- glutamine
97
- has a phenolic group
- together with aromatic groups of F and W, acounts for most of UV absorbance and fluorescence exhibited by proteins
tyrosine
98
tyrosine account for most of what
- UV absorbance
- fluorescence
exhibited by proteins
99
forms a disulfide bond to another residue through oxidation of their thiol groups
cysteine
100
how does the cysteine form a disulfide bond to another
through oxidation of thiol groups
101
what is formed between two cysteine residue after oxidaton of their thiol groups
disulfide bond
102
non-polar/hydrophobic amino acids
aliphatic
1. glycine
2. alanine
3. valine
4. leucine
5. isoleucine
6. methionine
7. proline
aromatic
1. phenylalanine
2. tryptophan
103
aliphatic non-polar/hydrophobic amino acids
1. glycine
2. alanine
3. valine
4. isoleucine
5. leucine
6. proline
7. methionine
104
aromatic non-polar/hydrophobic amino acid
1. phenylalanine
2. tryptophan
105
where are non-polar/hydrophobic amino acids found
- globular proteins
- insoluble core
106
has the smallest possible side chain, an H atom
glycine
107
has methyl group -CH3
alanine
108
has aliphatic hydrocarbon side chain
valine
109
has isomeric butyl groups
- leucine
- isoleucine
110
has thiol ether side chain that resembles an n-butyl group in many of its physical properties
methionine
111
methionine: C and S have nearly equal __ and S is about the size of a __ __
- electronegativities
- methylene group
112
cyclic secondary amino acid has conformational constraints imposed by the cyclic nature of its pyrrolidine side chain, which is unique among the standard amino acids
proline
113
side chain" from the α carbon connects to the nitrogen
pyrrolidine loop
114
has phenyl moiety
phenylalanine
115
with indole group, contain aromatic side chains, which are characterized by bulk as well as nonpolarity
tryptophan
116
D (position)
dexter (right)
117
L (position)
laevus (left)
118
electrically charged amino acids
Negative (acidic)
1. aspartic acid
2. glutamic acid
Positive (basic)
1. lysine
2. arginine
3. histidine
119
- negatively charged above pH 3
- aspartic acid
- glutamic acid
120
in its ionized state, aspartic acid is often referred to as what?
aspartate
121
in its ionized state, glutamic acid is often referred to as what?
glutamate
122
positively charged at pysiological pH values
- lysine
- arginine
- histidine
123
what kind of side chain does lysine have
butylammonium side chain
124
what group does arginine have
guanidino group
125
guanidino group contains __ __ __, rather than only one as in the lysine side chain, it shows a more diverse chemistry
two reactive nitrogens
126
what does histidine carry
imidazolium moiety
127
glycine one letter
G
128
alanine one letter
A
129
valine one letter
V
130
leucine one letter
L
131
isoleucine one letter
I
132
methionine one letter
M
133
proline one letter
P
134
phenylalanine one letter
F
135
tryptophan one letter
W
136
serine one letter
S
137
threonine one letter
T
138
asparagine one letter
N
139
glutamine one letter
Q
140
tyrosine one letter
Y
141
cysteine one letter
C
142
lysine one letter
K
143
arginine one letter
R
144
histidine one letter
H
145
aspartic acid one letter
D
146
glutamic acid one letter
E
147
Animal protein: complete
- egg
- milk
- meat, fish, poultry
148
Animal protein: incomplete
gelatin (denatured collagen)
149
what is missing in gelatin
Trp
150
vegetable protein: incomplete
Grains
- wheat
- corn
- rice (brown, white)
- oats
Legumes
- beans
- peas
Nuts
- almonds
- walnuts
151
what is missing in grains
lys (wheat, rice, oats)
lys, trp (corn)
152
what is missing in legumes
met (peas)
met, trp (beans)
153
what is missing in nuts
lys, trp
154
top 10 complete vegetarian protein foods with all the essential amino acids
1. firm tofu
2. lentils
3. low-fat yogurt
4. cottage cheese
5. green peas
6. squash and pumpkin seeds
7. quinoa
8. peanut butter
9. eggs
10. mushrooms
155
chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O)
peptide bond
156
how is peptide bond formed
dehydration synthesis
157
what does peptide bond have that limits rotation about this bond
partial double bond
158
what is formed from the condensind or dehydrating of two amino acids
dipeptide
159
amino acid with free -NH3+
amino terminal amino acid
160
short for amino terminal amino acid
N-terminal
161
amino acid with free -COO-
carboxyl terminal amino acid
162
short for carboxtyl terminal amino acid
C-terminal
163
how are amino acid structures written
N-terminal on the left
164
unbranched chain of amino acids
polypeptide chain
165
may consists of one or more polypeptide chains
protein
166
read from N to C terminal
simple peptide
167
naming:
ex. alanine
alanyl
167
naming peptides
1. far AA residue retains the name of amino acids
2. all AAs (except trp) --> -ine or -ic acid is replaced by -yl
3. tryptophan --> tryptophanyl
168
naming:
ex. glycine
glycyl
169
naming:
ex. serine
seryl
170
naming:
ex. alanine, glycine, serine
alanylglycylserine
(Ala-Gly-Ser)
171
4 steps of writing strucutre of peptides
1. write backbone
2. add oxygens to carboxyl carbons, and hydrogens to amino nitrogens
3. add hydrogens to alpha-carbon
4. add side chains
172
backbone of peptide
N-C-C-N-C-C-N-C-C
173
peptide chain of nine amino acid residues
nonapeptide
174
examples of nonapeptides
- oxytocin
- vasopressin
175
where do oxytocin and vasopressin differ
amino acid position
- 3
- 8
176
stimulates uterine contraction in labor
oxytocin
177
- antidiuretic hormone
- regulates blood pressure by adjusting amount of water reabsorved by kidneys
vasopressin
178
Variety of Functions of Peptides
1. hormones and pheromones
2. neuropeptides
3. antibiotics
4. protection
179
hormones and pheromones
- insulin (think sugar)
- oxytocin (think childbirth)
- sex-peptide (think fruit fly mating)
180
neuropeptides
substance P (pain mediator)
181
antibiotics
- polymyxin B (Gram - bacteria)
- bacitracin (Gram + bacteria)
182
ex. of toxins that protection proteins defend against
- amanitin
- conotoxin
- chlorotoxin
183
amanitin
mushrooms
184
conotoxin
cone snails
185
chlorotoxin
scorpions
186
fewer than 50 amino acids
peptides
187
2 amino acids
dipeptides
188
3 amino acids
tripeptides
189
more than 10 amino acids
polypeptides
190
more than 50 amino acids
proteins
191
proteins are typically __ to __ amino acids linked together
100 - 10,000 amino acids
192
how are chains of proteins synthesized
based on specific bodily DNA
193
Functions of proteins
1. enzymes
2. defense proteins
3. transport proteins
4. regulatory proteins
5. structural proteins
6. movement proteins
7. nutrient proteins
194
are biological catalysts
enzymes
195
include antibodies which are specific protein molecules produced by specialized cells of the immune system in response to foreign antigens
defense proteins
196
other term for antibodies
immunoglobulins
197
__ has regions that precisely fit and bind to a single __
- antibody
- antigen
198
carry materials from one place to another in the body
transport proteins
199
- carry lipids, vitamins, minerals, and oxygen in the body
- act as pumps in cell membranes, transferring compounds from one side of the cell to the other
transporters
200
responsible for transport and storage of oxygen in higher organisms, respectively
- hemoglobin
- myoglobin
201
myoglobin
1 subunit
1 heme group
202
hemoglobin
4 subunits
4 heme groups
203
- control many aspects of cell function, including metabolism and reproduction
- we can only function within limited set of conditions
regulatory proteins
204
where are insulin released
beta cells of pancreas
205
where are glucagon released
alpha cells of pancreas
206
promotes growth
growth hormone
207
regulate blood glucose
insulin and glucagon
208
regulates the body's metabolic rate
thyroxine
209
regulate blood calcium
- calcitonin
- parathormone
210
regulates fluid and electrolyte balance
antidiuretic hormone
211
provide mechanical support to large animals and provide them with outer coverings
structural proteins
212
hair and fingernail are composed of what
keratin
213
necessary for all forms of movement
movement proteins
214
how do muscles move
interaction of actin and myosin proteins
215
serve as sources of amino acids for embryos or infants
nutrient proteins
216
examples of nutrient storage proteins
- egg albumen
- casein in milk
217
Levels of protein structure
1. primary
2. secondary
3. tertiary
4. quaternary
218
primary structure
amino acid residues
219
secondary structure
three-dimensional spatial arrangements
220
tertiary structure
polypeptide chain
221
quaternary structure
assembled subunits
222
bond that holds primary structure
peptide bonds
223
smalles protein
insulin (51 amino acids in two chains)
224
what links the two chains of insulin
cysteine (disulfide) cross links
225
bonds in secondary strucure
hydrogen bond
(-NH group of peptide bond and carbonyl oxygen of another peptide bond)
226
two regular arrangements in secondary structure
1. α-Helix
2. beta sheet
227
stabilized by hydrogen bonds between nearby residues
α-Helix
228
stabilized by hydrogen bonds between adjacent segemtns that may not be nearby
beta sheet
229
most common type of secondary structure
α-Helix
230
shape of α-Helix
coiled, helical
231
important features of α-Helix
1. amide H and carbonyl O involved in H bonds
2. carbonly O links to amide H, 4 AA away
3. H bonds parallel to long axis of helix
4. right handed
5. 5.4 angstorms repeat distance
6. 3.6 amino acids per turn
232
second most common secondary structure appears similar to folds of fabric
β-pleated sheet
233
two possible orientations of β-pleated sheet
1. parallel
2. antiparallel
234
if the N-termini are head-to-head
parallel
235
if the N-terminus of one chin is aligned with the C-terminus of the other
antiparallel
236
- gives a specific three dimensional shape of the polypeptide chain
- involves interactions and cross links between different parts of peptide chain
tertiary structure
237
tertiary structure is stabilized by what
1. hydrophobic and hydrophilic interactions
2. salt bridges
3. hydrogen bonds
4. disulfide bonds
238
globular tertiary structure forms spontaneously and is maintained by what
interactions among side chains or R groups
239
between two cysteine residues
disulfide bridges
240
S-S linkage can occur within the same chain
intrachain
241
S-S linkage can occur between 2 or more chains
interchain
242
ionic interaction/electrostatic attraction between ionic side chains -COO- and - NH3+
salt bridges
243
interaction between polar residue chains
hydrogen bonds
244
interaction between nonpolar groups attracted by mutual repulsion of water
hydrophobic interactions
245
results from the aggregation of two or more polypeptide subunits
quaternary structure
246
fibrous protein of three polypeptides that are supercoiled like a rope
collagen
247
globular protein with two copies of two kinds of polypeptides
hemoglobin
248
Two major classes of protein
1. fibrous proteins
2. globular proteins
249
- typically insoluble inw ater and serve structural roles
- 3D structure is usually long and rod shaped
fibrous proteins
250
- coiled into compact shapes with hydrophilic outer surfaces making them water-soluble
- compact shape like a ball with irregular surfaces
- enzymes
globular proteins
251
α-keratin function
tough, rigid, hard (nails, horns)
252
α-keratin structure
- cross-linked α-helixes
- rigid linker (S--S)
253
collagen function
tensile strength, non-stretching (tendons, cartilage)
254
collagen structure
- cross linked triple-helixes
- flexible linker (Lys-HyLys)
255
silk fibroin function
soft, flexible non-stretchy (egg sac, nest, web)
256
silk fibroin structure
- non-covalently held β-sheets
- van der Waals interaction
257
shape of globular proteins
roughly circular
258
shape of fibrous proteins
long strands
259
amino acid sequence globular
irregular and wide range of R groups
260
amino acid sequence fibrous
repetitive with limited range of R groups
261
function globular
physiological/functional
262
function fibrous
structural
263
examples of globular
- hemoglobin
- enzymes
- insulin
- immunoglobulin
264
examples of fibrous
- collagen
- keratin
- myosin
- actin
- fibrin
265
solubility globular
generally soluble in water
266
solubility fibrous
generally insoluble in water
267
chemistry of permanent waving
- reduce
- curl
- oxidize
