Proteins Flashcards
(177 cards)
1
Q
What is a protein?
A
Linear polymers of amino acids
2
Q
What is a peptide bond formation?
A
The creation of an amide bond between the carboxyl group (-COO) of one amino acid and the amino group (-NH3) of another amino acid
3
Q
What is the structure of the backbone of a protein chain?
A
Repeated sequence (N-Ca-C)
3
Q
Three things that create a peptide bond formation
A
- Amide bond
Between - Carboxyl group (-COO) of amino acid
- Amino group (-NH3) of another amino acid
3
Q
Most proteins use _____ amino acids
A
all
3
Q
What is Ribonuclease?
A
The enzyme that breaks down RNA molecules
3
Q
R-side chains (inside) are _____
A
Hydrophobic
3
Q
The atoms around the peptide bond (CO-NH) are ____________
A
Coplanar
4
Q
Outside of proteins are __________
A
Hydrophilic
5
Q
How was the phylogenetic tree constructed?
A
By comparing the amino acid sequences of the protein cytochrome c
6
Q
What are the two terminal ends of proteins?
A
-Amino terminal end (HOOC)
- Carboxyl terminal end (NH2)
7
Q
What type of bond are disulfide bonds?
A
Covalent bonds
8
Q
Do proteins have spaces?
A
No
9
Q
What is lysosome?
A
An extracellular protein
10
Q
How many disulfide bonds are in a protein?
A
Any number
11
Q
List the sizes of proteins from smallest to largest
A
Insulin, cytochrome, ribonuclease, lysosome, myoglobin, hemoglobin, immunoglobin, glutamine sythetase
12
Q
Shape of insulin
A
A + B chain
13
Q
Shape of cytochrome
A
Single chain
14
Q
Shape of ribonuclease
A
Single chain
15
Q
Shape of lysozyme
A
Single chain
16
Q
Shape of myoglobin
A
Single chain
17
Q
Shape of hemoglobin
A
4 chains
(2 alpha)
(2 beta)
18
Q
Shape of immunoglobulin
A
4 chains
19
Q
Shape of glutamine synthetase
A
12 chains
20
Where are the number of amino acid changes listed on the phylogenetic tree?
The number of amino acid changes are given on the branches
21
What is released during a peptide/amide bond formation?
Water
22
A phylogentic tree compares amino acid sequences of the protein ______
Cytochrome C
23
_____ proteins require something bound to them to activate
Conjugated
24
The binding of nonprotein groups affect protein ____
Folding
25
Glycoproteins contain ____
Carbohydrates
26
Lipoproteins contain _____
Lipids
27
Nucleoprotein complexes contain ___
Nucleic acid
28
Phosphoproteins contain _____
Phosphate
29
Metalloproteins contain _____
Metal atoms
30
Hemoproteins contain _____
Heme
31
Flavoproteins contain ____
Flavin
32
Glyco means
Carbohydrate
33
Lipo means
Lipid
34
Nucleo means
DNA or RNA
35
Metallo means
Metal ion
36
Biological functions of proteins:
Enzymes
Ribonuclease, trypsin
37
Biological functions of proteins:
Regulatory proteins
Insulin, transcription factor NF -1
38
Biological functions of proteins:
Transport Proteins
Hemoglobin, glucose transporter
39
Biological functions of proteins:
Storage Proteins
Casein, ovalbumin
40
Biological functions of proteins:
Contractile, Motile Proteins
Actin, myosin, tubulin
41
Biological functions of proteins:
Structural Proteins
Collagen, a-keratin
(Hair & fingernails)
42
Biological functions of proteins:
Protective Proteins
Immunoglobulins, fibrinogen
(antibodies)
43
Biological functions of proteins:
Exotic Proteins
antifreeze proteins, glue proteins
44
Protein Techniques:
Chromatography
- ion exchange chromatography
- size exclusion chromatography
- affinity chromatography
45
Ion exchange chromatography
Separates proteins on the basis of their overall charge
46
Size exclusion chromatography
Separates proteins on the basis of size
47
Affinity chromatography
Separates proteins on the basis of affinity (specific binding to small molecules)
48
Protein Techniques:
Electrophoresis
- SDS-PAGE
- Isoelectric focusing
- Two dimensional gel electrophoresis
49
SDS-PAGE electrophoresis
Separates proteins on the basis of molecular weight
50
Isoelectric focusing
Separates proteins on the basis of Isoelectric point (pI)
51
Electrophoresis
The movement in an electric field
52
Two dimensional gel electrophoresis
Separates proteins on the basis of isoelectric point (pl) and molecular weight (a) + (b)
53
Protein Shape:
Fibrous Proteins
- Linear, serve structural roles
54
Protein Shape:
Globular Proteins (aq environment)
- Hydrophobic on amino acids on inside
- Hydrophilic amino acids on outside
55
Protein Shape:
Membrane Proteins (hydrophobic environment)
- Interact with membrane lipids
- Hydrophobic amino acids on *outside
* in entirely different environment than globular proteins
56
Collagen is an example of what protein shape?
Fibrous protein
57
Myoglobin is an example of what protein shape?
Globular protein
58
Bacteriorhodopsin is an example of what protein shape?
Membrane protein
59
What is primary structure?
Amino acid sequence of a protein
60
What is secondary structure?
- Short range 3D structure in a protein
- Localized conformation of the polypeptide backbone
61
What are the two types of secondary structure?
1. a-helix
2. b-strand
62
What causes a secondary structure?
Due to H-bonding of backbone atoms (-CO-NH-)
63
What is tertiary structure?
Folding of a polypeptide into its 3D shape
64
What causes a tertiary structure?
Due to R-side chain interactions
65
What are the 4 properties of tertiary structures?
1.Hydrophobic
2. H-bonding
3. Charge
4. Disulfide bonds
lots of weak interactions make strong interaction
66
What are quaternary structures?
- Numbers and kinds of polypeptide subunits in a protein
- Polypeptide chains in a protein with multiple subunits
67
What are the levels of protein structure?
Primary, secondary, tertiary, quaternary
68
What does the sequence of amino acids that go from the amino terminal end to the carboxyl terminal end tell you?
1. What type of protein
2. Function of protein
3. Everything you need to know about proteins
69
What causes the a-helix in secondary structure?
H-bonding along one strand
70
What causes the b-strand in secondary structure?
H-bonding between two or more strands
71
In secondary structure, each C=O is _____ _____ to the N-H group ____ ____ _____ along the chain
hydrogen bonded, four amino acids
72
What are the two types of the B-strand in secondary structures?
1. Parallel
2. Antiparallel
- Can both exist in the same protein
- Can form extensive B-pleated sheet structures
73
This type of secondary structure is formed by hydrogen bonding of C=O and N-H groups along the backbone of a single polypeptide chain
a-helix
74
How many amino acid residues per turn of the helix?
3.6 amino acids per turn of the helix
75
Is the a-helix left or right handed?
Right handed
76
What is the pitch of the a-helix?
5.4A
77
What is the diameter of the a-helix?
6A
78
What stabilizes the a-helix structure?
Hydrogen bonds
79
Are the B-strands hydrogen bonding between or within strands?
The hydrogen bonding is between strands
80
What is the arrangment of B-strands in the secondary structure?
Parallel and antiparallel
81
Are parallel B-strands linear or bent?
Bent
82
Are antiparallel B-strands linear or bent?
Linear
83
The ______ B-strand is the most common
Antiparallel
84
The ____ B-strand is the strongest
Antiparallel
85
The four horizontal ______ form an antiparallel B-Plated sheet with _____ strands in _____ directions
B-strands, adjacent, opposite
86
B-pleated sheets follow the __ and ____
peaks and valleys
87
Antiparallel B-plated sheets are very ____
stable
88
B-turn is a ____ _____ in the ______ _____ that allows the strand to _____ its direction
sharp bend
polypeptide chain
reverse
89
The B-turn ____ the direction of the strand
reverses
90
Tertiary structure is the _______ of a ____ _____ ___ in 3D
folding, single polypeptide chain
91
Globular proteins contain segments of both ____ and ____, while fibrous proteins have _____ ____ ____
a-helix, b-strand, specialized tertiary structure
92
What three things make up fibrous proteins?
1. Collagen
2. a-keratin
3. Fibroin and B-keratin
93
The special collagen helix consists of three interwined polypeptide chains
Collagen
94
Formed by the coiling of a-helices
a-keratin
95
Consists primarily of B-sheet
B-keratin
96
What is tropocollagen?
A triple helix
97
What is the main protein of connective tissue?
Collagen
98
Makes up 25-35% of the whole body
Collagen
99
How many common types of collagen are there?
28 types
100
Type l collagen -
Most abundant, found in tendons, ligaments, skin, blood vessels, bone
101
Type ll collagen -
Cartilage, found in joints between bones, rib cage, nose, ears
102
What is the sequence of formation of tropocollagen and collagen?
1. Procollagen
2. Tropocollagen
3. Cross-linked fiber
103
Amino & carboxyl terminal ends - peptides DO NOT twist together
Procollagen
104
Protein component of skin, hair, fingernails are made up of _____
a-keratin
104
Cute amino & carboxyl terminal ends of procollagen
Peptidases
104
2 coiled coils (4 a-helices)
protofilament
105
4 protofibrils (32 a-helices)
intermediate filament
105
2 protofilaments (8 a-helices)
protofibril
106
Two a-helices
coiled coil
107
Pair of coiled coils
protofilament
108
Four right hand twisted protofibrils
filament
109
Disulfide bond formation creates ____ in hair
curls
110
Main silk protein
Fibroin
111
B-sheet of _____
Fibroin
112
Component of bird feathers, beaks, claws
B-Keratin
113
Antiparallel arrangement of B-sheet
Strands in opposite directions
114
Parallel arrangement of B-sheet
Strands in same direction
115
Antiparallel or parallel arrangment most stable?
Antiparallel
116
Globular proteins can be classified according to the type and arrangement of secondary structure:
- All a-helix proteins
- All b-strand proteins
- a/B proteins
- Proteins with little secondary structure
117
What are the four classes of globular protein structures? (ABBA LSS)
- All a-helix proteins
- All b-strand proteins
- a/B proteins
- Proteins with little secondary structure
118
A typical globular protein is _____
ribonuclease
119
Example of a-helix
growth hormone
120
Example of a b-strand
yB-crystallin (lens cornea of eye)
121
Example of a/B proteins
Flavodoxin (bacteria)
122
Example of protein with little secondary structure
Tachystatin (antimicrobial peptide)
123
What type of globular protein is ribonuclease?
a/B protein
124
Protein domains are also known as ____
modules
125
Protein domains or modules are ___ ____ ____ that are used repeatedly in the same protein or that are found in different proteins
amino acid sequences
126
How main amino acids does a protein domain typically contain?
40-100
127
Produced by the duplication of DNA segments within a gene or by the insertion of a copy of DNA segment into another gene
Protein domains
128
Protein domains are produced by the _____ of DNA segments within a gene
protein domains
129
Protein domains can be produced by the ____ of a copy of a DNA segments into another gene
insertion
130
Protein domains are produced by _____ or _____ of DNA segments
duplication or insertation
131
___ ____ are amino acid sequences used repeatedly in a single protein or that are found in different proteins
Protein domains/modules
132
What type of protein domain is unusual and less common?
different proteins
133
Domains in the ____ occur from faulty DNA replication
same protein
134
Domains in ____ occur after the insertion of a copy of a DNA segment into another gene
different proteins
135
Some domains are ___ and their function is unknown
neutral
136
Domains ___ over time and become unrecognizable to the original
mutate
137
Protein folding is the process of folding a _____ ___ into a ___ ___ with a precise 3D structure
polypeptide chain, globular protein
138
Step 1 of protein folding
1. newly synthesized polypeptide first forms segments of secondary structure (a-helix & B-sheet)
139
Step 2 of protein folding
2. These coalesce into a globular structure, primarily through hydrophobic interactions
140
Step 3 of protein folding
3. The final stable tertiary structure is generated by small adjustments to the folded structure
141
Step 4 of protein folding
4. In the cell, protein folding may require the assistance of molecular chaperones
142
In general the #D of folding of extended protein chain is dependent upon the ___ ___ ___ of that protein chain
amino acid sequence
143
(1) protein folding: A newly synthesized protein first forms segments of ___ ___
secondary structure
144
(2) protein folding: secondary structure of polypeptides arrange into a ____ shape by _____ interactions
globular, hydrophobic
145
(3) protein folding: final stable tertiary structure is generated by ____ _____ to the folded structure
small adjustments
146
Secondary structure of polypeptide arrange into a globular shape by _____ ____
hydrophobic interactions
147
(4) protein folding: Protein folding may need the assistance of ___ ___
molecular chaperones
148
Amyloid deposits
misfolded, insoluble, and aggregated proteins in brain cells
149
Two examples of amyloid deposits
Alzheimer's disease
Parkinson's disease
150
What protein is misfolded in Alzheimers disease?
amyloid-B
151
What protein is misfolded in Parkinson's disease?
a-synuclein
152
(1) step globular protein folding
rapid and reversible formation of local secondary structure (a-helix, B-strand)
153
(2) step globular protein folding
establishment of partially folded intermediates
154
(3) step globular protein folding
final tertiary structure
155
The association of protein subunits to form multi-subunit complexes is ____
quaternary structure
156
Do all proteins have quaternary structure?
NO
157
Proteins with quaternary structure are composed of ____ subunits or ____ types of ____ ____
identical , different, protein chains
158
The ____ producing quaternary structure are the same as those responsible for tertiary structure
forces
159
What four forces are involved in tertiary and quaternary structures?
- hydrophobic int
- hydrogen bonding
- ionic int
- disulfide bons
160
Quaternary structure allows for ___ ____ between protein subunits
cooperative behavior
161
In hemoglobin, there are ___ subunits
4
162
How does hemoglobin exhibit cooperative behavior?
The binding of the first O2 molecule makes it easier for three other O2 molecules to each bind to a subunit
163
Hemoglobin aides in what physiological function?
rapid release of O2 into the lungs
164
What are the two types of quaternary structure?
- fixed number of subunits
- open structure of microtubules
165
What are microtubules?
long, hollow tubes
166
Where are microtubules found?
cytoskeletion (cell structure)
mitotic spindles (cell division process)
167
Tubulin dimers ___ to form microbtubules
polymerize
168
Microtubules are dynamic and can easily ___
increase or decrease in length
169
Microtubules have ___ quaternary structure
open
