Chapter 4 - Protein Structure And Function Flashcards
1
Q
What are the kind of transport proteins
A
Hemoglobin and myoglobin
2
Q
What are the function of specific transport proteins like hemoglobin and myoglobin
A
Carry O2 and CO2 in blood and muscles
3
Q
What are the kind of structural proteins
A
Collagen and keratin
4
Q
What is the function of structural proteins like collagen and keratin
A
Form cartilage, hair, and nails
5
Q
What are the motor proteins
A
Actin and myosin
6
Q
What is the function of motor proteins like actin and myosin
A
Allow muscles to contract
7
Q
What are the defense proteins
A
Immunoglobulins
8
Q
What are immunoglobulins
A
Antibodies produce by WBCs
9
Q
What are the functions of defense proteins
A
Recognize foreign organisms and cancer cells
10
Q
Enzymes
A
Are proteins that catalyze chemical reactions
11
Q
Pepsin
A
Enzyme that breaks down proteins in stomach
12
Q
What is an example of storage protein
A
Ferritin
13
Q
What is the function of a storage protein, ferritin
A
stores iron in the liver
14
Q
What is a signal protein that controls blood glucose levels
A
Insulin
15
Q
What cells produce insulin
A
Beta cells of pancreas
16
Q
How does insulin control blood glucose levels
A
By decreasing blood glucose levels
17
Q
Receptors
A
Are proteins that detect signals and transmit them to the cell’s response machinery`
18
Q
What is a type of regulatory protein
A
Transcription factors
19
Q
Transcription factors
A
Regulatory proteins that regulate gene expression
20
Q
GFP, green fluorescent protein
A
Is special purpose protein from jelly fish that emits green light
21
Q
Proteins are made up of many what, and what is that called
A
Monomers, polymers
22
Q
Polymers of proteins
A
Amino acids building block of protein
23
Q
Example Protein that is made of up one polypeptide or polypeptide chain
A
Myoglobin
24
Q
Example of proteins that are made up of two or more polypeptide
A
Hemoglobin
25
What groups make up a protein
Side chain (R group)
Amino group
Carboxyl group
26
Carboxyl group behaves as a what, what charge
Acids, donating H ions to solution, negative charge
27
Amino group behaves as what, what charge
Base by accepting h ions, positively charged
28
Who are amino acids joined together and forms what kind of bond
Dehydration synthesis to form peptide bonds
29
How are covalent bonds formed for amino acids
Carboxyl group of one amino acids shares electrons with the nitrogen atom from the amino group of second amino acid
30
Polar covalent bonds
Bond between atoms that don’t share their electrons equally because they have different electro negativities
31
Electronegativity
Atom’s attraction (pull) for shared electrons
32
Examples of polar covalent bonds
C-N
O-H
S-H
33
No polar covalent bonds
Bond between atoms that equally share their electrons because they have the same or similar electronegatives
34
Example of nonpolar covalent bonds
C-C
C-H
O=O
S=C
35
Peptide bonds are what kind of bonds
Polar covalent
36
Amino acids are linked together into
Polypeptide chain
37
What are unique to proteins
N and C terminus
38
Which way does amino acids link
N to C direction
39
N terminus
Amino terminus, positively charged
40
C terminus
Carboxyl terminus, negatively charged
41
Side chains aka
R groups
42
Why are side chain important
Determine chemical properties of amino acids
43
Side chain or r groups can be classified into what
Polar (hydrophilic) or non polar (hydrophobic)
44
How many amino acids are there
20
45
GeorgiA
What charge
Basic or acidic
Polar or nonpolar
Aspartic acid
Glutamic acid
Negative
Acidic
Polar, hydrophilic
46
Home in ALabama
What charge
Basic or acidic
Polar or nonpolar
Histidine
Lysine
Arginine
Positive charged
basic
Polar hydrophilic
47
Calls Sally and George by AT&T
What charge
Basic or acidic
Polar or nonpolar
```
Cysteine
Serine
Glutamine
Asparagine
Threonine
Tyrosine
```
Uncharged
Neither basic or acidic
Polar
48
What is unique to polar amino acids in their side chains
They have oxygen or hydroxyl groups (OH-)
49
LT GAV PIMP
What charge
Basic or acidic
Polar or nonpolar
Leucine, tryptophan, glycine, alanine, valine, proline, isoleucine, methionine, phenylalanine
No charge
Not basic or acidic
Non polar, hydrophobic
50
What is unique to nonpolar amino acids side chains
Have CH2, or methyl CH3 group in their side chains
51
What is the pneumonic to remember all 20 amino acids
LT GAV PIMP Calls Sally and George by AT&T from GeorgiA to their Home in ALabama
52
What determines the proteins function and with the help of what
The shape, with the help of three types of non covalent bonds
53
What are the three types of non-covalent bonds for proteins
Ionic bonds
Hydrogen
Van Dre Waals attraction
54
What happens when they are many of van der waals attraction
Causes bond to be strong
55
Ionic bonds
Bonds form between opposite charges
56
Van der waals
Weak attraction that form between atoms at very short differences due to their fluctuating electrical charges
57
Why are hydrogen bonds important for hydrogen bonds
Help stabilize proteins folded shape
58
What are the three types of hydrogen bonds
Backbone to backbone
Backbone to side chain
Side chain to side chain
59
Interactions that contribute to protein shape
Hydrophobic forces
60
What are so unique to hydrophobic forces to proteins
Help proteins fold into compact conformations (final folded structures)
61
In biology what bond is the strongest
Covalent
62
In chemistry was bonds are the strongest
Ionic
63
List the bonds to strongest to weakest
Covalent > Ionic > H bonds > hydrophobic forces > Van der waals attractions
64
What type of bond can be found in a single protein
H bonds
65
Denatured
Unfolded
66
How can proteins become denatured
Through exposure to heat, wrong pH or chemicals
67
How does desaturation works
It disrupts the noncovalent interactions holding the folded chain
68
Denatured proteins have only what bond
Peptide covalent bonds
69
Renaturation
Some proteins can be regenerated upon removal of denature good agent
70
What agent can causes denaturation to proteins
Urea
71
How can urea causes denaturation
Squeezes between H bonds
| Diminishes hydrophobic forces
72
Can denaturation be undone
In some cases, but mostly no
73
Protein aggregation
Occur when misfolded proteins aggregate
74
Protein aggregation causes underlying number of neurodegenerative disorders which are
Alzheimer’s disease and Huntington’s disease
75
Prion diseases causes what in sheep, cattle, and humans
Scrapie
Mad cow
CJD creutzfeld jacob disease
Protein aggregate
76
What disrupt brain function that can result in death due to aggregates
Amyloid fibril
77
How can abnormal prion proteins be transferred to normal individuals
Blood, food or surgical instruments
78
Chaperons
Proteins that help incorrectly folded and newly synthesized proteins fold correctly
79
Heat shock proteins HSP
Produce when cells are exposed to elevated temperatures and other stresses
80
What organelle has many chaperons
Rough ER
81
What does the alpha helix looks like and what bonds are formed
Spiral, which the N-H of every peptide bond is hydrogen bonded to the C=O neighboring peptide bond
82
How does alpha helixes form
Backbone to backbone h bonds
83
The b sheet resembles what
Picket fence
84
The b sheets are connected by
Which individual polypeptide chains strands in the sheet are held together by hydrogen bonding between peptide bonds in different strands
85
Hydrophobic side chains of the amino acids formin the alpha helix contact what
They hydrophobic hydrocarbon tails of the phospholipids
86
Hydrophilic parts of the polypeptide backbone form what
Hydrogen bonds with another interior of the helix
87
Two alpha helixes can wrap around each other with ...
Hydrophobic side chains
88
What is left exposed to the aqueous environment for intertwined alpha helices
Hydrophobic side chains
89
What are the proteins levels or organization
Primary, secondary, tertiary, quaternary structure
90
What are two types of protein secondary structures
Beta sheets and alpha helix
91
Primary structure
Sequence of amino acids, this is not functional
92
What types of bonds does primary structures have
Only peptide bonds, covalent
93
Secondary structures functional or non functional
Non functional
94
What kind of bonds does secondary structure protein has
Backbone to backbone, h bonds and peptide bonds
95
Tertiary structure
Final 3D shape of protein consisting of a single polypeptide chain
96
Quaternary structure
Arrangement of 2 or more polypeptide chains in space
97
What kind of bonds does quaternary structure
Back bone to backbone, h bonds, peptide bonds, and any other bonds
98
If a protein is made up of one polypeptide chain, how does it become functional
By reaching its tertiary structure
99
What is an example of a protein that is made of one polypeptide chain
Myoglobin
100
Denatured myoglobin loses what structures
Secondary and tertiary structures
101
How does a proteins that is made out of 2 or more polypeptides becomes functional
By reaching its quaternary structure
102
Example of a protein made out of 2 or more polypeptides
Hemoglobin
103
Hemoglobin is made out of how many polypeptides
4
104
Denatured hemoglobin loses what structures
Secondary, tertiary, and quaternary structures
105
Protein dissociation and how can this happen
2 or more polypeptides that makes up a protein come apart; loses quaternary structures, this happens by exposure to salts
106
How is protein dissociation related to denaturation
Easier to fix than denaturation
107
Protein is made up of only 1 polypeptide undergoes what...
Denaturation or dissociation
Denaturation only
108
Protein made 2 or more polypeptides undergoes what
Denaturation and dissociation
Both
109
Protein domain
Any segment of polypeptide chain that can fold independently into compact, stable structure
110
Unstructured regions in proteins
Separate proteins domains from each other
111
Protein family
Each family member has amino acids sequences and 3D conformation that closely resembles that of the other family members
112
Active site
Region of enzyme where peptide bond of its protein substrate is bound and cleaved by hydrolysis
113
Binding site
Any region on proteins surface that interacts with another molecule through sets of noncovalent bonds
114
What are the different subunits of hemoglobin
2 alpha globin subunits and 2 beta globin subunits
115
Each subunits contains what for hemoglobin
Heme group with iron atom for O2 binding
116
Dimer
A molecule consisting of two identical molecules linked together
117
Protein with just one binding site can form what
Dimer with another identical protien
118
Identical proteins with two different binding sites will often form what
Helical filament
119
How can proteins form a ring
Two binding sites of identical proteins are disposed appropriately to each other
120
Actin filament is what kind of structure
Helical structure
121
How is actin filaments formed
Many identical protein subunits
122
Single protein subunits can pack to form
Filaments, tube or spherical shell
123
Types of proteins that has elongated fibrous shapes
Collagen and elastin
124
Fibrous proteins
Relatively simple, elongated 3D shaped
125
Collagen
Triple helix formed by three polypeptide chains
126
Elastin
Cross linked together by covalent bonds to form rubberlike elastic fibers
127
Disulfide bonds are stronger or weaker than peptide bonds
Weaker
128
Are disulfide bonds polar or nonpolar
Non polar
129
Disulfide bonds
Covalent bonds that form between the sulfur atoms of adjacent cysteine side chains
130
What is important about the disulfide bonds
Help stabilize the tertiary and quarternary conformations
131
The activity of proteins depends on
Their ability to bind specifically to other molecules, allowing them to act as catalyst, structural supports, signal receptors and tiny motors
132
What is needed to enable protein to bind tightly to ligand
Many noncovalent bonds are needed
133
Binding sites allow protein to interact with ...
Specific ligand by forming noncovalent bonds
134
What is unique to the binding sites of antibodies
They are versatile
135
Antibodies
Immunoglobulins proteins that are produced by white blood cells called B sites
136
What are antibodies used for
Immune system to recognize foreign molecules found on the surface of cancer cells invade microorganisms
137
Antigen
Foreign molecules
138
Antibodies are composed of what
2 identical heavy chains and 2 identical light chains held together by disulfide bonds
139
How does antigen bonding site forms
When Vh and Vl domains come close together
140
What domain is closely involved in binding to antigen
Vl domain
141
Enzymes convert substrates to what
Products
142
Catalyst does what to activation energy
Lowers it
143
Each enzyme has its own _______ which binds to the __________
Substrate; active site
144
Hydrolase
General term for enzymes that catalyze a hydrolytic cleavage reaction
145
Nuclease
Breaks down nucleic acids by hydrolyzing bonds between nucleotides
146
Protease
Breaks down proteins by hydrolyzing peptide bonds between amino acids
147
Ligase
Joins two molecules together; DNA Ligase joins the two DNA strands together end to end
148
Isomerase
Catalyze the rearrangement of bonds within a single molecule
149
Polymerase
Catalyze polmerization reactions such as the synthesis of DNA and RNA
150
Kinase
Catalyze the addition of phosphate groups to molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins
151
Phosphatase
Catalyzes the hydrolytic removal of a phosphate group from a molecule
152
Oxide-reductase
General name for enzymes that catalyzes reactions in which one molecule is oxidized while the other is reduced.
153
ATPase
Hydrolyzes ATP. Many proteins have an energy harnessing ATPase activity as part of their function, including motor proteins such as myosin
154
DNase and RNase
Nucleases that break down DNA and RNA by hydrolyzing phosphodiester bonds
155
Ribozymes
Enzymes that RNA molecules in nature
156
Peptidyltranserase
rNA of the large ribosomal subunit that catalyzes the formation of peptide bonds between amino acids
157
Lysozyme
Enzyme which cleaves the polysaccharide chains that form the cell wall of the bacteria, act as a natural antibiotics
158
Polysaccharides are made up of what
Glycosidic links
159
What is true about enzymes and reactions,can it be consumed?
No, It can be reused in rxns
160
What happens of the active site of lysozymes
Bonds are bent and brokenness
161
Proteins are controlled by what
Inhibitors and activators
162
Allosteric enzymes has how many binding sites that influences one another
Two or more
163
Phosphorylation can control activity by causing
Conformational change
164
Regulatory GTP binding proteins are switched on and off by
The gain and loss of phosphate group become when GPD binds to them they become active.
165
Allosteric site
Region of enzyme where molecule other than substrate binds
166
Biochemical pathway
Consist of multiple chemical reaction that occur at the same area and the product of one enzyme becomes the substrate of the next
167
Where glycolysis occurs
Cytoplasm
168
Feedback inhibition (negative regulation)
Process in which late product of the pathway inhibits enzynme acting early in the pathway by binding to allosteric site, it will make site inactive
169
How does feedback inhibition triggers conformational change
By altering the enzymes active site
170
Competition inhibition
Competes with substrate for the enzymes active site while noncompeptitor inhibition does not, it binds to allosteric site.
171
Non competition inhibition or allosteric inhibitor
Allosteric activations help enzymes work better. They invade cofactors; some are inorganic copper zinc and iron
172
Positive feedback or positive regulation
Process in which the enzyme activity is stimulated by regulatory molecule
173
Production of what is an example of positive feedback
Oxytocin
174
Oxytocin
Hormone causes contractions of uterus
175
What is true about ATP levels
When they are low, ADP levels are high and ADP activates the enzyme that catalyzes the conversion of sugar to produce more ATP
176
The transfer of phosphate group from ATP to the hydroxyl group on serine, threonine, or tyrosine side chain of what target protein
Protein kinase
177
Protein phosphatases does what
Dephosphorylate phosphorylated proteins
178
Why is phosphorylation of a protein by protein kinase
Can either increase or decrease the protein’s activity depending on the site of phosphorylation and the structure of the protein
179
If protein is activated by phosphorylation, it is _________ by dephosphorylation
Inactivated
180
When GTP is bound to proteins, they are what
Active
181
What is GTP
Guanosine triphosphate
182
GTP is made up of what
5 c sugar, ribose
Guanine
3 phosphate groups
183
When does GTP becomes inactive
When GTP is hydrolyzed into GDP, releasing Pi (inorganic phosphate)
184
What 3 main things are motor proteins responsible for
Muscle contractions, separation of chromosomes during mitosis, and movement of materials and organelles within the cell.
185
What allows motor proteins to move continuously in one direction along the cytoskeletal filament
Three conformational changes
186
What covalent modification control the activity and degradation of the tumor suppressor protein p53
Phosphorylation, ubiquitylation, acetylation
187
Acetylation
Acetyl groups (COCH3) are added to protein
188
P53 regulates what
Cells response to DNA damage
189
What kind of gene is p53
A tumor suppressor gene
190
What makes p53 function
Acetylation and phosphorylation
191
What degrades p53
Ubiquitylation
192
When do we want p53 active and when do we not want it active
We want it active when there is DNA damage
When there is no damage, we don’t need p53
193
Will all the modifications for p53 be present
No
194
What is the most mutated gene
P53
195
What is the function of normal p53
Stops cell division when DNA is damaged
Triggers the production of the DNA repair enzymes
If DNA is fixed, the cell divides
If DNA is not fixed, p 53 proteins causes the cell to commit suicide or apoptosis
196
Ubiquitylation
Marks protein for degradation binds with another protein
197
Proteasome
Cylindrical complexes found in cytoplasm and nucleus of eukaryotes and are made of proteases
198
How are proteins studied
Centrifuge
Chromatography
Gel electrophoresis
Isoelectric focusing
199
Centrifugation
Separates cells components on the basis of size and density.
200
What are the three kinds of chromatography
Ion exchange chromatography
Gel filtration chromatography
Affinity Chromatography
201
What is the importance of affinity chromatography
Isolated the binding partner of protein of interest.
202
How is protein x related to insulin
Receptor protein
203
Where does glucagon made from
Alpha cells of pancreas
204
Adrenaline is made
Cells of adrenal glands
205
Insulin is made where
Beta cells of pancreas
206
What does SDS causes polypeptides to do
To unfold and makes them negatively charged
