Biochem #3 Flashcards
1
Q
motif
A
a repetitive organization of secondary structural elements together.
Gives proteins a fibrous nature
2
Q
what are the 5 structural proteins?
A
collagen, elastin, keratin, actin, tubulin
3
Q
collagen
A
Characteristic trihelical fiber
Extracellular matrix of connective tissue
Found throughout the body
Providing strength and flexibility
4
Q
elastin
A
Extracellular matrix of connective tissue
Stretch and recoil like a spring, which restores the original shape of the tissue
5
Q
keratin
A
Intermediate filament proteins found in epithelial cells.
Mechanical integrity of the cell
Regulatory proteins
The primary protein that makes up hair and nails.
6
Q
actin
A
Makes up microfilaments and thin filaments in myofibrils.
Most abundant protein in eukaryotic cells.
Has a positive side and a negative side which allows motor proteins to travel unidirectionally along an actin filament.
7
Q
tubulin
A
Makes up microtubules
Important for providing structure, chromosome separation in mitosis and meiosis, and intracellular transport with kinesin and dynein.
Also has polarity with the negative end located close to the nucleus.
8
Q
motor proteins
A
a class of molecular motors that can move along the cytoplasm of animal cells.
They convert chemical energy into mechanical work by the hydrolysis of ATP.
9
Q
ATPase
A
enzymatic activity, power the conformational change necessary for motor function.
10
Q
myosin
A
primary motor protein that interacts with actin.
Involved in muscles and cellular transport
Has a head and neck, neck responsible for the power stroke of sarcomere contraction.
11
Q
kinesin and dynein
A
motor proteins associated with microtubules
They have two heads with at least one of them remaining attached to tubulin at all times.
Kinesin:
• Align chromosomes during metaphase
• Depolymerizing MT during anaphase of mitosis.
Dynein:
• Sliding movement of cilia and flagella
Both:
• Vesicle transport in the cell (kinesin brings vesicles to + end of MT, dynein brings vesicles to – end of MT)
• Ex: kinesins bring vesicles of neurotransmitters to positive end of neuronal MT toward synaptic terminal and dynein bring vesicles of waste neurotransmitter back to negative end of MT
12
Q
kinesin specifically
A
- Align chromosomes during metaphase
* Depolymerizing MT during anaphase of mitosis.
13
Q
dynein specifically
A
• Sliding movement of cilia and flagella
14
Q
cell adhesion molecules
A
(CAMs): proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix or other cells. 3 main groups:
15
Q
what are the main groups of cell adhesion molecules
A
cadherins
integrins
selectins
16
Q
cadherins
A
Holds together two cells of the same or similar type using calcium
group of glycoproteins that mediate calcium-dependent cell adhesion
Often hold similar cell types together (epithelial cells)
Different cells have specific cadherins: E-cadherins for epithelial and N-cadherins for nerve cells
17
Q
integrins
A
have two membrane-spanning chains called α and β.
Important for binding to and communicating with the ECM.
Cell signaling: mitosis, apoptosis, etc.
18
Q
selectins
A
bind to carbohydrate molecules that project from other cell surfaces (weakest of the CAM bonds)
White blood cell migration and inflammation
19
Q
antibodies
A
proteins produced by B cells that function to neutralize targets in the body, such as toxins and bacteria, and then recruit other cells to eliminate the threat.
Y shaped made up of two identical heavy and 2 identical light chains.
20
Q
antigens
A
protein, antibody target
21
Q
antibody antigen binding region
A
at the tips of the Y, specific polypeptide sequences that will bind one, and only one, specific antigenic sequence.
22
Q
what are the 3 results of antibody binding to antigen
A
- Neutralizing the antigen, making the pathogen or toxin unable to exert its effect on the body
- Opsonization: Marking the pathogen for destruction by other white blood cells immediately
- Agglutinating: clumping together the antigen and antibody into large insoluble proteins complexes that can be phagocytized and digested by macrophages.
23
Q
opsonization
A
antibody
Marking the pathogen for destruction by other white blood cells immediately
24
Q
agglutinating
A
clumping together the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages.
25
biosignaling
a process in which cells receive and act on signals
o Ex: how proteins are involved: extracellular ligands, transporters for facilitated diffusion, receptor proteins, and second messengers.
26
ion channels
proteins that create specific pathways for charged molecules.
27
facilitated diffusion
all of the ion channels act this way, a type of passive transport, the diffusion of molecules down a concentration gradient through a pore in the membrane created by this transmembrane protein.
Used for molecules impermeable to the membrane: large, polar, charged
28
ungated ion channels
have no gates and are therefore unregulated
| • Ex: all cells have ungated potassium channels
29
voltage-gated ion channels
the gate is regulated by the membrane potential change near the channel.
• Ex: neurons possess voltage-gated sodium channels. The channels are closed under resting conditions, but membrane depolarization causes protein conformation change that allows them to quickly open and then quickly close as the voltage increases.
30
ligand-gated ion channels
: the binding of a specific substance or ligand to the channel causes it to open or close.
• Ex: neurotransmitters act at ligand-gated channels at the postsynaptic membrane: GABA binds to chloride channel and opens it.
o Km and Vmax can be applied: Km: the solute concentration at which the transporter is functioning at half of its maximum activity.
31
enzyme linked receptors
membrane receptors may also display catalytic activity in response to ligand binding
Have 3 primary protein domains (all one enzyme):
• 1. Membrane-spanning domain: anchors the receptor in the cell membrane
• 2. Ligand-binding domain: stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain
• 3. Catalytic domain: activation results in the initiation of a second messenger cascade.
o Second messenger cascade: second messenger continues the rest of the pathway.
Ex: RTK: receptor tyrosine kinase
32
why are second messenger pathways important?
generate amplified signals from low concentration of signal.
33
GPCR
large family of integral membrane proteins involved in signal transduction. Characterized by 7 membrane-spanning alpha-helices
Differ in the ligand-binding area found on the extracellular surface of the cell.
Use heterotrimeric G protein: intracellular link to Guanin nucleotides (GDP and ATP)
Binding of ligand increases the affinity of the receptor for the G protein. G proteins:
• Gs: stimulates adenylate cyclase, which increases levels of cAMP in the cell
• Gi: inhibits adenylate cyclase, which decreases levels of cAMP in the cell
• Gq activates phospholipase C, which cleaves phospholipid from membrane to form PIP2. PIP2 is then cleaved into DAG and IP3; IP3 can open calcium channels in the ER, increasing calcium levels in the cell.
• GPCR steps
o The three subunits that comprise the G protein are α, β, and γ. In inactive form, α subunit binds GDP and is a complex with β, and γ. GPCR binds ligand, the receptor becomes activated and engages the G protein. GTP replaces GDP, α dissociates from other two subunits, alters the activity of adenylate cyclase (example). When GTP is dephosphorylated back to GDP, subunits come back together and the G protein becomes inactive.
34
what are the steps of the GPCR pathway?
The three subunits that comprise the G protein are α, β, and γ. In inactive form, α subunit binds GDP and is a complex with β, and γ. GPCR binds ligand, the receptor becomes activated and engages the G protein. GTP replaces GDP, α dissociates from other two subunits, alters the activity of adenylate cyclase (example). When GTP is dephosphorylated back to GDP, subunits come back together and the G protein becomes inactive
35
what triggers the dissociation of the alpha subunit from the beta and gamma units on the G protein during GPCR pathway?
ligand binds, receptor becomes activated, engages the G protein, binding of GTP to the G protein
36
homogenization
crushing, grinding, or blending the tissue of interest into an evenly mixed solution
37
centrifugation
distinguish proteins of different sizes.
o Centrifugation is a technique used for the separation of particles from a solution according to their size, shape, density, viscosity of the medium and rotor speed. The particles are suspended in a liquid medium and placed in a centrifuge tube. The tube is then placed in a rotor and spun at a define speed
the larger the size and density of the particles, the more they separate from the mixture and end up in the pellet.
38
electrophoresis
subjecting compounds to an electric field, which moves them according to their net charge and size.
o Positive charge compounds: migrate to negatively charged cathode cations to cathode
o Negative charge compounds: migrate to positively charged anode anions to anode
o Migration velocity: the velocity of migration of the compound.
E = electric field strength, z = net charge on the molecule, f = frictional coefficient
v = Ez/f
o Polyacrylamide gel: the standard medium for protein electrophoresis
Slightly porous matrix mixture, solidifies at room temperature.
Slower particles move faster through it.
o Native PAGE: Polyacrylamide gel electrophoresis (PAGE): a method for analyzing proteins in their native states
Limited as some different proteins may travel the same distance.
Most useful for: compare the molecular size or the charge of proteins known to be similar in size from other analytical methods (SDS PAGE or size-exclusion chromatography)
o SDS-PAGE
Sodium dodecyl sulfate (SDS) PAGE is useful because it separates based on relative molecular mass alone.
SDS is a detergent that denatures the protein and makes it have a net 0 charge.
Velocity through the gel is only affected by E and f (depends on mass).
39
in electrophoresis, where do the positively and negatively charged components migrate?
postive (cations to cathode
| negative (anions) to anode
40
migration velocity
the velocity of migration of the compound.
E = electric field strength, z = net charge on the molecule, f = frictional coefficient
v = Ez/f
41
polyacrylamide gel
the standard medium for protein electrophoresis
Slightly porous matrix mixture, solidifies at room temperature.
Slower particles move faster through it.
42
Native PAGE
a method for analyzing proteins in their native states
| Limited as some different proteins may travel the same distance.
43
SDS-PAGE
Sodium dodecyl sulfate (SDS) PAGE is useful because it separates based on relative molecular mass alone.
SDS is a detergent that denatures the protein and makes it have a net 0 charge.
Velocity through the gel is only affected by E and f (depends on mass).
44
isoelectric focusing
separate proteins based on their isoelectric point. Exploits the acidic and basic properties of amino acids by separating on the basis of pI.
o pI: the pH at which the protein or amino acid is electrically neutral.
o Process: Placed in gel, acidic gel at the anode, basic gel at the cathode. Electric field is generated across the gel. As the protein gets to a point on the gel at which the pH is equal to the protein’s pI, it takes on a neutral charge and stops.
45
chromatography
uses physical and chemical properties to separate and identify compounds from a complex mixture.
o Useful: isolated proteins are immediately available for identification and quantification.
o Overall: the more similar the compound to its surroundings, the more it will stick and move slowly. only differs for size exclusion chromatography
Preferred over electrophoresis when separating large amounts of protein.
46
describe the process of chromatography
sample is placed onto a solid medium (stationary phase or adsorbent). Run the mobile phase through the stationary phase. This allows the sample to elute through the stationary phase. Sample migrates depending on affinity to mobile or stationary phase.
Retention time: amount of time a compound spends in the stationary phase
• Partitioning: varying retention times of each compound results in separation of the components.
47
retention time
amount of time a compound spends in the stationary phase
48
partitioning
chromatography
| varying retention times of each compound results in separation of the components within the stationary phase.
49
column chromatography
A column is filled with silica or alumina beads as an absorbent, and gravity moves the solvent and compounds down the column. Silica gel is polar. Less polar the compound, the faster it elutes out.
The sample is added at the top of the column and a solvent is poured over it. The more similar the sample is to the solvent (mobile phase), the quicker it will elute; the more similar it is to the alumina or silica (stationary phase), the more slowly it will elute (if at all).
50
ion exchange chromatography
the beads in the column are coated with charged substances so they attract or bind compounds that have an opposite charge.
After all other compounds have moved through the column, a salt gradient is used to elute the charged molecules that have stuck to the column.
51
size exclusion chromatography
the beads in the column contain tiny pores of varying sizes.
Smaller compounds fit in the beads and actually elute slower. Large elute first!
Can do ion exchange and then size exclusion
52
affinity chromatography
bind any protein of interest by manipulating the column with things such as a receptor that binds the protein or an antibody.
Protein of interest is retained in the column.
Ex: nickel and histidine tag on POI
Use something that competes with the binding to get it off.
53
x ray crystallography
measures electron density on an extremely high-resolution scale and can also be used for nucleic acids.
o Generates an x-ray diffraction pattern, can be analyzed for protein structure
o The experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions
54
methods used to determine protein structure
x ray crystallography and NMR spectroscopy
55
methods used to determine amino acid composition
• To determine the exact sequence of a protein, can’t just cut randomly at different spots.
o Need specific cleavage enzymes.
• Edman degradation: uses cleavage to sequence proteins of up to 50-70 AA
o Selectively and sequentially removes the N-terminal amino acid of the protein, which can be analyzed via mass spec.
o Other methods are used for bigger structures: chymotrypsin and trypsin cannot determine location of disulfide links or salt bridges
56
measuring activity of a protein
* Monitoring a known reaction with a given concentration of substrate and comparing it to a standard.
* Concentration and purification affect it.
57
protein concentration determination
• Almost determined exclusively through spectroscopy.
• UV spectroscopy: due to aromatic side chains.
o Sensitive to sample contaminants
• Proteins cause colorimetric changes with specific reactions: bicinchoninic acid (BCA) assay, Lowry reagent assay, and Bradford protein assay
o Bradford Protein Assay: mixes a protein in solution with Coomassie Brilliant Blue Dye. Protonated and green-brown in color prior to mixing with proteins.
Increased protein concentrations correspond to a larger concentration of blue dye in the solution.
Make a standard curve first with known protein concentrations.
Limited by: excessive buffer, detergent in sample, multiple proteins in sample
58
UV spec
due to aromatic side chains.
| o Sensitive to sample contaminants
59
proteins cause _______ changes with specific reactions: bicinchoninic acid (BCA) assay, Lowry reagent assay, and Bradford protein assay
colorimetric
60
bradford protein assay
mixes a protein in solution with Coomassie Brilliant Blue Dye. Protonated and green-brown in color prior to mixing with proteins.
Increased protein concentrations correspond to a larger concentration of blue dye in the solution.
Make a standard curve first with known protein concentrations.
Limited by: excessive buffer, detergent in sample, multiple proteins in sample
61
where are the negative and positive ends of the microtubule located?
positive: periphery of the cell
negative: near the nucleus
62
motor proteins can have _____ and ____ roles.
enzymatic and structural roles.
| they can act as ATPases
63
compare the number of heads of myosin vs. kinesin and dynein
myosin has one head while myosin and kinesin have 2
64
kinesin brings vesicles toward the ____ of the microtubule, while dynein brings vesicles to the ____ end
positive
| negative
65
give some examples of the role of binding proteins
can play stabilizing functions, transport molecules (hemoglobin), DNA binding proteins (transcription factors)
66
describe the role of integrin and selectin in host defense
integrin allows platelets to stick to fibrinogen and cause activation of platelets to stabilize a blood clot
selectin allows white blood cells to squeeze through endothelial cells
67
what is another name for antibodies? Are antibodies proteins?
immunoglobulin
| yes
68
how are the heavy and light chains of antibodies held together?
disulfide linkages and noncovalent interactions
69
What is the shape of an antibody and where is the antigen binding region on an antibody?
Y. On the Y.
70
describe the type of adhesion of the 3 cell adhesion molecules
cadherin: 2 cells of the same or similar type using calcium
integrin: one cell to proteins in the extracellular matrix
selectin: one cell to carbohydrates usually on the surface of other cells
71
list some functions of proteins in biosignaling
extracellular ligands, transporters, receptor proteins, second messengers
72
what type of molecules are impermeable to the cell membrane
large, polar, charged
73
what are the types of ion channels
ungated, voltage-gated, ligand-gated
74
pacemaker current in cells of the sinoatrial node of the heart
voltage-gated non-specific sodium-potassium channels
75
how do protein receptors related to Michaelis Menten kinetics?
the Km refers to the solute concentration at which the transporter is functioning at half its maximum capacity
76
explain voltage gated and ligand gated ion channels in the nervous system
neurotransmitters bind to ligand gated channels at the postsynaptic membrane
voltage gated ion channels allow the action potential to travel down an axon
77
how do enzyme linked receptors work?
the ligand-binding domain is stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain. Can result in the initiation of a second messenger cascade.
78
describe receptor tyrosin kinases
type of enzyme-linked receptor
| upon binding of the ligand, dimerizes and can phosphorylate intracellular enzymes and itself.
79
in order for G protein couple receptors to transmit signals to an effector in the cell, they utilize _____
heterotrimeric G protein
80
what are the main types of G proteins?
Gs: stimulates adenylate cyclase which increases cAMP levels in the cell
Gi: inhibits adenylate cyclase which decreases cAMP levels in the cell
Gq: activates phospholipase C, end of reaction is increased calcium levels in the cell upon release from the endoplasmic reticulum.
81
how are transport kinetics similar and different from enzyme kinetics
there is a Km and vmax based on how efficient the transporter is
there is no Keq because no catalysis is actually happening.
82
are electrophoresis and chromatograph used for native or denatured proteins?
both for both
83
in electrophoresis, the anode is ___ charged and the cathode is ___ charged
anode: positive
cathode: negative
84
polyacrylamide gel acts as a _____, allowing smaller particles to pass through easily while retaining large particles
sieve
85
in electrophoresis, which particles move the fastest?
highest charge and smallest mass
86
what method is used to analyze proteins in their native states?
polyacrylamide gel electrophoresis (PAGE)
87
what are the uses of native PAGE electrophoresis?
compare the molecular size or the charge of proteins known to be similar in charge (discovered from SDS-PAGE or size exclusion chromatography)
88
protein atomic mass is usually expressed in ____. The average mass of an amino acid is ____.
```
daltons (Da), same as g/mol
100 daltons (100 g/mol)
```
89
what does SDS stand for?
sodium dodecyl sulfate
90
what is the isoelectric point?
the pH at which the protein or amino acid is electrically neutral
91
explain the pH gradient in isoelectric focusing
acidic gel at the positive anode, neutral in the middle, basic gel at the negative cathode
92
why is chromatography super valuable?
the isolated proteins are immediately available for identification and quantification
93
what is it called when the mobile phase runs by the stationary phase in chromatography?
eluting
94
in ion exchange chromatography, what is used to elute the material stuck to the column at the end?
salt gradient
95
what are two drawbacks of affinity chromatography?
the POI may have too high affinity to the stationary phase and will not come out (elute)
the POI is permanently stuck to the eluent
96
how is protein structure determined?
x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy
97
edman degradation
uses cleavage to sequence proteins of up to 50-70 AA. Sequentially removes the N-terminal amino acid which can be analyzed via mass spectroscopy
98
UV spectroscopy can be used to look at proteins with _____
aromatic side chains
99
activity analysis
observe concentration in comparison to a standard and can also look at color change as the reaction progresses
100
amino acid composition can be determined by ____, but amino acid sequencing requires ____
```
simple hydrolysis
sequential degradation (Edman degradation)
```
101
bradford protein assay has what color change
brown/green to blue
102
are centrioles or actin involved in cell movement?
only actin (actin polymerization at the leading edge of the cell)
103
both GPCR and enzyme-linked receptors are ______ systems
second messenger systems
104
calcium must be sequestered because ____
it is involved in muscle contraction, exocytosis of NT, and other tightly regulated cellular processes. `
105
___ channels promote the resting membrane potential
ungated ion channels
106
Gs, Gi, and Gq are all subtypes of the G____ subunit of trimeric G protein
Galpha
107
UV spectroscopy is for _____ systems
conjugated
