Lectures 1-7 Flashcards
(106 cards)
1
Q
What are the 4 allosteric effectors of hemoglobin?
A
- oxygen itself affects the binding of additional molecules of oxygen
- CO2
- protons
- 2,3-bisphosphoglycerate (2,3-BPG)
2
Q
Lowered pH shifts the p02 curve to the…
A
Right
3
Q
This lowering of the pH causes a BLANK in the affinity of hemoglobin for oxygen, a phenomenon known as the BLANK.
A
Decrease; Bohr Effect
4
Q
The Bohr effect allows…
A
More oxygen to be released from hemoglobin in active tissues where the pH is low.
5
Q
Binding of CO2 to hemoglobin BLANK it’s affinity for oxygen.
A
Decreases
6
Q
CO2 binding to hemoglobin results in
A
Release of more oxygen in tissues that contain a high concentration of CO2.
7
Q
Binding of 2,3-BPG BLANK the affinity of hemoglobin for oxygen.
A
Decreases
8
Q
Binding of 2,3-BPG shifts the oxygen curve to the…
A
Right
9
Q
For a drug that binds to a receptor to be efficacious, should it have a lower or higher KD than the natural ligand? Why?
A
Yes, because the lower the KD the higher the ligand’s affinity for the protein and you would want the drug’s affinity to be higher than the natural ligand.
10
Q
Explain why cooperative binding of oxygen to hemoglobin is important for the normal transport of oxygen from lungs to tissues.
A
Cooperative binding allows hemoglobin to become completely saturated with oxygen in the lungs and release it in the tissues.
11
Q
How does 2,3-BPG affect oxygen exchange in high altitudes?
A
It allows oxygen to be released at higher partial pressures of oxygen.
12
Q
3 most abundant glycerophospholipids…
A
phosphatidylethanolamine (PE), phosphatidylcholine (PC), and phosphatidylserine (PS).
13
Q
What makes up a glycerophospholipid?
A
It is a derivative of glycerol. Two of the hydroxyl groups in glycerol are in ester linkages to fatty acids and the third is attached to a polar headgroup through a phosphate group. The backbone of glycerophospholipids is called phosphatidic acid.
14
Q
What makes up a sphingolipid?
A
There is a sphingosine backbone that contains two long hydrocarbon chains but does not contain a phosphate group. This family includes ceramide, sphingomyelin, and the glycolipids.
15
Q
Defects in the metabolism of sphingolipids are responsible for?
A
Several types of lysosomal storage diseases.
16
Q
Cholesterol composition?
A
Multi-ring structure (called the steroid nucleus), a hydrocarbon tail, and a hydroxyl group. The hydroxyl group is the only polar portion of the structure.
17
Q
Another glycophospholipid found in the membrane?
A
Phosphatidylinositol (PI) plays an key role by functioning as a precursor for signaling molecules that are generated in response to extracellular signals.
18
Q
What lipids are predominantly on the cytosolic side of the bilayer?
A
The negatively charged phospholipids, PS and PI, and the neutral phospholipid PE are all predominantly found on the cytosolic side of the bilayer.
19
Q
What lipids are predominantly on the extracellular side of the bilayer?
A
PC, sphingomyelin, and glycolipids are predominantly found on the extracellular side of the bilayer.
20
Q
What lipid is found relatively equally in both monolayers of the bilayer?
A
Cholesterol
21
Q
Increasing the concentration of cholesterol in a membrane….
A
Decreases the permeability to small polar molecules such as water.
22
Q
For a typical membrane, the ratio of lipid molecules to protein molecules is about…
A
50:1
23
Q
What are 3 characteristics of membrane spanning regions of alpha helix transmembrane proteins?
A
First, they contain predominantly hydrophobic side chains that interact with the lipid bilayer. Second, residues that interact with the phospholipid head groups tend to have positive side chains because of the negative charge of the phospholipids. Third, intracellular regions close to the membrane tend to be abundant with positively charged residues, which often interact with the particular lipids in these regions (“Positive Inside Out Rule”).
24
Q
What are the three major classes of lipids found in the plasma membrane?
A
Glycerophospholipids, sphingolipids, and cholesterols.
25
How do we name fatty acids?
The name of a fatty acid is composed of the number of carbons, the number of double bonds, and the position of the double bonds.
26
Explain why triglycerides are not found in cell membranes.
Triglycerides are entirely hydrophobic and membrane lipids need to be both hydrophobic and hydrophilic.
27
How does a binding ligand activate a receptor and allow interaction with a G protein?
The receptor interacts with the ligand, which binds extracellularly and causes a conformational change in the receptor. This change allows the intracellular domain of the receptor to interact with a heterotrimeric G protein.
28
Subunits of a G protein? How many and what are they?
Has 3 subunits: α, β, and γ. The β and γ subunits are always found together. The α subunit is able to bind to GTP and hydrolyze the bound GTP to GDP.
29
Describe the 3 steps to activate a heterotrimeric G-protein.
Activation
A. The heterotrimeric G protein is inactive when it is bound to GDP and the three subunits are all interacting.
B. Upon ligand binding, the receptor adopts a conformation allowing interaction with the α subunit of the heterotrimeric G-protein.
C. The α subunit releases GDP and binds GTP. The α subunit bound to GTP dissociates from the βγ subunit. In this state the GTP-bound α subunit and the βγ subunit are active and can interact with downstream effectors.
30
How does a G-Protein inactivate?
Inactivation
After activating its target protein, the α subunit hydrolyzes GTP to GDP; the GDP-bound α subunit is inactive. In this form it re-associates with the βγ subunit.
31
The α subunit is not an efficient GTPase. What can speed it up?
Binding to a membrane-bound RGS protein increases the GTPase activity of the α subunit and allows it to inactivate and “reset” much faster.
32
What is the downstream target of Gs?
Gs activated Adenyl Cyclase via its alpha subunit.
33
What does adenyl cyclase do?
Converts ATP to cyclic AMP (cAMP)
34
What is one important target of cAMP?
PKA
35
What does cAMP do to PKA?
Upon binding of cAMP, the regulatory subunits dissociate and release the catalytic subunits which now become active, and can phosphorylate their targets.
36
What is Glycogen phosphorylase?
A target of PKA. When it is phosphorylated by PKA it becomes activated and starts to break down glycogen.
37
What is glycogen synthase?
A target of PKA that is INACTIVATED when phosphorylated by PKA. This ensures that glycogen is not being synthesized at the same time as it’s being broken down (glycogen phosphorylase).
38
What does Gi do?
Inhibits adenyl cyclase.
39
What does Gq do?
Activates phospholipase Cβ. This enzyme breaks down the membrane phospholipid PIP2 (phosphoinositol 4,5 bisphosphate) into IP3 (inositol 1,4,5- trisphosphate) and DAG (diacylglycerol.)
40
What does IP3 do?
Can activate the release of calcium inside the cell, which activates another protein kinase, PKC, and has many other signaling functions.
41
What does DAG do?
Can directly activate PKC.
42
What are two ways to activate PKC?
Through calcium release inside the cell and directly with DAG.
43
How does IP3 lead to calcium release within the cell?
The production of IP3 from the break down of PIP2 by phospholipase Cβ leads to the opening of the IP3-gated calcium release channels on the endoplasmic reticulum and the calcium escapes from the lumen of the ER into the cytosol which can then stimulate the activation of PKC.
44
How is Gt activated?
By the rhodopsin receptor.
45
What does Gt do?
Activates cGMP phosphodiesterase, which breaks down cGMP.
46
How does Cholera Toxin cause watery diarrhea from a cell signaling perspective?
Cholera toxin is an enzyme which ADP-ribosylates the α subunit of Gs (adds an ADP-ribose molecule
to it.) The ADP-ribosylated α subunit can no longer catalyze hydrolysis of GTP to GDP. The α subunit thus remains permanently activated, and keeps activating adenylyl cyclase which causes a prolonged rise in cAMP levels and the activation of PKA. The prolonged upregulation of PKA activity in cells of the intestinal epithelium causes an efflux of Cl- and water into the gut (PKA phosphorylates certain ion channels in these cells.) This results in the copious, watery diarrhea which is the defining symptom of cholera.
47
What G protein does pertussis toxin affect and how does it work?
Pertussis toxin ADP-ribosylates the α subunit of Gi, which prevents its binding to GPCR’s and thus preventing its activation. This bacteria causes whooping cough.
48
What are the steps of signal transduction for receptor tyrosine kinases?
The receptors are single-pass transmembrane proteins. Binding of the ligand to the receptor causes the receptor to dimerize. Dimerization causes auto/trans phosphorylation and the receptors become active. Phosphorylation leads to two separate events: it activates the receptor’s catalytic function and it creates sites for target protein recruitment
49
Describe the MAP Kinase cascade.
After the RTK is phosphorylated, Grb2 can bind to it via a SH2 domain (phospho-tyrosine
binding.)
• SOS is constitutively bound to Grb2 via its SH3 domain (which recognizes proline-rich regions in
Grb2.)
• SOS activates Ras.
o RasisasmallG-protein,aclassofproteins(differentfromheterotrimericGproteins) which can bind GTP and GDP, and have GTPase activity.
o Small G proteins are active when bound to GTP and inactive when bound to GDP. Guanine nucleotide exchange factors (GEFs) cause small G proteins to dissociate from GDP and to bind GTP, therefore activating them. SOS is a GEF for Ras.
o GTPaseactivatingproteins(GAPs)acceleratetherateofGTPhydrolysisbythesmall G proteins and thereby inactivate them (not shown)
• Ras activates Raf, a ser/thr kinase that phosphorylates MEK (a MAPKK), which in turn phosphorylates ERK (a MAPK).
50
How does Grb2 bind to RTK?
RTK must first be phosphorylated. Then Grb2 can bind via an SH2 domain. (phospho-tyrosine binding)
51
What is constitutively bound to Grb2 and how?
SOS; via an SH3 domain.
52
What does SOS activate?
Ras
53
What is ras?
Ras is a small G protein, (different from heterotrimeric G proteins) a class which can bind GTP and GDP and has GTPase activity.
54
When are small G proteins active and inactive?
Small G proteins are active when bound to GTP and inactive when bound to GDP.
55
What do Guanine nucleotide exchange factors (GEFs) do?
Guanine nucleotide exchange factors (GEFs) cause small G proteins to dissociate from GDP and to bind GTP, therefore activating them.
56
What activates ras?
GEF's. SOS is one of them.
57
What does SOS do to ras?
It is a GEF for ras so it activates it.
58
What do GTPase activating proteins (GAPs) do?
GAPs accelerate the rate of GTP hydrolysis and thereby inactivate them.
59
What does Ras activate?
Ras activates Raf, a set/thr kinase that phsophorylates MEK, which then in turn phosphorylates ERK.
60
What is PI-3K?
A complex of a regulatory subunit (p85) and a catalytic subunit (p110).
61
How does p85 allow for activation of p110?
p85 has an SH2 domain that binds to activated RTK's and allows access of p110 to PIP and PIP2.
62
What does p110 do to PIP and PIP2?
It phosphorylates them on the 3 position of the inositol ring (hence the name PI-3K).
63
What do phosphoinositides phosphorylated on the 3 position activate?
The directly and indirectly activate a ser/thr
| kinase called Akt (sometimes also called PKB).
64
What does AKT do when it becomes activated?
It phosphorylates substrates that
| promote cell survival and inhibit programmed cell death (a process called apoptosis).
65
What is PTEN?
PTEN is a phosphatase that which removes phosphate from the 3 position of phosphoinositides
previously phosphorylated by PI-3K. It is a tumor suppressor that is often mutated in cancer.
66
What does TGFB binding do?
Causes the Type-II TGFB receptor to phosphorylate the Type-I receptor.
67
What does the phosphorylated TGFB type 1 receptor do?
It recruits and phosphorylates SMAD2 or SMAD3.
68
What does phosphorylated SMAD2 or 3 do?
Dissociates from the receptor and oligomerizes with SMAD4.
69
What does the SMAD2/3 and 4 oligomer do?
Translocates to the nucleus, recruits other regulatory genes and induces transcription of specific target genes.
70
What is one downstream target of AKT when it's phosphorylate/activated by PDK1 and mTOR?
It phosphorylates Bad, therefore activating the apoptosis inhibitory protein previously in complex with bad. This inhibits apoptosis.
71
What phosphorylates AKT?
PDK1 and mTOR
72
A survival signal to the RTK in the PI-3K pathway triggers what?
The RTK becomes activated (phosphorylated). This activates PI-3 Kinase which then phosphorylates PIP2 to PIP3 or PI (345)3 which can then act on PDK1 etc.
73
What happens when Prolactin binds to it's receptors?
JAK1 and JAK2 cross phosphorylate to activate one another and then phosphorylate a domain on the receptor that recruits and activates STAT 5
74
When STAT 5 is activated, what does it do?
It dissociates from the receptor and dimerizes. It can then translocate into the nucleus and along with other transcription regulators triggers the transcription of MILK protein genes.
75
What does a membrane bound inhibitory signal (delta) bind to?
A receptor protein (notch) on a nearby cell. This interaction allows a developing nerve cell inhibit other surrounding epithelial cells from all developing into nerve cells. Just aids in neuronal differentiation and diversity in development.
76
Why is the maximum buffering capacity of a weak acid at + 1 pH unit of its pKa?
The maximum buffering capacity of a weak acid occurs at one pH unit above or below the pKa, because in this pH range both the acid and its conjugate base are present and can consume the added ions.
77
How does a buffer reduce the effect of added acid or base on the pH of a solution?
Weak acids and weak bases function as buffers because they only partially dissociate into charged species. Buffers dampen pH changes by providing a reservoir of acid that consumes added base and a reservoir of base that consumes added acid.
78
Is a weak acid charged or uncharged at 2 pH units above its pKa?
Unprotonated, charged.
79
Is a weak base charged or uncharged at 2 pH units above its pKa?
Unprotonated, neutral.
80
What is the general form of the Henderson-Hasselbalch equation?
pH = pKa + log([conjugate base]/ [conjugate acid])
81
Why is the carbonic acid/bicarbonate system an effective buffer of blood even though its combined pKa is more than one pH unit below that of blood pH?
Blood is maintained at a pH of about 7.4, and at this pH the ratio of [H2CO3] to [HCO3-] is 1:20. This buffering system works well even though there is much more bicarbonate than carbonic acid because the concentration of these components can be regulated by physiological mechanisms. The concentration of H2CO3 can be modulated by changing the breathing rate, which affects the level of CO2 in blood. The concentration of HCO3- can be modulated by changing the rate of its elimination by the kidney.
82
What is the isoelectric point of a molecule?
pH at which a molecule's net charge is zero.
83
At what pH ranges are amino acids effective buffers?
The pKa of the basic amino group is between 9 and 10, and the pKa of the acidic carboxyl group is approximately 2.
84
What's the dissociation of a weak base?
RNH3+ (conjugate acid) -> RNH2 (Conjugate base) (LOOK UP)
85
What is the pKa of a weak acid?
The pH at which one half of the molecules are dissociated into ions.
86
What is the most useful form of the Henderson-Hasselbalch equation for the bicarbonate buffering system?
pH = 6.1 + log([HCO3-] / 0.03[PaCO2]) Where pKa is a combined pKa that includes both K1 and K2
87
How can the levels of H2CO3 and HCO3- be modulated in the body?
The concentration of H2C03 can be modulated by changing the breathing rate, which affects the level of CO2 in blood. The concentration of HCO3- can be modulated by changing the rate of its elimination by the kidney.
88
Which amino acids can be glycosolated?
Serine, threonine, and asparagine.
89
Which amino acid can have hydrogen chain added, such as a farnesyl group?
Cysteine
90
Which amino acids are basic?
Histidine, Lysine, Arginine
91
How are small peptides named?
Small peptides are named for their constituent amino acids, starting at the amino terminus and adding "yl" to the name of the each amino acid except for the one at the carboxyl terminus .
92
What is an alpha helix and how is it formed?
An α-helix is depicted as a spiral in a ribbon diagram of the structure of a protein, which traces out the peptide bond backbone of the protein in three-dimensional space. In an α-helix, the oxygen in the carbonyl group of amino acid R1 forms a hydrogen bond with the hydrogen in the amino group of amino acid R5, forming a turn of 3.6 amino acids.
93
What is a beta sheet
A β-sheet hydrogen bonds are formed between atoms in peptide bonds of the same or different linear chains. β-sheets can be oriented in antiparallel or parallel configurations. A β-sheet is depicted as a wide arrow in a ribbon diagram.
94
What is a cysteine residue?
Two cysteines can undergo formation of a covalent disulfide bond
95
Which amino acid side chains can participate in hydrogen bond formation?
All. A peptide bond is polar and presents an opportunity for hydrogen bonding.
96
In an alpha helix what bonds with what?
The oxygen in the carbonyl group of amino acid R1 forms a hydrogen bond with the hydrogen in the amino group of amino acid R5
97
What determines the overall three-dimensional conformation of a protein?
The amino acid sequence determines the overall 3D conformation of a protein. Interactions involving both the peptide bond backbone and the amino acid side chains contribute to tertiary structure. Interactions between side chains can occur between amino acids that are far apart in the linear sequence because they are close together in the three-dimensional structure of the folded protein.
98
What interactions stabilize tertiary and subunit composition of a protein?
Noncovalent interactions like ionic bonds are due to electrostatic interactions between amino acid side chains that have opposite charges. Such electrostatic interactions can also occur between a charged amino acid and a polar amino acid. Furthermore, non-polar side chains can form van der Waals interactions that usually involve hydrocarbon side chains.
99
What is a ligand?
Ligands are molecules that bind REVERSIBLY to specific sites in proteins with extremely high specificity.
100
What is Kd?
The dissociation constant, KD, is the equilibrium constant for the dissociation reaction. When half of the protein is bound to the ligand, [P] = [PL], and KD = [L]. Therefore, the KD is the concentration of ligand at which half of the protein is bound to ligand.
101
What does a lower Kd mean?
The lower the value of KD, the higher the affinity of ligand for protein, because it takes a smaller amount of ligand to half- saturate its binding partner.
102
Which state is hemoglobin in when NOT bound to oxygen?
Taut or T
103
Which state is hemoglobin in when bound to oxygen?
Relaxed or R
104
If blood is too acidic how could you remedy that?
Breath faster. This would give off more CO2 and push the bicarbonate equilibrium towards the left to make more CO2 which would decrease the H+. Therefore the pH would rise.
105
How does 2,3 BPG affect oxygen binding to Hb?
It inhibits it.
106
Higher Kd means what for binding?
Worse binding affinity. A higher dissociation constant for 2,3 BPG means it would bind worse, which would increase HB's affinity for oxygen.
