Midterm 2 Flashcards
(245 cards)
1
Q
What are the important characteristics of a biological membrane?
A
It must be selectively permeable. It is used to store energy in the form of gradients. One important characteristic is the fact that it is self-sealing, which means that when it forms, the membrane will fuse together through noncovalent bonds. This is important or else the content of the cell will fall out. The membrane also allows for adaptability for cell conditions and functions
2
Q
What are glycerophospholipids?
A
They are a building block to the cell membrane where the building block of the glycerophospholipids are fatty acids.
3
Q
What are fatty acids a building block to?
A
Many things including glycerophospholipids, sphingolipids, and fats
4
Q
What are the four key biological roles of fatty acids?
A
They are necessary for the construction of the membrane. Fatty acids also aid in post translational modifications of proteins by aiding in protein localization. They also aid in both intra and inter cellular signaling of molecules. Fatty acids lastly are used to store energy in the form of fats.
5
Q
At what angle is a kink created when a double bond is created in a hydrocarbon chain?
A
Thirty degrees
6
Q
Describe the intermolecular movement around a single bonded fatty acid
A
Because there are just single bonds, that means that the carbon chains can rotate about them, more fluid.
7
Q
What does it mean when name a fatty acid 18:0?
A
The first number means how many carbon are in the carbon chain while the second number means how many double bonds are in the molecule. In this case, this fatty acid has 18 carbons and no double bonds in it.
8
Q
What does it mean to name a fatty acid 18:1(∆9)?
A
The right side of the colon shows how many double bonds are in the carbon chain, and the ∆ superscript is the carbon number of the start of the double bond.
9
Q
What is the most naturally occurring conformation of double bonds in fatty acids?
A
The cis double bond
10
Q
On a fatty acid chain, what are the α, β, and ω carbons?
A
The α carbon is the first carbon in the chain that is the carboxylic acid carbon. The β carbon is the carbon right after the α. And the ω carbon is the last one
11
Q
What does it mean that a fatty acid is an ω-3 fatty acid?
A
The carbon number from the ω carbon that the first double bond at the end occurs
12
Q
As the number of carbons in a fatty acid chain increases, what happens to the melting point?
A
It will increase
13
Q
As the number of double bonds in a fatty acid increases, what happens to the melting point?
A
It decreases greatly
14
Q
What are the important structural components of the membrane lipids?
A
Glycerophospholipids, sterols and sphingolipids
15
Q
What are some of the important roles of a lipid?
A
Enzyme cofactor, additional signaling molecule, and it acts as a pigment, along with other roles.
16
Q
Describe the building block of a regular lipid.
A
It first starts off with a backbone, this can be Glycerol (three carbon chain with three hydroxyl groups attached to it) or L-serine (same three carbon chain but a hydroxyl, amine, and carboxylic acid is attached. Then the biological lipid contains fatty acids and a common polar head, such as a phosphate group
17
Q
What is the most important characteristic of lipids that allow them to be great membrane creators?
A
It is hydrophobic allowing it to be insoluble in water.
18
Q
What are triglycerides?
A
These are also what we see as fats. They are very hydrophobic allowing them to exclude water as well as store energy. These are usually clumped together in adipocytes and work as energy storage molecules
19
Q
What is a saturated fatty acid vs. an unsaturated fatty acid?
A
A saturated fatty acid means it has no double bonds while the more unsaturated a fatty acid is, the more double bonds it has.
20
Q
Will you most likely find saturated or unsaturated fats as a solid at room temperature?
A
Saturated because they have no kinks, they stack very easily
21
Q
What is the set-up for a phosphoglyceride?
A
There are two fatty acyl chains attached to the backbone and a polar group usually attached to the middle of the back bone away from the two fatty acids
22
Q
What is a cardiolipin?
A
A di-phosphoglyceride. That has four fatty acid tails because on the inside, the polar heads of two phosphoglycerides are attached by an inner molecule.
23
Q
What is the role of cardiolipin?
A
It acts as an insulator. It also aids in the stabilization of electron transport chain complexes on the membrane
24
Q
What is a sphingolipid?
A
This is when the fatty acids, instead of glycerol or other backbone, it is attached to a serine backbone. The carboxylic acid conformation change when the fatty acid is attached to the serine results in a trans double bond on the fatty acid:
25
What are ceramides?
This is like a sphingolipid, except another fatty acid attached to the hydroxyl group creating the double oxygen bond. There is also a polar head attached to the carbon between the first fatty acid carbon and the amide group
26
Name some shingolipids
Sphingomyelin, cerebrosides, and gangliosides
27
What is a ganglioside?
An oligosaccharide head group with one or more sialic acid attached to it. It has a lot of rings in it making it a bulky molecule
28
What is the purpose of a complex carbohydrate head group?
It allows for specificity in binding to other proteins. It aids in cell-cell recognition, specifically in the roles of growth and differentiation.
29
What is cholesterol?
This a hydrocarbon chain attached to a steroid with a hydroxy group on the other side?
30
What is a steroid?
A compound with four non-planar rings attached to it.
31
What drives the formation of lipid membranes?
The formation of hydrophobic membranes allows for an increase In the entropy of water due to increase space for the water to move around. This makes the self-sealing capabilities of the phospholipid more important. This formation is cooperative
32
What are the two organizations of the lipid bilayer?
Miscellar organization and a lamellar membrane
33
What types of lipids form the micellar conformation?
Inverted cone shapes allowing it to enter a circular conformation.
34
What type of lipids allow for the lamellar organization of a membrane?
cylindrical, roughly symmetric in shape lipids
35
What kind of interactions hold the lipid bilayer together?
Non-covalent bonds
36
What compounds can diffuse through the lipid membrane?
Lipids and proteins
37
Are membranes uniform throughout the cell in composition?
No
38
How can you measure diffusion in a bilayer?
Using Fluorescence Recovery After Photobleaching (FRAP)
39
How does temperature affect the fluidity of the phospholipid membrane?
With an increase in temperature, there is an increase in fluidity, but there does become a point when he membrane is maximally fluid. If you look at the graph, it is sinusoidal. At the top, the long fats move around more and are less straight. At lower temperatures, the fats lie almost strait and ordered.
40
What would happen to the Tm if the lipid chains were shorter? What about longer?
The shorter the chain the faster the increase in fluidity in the graph, meaning that middle slope would be moved to the left. While longer chains will need a larger increase in temperature to increase fluidity more, so Tm instead would move to the right.
41
What would happen to Tm if the lipid chains were unsaturated?
If the lipid chains are more unsaturated, that means there are much more kinks allowing for an increase in fluidity overall, so the more unsaturated the fatty acid chain, the more TM moves to the left
42
How does the temperature of the environment effect the lipid composition of the membrane of the cell?
The molecular composition of the membrane will change with changing temperatures of the environment. For example, at high temperatures, there will be less unsaturated fatty acids than in low temperatures, or longer chains instead of short chains comprising the membrane. This is to create a balance in permeability. So the shorter, more kinked membranes are much more leaky making them favorable in lower temperature to promote permeability, but in high temps, since the membrane is more fluid, the composition will be more favorable when the membrane is less permeable, to make up for the temp disadvantage
43
How does the membrane fluidity vs. temperature graph change when cholesterol is added to the mix?
The graph moves from sinusoidal to linear. But if you notice, TM stays same
44
What is the basic structure of cholesterol?
It is big bulky molecule with four rings. It is rigid as well
45
Where is cholesterol found?
Only in Eukaryotic Membranes
46
How does the presence of cholesterol effect the fluidity of the membrane?
It makes it more rigid because it inserts itself in the empty spaces of the lipid membrane. The composition of lipids does not vary across the lipid membrane, but at higher temperatures, the presence of cholesterol decreases lipid movement at higher temperatures, while at lower temperatures, the cholesterol allows the membrane to be more solid and packed.
47
What kind of fatty acid tails does cholesterol associate itself with?
Long, saturated fatty acyl tails. This can include sphingolipids and glycolipids
48
What is a lipid raft?
When the cholesterol and sphingolipids combine to create a microbiome in the plasma membrane. The sphingolipids are usually pretty long so they slightly go above the lipid membrane to create a thicker membrane portion. These lipid rafts aid in cellular signaling and membrane budding.
49
What is the disadvantage of the lipid raft?
Viruses tend to localize on lipid rafts
50
Is lipid composition of membranes on the Eukaryotes conserved?
No it varies between eukaryotes
51
What lipids are generally found on the outer leaflet of the phospholipid membrane?
Cerebrosides and gangliosides
52
What lipids are generally found on the inner leaflet of the phospholipid membrane?
Phosphatidyl serine, and phosphatidyl ethanolamine
53
What is transverse diffusion?
Diffusion of a polar head across the hydrophobic membrane. This is highly unfavorable and usually take a lot of energy and time to happen. The polar head almost flips across the membrane. The groves in the membrane allow for a faster movement of polar heads on the phospholipid
54
Why is asymmetry between the top and bottom membrane important?
It allows for uneven proteins that sit in the membrane to rest comfortably. It accommodates for the uneven sides of the proteins basically. Therefore, transverse diffusion is so important when establishing the membrane. Asymmetry fills in the holes caused by membrane proteins
55
How much of the genome encodes membrane proteins?
About thirty percent
56
What are the two types of membrane proteins?
Integral membrane proteins and peripheral membrane proteins.
57
What is an integral membrane protein?
A protein that spans most of the lipid bilayer with huge contact in the inner hydrophobic region of the membrane. Because of these interactions, integral membrane proteins are strongly stuck on the lipid membrane. What is unique about it is that it only has one orientation. For example, the ATP synthase has the head region only on one side of the membrane.
58
What do you need to remove an integral membrane protein from the membrane it is attached to?
A strong detergent
59
What is a peripheral membrane protein?
This is a protein that has art of its structure on the membrane, but it usually just interacts with the surface of the membrane. It is on the edge of the membrane.
60
How can you get rid of a peripheral membrane protein?
Use a solution of high salt, or change the pH. It is much easier to obtain than the peripheral membrane proteins
61
What are the most common motifs of integral membrane proteins inside the hydrophobic layer?
It is usually has a β-barrel structure inside the hydrophobic layer or an alpha helix structure that allows all of the non-polar R-groups to remain on the outside to interact with the hydrophobic layer.
62
What are the properties of the integral membrane spanning protein that has an α-helix as the hydrophobic integral region?
The α-helix must be at least 20 residues long and most of the R-groups in this 20-residue section must be non-polar.
63
For an integral membrane protein, what is the most common characteristic of the protein structures that is outside of the hydrophobic region?
These regions are usually polar because there is water on the exterior.
64
What is the hydropathy score of an amino acid?
This is how hydrophobic the amino acid R group is. The higher the number, the more hydrophobic it is.
65
How do you create a hydrophobicity graph for a protein?
You take primary sequence of the protein and look at the first seven amino acids and take the average hydrophobicity of that group. So add the hydropathy scores all up and divide by seven. Then plot that point. Then move over one amino acid and plot that group continuously until you get a plot. When looking at the hydropathy plot, any clear regions that are above zero are categorized as hydrophobic while any clear regions that are below the zero line are hydrophilic regions
66
What is an aquaporin?
A pore in the lipid membrane that allows for a faster movement of water across the membrane
67
What are annular lipids?
The phospholipids that surround the protein on the membrane. These have acyl chains that will be fluid to the shape of the protein interacting with the hydrophobic patch of the protein. The annular lipids at the ends have salt bridges and hydrogen bonds that will interact with the polar ends of the proteins. Annular lipids provide a strong interaction with the integral membrane protein that allows the protein to be strongly connected to the membrane. Therefore, it requires a strong detergent to remove it.
68
How can you anchor protein to the membrane?
Through post translational modification of the protein by attaching a lipid to the protein that will act as an anchor on the membrane.
69
What are the three lipid modifications that allow for the anchoring of a protein to the membrane?
Fatty acylation, glycosyl-phosphatidyl-Inositol (GPI)-linked, and Prenylation. These names are based off what is attached to the protein. Which lipid is attached to the protein will determine the localization of the protein.
70
What is the localization effect of a protein that had lipid modification to make GPI-anchored protein?
The protein will be anchored on the outer leaflet of the plasma membrane, exterior.
71
What is the localization effect of a protein that had lipid modification to make prenylated proteins?
These proteins localize on the inner leaflet of the membrane and they do not interact with rafts
72
What is the localization effect of a protein that had lipid modification to make Palmitoyl-dependent protein (fatty acylation)?
This causes the protein to localize with rafts
73
What is a caveola?
This is a dip in the membrane that will form dimers, become palmitoylated and it binds to cholesterol. It is enriched with cholesterol, sphinglipids, and GPI- anchored proteins. It aids in the creation of membrane curvature as well as associating with lipid rafts.
74
What component aids in creating the structure of the cell membrane?
The cytoskeleton
75
What is a common component of the cytoskeleton?
Actin
76
What is a biconcave disk?
This is that bend in red blood cells that allow for an increase in surface area of the red blood cell for an increase in diffusion of oxygen to the hemoglobin. This shape is set up by the cytoskeleton. This cytoskeletal structure allows for the red blood cells to retain their shape when they move through the small capillaries
77
What does the cytoskeleton do for a cell?
It gives it shape and structure
78
What is it called when molecules are moved using a concentration gradient?
Diffusion and facilitated diffusion
79
What proteins allow for facilitated diffusion to happen across a membrane?
Ionophores, ion channels, and transporters
80
What is it called when molecules move against a concentration gradient?
Active transport which requires energy
81
What protein allow for active transport to happen?
Active transporters, or pumps that use proton, ions, or other concentration gradients. There is also ATP-dependent transport
82
How would very large molecules be moved across a membrane?
Clathrin-mediated Endocytosis
83
Give two examples of how information is transferred across a membrane?
Through an insulin receptor or a G-Protein coupled receptor
84
What is it called when a molecule moves down its concentration gradient?
Passive transport
85
What is it called when a molecule moves against its concentration gradient?
Active transport
86
What is the difference in Gibbs free energy change between active and passive transport?
The ∆G for passive transport is negative meaning it is favorable while the ∆G for active transport is positive which means that it is unfavorable. Therefore, active transport need to be driven by ATP or another molecules concentration gradient
87
What must happen for a molecule to be able to enter a cell across the lipid bilayer without the aid of another protein?
It must be permeable to the lipid bilayer and it will result in movement using a concentration gradient where the external concentration is great than what is inside the cell. Molecules such as H2O, CO2, and O2 can easily cross the membrane but ions have a much harder time crossing the membrane because of the hydration shell that surrounds the ion when in water.
88
How does facilitated diffusion work?
This is generally for ions where there is a channel or peptide inside the membrane that will create an energetically favorable area for the ion to enter, better than when compared to the lipid bilayer. This will result in the ion traveling with its electrical or chemical gradient in the end.
89
What is Valinomycin?
This is an ionophore that allows for a great increase in the movement of potassium across the membrane. It does not favor movement of other ions because Potassium is the perfect size. It will surround the potassium getting rid of the hydration shell and it will travel across the membrane so that potassium can enter the cell.
90
What is an ionophore?
A protein that can move across the membrane to facilitate the movement of ions. Its hydrophobic exterior allows for the movement when interacting with the lipid bilayer.
91
What is the structure of the potassium ion channel and how does it work?
It is a tetramer with C4 symmetry. It consists of just alpha helices which gives it a carbonyl backbone allowing the channel to favorably sit in the lipid bilayer membrane. It has a pore seeping through the middle which perfectly fits potassium so it can move along its chemical or electrical gradient.
92
How is the potassium ion channel a selective filter?
For the potassium ion channel, for it to work, it will exchange the hydration shell surrounding the potassium with carbonyl groups on the backbone of the channel to facilitate the passing of the potassium past the channel.
93
How can other channels have a selective filter for the transport of molecules or ions?
Ion channels can have varying induced closed and open conformations. Ion channels can also be voltage gated or ligand gated.
94
What does an aquaporin do for a cell?
It allows for the rapid movement of water across a cell membrane so that osmotic pressure inside and outside the cell can be in equilibrium with each other.
95
What does an aquaporin transport?
Only water, not its H+ or H3O+ products. The internal charged components of the aquaporin repel the H+ and H3O+
96
What is the structure of an aquaporin?
It has C4 conformation and it is made up of a bunch of alpha helices that sit in the membrane of the cell.
97
What does facilitated diffusion do?
It allows for an increase in the transport of a certain molecule making the cell more permeable to the specific molecule.
98
What does it mean when the rate of diffusion is saturated?
That means the rate of transport will at first greatly increase, but then as the amount of transport molecules are becoming all used up, the rate of transport will begin to plateau off.
99
What does the rate of transport graph vs. the concentration difference across a membrane look like for both facilitated transport and Non-Mediated Transport?
The facilitated transport will have a sharp increase and then plateau off as the transport channels get all used up. While non-mediated transport will just have a small sloped linear graph
100
Name a protein that conducts facilitated Diffusion.
A glucose transporter
101
What does a glucose transporter do?
It allows for the transport of glucose across the cell membrane by having glucose bind to the glucose transporter, which will induce a conformation change in the glucose transporter that will open the glucose to the inside of the cell.
102
What is the Glut1 permease?
It is a glucose transporter that is composed of 12 helices. It allows for the passive diffusion of glucose across the cell membrane so that it can follow its concentration gradient. It is also found on erythrocytes (red blood cells)
103
Can the Glut1 permease be saturate?
yes
104
What does Glut2 do and where is it found?
Glut 2 facilitates the transfer of glucose out of the liver cell.
105
What does Glut3 do and where is it found?
This is found in the neurons and it has a high affinity for glucose which is very important because the neurons need energy. It facilitates the transfer of glucose into the neurons
106
What does Glut4 do and where is it found?
This facilitate the transport of glucose and it is found in adipose and muscle tissue. It is also the Glut transport protein that is found on the intracellular vesicles that responds to insulin.
107
What does primary active transport require?
Energy so it can pump the movement of molecules or ions against their concentration gradient.
108
What are the two types of Primary active transporters?
P-type ATPase and ABC-transporter
109
What does a P-type ATPase do?
It is used to maintain an ion gradient in the cell
110
In a P-type ATPase, what residue is phosphorylated and de-phosphorylated that will result in the conformation change so that an ion can be transported?
Asp
111
What are the two main states of the P-type ATPase?
The E2 state and the E1 state
112
Describe the E2 state of the P-type ATPase
Here the ATPase is open on the outside of the cell membrane and it will have an open area for the specific ion to bind to. Then ATP will come in and phosphorylate the Asp after the ion binds to the ATPase resulting in the ATPase closing and moving to its E1 conformation
113
Describe the E1 state of the P-type ATPase
In the E1 state, the ATPase is open on the inside of the cell. Here ADP is released from the ATPase that will result in the ion to be moved into the cell
114
What does and ABC transporter do?
It allows for the transport of amino acids, peptides, metal ions, lipids, bile salts, toxins, and drugs against their concentration gradient.
115
Why are ABC transporters important in the medical field?
They allow for the transport of drugs, but how antibiotic resistance arises is when there is a mutation to the transporters that will not allow for the drug to enter the cell.
116
Describe the structure of a general ABC transporter
It is made up of a bunch of alpha helices that can open and close like a bridge. On the cytoplasm side of the transporter, there is a nucleotide binding domain that will bind to the ligand and use ATP to push the molecule out of the cell
117
Name a protein that works through secondary active transport
A glucose/Na+ Symporter
118
What mode of transport is the Glucose/Na+ symporter?
Secondary active transport because the sodium will move with its concentration gradient to drive glucose to move against its concentration gradient
119
What does symport mean?
The molecules are moving in the same direction
120
What does antiport mean?
The molecules are moving in opposite directions
121
What does modularity mean?
When similar structures are used to respond to different signals
122
What does amplification mean?
When a small signal gets amplified to a much larger signal.
123
What is the Receptor Tyrosine Kinase (RTK)?
It is a dimer (consists of two structures) where on the extra cellular side, there is a large structure that is attached by two α-helical trans membrane segment. On the intracellular side, attached to each of the α helical trans membrane domains, there is a Tyrosine kinase domain.
124
How does the Receptor Tyrosine Kinase get activated?
As insulin is floating around, it will bind to the insulin receptor ligand binding domain which will induce the activation of the Tyrosine Kinase inside the cell. The two receptor tyrosine kinases will auto phosphorylate each other because the conformational change brought the two together. This will lead to the IRS-1 protein to be phosphorylated (on the cell membrane), and then the PI3 kinase, resulting in PIP2 to be phosphorylated and become PIP3 leading to the activation of PDK1
125
What is PDK1?
PIP3-dependent protein kinase
126
What does PDK1 do?
When it is activated, it will induce a signal cascade with the activation of a bunch of other kinases, which will induce the Glut4 transporter vesicle in the adipose or muscle cells to fuse to the plasma membrane of the cell so that more glucose can be taken up by the cell
127
What are the structural changes behind activation of the insulin receptor tyrosine kinase domain?
Upon binding of insulin, the Receptor tyrosine kinase will expose an activation loop that will allow it to become a kinase.
128
What happened when a ligand binds to a G-protein binding GDP/GTP exchanger?
Upon binding, the receptor will interact with the G protein by inducing a conformation change leading to the transfer of a phosphate group from GTP to the G-protein that will then lead to the dissociation of the alpha-beta-gamma subunit. Alpha will dissociate from the beta-gamma side. It is the subunit that gets phosphorylated, therefore it will act as a scecondary messenger to induc protein kinase C to activate PIP2 leading to the release of DAG and IP3.
129
How does the GPCR get put back together?
The GTP will slowly hydrolyze causing an inactivation of the alpha subunit which will lead to the re-assembling of the GPCR. This is kind of like an internal timer. The internal mechanism that does this is a GTPase inside the alpha subunit
130
What are the two types of secondary messenger for a GPCR?
cAMP and PIP2. cAMP is triggered by adenylate cyclase while PIP2 is triggered by the activation of protein kinase C
131
What are carbohydrates made up of?
Carbon and water
| (CH2O)n
132
What do carbohydrates do?
They aid in providing an energy source or structure, and they do not have any catalytic activity
133
What do carbohydrates do?
They aid in providing an energy source or structure, and they do not have any catalytic activity
134
What is the most common conformation for a carbohydrate?
D-sugar
135
What are the two types of monosaccharides?
Aldehydes and ketones. Aldehydes have the carbonyl group at the end, while ketones have the carbonyl group second to last.
Ketoses have one fewer asymmetric carbon than aldoses
136
What are enantiomer?
Molecules that are mirror images of each other
137
What are tautomer’s?
When two compounds have the same atomic composition, but the structure is different
138
What are stereoisomers?
When the connectivity of the two molecules are the same
139
What are the four types of stereoisomers?
Diastereoisomers
Enantiomers
Epimers
Anomers
140
What are anomers?
When the ring conformation of the sugar results in a variation in the conformation of one of the carbon atoms in the ring. In this case, and example would be the β and α conformations
141
When finding the D or L conformation of a carbohydrate, which chiral carbon would you look at?
The chiral carbon furthest away from the carbonyl group
142
What is an aldehyde with three carbons called? Four carbons? Five? Six?
Aldotriose, aldotetroses, aldopentoses, aldohexoses
143
What is the difference between glucose and fructose?
Both are 6 carbon carbohydrates, but glucose is an aldose, while fructose is a ketose
144
What molecules is the smallest ketose?
Dihydroxyacetone, it does not have any chiral centers
145
How would you distinguish a ketose and an aldose by looking at the name?
A ketose usually has the same name as an aldose, it just has the -ul- in the middle of its name, such as ribulose
146
What is a hemiacetal?
When an aldehyde reacts with an alcohol
| When a ketone reacts with an alcohol
147
Describe the Haworth projections for a 5-membered ring and a 6-membered ring
A five-membered ring has 4 carbons in the ring and one oxygen. A 5-membered ring is known as furan. A six membered ring has 5 carbons in the ring and one oxygen, this is known as a pyran
148
If a carbohydrate is has 5 carbons, will it prefer the five-membered ring, or the six-membered ring?
It will always prefer the ring with the most amount of carbon because there is less hindrance. The carbohydrate will not just consist of one ring conformation, it will exist in equilibrium with the two ring structures, with the six-membered ring having the highest dominance
149
What is the difference between the α and β sugar conformation in the Haworth projections?
The α ring has its hydroxyl group on the C1 carbon pointing down, while the β ring has its hydroxyl group on the C1 carbon, pointing up
The C1 carbon is the anomeric carbon
150
Which position between α, β, and the linear structure of glucose is preferred?
The pyranose form is preferred much over the linear form. Then the β glucopyranose conformation dominates over the α glucopyranose conformation
151
How are glycosidic bonds formed?
When the anomeric carbon hydroxyl group reacts with an alcohol
152
How is lactose formed?
Through the glycosidic linkage of the β anomeric carbon of galactose, to the C4 hydroxyl group carbon of glucose. It is a reducing sugar because there is a free anomeric carbon end
153
What are galactose and glucose to each other?
Epimers
154
What breaks up lactose?
Lactase and it breaks it up into galactose and glucose
155
How is sucrose formed?
Through the glycolytic bond between the anomeric carbon hydroxyl group of α glucose and the C2 carbon of β fructose. This is a non-reducing sugar because there are no anomeric carbon ends
156
What is Maillard Reaction?
When an open reducing sugar reacts with a nucleophilic amino group of amino acids to create a new substance.
157
What happens when someone has a high level of HbA1c?
This means that a person is usually diabetic. The HbA1c is the mix of D-glucose with hemoglobin to form N-fructosyl-valine-hemoglobin due to large amounts of glucose in the person’s blood.
158
Give a few examples of polysaccharides
Cellulose, chitin, glycogen, and starch
159
What is cellulose?
A material found in plants that is not digestible by humane. It is a long chain of glucose molecules linked together. The long chains forms sheet like structures that form hydrogen bonds with each other allowing it to be very strong. It is the most abundant polysaccharide
160
How is cellulose made?
This is a long chain of glucose molecules that are glycosidically linked at the anomeric β carbon and the C4 carbon of another glucose.
161
What is Chitin?
This is the second most abundant polysaccharide in the world and it is composed of a long chain of N-Acetylglucosamine molecules.
162
How is Chitin formed?
Just like cellulose, it is formed when the β anomeric carbon of the N-acetylglucosamine forms a glycosidic bond with the C4 carbon of another N-Acetylglucosamine
163
What is α-amylose?
This is starch that is broken down by amylase in the body. It is made up of a long chain of glucose molecules?
164
How is α amylase made?
This is the opposite of Cellulose basically. It is created by having the α anomeric carbon (not β) form a glycosidic bond with the C4 carbon of glucose
165
What is Amylopectin?
This is a series of glucose molecules linked like the α amylase, but every 24-30 residues, there is a glycosidic link of the α anomeric carbon of one glucose to the C6 carbon of the chain glucose. This creates a branching point in the molecule.
166
What is glycogen?
A way to store glucose. This is set up just like amylopectin but the branching occurs every 8-14 residues
167
What does glucose isomerase do?
It breaks down starch to glucose monomers
168
What is the difference between a reducing and a non-reducing end?
The reducing end is an open end in a polysaccharide where the anomeric carbon is open while the non-reducing end is the end without the anomeric carbon open
169
What is a non-reducing sugar?
This is when there are no anomeric carbon ends. In the case of the saccharides we learned, sucrose is a non-reducing sugar because it does not have an open anomeric carbon end.
170
Give two monosaccharides and the disaccharide they form, which state has lower free energy?
The two monosaccharides because there are more possible conformation states than when the two monosaccharides are linked, thus increasing probability and making Gibbs free energy more favorable. Hydrolysis of a polysaccharide is greatly favored over the condensation
171
What kind of reaction is respiration?
Redox, here glucose is oxidized to CO2 and oxygen is reduced
172
How does cellular respiration gain energy?
It oxidizes food
173
What is oxidation?
Loss of electrons (more positive since electrons are negatively charged)
174
What is reduction?
Gain of electrons (more negative)
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How many oxidation states are in carbon?
9
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What are the guidelines for assigning oxidation number in for carbon?
When looking at the atoms that are linked to carbon, hydrogen is assigned a (-1) oxidation state, carbon is assigned a (0) oxidation state, and any bond attached to either O, N, or S gets an oxidation state of (+1). The total oxidation state is the sum of these.
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The higher the oxidation number the more _____ something is
Oxidized
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The more negative the oxidation number, the more _____ something is
Reduced
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Molecules with what kind of carbons lead to a larger release in energy when the molecule is oxidized?
Reduced
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What are the key metabolic energy carriers in cells?
ATP and NADH
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What is the most common metabolic energy carrier used?
ATP (adenosine triphosphate). This is an adenosine nucleotide with three phosphate groups attached to the C4 carbon through a phosphodiester bond. The phosphate groups are attached by a phosphoanhydride bonds
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How is ATP used in the cell?
It is hydrolyzed to form ADP and a phosphate group which in turn releases a lot of energy
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Why is the hydrolysis of ATP favored?
Because the release of a phosphate group causes a relief in the repulsion of charge and resonance stabilization
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Describe the process of ATP hydrolysis
A water molecule will attach to the end phosphate of ATP causing it to leave. The attached oxygen to the phosphate that left results in resonance stabilization of charge on the molecule. The ADP will undergo favorable ionization resulting in a charge (-) where the phosphate group left. All of this is favorable resulting in a large release of energy.
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What is the most widely used electron carrier in the cell?
NADH which is Nicotinamide adenine dinucleotide.
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What is the structure of NADH?
It has an adenine attached to a ribose. That ribose is attached to another ribose that is attached to nicotinamide.
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Where is the reactive site on NADH?
On the ring of nicotinamide
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What are coupling reactions?
Since a lot of necessary biological reactions are endergonic, this means they need energy to proceed. Therefore, endergonic reactions are usually coupled with exergonic reactions. The energy released from the exergonic reaction results in the release of energy that the endergonic reaction can use to power its reaction. The energy released by the exergonic must be equal to the energy required for the endergonic reaction, or greater making the reaction exergonic overall.
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How do you find the ∆G for a coupling reaction?
Add up all the ∆G’s of each reaction
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How many reactions are in glycolysis?
10
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What is glycolysis?
It is the oxidation of glucose to pyruvate, NADH, and ATP
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How does the dephosphorylation of Phosphocreatine occur?
ADP takes the phosphate group from the phosphocreatine to create creatine and ATP molecule. A creatine kinase is used to make this reaction proceed forward.
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When a person sprints, where does the person get their energy source?
Through pre-existing ATP, the synthesis of ATP through by a creatine kinase, synthesis of glucose by glycolysis and/or respiration.
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During a sprint, create a graph with energy as the y-axis and time of exercise on the x-axis.
Here we see that in short exercise, ATP is the major source of energy but it decreases very quickly. Then Creatine phosphate is the major source of energy.
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When exercising, what does phosphocreatine do for the body?
It allows ATP concentration to remain constant.
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How is glucose transported?
Through glucose transporters that use facilitated diffusion
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What is the difference between GLUT1, GLUT2, and GLUT4?
GLUT1 has a high affinity for glucose, GLUT 2 has a low affinity for glucose, and the GLUT4 transporter is used when a response from insulin is received
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What is the overall reaction of glycolysis?
Reactants: Glucose + 2Pi + 2 ADP + 2NAD+
Products: 2 pyruvates + 2ATP +2NADH + 2H+ + 2 H2O
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What is the first step of glycolysis?
When a hexokinase is used to activate glucose by adding a phosphate group to C6 to create Glucos-6-phosphate (G6P)
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What are the different types of hexokinases?
Types I and II are found in the brain, skeletal, muscle, and fat, and it has a high affinity for glucose. Type IV is a glucokinase and it is found in the liver so it can sense glucose levels, therefore it has a low affinity for glucose.
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What kind of mechanism does hexokinase use to bind to glucose?
Induced fit mechanism
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What is the induced fit mechanism used by hexokinase?
When the binding of glucose causes a conformational change that will allow glucose to fit better in the hexokinase so that it can become phosphorylated
203
In glycolysis, what is made directly after Glucose-6 phosphate?
Fructose 6 phosphate where a phosphoglucose isomerase is used to make the 6-membered ring, a 5-membered ring.
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In glycolysis, what is made directly after Fructose 6 phosphate?
A phosphofructokinase is used to make Fructose 1,6-bisphosphate so that it has two phosphate groups attached to each end out of the ring. ATP is used to synthesize this step
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What is the commitment step in glycolysis?
When the glucose becomes Glucose-6 phosphate because it can no longer go through the glucose transport through passive diffusion
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What are the two molecules that Fructose 1,6 bisphosphate can be cleave to?
DHAP and GAP
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What is the second step of glycolysis?
When Glucose 6 phosphate (G6P) becomes Fructose 6 phosphate (F6P). This reaction is catalyzed by phosphoglucose isomerase (PGI). Phosphoglucose is a hexokinase that will phosphorylate the glucose.
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Why is the transfer for the glucose 6 phosphate to become Fructose 6 phosphate important?
It will open the molecule to becoming phosphorylated a second time. Originally the C1 is at a hemiacetal position which is unfavorable. It will become a primary hydroxyl group after the phosphoglucose isomerase, allowing it to become phosphorylated much easier.
The aldose carbon is shifted to a ketose carbon to allow for the cleavage of the molecule to result in two three carbon molecules
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What is the third step in glycolysis?
When fructose 6 phosphate becomes phosphorylated through the addition of ATP to make fructose 1,6 bisphosphate. Phosphofructokinase I phosphorylates this reaction
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What does phosphofructokinase I do?
It takes the Phosphate off of the ATP molecule and attaches it to the fructose 6 phosphate to become fructose 1,6 bisphosphate
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What is the difference between a bisphosphate and a diphosphate?
Diphosphate are two attached phosphate groups and bisphosphate are two phosphates attached to a molecule at different placements.
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Why is the third step of glycolysis important?
This is when fructose 6 phosphate becomes fructose 1,6 bisphosphate and it is important because when the molecule is cleaved it allows for each half to have a phosphate group attached to it.
213
What is the fourth step of glycolysis?
Aldolase step. This is the split of the fructose 1,6 bisphosphate which will result in the creation of dihydroxyacetone phosphate (DHAP) and Glyceraldehyde 3-phosphate (GAP). The fructose 1,6 bisphosphate is cleaved between the 3 and 4 carbon. The enzyme aldolase will cleave the molecule
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What is the aldolase?
The enzyme that cleaves the fructose 1,6 bisphosphate
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Why is the fourth step of glycolysis important?
It doubles the amount of substrate used
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What allows the dihydroxyacetone phosphate (DHAP) and Glyceraldehyde 3-phosphate (GAP) to become interchangeable?
The Triose phosphate isomerase (TIM)
217
What form is the glyceraldehyde 3-phosphate in?
The aldose form
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If you have one molar of glyceraldehyde 6 phosphate and dihydroxyacetone phosphate, as well as the Triose phosphate isomerase (TIM), which molecule will be favored?
The dihydroxyacetone phosphate form, aldose form is less favorable
219
What happens after the glyceraldehyde 3 phosphate enters the chaos phase, or step 6 of glycolysis?
It will immediately get phosphorylated to become 1,3 bisphosphoglycerate through the enzyme glyceraldehyde 3 phosphate dehydrogenase. NAD oxidizes the carbon. The 1,3 bisphosphoglycerate will end up having two charge phosphate group, making the molecule super charge and therefore the next step of glycolysis very favorable by inducing the phosphoglycerate kinase to come in
220
What is the 7th step of glycolysis?
When the phosphoglycerate kinase attaches to the 1,3 bisphosphoglycerate and with the help of ADP, take off a phosphate group to create 3-phosphoglycerate. Here ATP is created
221
What is substrate level phosphorylation and which step of glycolysis is this found?
This is when a substrates phosphate group ends up phosphorylating ADP to make ATP. This is found in the seventh step of glycolysis when the 1,6 bisphosphoglycerate becomes 4 phosphoglycerate.
222
Describe the sixth and seventh step of glycolysis in terms of energy
The sixth step is slightly endergonic, while because such a high energy molecule is created (1,3 bisphosphoglycerate), the seventh step is exergonic, resulting in the release of energy. These two reactions are coupled together to allow the glyceraldehyde 3 phosphate to be driven to the sixth step.
223
What is the eighth step of glycolysis?
This is when the 3 phosphoglycerate becomes 2 phosphoglycerate through the help of a phosphoglycerate mutase (PGM). The phosphate is transferred to the second position.
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What does the transfer of the phosphate in step eight of glycolysis from the third carbon to the second carbon do?
It makes the removal of the phosphate group for ATP creation more favorable
225
What do mutase enzymes do?
They allow for an intramolecular shift of chemical groups. Phosphorylation of an internal histidine allows for this to happen. The second phosphorylation will result in a conformational change that will allow the mutase to take off another phosphate.
226
What is the intermediate between 3 phosphoglycerate and 2 phosphoglycerate in glycolysis by the phosphoglycerate mutase?
A 2,3-bisphosphoglycerate. So, there are two phosphate groups attached to the glycate.
227
Where else have we seen the 2,3 bisphosphoglycerate?
This is the BPG we saw that aids in the decreased affinity of hemoglobin in the blood to allow for more oxygen to be delivered to the muscles.
228
What does hyperventilation do to the blood?
It raises pH of the blood because more CO2 is taken in which results in le chatlier’s principle to move to the left, removing protons from the blood leading to pH to increase, which will cause the affinity of hemoglobin to go up, due to bohr’s effect. Therefore, it becomes harder to deliver oxygen to the muscles and tissue
229
How do the red blood cells overcome the hyperventilation high pH?
3,6 bisphosphoglycerate. Bisphosphoglycerate mutase will pull some of the 3 phosphoglycerate to make the 3,6 bisphosphoglycerate. This enzyme increase when the pH will increase. This will allow the BPG to be free flowing instead of being attached to an enzyme.
230
What is the downside to the use of the 3,6 bisphosphoglycerate mutase?
Since the reaction pulls away the 3 phosphoglycerate from glycolysis, this results in a decrease in the ATP production overall
231
How does a hexokinase deficiency effect the affinity of hemoglobin in high altitudes?
This will result in an overall lower amount of 3 phosphoglycerates to be created which will lead to an overall lower amount of 3,6 bisphosphoglycerate to be created and so the affinity of oxygen will remain high.
232
How does a pyruvate kinase deficiency affect the affinity of hemoglobin at high altitudes?
It will result in a large decrease in hemoglobin affinity because the deficiency prevents the creation of pyruvate leading to a buildup of BPG.
233
What is step 9 of glycolysis?
When the 2 phosphoglycerate is dehydrated to become phosphoenolpyruvate. The phosphoenolpyruvate will have a double bond on one of the carbons when the water is removed causing the reaction to be super charged. The enzyme that allows this to proceed is an enolase?
234
What enzyme catalyzes the 2 phosphoglycerate to become phosphoenolpyruvate?
Enolase
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What is step 10 of glycolysis?
When the phosphoenolpyruvate will make ATP by having a pyruvate kinase take off the phosphate group, add it to ADP to make ATP and thus, make pyruvate.
236
Why is the reaction of phosphoenolpyruvate to pyruvate important?
Substrate level phosphorylation makes ATP making a total net gain of 2 ATP from glycolysis.
237
In glycolysis, which molecule has the highest energy?
The phosphoenolpyruvate which will make the creation of ATP much more favorable
238
What is the investment phase of glycolysis?
The steps between glucose to glyceraldehyde 3 phosphate
239
What is the payoff phase of glycolysis?
What is the payoff phase of glycolysis?
240
What does glycolysis use up?
NAD+ therefore it must be replenished
241
How is NAD+ regenerated for glycolysis?
Using mitochondria, or anaerobic methods such as turning pyruvate to lactate
242
What is homolactic fermentation?
When pyruvate is reduced to lactate (its alcohol form) which will use NADH and result in NAD+ to be made. The enzyme that allows this reaction to proceed is the lactase dehydrogenase. In fermentation, there is no net change of oxidation state
243
How does yeast replace NAD+?
By turning Pyruvate into acetaldehyde and then making ethanol which is the step that uses up NADH. The pyruvate has a CO2 removed by pyruvate dehydrogenase to make the acetaldehyde. The acetaldehyde is reduced by alcohol dehydrogenase to make ethanol.
244
What is Thiamine pyrophosphate?
It is found in the B1 vitamin. It has a critical carbon that has a hydrogen fall off causing it to have a positive charge that will result in the reaction with pyruvate allowing it to lose CO2.
245
What does consuming alcohol do for your body?
It will increase the amount of NADH in your body resulting in a decreased driving force for glycolysis, resulting in a decrease in the amount of ATP created. The ethanol will turn to acetaldehyde through alcohol dehydrogenase, which in turn will turn to acetate by aldehyde dehydrogenase.
