1
Q
What are the five major functional classes of proteins?
A
- Metabolic enzymes
- Structural proteins
- Transport protein
- Cell signaling proteins
- Genomic caretaker proteins
2
Q
Describe the function of Metabolic enzymes and give an example.
A
- Reaction catalysts that control metabolic flux
- Catalyze reactions in energy conversion pathways
- Lower Activation energy
- Increased product formation
- Responsible for synthesis and degradation of macro molecules
Ex. Malate dehydrogenase
3
Q
Describe the function of structural proteins and give an example.
A
- Maintain integrity of cell structure and promote changes in cell shape
- Serve as framework for individual cells, tissues, and organs
- Structure proteins that are responsible for cell shape, cell migration, and cell signaling are Actin Tubulin, and Collagen
Ex. Cytoskeletal proteins
- Structure proteins that are responsible for cell shape, cell migration, and cell signaling are Actin Tubulin, and Collagen
4
Q
What is Actin? What category of protein does it fall under and what is its function?
A
- A structural protein that is abundant in cytoskeleton of animals
- Subunits self assemble form actin monomers and form thin filaments (polymer)
- Also found in muscles which with myosin can cause a contraction
5
Q
What is Tubulin? What category of protein does it fall under and what is its function?
A
- A structural protein abundant in Cytoskeleton of animals
- self assembled monomers of tubulin form microtubules (polymers)
- Microtubules act as roads for movement of organelles and chromosomes during cell division
6
Q
What is Collagen? What category of protein does it fall under and what is its function?
A
- A major structural protein in animals
- Primary component of connective tissue
- Gives strength to tendons, cartilage, bones, and teeth
7
Q
What is the function of transport enzymes?
A
- Facilitate movement of molecules within and between cells
- Abundant in the plasma membrane
- Allow entrance and exit of polar molecules
- Two types of transportation
- Active
- Passive
8
Q
Outline the proteins involved in a cell signaling protein pathway
A
- First messenger
- Receptor protein
- Upstream signaling proteins
- Second messenger
- Downstream signaling protein
- Target protein
9
Q
What are the two large classes of membrane receptors?
A
- G-protein coupled receptors (GPCR)
- Glucagon
- Receptor tyrosine kinases
- Insulin
10
Q
What activates a nuclear receptor?
A
- Steroid hormones such as Estrogen and Progesterone
11
Q
What are two examples of Intracellular signaling proteins and what do they do?
A
- Protein phosphorylation
- Kinases and phosphotases
- They act as molecular switches
12
Q
What is a Genomic caretaker protein and what are some examples?
A
- Protein that maintains integrity and accessibility of genomic information
- Important to remairing mutations in DNA of reproductive cells
- Includes proteins involved in DNA replication, repair, and recombination
- DNA Polymerase, DNA Ligase, Topoisomerase, and DNA Primase
- Includes Gene expression (RNA Polymerase)
13
Q
Compare and contrast Myoglobin and Hemoglobin?
A
Myoglobin:
- Concentrates in muscle
- Storage depot for O2
Hemoglobin:
- Major protein in blood cells
- 35% of dry weight in red blood cell
- Transports O2 from lungs and tissue through circulatory system
Both:
- Both reversibly bind O2 to Fe(2+) using a porphyrin ring tightly bound to the protein.
14
Q
What is Heme and why is it important?
A
- It is a prosthetic group
- Organic group permanently attached to enzyme to provide specific function
- Fe(2+) porphyrin complex binds O2
- Vital because no amino acid can reversibly bind to oxygen
- O2 binds to prosthetic group with iron in its reduced state Fe(2+)
- Heme Alone cannot bind as it is too strong and will not release the oxygen
- Protein environment allows for regulation of O2 binding
15
Q
How many heme groups does myoglobin have?
A
- Single polypeptide with one heme group
16
Q
How many subunit and heme groups does hemoglobin have?
A
- Tetrameric structure of four polypeptides with two alpha and two beta subunits
- Each subunit has one heme group adding up to 4 O2 binding sites
17
Q
How many alpha helices does a Globin fold have?
A
- 8 (Each letter is a helix)
- About 150 aa residues and 1 heme
18
Q
How does heme bind oxygen and what amino acid is crucial?
A
- Heme has 6 coordination bonds
- Myoglobin and hemoglobin bind to 6th coordination bond
- Two histidines are needed for binding to occur
19
Q
How does oxygen binding to heme change its structure?
A
- Heme is not naturally planar(because it is too big) but becomes planar when oxygen binds
- The binding of O2 causes smaller Fe(2+) which is facilitated by Helix F movement which results in larger conformational change
20
Q
What effect does O2 binding have on other subunit affinity? (deoxyhemoglobin to oxyhemoglobin)
A
- Binding of O2 in one subunit leads to conformation change in other subunits increasing their O2 affinity
21
Q
Describe cooperativity in O2 affinity
A
- a protein that has multiple binding sites that can influence each other can experience cooperativity
Positive Cooperativity
- First binding site increase O2 affinity in the remaining sites
Negative Cooperativity
- First binding reduces affinity at remaining binding sites
22
Q
What is the association constant equation? (at eq)
A
- Ka
- [P] is protein and [L] is ligand
(Insert picture)
23
Q
What is the dissociation constant equation? What is strong vs weak binding
A
- Kd
- [P] is protein and [L] is ligand
- Strong binding Kd < 10 nM
- Weak binding Kd > 10 uM
24
Q
What is the equation used to calculate for (fractional) occupied binding sites?
A
25
Where is Kd on a fractional saturation plot?
- Where fractional saturation is at .5
26
How much O2 can be released from myoglobin as opposed to hemoglobin?
These graphs can be read by subtracting the fractional saturation at resting and subtracting the active saturation which can then be calculated into a percent
- These graphs show that myoglobin can only release about 20% of oxygen bound to it while hemoglobin can release about 60% of the oxygen bound to it
27
Compare and contrast T and R conformations of Hemoglobin
T State
- Tense
- Oxygen is unbound
-deoxyhemoglobin
R state
- Relaxed
- Bound oxygen
- Oxyhemoglobin
- Affinity for O2 about 100 times higher than T state
28
How does the T state change to the R state?
- Helix F moves
- Movement induces conformational change in other subunits
- 15 degree rotation of alpha and beta one and alpha and beta two
29
Outline the points of this sigmoidal plot
- Binding of first O2 is weak
- Conformational change occurs T->R
- Binding of second O2 is stronger
- Third and fourth binding are increasingly stronger than the first
- Fourth is about 100 times stronger than the first
30
Compare and contrast the Concerted and Sequential model
Concerted model:
- Tetramer can either be in low affinity (T) or high affinity (R) state
Sequential model:
- Subunits of tetramer can be either low affinity (T) or high affinity (R)
31
Describe the role of O2 as a positive allosteric effector.
- Changes conformation of hemoglobin
- Increases O2 affinity
- An example of homotropic allostery, substrate binding changes affinity
32
What are three heterotrophic allosteric effectors for hemoglobin? (not substrates)
- CO2, H+, 2,3 bisphosphoglycerate (BPG)
- Cannot be substrates because they do not bind to O2 binding site
33
What effect does aerobic respiration have on blood pH in the lungs and tissue? What effect does it have on O2 affinity?
- CO2 released from aerobic respiration
- Produces H+ which decreases pH
- Blood pH is 7.6 and 7.2 in tissues
- Lower O2 affinity in tissue promotes O2 release
34
What does protenation of hemoglobin cause?
- Affects salt bridges between Asp, Glu, His, Lys
- Favors T state
- Promotes release of O2 in tissue
35
Where does Bicarbonate bind to Hemoglobin?
- Binds as CO2 to the N terminus causing T state to be more favorable
36
What is 2,3 Bisphosphoglycerate (2,3BPG) and what does it do?
- Found in red blood cells
- Traps hemoglobin in T state acting as negative effector to O2 binding
- Only one 2,3BPG can bind to tetramer
- Binds in center cavity
- Forms salt bridges with His-2, Lys-82, and His-143 on each beta subunit
37
Give an overview of how allosteric regulation works between the lungs and tissue.
- BPG concentration is constant in red blood cell regardless of where it is
- High O2(lungs) favors R state and leads to release of BPG
- Low O2 (tissue) favors T state which is stabilized by BPG
- Effects(Bohr) are enhanced by CO2 and H+
38
How does high altitude affect BPG concentration?
- High altitude increases BPG concentration resulting in a larger difference between the fractional saturations in the lungs and tissue
- Larger difference in fractional saturation means increased O2 transport capacity
39
What is the difference between hemoglobin and fetal hemoglobin? What effect does this have?
- Contains γ instead of β subunits (His ->Ser)
- Eliminates 2 charges and reduces BPG affinity
- Mostly R state
- After birth γ is replaced by β
40
What is Anemia?
- Reduced oxygen transport efficiency from the lungs to the tissue
- Altered hemoglobin function or reduced number of red blood cells
Example: Sickle cell anemia
41
What causes sickle cell anemia and what are the effects?
- (Glu6-> Val6)
- Hydrophobic amino acids on the surface of beta subunit
- Causes folding on another beta subunit
- Aggregates and forms long chains of hemoglobins resulting in altered cell shape
42
What form of hemoglobin aggregates in sickle cell anemia?
Deoxyhemoglobin S
43
What type of disease is Sickle cell anemia?
- Autosomal Recessive
- Capillaries can become blocked and it can be very painful
- Homozygous individuals usually die in childhood
- If one allele has the sickle cell trait, 1% of erythrocytes become sickled which protects against malaria
44
How does Sickle Cell Anemia (HbS) combat Malaria?
Decreases pH (by 0.4)
45
What is used to treat Sickle Cell Anemia?
Hydroxyurea elevates expression of γ subunit which means α2γβs cannot aggregate
46
What does carbon monoxide do to hemoglobin?
It binds to O2(CO has better binding affinity than O2) binding sites and is highly toxic
- Blocks function of hemoglobin, myoglobin, and mitochondrial cytochromes
47
What would happen to the COHb individual? Will the same thing happen to the Anemic individual? Why?
- COHb individual will die because the pO2 in tissue is very high relative to the pO2 in the lungs
- No the same thing will not happen because the anemic individual has the same shaped curve as the normal individual with 50% capacity meaning O2 can still be released in the tissue
48
What are the three major classes if membrane proteins?
- Membrane receptor proteins
- Involved in transduction of a signal across the plasma membrane
- Membrane-bound metabolic enzymes
- Membrane proteins embedded in the inner mitochondrial membrane (similar to chloroplast thylakoid membrane)
- Membrane transport proteins
-Facilitate movement of polar molecules across the hydrophobic membrane
49
Compare and contrast active and passive transport.
Active:
- Moves biomolecules against a concentration gradient
- Requires energy: ATP hydrolysis
Passive:
- Movement across a membrne in the direction of the concentration gradient
- Does not require energy
50
What molecules can pass the membrane bilayer? Which cannot?
- Hydrophobic molecules can diffuse across the bilayer (from high to low concentration)
- Polar molecules must be transported via membrane proteins
51
What is the ΔG of passive transport? Active transport?
- ΔG is negative for passive transport
- ΔG is positive for active transport
52
What equation is used to calculate ΔG of transport?
ΔG = RTln(C2/C1) + ZFΔV
R = 8.314
T = Kelvin
C2 = Concentration at destination
C1 = Concentration at starting point
Z = Charge of solute
F = 96500 coulombs per mol
ΔV = Membrane potential difference
53
What is Gramicidin A and what does it do?
- A basic passive transporter
- Dimer made of two stacked helices
- Pore is wide enough for Na+ and K+ to pass
- Great antibiotic
- disrupts electrochemical gradient of bacteria
54
How does porin passive transport work?
1. Ion or small molecule is transported via porin passive transport protein
2. Substrate carrier protein transports ion or small molecule through the periplasmic space
3. Substrate carrier protein transports ion to coupled ABC active transport protein
55
What is a K+ ion channel and what does it do?
- Responsible for K+ transport
- Does not allow passage of Na+
- Diameter of Na+ is smaller than that of K+
- selectivity filter of TVGYG sequence means Na+ is too small to interact with the amino acids which means dehydration cannot occur and it must be dehydrated to pass through small channel
- K+ channel directs K+ out of the intracellular space
56
What is an Aquaporin?
- Membrane transport protein that transports water passively across the hydrophobic membrane
- Can also transport Urea and glycerol
- Tetramer can transport 3 billion H2O per second
- Responsive to osmotic pressure
57
What is Proton Hopping?
- The transfer of a proton from a hydronium ion to a water molecule
58
What is active membrane transport? What are the two types?
- Transport which requires energy to "pump" molecules across the membrane
- Two Types of Active transport
- Primary active
- Secondary active
- Symport
- Anitport
59
Describe primary active transport, secondary active antiporter, and secondary active symporter.
Primary active transport:
- ATP drives molecule up its concentration gradient
Secondary active antiporter:
- Molecule traveling down its concentration gradient drives another molecule up its gradient
Secondary active symporter:
- A molecule moves down its concentration gradient which drives another molecule up its gradient in the same direction
60
What are the two most abundant types of primary active transporters? How do they work?
- P-type (phosphorylated)
- ABC (ATP binding cassette)
- Both use ATP hydrolysis that drive conformational change in protein complex
61
What are P-type transporters and what do they do?
- Use phosphorylation to drive protein conformational changes
- Na+K+ ATPase
- 3 Na+ out for 2 K+ in
- 1/4 of atp used in cell is to maintain Na+/K+ electrochemical gradient
62
What are ABC transporters?
- ATP dependent importers/exporters
- ATP Binding Cassette
- ATP hydrolysis causes conformational change in membrane protein (facing out to facing in)
Examples: Multidrug resistant protein and cystic fibrosis transmembrane conductance regulator protein
63
How many trans membrane domains does Na+/K+ ATPase have?
4: Transmembrane domain (M), Regulatory domain (A), Phosphoryl domain (P), and ATP binding domain (N)
64
What are two examples of important molecules bacterial ABC transporter proteins transport?
- Molybdate and tungstate transporter
- Maltose transporter
65
Outline the steps of ABC transport mechanism
1. Binding of substrate carrier causes conformational change exposing substrate binding site
2. ATP hydrolysis causes conformational change releasing substrate
3. Release of ADP + Pi and the binding of ATP resets transport protein
66
How does secondary active transport work?
- Uses energy from downhill electrochemical gradient to co-transport a second molecule against its gradient
- Coupled to ATP hydrolysis
Example: Lactose permease in bacteria
67
Describe how the Na+/I- symporter works.
Na+ gradient is used to drive I- against its concentration gradient
68
What do thyroid glands regulate? What does it uptake?
- Metabolic rate
- Uptakes iodine, otherwise goiter occurs
69
What does sliding filament model show?
- Muscle filaments made of actin and myosin slide over one another during muscle contraction using chemical energy from ATP hydrolysis
70
What is a myoblast and what is a unique feature?
- Muscle cells which consists of larged fuzed cells with many nuclei and a shared plasmamembrane known as a sarcolemma
CHEM 441A+B
flashcards
Decks in class (22)
# Cards
-
Chapter 2: Physical Biochemistry25
-
Amino Acid Structures20
-
Amino Acid Abbreviations20
-
Chapter 3: Nucleic Acid Structure and Function19
-
Chapter 4: Protein Structure18
-
Chapter 5: Methods in Protein Biochemistry44
-
Chapter 6: Protein Function70
-
Chapter 7: Enzyme Mechanisms86
-
Chapter 8: Cell Signaling Systems31
-
Chapter 9: Glycolysis46
-
Chapter 10: The Citrate Cycle41
-
Chapter 11: Oxidative Phosphorylation59
-
Chapter 12: Photosynthesis60
-
Chapter 13: Carbohydrate Structure and Function47
-
Chapter 14: Carbohydrate Metabolism87
-
Chapter 15: Lipids47
-
Chapter 16: Lipid Metabolism51
-
Chapter 17: Amino Acid Metabolism34
-
Chapter 19: Metabolic Integration18
-
Chapter 20: DNA Replication36
-
Chapter 21: Transcription38
-
Chapter 22: Translation30
