Term
|
Definition
| metabolites, coenzymes, inorganic ions, and enzymes |
|
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Term
|
Definition
| plasma membrane, cytosol, genes |
|
|
Term
| Bacterial cells contain (3) |
|
Definition
| cytosol, nucleoid, plasmids |
|
|
Term
| Eukaryotic cells have (2) |
|
Definition
| a nucleus and membrane bound organelles |
|
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Term
|
Definition
| linear polymers of amino acids which serve a wide range of biological functions (enzymes, receptors, transporters, etc) |
|
|
Term
|
Definition
| linear polymers of nucleic acids that are involved in all aspects of storage and utilization of genetic information |
|
|
Term
|
Definition
| polymers of sugars that serve in structural, energy storage and cellular recognition roles |
|
|
Term
|
Definition
| Fats, and aggregates of fats, that serve in energy storage, formation of membrane and signaling. |
|
|
Term
| Carbon's bonding versatility allows it to: |
|
Definition
| produce a broad array of carbon-carbon skeletons with a variety of functional groups. |
|
|
Term
|
Definition
| give biomolecules their biological and chemical personalities |
|
|
Term
| Molecular configuration can be changed only by: |
|
Definition
|
|
Term
| Molecular confirmation is: |
|
Definition
| the position of atoms in space that can be changed by rotation about single bonds, without breaking covalent bonds. |
|
|
Term
| Interactions between biological molecules are almost invariability stereospecific: |
|
Definition
| they require complementary match between the interacting molecules. |
|
|
Term
| Living Cells are: Open Systems |
|
Definition
| exchanging matter and energy with their surroundings, extracting and channelling energy to maintain themselves in a dynamic steady state distant from equilibrium. |
|
|
Term
| How is energy obtained from sunlight or fuels in cells? |
|
Definition
| by converting the energy from electron flow into chemical bonds of ATP. |
|
|
Term
| Free Energy Change, DeltaG |
|
Definition
| the tendency for a chemical reaction to proceed toward equilibrium |
|
|
Term
|
Definition
| enthalphy change. Reflects the number of kinds of bonds. |
|
|
Term
|
Definition
| entropy change. The degree of randomness |
|
|
Term
| Free energy change equation |
|
Definition
|
|
Term
| Delta G of reaction is negative.. |
|
Definition
| the reaction is exergonic, tends to go towards completion. Spontaneous, releases energy which can be used to do work, proceeds until equilibrium is reached. |
|
|
Term
| Delta G of reaction is positive.. |
|
Definition
| the reaction is endergonic and tends to go in the reverse direction. Non-spontaneous, needs input of energy to proceed. |
|
|
Term
| When two reactions can be summed to yield a third reaction.. |
|
Definition
| the delta G for this overall reaction is the sum of the Gs of the two separate reactions. |
|
|
Term
|
Definition
| the standard free-energy change for reaction that is related to the equilibrium constant by the equation DeltaGdegrees=-RT inKeq |
|
|
Term
|
Definition
| the study of life at a molecular level. The study of the molecular logic of life. |
|
|
Term
| Living organisms have:(6) |
|
Definition
Chemical complexity and microscopic organization.
system for extracting, transforming, and using energy from the environment.
Defined functions of each component and regulated interactions.
Sensory mechanisms and ability to respond.
Self-replication and assembly.
Gradual Evolution/change over time. |
|
|
Term
|
Definition
1. cellular foundation
2. chemical foundations
3. physical foundations
4. genetic foundations
5. evolutionary foundations |
|
|
Term
|
Definition
| a thin, hydrophobic barrier that regulates the movement of molecules in and out of the cell |
|
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Term
|
Definition
| the interior volume of the cell. Consists of cytosol and dissolved biomolecules |
|
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Term
|
Definition
| a nucleoid or nucleus that contains the genetic material of the cell. In bacteria genetic material is contained in the nucleod which is not separated from the cytosol. In eukaryotic genetic material is contained in specialized organelles called nucleus. |
|
|
Term
| All living things need (3) |
|
Definition
| Plasma Membrane, Cytoplasm, Nucleic Acid |
|
|
Term
|
Definition
| before nucleus. Small, simple, single-celled organisms such as bacteria. Their potential for rapid growth and division allow for quick adaption to changing environment conditions. |
|
|
Term
|
Definition
| large complex cells. Make up multi-cellular organisms such as yeasts, plants, fungi, vertebrates. Organelles to support specialized functions. Differentiation of cells to unique and specialized cell types. |
|
|
Term
|
Definition
| linear polymers of amino acids which serve as a wide range of biological functions. Enzymes, receptors, transporters, etc. |
|
|
Term
|
Definition
| linear polymers of nucleic acids that are involved in all aspects storage and utilization of genetic information. |
|
|
Term
|
Definition
| polymers of sugars that serve in structural, energy storage and cellular recognition roles. |
|
|
Term
|
Definition
| Fats, and aggregates of fats, that serve in energy storage, formation of membrane and signaling. |
|
|
Term
|
Definition
| Water (70%), 3000 Proteins (15%), DNA (1%), over 3000 RNA (6%), 5 Polysaccharides (3%), 20 Lipids (2%), 500 Subunits and intermediates (2%), 20 inorganic ions (1%). |
|
|
Term
| Complex Molecules from Simple Precursors: 4 Levels |
|
Definition
1. monomeric units
2. macromolecules
3. supramolecular complexes
4. the cell and its organelles |
|
|
Term
|
Definition
| in glass. studies the behaviour of molecules outside the context of the cell and organism |
|
|
Term
|
Definition
| in the living. Studies occur within the context and complexity of the cell or organism |
|
|
Term
| Experiments which are successful in vitro often fail in vivo because... |
|
Definition
| of the greater complexity of the system |
|
|
Term
| Chemical Foundations: 97% of the weight of most organisms in made up of: (6) |
|
Definition
| Carbon, Oxygen, Hydrogen, nitrogen, phosphorus and sulfur |
|
|
Term
|
Definition
| flexible spatial arrangement of atoms within a molecule(can be changed without breaking bonds) |
|
|
Term
|
Definition
| fixed spatial arrangement of atoms within a molecule (cannot be changed without breaking bonds). Conferred by either presence of double bonds (no freedom of rotation or chiral centers (substituent groups are arranged in a specific positioning) |
|
|
Term
| Configuration is conferred by (2) |
|
Definition
1. presence of double bonds (no freedom of rotation)
2. chiral centers, around which substituent groups are arranged in a specific positioning. |
|
|
Term
|
Definition
| Cis and Trans. Have the same chemical formula but differ in the arrangement of groups with respect to non-rotating double bond. |
|
|
Term
|
Definition
| have 4 different substituents attached. These groups may be arranged in different ways in space yielding 2 stereoisomers that differ in their configuration. |
|
|
Term
| How many stereoisomers will a molecule with 3 chiral carbons have? |
|
Definition
8.
n chiral carbons=2tothepowerofN stereoisomers. |
|
|
Term
|
Definition
| non-superimposable molecules that differ in configurations at a chiral center |
|
|
Term
|
Definition
| stereoisomers that are mirror images. Have nearly identical chemical properties but rotate the plane of polarized light in equal but opposite directions. |
|
|
Term
|
Definition
| stereoisomers that are not mirror images. |
|
|
Term
|
Definition
| An equimolar solution of enataniomers. Shows no optical rotation |
|
|
Term
| Biomolecules are often constructed exclusively from one building block stereoisomer |
|
Definition
| Proteins are built entirely from L-amino acids |
|
|
Term
| interactions between biomolecules, as well as between biomolecules and small molecule ligands are... |
|
Definition
|
|
Term
|
Definition
| constituent reactants and products, the solvent that contains them, and the immediate atmosphere. |
|
|
Term
|
Definition
| system and its surroundings |
|
|
Term
|
Definition
| does not exchange energy or matter with its surroundings |
|
|
Term
|
Definition
| exchanges energy but not matter with the surroundings |
|
|
Term
|
Definition
| exchanges energy and matter with the surroundings. |
|
|
Term
| Organisms derive energy from their surroundings in 2 ways |
|
Definition
1. taking up energy fuels (such as glucose) from the environment and extracting energy by oxidizing them.
2. absorbing energy from sunlight |
|
|
Term
| First Law of thermodynamics |
|
Definition
| in any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change. |
|
|
Term
| First law of thermodynamics in Cells |
|
Definition
| cells are highly effective transducers of energy, converting the energy of metabolized nutrients, or energy of the sun, into work, heat and generation of complex molecules. |
|
|
Term
| Second Law of thermodynamics |
|
Definition
| the tendency in nature is toward ever greater disorder in the universe: the total entropy (disorder) of the universe is continually increasing. The universe moves towards greater disorder but biomolecules and living systems require a high degree of organization. |
|
|
Term
|
Definition
| System is at equilibrium-the rate of the forward reaction equals the rate of the reverse reaction. There is no change in free energy in the system |
|
|
Term
| What is the link between catabolic (breakdown) reactions and anabolic (building) reactions? |
|
Definition
|
|
Term
| What is metabolic efficiency? |
|
Definition
|
|
Term
|
Definition
| provides the instructions for forming all other cellular components and provides a template for the production of identical DNA molecules to be distributed to the progeny when a cell divides |
|
|
Term
Nucleotide sequence within genes dictates-
The amino acid sequence dictates-
the structure dictates- |
|
Definition
sequence of amino acids.
structure of the protein.
biological activity of the protein |
|
|
Term
| Central Dogma of Biochemistry |
|
Definition
| Describes the fundamental information flow in biological systems. DNA is replicated to form new DNA, which is transcribed into RNA. The RNA is translated to protein. James Watson. |
|
|
Term
| Biomolecules First arose by chemical evolution |
|
Definition
| stanley miller demonstrated that exposing a gaseous mixture thought to resemble the atmospheric conditions of pre-biotic earth to a series of electric shocks (lightening) generated a variety of organic compounds associated with life. |
|
|
Term
|
Definition
| the structures of biomolecules (proteins, membrances, nucleic acids) are formed in response to their interaction with water. |
|
|
Term
|
Definition
| water is a participant in many biological reactions |
|
|
Term
| Waters ability to interact with other water molecules and other biomolecules is due to |
|
Definition
|
|
Term
| The dipole of water will dictate its ability to (2) |
|
Definition
1. form electrostatic interactions with charged molecules which includes other water molecules.
2. form hydrogen bonds, including with other water moleucles |
|
|
Term
|
Definition
| an electrostatic interaction between an electronegative atom with a hydrogen linked (donor) to another electronegative atom with a free electron pair (acceptor) |
|
|
Term
| Characteristics of Hydrogen bonds (3) |
|
Definition
form individually weak, non covalent interactions.
approx double the length of a covalent bond.
Strength depends on its geometry |
|
|
Term
| The large number of hydrogen bonds in water contribute to (2) |
|
Definition
| its high heat of vaporization and specific heat capacity (higher melting point and boiling point) |
|
|
Term
|
Definition
| the amount of heat to raise the temperature of a substance one degree |
|
|
Term
| Cohesion of water is due to |
|
Definition
| each water molecule can donate two hydrogen bonds and accept two hydrogen bonds. These interactions occur with other water molecules. The sum of all the hydrogen bonds between water molecules confers great internal cohesion on liquid water. Adjacent water molecules give liquid water great internal cohesion. |
|
|
Term
| Biological Significance of High specific heat capacity of water: |
|
Definition
| The high composition of water within our bodies, coupled with the high specific heat capacity of water helps us to stay cool. |
|
|
Term
|
Definition
| in ice each water molecule participates in 4 hydrogen bonds with other water molecules. The ordered arrangement of ice has a lower density than liquid water. |
|
|
Term
|
Definition
| soviet physicist. water forced through quartz capillary tubes. higher boiling point, lower freezing point, much high viscosity than ordinary water. Infectious. BS. |
|
|
Term
| Water is an extremely effective hydrogen-bonder for two reasons: |
|
Definition
1. water can accept and donate hydrogen bonds.
2. waters small size allows it to adapt optimal positioning for optimal geometry of hydrogen bonding. |
|
|
Term
| Water has the ability to act as a solvent because... |
|
Definition
| it forms hydrogen bonds with polar solutes. like dissolves like. Water molecules can interact, and dissolve, charged solutes through formation of layers of hydration. Water can interact with both positively and negatively charged groups. |
|
|
Term
| Solubilities of molecules in water depend on: |
|
Definition
| its ratio of polar to nonpolar groups. the larger portion of nonpolar groups the less soluble the molecule is in water. |
|
|
Term
| Biological Significance of solubilities of molecules in water: Gas exchange |
|
Definition
| CO2 and O2 are nonpolar and have limited solubility in water (and blood). This present s a challenge for the transport of these vital gases between tissues and the lungs. Specialized transport proteins and strategies are required |
|
|
Term
| What is the primary driving force in formation and stabilization of biomolecular structures and interactions |
|
Definition
| hydrophobic drive (hydrophobic interactions) |
|
|
Term
| Non-Covalent Forces Include (3) |
|
Definition
formation and stabilization of structures of biomolecules.
Recognition/interactions of one biomolecules with another.
Binding of reactants to enzymes. |
|
|
Term
| Non-Colvalent interactions that are of importance to biomolecules include: (4) |
|
Definition
hydrogen bonds.
ionic interactions.
hydrophobic interactions.
van der Waals interactions |
|
|
Term
| Many biomolecules possess groups which accept and donate hydrogen bonds. These groups form hydrogen bonds with (3)`` |
|
Definition
water.
Groups with the same molecule (Intramolecular).
Groups with other molecules (intermolecular) |
|
|
Term
|
Definition
| electrostatic interactions between charged groups. Can be attractive or repulsive. The magnitude of contribution of ionic interactions to biomolecular structures is greatly reduced by the shielding of these groups by water molecules. |
|
|
Term
|
Definition
When 2 uncharged atoms are brought very close together their surrounding electron clouds influence each other. Interaction between permanent and induced dipoles; short range, low magnitude interactions.
Abundant in the core of protein due to close packing of hydrophobic side chains. When two atoms are separated by the sum of the van der Waals radii the attraction is maximal. |
|
|
Term
| Dissociation of water equation |
|
Definition
|
|
Term
Keq of water
[H+][OH-]/[H2O] |
|
Definition
|
|
Term
|
Definition
|
|
Term
Kw=[H+][OH-]
Kw of water =
the ion product of water |
|
Definition
|
|
Term
|
Definition
| A difference of 1 pH unit is a 10-fold difference in [H+] |
|
|
Term
| Ka=[H+][CH3COO-]/[CH3COOH] |
|
Definition
| Ka values are often expressed as pKa's (pKa=-logKa) |
|
|
Term
|
Definition
| extends one pH unit on either side of the pKa point. when pH=pKa the solution is best able to resist changes in pH. |
|
|
Term
| the lower the pKa the ____ the acid. |
|
Definition
|
|
Term
| the higher the pKa the ____ the acid. |
|
Definition
|
|
Term
| The henderson-hasselbalch equation describes the relationship between: (3) |
|
Definition
1. the pH of the solution
2. the pKa of the weak acid
3. the relative concentrations of the weak acid (HA) and conjugate base (A-) |
|
|
Term
| The henderson-hasselbalch equation |
|
Definition
|
|
Term
|
Definition
| a solution that can resist changes in pH with the addition of acid or base. Arise from weak acids and bases. Common in biological systems (phosphate and bicarbonate) and are required to maintain physiological pH in cells and tissues |
|
|
Term
|
Definition
| a increased acidity in the blood and other body tissue (pH lower than 7.35) |
|
|
Term
|
Definition
| a decreased acidity in the blood and other body tissue (pH higher than 7.45) |
|
|
Term
| Amino acids are bi-functional compounds due to |
|
Definition
|
|
Term
| Except for ____, all amino acids have a chiral carbon and are therefore stereoisomers |
|
Definition
|
|
Term
| A peptide with three residues could be produced ____ ways |
|
Definition
|
|
Term
| a protein of 100 residues would have _____ possible sequences |
|
Definition
|
|
Term
|
Definition
1. carboxyl group
2. Amino group
3. Alpha carbon
4. R group |
|
|
Term
| For all amino acids but glycine the alpha carbon is bonded to 4 different groups creating a ______ |
|
Definition
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Term
|
Definition
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Term
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Definition
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Definition
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Definition
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Definition
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Definition
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Term
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Definition
Glutamate.
carries a net charge of -1 at pH7. Used as a flavor enhancer |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Nonpolar, aaliphatic R Groups (7) |
|
Definition
Gly, Ala, Pro, Val, Leu, Ile, Met
Non-polar hydrophobic side chains tend to be buried in the core of the protein. |
|
|
Term
| Polar, uncharged R Goups (5) |
|
Definition
|
|
Term
| Positively charged R groups (3) |
|
Definition
|
|
Term
| Negatively charged R groups (2) |
|
Definition
|
|
Term
| Phosphorylation of Amino Acids |
|
Definition
| protein phosphorylation is a central mechanism to regulate the activities of select proteins. These modifications are post-translational. These phosphoryl groups are added by kinases to specific, hydroxyl-group containing amino acids. These modifications are reversible; the phosphoryl group can be removed by phosphatases. |
|
|
Term
|
Definition
| form through the oxidation of the sulfhydryl groups of two cysteines to form a covalent linkage. Can help to stabilize the structures of proteins. |
|
|
Term
|
Definition
| can act as both weak acids and bases. |
|
|
Term
|
Definition
| the dipolar ion of an amino acid |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Triprotic Amino Acids (7) |
|
Definition
| Lys, Arg, His, Asp, Glu, Cys, Tyr |
|
|
Term
|
Definition
isoelectric point.
Is equal to the average of hte pKas on either side of the region where the net charge on teh molecule is equal to zero.
is the pH at which the net charge on the molecule is equal to zero. |
|
|
Term
|
Definition
| the protonated form predominates (HA) |
|
|
Term
|
Definition
| unprotonated form predominates (A-) |
|
|
Term
|
Definition
|
|
Term
|
Definition
| form by condensation reactions between carboxyl of one amino acid and the amino group of another acid. |
|
|
Term
| Retro-inverso (RI) peptides |
|
Definition
| isomers of natural peptides in which the sequence in reversed the D-amino acids are employed. |
|
|
Term
| Physiological Roles of Proteins (7) |
|
Definition
1. engymes
2. storage and transport
3. physical cell support and shape
4. mechanical movement
5. decoding cell information
6. hormones and/or hormone receptors
7. other specialized functions |
|
|
Term
|
Definition
|
|
Term
|
Definition
| titin. 34,350 amino acids |
|
|
Term
| The number of amino acids in a protein can be approx by dividing the molecular weight of the protein by___` |
|
Definition
|
|
Term
|
Definition
defined as the tendency to maintain native conformation.
Weak interactions predominate as a stabilizing force in protein structure. The stability of a protein is not the sum of the energies of formation of many weak interactions but rather the difference in the free energies of the folded and unfolded states. |
|
|
Term
| Why is the native structure more stable? |
|
Definition
| because folded proteins occupy a low-energy state. Protein folding and unfolding is a cooperative process |
|
|
Term
|
Definition
| disruption of native conformation with loss of activity. energy require is small (equivalent to a few hydrogen bonds).a cooperative process. Some proteins can be renatured. |
|
|
Term
|
Definition
| linear sequence of amino acids. Presented from N terminus to C terminus. Repeating structural pattern of NCCNCC |
|
|
Term
|
Definition
| localized interactions within the polypeptide. Regularities in local conformation maintained by main chain hydrogen bonds between amide hydrogen and carbonyl oxygen groups. Characterized by a specific pattern of hydrogen bonding. Restricted by the limited flexibility of the peptide bond. a-helicies and b-sheets |
|
|
Term
|
Definition
final structure of a single poplypeptide.
Residues separated by great distance in primary structure may be in close proximity in tertiary structure. Relates to proteins function. very in their content of alpha helicies and beta sheets |
|
|
Term
|
Definition
folding pattern with multiple polypeptides.
composed of multiple subunits where each subunit is a separate polypeptide chain. Subunits are held together by non-covalent interactions. More complex biological function. |
|
|
Term
| 2 Rules that must be followed for formation of secondary structure. |
|
Definition
1. optimize the hydrogen bonding potential of the main-chain carbonly and amide groups.
2. represent a favored conformation of the polypeptide chain. |
|
|
Term
|
Definition
| spatial arrangement of atoms around double bonds or chiral centers, can only be changed by breaking bonds. |
|
|
Term
|
Definition
| spatial arrangement of groups that are free to assume different positions in space without breaking bonds. The possible conformations of a protein include any structural state that can be achieved without breaking covalent bonds. |
|
|
Term
|
Definition
| each protein folds into a single stable shape (physiological conditions). Biological function of a protein depends on its native conformation. |
|
|
Term
| Configuration of the Peptide Bond |
|
Definition
| rotation around C-N bond is restricted due to the partial double bond nature of the peptide bond (no freedom of rotation). The six atoms of the peptide group are planar, the oxygen of the carbonyl group and they hydrogen of the amide nitrogen are trans to each other. The side chain groups also tend to be in the trans configuration |
|
|
Term
| Conformation of the Polypeptide Chain |
|
Definition
| Each a-Carbon is held within the main-chain through single bonds, about which there is complete freedom of rotation. Phi and Psi bonds. They can range from -180 to +180 but steric interference prevents the formation of most conformations. |
|
|
Term
|
Definition
| illustrates all possible combinations of phi and psi and highlight combinations that are observed in actual proteins. The most favored conformations define the common secondary structures (lowest energy conformations) |
|
|
Term
| The Peptide Bond and hydrogen bonding |
|
Definition
| each peptide bond has both a hydrogen bond donor as well as a hydrogen bond acceptor. There are an equal number of hydrogen bond donors and acceptors within the polypeptide main-chain which is important from the perspective of optimizing hydrogen bonds. |
|
|
Term
|
Definition
| 3.6 residues/turn. Each C=O (residue n) forms a hydrogen bond with the amide hydrogen of reside n+4. All C=O groups point toward the C terminus. The entire helix is a dipole with (+) N, (-) C termini. The phi and psi angles of each residue are similar. |
|
|
Term
|
Definition
| 1948. Discovered Alpha-Helix. Recieved a nobel price in chemistry in 1954. |
|
|
Term
| Amino Acid Sequence Affects Helix Stability |
|
Definition
| Residues separated by 3-4 positions in the primary structure are close together in helical structure; positively and negatively charged residues found 3 or 4 positions away from each other. Aromatic Residues also often separated by 3 or 4 positions to enable hydrophobic interactions |
|
|
Term
|
Definition
| its rigidity its known as a helix breaker and is not usually found |
|
|
Term
|
Definition
| flexibility it imparts, usually not found |
|
|
Term
| Helix Stability: Stretches of similarly charged residues |
|
Definition
| no observed as they will destabilize the helix due to electrostatic repulsion |
|
|
Term
|
Definition
| Small electrical dipole exists in each peptide bond. This dipole is communicated through the helix by hydrogen bonding. As a result the helix has a net dipole whereby the N terminus of the helix has a partial +charge and the C terminus has a partial +charge. The sequence of the helix can help stabilize this dipole by the positioning of charged residues at the termini (- at N and +at C). Amino Terminus =+ and carboxyl terminus = - |
|
|
Term
|
Definition
| residues which are 4 residues away from each other in the primary sequence will be on the same side of an alpha-helix. Strategic positioning of hydrophobic and hydrophilic residues with the primary structure can generate an amphipathic helix with hydrophobic and hydrophilic faces. |
|
|
Term
| Constraints on the Alpha-helix Staility (5) |
|
Definition
1. Electrostatic repulsion (or attraction) between successive residues with charged R groups.
2. the bulkiness of adjascent R groups
3. The interactions between residues spaced by three or four residues
4. the occurrence of Proline and glycine
5. the interaction between amino acids at each end of the helix and helix dipole. |
|
|
Term
| What are B sheets made up of? |
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Definition
B strands
arranged side by side |
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Term
| Conformation of B strands |
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Definition
| polypeptide chains that are almost fully extended. B sheet side chains project alternately above and below the plane of the B strands. |
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Term
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Definition
| one surface of a B sheet consists of hydrophobic side chains |
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Term
| Hydrogen Bonding Pattern of B Strands |
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Definition
| stabilize by hydrogen bonds between C=O and -NH on adjacent strands. |
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Term
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Definition
| strands run in the same N to C direction |
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Term
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Definition
| strands run in opposite N to C direction. are more stable due to better geometry of hydrogen bonding. |
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Term
| Biological Advantages associated with formation of quaternary structure (4) |
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Definition
1. help stabilize subunits and prolong life of protein
2. unique active sites produced at interface between subunits
3. help facilitate unique and dynamic combinations of structure/function through physiological changes in tertiary and quaternary structure (hemoglobin)
4. Conservation of functional subunits more efficient than selection for new protein with ideal function |
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Term
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Definition
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Term
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Definition
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Term
| Keratin: Primary Structure |
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Definition
pseudo-seven repeat where positions a and d are hydrophobic
abcdefgabcdefgabcdefgabcdefg |
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Term
| Keratin: Secondary Structure |
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Definition
| Keratin forms right-handed amphipathic alpha helicies. Residues from positions a and d end up on the same face of the helix resulting in a hydrophobic strip along the length of the helix |
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Term
| Keratin: Tertiary Structure |
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Definition
| dominated by the polypeptide strand presenting an alpha-helical rod. the hydrophobic strip running the length of this rod is looking for a hydrophobic environment |
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Term
| Keratin: Quaternary Structure |
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Definition
| the pseudoseven repeat generates hydrophobic surfaces along the length of the helix. Through these hydrophobic surfaces interact to the formation of a coiled-coil.q |
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Term
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Definition
| involves two right-handed helicies wrapping around each other in a left-handed fashion. |
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Term
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Definition
| arise from the successive linking of individual units into higher-order structures. The individual units are linked together through disulfide bonds. the extend of disulfide bonding will determine the strength of the overall structure |
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Term
| Collagen: Primary Structure |
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Definition
| multiple repeats of Gly-X-Y where x is often proline and y is often hydroxyproline. |
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Term
| Collagen: Secondary Structure |
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Definition
| Formation of left-handed helicies of three residues per turn (as opposed to 3.6/turn on right handed alpha helixes) |
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Term
| Collagen: tertiary structure |
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Definition
| nearly the full length of the polypeptide is helical |
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Term
| Collagen: quaternary structure |
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Definition
| formation of coiled-coils. Three left-handed helicies wrappign around each other in a right handed fashion. |
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Term
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Definition
| arise from the successive linking of individual units into higher order structures. occur from amino acid residues that undergo post-translational modification (hydroxyproline, hydroxylysine). More of these cross link occur with age accounting for the increasingly brittle character of aging connective tissue and tougher meat |
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Term
| Post-Translational modifications of collagen |
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Definition
| The enzyme that performs these require Vitamin C for its activity. Without these modified residues, as would occur in the absence of vitamin C, collagen cannot form the stabilizing crosslinks. The weakened structure of collagen manifests as scurvy. Leading to defective triple helix |
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Term
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Definition
| bruises, tooth loss, poor wound healing, bone pain, eventual heart failure, bleeding gums, fragile blood vessels. Milder cases cause fatigue, irritability and susceptibility to respiratory infections. 10% of university students have a vitamin C deficiency. |
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Term
| Osterogenesis imperfecta, Marfan's syndrome, Stickler syndrome and Ehlers-Danlos syndrome |
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Definition
| genetic diseases involving collagen. Associated with brittle and abnormal bone structure, weakened cardiovascular capabilities, abnormal facial features, loose skin and joints and hyperflexibility. |
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Term
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Definition
| born oct 27, 1782. greatest violin virtuosi. capable of playing three octaves across 4 strings in a hand span, nearly impossible feat. believed to have had marfan's syndrome that resulted in hyperextendible joints allowing him to play music beyond the range of normal individuals. |
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Term
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Definition
6 reside repeat that is rich in small amino acids
GSGAGA GSGAGA GSGAGA |
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Term
| Silk: Secondary Structure |
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Definition
| silk is composed primary from beta sheets the fully extended polypeptides of the beta strands offer considerable strength. very high strength and is highly flexiable |
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Term
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Definition
| orb-weaver spider that produces one of the largest known orb webs with anchor lines spanning up to 25 meters. Its silk is the toughest biological material ever studied, over ten times tougher than kelvar |
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Term
| 3 Dimensions of Silks Structure Considered: |
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Definition
1. fully extended polypeptide chains (strength)
2. association of strands by hydrogen bonding (flexible)
3. Association of sheets by van der Waals and hydrophobic interactions (flexible) |
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Term
| Genetically Engineered Silk |
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Definition
| Spiders dragline silk gene into goats such that the goats would make the protein in their milk |
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Term
| Prion Disease: Transmissible spongiform Encephalopathies |
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Definition
| misfolding of a self-protein into a pathological, infectious conformation. Includes mad cow disease, chronic wasting disease of elk and deer, and a number of human diseases. Are progressive and neurogenerative diseases. |
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Term
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Definition
| molecule reversibly bound by protein. called the substrate |
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Term
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Definition
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Term
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Definition
| site on the protein where the ligand binds. Complementary to the ligand |
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Term
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Definition
| binding of a ligand causing a conformational change in the protein that alters the function of the protein |
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Term
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Definition
| monomeric protein that facilitates oxygen storage in peripheral tissue |
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Term
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Definition
| tetrameric protein found in erythrocytes that transports oxygen from lungs to the periphery |
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Term
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Definition
| consists of a protoporphyrin ring system bound to a single (Fe2+) iron atom; Fe2+ bind oxygen reversibly, Fe3+ does not bind oxygen. The ring system provides four coordinating interactions with the iron atom. The electron donating characteristic of nitrogen prevent conversion to Fe3+. The heme group is bonded within a specific pocket. |
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Term
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Definition
| seeks 6 coordinating interactions. 4 come from interactions with heme, a fifth comes with a histidine imidazole group and the sixth is for oxygen binding. |
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Term
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Definition
| provides a stabilizing interaction for bound oxygen. |
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Term
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Definition
| small globular protein which consists of a single polypeptide of 153 residues arranged in 8 alpha helicies. Contains a heme group |
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Term
| Oxygen Saturation curve of myoglobin |
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Definition
| hyperboloic, indicating a single oxygen bindinging constant. |
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Term
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Definition
| the amount of oxygen required to half saturate the protein. pO2 in the lungs is 13.5 kPa (where o M is the highest) and 4.0 kPa in the periphery (where o M is are the lowest) |
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Term
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Definition
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Term
| Saturation of Mb with O2 in peripheral tissues 0=4.0/4.0+0.26= |
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Definition
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Term
| In the lungs the partial pressure of O2 is 0=13.5/13.5+0.26= saturation of Mb |
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Definition
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Term
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Definition
| derived from two greek words: allos= other and stereos= site. other site |
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Term
| Allosteric Effectors (modulators) |
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Definition
| bind to allosteric proteins at sites separate from the functional binding site. Can be either activators or inhibitors. |
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Term
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Definition
| when a normal ligand and modulator are the same. oxygen is a homotrophic allosteric activator of hemoglobin |
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Term
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Definition
| when the modulator is different from the normal ligand |
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Term
| Active state on an allosteric protein |
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Definition
| R state. stabilize the r state |
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Term
| inactive state on an allosteric protein |
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Definition
| T state. stabilize the t state |
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Term
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Definition
| binding of the first O2 by hemoglobin causes a conformational change making it easier to bind subsequent oxygens |
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Term
| O2 binding promotes and stabilizes the __ state which has a higher oxygen affinity than the ___state |
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Definition
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Term
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Definition
| iron atom is just outside the plane of the heme ring |
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Term
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Definition
| oxygen bound, the iron moves into plane of the ring. This minor movement within the tertiary structure of one subunit causes structural changes that are translated to cause major changes in the quarternary structure of the protein. |
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Term
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Definition
| partial pressure of oxygen found in the lungs, hemoglobin will completely saturate with oxygen. |
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Term
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Definition
| partial pressures of oxygen typically found in the extremes of the body Hb will release approx half of its oxygen load. |
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Term
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Definition
| closely matches the partial pressures of oxygen found in periphery |
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Term
| Hemoglobin has the greatest sensitivity for oxygen release |
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Definition
| at the peripheral partial pressures of oxygen. allowing hemoglobin to rapidly sense and respond to changes in oxygen levels in regions at greatest risk for oxygen deprivation. |
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Term
| A heterotropic allosteric inhibitor of hemoglobin |
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Definition
| 2,3 Bisphospho-D-glycerate |
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Term
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Definition
| decreases hemoblobins affinity for oxygen. Carries 5 units of negative charge and binds to the positively charged pockets that if formed at the interface between the subunits of deoxyhemoglobin |
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Term
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Definition
| has a lower 2,3 BPG affinity than Adult Hb. A fetus breathes inside the womb by stripping oxygen away from the maternal blood. High oxygen affinity than adult Hb. Adult Hb has six residues at the 2,3 BPG binding site, fetal Hb has five. Decreased affinity for 2,3BPG translates into higher oxygen affinty for fetal Hb. Lower affinity for the allosteric inhibitor bestows higher affinity for oxygen. |
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Term
| 2,3 BPG and High Altitude Adaptation |
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Definition
| At high altitudes the partial pressure of oxygen in the air, hence lungs, decreases. Adaptation to high altitude can rapidly occur through increased production of 2,3 BPG from 5mM to 8mM. This decreases the oxygen affinity of hemoglobin to ensure maintained oxygen delivery to the periphery. |
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Term
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Definition
| describes the pH dependence of hemoglobin's affinity for oxygen. |
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Term
| Hemoglobin has a lower affinity for oxygen at a ph of |
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Definition
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Term
| The physiological significance of the Bohr effect is that active tissues have lower pH than resting tissues through 2 primary mechanisms |
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Definition
1. during moderate exercise increased muscle activity increases the rate of the carbon dioxide production.
2. in extreme exercise muscle may produce lactic acid to further drop pH |
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Term
| 2 Primary challanges to cellular respiration and metabolism: |
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Definition
1. providing sufficient oxygen to the tissues
2. removing carbon dioxide, the "exhaust" of metabolism, from the periphery |
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Term
| Coordination of oxygen delivery and carbon dioxide removal: mechanism #1 |
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Definition
| Carbon dioxide is taken up into red blood cells and converted to bicarbonate and a proton by the enzyme carbonic anhydrase |
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Term
Carbon dioxide + water = H+ + HCO-3
Through this reaction (2) |
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Definition
1. carbon dioxide is converted into a soluble form for transport to the lungs.
2. the decreased pH in the red blood cells decreases Hb's Oxygen affinity through the Bohr Effect to promote oxygen release to active tissues. The more active the tissues the greater the production of carbon dioxide, the greater the production of carbon dioxide the greater the release of oxygen |
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Term
| Coordination of oxygen delivery and carbon dioxide removal: Mechanism 2 |
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Definition
| Carbon dioxide is produced in the tissues can form a covalent carbamate linkage to the N terminus of each chain of hemoglobin chain to form carbaminohemoglobin. |
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Term
| Coordination of oxygen delivery and carbon dioxide removal: 3 important outcomes of mechanism 2 |
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Definition
1. it converts carbon dioxide into a more soluble form to assist in its transport to the lungs
2. carbamino hemoglobin has a lower oxygen affinity than hemoglobin to promote oxygen release
3. the proton released by the reaction will contribute to oxygen release through the Bohr Effect |
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Term
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Definition
| results from a single amino acid change(Glu6Val). Formation of fibers only occurs at low partial pressures of oxygen involving deoxy forms of HbS. Fibers tend to form in the capillaries (where oxygen concentration is the lowest) blocks blood flow to the extremities of the body |
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Term
| Mutation that causes sickle cell anemia |
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Definition
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