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878 Cards in this Set
- Front
- Back
what cell has membrane bound nucleus and organelles?
|
eukaryotic cell
|
|
what are the four levels of cell to molecules?
|
-the cell and its organelles (cell)
-Supramolecular complexes (organelles) -macromolecules -monomeric units (monomers) |
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out of 92 chemical elements, how many are found to be organic matter?
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25 out of 92
|
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what percent does carbon, oxygen, nitrogen and hydrogen make up the elements of life?
|
96%
|
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what percent does phosphorus, sulphur, calcium and potassium make up the essential elements of life?
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4%
|
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what two trace elements are required in the essential elements of life?
|
Iron (Fe) and Iodine (I)
|
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what three bonds are involved in life?
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-Ionic bonds
-Covalent bonds -Hydrogen bonds |
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what is the electrical attractions between ions of opposite charge in a crystal. they are oppositely attracted and are said to be what kind of bond?
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Ionic bond
|
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what kind of bond is formed when there is a sharing of electrons between atoms?
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covalent bond
|
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what is the attraction between a hydrogen atom bonded to an electronegative O, N or F atom and another nearby electronegative O, N or F atom?
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Hydrogen bond
|
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when a H atom is bonded to an electronegative atom it produces a
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delta plus (d+) charge
|
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what is the delta plus (d+) of a H atom attracted to?
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the delta negative (d-) of an electronegative atom
|
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what is a weak intermolecular force produced between neutral atoms by transient electrostatic interactions. the force is strongest when atoms are separated by the sum of their radii, and the force is the strongest when bonds are closer together
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Van der Waals force
|
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what interactions occurs when there is an attraction between non polar molecules and only occur when molecules are very close together?
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Van der Waals interactions
|
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what is the other name for london forces?
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Van der Waals forces
|
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what is responsible for allowing geckos to walk up walls?
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Van der Waals forces
|
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which of the following is not among the four most abundant elements in living organisms?
A) Carbon B) Hydrogen C) Nitrogen D) Oxygen E) Phosphorus |
Phosphorus
|
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what bond does a carbon skeleton form?
|
Covalent bonds
|
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what is the difference between an aldehyde and a ketone?
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an aldehyde is a carbon that has a double bond to an oxygen and the carbon has a bond to a carbon and a hydrogen.
CH3 -- C -- H This is an aldehyde (with an O double bonded to the center C). The CH3 group can be any alkyl chain, but the other group is always a hydrogen. a ketone is a carbon that has a double bond to an oxygen and the carbon also has bonds to two other carbons CH3 -- C -- CH3 This is a ketone (with an O double bonded to the center C). the CH3 groups can be any alkyl chain |
|
describe a ketone
|
a ketone is a carbon that has a double bond to an oxygen and the carbon also has bonds to two other carbons
CH3 -- C -- CH3 This is a ketone (with an O double bonded to the center C). the CH3 groups can be any alkyl chain |
|
describe an aldehyde
|
an aldehyde is a carbon that has a double bond to an oxygen and the carbon has a bond to a carbon and a hydrogen.
CH3 -- C -- H This is an aldehyde (with an O double bonded to the center C). The CH3 group can be any alkyl chain, but the other group is always a hydrogen. |
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what bond is commonly found in proteins?
|
disulfide bonds
|
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what functional group is important in energy transfer?
|
thioester
|
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what are molecules that have the same chemical formula but different chemical structures
|
isomers
|
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Two mirror images of a chiral molecule are called
|
enantiomers or optical isomers.
|
|
what is a chiral centre?
|
where a chiral molecule is rotated and yet cannot be superimposed on its mirror images
|
|
stereoisomers that are nonsuperimposable mirror images of each other are known as
|
enantiomers
|
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what is an anomer
|
Diastereoisomers of glycosides, hemiacetals or related cyclic forms of sugars, or related molecules differing in configuration only at C-1 of an aldose, C-2 of a 2-ketose, etc.
|
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what is a cis-trans isomer
|
In organic chemistry, cis/trans isomerism (also known as geometric isomerism) is a form of stereoisomerism describing the relative orientation of functional groups within a molecule.
such isomers contain double bonds, which cannot rotate, but they can also arise from ring structures, wherein the rotation of bonds is greatly restricted. Cis and trans isomers occur both in organic molecules and in inorganic coordination complexes |
|
what is diastereoisomers
|
Diastereomers are stereoisomers that are not mirror images of one another and are non-superimposable on one another. Stereoisomers with two or more stereocenters can be diastereomers. It is sometimes difficult to determine whether or not two molecules are diastereomers
|
|
what are geometric isomers?
|
each of two or more chemical compounds having the same molecular formula but a different geometric arrangement; an unsaturated compound or ring compound in which rotation around a carbon bond is restricted, as in cis- and trans- configurations.
|
|
what is the first law of thermodynamics (principle of conservation)?
|
energy can be transferred and transformed. it cannot be created of destroyed
e.g. plant (light --> chemical energy) e.g. cheetah animal ( chemical energy -->kinetic energy) |
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what is the second law of thermodynamics?
|
during energy transfer some of the energy becomes unavailable to do work (energy --> heat)
when energy is lost as heat, it makes the universe more disordered energy transfer or transformation increases the entropy of the universe |
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what is the measure of a systems disorder and allows understanding of why a process will occur spontaneously?
|
entropy
|
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if there is in increase in disorder, will the process be spontaneous or non spontaneous?
|
the process will be spontaneous if it involves in increase in disorder
|
|
if there is a decrease in disorder (increase in order) will the process be spontaneous or non spontaneous?
|
a process will not be spontaneous if there is a decrease in disorder, and so the process will only occur if energy is added to the system
|
|
what is a portion of a systems energy that can perform work when temperature and pressure are constant?
|
free energy
|
|
what is the formular for delta G or Gibbs free energy?
|
delta G = delta H -T delta S
|
|
in gibbs free energy formular what does delta H represent?
|
change in enthalpy (change in heat)
|
|
in gibbs free energy formlar what does T delta S represent?
|
change in entropy (order of the system)
|
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what are the symptoms of an increase in entropy? (delta G = < 0)
|
-increase in temperature
-increase in volume -increase number of independently moving particles |
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what is the outcome of spontaneity when delta G < 0
|
process is spontaneous
|
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what is the outcome of spontaneity when delta G = 0
|
process is at equilibrium
|
|
what is the outcome of spontaneity when delta G > 0
|
process is not spontaneous
|
|
when the reactants are greater than the products, what kind of reaction is it in regards to free energy change?
|
exergonic reaction (energy released)
|
|
when the reactants are less than the products, what kind of reaction is it in regards to free energy change?
|
endergonic reaction (energy absorbed and thus needed)
|
|
what is the formular for free energy change? and what does it calculate?
|
delta G = G final state - G initial state
it shows if the process is exergonic(-) or endergonic (+) |
|
describe spontaneity in endergonic reactions?
|
delta G is positive, reaction is not spontaneous
|
|
describe spontaneity in exergonic reactions?
|
delta G is negative, reaction is spontaneous
|
|
describe spontaneity in coupled reactions?
|
overall delta G is negative; together, reactions are spontaneous
|
|
in oxidation describe spontaneity?
|
OIL = delta G = < 0
therefore reaction is spontaneous in oxidation reactions where electrons are lost (increase in entropy or disorder) |
|
in reduction describe spontaneity?
|
RIG = delta G = > 0
therefore reaction is not spontaneous in reduction where electrons are gained (decrease in entropy or disorder) |
|
what oxidises another species and in itself is reduced?
|
oxidising agent
|
|
what reduces another species and in itself is oxidised?
|
reducing agent
|
|
Biochemistry is about
|
Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms
|
|
The principles of Biochemistry differ for bacteria, plants and humans!
True or False? |
false
|
|
Biomolecules
that contain the same chemical bonds but differ in their configuration are called |
geometric isomers
|
|
A
carbon with 4 different constituents is referred to as |
chiral
|
|
Stereoisomers
that are mirror images of each other are called |
Enantiomers
|
|
Stereoisomers
that are not mirror images of each other are called |
Diastereomers
|
|
describe biochemistry
|
biochemistry is the discipline that uses the principles and language of chemistry to explain biology
|
|
which six non metalic elements account for more than 97% of the weight of most organisms and can all form stable covalent bonds?
|
carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur (CHNOS)
|
|
which elements are very common in earths crust but are only present in trace amounts in cells?
|
silicon, aluminum and iron
|
|
there are 23 other elements found in living organisms which include which five ions that are essential in all species?
|
calcium, potassium, sodium, magnesium and chloride (CPSMC)
|
|
which way does molecular information flow
|
DNA <-> RNA -> protein
which is replication, transcription and translation |
|
what obey the standard laws of physics and chemistry.
|
Living things obey the standard laws of physics and chemistry. No vitalistic force is required to explain life at the molecular level
|
|
biochemical reactions involve specific chemical bonds or parts of molecules called
|
functional groups
|
|
what kind of linkages are common in fatty acids and lipids
|
ester and ether linkages
|
|
what kind of linkages are found in proteins?
|
amide
|
|
what kind of linkages occur in nucleotides?
|
phosphate ester and phosphoanhydride linkages
|
|
an important theme of biochemistry is that the chemical reactions occurring inside cells are the same kinds of reactions that take place in a chemistry lab. the most important difference is that almost all reactions in living cells are
|
catalyzed by enzymes and thus proceed at very high rates
|
|
biochemical reactions that occur in an organism is called
|
in vivo
|
|
biochemical reactions that occur under laboratory conditions is called
|
in vitro
|
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many important macromolecules are
|
polymers
|
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biological macromolecules are a form of polymer created by joining many smaller organic molecules, or monomers, via what reaction?
|
condensation reaction (removal of the elements of water)
|
|
the levels of organisation in increasing order are
|
atoms,
molecules, macromolecules organelles, cells tissues, organs and whole organs (ammoctow) |
|
amino acids contain
|
an amino group and a carboxylate group as well as a side chain (R group)
|
|
different amino acids contain different
|
side chains
|
|
how is a dipeptide produced
|
when the amino group of one amino acid reacts with the carboxylate group of another to form a peptide bond
|
|
biochemical molecules are what shape?
|
three dimensional objects
|
|
how many common amino acids are incorporated into proteins in all cells
|
twenty
|
|
the amino group of one amino acids and the carboxylate group of another are condensed during protein synthesis to form
|
an amide linkage
|
|
the bond between the carbon atoms of one amino acid residue and the nitrogen atom of the next residue is called
|
a peptide bond
|
|
can proteins function as enzymes?
|
yes
|
|
the function of a protein depends on
|
its three dimensional structure or conformation
|
|
cabohydrates or saccharides are composed mainly of
|
carbon, oxygen and hydrogen
|
|
all monosaccharides and all residues of polysaccharides contain
|
several hydroxyl groups and are therefore polyalcahols
|
|
the linear representation of a molecule is called a
|
Fischer projection (after Emil Fischer)
|
|
most biochemical molecules exist as a
|
collection structures with different conformations
|
|
a change from one conformation to antoher does not require the breaking of
|
covalent bonds
|
|
the two basic forms of carbohydrate structures, linear and ring forms, do require the breaking and forming of
|
covalent bonds
|
|
what is the most abundant biopolymer ono earth
|
cellulose, because it is a major component of flowering plant stems including tree trunks
|
|
what is the most abundant six carbon sugar
|
glucose
it is the monomeric units of cellulose a structural polysaccharide joined by covalent bonds |
|
what bond is formed when one glucose molecule is joined to a C-4 hydroxyl group
|
glycosidic bond
|
|
nucleic acids are large macromolecules composed of monomers called
|
nucleotides
|
|
most of the energy required for life is supplied by
|
light from the sun
|
|
the rate of a chemical reaction depends on the
|
concentration of the reactants
the higher the concentration the faster the reaction |
|
almost all biochemical reactions are reversible. when the forward and reverse reactions are equal, the reaction is t
|
equilibrium
|
|
the gibbs free energy change (delta G) is the
|
difference between the free energy of the products of a reaction and that of the reactants (substrates)
|
|
what is the formular for the gibs free energy change
|
delta G = delta H -T delta S
|
|
what is the formula for gibbs free energy change for a reaction (products and reactants)
|
Delta G (reaction) = Delta G (products) - Delta G (reactants)
|
|
the standard gibbs free energy change tells us the
|
-direction of a reaction when the concentrations of all products and reactants are at 1 M concentration
-the relative concentration of reactants and products when the reaction reaches equilibrium |
|
the rate of reaction is not determined by the
|
Gibbs free energy change
|
|
if in a reaction, the activation energies (barrier) is high, the reaction will proceed
|
very slowly
If activation energies are low however, reaction will proceed quickly |
|
what are the two main groups of prokaryotes
|
the Eubacteria and Archaea
|
|
what is the basic unit for life?
|
the cell
|
|
what are usually single celled organisms?
|
prokaryotes
|
|
what accounts for most of the biomass on earth?
|
prokaryotes
|
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what kind of cell is the following?
they lack a nucleus, their DNA is packed in a region of the cytoplasm called the nucleotide region, they are a bacteria and lack an internal organ compartment |
prokaryotes
|
|
what does eukaryotes include?
|
plants, animals, fungi and protist (which make the Eubacteria and archaea kingdoms)
|
|
what kind of cell is surrounded by a single plasma membrane unlike bacteria which have a double membrane?
|
Eukaryotic cells
|
|
the most obvious feature that distinguishes eukaryotes from prokaryotes is
|
the presence of a membrane bound nucleus in eukaryotes
|
|
what cell is larger, a euk or pro?
|
a eukaryotic cell is 1000 times larger than a prokaryotic cell
|
|
what is the difference between plant and animal cells?
|
plant cells contain cellulose and chloroplasts where they get their energy, rather than animal cells which get their energy from mitochondria, which is bacteria derived
|
|
what is the difference between eukaryotic DNA and protylitic DNA?
|
-most eukaryotic cells contain more DNA than prokaryotes do
-the genetic material of prokaryotes is singular and circular molecule of DNA -the eukaryotic DNA is organised (genome) is organized as multiple linear chromosomes |
|
can eukaryotes undergo mitosis and meiosis?
|
yes
|
|
eukaryotic cells have what kind of endoplasmic reticulum
|
rough ER and smooth ER
|
|
what kind of cells contain both mitochondria and chloroplasts?
|
photosynthetic plant cells
|
|
in chloroplasts the energy captured from light is used to
|
drive the formation of carbohydrates from carbon dioxide and water
|
|
where are mitochondria derived?
|
proteobacteria
|
|
where are chloroplasts descended from
|
cynobacteria
|
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what cells contain lysosomes?
|
eukaryotic cells
|
|
what is the defenition for, the loss of electrons from a substance through transfer to another substance (the oxidizing agent). It can take several forms, including the addition of oxygen to a compound, the removal of hydrogen from a compound to create a double bond, or an increase in the valence of a metal ion?
|
Oxidation
|
|
what is the definition for a substance that accepts electrons in an oxidation-reduction reaction and thereby becomes reduced?
|
oxidizing agent
|
|
what is the defenition for the gain of electrons by a substance through transfer from another substance (the reducing agent). they can take several forms, including the loss of oxygen from a compound, the addition of hydrogen to a double bond of a compound, or a decrease in the valence of a metal ion?
|
reduction
|
|
what is the definition of a substance that loses electrons in an oxidation-reduction reaction and thereby becomes oxidized
|
reducing agent
|
|
what is the definition of an optical (chiral) isomer?
|
A chiral molecule /ˈkaɪərəl/ is a type of molecule that has a non-superposable mirror image. The presence of an asymmetric carbon atom is often the feature that causes chirality in molecules
Human hands are perhaps the most universally recognized example of chirality: the left hand is a non-superposable mirror image of the right hand; no matter how the two hands are oriented, it is impossible for all the major features of both hands to coincide. This difference in symmetry becomes obvious if a left-handed glove is placed on a right hand. The term chirality is derived from the Greek word for hand, χειρ (kheir). It is a mathematical approach to the concept of "handedness". In chemistry, chirality usually refers to molecules. Two mirror images of a chiral molecule are called enantiomers or optical isomers. Pairs of enantiomers are often designated as "right-" and "left-handed". |
|
what is a chiral carbon?
|
A chiral carbon is one that has four different "groups" attached to it. The groups can be anything from a single H to functional groups to one or more other carbons
|
|
what type of chemical bond is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions
|
Ionic bond
|
|
what type of bond is a chemical bond that involves the sharing of electron pairs between atoms.
|
covalent bond
|
|
what kind of bond is the electromagnetic attractive interaction between polar molecules, in which hydrogen (H) is bound to a highly electronegative atom, such as nitrogen (N), oxygen (O) or fluorine (F)
|
hydrogen bond
|
|
what kind of bond is the sum of the attractive or repulsive forces between molecules (or between parts of the same molecule) other than those due to covalent bonds, the hydrogen bonds, or the electrostatic interaction of ions with one another or with neutral molecules or charged molecules.[1] The term includes:
force between two permanent dipoles (Keesom force) force between a permanent dipole and a corresponding induced dipole (Debye force) force between two instantaneously induced dipoles (London dispersion force). It is also sometimes used loosely as a synonym for the totality of intermolecular forces |
Van der Waal interactions
|
|
what has a high melting point, boiling point and heat of vaporisation?
|
water
|
|
water can form what bond?
|
Hydrogen (H) bond (90% electrostatic)
and covalent bond (10%) |
|
what bond forms the highest percentage in water? H bond or covalent bond?
|
H bond at 90%
|
|
when are H bonds weak, when are they strong?
|
H bonds on their own are weak, but in a group are strong
|
|
what allow water to be pulled up inner water pipes from roots to leaves?
|
H bonds
|
|
water surface tension is due to
|
H bonding
|
|
what are the phases of water?
|
there are three phases of water, Gas, liquid and solid
|
|
during what phase is water in when the following happens:
-Molecules possess a lot of kinetic energy -fast moving -occupy a given volume -too much kinetic energy to H bond |
Gas phase
|
|
when water is in liquid phase, what happens to H bonds?
|
H bonds broken and reformed in a continuous motion
|
|
water molecules can form up to how many bonds?
|
4
|
|
solid is less dense than
|
water
|
|
why does ice float on water?
|
because solid ice is less dense than water
|
|
when is waters density greatest?
|
4 degrees celsius
when molecules are lowest in kinetic energy, the H bonds keep molecules apart, hence why their is a lower density |
|
water can dissolve ionically bonded
|
salts (eg. NaCl)
|
|
what kind of biological molecules can be dissolved in water?
|
proteins with charges and polar groups
|
|
what compounds cannot be dissolved in water?
|
Hydrophilic, Hydrophobic and Amphipathic compounds
|
|
what compounds can easily dissolve in water?
|
Hydrophilic compounds
|
|
what compounds cannot be easily dissolved in water and dissolve in non polar solvents?
|
hydrophobic compounds
|
|
what kind of compounds has polar and non polar regions, with the polar regions associated with water and the non polar regions associated together?
|
Amphipathic compounds
|
|
does an ordered H2O molecules have an increase or decrease in entropy (delta S)
|
decrease in entropy
|
|
during dispersion of lipids in H2O, what happens and what effect does this have on entropy (Delta S)?
|
each lipid molecule forces the surrounding H2O molecules to become highly ordered, therefore this represents a great decrease in entropy
|
|
what happens in clusters of lipid molecules and what effect does this have on entropy?
|
only the lipid portions at the edge of the cluster force the ordering of water. fewer water molecules are ordered, and entropy increases
|
|
what are hydrophobic groups sequestered from water, with an ordered minimised shell of water molecules with an increased entropy?
|
micelles
|
|
what chemical and structural properties explain why water has a high melting and boiling point?
|
-lone pair electrons
-the bent shape of water causes it to be a highly electronegative molecule caused by its polarity -much more effort is required to break the bonds in the polar molecule |
|
what are proton donors?
|
acids
|
|
what are proton acceptors?
|
bases
|
|
what completely dissociate in solution?
|
strong acids and strong bases
|
|
what does not completley dissociate in solution?
|
weak acids, and weak bases
|
|
weak bases react with water to form
|
equilibrium
|
|
1 mol of HCl + 0.5 mol NaOH.
-write the chemical equation -how much HCl is left? -how much NaCl is produced? |
GCl + NaOH --> NaCl + H2O
-0.5 HCl left over - 0.5 mol NaCl produced |
|
1 mol of Acetic acid (CH3COOH) + 0.25 mol NaCl
-write the chemical equation -how much acetate (CH3COO-) and acetic acid is there after the reaction? |
CH3OOH + NaOH --> CH3COONa + H2O
-0.75 mol of CH3COOH left over -0.25 mol of CH3COONa left over |
|
what are buffers?
|
-compounds that keep the pH of a solution relatively constant
-weak acids/bases -in solution dissociate to form equilibrium |
|
how do buffer maintain pH?
|
-donating protons (H+) when [H+] drops
-absorbing protons when [H+] increases |
|
when do buffers work best?
|
-when [base] = [acid]
-when there is a high concentration of both species to absorb and donate protons (H+) -when pH = pKa +- 1 |
|
what is the buffering range of pKa - 6.86?
|
5.86-7.86
|
|
if the molar ratio acetate: acetic acid is 2:1 and the pKa = 4.76 then calculate the pH
|
pH = pKa + log ([B]/[A])
therefore: pH = 4.76 + log (2/1) = 5.06 |
|
buffer contains 0.010 mol of lactic acid (pKa =3.86) and 0.050 mol Na lactate
-calculate the pH of the buffer -calculate the pH when 5mL of 0.5 M HCL is added to 1L of this buffer |
pH =pKa + log ([lactate]/ [lactic acid])
pH =3.86 + log (0.05 mol/ 0.01 mol) pH = 3.86 + log 5 pH = 3.86 + 0.70 = 4.55 at start: mol of lactic acid = 0.01 mol mol of lactate = 0.05 mol mol of HCL added = 5mL (0.005L) which is 0.005 x 0.5M HCL = 0.0025 mol (using n=c x v) after addition of 0.0025 mol HCL: new lactate (Base) = 0.05 - 0.0025 mol =0.0475 mol new lactic acid (acid) = 0.01 + 0.0025 = 0.0125 mol pKa = 3.86 pH= 3.86 + log (0.0475/0.0125) pH = 3.86 + log 3.8 = 3.86 + 0.5798 =4.439 pH decreased by = 4.55 =4.439 = 0.111 |
|
what is the ion product of water?
|
H3O+ (also called H+)
|
|
what is the pKb a measure of?
|
the strength of a base and is defined by pKb = -logKb
|
|
buffers are compounds that keep the pH of a solution
|
relatively constant
|
|
buffers are composed of
|
weak acids or weak bases that dissociate in solution to form an equilibrium
|
|
buffers maintain pH by
|
-donating protons when [H+] decreases
-accepting protons when [H+] increases |
|
buffers work best when
|
base = acid
|
|
why do buffers work best when base =acid?
|
because of the high concentration of both species is able to absorb and donate [H+]. this is the case when pH =pKa
|
|
describe a water molecules
|
-it is V shapes
-polar -has a bond angle of 104.5 degrees |
|
what is more electronegative in water, oxygen or hydrogen?
|
oxygen, as they have more lone pair electrons that attract electrons
|
|
what kind of molecules are molecules with an unequal distribution of charge so that one end of the molecule is more negative and another end is more positive?
|
polar moelcules
|
|
when do hydrogen bonds form?
|
hydrogen bonds form when a hydrogen atom with a partially positive charge is shared between two electronegative atoms. hydrogen bonds are much weaker than covalent bonds
|
|
how many hydrogen bonds can water form?
|
four
|
|
why does ice float?
|
because it is less dense than water. however, it is only slightly less dense than water so most of the mass of floating ice lies underwater
|
|
what form of water (liquid, solid, or gas) does a water molecule form an open hexagonal lattice in which every water molecule is hydrogen bonded to gour others. which contributes to its strength
|
when water is in the form of ice
|
|
why does the density of most substances increase upon freezing
|
because molecular motion slows and tightly packs into crystal form
|
|
when does the desnity of water increase?
|
as it cools, until it reaches 4 degrees celcius
|
|
what two properties of water are related to its hydrogen bonding characteristics
|
-its specific heat
-its vaporation |
|
how is water an excellent solvent?
|
the physical properties of water combine to make it an excellent solvent.
-being polar molecule is an important property -water has a low intrinsic viscosity that does not greatly impede the movement of dissolved molecules -water molecules are small compared to other solvent such as ethanol and benzene -the small size of water molecules means that many of them can associate with solute particles to make them more soluble |
|
how do ionic and polar substances dissolve in water?
|
-water can interact with and dissolve other polar compounds and compounds that ionize
-ionization is associated with the gain or loss of an electron, or an H+ ion, giving rise to an atom or a molecule that carries a net charge -molecules that can dissociate to form ions are called electrolytes -substances that readily disslve in water are said to be hydrophilic |
|
why are electrolytes soluble in water?
|
water molecules are polar, this means they can align themselves around electrolytes so that the negative oxygen atoms of the water molecules are oriented toward the cations of the electrolytes and the positive hydrogen atoms are oriented toward the anions
|
|
what kind of substances are insoluble in water?
|
non polar substances
|
|
what kind of non polar substances are insoluble in water?
|
Hydrocarbons and other nonpolar substances have very low solubility in water
|
|
why do non polar substances not dissolve in water?
|
because water molecules tend to interact with other water molecules rather than with nonpolar molecules, as a result water molecules exclude non polar substances forcing hem to associate with each other
|
|
non polar substances are said to be
|
hydrophobic
|
|
detergents sometimes called surfactants, are molecules that are both hydrophilic and hydrophobic. they usually have a hydrophobic chain at least 12 carbon atoms long and an ionic or polar end, such molecules are said to be
|
amphipathic
|
|
detergents (amphipathic) molecules can form
|
-monolayers at the air-water interface. they can also form micelles, aggregates of detergent molecules in which the hydrocarbon tails associate in the water free interior and the polar head groups are hydrated
|
|
what are the four major noncovalent bonds or forces?
|
-hydrogen bonds
-hydrophobic interactions -charge-charge interactions -van der waals forces |
|
what kind of interaction plays an extremely important role in determining the structures and functions of macromolecules? these weak forces are also involved in the recognition of one of one macromolecule by another and in the binding of reactants to enzymes
|
hydrogen bonds and hydrophobic interactions
|
|
what kind of forces and interactions are variations of a more general type of forces called electrostatic interactions?
|
charge charge interactions, hydrogen bonds and van der waals forces
|
|
what kind of interactions are electrostatic interactions between two charged particles? these interactions are potentially the strongest noncovalent forces and can extend over greater distances than other noncovalent interactions
|
charge-charge interactions
|
|
what is an example of charge charge interactions in proteins
|
when oppositely charged functional groups attract one another. the interaction is sometimes called a salt bridge and its usually buried deep within the hydrophobic interior of a protein where it cant be disrupted by water molecules. the most accurate term for such interactions is ion pairing
|
|
what kind of bond are a type of electrostatic interaction, and occur in many macromolecules and are among the strongest noncovalent forces in biological systems?
|
hydrogen bonds
|
|
a hydrogen bond has many of the characteristics of a covalent bond but
|
it is much weaker
|
|
what kind of bonding between base pairs in double stranded DNA makes only a small contribution to the stability of DNA?
|
Hydrogen bonding
|
|
hydrogen bonds between and within biological molecules are easily disrupted by
|
competition with water molecules
|
|
what kind of weak force involves the interactions between permanent or transient dipoles of two molecules?
|
Van der Waals forces
|
|
when do van der waals forces occur?
|
they only occur when atoms are very close together, the forces involve both attraction and repulsion. the attractive forces are known as london dispersion forces, originated from the infinitesimal dipole generated in atoms b the random movement of the negatively charged electrons around the positively charged nucleus
|
|
what forces are dipolar or electrostatic
|
van der waals forces
|
|
the association of a relatively nonpolar molecule or group with other nonpolar molecules is termed a
|
hydrophobic interaction
|
|
water is
|
nucleophilic
|
|
the chemical properties of water are also important in biochemistry because water molecules can react with biological molecules. the electron rich oxygen atom determines much of water reactivity in chemical reactions. Electron rich chemical are called
|
nucleophiles (nucleus lovers) because they seek positively charged species called electrophiles
|
|
weak interactions are individually weka but the combined effect of a large number of weak interactions is a
|
significant organizing force
|
|
charge-charge interactions, hydrogen bonds and van der waals interaction are
|
electrostatic interactions
|
|
hydrophobic interactions depend on
|
the increased entropy of the surrounding water molecules rather than on direct attraction between nonpolar groups
|
|
the density of water varies with
|
temperature
|
|
one of the important propertoes opf water is its slight tendency to
|
ionize
pure water contains a low concentration of hydronium ions and an equal concentration of hydroxide ions. the hydronium ion and hydroxide ion are formed by a nucleophilic attack of oxygen on one of the protons in an adjacent water molecule |
|
hydronium (H30+) ions are capable of donating a proton to another ion. such proton donors are referred to as
|
acids
|
|
hydroxide (OH-) ions can accept a proton and be converted back into water molecules. Proton acceptors are called
|
bases
|
|
the product obtained by multiplying the proton and hydroxide ion concentration ([H+][OH-]) is called the
|
ion product for water. this is a constant designated Kw where
Kw = [H+][OH-] + 1.0 x 10-^14 M^2 |
|
what compounds only partially dissociate in water?
|
weak acids and weak bases
|
|
the chloride ion is the base that corresponds to HCl after it has given up[ its proton, Cl- is called the
|
conjugate base of HCl
|
|
H3O+ is the what of water?
|
conjugate acid of H2O
|
|
the contribution of water is implied in
|
most acid/base dissociation reactions
|
|
the pKa values are determined by
|
titration
|
|
if the pH of a solution remains nearly constant when small amounts of strong acid or strong base are added the solution is said to be
|
buffered
|
|
the ability of a solution to resist changes in pH is known as its
|
buffer capacity
|
|
the water molecule has a permanent dipole because of
|
the uneven distribution of charge in O-H bonds and their angled arrangement
|
|
water molecules can form hydrogen bonds with each other. hydrogen bonding contributes to the
|
high specific heat and heat of vapourization of water
|
|
because it is polar, water can dissolve ions. water molecules form a solvation sphere around each dissolved ion. organic molecules may be soluble in water if they contain ionic or polar functional groups that can form
|
hydrogen bonds with water molecules
|
|
the major noncovalent interactions that determine the structure and function of biomolecules are
|
electrostatic and hydrophobic interactions.
Electrostatic interactions include charge-charge interactions, hydrogen bonds and can der Waal forces |
|
under cellular conditions, macromolecules do not spontaneously
|
hydrolyze. despite presence of high concentrations of water, specific enzymes catalyze their hydrolysis, and other enzymes catalyze their energy requiring biosynthesis
|
|
the acidity or basicity of an aqueous solution depends on the
|
concentration of H+
|
|
buffered solutions resist changes in
|
pH
in human blood, a constant pH of 7.4 is maintained by the carbon dioxide-carbonic acid-bicarbonate buffer system |
|
amino acids are
|
chiral
|
|
what kind of molecule are mirror images-enantiomers and cannot be superimposed on each other?
|
chiral molecules
|
|
only what kind of amino acids exist in nature?
|
only L-amino acids
|
|
what is the pKa of carboxyl group?
|
2.3
|
|
what is the pKA of amino group?
|
9.6
|
|
what is a zwitterion?
|
a dipolar ion with both positive and negative charges
|
|
what are two "small" non polar (hydrophobic) amino acids?
|
Glycine and Alanine
|
|
is Glycine Achiral or chiral?
|
Achiral
|
|
is Alanine chiral or achiral?
|
chiral
|
|
Leucine, Isoleucine and Valine are what sort of amino acids?
|
nonpolar (hydrophiobic) amino acids
|
|
which amino acids have a larger aliphatic side chain in their R group?
|
Leucine, Isoleucine and Valine
|
|
what does aliphatic relate to?
|
relating to or donating organic compounds in which carbons atoms form open chains(as an alkanes, not aromatic rings)
|
|
which amino acids are aliphatic?
|
Glycine
there are 6 Alanine Valine Leucine Isoleucine |
|
which amino acids are aromatic?
|
there are 3
Phenylalanine Tryosine Tryptophan |
|
which amino acids have a sulphur containing group?
|
Methionine and Cysteine
|
|
which amino acids have an alcahole group?
|
Serine and Threonine
|
|
which amino acids are basic?
|
Lysine and Arganine
|
|
which amino acids are neutral?
|
Histidine
|
|
which amino acids are acidic?
|
there are 4
Aspartate, Glutamate Aspargine Glutamine |
|
which amino acids have a highly hydrophobic (polar) group?
|
there are 4
Valine Leucine Isoleucine Phenylalanine Methionine |
|
which amino acids have a highly acidic group?
|
there are seven:
Lysine, Arginine Histidine Aspartate Glutamate Aspargine Glutamine |
|
what is the defenition of relative hydrophobicity or hydrophilicity or amino acids, and is important for determining protein folding with the hydrophobic amino acids usually inside and the hydrophilic amino acids outside?
|
hydropathy
|
|
which groups in amino acids are ionisable?
|
Carboxyl and amino groups
|
|
when pH < pKa
|
groups are protonated
-e.g. NH4+ -acid |
|
when pH > pKa
|
-groups are deprotonated
-e.g. COO- -conjugate base |
|
when is a group proteated?
|
when pH < pKa
|
|
when is a group deprotonated?
|
when pH > pKa
|
|
what is an isoelectric point?
|
The isoelectric point, sometimes abbreviated to IEP, is the pH at which a particular molecule or surface carries no net electrical charge. The net charge on the molecule is affected by pH of its surrounding environment and can become more positively or negatively charged due to the gain or loss, respectively, of protons (H+). The pI is the pH value at which the molecule carries no electrical charge or the negative and positive charges are equal.
|
|
what is the formula for calculating pI (Isoelectric point)?
|
pI = 1/2 (pK1 + pK2)
|
|
when you have an unknown amino acids how do you figure out the pKa to find the amino acid?
|
-use a titration curve to figure out pKa and from the pKa you can identify the amino acid
|
|
what joins amino acids together?
|
a peptide bond
|
|
how does a peptide bond join amino acids together?
|
via a dehydration or condensation reaction, where the H2O is removed from the alpha carboxyl and alpha amino group
|
|
what are peptides?
|
amino acids joined together
|
|
what are oligopeptides?
|
a few amino acids jopined together
|
|
what are polypeptides?
|
lots of amino acids joined together
the word polypeptide is used interchangeably with protein |
|
what is residue?
|
an amino acid in a peptide
|
|
in the peptide order, the amino terminal or N terminal ends with
|
free alpha-amino group
|
|
in then peptide order the carboxyl terminal or C terminal end with
|
free alpha-carboxyl group
|
|
in what direction do amino acids flow in regards to amino terminal and carboxyl terminal?
|
from the amino terminal to the carboxyl terminal
|
|
where is the unuasual amino acid 4-hydroxyproline found?
|
in collagen
|
|
where is the unusual amino acid 5-hydroxylysine found?
|
in plant cell walls
|
|
what is the unusual amino acid found in myosin contractile protein?
|
6-N-methyllysine
|
|
on a molar basis, tryptophan absorbs more UV light than
|
tyrosine
|
|
what is the difference between phenylalanine and tyrosine structure
|
the tyrosine has a OH group attached to its aromatic ring strucutre
|
|
what is the dominant form of glycine?
|
NH3+--CH2--COO-
|
|
the formation of a peptide bond between two amino acdisd is an example of a
|
condensation reaction
|
|
Enzymes catalyze nearly all reactions that occur in
|
living organisms
|
|
many proteins function as enzymes, the biochemical
|
catalysts
|
|
the protein hemoglobin binds and transports
|
oxygen and carbon dioxide in red blood cells
|
|
several types of proteins such as tubulin, actin and collagen, provide
|
support and shape to cells and hence to tissues and organisms
|
|
assemblies of proteins can do mechanical work such as
|
the movement of flagella,
the separation of chromosomes at mitosis, and the contraction of muscles |
|
many proteins play a role in information flow in the cells, some are involved in translation whereas others pla a role in regulating gene expression by
|
binding to nucleic acids
|
|
the functions of biochemical molecules can only be understood by
|
knowing their structures
|
|
there are many different kinds of proteins with many ifferent roles in
|
metabolism and cell structure
|
|
proteins on the cell surface can act as receptors for various
|
ligands and as modifiers of cell-cell interaction
|
|
some proteins have highly
|
specialised functions
|
|
all organisms use the same 20 amino acids as
|
building blocks for the assembly of protein molecules
|
|
the 20 amino acdids are called the
|
common or standard amino acids
|
|
a variety of different polypeptides can be produced by connecting the
|
20 common amino acids in various combinations
|
|
amino acids are called amino acids because
|
they are amino derivatives of carboxylic acids
|
|
in the 20 common amino acids the amino groups and carboxyl group are bonded to the same
|
carbon atom alpha(a) carbon atom
|
|
all of the standard amino acids found in proteins are
|
alpha-amino acids
|
|
two other substituents are bound to the alpha carbon,
|
a hydrogen atoms and a side chain (R) that is distinctive for each amino acids
|
|
inside a cell, under normal physiological conditions, the amino group is
|
(NH3+) protonated because the pKa of this grouo is close to 9
|
|
inside a cell under normal physiological conditions, the carboxyl group is
|
(COO-) ionized, because the pKa of that group is below 3
|
|
in the physiological pH range of 6.8 to 7.4 amino acids are
|
zwitterions, or dipolar ions, even thought their net charge may be zero
|
|
in 19 of the 20 amino acids the alpha-carbon is
|
chiral, or asymmetric, since it has gour different groups bonded to it
|
|
the exception of the 19 chiral amino acids is
|
glycine, whose R group is simple a hydrogen atom
|
|
why isn't glycine chiral?
|
because the alpha-carbon atoms is bonded to two identical hydrogen atoms
|
|
the 19 chiral isomers can exsit as
|
stereoisomers
|
|
stereoisomers are compounds that have
|
the same molecular formula but differ in the arrangement or configuration of their atoms in space
|
|
the two stereoisomers are distinct molecules that cant be easily converted from one form to the other since
|
a change in configuration requires the brekaing of one or more bonds
|
|
amino acid stereoisomers are nonsuperimposable mirror images called
|
enantiomers
|
|
which two of the 19 chiral amino acids, have two chiral carbon atoms each
|
Isoleucine and
Threonine (IT) |
|
which two amino acids can each form four different stereoisomers?
|
Isoleucine and Threonine (IT)
|
|
describe the location of the alpha-amino groups location on a L and D isomer
|
the alpha-amino group of the L isomer is on the Left of the alpha carbon
and that of the D isomer is on the right |
|
the 19 chiral amino acids used in the assembly of proteins are all of the
|
L isomer configuration
although a few D amino acids occur in anture |
|
amino acids are assumed to be
|
L-isomer configurations unless specifically designated D
|
|
the fact that all living organisms use the same standard amino acids in protein synthesis is evidence that
|
all species on earth are descende from a comon ancestor
|
|
what is the one letter representation for the amino acids theonine?
|
T
|
|
what is the one letter representation for the amino acids tyrosine?
|
Y
|
|
what is the one letter representation for the amino acids tryptophan?
|
W
|
|
the side chains of amino acids fall into what 7 classes?
|
-aliphatic
-aromatic Sulfur containing -alcohols -positively charged -negatively charged -amides (AAAPNA) |
|
of the 20 amino acids 5 are further classified as
|
highly hydrophobic
(keyword: hive) |
|
of the 20 amino acids 7 are classified as
|
highly hydrophilic
(keyword: heaven) |
|
what is the 3 letter and 1 letter code for Glycine?
|
(Gly, G)
|
|
which is the smallest amino acid?
|
Glycine
because its R group is simply a H atom the aplha carbon of glycine is not chiral |
|
how does glycine play a unique role in the structure of many proteins?
|
because its side chain is small enough to fit into niches that canot accommodate ant other amino acid
|
|
what is the 3 letter and 1 letter code for alanine?
|
(Ala, A)
|
|
what is the 3 letter and 1 letter code for Valine?
|
(Val, V)
|
|
what is the 3 letter and 1 letter code for Leucine?
|
(Leu, L)
|
|
what is the 3 letter and 1 letter code for the structural isomer of leucine, being Isoleucine?
|
(Ile, I)
|
|
which four amino acids and a structural isomer of leucine have saturated aliphatic side chains?
|
Ala, A
Val, V Leu, L ILe, I |
|
both the alpha and beta carbon atoms of isoleucine are
|
asymmetric
|
|
Isoleucine has how many chiral centres and possible stereoisomers?
|
it has two chiral centers, and has four possible stereoisomers
|
|
Alanine, valine, leucine and isoleucine play an important role in
(AVLI) |
establishing and maintaining the three dimensional structures of proteins because of their tendency to cluster away from water
|
|
which amino acids are known as the branched amino acids
|
Valine, Leucine, and Isoleucine are known as the branched chain amino aids because their side chains of carbon atoms contain branches
(VLI) |
|
valine, luecine and isoleucine are highly
|
hydrophobic
|
|
What is the three letter and one letter code for Proline?
|
Pro, P
|
|
How does Proline differ from the other 19 amino acids?
|
its three-carbon side chain is bonded to the nitrogen of its alpha amino group as well as to the alpha carbon creating a cyclic molecule
|
|
the cyclic structure of proline makes it much less
|
much less hydrophobic than valine, leucine and isoluecine?
|
|
which three amino acids have side groups with aromatic groups?
|
Phenylalanine (Phe, F)
Tyrosine (tyr, Y) Tryptophan (Trp, W) have side chains with aromatic groups |
|
Why are Tyrosine and tryptophan not as hydrophobic as phenylalanine?
|
because their side chains include polar groups
|
|
which three amino acids absorb UV light?
|
all three aromatic amino acids Tyrosine, Tryptophan and Phenylalanine
|
|
why do the three aromatic amino acids absorb Uv light?
|
because unlike the saturated aliphatic amino acids, the aromatic amino acids contain delocalized pie-electrons
|
|
at neutral pH both tryptophan and tyrosine absorb light at a wavelength of
|
280 nm
|
|
Phenylalanine is almost transparant at 280nm and absorbs light weakly at
|
260nm
|
|
which amino acids have sulfur containing R groups?
|
Methionine (Met, M) and
Cysteine (Cys, C) (MC) |
|
methionine contains a nonpolar methyl thioether group in its side chain and this makes it one of the more
|
hydrophobic amino acids
|
|
cystine is formed from two oxidized cysteine molecules linked by a
|
disulfide bond
|
|
which amino acids have side chains with alcohol groups?
|
Serine (Ser, S) and Threonine (Thr, T)
|
|
when oxidation links the sulfhydryl groups of two cysteine molecules, the resulting compound is a disulfide called
|
cystine
|
|
which amino acids have positively charged R groups?
|
-Histidine (His, H)
Lysine (Lys, K) and Arginine (Arg, R) they have hydrophilic side chains that are nitrogenous bases. the side chains can be positively charged at physiological pH |
|
why is arginine the most basic of the 20 amino acids?
|
because its side chain guanidinium ion is protonated under all conditions normally found within a cell.
|
|
which amino acids have negatively charged R groups?
|
-Aspartate (Asp, D) and Glutamate (Glu, E) are dicarboxylic amino acids have negatively charged hydrophilic side chains at pH7
|
|
the relative hydrophobicity or hydrophlicity of each amino acid is called its
|
hydropathy
|
|
which compounds are derived from common amino acids?
|
-Y-Aminobutyrate (GABA)
-Histamine -Epinephrine (Adreneline) -Thyroxine/Triiodothyronine |
|
the physical propertes of amino acids are influenced by the ionic states of the
|
alpha-carboxyl and
alpha-amino groups and of any ionizable groups in the side chains |
|
for every acid-base pair the pKa is the pH at which the concentrations of the two forms are
|
equal
|
|
when the pH of the solution is below the pKa the protonated form predominates and the amino acids is then a true acid that is capable of
|
donating a proton
|
|
when the pH of the solution is above the pKa of the ionizable group the unprotonated form of that group predominates the amino acid exist as the conjugate base which is a
|
proton acceptor
|
|
the pKa of an ionizable group corresponds to a midpoint of its
|
titration curve, it is the pH at which the concentration of the acid form (proton donor) exactly equals the concentration of its conjugate base (proton acceptor)
|
|
what bonds link amino acids in proteins?
|
peptide bonds
|
|
the linear sequence of amino acids in a polypeptide chain is called the
|
primary structure of a protein
|
|
the linkage formed between amino acids is an amide bond called a
|
peptide bond
this linkage can be thought of as the product of a condensation reaction between the apha-carboxyl group of one amino acid and the alpha amino group of another |
|
linked amino acids in a polypeptide chain are called amino acid
|
residues
|
|
The oxygen atom of water is nucleophilic because
|
it has two unshared pair of electrons.
|
|
What is the maximum number of hydrogen bonds that one water molecule can have with neighboring water molecules?
|
4
|
|
Electrolytes dissolve readily in water because
|
water molecules can cluster about cations and anions.
|
|
A molecule or ion is said to be hydrated when it ________.
|
is surrounded by water molecules
|
|
Hydrogen bonds can occur when hydrogen is covalently bonded to atoms like nitrogen and oxygen. What property of nitrogen and oxygen is important for this?
|
electronegativity
|
|
Attractions of oppositely charged functional groups of proteins are sometimes called ________.
|
salt bridges or ion pairing
|
|
Molecules that are both hydrophobic and hydrophilic are ________.
|
amphipathic
|
|
Which molecule or ion below is amphipathic?
|
CH3(CH2)14COO-
|
|
Which statement explains the cleaning action of soap on greasy dishes?
|
CH3(CH2)14COO-
|
|
A solution containing 10-8 M HCl and 10-8 M acetic acid contains H+ which is supplied mostly by
|
water.
|
|
The pH of a 10-4 M solution of HCl is
|
4.
|
|
Compare solution A with pH = 4 to solution B with pH = 6.
|
The concentration of hydronium ion in solution A is 100 times that in solution B.
|
|
The Henderson-Hasselbalch equation can be used to calculate
|
the pKa of a weak acid.
the amount of salt and acid to add to form a specific buffer. the pH of a solution of an organic acid |
|
The ratio of the concentration of a ________ over ________ describes the proportions of forms of a weak acid necessary to satisfy the Henderson-Hasselbalch equation
|
conjugate base; conjugate acid
proton acceptor; proton donor |
|
pKa values of phosphoric acid are 2.2, 7.2 and 12.7. A phosphate buffer of pH = 7.4 can be prepared using
|
H2PO4- and HPO42-.
|
|
Acetic acid has a pKa of 4.8. How many milliliters of 0.2 M acetic acid and 0.1 M sodium acetate are required to prepare 1 liter of 0.1 M buffer solution having a pH of 4.8?
|
250 ml acetic acid and 500 ml sodium acetate, then 250 ml water
|
|
At the midpoint of a titration curve
|
the pH equals the pKa
the ability of the solution to buffer is best the concentration of a conjugate base is equal to the concentration of a conjugate acid |
|
The tendency of a metabolic reaction to proceed is due to the free energy of both the reactants and products as well as the change in randomness of that reaction.
True or False |
True
|
|
The buffering capacity of a weak acid and its conjugate base is strongest when the pH = pKa.
true or false |
true
|
|
what are the levels of protein structure?
|
-primary
-secondary -tertiary -quaternary |
|
describe the primary structure of a protein
|
its a sequence of amino acids
|
|
describe a secondary structure protein
|
an arrangement of nearby amino acids which include alpha-helices and beta pleated sheets
|
|
describe a proteins tertiary structure
|
its the overall folding of a protein
|
|
describe the quaternary structure of a protein
|
an arrangement of two or more polypeptides to form a functional protein
|
|
proteins have a unique sequence specified by _________
|
genes
|
|
like letters in a sentence, ___________________ give proteins meaning
|
amino acids
|
|
what determines a proteins function (Catalytic for enzymes) and structure?
|
amino acids
|
|
alterations in an amino acid sequence can do what to a protein?
|
drastically alter the function of the protein
|
|
the amino acid sequence is specified by the
|
DNA sequence in genes
|
|
what prescribe the amino acid sequence of proteins?
|
specific codons (combinations of DNA bases)
|
|
when amino acids are joined together what bond is formed?
|
a peptide bond
|
|
a peptide bond is formed via
|
dehydration or condensation reaction
|
|
describe a dehydration or condensation reaction
|
a H2O (water) molecule is removed from the alpha carboxyl (COO-) and alpha amino group (NH3+)
|
|
peptide bonds are what kind of shape?
|
planar
|
|
what gives a peptide bond its character and restricts its rotation
|
its partial double bond that forms its peptide bond
|
|
peptide bonds are flexible yet
|
conformationally restricted
|
|
what are peptide bonds flexible yet restricted?
|
they have some double bond character, this restricts the rotation around the peptide bond, also the bond is uncharged (not charged) which allows tight globular structure
|
|
what allows the tight globular structure of a peptide bond?
|
because a peptide bond is uncharged
|
|
in a normal bond between C-N the Armostrong length is
|
1.49
|
|
in a "peptide" bond between C-N, the armstrong length is
|
1.32 armstrongs
|
|
in a normal double bond between C=N, the armstrong length is
|
1.27 armstrongs ( the double bond character decreases the bond length when it is a peptide bond)
|
|
peptide bonds can exsist in _______ or _______ configuration
|
cis or trans
|
|
in a Cis configuration, what side are the alpha carbons on?
|
the same side
|
|
in a Trans configuration what side are the alpha carbons on
|
different sides
|
|
which configuration is preferred, the cis or trans, why?
|
the trans is preferred, because there are no steric clashes between the R groups attached to the alpha carbon
|
|
Proline linkages are mostly in ________ form
|
cis form
|
|
since most proline linkages are in cis form, what does this do
|
since the Nitrogen is bonded to the tetrahedral carbon, this limits steric clashes, and allows a U turn in the peptide bond
|
|
what creates a stiff bond?
|
when there is a "peptide bond" between the alpha carbon and carbonyl carbon, the protein can fold in many different ways however this causes a stiff bond
the peptide bond is stiff and not free to rotate |
|
what do single bonds allow
|
when the bond between alpha carbon and amino group, this is a single bond which allow rotation
in simple : single bonds are free to rotate |
|
what kind of rotation of a bond is between the Nitrogen (N) and the alpha-carbon?
|
the Phi bond
|
|
what kind of rotation of a bond is between the alpha-carbon and the carbonyl carbon?
|
the Psi bond
|
|
which bond has a anti clockwise negative angle of -80 degrees?
|
the phi bond
|
|
what bond has an positive clockwise angle of +85 degrees?
|
the psi bond
|
|
an anti clockwise negative bond is
|
phi
|
|
a clockwise positive angle is
|
psi
|
|
not all combinations of _____ and _____ are possible
|
phi and psi
|
|
why are not all combinations of phi and psi not possible
|
because of steric hindrance;
Ramachandran plots recognise which combinations are possible |
|
on a Ramachandran plot, Antiparallel Beta sheets, Type II turn,Parallel Beta sheets and alpha helix (right handed) are:
|
highly favoured
|
|
on the Ramachandran plot, an alpha helix (left handed) and a 3^10 helix are
|
favoured (not highly favoured)
|
|
on a ramachandran plot, Type II turns (on their own) are
|
unfavoured
|
|
what is more highly favoured, an antiparallel beta sheet or a parallel beta sheet?
|
they are both highly favoured, but the antiparallel beta sheet is more favoured
|
|
on the ramachandran plot, what is the cause of it being unfavoured?
|
steric hinderence
|
|
what is a peptide bond?
|
a bond between two amino acids
|
|
why are peptide bonds planar?
|
because of a partial double bond character
|
|
what does the secondary protein structure, the alpha-helix appear like?
|
it looks like a ribbon spiral
|
|
describe the alpha helix found within the secondary structure of proteins, where is its R group and describe its backbone
|
its R group extends outwards from the alpha helix
its peptide backbone forms a tightly coiled backbone |
|
what is the alpha helical structure stabilised by?
|
hydrogen bonding
|
|
in the secondary protein structure of the alpha helix, between which atoms or groups does hydrogen bond between?
|
in the secondary structure of the alpha helics, Hydrogen bonding occurs between the N -H and CO of the backbone
|
|
in the alpha helix, hydrogen is bonded to every ____________ amino acid giving _________ amino acids per turn
|
i + 4th amino acid starting from right, giving 3.6 amino acids per turn
(i standing for original/initial amino acid; and 4th represents 4th carbon-hence there is only one central alpha carbon per amino acid) |
|
the pitch (angle) of the alpha helix is _______nm
|
5.4 nm
|
|
in the alpha helix, protein have ________% alpha helix, the average length are ________ residues (range 4-40 residues)
|
26%;
12 residues |
|
in the secondary alpha helix structure, a hydrogen is bonded to every
|
4th amino acid
|
|
most alpha helices are________________
|
amphipathic
|
|
why are most alpha helices amphipathic?
|
they have a hydrophilic amino acids on one side facing the outside of the protein, and
they have hydrophobic amino acids on the other side facing the inside of the protein |
|
describe a left handed helices
|
it moves in an anti clockwise direction (left) from the N terminus to the C terminus
|
|
describe a right handed helices
|
it moves in a clockwise direction (right) from the N terminus to the C terminus
|
|
it is possible to have both _______ and ________ helices
|
right and left
|
|
which helicix is more energetically favourable, the right or left?
|
the Right helices is more energetically favourable
|
|
nearly all helices are _______ handed
|
right handed
|
|
what are four examples of secondary alpha helical proteins?
|
-Myosin (found in muscle)
-Tropomyosin (found in cells cytoskeleton) -alpha-keratin (found in hair) -collagen (found in skin) (Key: Mr CaKt tells the class, four examples of secondary alpha helical 'proteins') |
|
describe the type of helices of a-Keratin protein
|
it has two right handed helices in its structure
|
|
a-Keratin has _____ amino acids per turn instead of ____ amino acids per turn
|
3.5 instead of 3.6
|
|
in a-keratin, there are ____ amino acid repeats that allow ___________________
|
in a-keratin , there are 7 amino acid repeats that allow cross linking
|
|
in a-keratin, cross linking occurs via which forces?
|
by three forces:
-Van der waals forces -ionic interactions and -disulfide bonds |
|
why does hair straighten and then recoil after a long while after straightening with heat or chemicals?
|
because of the Di-sulfide bonds being denatured via heat or chemicals breaking the disulfide bonds and then over time going back to original helical structure
|
|
a primary helical structure has an arrangement of amino acids in
|
in a straight line/row
|
|
a secondary helical structure has an what kind of amino acid arrangement?
|
a nearby arrangement of amino acids
|
|
in relation to the a-helix, where are the side chains of the amino acids?
|
an example is seen in alanine where the sidechains angle slightly downward, toward the N-terminus, while the peptide oxygens point up and the peptide NHs point down.
|
|
besides the alpha helix being one of the secondary helical structures, what is the other one?
|
Beta-pleated sheet
|
|
in the beta strands, there how is the polypeptide chain arranged?
|
it is an extended polypeptide chain
|
|
what forms the Beta sheets? what is the arrangement?
|
Beta strands in a side by side arrangement
|
|
how many types of Beta strands are their?
|
there are two types:
-Antiparallel ( run in opposite direction) -parallel (run in same direction) |
|
in antiparallel beta sheets, Hydrogen bonding occurs between:
|
"Adjacent" polypeptide chains which connect between both "Carbonyl O and Amide H"
(Key: antiparallel ACA) |
|
what causes Hydrogen bonding in the antiparallel Beta pleated sheets?
|
the fact that the helices run in opposite directions (from N to C terminus) which gives two adjacent polypeptide backbones next to each other, causing hydrogen bonding
|
|
in parallel Beta sheets, which way do the helices run?
|
the two helices run from the N terminus to the C terminus in the same direction (parallel)
|
|
where does hydrogen bonding occur in a parallel beta sheet?
|
Hydrogen bonding occurs between the +1 residue (a residue may be one amino acid in a polypeptide chain)
|
|
in a beta pleated sheet, __________ peptide bonds meet each other at __________, creating a pleated _________________________________
|
in B-pleated sheet, planar peptide bonds meet each other at angles, creating a pleated "accordion effect"
|
|
what creates the accordion effect in beta pleated sheets?
|
the planar peptide bonds in the polypeptide backbone that meet each other at angles via causative hydrogen bonding
|
|
in a B-pleated sheet, where are the side chains located?
|
above and below (steric hindrance dictates location)
|
|
in the Ramachandran plot (R plot), what region does the Beta-pleated strands stand?
|
in the highly favourable region
|
|
why do Beta pleated sheets stand in the highly favourable region of R plot?
|
because their R groups are above and below, with very little steric hindrance, so they can react favourable
|
|
what is an example of a secondary helical Beta pleated sheet protein?
|
Grass pollen protein
(Key: The grass pollen protein nicknamed "SBS", for secondary Beta sheet) |
|
in the Grass pollen protein, which is a secondary heical beta pleated sheet structure, how are the R groups arranged? what does its arrangement mean?
|
one side has hydrophobic side chains which face the protein core, and the other side which is above has hydrophilic chains which face the solvent; meaning this is amphipathic
|
|
Beta-pleated sheets can be ___________, an example is the Grass pollen protein
|
amphipathic
|
|
how many strands can make a Beta sheet?
|
usually 4 or 5, but can go up to 10 strands
|
|
how are B-pleated sheets represented?
|
by "arrows" that depict the "Orientation of the "Peptide"
|
|
besides the Grass pollen protein being one example of a secondary Beta sheet structure, what are some more?
|
-Fatty acid binding protein,
-silk Fibrion |
|
nearly all fatty acids binding proteins are_________________
|
Beta-pleated
|
|
silk fibroin, it has beta sheets in its polypeptide backbone and has tightly packed structure which is rich in
|
ala (alanine) and gly (glycine)
|
|
what is silk fibroin structure stabilized by?
|
Hydrogen bonding in beta sheets
|
|
silk fibroin has an extended Beta conformation therefore
|
no stretch
|
|
what kind of interactions/forces are in the silk fibroin beta sheets? what does it provide?
|
Van der Waals interactions between sheets, which provides flexibility
|
|
Reverse turns (B-turn or hairpin) are common in
|
antiparallel Beta sheets
|
|
how many degrees does a Reverse turn, turn?
|
180 degrees
|
|
in a Reverse turn, the CO group of residue 1 is H bonded to the
|
NH group of residue 4
|
|
hydrophilic residues are common where loops are on
|
the outside
|
|
loops that are the result of reverse turns are
|
hydrophilic
|
|
DNA binding protein is an example of _____________________________ and __ helices, where its helix-turn-helix loop is _____________
|
reverse turns, and alpha helices, where its helix turn loop is hydrophilic
|
|
a tertiary protein structure is known as the
|
overal folding of a protein
|
|
in a tertiary protein, the hydrophilic amino acids are on the
|
outside
|
|
in a tertiary protien, the hydrophobic amino acids are on the
|
inside
|
|
in a tertiary protein what groups are on the main chain in the middle of the the protein?
|
CO and NH
|
|
CO and NH of the main chain in the middle of the tertiary protein are involve in what kind of bonding?
|
hydrogen bonding via alpha helices and Beta sheets
|
|
how are tertiary proteins stabilised?
|
via non covalent interactions such as:
-the hydrophobic effects (gets rid of water) and -some disulfide bridges-extracellular proteins |
|
what is an example of a tertiary protein?
|
Myoglobin (its stores oxygen in muscle)
|
|
in myoglobin, what are the hydrophobic residues that are on the inside of the structure?
|
-Leucine (Leu)
-Valine (Val) -Methionine (Met) -Phenylalanine (Phe) |
|
what are secondary motifs?
|
combinations of alpha-helices and Beta-sheets
|
|
what is an example of a secondary motif structure?
|
a "Helix-loop-helix" found in Calcium binding and DNA binding proteins
and Beta-sandwich (Beta sheets stacked on top of each other) |
|
membrane proteins are
|
"hydrophobic" proteins on the outside in membrane spanning segments of the protein (note they are not hydrophilic even thought they on the outside)
|
|
name a membrane protein?
|
aqua porin protein
|
|
describe the hydrophobic and hydrophilic locations of the protein
|
-aqua porins are different than normal, they have -"hydrophobic" amino acids on the "Outside"
and -"Hydrophilic" amino acids on the "Inside" lining of the pore |
|
what are the three levels of protein structure?
|
-primary structure
-secondary structure -tertiary structures -quaternary structure |
|
what protein strcture has an arrangement of adjacent amino acids (Alpha and beta sheets)?
|
secondary structure
|
|
what protein structure has a sequence of amino acids?
|
primary structure
|
|
what protein structure has an overall protein folding?
|
tertiary structure
|
|
protein domains are
|
seperate folded comact units joined by a polypeptide chain
|
|
protein domains may serve what different functions?
|
-fungal cellulases-
binding domain + catalytic domain |
|
describe the evolutionary conservation of a proteins structure
|
-proteins group into families (which have similar domain structures and amino acid sequences)
-proteins in families descended from a common ancestral protein -all modern proteins may have evolved from a few 1000 proteins in a common ancestor (3 billion years ago) |
|
an example of evolutionary conservation of proteins are the proteins
|
-Lactate DH and Malate DH
|
|
why are lactate DH and Malate DH good examples of evolutionary conservation proteins
|
-they are similar structures, with 23% of their amino acid sequences identical, they descended from a common protein via gene duplication
|
|
A Quaternary protein structure is the
|
arrangement of different polypeptides to form a functional protein
(where you take 2 or 3 polypeptides and assemble it into a structure) |
|
what is an example of a quaternary structure protein?
|
hemoglobin
|
|
in haemoglobin, alpha and Beta subunits are arranged to form a
|
functional protein
|
|
protein denaturation is the loss of
|
secondary and tertiary structures
|
|
what are ways to denature proteins?
|
-increase temperature
-chaotropic agents (Urea, Vinigar) -Detergents-SDS |
|
how does temperature unfold and denature a protein? give an example
|
an example is egg white turning white
heat disrupts the hydrogen bonds and hydrophobic interactions leaving the protein to unfold when heated. Since heat is not strong enough to break the peptide bonds between the amino acid subunits, the primary structure remains intact. Once the protein is cooled again, the hydrogen bonds and hydrophobic interactions can reform since they are based on the makeup of the primary structure and it hasn't changed. |
|
how does Chaotropic agents such as Urea denature a protein?
|
Urea is acidic such as vinegar and so water molecules get into (sulvates) the interior which disrupts the hydrophobic interactions in the protein
|
|
how does detergent SDS denature a protein?
|
the hydrophobic tails penetrate the interior and disrupt the hydrophobic interactions
|
|
protein denaturing is a _________________ process
|
protein denaturing is a cooperative process
|
|
how is protein denaturing a cooperative process?
|
-denaturing occurs over a small temperature range, and it is a all or none process. Cooperative process means that once it starts to denature, all become unfolded and denatured
|
|
what is the only things that determines the 3D structure of a protein?
|
amino acids
|
|
how did a scientist discover amino acid sequence alone determines the 3D structure of a protein
|
-a scientist experimented and denatured Ribonuclease by 8Moles of Urea and mercaptoethanol which then after being denatured lost its shape and function
|
|
how did the scientist that discovered that an amino acid alone determines protein structure, then show the refolding or Ribonuclease?
|
he removed Urea and mercapto and the protein refolded to its native structure and resumed its normal activity, which proved that the Amino acid sequence determines overall 3D shape
|
|
what does Levithals paradox state:
|
if 100 amino acid proteins were to undergo all possible folding combinations randomly it could take the protein 1.6 x10^27 years
this does not naturally occur however |
|
as proteins fold, only the correct folding is keps and the incorrect folding is
|
not kept, this continues until the protein is folded properly
|
|
what is the driving force of protein folding?
|
a decrease in free energy (entropy)
|
|
what are the three forces involved in protein folding?
|
-hydrophobic effect
-Hydrogen bonding -Van der Waal forces |
|
hydrophobic effect and how does it work in protein folding?
|
hydrophobic parts collapse together to release water causing an increase in entropy
|
|
hydrogen bonding and how does it work in protein folding?
|
1st in alpha helices and Beta sheets, more stable in protein core, no water to compete with because of other force (hydrophobic effect)
|
|
Wan der Waals forces and how they work in protein folding?
|
the forces occur between "non polar" side chains
|
|
what do molecular chaperone proteins assist?
|
chaperone proteins assist in protein folding
|
|
how do chaperones assist in protein folding?
|
they bind newly made polypeptides ans assist in folding
|
|
what is an example of a chaperone protein?
|
the heat shock protein MW 70000 (HSP70)
|
|
what does the heat shock protein (Chaperone) do?
|
helps repair damage caused by heat, its normal function is to bind and fold new proteins, and stop proteins from aggregating with other proteins in their incorrect protein form, they are highly conserved and present in all species except ARCHAEBACTERIA
|
|
heat shock proteins are present in all species except
|
archaebacteria
|
|
the chaperone protein (HSP60) is involved in
|
protein folding and heat shock
|
|
HSP60 chaperone has two protein
|
rings/subunits (GroEL) with hydrophobic cavity
|
|
what does each of the two subunits with hydrophobic cavity do in HSP60?
|
they each bind to ATP and fold small to medium proteins
|
|
how many amino aids can the two protein ring/subunits in the chaperone HSP60 accommodate?
|
630 amino acids
|
|
what does HSP60 do to incorrect folding of proteins?
|
it inhibits it
|
|
describe how the chaperonin (HSP60) folds a polypeptide
|
an unfolded polypeptide enters the chaperone cavity binds with ATP for energy, then the protein becomes bound in the cavity and folds, and then ATP becomes ADP + Phosphate, and then the folded polypeptide is released. the end result is that the polypeptide is ATP hydrolyzed and protein is released
|
|
how many basic amino acids are their?
|
there are around 3 main ones
|
|
what are the three main basic amino acids?
|
Lys, Arg and Tyr
|
|
what is the pKa for Lysine (Lys)?
|
10.8
|
|
what is the pKa for Arganine (Arg)?
|
12.5
|
|
what is the pKa for Tyrosine (Tyr)?
|
10.8
|
|
what is the pKa for COO-?
|
2.5
|
|
what is the pKa for NH3?
|
9.5
|
|
what are the aliphatic amino acids?
|
Gly, Ala, Val, Leu, Iso
|
|
what are the aromatic amino acids?
|
Phe, Tyr, Trp
|
|
what are the sulphur containing amino acids?
|
Met, Cys
|
|
qwhat are the alcahol amino acids?
|
Ser, Thr
|
|
what are the two main basic amino acids?
|
Lys and Arg
|
|
what are the nuetral amino acids?
|
His
|
|
what are the acidic amino acids?
|
Asp, Glu, Asn, Gln
|
|
how many levels of protein structure are their?
|
four
|
|
what are the four levels of protein structure?
|
-primary
-secondary -tertiary -quaternary |
|
a linear sequence of amino acid residues defines which structure?
|
primary structure
|
|
which structure consists of regions of regularly repeating conformations of the peptide chain such as alpha helices and beta sheets
|
secondary stucture
|
|
which structure describes the shape of the fully folded polypeptide chain, and has domains?
|
teriary structure
|
|
which structure refers to the arrangement f two or more polypeptide chains into a multi subunit molecule?
|
quaternary structure
|
|
which structure is maintained by hydrogen bonds between the amide hydrogens and carbonyl oxygens of the peptide backbone?
|
secondary structure
|
|
which structure has many folded polypeptides that consist of several distinct globular units linked by a short stretch of amino acid residues called domains
|
tertiary structure
|
|
which structure has the association of two or more polypeptide chains into a multisubunit, or oligomeric, protein. with the polypeptide chains of an oligomeric protein may be identical or different
|
quaternary structure
|
|
the amino acid sequence of polypeptides can be determined by
|
by directly sequencing the protein or indirectly by sequencing the gene
|
|
X-ray crystallographic analysis of small peptides reveal analysis of small peptides reveal that the bond between the carbonyl carbon and the nitrogen is
|
shorter than typical C-N single bonds but longer than typical C=N double bonds. In addition, the bond between the carbonyl carbon and the oxygen is slightly longer than typical C=O double bonds. these measurements reveal that peptide bonds have some double bond properties and can best be represented as resonance hybrid
|
|
the planar peptide groups in a polypeptide chain have their peptide groups consisting of the
|
N-H and C=O groups, which are involved in the formation of the peptide bond, as well as the alpha carbons on each side of the peptdie bond
|
|
nearly all peptide gruops in prtoeins are in the
|
trans conformation
which minimizes steric interference between adjacent side chains. |
|
the three dimensional conformation of a polypeptide backbone is defined by the
|
phi and psi angles of roation around each peptide group
|
|
the known frequencies of various amino acid residues in alpha helices are used to predict the
|
secondary structure based on the primary sequence alone
|
|
there are only thee different kins of common secndary structures
|
-alpha helix,
-Beta strands and -turns |
|
loops often contain
|
hydrophilic residues and are usually found on the surfaces of proteins where they are exposed to solvent and form hydrogen bond with water
|
|
loops containing only a few residues are referred to as________ if they cause an abrupt change in direction of a polypeptide chain
|
turns
|
|
the most common types of turns are called
|
reverse turns, they are also called Beta turns
|
|
describe how there are two common types of Beta turns designated type 1 and type 2?
|
both types of turn contain four amino acid residues and are stabilized by hydrogen bonding between the carbonyl oxygen of the first residue and the amide hydrogen of the fourth residue. both type 1 and type 2 turns produce an abrupt (around 180 degree) change in the direction of the polypeptide chain. in type 2 turns, the third residue is glycine about 60% of the time.
Proline is often the second residue in both types of turns |
|
which amino acid is the second residue in both type 1 and type 2 beta turns?
|
proline
|
|
ramachandran plots usually show only the permitted regions for all residues except ________, this is why the rotation angles of type 2 appear to lie in a restricted area (hence why type II is unfavoured)
|
glycine
|
|
in folded proteins, alpha helices and Beta strands are commonly connceted by loops and turns to form supersecondary structures called
|
common motifs
|
|
what are the names of the 8 common motifs
|
-helic loop helix
-coiled coil -helix bundle -Beta alpha Beta unit -hairpin -Beta meander -Green key -Beta sandwhich |
|
many proteins are composed of several discrete, indeendelny folden, compact units called
|
domains
|
|
domains may consist of combinations of
|
motifs
|
|
the size of a domain varies from
|
as few as 25 to 30 amino acid residues to more than 300
|
|
an example of a protein with multiple domains is
|
pyruvate kinase from cat
|
|
each domain is a distinct compact unit consisting of
|
various elements of secondary structure
|
|
domains are usually connected by loops but they are also bound to each other through
|
weak interactions formed by the amino acid side chains on the surgace of each domain
|
|
in general, domains consist of a contiguous
|
stretch of amino acid residues
|
|
what is the most important observations that has emerged from the study of proteins in past few decades?
|
the evolutionary conservation of protein structure
|
|
where is protein conservation seen most easily?
|
in the the case of single domain homologous proteins from different species,
all of the members of a protein family phylogeny have descended from a common ancestral protein |
|
there are only three basic types of secondary structures but thousands of
|
tertiary folds and domains
|
|
many proteins exhibit an aditional level of organisation called
|
quaternary strcture
|
|
quaternary structure refers to the organization and arrangement of
|
subunits in a protein with multiple subunits, each subunit is a separate polypeptide chain. A multisubunit protein is referred to as an oligomer
|
|
the fact that a large proportion of proteins consist of multiple subunits is probably related to what several factors?
|
-oligomers are usually more stable that their dissociated subunits suggesting that quaternary structure prolongs the life of a protein in vivo
-the active sites of some oligomeric enzymes are formed by residues from adjacent polypeptide chains |
|
the most occurring oligomeric state of a protein is a
|
dimer
|
|
the numbering convention for amino acid residues in a polypeptide starts at the
|
N terminal end
|
|
when a protein is treated with excess 2-mercaptoethanol, what reaction takes place?
|
a disulfide exchange reaction occurs in which each cysteine residue is reduced to two cysteine residues and 2-mercaptoethanol is oxidized to a disulfide
|
|
what will heatin a protein do?
|
a modest increase in temperature will result in unfolding and loss of secondary and tertiary structure. Denaturation takes place over a small range of temperature, indicating that unfolding is a cooperative process where the destabilization of just a few weak interactions leads to almost complete loss of native conformation
|
|
proteins can be denatured by two types of chemicals, which are
|
chaotropic agents and detergents
|
|
high amounts of chaotropic agents such as urea and guanidinium salts, denature proteins by allowing
|
water molecules to solvate nonpolar groups in the interior of proteins, the water molecules disrupt the hydrophobic interactions that normally stabilize the native conformation
|
|
the hydrophobic tails of detergent such as sodium dodecyl sulfate, also denature proteins by
|
penetrating the protein interior and distrucping hydrophobic interactions
|
|
the native conformation of some proteins is stabilized by
|
disulfide bonds
|
|
the presence of disulfide bonds stabolozes proteins by
|
making them less susceptible to unfolding and subsequent degradation when they are exposed to external environment
|
|
complete denaturation of proteins containing disulfide bonds requires
|
cleavage of these bonds in addition to disruption of hydrophobic interactions and hydrogen bonds
|
|
treatment of native ribonuclease with urea in the presence of 2 mercaptoethanol unfolds the protein and disrupts disulfide bonds to produce reduced, reversibly denatured ribonuclease. when the denatured protein is returned to physiological conditions in the absence of 2 mercaptoethanol, it refolds into its native conformation and the correct disulfide bond forms, however when 2 mercaptoethanol alone is removed, ribonuclease
|
re oxidizes in the presence of air, but the disulfide bonds form randomly, producing inactive protein. when urea is removed, a trace of 2 mercaptoethanol is added to the randomly reoxidised protein, and the solution is warmed gently, the disulfide bonds break and re form correctly to produce native ribonuclease
|
|
which scientist discovered denaturation and renaturation of ribonuclease A?
|
Christian B. Anfinsen
|
|
most proteins fold spontaneously into a conformation with the
|
lowest energy
|
|
proteins are more stable in water when their hydrophobic side chains are aggregated in the protein interior rather than exposed on the surface to the aqueous medium because
|
water molecules interact more strongly with each other than with the nonpolar side chains of a protein, the side chains are forced to associate with one another causing the polypeptide chain to collapse into a more compact molten globule. the entropy of the polypeptide decreases as it becomes more ordered
|
|
the overall increase in the entropy of the system of the ordered protein proved the major
|
driving force for protein folding
|
|
in the case of hydrophobic interactions, the change in entropy is mostly due to the
|
release of ordered water molecules that shield hydrophobic groups
|
|
protein folding is assisted by molecular
|
chaperones
|
|
protein folding is cooperative, sequential process in which formation of the fist few structural elements assist in the alignment of features
the the folding pattern and the final conformation of a protein depend on its |
primary structure
|
|
larger priteins rae more liely to become temporarily tyrapped in a local energy well. the presence of such metastable incorrect conformations at best slows the rate of protein folding ad at worst causes the folding intermediates to aggregate and fall out of solution. in order to overcome this problem inside the cell,m the rate of correct protein folding is enhanced by a group of special proteins called
|
molecular chaperones
|
|
chaperones increase the rate of correct folding of some proteins by
|
binding newly synthesised polypeptides before they are completely folding. they prevent the formation of incorrectly folded intermediates that may trap the polypeptide in aberrant form. chaperones can also bind to unassembled protein subunits to prevent incorrect aggregation
|
|
there are many different chaperones, most of them are
|
heat shock proteins
|
|
heat shock proeinst are prtoeins that are synthesised in response to
|
temperature increase (heat shock) or other changes that cause protein dnaturation in vivo
|
|
the role of heat shock proteins (chaperones) is to
|
repair damage caused by temperature increases by binding to denatured proteins and helping them to refold rapidly into their native conformation
|
|
the major heat shiocjk protine is
|
HSP70 (Mr=70000)
|
|
HSP70 the major heat shock protein is present in all species except for some species of
|
archaebacteria
|
|
what is required for chaperonin function?
|
the hydrolysis of several ATP molecules
|
|
except for one, amino acids exist as what chiral isomer?
|
L-isomer
|
|
which amino acid is not chiral?
|
Glycine
|
|
name 3 hydrophobic amino acids?
|
any three:
Valine, Leucine, Isoleucine, Phenylalanine, Methionine |
|
another name for dipolar molecules is
|
zwitterions
|
|
disulfide bonds are formed by pairs of which amino acid??
|
cysteine
|
|
when a peptide bond is formed, what molecule is also made
|
water
|
|
the amino acid residue disrupts the alpha helix because its side chain contains a unique ring structure that restrict bond rotations
|
proline
|
|
the amino acid asp is hydrophilic or hydrophobic?
|
hydrophilic
|
|
the amino acid Phe is hydrophilic or hydrophobic?
|
hydrophobic
|
|
the amino acid Lysine is hydrophilic or hydrophobic?
|
hydrophilic
|
|
the amino acid Gln is hydrophilic or hydrophobic?
|
hydrophilic
|
|
the delivery of O2 to the tissues requires
|
-a circulatory system to carry O2 fluid to the tissue and the oxygen carrier increases the amount of dissolved O2
|
|
what is the oxygen transport protein?
|
haemoglobin
|
|
haemoglobin transports O2 from the
|
lungs to the tissues
|
|
what is the oxygen storage protein?
|
Myoglobin
|
|
what does Myoglobins function
|
it functions to reserve O2 in muscle
|
|
what is the first protein to be sequenced from wale sperm, Myoglobin or haemaglobin?
|
Myoglobin
|
|
what kind of structure is myoglobin protein?
|
-a secondary structure, and a globular protein
|
|
what two main characteristics does myoglobin have?
|
a haem- prosthetic group and
alpha helices |
|
what does the haem prosthetic group do in myoglobin?
|
it binds to )2
|
|
how many Alpha helices does myoglobin structure have?
|
8
|
|
what gives muscle and blood its red color?
|
the heme group
|
|
what does Haem group consist of?
|
an organic compoenent called a protophorphyrin and
Fe (Iron) at the centre |
|
when oxygen is bound to the haem group. what is the charge of the Fe (Iron)?
|
2+ charge (Ferrous state)
|
|
Fe (Iron) bonded to 4 Nitrogen atoms can form another
|
2 bonds
|
|
what are the 5th and 6th co-ordination sites of Fe2+?
|
below is the 5th Co-ordination site of Histidine (His-93) and
the above the 6th co-ordination site for O2 binding |
|
what happens to the Fe2+ atom when it binds to O2?
|
upon binding the Fe2+ becomes smaller and moves in line with the plane of the molecule
|
|
before the haem is bound to oxygen it is called
|
deoxyhemoglobin
|
|
after oxygen is bound to the Haem what is it called?
|
oxyhemoglobin
|
|
before Fe2+ is bound to oxygen, where does it lie on the plane of the molecule?
|
Fe2+ lies below the plane
|
|
what happens after Fe2+ is bound the oxygen, where does it move
|
it moves upwards in line with the plane
|
|
when O2 binds to the haem group, there is a partial electron transfer between
|
Fe2+ and O2
|
|
what is formed with Fe and O2 bond
|
a complex between O2 (superoxide anion) and Fe3+
|
|
why must oxygen leave after binding to O2?
|
because O2 is a highly reactive free radical that can damage molecule and Fe3+ is unable to bind O2
|
|
how does haem stabilize the O2 and Fe3+ complex?
|
the Distal histidine stabilised the O2 complex and makes it less likely that O2 is released because of its new stability
|
|
what kind of bond does histidine form when it binds to the O2 and Fe3+ complex?
|
it forms a Hydrogen bond
|
|
What is myoglobin composed of?
• Which part is responsible for binding oxygen? |
myoglobin consists of a secondary structure with 8 alpha helices,
the Fe iron in the haem group is responsible for binding to oxygen |
|
in myoglobin, what is the oxidation state of Fe at the centre of the protoporphyrin ring?
|
Fe2+
|
|
what two main features does a haemoglobin molecule contain?
|
- 4 myoglobin like subunits
-2 alpha chains and 2 Beta chains (a total of 4 chains) |
|
in the haemoglobin molecule, where is the Beta 1 chain located?
|
on the top right
|
|
where is the Beta 2 chain lcoated
|
top left
|
|
where is the alpha 1 located
|
bottom right
|
|
where is the alpha 2 chain located
|
bottom left
|
|
what is evidence that Myoglobin and haemoglobin related?
|
the alpha chains are 25% relatedness and
Beta chains are 24% relatededness similarity in amino acid sequence |
|
how are myoglobion and haemoglobin proposed to be related?
|
having evolved from the same ancestor and diverged through evolution
|
|
how does haemoglobin form a tetramer?
|
it has 2 alpha Beta dimers which form a tetramer
(this is where two secondary structures come together and form a quaternary structure) |
|
imagining the oxygen binding curve, out of haemoglobin and myoglobin, which requires alot more oxygen at p-50
|
haemoglobin requires alot more oxygen at p-50 compared to myoglobin,
|
|
who has a higher affinity for oxygen, haemoglobin of myoglobnin?
|
haemoglobin has a lower affinity for O2 than the affinity of myoglobin
|
|
what type of binding curve is myoglobin represented by?
|
a simple binding curve
|
|
what type of binding curve is haemoglobin represented by?
|
a sigmoid curve (S shaped)
|
|
what does the O2 binding curve for haemoglobin tell about its affinity for O2 compared to myoglobin?
|
Haemoglobin has less affinity for O2 than myoglobin
|
|
what partial pressure of O2 does haemoglobin require to bind?
|
P50 = 26 torr (26mmHg)
|
|
what partial pressure of )2 is required for the binding of myoglobin?
|
P1/2 = 2 torr (2mmHg)
|
|
what does the pressure difference mean for haemoglobin and myoglobin?
|
it will take more time for haemoglobin to bind to oxygen than myoglobin because of the partial pressure difference.
Haemoglobin gives up more pressure than myoglobin in order to bind oxygen |
|
haemoglobin binds to O2 in what manner?
|
in a co-operative manner
|
|
what does haemoglobins co-operative binding/releasing manner mean?
|
if 1 O2 binds then it is easier for the next O2 to bind, conversely if 1 O2 is released then it is easier for the next O2 to be released
|
|
what is the physiological significance of the Binding Curve for hemoglobin's "Sigmoid Curve"?
|
the Sigmoid curve allows more O2 to be released at the tissues (as seen in the steep part of the curve)
|
|
what is the pressure of O2 in the tissues?
|
20 torr (20mmHg)
|
|
what is the pressure of O2 in the lungs?
|
100 Torr (100mmHg)
|
|
what percent of partial pressure does Haemoglobin release when binding oxygen?
|
66%
|
|
what percent of partial pressure does myoglobin release in order to bind oxygen?
|
7%
|
|
Haemoglobins co-operative process allows it to
|
deliver 10 times more Oxygen (O2) than myglobin
|
|
haemoglobin delivers 1.7 times more oxygen than a
|
noncoperative protein (a noncooperative protein releases 38% partial pressure to bind to O2)
|
|
what protein is efficient at delivering Oxygen at rest and during exercise?
|
haemoglobin
|
|
imagining at oxygen binding curve, how is haemoglobin efficient at O2 delivery at rest and during exercise?
|
haemoglobin delivers 45% more Oxygen during Exercise due to its Sigmoid curve being steeper from 40 to 20 too (mmHg)
|
|
what does the steep curve from 40 to 20 Torr (mmHg) for haemoglobin tell about its ability?
|
haemoglobin delivers 45% more oxygen during exercise than myoglobin
|
|
what happens to the haemoglobin structure after it binds to oxygen?
|
the binding of O2 on haemoglobin affects the structure of tetramer
|
|
to what degree does deoxyhemoglobin twist when it becomes oxyhemoglobin?
|
it twists 15 degrees to the right
|
|
what does haemoglobin rotate by 15 degrees?
|
it rotates its dimers (a1, B1 and a2, B2)
|
|
when is a haemoglobin in a T (tense) state?
|
when it is deoxyhemoglobin
|
|
when is haemoglobin in a R (relaxed) state?
|
when it is Oxyhemoglobin
|
|
in which state does haemoglobin have a low affinity for O2?
|
in its T state
|
|
in which state does haemoglobin have a high affinity for O2 (more likely to bind O2)?
|
in R state
|
|
how are T and R states in equilibrium?
|
as haemoglobin goes from T --> R state, binding of O2 at the first site increase the O2 affinity at another site. ans so there is a shift in equilibrium from T --> R
|
|
the sigmoid curve is a mixture of the
|
R state and T state binding curves being in equilibrium
|
|
how does the overall haemoglobin structure change during the binding of O2 at the haem group?
|
-movement of Fe2+ move Histidine which moves the alpha helix and
-C terminal of alpha helix at junction of the 2 subunits also move |
|
which amino acids are charged?
|
Charged:
• Arginine - Arg - R • Lysine - Lys - K • Aspartic acid - Asp - D • Glutamic acid - Glu - E |
|
which amino acids are polar (Hydrophilic)?
|
Polar (may participate in hydrogen bonds):
• Glutamine - Gln - Q • Asparagine - Asn - N • Histidine - His - H • Serine - Ser - S • Threonine - Thr - T • Tyrosine - Tyr - Y • Cysteine - Cys - C • Methionine - Met - M • Tryptophan - Trp - W |
|
which amino acids are non polar (Hydrophobic)?
|
Hydrophobic (normally buried inside the protein core):
• Alanine - Ala - A • Isoleucine - Ile - I • Leucine - Leu - L • Phenylalanine - Phe - F • Valine - Val - V • Proline - Pro - P • Glycine - Gly - G |
|
the structure of a normal adult hemoglobin can be described as
|
a tetramer composed of two alphaBeta dumers
|
|
chemical cofactors that alter haemoglobin
|
binding curves
|
|
haemoglobins Relaxed and Tense states are in
|
equilibrium
|
|
what does the equilibrium lie towards, R or T state?
|
R state
|
|
in order for the T state to become stabilised it its shifts the equilibrium towards
|
T state
|
|
which state (R or T) forms less affinity for O2?
|
T (tense state) forms less affinity for O2 than the R (relaxed form)
hence why the T state gives a reduced O2 binding affinity to haemoglobin |
|
the presence of 2,3-BPG (2,3-Bisphoglycerate) dramatically
|
decreases haemoglobins O2 affinity
|
|
when the T state is unstable and the equilibrium lies to the R state side, what is needed to stabilise with the T state?
|
2,3-BPG
|
|
without 2,3-BPG, the R state would
|
the R state would predominate and little O2 would be released
|
|
where does 2,3-BPG bind on the haemoglobin molecule?
|
2,3-BPG binds to a pocket between the dimers only in its T form
|
|
what is the only form that 2,3-BPG can bind to the centre circle pocket in haemoglobin:
|
in its T form (tense)
|
|
when 2,3-BPG is bound to haemoglobins centre pocket, what happens when O2 binds?
|
as O2 binds, it gets to a state where the R (relaxed) state is preferred and the pocekt then clsoes and 2,3-BPG is released from the pocket
|
|
2,3-BPG is an allosteric effector, what does this mean?
|
an allosteric effector (allosteric modulator) is a biomolecule that binds to the regulatory site of an allosteric protein and modulates its activity. a allosteric modulator may be an activator or an inhibitor.
|
|
how does 2,3-BPG have characteristics of an allosteric effector?
|
-it is a different compound than O2 the normal binding molecule to haemoglobin
-it binds to the site distinct from O2 |
|
llama's have low 2,3-DPG sensitivity, they have a mutation in their
|
'B2 chain' where histidine becomes Asparagine
|
|
why do llamas have low 2,3-BPG sensitivity?
|
the histidine in their Beta chain becomes mutated to asparagine to increase the O2 capacity, to adapt in high climates and survival
|
|
what binds in the central cavity in the T form of hemoglobin, and preferentially binds to deoxyhemoglobin and stabilizes it and is present in red blood cells?
|
2,3-Bisphosphaoglycerate
|
|
how does 2,3-Bisphosphoglycerate reduce the oxygen affinity of haemoglobin?
|
it stabilizes the T state by binding to the middle pocket of haemoglobin, after O2 binds, the T (tense) state becomes the R (relaxed) state and the pocket hole closes and then the 2,3-BPS molecule is released
|
|
what does the Bohr effect, H+ and CO2 all do to the oxygen affinity of haemoglobin?
|
they all decrease haemoglobins O2 binding affinity
|
|
where is H+ and CO2 produced?
|
at the tissues where O2 is needed most
|
|
what does a decrease in O2 affinity help do?
|
load off more O2 from haemoglobins binding sites
|
|
explain the biochemical mechanisms which cause haemoglobin to reduce its oxygen affinity in the presence of CO2?
|
CO2 reacts with H2O to give:
[CO2 + H2O <-_> H2CO3 <__> HCO3 - + H+] and CO2 by itself can decrease O2 affinity by decreasing pH and also CO2 reacts with amino group and forms carbomate with negative charge, thus participates in salt bridges and stabolises the T state and this decreases O2 affinity |
|
explain the biochemical mechanisms which cause haemoglobin to reduce its oxygen affinity in the presence of H+?
|
H+ reacts with Histidine making it positively charged, by adding a proton (H+) then it reacts with Aspartates negative COO_ (Carboxyl group) forming a salt bridge (charge-charge interactions). and the salt bridge stabilises the T (tense) state and lowers the O2 affinity
|
|
what is a salt bridge?
|
also knwn as charge charge interactions, which is a noncovalent electrostatic interaction between two charged particles
|
|
in deoxyhaemoglobin, Carboxyl group can form salt bridge with
|
Lys 40
|
|
Protonated his (histidine) can form a salt bridge with
|
Asp 94
|
|
what locks in the amino acid chain and staboloses T form?
|
protonates histidine that forms a salt bridge with Asp (asparagine)94
|
|
when the amino acid chain is locked in and the T state is stabilized, what does this do for O2?
|
more O2 can be released
|
|
at high pH (basic) Histidine is not
|
protonated
|
|
when Histidine is not protonated at high pH (basic) a salt bridge...
|
cannot form
|
|
when a salt bridge cannot form, a T state..
|
cannot be locked in, and lower O2 binding affinity to release more O2
|
|
in a salt bridge, positive histidine is attracted to
|
negatrively charged Asp (asparagine)
|
|
CO2 alone can decrease the
|
O2 affinity of Hb
|
|
with CO2 present, it can lower the pH to
|
pH7.2 (40 Torr (40mmHg))
|
|
how is carbamate formed?
|
CO2 reacts with amino groups at the end of N terminus to form cabamate
|
|
carbamate has a negative charge and so can participate in
|
salt bridges
|
|
when carbamate participates in salt bridges it can stabilise the T state to reduce
|
haemoglobins oxygen binding affinity
|
|
what is the bohr effect?
|
the regulation of hemoglobin-binding by hydrogen ions and carbon dioxide
|
|
what does CO2 do to the oxygen binding affinity of haemoglobin?
|
decreases it
|
|
in sickle cell anaemia haemoglobin forms
|
fibers that distort the blood cell shape and clog capillaries and disrupt blood flow
|
|
what happens in sickle cell anaemia when the abnormal blood cells are removed?
|
the person becomes anaemic
|
|
what causese sickle cell anaemia?
|
a one amino acid mutation
|
|
which amino acid and chain is mutated in haemoglobin that causes sickle cell anaemia?
|
a mutation in the Beta (B) chain,
Glu 6 becomes Val 6 |
|
what does the beta chain and amino acid (Glu 6 --> Val6) mutation in haemoglobin do to the molecule?
|
it creates a hydrophoic patch on surface
|
|
in sickle cell, what two molecules interact that causes the sickle cell shape?
|
Val 6 interacts with Phe 85 and Val 88 on another Beta chain
|
|
when Val 6 interacts with Phe 85 and Val 88 on another beta chain in haemoglobin, what does it caues?
|
haemoglobin chains to form, which causes the sickle cell shape
|
|
haemoglobin chains only form in
|
deoxyhaemoglobin, not in oxyhaemoglobin
|
|
why does sickle cell shape only occur in deoxyhaemoglobin and not oxyhaemoglobion
|
because in oxyhaemoglobin the centre pocket is filled with O2 and its shape is closed to any other molecule, however in deoxyhaemoglobin the pocket centre in the haemoglobin molecule is open and so the molecule becomes vulnerable to react with the mutated amino acid (Glu 6--> Val 6) which causes the haemoglobin chains to form to sickle shape
|
|
in malaria, which is more prone to survival of malaria?
|
Heterozygotes survive more than homozygotes in malaria heterozygotes
|
|
is heterozygote or homozygote malaria resistant?who is more prone to getting sickle cell?
|
homozygotes
(heterozygote advantage) |
|
natural selection maintains how many phenotypes for heterozygotes?
|
2 phenotypes
|
|
sickle cell is a what sort of genetic disease
|
recessive
|
|
sickle cell anemia is caused by
|
a substitution of a Val residue for a Glu residue at the B6 position
|
|
the humoral immune system produces antibodies called
|
Immunoglobins (Ig)
|
|
immunoglobins bind to
|
bacteria and viruses (targets them for distruction), Ig also bind to molecules called antigens
|
|
immunoglobins (Ig) are produced by
|
B lymphocytes or B cells which are produced in bone marrow
|
|
what is a molecule that elicits an immune response?
|
Antigen
|
|
what is part of a molecule that binds to the antibody?
|
Epitome
|
|
the Cellular immune system includes
|
T lymphocytes, that recognise cells infected with viruses and parasites
|
|
Helper T cells produce
|
signalling molecules
|
|
how many chains do immunoglobulins have?
|
4 chains
|
|
describe the four chains of Immunoglobins (Ig)
|
2 are light and 2 are heavy
|
|
what is the MW of the 4 chains of an immunoglobin?
|
150 KDa
|
|
where is the light chains located?
|
the top
|
|
where is the heavy chains located
|
the bottom
|
|
in the heavy chains, how many constant regions are there, and how many variable regions?
|
there are 3 constant and 1 variable
|
|
what happens to the hinges that hold the four chains together in the immunoglobulin?
|
the hinges can be cleaved with proteases producing two fragments
|
|
what are the two fragments released once proteases cleave the immunoglobulins hinges?
|
Fc-Crystallises fragment and
Fab - antigen binding fragment |
|
how many constant and how many variable regions are theire in a light chain?
|
there is 1 constant and 1 variable
|
|
why are all theoretical combinations of phi and psi not possible?
|
because of steric hinderence
|
|
what do Phi and psi represent?
|
they represent rotation/angle of peptide bond (joins amino acid toegether)
|
|
why cant a peptide bonmd roptate?
|
steric hinderence, because the double bond character (limits rotation)
|
|
when asked to identify a phi and psi bond, what are the only bonds that can rotate?
|
single bonds
|
|
how does carbon dioxide mainly travel in the blood?
|
HCO3- (as the bicarbonate ion) it can also travel on carbomate, however that is only 20% of its travel preference
|
|
when is the haemoglobin pocket hole open?
|
in the T state when there is low oxygen binding affinity
|
|
when is the pocket hole in haemoglobin closed?
|
in the R state when oxygen affinity is high
|
|
how is the T state represented on a Hb O2 binding curve?
|
it is draw in a straight line underneath the main curve
|
|
how is a R state represented on a O2 binding curve?
|
it is above the initial curve, and has the same shape as the initial, it is not in a straight line
|
|
when pH is 7.4 what does it change to when CO2 is produced in the blood?
|
it changes to pH 7.2
|
|
the reversible binding of oxygen is called
|
oxygenation
|
|
oxygen free myoglobin is called
|
deoxymyoglobin
|
|
oxygen bearing myoglobin molecule is called
|
oxymyoglobin
|
|
the two forms of hemoglobin are called
|
-deoxyhemoglobin and
-oxyhaemoglobin |
|
some substituents of the heme prothetic group are
|
hydrophobic
|
|
what does the hydrophobic region of heme prosthetic group allow?
|
allows prosthetic group to be partially buried in the hydrophobic interior of the myoglobin molecule
|
|
what are the two polar residues located near the heme group?
|
His-64 and
His-93 |
|
his 93 is the
|
proximal histidine
|
|
His 64 is the
|
distal histidine
|
|
in oxymyoglobin, how many ligands are coordinated to the ferrous iron with the ligands in an octahedral geometry around the metal cation
|
six
|
|
describe the 6 ligands around Iron (Fe) in Hb
|
Four of the ligands are the nitrogen atoms of the tetrapyrrole ring system; the fifth ligand is molecular oxygen bound betwen the iron and the imidazole nitrogen from His 93 (proximal histidine), and the sixth ligand is molecular oxygen bound between iron and the imidazole side chain of His 64 (distal histidine)
|
|
in deoxymyoglobin, the iron is coordinated to how many ligands
|
only 5 ligands because oxygen is not present
|
|
the nonpolar side chains of Val 68 and Phe 43, contribute to the
|
hydrophobicity of the oxygen binding pocket and help hold the heme group in place
|
|
what blocks the entrance to the heme containing pocket in both oxymyoglobin and deoxymyoglobin?
|
several side chains
|
|
what must happen to allow oxygen to bind and dissociate in the blocked pocket of oxy and deoxy Hb
|
must vibrate, breathe rapidly to allow O2 to bind
|
|
the structure of myoglobin and hemoglobin prevents the permanent transfer of an
|
electron or irreversible oxidation and thereby ensuring the reversible binding of molecule oxygen for transport
|
|
the ferrous iron atom of heme in hemoglobin is partially oxidized when
|
O2 is bound
|
|
an electron is temporarily tranferred towards the oxygen atom that is attached to the iron so that the molecule of dioxygen is partially reduced. If the electron were tranferred completely to the oxygen, the complex would be
|
Fe+3 --O2- (a superoxide anion attached to ferric iron)
|
|
the globin crevice prevents
|
complete electron transfer and enforces return of the electron to the iron atom when OP2 dissociates
|
|
oxygen binds reversible to
|
myoglobin and hemoglobin
|
|
the extent of O2 binding at equilibrium depends on the
|
concentration of the protein and the concetration of oxygen
|
|
the oxygen binding curve of myoglobin is hyperbolic indicating that there is a
|
single equilibrium constant for the binding of O2 to the macromolecule
|
|
the O2 binding curve depicts the relationship between oxygen concentrations and binding to hemoglobin is
|
sigmoidal
|
|
signoidal (S shaped) binding curves indicate that
|
more than one molecule of ligand is binding to each protein ( in this case, up to four molecules of O2 bind to hemoglobin, one per heme group of the tetrameric protein)
|
|
the shape of the S curve indicates that the oxygen binding sites of hemoglobin interact such that the
|
binding of one molecule of oxygen to one heme group facilitates the binding of oxygen molecules to other hemes
|
|
the oxygen affinity of hemoglobin increases as each oxygen molecule is bound, this interactive binding phenomenon is termed
|
positive cooperativity of binding
|
|
the partial pressure of half saturation (P50) is a measure of
|
the affinity of the protein for O2.
|
|
A low P50 indicates a
|
high affinity for oxygen since the protein is half saturated with oxygen at a low oxygen concetration
|
|
a high p50 indiactes a
|
low affinity
|
|
myoglobin molecules are half saturated at a pO2 of 2.8 torr
|
the p50 of hemogloin is much higher at (26 torr) reflecting its lower affinity for oxygen
|
|
the heme prosthetic groups of myoglobin and hemoglobin are identical but the affinities of these groups for oxygen differ because
|
the microenvironments provided by the proteins are slighly different
|
|
the cooperative binding of oxygen by hemoglobin can be related to changes in the protein conformation that occur on
|
oxygenation
|
|
deoxyhemoglobin is stabilized by
|
several intra-and intersubunit ion pairs
|
|
which amino acid has the one letter key word G
|
Glycine
|
|
which amino acid has the one letter key word A
|
Alanine
|
|
which amino acid has the one letter key word V
|
Valine
|
|
which amino acid has the one letter key word L
|
Leucine
|
|
which amino acid has the one letter key word I
|
Isoleucine
|
|
which amino acid has the one letter key word F
|
Phenylalanine
|
|
which amino acid has the one letter key word Y
|
Tyrosine
|
|
which amino acid has the one letter key word W
|
Tryptophan
|
|
which amino acid has the one letter key word M
|
Methionine
|
|
which amino acid has the one letter key word C
|
Cysteine
|
|
which amino acid has the one letter key word
|
Serine
|
|
which amino acid has the one letter key word T
|
Threonine
|
|
which amino acid has the one letter key word K
|
lysine
|
|
which amino acid has the one letter key word R
|
Arginine
|
|
which amino acid has the one letter key word H
|
Histidine
|
|
which amino acid has the one letter key word P
|
Proline
|
|
which amino acid has the one letter key word D
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Aspartate
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which amino acid has the one letter key word E
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Glutamate
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which amino acid has the one letter key word N
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Asparagine
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which amino acid has the one letter key word Q
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Glutamine
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name the hydrophobic amino acids
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G
A V L I F Y M P |
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name the hydrophilic amino acids
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W
C S T K R H D E N Q |
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name the aliphatic amino acids
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G
A V L I |
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name the aromatic amino acids
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F
Y W |
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name the sulphur containing amino acids
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M
C |
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name the alcahole amino acids
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S
T |
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name the basic amino acids
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K
R |
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name the neutral amino acids
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H
P |
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name the acidic amino acids
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D
E N Q |
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which amino acids have a pKa value of 2.4 for their Carboxyl group?
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Glycine
Alanine |
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Asparagine and glutamine are both amides of aspartic acid and because they have uncharged sidechains are often found on the interior of proteins.
Question 1 options: True False |
False
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Amino acids are neutral at the isoelectric pH.
Question 2 options: True False |
True
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Amino acids are named that because each one
Question 3 options: is an amino derivative of a carboxylic acid. is a unique carboxylic acid. has a standard configuration. is a carboxyl derivative of an amide acid. |
is an amino derivative of a carboxylic acid.
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The last common ancestor of modern organisms must have used
Question 4 options: either D or L amino acids. D amino acids. L amino acids. both D and L amino acids. |
L amino acids.
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Amino acids with non-ionizable side chains are zwitterions when they are ________.
Question 5 options: in alkaline solutions only in any solution at physiological pH, pH = 7.4 in acidic solutions only All of the above |
at physiological pH, pH = 7.4
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Glycine is not a stereoisomer because
Question 6 options: it does not exist in two non-superimposable mirror-image forms. it does not form enantiomers. it has no chiral carbon. All of the above A and B only |
All of the above
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The R group of an amino acid determines if it is
Question 7 options: polar or nonpolar. charged or uncharged. an acid or a base. hyrophilic or hydrophobic. All of the above |
All of the above
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Proline is distinct among the 20 commonly found amino acids because
Question 8 options: it is a ring compound. the nitrogen of the amino group is in a ring. it has little effect on protein structure. it is hydrophilic and ionic. the carbon of the carboxyl group is in a ring. |
the nitrogen of the amino group is in a ring.
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Which structure below is appropriate for glycine at neutral pH?
Question 9 options: +H3NCH2COO- H2NCH2COO- H2NCH2COOH +H3NCH2COOH |
+H3NCH2COO-
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The pKa of a certain weak acid is 4.0. Calculate the ratio of proton acceptor to proton donor at pH 7.0.
Question 10 options: 1:1 1000:1 3:1 20:1 The ratio cannot be calculated without knowing the structure of the weak acid. |
1000:1
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According to the Henderson-Hasselbalch equation, when the concentrations of proton acceptor and proton donor are the same, then
Question 11 options: pH = pKa. pKa = log[proton acceptor]/[proton donor]. the carboxylic acid is totally neutralized. only salt forms are present. |
pH = pKa.
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For the amino acid lysine, the Henderson-Hasselbalch equation can be applied to ________ ionization group(s).
Question 12 options: one three four two |
three (because it has three ionizable groups)
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All 20 common amino acids have an amino group and a carboxyl group bonded to the same carbon atom.
Question 13 options: True False |
True
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All 20 common amino acids exist in nature equally as both the D and L stereoisomers.
Question 14 options: True False |
False
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Ultraviolet (UV) light can be used to estimate concentrations of proteins in solutions because tryptophan and tyrosine absorb light at a wavelength of 280 nm.
Question 15 options: True False |
True
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The amino acids in polypeptide chains which contain sulfur (S) are
Question 16 options: cysteine and methionine. cystine. methionine only. cysteine only. cysteine, cystine, and methionine. |
cysteine and methionine.
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Basic amino acids are ________ (positive, negative) at pH 7 and acidic R group amino acids are ________ (positive, negative) at pH 7.
Question 17 options: positive; positive negative; positive positive; negative negative; negative |
positive; negative
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An amino acid named for a plant from which it was first isolated is
Question 18 options: methionine. threonine. proline. asparagine. |
asparagine.
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A protein that contains more isoleucine, phenylalanine and leucine than asparagine, lysine and arginine is most likely
Question 19 options: hydrophobic. low on the hydropathy index scale. hydrophilic. neutral. |
hydrophobic.
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At the isoelectric pH of an amino acid which has two pKa values the net charge is
Question 20 options: 0. 1. -1. 0.5. |
0
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Histidine has pKa values of 1.8, 6.0 (R-group) and 9.3 . At pH 8.0, the net charge on histidine is
Question 21 options: negative. neutral (uncharged). positive. insufficient information to tell. |
neutral (uncharged).
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Which amino acid is ideal for the transfer of protons within the catalytic site of enzymes due to the presence of significant amounts of both the protonated and deprotonated forms of its side chain at biological pH?
Question 22 options: Cysteine Lysine Histidine Tyrosine Asparagine |
Histidine
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The ________ is the single shape a protein adopts under physiological conditions.
Question 1 options: primary structure most stable enantiomer native conformation minimal configuration |
native conformation
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To what level of structure do α-helices belong?
Question 2 options: primary secondary quaternary tertiary |
secondary
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What does it mean to say a protein is oligomeric?
Question 3 options: In vivo it establishes an equilibrium between two or more active conformations. The active protein involves the association of two or more polypeptide chains. The protein has multiple α-helices. It has more than fifty amino acids. |
The active protein involves the association of two or more polypeptide chains.
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Which statement is not true about the peptide bond?
Question 4 options: The carbonyl oxygen and the amide hydrogen are most often in a trans configuration with respect to one another. The peptide bond is longer than the typical carbon-nitrogen bond. The peptide bond has partial double-bond character. Rotation is restricted about the peptide bond. |
The peptide bond is longer than the typical carbon-nitrogen bond.
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Supersecondary structures that contain recognizable combinations of α-helices, β-strands and loops (e.g. the Greek Key) are called ________.
Question 6 options: homologous regions motifs domains folds |
motifs
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Which is true about the side chains of residues in an α-helix?
Question 7 options: They extend radially outward from the helix axis. They hydrogen bond extensively with each other. They extend above or below the pleats. They point toward the center of the helix. |
They extend radially outward from the helix axis.
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Ramachandran determined the "allowed" values of the phi and psi angles primarily by considering ________.
Question 8 options: steric hindrance pKa values of the amino acids the hydropathy of amino acids hydrogen bonding effects |
steric hindrance
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What is true about the rotation about bonds in a protein backbone?
Question 9 options: The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues. All bonds in the backbone have restricted rotation and partial double-bond character. The rotation is free about all bonds in the backbone, except for the bond between the nitrogen and the alpha carbon in proline residues. The rotation is free only about the peptide bond. The other bonds are restricted by steric hindrance and the presence of proline residues. |
The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues
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Which demonstrates that the primary structure of a protein determines its tertiary structure?
Question 10 options: Proteins refold when the amino acid sequence is the same as in the native conformation. Proteins can refold even when the amino acid sequence is changed. Chaotropic agents cannot denature the native conformation. How the disulfide bonds hold it in the correct shape. All of the above |
Proteins refold when the amino acid sequence is the same as in the native conformation
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In addition to self assembly, some proteins fold with the help of
Question 11 options: low entropy pickets. energy stabilizers. weak chemical interactions. other proteins. All of the above |
other proteins.
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All proteins possess primary, secondary, tertiary and quaternary structure.
Question 12 options: True False |
False
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β-strands are a type of secondary structure.
Question 13 options: True False |
True
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Proline exists in the cis configuration more frequently than any other amino acid.
Question 14 options: True False |
True
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In oligomeric proteins all the subunits are always identical.
Question 15 options: True False |
False
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Chaperones are proteins which prevent incorrect folding of proteins as well as preventing some proteins from aggregating.
Question 16 options: True False |
True
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The principle forces holding subunits of an oligomeric protein to each other are ________.
Question 1 options: covalent bonds disulfide bonds peptide bonds hydrophobic interactions |
hydrophobic interactions
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A tetrameric protein contains
Question 2 options: four identical subunits. four different subunits. three subunits and one prosthetic group. A or B only A, B or C |
A or B only
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Hydrophobic amino acid sequences in myoglobin are responsible for
Question 3 options: the irreversible binding of oxygen. the folding of the polypeptide chain. covalent bonding to the heme prosthetic group. A and B above |
the folding of the polypeptide chain.
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The main property of myoglobin and hemoglobin that makes them an efficient system for oxygen delivery from lungs to muscles is
Question 4 options: different binding affinities for oxygen. hydrophobicity. movement of the protein shapes. cooperativity. All of the above |
different binding affinities for oxygen
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Cooperative binding of oxygen by hemoglobin
Question 5 options: is induced by oxygenation. is a result of different affinities for oxygen by each subunit protein. is induced by hemoglobin. is a result of interaction with myoglobin. |
is induced by oxygenation.
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Which statement is false about the heme group?
Question 6 options: The heme group is tightly, but non-covalently, held in myoglobin molecule. When oxygen binds to heme, the iron ion is oxidized from Fe2+ to Fe3+. The chemical structure of the heme groups in myoglobin and hemoglobin are identical. If exposed to air, a free heme group (not associated with hemoglobin) is readily oxidized converting Fe2+ to Fe3+ and can no longer bind oxygen. |
When oxygen binds to heme, the iron ion is oxidized from Fe2+ to Fe3+.
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Conditions in the tissues which enhance the delivery of oxygen by hemoglobin are the presence of
Question 7 options: 2,3 BPG. carbon dioxide. protons. All of the above A and B above |
All of the above
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Antibodies bind antigens at
Question 8 options: light chains. heavy chains. glycoprotein regions. hypervariable regions. All of the above |
hypervariable regions.
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Antibodies are suitable for diagnostic tests because
Question 9 options: they are found everywhere. they can be readily purified. they can be made radioactive. they are found in very small quantities. they bind very specifically to antigens. |
they bind very specifically to antigens.
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The porphyrin prosthetic group is held into the interior of globin molecules by covalent bonds to specific amino acid residues.
Question 10 options: True False |
False
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Myoglobin has a greater affinity for oxygen than hemoglobin.
Question 11 options: True False |
True
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Cooperative binding and allosterism of hemoglobin allow oxygen to be unloaded at low partial pressures of oxygen in the tissues.
Question 12 options: True False |
True
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The Bohr effect describes the effect of pH on hemoglobin's ability to bind oxygen. Oxygen binds more tightly at low pH and less tightly at higher pH values.
Question 13 options: True False |
False
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Part of immunoglobulin molecules can be changed in order to bind to a variety of antigens while the amino acid sequence of another part does not change.
Question 14 options: True False |
True
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