Sle212 Biochemistry

Front 1

what cell has membrane bound nucleus and organelles?

Back 1

eukaryotic cell

Front 2

what are the four levels of cell to molecules?

Back 2

-the cell and its organelles (cell)
-Supramolecular complexes (organelles)
-macromolecules
-monomeric units (monomers)

Front 3

out of 92 chemical elements, how many are found to be organic matter?

Back 3

25 out of 92

Front 4

what percent does carbon, oxygen, nitrogen and hydrogen make up the elements of life?

Back 4

96%

Front 5

what percent does phosphorus, sulphur, calcium and potassium make up the essential elements of life?

Back 5

4%

Front 6

what two trace elements are required in the essential elements of life?

Back 6

Iron (Fe) and Iodine (I)

Front 7

what three bonds are involved in life?

Back 7

-Ionic bonds
-Covalent bonds
-Hydrogen bonds

Front 8

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?

Back 8

Ionic bond

Front 9

what kind of bond is formed when there is a sharing of electrons between atoms?

Back 9

covalent bond

Front 10

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?

Back 10

Hydrogen bond

Front 11

when a H atom is bonded to an electronegative atom it produces a

Back 11

delta plus (d+) charge

Front 12

what is the delta plus (d+) of a H atom attracted to?

Back 12

the delta negative (d-) of an electronegative atom

Front 13

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

Back 13

Van der Waals force

Front 14

what interactions occurs when there is an attraction between non polar molecules and only occur when molecules are very close together?

Back 14

Van der Waals interactions

Front 15

what is the other name for london forces?

Back 15

Van der Waals forces

Front 16

what is responsible for allowing geckos to walk up walls?

Back 16

Van der Waals forces

Front 17

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

Back 17

Phosphorus

Front 18

what bond does a carbon skeleton form?

Back 18

Covalent bonds

Front 19

what is the difference between an aldehyde and a ketone?

Back 19

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

Front 20

describe a ketone

Back 20

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

Front 21

describe an aldehyde

Back 21

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.

Front 22

what bond is commonly found in proteins?

Back 22

disulfide bonds

Front 23

what functional group is important in energy transfer?

Back 23

thioester

Front 24

what are molecules that have the same chemical formula but different chemical structures

Back 24

isomers

Front 25

Two mirror images of a chiral molecule are called

Back 25

enantiomers or optical isomers.

Front 26

what is a chiral centre?

Back 26

where a chiral molecule is rotated and yet cannot be superimposed on its mirror images

Front 27

stereoisomers that are nonsuperimposable mirror images of each other are known as

Back 27

enantiomers

Front 28

what is an anomer

Back 28

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.

Front 29

what is a cis-trans isomer

Back 29

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

Front 30

what is diastereoisomers

Back 30

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

Front 31

what are geometric isomers?

Back 31

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.

Front 32

what is the first law of thermodynamics (principle of conservation)?

Back 32

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)

Front 33

what is the second law of thermodynamics?

Back 33

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

Front 34

what is the measure of a systems disorder and allows understanding of why a process will occur spontaneously?

Back 34

entropy

Front 35

if there is in increase in disorder, will the process be spontaneous or non spontaneous?

Back 35

the process will be spontaneous if it involves in increase in disorder

Front 36

if there is a decrease in disorder (increase in order) will the process be spontaneous or non spontaneous?

Back 36

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

Front 37

what is a portion of a systems energy that can perform work when temperature and pressure are constant?

Back 37

free energy

Front 38

what is the formular for delta G or Gibbs free energy?

Back 38

delta G = delta H -T delta S

Front 39

in gibbs free energy formular what does delta H represent?

Back 39

change in enthalpy (change in heat)

Front 40

in gibbs free energy formlar what does T delta S represent?

Back 40

change in entropy (order of the system)

Front 41

what are the symptoms of an increase in entropy? (delta G = < 0)

Back 41

-increase in temperature
-increase in volume
-increase number of independently moving particles

Front 42

what is the outcome of spontaneity when delta G < 0

Back 42

process is spontaneous

Front 43

what is the outcome of spontaneity when delta G = 0

Back 43

process is at equilibrium

Front 44

what is the outcome of spontaneity when delta G > 0

Back 44

process is not spontaneous

Front 45

when the reactants are greater than the products, what kind of reaction is it in regards to free energy change?

Back 45

exergonic reaction (energy released)

Front 46

when the reactants are less than the products, what kind of reaction is it in regards to free energy change?

Back 46

endergonic reaction (energy absorbed and thus needed)

Front 47

what is the formular for free energy change? and what does it calculate?

Back 47

delta G = G final state - G initial state

it shows if the process is exergonic(-) or endergonic (+)

Front 48

describe spontaneity in endergonic reactions?

Back 48

delta G is positive, reaction is not spontaneous

Front 49

describe spontaneity in exergonic reactions?

Back 49

delta G is negative, reaction is spontaneous

Front 50

describe spontaneity in coupled reactions?

Back 50

overall delta G is negative; together, reactions are spontaneous

Front 51

in oxidation describe spontaneity?

Back 51

OIL = delta G = < 0

therefore reaction is spontaneous in oxidation reactions where electrons are lost (increase in entropy or disorder)

Front 52

in reduction describe spontaneity?

Back 52

RIG = delta G = > 0

therefore reaction is not spontaneous in reduction where electrons are gained (decrease in entropy or disorder)

Front 53

what oxidises another species and in itself is reduced?

Back 53

oxidising agent

Front 54

what reduces another species and in itself is oxidised?

Back 54

reducing agent

Front 55

Biochemistry is about

Back 55

Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms

Front 56

The principles of Biochemistry differ for bacteria, plants and humans!

True or False?

Back 56

false

Front 57

Biomolecules
that
contain
the
same
chemical
bonds
but
differ
in
their
configuration
are
called

Back 57

geometric isomers

Front 58

A
carbon
with
4
different
constituents
is
referred
to
as

Back 58

chiral

Front 59

Stereoisomers
that
are
mirror
images
of
each
other
are
called

Back 59

Enantiomers

Front 60

Stereoisomers
that
are
not
mirror
images
of
each
other
are
called

Back 60

Diastereomers

Front 61

describe biochemistry

Back 61

biochemistry is the discipline that uses the principles and language of chemistry to explain biology

Front 62

which six non metalic elements account for more than 97% of the weight of most organisms and can all form stable covalent bonds?

Back 62

carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur (CHNOS)

Front 63

which elements are very common in earths crust but are only present in trace amounts in cells?

Back 63

silicon, aluminum and iron

Front 64

there are 23 other elements found in living organisms which include which five ions that are essential in all species?

Back 64

calcium, potassium, sodium, magnesium and chloride (CPSMC)

Front 65

which way does molecular information flow

Back 65

DNA <-> RNA -> protein

which is replication, transcription and translation

Front 66

what obey the standard laws of physics and chemistry.

Back 66

Living things obey the standard laws of physics and chemistry. No vitalistic force is required to explain life at the molecular level

Front 67

biochemical reactions involve specific chemical bonds or parts of molecules called

Back 67

functional groups

Front 68

what kind of linkages are common in fatty acids and lipids

Back 68

ester and ether linkages

Front 69

what kind of linkages are found in proteins?

Back 69

amide

Front 70

what kind of linkages occur in nucleotides?

Back 70

phosphate ester and phosphoanhydride linkages

Front 71

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

Back 71

catalyzed by enzymes and thus proceed at very high rates

Front 72

biochemical reactions that occur in an organism is called

Back 72

in vivo

Front 73

biochemical reactions that occur under laboratory conditions is called

Back 73

in vitro

Front 74

many important macromolecules are

Back 74

polymers

Front 75

biological macromolecules are a form of polymer created by joining many smaller organic molecules, or monomers, via what reaction?

Back 75

condensation reaction (removal of the elements of water)

Front 76

the levels of organisation in increasing order are

Back 76

atoms,
molecules,
macromolecules
organelles,
cells
tissues,
organs and
whole organs

(ammoctow)

Front 77

amino acids contain

Back 77

an amino group and a carboxylate group as well as a side chain (R group)

Front 78

different amino acids contain different

Back 78

side chains

Front 79

how is a dipeptide produced

Back 79

when the amino group of one amino acid reacts with the carboxylate group of another to form a peptide bond

Front 80

biochemical molecules are what shape?

Back 80

three dimensional objects

Front 81

how many common amino acids are incorporated into proteins in all cells

Back 81

twenty

Front 82

the amino group of one amino acids and the carboxylate group of another are condensed during protein synthesis to form

Back 82

an amide linkage

Front 83

the bond between the carbon atoms of one amino acid residue and the nitrogen atom of the next residue is called

Back 83

a peptide bond

Front 84

can proteins function as enzymes?

Back 84

yes

Front 85

the function of a protein depends on

Back 85

its three dimensional structure or conformation

Front 86

cabohydrates or saccharides are composed mainly of

Back 86

carbon, oxygen and hydrogen

Front 87

all monosaccharides and all residues of polysaccharides contain

Back 87

several hydroxyl groups and are therefore polyalcahols

Front 88

the linear representation of a molecule is called a

Back 88

Fischer projection (after Emil Fischer)

Front 89

most biochemical molecules exist as a

Back 89

collection structures with different conformations

Front 90

a change from one conformation to antoher does not require the breaking of

Back 90

covalent bonds

Front 91

the two basic forms of carbohydrate structures, linear and ring forms, do require the breaking and forming of

Back 91

covalent bonds

Front 92

what is the most abundant biopolymer ono earth

Back 92

cellulose, because it is a major component of flowering plant stems including tree trunks

Front 93

what is the most abundant six carbon sugar

Back 93

glucose

it is the monomeric units of cellulose a structural polysaccharide joined by covalent bonds

Front 94

what bond is formed when one glucose molecule is joined to a C-4 hydroxyl group

Back 94

glycosidic bond

Front 95

nucleic acids are large macromolecules composed of monomers called

Back 95

nucleotides

Front 96

most of the energy required for life is supplied by

Back 96

light from the sun

Front 97

the rate of a chemical reaction depends on the

Back 97

concentration of the reactants

the higher the concentration the faster the reaction

Front 98

almost all biochemical reactions are reversible. when the forward and reverse reactions are equal, the reaction is t

Back 98

equilibrium

Front 99

the gibbs free energy change (delta G) is the

Back 99

difference between the free energy of the products of a reaction and that of the reactants (substrates)

Front 100

what is the formular for the gibs free energy change

Back 100

delta G = delta H -T delta S

Front 101

what is the formula for gibbs free energy change for a reaction (products and reactants)

Back 101

Delta G (reaction) = Delta G (products) - Delta G (reactants)

Front 102

the standard gibbs free energy change tells us the

Back 102

-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

Front 103

the rate of reaction is not determined by the

Back 103

Gibbs free energy change

Front 104

if in a reaction, the activation energies (barrier) is high, the reaction will proceed

Back 104

very slowly

If activation energies are low however, reaction will proceed quickly

Front 105

what are the two main groups of prokaryotes

Back 105

the Eubacteria and Archaea

Front 106

what is the basic unit for life?

Back 106

the cell

Front 107

what are usually single celled organisms?

Back 107

prokaryotes

Front 108

what accounts for most of the biomass on earth?

Back 108

prokaryotes

Front 109

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

Back 109

prokaryotes

Front 110

what does eukaryotes include?

Back 110

plants, animals, fungi and protist (which make the Eubacteria and archaea kingdoms)

Front 111

what kind of cell is surrounded by a single plasma membrane unlike bacteria which have a double membrane?

Back 111

Eukaryotic cells

Front 112

the most obvious feature that distinguishes eukaryotes from prokaryotes is

Back 112

the presence of a membrane bound nucleus in eukaryotes

Front 113

what cell is larger, a euk or pro?

Back 113

a eukaryotic cell is 1000 times larger than a prokaryotic cell

Front 114

what is the difference between plant and animal cells?

Back 114

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

Front 115

what is the difference between eukaryotic DNA and protylitic DNA?

Back 115

-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

Front 116

can eukaryotes undergo mitosis and meiosis?

Back 116

yes

Front 117

eukaryotic cells have what kind of endoplasmic reticulum

Back 117

rough ER and smooth ER

Front 118

what kind of cells contain both mitochondria and chloroplasts?

Back 118

photosynthetic plant cells

Front 119

in chloroplasts the energy captured from light is used to

Back 119

drive the formation of carbohydrates from carbon dioxide and water

Front 120

where are mitochondria derived?

Back 120

proteobacteria

Front 121

where are chloroplasts descended from

Back 121

cynobacteria

Front 122

what cells contain lysosomes?

Back 122

eukaryotic cells

Front 123

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?

Back 123

Oxidation

Front 124

what is the definition for a substance that accepts electrons in an oxidation-reduction reaction and thereby becomes reduced?

Back 124

oxidizing agent

Front 125

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?

Back 125

reduction

Front 126

what is the definition of a substance that loses electrons in an oxidation-reduction reaction and thereby becomes oxidized

Back 126

reducing agent

Front 127

what is the definition of an optical (chiral) isomer?

Back 127

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".

Front 128

what is a chiral carbon?

Back 128

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

Front 129

what type of chemical bond is a type of chemical bonding that involves the electrostatic attraction between oppositely charged ions

Back 129

Ionic bond

Front 130

what type of bond is a chemical bond that involves the sharing of electron pairs between atoms.

Back 130

covalent bond

Front 131

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)

Back 131

hydrogen bond

Front 132

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

Back 132

Van der Waal interactions

Front 133

what has a high melting point, boiling point and heat of vaporisation?

Back 133

water

Front 134

water can form what bond?

Back 134

Hydrogen (H) bond (90% electrostatic)
and covalent bond (10%)

Front 135

what bond forms the highest percentage in water? H bond or covalent bond?

Back 135

H bond at 90%

Front 136

when are H bonds weak, when are they strong?

Back 136

H bonds on their own are weak, but in a group are strong

Front 137

what allow water to be pulled up inner water pipes from roots to leaves?

Back 137

H bonds

Front 138

water surface tension is due to

Back 138

H bonding

Front 139

what are the phases of water?

Back 139

there are three phases of water, Gas, liquid and solid

Front 140

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

Back 140

Gas phase

Front 141

when water is in liquid phase, what happens to H bonds?

Back 141

H bonds broken and reformed in a continuous motion

Front 142

water molecules can form up to how many bonds?

Back 142

4

Front 143

solid is less dense than

Back 143

water

Front 144

why does ice float on water?

Back 144

because solid ice is less dense than water

Front 145

when is waters density greatest?

Back 145

4 degrees celsius

when molecules are lowest in kinetic energy, the H bonds keep molecules apart, hence why their is a lower density

Front 146

water can dissolve ionically bonded

Back 146

salts (eg. NaCl)

Front 147

what kind of biological molecules can be dissolved in water?

Back 147

proteins with charges and polar groups

Front 148

what compounds cannot be dissolved in water?

Back 148

Hydrophilic, Hydrophobic and Amphipathic compounds

Front 149

what compounds can easily dissolve in water?

Back 149

Hydrophilic compounds

Front 150

what compounds cannot be easily dissolved in water and dissolve in non polar solvents?

Back 150

hydrophobic compounds

Front 151

what kind of compounds has polar and non polar regions, with the polar regions associated with water and the non polar regions associated together?

Back 151

Amphipathic compounds

Front 152

does an ordered H2O molecules have an increase or decrease in entropy (delta S)

Back 152

decrease in entropy

Front 153

during dispersion of lipids in H2O, what happens and what effect does this have on entropy (Delta S)?

Back 153

each lipid molecule forces the surrounding H2O molecules to become highly ordered, therefore this represents a great decrease in entropy

Front 154

what happens in clusters of lipid molecules and what effect does this have on entropy?

Back 154

only the lipid portions at the edge of the cluster force the ordering of water. fewer water molecules are ordered, and entropy increases

Front 155

what are hydrophobic groups sequestered from water, with an ordered minimised shell of water molecules with an increased entropy?

Back 155

micelles

Front 156

what chemical and structural properties explain why water has a high melting and boiling point?

Back 156

-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

Front 157

what are proton donors?

Back 157

acids

Front 158

what are proton acceptors?

Back 158

bases

Front 159

what completely dissociate in solution?

Back 159

strong acids and strong bases

Front 160

what does not completley dissociate in solution?

Back 160

weak acids, and weak bases

Front 161

weak bases react with water to form

Back 161

equilibrium

Front 162

1 mol of HCl + 0.5 mol NaOH.
-write the chemical equation
-how much HCl is left?
-how much NaCl is produced?

Back 162

GCl + NaOH --> NaCl + H2O

-0.5 HCl left over
- 0.5 mol NaCl produced

Front 163

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?

Back 163

CH3OOH + NaOH --> CH3COONa + H2O
-0.75 mol of CH3COOH left over
-0.25 mol of CH3COONa left over

Front 164

what are buffers?

Back 164

-compounds that keep the pH of a solution relatively constant
-weak acids/bases
-in solution dissociate to form equilibrium

Front 165

how do buffer maintain pH?

Back 165

-donating protons (H+) when [H+] drops
-absorbing protons when [H+] increases

Front 166

when do buffers work best?

Back 166

-when [base] = [acid]
-when there is a high concentration of both species to absorb and donate protons (H+)
-when pH = pKa +- 1

Front 167

what is the buffering range of pKa - 6.86?

Back 167

5.86-7.86

Front 168

if the molar ratio acetate: acetic acid is 2:1 and the pKa = 4.76 then calculate the pH

Back 168

pH = pKa + log ([B]/[A])

therefore:

pH = 4.76 + log (2/1) = 5.06

Front 169

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

Back 169

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

Front 170

what is the ion product of water?

Back 170

H3O+ (also called H+)

Front 171

what is the pKb a measure of?

Back 171

the strength of a base and is defined by pKb = -logKb

Front 172

buffers are compounds that keep the pH of a solution

Back 172

relatively constant

Front 173

buffers are composed of

Back 173

weak acids or weak bases that dissociate in solution to form an equilibrium

Front 174

buffers maintain pH by

Back 174

-donating protons when [H+] decreases
-accepting protons when [H+] increases

Front 175

buffers work best when

Back 175

base = acid

Front 176

why do buffers work best when base =acid?

Back 176

because of the high concentration of both species is able to absorb and donate [H+]. this is the case when pH =pKa

Front 177

describe a water molecules

Back 177

-it is V shapes
-polar
-has a bond angle of 104.5 degrees

Front 178

what is more electronegative in water, oxygen or hydrogen?

Back 178

oxygen, as they have more lone pair electrons that attract electrons

Front 179

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?

Back 179

polar moelcules

Front 180

when do hydrogen bonds form?

Back 180

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

Front 181

how many hydrogen bonds can water form?

Back 181

four

Front 182

why does ice float?

Back 182

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

Front 183

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

Back 183

when water is in the form of ice

Front 184

why does the density of most substances increase upon freezing

Back 184

because molecular motion slows and tightly packs into crystal form

Front 185

when does the desnity of water increase?

Back 185

as it cools, until it reaches 4 degrees celcius

Front 186

what two properties of water are related to its hydrogen bonding characteristics

Back 186

-its specific heat
-its vaporation

Front 187

how is water an excellent solvent?

Back 187

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

Front 188

how do ionic and polar substances dissolve in water?

Back 188

-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

Front 189

why are electrolytes soluble in water?

Back 189

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

Front 190

what kind of substances are insoluble in water?

Back 190

non polar substances

Front 191

what kind of non polar substances are insoluble in water?

Back 191

Hydrocarbons and other nonpolar substances have very low solubility in water

Front 192

why do non polar substances not dissolve in water?

Back 192

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

Front 193

non polar substances are said to be

Back 193

hydrophobic

Front 194

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

Back 194

amphipathic

Front 195

detergents (amphipathic) molecules can form

Back 195

-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

Front 196

what are the four major noncovalent bonds or forces?

Back 196

-hydrogen bonds
-hydrophobic interactions
-charge-charge interactions
-van der waals forces

Front 197

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

Back 197

hydrogen bonds and hydrophobic interactions

Front 198

what kind of forces and interactions are variations of a more general type of forces called electrostatic interactions?

Back 198

charge charge interactions, hydrogen bonds and van der waals forces

Front 199

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

Back 199

charge-charge interactions

Front 200

what is an example of charge charge interactions in proteins

Back 200

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

Front 201

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?

Back 201

hydrogen bonds

Front 202

a hydrogen bond has many of the characteristics of a covalent bond but

Back 202

it is much weaker

Front 203

what kind of bonding between base pairs in double stranded DNA makes only a small contribution to the stability of DNA?

Back 203

Hydrogen bonding

Front 204

hydrogen bonds between and within biological molecules are easily disrupted by

Back 204

competition with water molecules

Front 205

what kind of weak force involves the interactions between permanent or transient dipoles of two molecules?

Back 205

Van der Waals forces

Front 206

when do van der waals forces occur?

Back 206

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

Front 207

what forces are dipolar or electrostatic

Back 207

van der waals forces

Front 208

the association of a relatively nonpolar molecule or group with other nonpolar molecules is termed a

Back 208

hydrophobic interaction

Front 209

water is

Back 209

nucleophilic

Front 210

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

Back 210

nucleophiles (nucleus lovers) because they seek positively charged species called electrophiles

Front 211

weak interactions are individually weka but the combined effect of a large number of weak interactions is a

Back 211

significant organizing force

Front 212

charge-charge interactions, hydrogen bonds and van der waals interaction are

Back 212

electrostatic interactions

Front 213

hydrophobic interactions depend on

Back 213

the increased entropy of the surrounding water molecules rather than on direct attraction between nonpolar groups

Front 214

the density of water varies with

Back 214

temperature

Front 215

one of the important propertoes opf water is its slight tendency to

Back 215

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

Front 216

hydronium (H30+) ions are capable of donating a proton to another ion. such proton donors are referred to as

Back 216

acids

Front 217

hydroxide (OH-) ions can accept a proton and be converted back into water molecules. Proton acceptors are called

Back 217

bases

Front 218

the product obtained by multiplying the proton and hydroxide ion concentration ([H+][OH-]) is called the

Back 218

ion product for water. this is a constant designated Kw where

Kw = [H+][OH-] + 1.0 x 10-^14 M^2

Front 219

what compounds only partially dissociate in water?

Back 219

weak acids and weak bases

Front 220

the chloride ion is the base that corresponds to HCl after it has given up[ its proton, Cl- is called the

Back 220

conjugate base of HCl

Front 221

H3O+ is the what of water?

Back 221

conjugate acid of H2O

Front 222

the contribution of water is implied in

Back 222

most acid/base dissociation reactions

Front 223

the pKa values are determined by

Back 223

titration

Front 224

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

Back 224

buffered

Front 225

the ability of a solution to resist changes in pH is known as its

Back 225

buffer capacity

Front 226

the water molecule has a permanent dipole because of

Back 226

the uneven distribution of charge in O-H bonds and their angled arrangement

Front 227

water molecules can form hydrogen bonds with each other. hydrogen bonding contributes to the

Back 227

high specific heat and heat of vapourization of water

Front 228

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

Back 228

hydrogen bonds with water molecules

Front 229

the major noncovalent interactions that determine the structure and function of biomolecules are

Back 229

electrostatic and hydrophobic interactions.

Electrostatic interactions include charge-charge interactions, hydrogen bonds and can der Waal forces

Front 230

under cellular conditions, macromolecules do not spontaneously

Back 230

hydrolyze. despite presence of high concentrations of water, specific enzymes catalyze their hydrolysis, and other enzymes catalyze their energy requiring biosynthesis

Front 231

the acidity or basicity of an aqueous solution depends on the

Back 231

concentration of H+

Front 232

buffered solutions resist changes in

Back 232

pH

in human blood, a constant pH of 7.4 is maintained by the carbon dioxide-carbonic acid-bicarbonate buffer system

Front 233

amino acids are

Back 233

chiral

Front 234

what kind of molecule are mirror images-enantiomers and cannot be superimposed on each other?

Back 234

chiral molecules

Front 235

only what kind of amino acids exist in nature?

Back 235

only L-amino acids

Front 236

what is the pKa of carboxyl group?

Back 236

2.3

Front 237

what is the pKA of amino group?

Back 237

9.6

Front 238

what is a zwitterion?

Back 238

a dipolar ion with both positive and negative charges

Front 239

what are two "small" non polar (hydrophobic) amino acids?

Back 239

Glycine and Alanine

Front 240

is Glycine Achiral or chiral?

Back 240

Achiral

Front 241

is Alanine chiral or achiral?

Back 241

chiral

Front 242

Leucine, Isoleucine and Valine are what sort of amino acids?

Back 242

nonpolar (hydrophiobic) amino acids

Front 243

which amino acids have a larger aliphatic side chain in their R group?

Back 243

Leucine, Isoleucine and Valine

Front 244

what does aliphatic relate to?

Back 244

relating to or donating organic compounds in which carbons atoms form open chains(as an alkanes, not aromatic rings)

Front 245

which amino acids are aliphatic?

Back 245

Glycine
there are 6
Alanine
Valine
Leucine
Isoleucine

Front 246

which amino acids are aromatic?

Back 246

there are 3
Phenylalanine
Tryosine
Tryptophan

Front 247

which amino acids have a sulphur containing group?

Back 247

Methionine and Cysteine

Front 248

which amino acids have an alcahole group?

Back 248

Serine and Threonine

Front 249

which amino acids are basic?

Back 249

Lysine and Arganine

Front 250

which amino acids are neutral?

Back 250

Histidine

Front 251

which amino acids are acidic?

Back 251

there are 4

Aspartate,
Glutamate
Aspargine
Glutamine

Front 252

which amino acids have a highly hydrophobic (polar) group?

Back 252

there are 4

Valine
Leucine
Isoleucine
Phenylalanine
Methionine

Front 253

which amino acids have a highly acidic group?

Back 253

there are seven:
Lysine,
Arginine
Histidine
Aspartate
Glutamate
Aspargine
Glutamine

Front 254

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?

Back 254

hydropathy

Front 255

which groups in amino acids are ionisable?

Back 255

Carboxyl and amino groups

Front 256

when pH < pKa

Back 256

groups are protonated
-e.g. NH4+
-acid

Front 257

when pH > pKa

Back 257

-groups are deprotonated
-e.g. COO-
-conjugate base

Front 258

when is a group proteated?

Back 258

when pH < pKa

Front 259

when is a group deprotonated?

Back 259

when pH > pKa

Front 260

what is an isoelectric point?

Back 260

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.

Front 261

what is the formula for calculating pI (Isoelectric point)?

Back 261

pI = 1/2 (pK1 + pK2)

Front 262

when you have an unknown amino acids how do you figure out the pKa to find the amino acid?

Back 262

-use a titration curve to figure out pKa and from the pKa you can identify the amino acid

Front 263

what joins amino acids together?

Back 263

a peptide bond

Front 264

how does a peptide bond join amino acids together?

Back 264

via a dehydration or condensation reaction, where the H2O is removed from the alpha carboxyl and alpha amino group

Front 265

what are peptides?

Back 265

amino acids joined together

Front 266

what are oligopeptides?

Back 266

a few amino acids jopined together

Front 267

what are polypeptides?

Back 267

lots of amino acids joined together

the word polypeptide is used interchangeably with protein

Front 268

what is residue?

Back 268

an amino acid in a peptide

Front 269

in the peptide order, the amino terminal or N terminal ends with

Back 269

free alpha-amino group

Front 270

in then peptide order the carboxyl terminal or C terminal end with

Back 270

free alpha-carboxyl group

Front 271

in what direction do amino acids flow in regards to amino terminal and carboxyl terminal?

Back 271

from the amino terminal to the carboxyl terminal

Front 272

where is the unuasual amino acid 4-hydroxyproline found?

Back 272

in collagen

Front 273

where is the unusual amino acid 5-hydroxylysine found?

Back 273

in plant cell walls

Front 274

what is the unusual amino acid found in myosin contractile protein?

Back 274

6-N-methyllysine

Front 275

on a molar basis, tryptophan absorbs more UV light than

Back 275

tyrosine

Front 276

what is the difference between phenylalanine and tyrosine structure

Back 276

the tyrosine has a OH group attached to its aromatic ring strucutre

Front 277

what is the dominant form of glycine?

Back 277

NH3+--CH2--COO-

Front 278

the formation of a peptide bond between two amino acdisd is an example of a

Back 278

condensation reaction

Front 279

Enzymes catalyze nearly all reactions that occur in

Back 279

living organisms

Front 280

many proteins function as enzymes, the biochemical

Back 280

catalysts

Front 281

the protein hemoglobin binds and transports

Back 281

oxygen and carbon dioxide in red blood cells

Front 282

several types of proteins such as tubulin, actin and collagen, provide

Back 282

support and shape to cells and hence to tissues and organisms

Front 283

assemblies of proteins can do mechanical work such as

Back 283

the movement of flagella,
the separation of chromosomes at mitosis, and
the contraction of muscles

Front 284

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

Back 284

binding to nucleic acids

Front 285

the functions of biochemical molecules can only be understood by

Back 285

knowing their structures

Front 286

there are many different kinds of proteins with many ifferent roles in

Back 286

metabolism and cell structure

Front 287

proteins on the cell surface can act as receptors for various

Back 287

ligands and as modifiers of cell-cell interaction

Front 288

some proteins have highly

Back 288

specialised functions

Front 289

all organisms use the same 20 amino acids as

Back 289

building blocks for the assembly of protein molecules

Front 290

the 20 amino acdids are called the

Back 290

common or standard amino acids

Front 291

a variety of different polypeptides can be produced by connecting the

Back 291

20 common amino acids in various combinations

Front 292

amino acids are called amino acids because

Back 292

they are amino derivatives of carboxylic acids

Front 293

in the 20 common amino acids the amino groups and carboxyl group are bonded to the same

Back 293

carbon atom alpha(a) carbon atom

Front 294

all of the standard amino acids found in proteins are

Back 294

alpha-amino acids

Front 295

two other substituents are bound to the alpha carbon,

Back 295

a hydrogen atoms and a side chain (R) that is distinctive for each amino acids

Front 296

inside a cell, under normal physiological conditions, the amino group is

Back 296

(NH3+) protonated because the pKa of this grouo is close to 9

Front 297

inside a cell under normal physiological conditions, the carboxyl group is

Back 297

(COO-) ionized, because the pKa of that group is below 3

Front 298

in the physiological pH range of 6.8 to 7.4 amino acids are

Back 298

zwitterions, or dipolar ions, even thought their net charge may be zero

Front 299

in 19 of the 20 amino acids the alpha-carbon is

Back 299

chiral, or asymmetric, since it has gour different groups bonded to it

Front 300

the exception of the 19 chiral amino acids is

Back 300

glycine, whose R group is simple a hydrogen atom

Front 301

why isn't glycine chiral?

Back 301

because the alpha-carbon atoms is bonded to two identical hydrogen atoms

Front 302

the 19 chiral isomers can exsit as

Back 302

stereoisomers

Front 303

stereoisomers are compounds that have

Back 303

the same molecular formula but differ in the arrangement or configuration of their atoms in space

Front 304

the two stereoisomers are distinct molecules that cant be easily converted from one form to the other since

Back 304

a change in configuration requires the brekaing of one or more bonds

Front 305

amino acid stereoisomers are nonsuperimposable mirror images called

Back 305

enantiomers

Front 306

which two of the 19 chiral amino acids, have two chiral carbon atoms each

Back 306

Isoleucine and
Threonine

(IT)

Front 307

which two amino acids can each form four different stereoisomers?

Back 307

Isoleucine and Threonine (IT)

Front 308

describe the location of the alpha-amino groups location on a L and D isomer

Back 308

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

Front 309

the 19 chiral amino acids used in the assembly of proteins are all of the

Back 309

L isomer configuration

although a few D amino acids occur in anture

Front 310

amino acids are assumed to be

Back 310

L-isomer configurations unless specifically designated D

Front 311

the fact that all living organisms use the same standard amino acids in protein synthesis is evidence that

Back 311

all species on earth are descende from a comon ancestor

Front 312

what is the one letter representation for the amino acids theonine?

Back 312

T

Front 313

what is the one letter representation for the amino acids tyrosine?

Back 313

Y

Front 314

what is the one letter representation for the amino acids tryptophan?

Back 314

W

Front 315

the side chains of amino acids fall into what 7 classes?

Back 315

-aliphatic
-aromatic
Sulfur containing
-alcohols
-positively charged
-negatively charged
-amides

(AAAPNA)

Front 316

of the 20 amino acids 5 are further classified as

Back 316

highly hydrophobic

(keyword: hive)

Front 317

of the 20 amino acids 7 are classified as

Back 317

highly hydrophilic

(keyword: heaven)

Front 318

what is the 3 letter and 1 letter code for Glycine?

Back 318

(Gly, G)

Front 319

which is the smallest amino acid?

Back 319

Glycine

because its R group is simply a H atom

the aplha carbon of glycine is not chiral

Front 320

how does glycine play a unique role in the structure of many proteins?

Back 320

because its side chain is small enough to fit into niches that canot accommodate ant other amino acid

Front 321

what is the 3 letter and 1 letter code for alanine?

Back 321

(Ala, A)

Front 322

what is the 3 letter and 1 letter code for Valine?

Back 322

(Val, V)

Front 323

what is the 3 letter and 1 letter code for Leucine?

Back 323

(Leu, L)

Front 324

what is the 3 letter and 1 letter code for the structural isomer of leucine, being Isoleucine?

Back 324

(Ile, I)

Front 325

which four amino acids and a structural isomer of leucine have saturated aliphatic side chains?

Back 325

Ala, A
Val, V
Leu, L
ILe, I

Front 326

both the alpha and beta carbon atoms of isoleucine are

Back 326

asymmetric

Front 327

Isoleucine has how many chiral centres and possible stereoisomers?

Back 327

it has two chiral centers, and has four possible stereoisomers

Front 328

Alanine, valine, leucine and isoleucine play an important role in

(AVLI)

Back 328

establishing and maintaining the three dimensional structures of proteins because of their tendency to cluster away from water

Front 329

which amino acids are known as the branched amino acids

Back 329

Valine, Leucine, and Isoleucine are known as the branched chain amino aids because their side chains of carbon atoms contain branches

(VLI)

Front 330

valine, luecine and isoleucine are highly

Back 330

hydrophobic

Front 331

What is the three letter and one letter code for Proline?

Back 331

Pro, P

Front 332

How does Proline differ from the other 19 amino acids?

Back 332

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

Front 333

the cyclic structure of proline makes it much less

Back 333

much less hydrophobic than valine, leucine and isoluecine?

Front 334

which three amino acids have side groups with aromatic groups?

Back 334

Phenylalanine (Phe, F)
Tyrosine (tyr, Y)
Tryptophan (Trp, W)
have side chains with aromatic groups

Front 335

Why are Tyrosine and tryptophan not as hydrophobic as phenylalanine?

Back 335

because their side chains include polar groups

Front 336

which three amino acids absorb UV light?

Back 336

all three aromatic amino acids Tyrosine, Tryptophan and Phenylalanine

Front 337

why do the three aromatic amino acids absorb Uv light?

Back 337

because unlike the saturated aliphatic amino acids, the aromatic amino acids contain delocalized pie-electrons

Front 338

at neutral pH both tryptophan and tyrosine absorb light at a wavelength of

Back 338

280 nm

Front 339

Phenylalanine is almost transparant at 280nm and absorbs light weakly at

Back 339

260nm

Front 340

which amino acids have sulfur containing R groups?

Back 340

Methionine (Met, M) and
Cysteine (Cys, C)

(MC)

Front 341

methionine contains a nonpolar methyl thioether group in its side chain and this makes it one of the more

Back 341

hydrophobic amino acids

Front 342

cystine is formed from two oxidized cysteine molecules linked by a

Back 342

disulfide bond

Front 343

which amino acids have side chains with alcohol groups?

Back 343

Serine (Ser, S) and Threonine (Thr, T)

Front 344

when oxidation links the sulfhydryl groups of two cysteine molecules, the resulting compound is a disulfide called

Back 344

cystine

Front 345

which amino acids have positively charged R groups?

Back 345

-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

Front 346

why is arginine the most basic of the 20 amino acids?

Back 346

because its side chain guanidinium ion is protonated under all conditions normally found within a cell.

Front 347

which amino acids have negatively charged R groups?

Back 347

-Aspartate (Asp, D) and Glutamate (Glu, E) are dicarboxylic amino acids have negatively charged hydrophilic side chains at pH7

Front 348

the relative hydrophobicity or hydrophlicity of each amino acid is called its

Back 348

hydropathy

Front 349

which compounds are derived from common amino acids?

Back 349

-Y-Aminobutyrate (GABA)
-Histamine
-Epinephrine (Adreneline)
-Thyroxine/Triiodothyronine

Front 350

the physical propertes of amino acids are influenced by the ionic states of the

Back 350

alpha-carboxyl and
alpha-amino groups and of any ionizable groups in the side chains

Front 351

for every acid-base pair the pKa is the pH at which the concentrations of the two forms are

Back 351

equal

Front 352

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

Back 352

donating a proton

Front 353

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

Back 353

proton acceptor

Front 354

the pKa of an ionizable group corresponds to a midpoint of its

Back 354

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)

Front 355

what bonds link amino acids in proteins?

Back 355

peptide bonds

Front 356

the linear sequence of amino acids in a polypeptide chain is called the

Back 356

primary structure of a protein

Front 357

the linkage formed between amino acids is an amide bond called a

Back 357

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

Front 358

linked amino acids in a polypeptide chain are called amino acid

Back 358

residues

Front 359

The oxygen atom of water is nucleophilic because

Back 359

it has two unshared pair of electrons.

Front 360

What is the maximum number of hydrogen bonds that one water molecule can have with neighboring water molecules?

Back 360

4

Front 361

Electrolytes dissolve readily in water because

Back 361

water molecules can cluster about cations and anions.

Front 362

A molecule or ion is said to be hydrated when it ________.

Back 362

is surrounded by water molecules

Front 363

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?

Back 363

electronegativity

Front 364

Attractions of oppositely charged functional groups of proteins are sometimes called ________.

Back 364

salt bridges or ion pairing

Front 365

Molecules that are both hydrophobic and hydrophilic are ________.

Back 365

amphipathic

Front 366

Which molecule or ion below is amphipathic?

Back 366

CH3(CH2)14COO-

Front 367

Which statement explains the cleaning action of soap on greasy dishes?

Back 367

CH3(CH2)14COO-

Front 368

A solution containing 10-8 M HCl and 10-8 M acetic acid contains H+ which is supplied mostly by

Back 368

water.

Front 369

The pH of a 10-4 M solution of HCl is

Back 369

4.

Front 370

Compare solution A with pH = 4 to solution B with pH = 6.

Back 370

The concentration of hydronium ion in solution A is 100 times that in solution B.

Front 371

The Henderson-Hasselbalch equation can be used to calculate

Back 371

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

Front 372

The ratio of the concentration of a ________ over ________ describes the proportions of forms of a weak acid necessary to satisfy the Henderson-Hasselbalch equation

Back 372

conjugate base; conjugate acid

proton acceptor; proton donor

Front 373

pKa values of phosphoric acid are 2.2, 7.2 and 12.7. A phosphate buffer of pH = 7.4 can be prepared using

Back 373

H2PO4- and HPO42-.

Front 374

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?

Back 374

250 ml acetic acid and 500 ml sodium acetate, then 250 ml water

Front 375

At the midpoint of a titration curve

Back 375

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

Front 376

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

Back 376

True

Front 377

The buffering capacity of a weak acid and its conjugate base is strongest when the pH = pKa.
true or false

Back 377

true

Front 378

what are the levels of protein structure?

Back 378

-primary
-secondary
-tertiary
-quaternary

Front 379

describe the primary structure of a protein

Back 379

its a sequence of amino acids

Front 380

describe a secondary structure protein

Back 380

an arrangement of nearby amino acids which include alpha-helices and beta pleated sheets

Front 381

describe a proteins tertiary structure

Back 381

its the overall folding of a protein

Front 382

describe the quaternary structure of a protein

Back 382

an arrangement of two or more polypeptides to form a functional protein

Front 383

proteins have a unique sequence specified by _________

Back 383

genes

Front 384

like letters in a sentence, ___________________ give proteins meaning

Back 384

amino acids

Front 385

what determines a proteins function (Catalytic for enzymes) and structure?

Back 385

amino acids

Front 386

alterations in an amino acid sequence can do what to a protein?

Back 386

drastically alter the function of the protein

Front 387

the amino acid sequence is specified by the

Back 387

DNA sequence in genes

Front 388

what prescribe the amino acid sequence of proteins?

Back 388

specific codons (combinations of DNA bases)

Front 389

when amino acids are joined together what bond is formed?

Back 389

a peptide bond

Front 390

a peptide bond is formed via

Back 390

dehydration or condensation reaction

Front 391

describe a dehydration or condensation reaction

Back 391

a H2O (water) molecule is removed from the alpha carboxyl (COO-) and alpha amino group (NH3+)

Front 392

peptide bonds are what kind of shape?

Back 392

planar

Front 393

what gives a peptide bond its character and restricts its rotation

Back 393

its partial double bond that forms its peptide bond

Front 394

peptide bonds are flexible yet

Back 394

conformationally restricted

Front 395

what are peptide bonds flexible yet restricted?

Back 395

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

Front 396

what allows the tight globular structure of a peptide bond?

Back 396

because a peptide bond is uncharged

Front 397

in a normal bond between C-N the Armostrong length is

Back 397

1.49

Front 398

in a "peptide" bond between C-N, the armstrong length is

Back 398

1.32 armstrongs

Front 399

in a normal double bond between C=N, the armstrong length is

Back 399

1.27 armstrongs ( the double bond character decreases the bond length when it is a peptide bond)

Front 400

peptide bonds can exsist in _______ or _______ configuration

Back 400

cis or trans

Front 401

in a Cis configuration, what side are the alpha carbons on?

Back 401

the same side

Front 402

in a Trans configuration what side are the alpha carbons on

Back 402

different sides

Front 403

which configuration is preferred, the cis or trans, why?

Back 403

the trans is preferred, because there are no steric clashes between the R groups attached to the alpha carbon

Front 404

Proline linkages are mostly in ________ form

Back 404

cis form

Front 405

since most proline linkages are in cis form, what does this do

Back 405

since the Nitrogen is bonded to the tetrahedral carbon, this limits steric clashes, and allows a U turn in the peptide bond

Front 406

what creates a stiff bond?

Back 406

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

Front 407

what do single bonds allow

Back 407

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

Front 408

what kind of rotation of a bond is between the Nitrogen (N) and the alpha-carbon?

Back 408

the Phi bond

Front 409

what kind of rotation of a bond is between the alpha-carbon and the carbonyl carbon?

Back 409

the Psi bond

Front 410

which bond has a anti clockwise negative angle of -80 degrees?

Back 410

the phi bond

Front 411

what bond has an positive clockwise angle of +85 degrees?

Back 411

the psi bond

Front 412

an anti clockwise negative bond is

Back 412

phi

Front 413

a clockwise positive angle is

Back 413

psi

Front 414

not all combinations of _____ and _____ are possible

Back 414

phi and psi

Front 415

why are not all combinations of phi and psi not possible

Back 415

because of steric hindrance;
Ramachandran plots recognise which combinations are possible

Front 416

on a Ramachandran plot, Antiparallel Beta sheets, Type II turn,Parallel Beta sheets and alpha helix (right handed) are:

Back 416

highly favoured

Front 417

on the Ramachandran plot, an alpha helix (left handed) and a 3^10 helix are

Back 417

favoured (not highly favoured)

Front 418

on a ramachandran plot, Type II turns (on their own) are

Back 418

unfavoured

Front 419

what is more highly favoured, an antiparallel beta sheet or a parallel beta sheet?

Back 419

they are both highly favoured, but the antiparallel beta sheet is more favoured

Front 420

on the ramachandran plot, what is the cause of it being unfavoured?

Back 420

steric hinderence

Front 421

what is a peptide bond?

Back 421

a bond between two amino acids

Front 422

why are peptide bonds planar?

Back 422

because of a partial double bond character

Front 423

what does the secondary protein structure, the alpha-helix appear like?

Back 423

it looks like a ribbon spiral

Front 424

describe the alpha helix found within the secondary structure of proteins, where is its R group and describe its backbone

Back 424

its R group extends outwards from the alpha helix

its peptide backbone forms a tightly coiled backbone

Front 425

what is the alpha helical structure stabilised by?

Back 425

hydrogen bonding

Front 426

in the secondary protein structure of the alpha helix, between which atoms or groups does hydrogen bond between?

Back 426

in the secondary structure of the alpha helics, Hydrogen bonding occurs between the N -H and CO of the backbone

Front 427

in the alpha helix, hydrogen is bonded to every ____________ amino acid giving _________ amino acids per turn

Back 427

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)

Front 428

the pitch (angle) of the alpha helix is _______nm

Back 428

5.4 nm

Front 429

in the alpha helix, protein have ________% alpha helix, the average length are ________ residues (range 4-40 residues)

Back 429

26%;
12 residues

Front 430

in the secondary alpha helix structure, a hydrogen is bonded to every

Back 430

4th amino acid

Front 431

most alpha helices are________________

Back 431

amphipathic

Front 432

why are most alpha helices amphipathic?

Back 432

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

Front 433

describe a left handed helices

Back 433

it moves in an anti clockwise direction (left) from the N terminus to the C terminus

Front 434

describe a right handed helices

Back 434

it moves in a clockwise direction (right) from the N terminus to the C terminus

Front 435

it is possible to have both _______ and ________ helices

Back 435

right and left

Front 436

which helicix is more energetically favourable, the right or left?

Back 436

the Right helices is more energetically favourable

Front 437

nearly all helices are _______ handed

Back 437

right handed

Front 438

what are four examples of secondary alpha helical proteins?

Back 438

-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')

Front 439

describe the type of helices of a-Keratin protein

Back 439

it has two right handed helices in its structure

Front 440

a-Keratin has _____ amino acids per turn instead of ____ amino acids per turn

Back 440

3.5 instead of 3.6

Front 441

in a-keratin, there are ____ amino acid repeats that allow ___________________

Back 441

in a-keratin , there are 7 amino acid repeats that allow cross linking

Front 442

in a-keratin, cross linking occurs via which forces?

Back 442

by three forces:
-Van der waals forces
-ionic interactions and
-disulfide bonds

Front 443

why does hair straighten and then recoil after a long while after straightening with heat or chemicals?

Back 443

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

Front 444

a primary helical structure has an arrangement of amino acids in

Back 444

in a straight line/row

Front 445

a secondary helical structure has an what kind of amino acid arrangement?

Back 445

a nearby arrangement of amino acids

Front 446

in relation to the a-helix, where are the side chains of the amino acids?

Back 446

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.

Front 447

besides the alpha helix being one of the secondary helical structures, what is the other one?

Back 447

Beta-pleated sheet

Front 448

in the beta strands, there how is the polypeptide chain arranged?

Back 448

it is an extended polypeptide chain

Front 449

what forms the Beta sheets? what is the arrangement?

Back 449

Beta strands in a side by side arrangement

Front 450

how many types of Beta strands are their?

Back 450

there are two types:
-Antiparallel ( run in opposite direction)
-parallel (run in same direction)

Front 451

in antiparallel beta sheets, Hydrogen bonding occurs between:

Back 451

"Adjacent" polypeptide chains which connect between both "Carbonyl O and Amide H"

(Key: antiparallel ACA)

Front 452

what causes Hydrogen bonding in the antiparallel Beta pleated sheets?

Back 452

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

Front 453

in parallel Beta sheets, which way do the helices run?

Back 453

the two helices run from the N terminus to the C terminus in the same direction (parallel)

Front 454

where does hydrogen bonding occur in a parallel beta sheet?

Back 454

Hydrogen bonding occurs between the +1 residue (a residue may be one amino acid in a polypeptide chain)

Front 455

in a beta pleated sheet, __________ peptide bonds meet each other at __________, creating a pleated _________________________________

Back 455

in B-pleated sheet, planar peptide bonds meet each other at angles, creating a pleated "accordion effect"

Front 456

what creates the accordion effect in beta pleated sheets?

Back 456

the planar peptide bonds in the polypeptide backbone that meet each other at angles via causative hydrogen bonding

Front 457

in a B-pleated sheet, where are the side chains located?

Back 457

above and below (steric hindrance dictates location)

Front 458

in the Ramachandran plot (R plot), what region does the Beta-pleated strands stand?

Back 458

in the highly favourable region

Front 459

why do Beta pleated sheets stand in the highly favourable region of R plot?

Back 459

because their R groups are above and below, with very little steric hindrance, so they can react favourable

Front 460

what is an example of a secondary helical Beta pleated sheet protein?

Back 460

Grass pollen protein

(Key: The grass pollen protein nicknamed "SBS", for secondary Beta sheet)

Front 461

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?

Back 461

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

Front 462

Beta-pleated sheets can be ___________, an example is the Grass pollen protein

Back 462

amphipathic

Front 463

how many strands can make a Beta sheet?

Back 463

usually 4 or 5, but can go up to 10 strands

Front 464

how are B-pleated sheets represented?

Back 464

by "arrows" that depict the "Orientation of the "Peptide"

Front 465

besides the Grass pollen protein being one example of a secondary Beta sheet structure, what are some more?

Back 465

-Fatty acid binding protein,
-silk Fibrion

Front 466

nearly all fatty acids binding proteins are_________________

Back 466

Beta-pleated

Front 467

silk fibroin, it has beta sheets in its polypeptide backbone and has tightly packed structure which is rich in

Back 467

ala (alanine) and gly (glycine)

Front 468

what is silk fibroin structure stabilized by?

Back 468

Hydrogen bonding in beta sheets

Front 469

silk fibroin has an extended Beta conformation therefore

Back 469

no stretch

Front 470

what kind of interactions/forces are in the silk fibroin beta sheets? what does it provide?

Back 470

Van der Waals interactions between sheets, which provides flexibility

Front 471

Reverse turns (B-turn or hairpin) are common in

Back 471

antiparallel Beta sheets

Front 472

how many degrees does a Reverse turn, turn?

Back 472

180 degrees

Front 473

in a Reverse turn, the CO group of residue 1 is H bonded to the

Back 473

NH group of residue 4

Front 474

hydrophilic residues are common where loops are on

Back 474

the outside

Front 475

loops that are the result of reverse turns are

Back 475

hydrophilic

Front 476

DNA binding protein is an example of _____________________________ and __ helices, where its helix-turn-helix loop is _____________

Back 476

reverse turns, and alpha helices, where its helix turn loop is hydrophilic

Front 477

a tertiary protein structure is known as the

Back 477

overal folding of a protein

Front 478

in a tertiary protein, the hydrophilic amino acids are on the

Back 478

outside

Front 479

in a tertiary protien, the hydrophobic amino acids are on the

Back 479

inside

Front 480

in a tertiary protein what groups are on the main chain in the middle of the the protein?

Back 480

CO and NH

Front 481

CO and NH of the main chain in the middle of the tertiary protein are involve in what kind of bonding?

Back 481

hydrogen bonding via alpha helices and Beta sheets

Front 482

how are tertiary proteins stabilised?

Back 482

via non covalent interactions such as:
-the hydrophobic effects (gets rid of water) and
-some disulfide bridges-extracellular proteins

Front 483

what is an example of a tertiary protein?

Back 483

Myoglobin (its stores oxygen in muscle)

Front 484

in myoglobin, what are the hydrophobic residues that are on the inside of the structure?

Back 484

-Leucine (Leu)
-Valine (Val)
-Methionine (Met)
-Phenylalanine (Phe)

Front 485

what are secondary motifs?

Back 485

combinations of alpha-helices and Beta-sheets

Front 486

what is an example of a secondary motif structure?

Back 486

a "Helix-loop-helix" found in Calcium binding and DNA binding proteins
and
Beta-sandwich (Beta sheets stacked on top of each other)

Front 487

membrane proteins are

Back 487

"hydrophobic" proteins on the outside in membrane spanning segments of the protein (note they are not hydrophilic even thought they on the outside)

Front 488

name a membrane protein?

Back 488

aqua porin protein

Front 489

describe the hydrophobic and hydrophilic locations of the protein

Back 489

-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

Front 490

what are the three levels of protein structure?

Back 490

-primary structure
-secondary structure
-tertiary structures
-quaternary structure

Front 491

what protein strcture has an arrangement of adjacent amino acids (Alpha and beta sheets)?

Back 491

secondary structure

Front 492

what protein structure has a sequence of amino acids?

Back 492

primary structure

Front 493

what protein structure has an overall protein folding?

Back 493

tertiary structure

Front 494

protein domains are

Back 494

seperate folded comact units joined by a polypeptide chain

Front 495

protein domains may serve what different functions?

Back 495

-fungal cellulases-
binding domain +
catalytic domain

Front 496

describe the evolutionary conservation of a proteins structure

Back 496

-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)

Front 497

an example of evolutionary conservation of proteins are the proteins

Back 497

-Lactate DH and Malate DH

Front 498

why are lactate DH and Malate DH good examples of evolutionary conservation proteins

Back 498

-they are similar structures, with 23% of their amino acid sequences identical, they descended from a common protein via gene duplication

Front 499

A Quaternary protein structure is the

Back 499

arrangement of different polypeptides to form a functional protein

(where you take 2 or 3 polypeptides and assemble it into a structure)

Front 500

what is an example of a quaternary structure protein?

Back 500

hemoglobin

Front 501

in haemoglobin, alpha and Beta subunits are arranged to form a

Back 501

functional protein

Front 502

protein denaturation is the loss of

Back 502

secondary and tertiary structures

Front 503

what are ways to denature proteins?

Back 503

-increase temperature
-chaotropic agents (Urea, Vinigar)
-Detergents-SDS

Front 504

how does temperature unfold and denature a protein? give an example

Back 504

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.

Front 505

how does Chaotropic agents such as Urea denature a protein?

Back 505

Urea is acidic such as vinegar and so water molecules get into (sulvates) the interior which disrupts the hydrophobic interactions in the protein

Front 506

how does detergent SDS denature a protein?

Back 506

the hydrophobic tails penetrate the interior and disrupt the hydrophobic interactions

Front 507

protein denaturing is a _________________ process

Back 507

protein denaturing is a cooperative process

Front 508

how is protein denaturing a cooperative process?

Back 508

-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

Front 509

what is the only things that determines the 3D structure of a protein?

Back 509

amino acids

Front 510

how did a scientist discover amino acid sequence alone determines the 3D structure of a protein

Back 510

-a scientist experimented and denatured Ribonuclease by 8Moles of Urea and mercaptoethanol which then after being denatured lost its shape and function

Front 511

how did the scientist that discovered that an amino acid alone determines protein structure, then show the refolding or Ribonuclease?

Back 511

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

Front 512

what does Levithals paradox state:

Back 512

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

Front 513

as proteins fold, only the correct folding is keps and the incorrect folding is

Back 513

not kept, this continues until the protein is folded properly

Front 514

what is the driving force of protein folding?

Back 514

a decrease in free energy (entropy)

Front 515

what are the three forces involved in protein folding?

Back 515

-hydrophobic effect
-Hydrogen bonding
-Van der Waal forces

Front 516

hydrophobic effect and how does it work in protein folding?

Back 516

hydrophobic parts collapse together to release water causing an increase in entropy

Front 517

hydrogen bonding and how does it work in protein folding?

Back 517

1st in alpha helices and Beta sheets, more stable in protein core, no water to compete with because of other force (hydrophobic effect)

Front 518

Wan der Waals forces and how they work in protein folding?

Back 518

the forces occur between "non polar" side chains

Front 519

what do molecular chaperone proteins assist?

Back 519

chaperone proteins assist in protein folding

Front 520

how do chaperones assist in protein folding?

Back 520

they bind newly made polypeptides ans assist in folding

Front 521

what is an example of a chaperone protein?

Back 521

the heat shock protein MW 70000 (HSP70)

Front 522

what does the heat shock protein (Chaperone) do?

Back 522

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

Front 523

heat shock proteins are present in all species except

Back 523

archaebacteria

Front 524

the chaperone protein (HSP60) is involved in

Back 524

protein folding and heat shock

Front 525

HSP60 chaperone has two protein

Back 525

rings/subunits (GroEL) with hydrophobic cavity

Front 526

what does each of the two subunits with hydrophobic cavity do in HSP60?

Back 526

they each bind to ATP and fold small to medium proteins

Front 527

how many amino aids can the two protein ring/subunits in the chaperone HSP60 accommodate?

Back 527

630 amino acids

Front 528

what does HSP60 do to incorrect folding of proteins?

Back 528

it inhibits it

Front 529

describe how the chaperonin (HSP60) folds a polypeptide

Back 529

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

Front 530

how many basic amino acids are their?

Back 530

there are around 3 main ones

Front 531

what are the three main basic amino acids?

Back 531

Lys, Arg and Tyr

Front 532

what is the pKa for Lysine (Lys)?

Back 532

10.8

Front 533

what is the pKa for Arganine (Arg)?

Back 533

12.5

Front 534

what is the pKa for Tyrosine (Tyr)?

Back 534

10.8

Front 535

what is the pKa for COO-?

Back 535

2.5

Front 536

what is the pKa for NH3?

Back 536

9.5

Front 537

what are the aliphatic amino acids?

Back 537

Gly, Ala, Val, Leu, Iso

Front 538

what are the aromatic amino acids?

Back 538

Phe, Tyr, Trp

Front 539

what are the sulphur containing amino acids?

Back 539

Met, Cys

Front 540

qwhat are the alcahol amino acids?

Back 540

Ser, Thr

Front 541

what are the two main basic amino acids?

Back 541

Lys and Arg

Front 542

what are the nuetral amino acids?

Back 542

His

Front 543

what are the acidic amino acids?

Back 543

Asp, Glu, Asn, Gln

Front 544

how many levels of protein structure are their?

Back 544

four

Front 545

what are the four levels of protein structure?

Back 545

-primary
-secondary
-tertiary
-quaternary

Front 546

a linear sequence of amino acid residues defines which structure?

Back 546

primary structure

Front 547

which structure consists of regions of regularly repeating conformations of the peptide chain such as alpha helices and beta sheets

Back 547

secondary stucture

Front 548

which structure describes the shape of the fully folded polypeptide chain, and has domains?

Back 548

teriary structure

Front 549

which structure refers to the arrangement f two or more polypeptide chains into a multi subunit molecule?

Back 549

quaternary structure

Front 550

which structure is maintained by hydrogen bonds between the amide hydrogens and carbonyl oxygens of the peptide backbone?

Back 550

secondary structure

Front 551

which structure has many folded polypeptides that consist of several distinct globular units linked by a short stretch of amino acid residues called domains

Back 551

tertiary structure

Front 552

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

Back 552

quaternary structure

Front 553

the amino acid sequence of polypeptides can be determined by

Back 553

by directly sequencing the protein or indirectly by sequencing the gene

Front 554

X-ray crystallographic analysis of small peptides reveal analysis of small peptides reveal that the bond between the carbonyl carbon and the nitrogen is

Back 554

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

Front 555

the planar peptide groups in a polypeptide chain have their peptide groups consisting of the

Back 555

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

Front 556

nearly all peptide gruops in prtoeins are in the

Back 556

trans conformation
which minimizes steric interference between adjacent side chains.

Front 557

the three dimensional conformation of a polypeptide backbone is defined by the

Back 557

phi and psi angles of roation around each peptide group

Front 558

the known frequencies of various amino acid residues in alpha helices are used to predict the

Back 558

secondary structure based on the primary sequence alone

Front 559

there are only thee different kins of common secndary structures

Back 559

-alpha helix,
-Beta strands and
-turns

Front 560

loops often contain

Back 560

hydrophilic residues and are usually found on the surfaces of proteins where they are exposed to solvent and form hydrogen bond with water

Front 561

loops containing only a few residues are referred to as________ if they cause an abrupt change in direction of a polypeptide chain

Back 561

turns

Front 562

the most common types of turns are called

Back 562

reverse turns, they are also called Beta turns

Front 563

describe how there are two common types of Beta turns designated type 1 and type 2?

Back 563

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

Front 564

which amino acid is the second residue in both type 1 and type 2 beta turns?

Back 564

proline

Front 565

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)

Back 565

glycine

Front 566

in folded proteins, alpha helices and Beta strands are commonly connceted by loops and turns to form supersecondary structures called

Back 566

common motifs

Front 567

what are the names of the 8 common motifs

Back 567

-helic loop helix
-coiled coil
-helix bundle
-Beta alpha Beta unit
-hairpin
-Beta meander
-Green key
-Beta sandwhich

Front 568

many proteins are composed of several discrete, indeendelny folden, compact units called

Back 568

domains

Front 569

domains may consist of combinations of

Back 569

motifs

Front 570

the size of a domain varies from

Back 570

as few as 25 to 30 amino acid residues to more than 300

Front 571

an example of a protein with multiple domains is

Back 571

pyruvate kinase from cat

Front 572

each domain is a distinct compact unit consisting of

Back 572

various elements of secondary structure

Front 573

domains are usually connected by loops but they are also bound to each other through

Back 573

weak interactions formed by the amino acid side chains on the surgace of each domain

Front 574

in general, domains consist of a contiguous

Back 574

stretch of amino acid residues

Front 575

what is the most important observations that has emerged from the study of proteins in past few decades?

Back 575

the evolutionary conservation of protein structure

Front 576

where is protein conservation seen most easily?

Back 576

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

Front 577

there are only three basic types of secondary structures but thousands of

Back 577

tertiary folds and domains

Front 578

many proteins exhibit an aditional level of organisation called

Back 578

quaternary strcture

Front 579

quaternary structure refers to the organization and arrangement of

Back 579

subunits in a protein with multiple subunits, each subunit is a separate polypeptide chain. A multisubunit protein is referred to as an oligomer

Front 580

the fact that a large proportion of proteins consist of multiple subunits is probably related to what several factors?

Back 580

-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

Front 581

the most occurring oligomeric state of a protein is a

Back 581

dimer

Front 582

the numbering convention for amino acid residues in a polypeptide starts at the

Back 582

N terminal end

Front 583

when a protein is treated with excess 2-mercaptoethanol, what reaction takes place?

Back 583

a disulfide exchange reaction occurs in which each cysteine residue is reduced to two cysteine residues and 2-mercaptoethanol is oxidized to a disulfide

Front 584

what will heatin a protein do?

Back 584

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

Front 585

proteins can be denatured by two types of chemicals, which are

Back 585

chaotropic agents and detergents

Front 586

high amounts of chaotropic agents such as urea and guanidinium salts, denature proteins by allowing

Back 586

water molecules to solvate nonpolar groups in the interior of proteins, the water molecules disrupt the hydrophobic interactions that normally stabilize the native conformation

Front 587

the hydrophobic tails of detergent such as sodium dodecyl sulfate, also denature proteins by

Back 587

penetrating the protein interior and distrucping hydrophobic interactions

Front 588

the native conformation of some proteins is stabilized by

Back 588

disulfide bonds

Front 589

the presence of disulfide bonds stabolozes proteins by

Back 589

making them less susceptible to unfolding and subsequent degradation when they are exposed to external environment

Front 590

complete denaturation of proteins containing disulfide bonds requires

Back 590

cleavage of these bonds in addition to disruption of hydrophobic interactions and hydrogen bonds

Front 591

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

Back 591

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

Front 592

which scientist discovered denaturation and renaturation of ribonuclease A?

Back 592

Christian B. Anfinsen

Front 593

most proteins fold spontaneously into a conformation with the

Back 593

lowest energy

Front 594

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

Back 594

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

Front 595

the overall increase in the entropy of the system of the ordered protein proved the major

Back 595

driving force for protein folding

Front 596

in the case of hydrophobic interactions, the change in entropy is mostly due to the

Back 596

release of ordered water molecules that shield hydrophobic groups

Front 597

protein folding is assisted by molecular

Back 597

chaperones

Front 598

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

Back 598

primary structure

Front 599

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

Back 599

molecular chaperones

Front 600

chaperones increase the rate of correct folding of some proteins by

Back 600

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

Front 601

there are many different chaperones, most of them are

Back 601

heat shock proteins

Front 602

heat shock proeinst are prtoeins that are synthesised in response to

Back 602

temperature increase (heat shock) or other changes that cause protein dnaturation in vivo

Front 603

the role of heat shock proteins (chaperones) is to

Back 603

repair damage caused by temperature increases by binding to denatured proteins and helping them to refold rapidly into their native conformation

Front 604

the major heat shiocjk protine is

Back 604

HSP70 (Mr=70000)

Front 605

HSP70 the major heat shock protein is present in all species except for some species of

Back 605

archaebacteria

Front 606

what is required for chaperonin function?

Back 606

the hydrolysis of several ATP molecules

Front 607

except for one, amino acids exist as what chiral isomer?

Back 607

L-isomer

Front 608

which amino acid is not chiral?

Back 608

Glycine

Front 609

name 3 hydrophobic amino acids?

Back 609

any three:
Valine, Leucine, Isoleucine, Phenylalanine, Methionine

Front 610

another name for dipolar molecules is

Back 610

zwitterions

Front 611

disulfide bonds are formed by pairs of which amino acid??

Back 611

cysteine

Front 612

when a peptide bond is formed, what molecule is also made

Back 612

water

Front 613

the amino acid residue disrupts the alpha helix because its side chain contains a unique ring structure that restrict bond rotations

Back 613

proline

Front 614

the amino acid asp is hydrophilic or hydrophobic?

Back 614

hydrophilic

Front 615

the amino acid Phe is hydrophilic or hydrophobic?

Back 615

hydrophobic

Front 616

the amino acid Lysine is hydrophilic or hydrophobic?

Back 616

hydrophilic

Front 617

the amino acid Gln is hydrophilic or hydrophobic?

Back 617

hydrophilic

Front 618

the delivery of O2 to the tissues requires

Back 618

-a circulatory system to carry O2 fluid to the tissue and the oxygen carrier increases the amount of dissolved O2

Front 619

what is the oxygen transport protein?

Back 619

haemoglobin

Front 620

haemoglobin transports O2 from the

Back 620

lungs to the tissues

Front 621

what is the oxygen storage protein?

Back 621

Myoglobin

Front 622

what does Myoglobins function

Back 622

it functions to reserve O2 in muscle

Front 623

what is the first protein to be sequenced from wale sperm, Myoglobin or haemaglobin?

Back 623

Myoglobin

Front 624

what kind of structure is myoglobin protein?

Back 624

-a secondary structure, and a globular protein

Front 625

what two main characteristics does myoglobin have?

Back 625

a haem- prosthetic group and
alpha helices

Front 626

what does the haem prosthetic group do in myoglobin?

Back 626

it binds to )2

Front 627

how many Alpha helices does myoglobin structure have?

Back 627

8

Front 628

what gives muscle and blood its red color?

Back 628

the heme group

Front 629

what does Haem group consist of?

Back 629

an organic compoenent called a protophorphyrin and
Fe (Iron) at the centre

Front 630

when oxygen is bound to the haem group. what is the charge of the Fe (Iron)?

Back 630

2+ charge (Ferrous state)

Front 631

Fe (Iron) bonded to 4 Nitrogen atoms can form another

Back 631

2 bonds

Front 632

what are the 5th and 6th co-ordination sites of Fe2+?

Back 632

below is the 5th Co-ordination site of Histidine (His-93) and
the above the 6th co-ordination site for O2 binding

Front 633

what happens to the Fe2+ atom when it binds to O2?

Back 633

upon binding the Fe2+ becomes smaller and moves in line with the plane of the molecule

Front 634

before the haem is bound to oxygen it is called

Back 634

deoxyhemoglobin

Front 635

after oxygen is bound to the Haem what is it called?

Back 635

oxyhemoglobin

Front 636

before Fe2+ is bound to oxygen, where does it lie on the plane of the molecule?

Back 636

Fe2+ lies below the plane

Front 637

what happens after Fe2+ is bound the oxygen, where does it move

Back 637

it moves upwards in line with the plane

Front 638

when O2 binds to the haem group, there is a partial electron transfer between

Back 638

Fe2+ and O2

Front 639

what is formed with Fe and O2 bond

Back 639

a complex between O2 (superoxide anion) and Fe3+

Front 640

why must oxygen leave after binding to O2?

Back 640

because O2 is a highly reactive free radical that can damage molecule and Fe3+ is unable to bind O2

Front 641

how does haem stabilize the O2 and Fe3+ complex?

Back 641

the Distal histidine stabilised the O2 complex and makes it less likely that O2 is released because of its new stability

Front 642

what kind of bond does histidine form when it binds to the O2 and Fe3+ complex?

Back 642

it forms a Hydrogen bond

Front 643

What is myoglobin composed of?
• Which part is responsible for binding oxygen?

Back 643

myoglobin consists of a secondary structure with 8 alpha helices,
the Fe iron in the haem group is responsible for binding to oxygen

Front 644

in myoglobin, what is the oxidation state of Fe at the centre of the protoporphyrin ring?

Back 644

Fe2+

Front 645

what two main features does a haemoglobin molecule contain?

Back 645

- 4 myoglobin like subunits
-2 alpha chains and 2 Beta chains (a total of 4 chains)

Front 646

in the haemoglobin molecule, where is the Beta 1 chain located?

Back 646

on the top right

Front 647

where is the Beta 2 chain lcoated

Back 647

top left

Front 648

where is the alpha 1 located

Back 648

bottom right

Front 649

where is the alpha 2 chain located

Back 649

bottom left

Front 650

what is evidence that Myoglobin and haemoglobin related?

Back 650

the alpha chains are 25% relatedness and
Beta chains are 24% relatededness

similarity in amino acid sequence

Front 651

how are myoglobion and haemoglobin proposed to be related?

Back 651

having evolved from the same ancestor and diverged through evolution

Front 652

how does haemoglobin form a tetramer?

Back 652

it has 2 alpha Beta dimers which form a tetramer

(this is where two secondary structures come together and form a quaternary structure)

Front 653

imagining the oxygen binding curve, out of haemoglobin and myoglobin, which requires alot more oxygen at p-50

Back 653

haemoglobin requires alot more oxygen at p-50 compared to myoglobin,

Front 654

who has a higher affinity for oxygen, haemoglobin of myoglobnin?

Back 654

haemoglobin has a lower affinity for O2 than the affinity of myoglobin

Front 655

what type of binding curve is myoglobin represented by?

Back 655

a simple binding curve

Front 656

what type of binding curve is haemoglobin represented by?

Back 656

a sigmoid curve (S shaped)

Front 657

what does the O2 binding curve for haemoglobin tell about its affinity for O2 compared to myoglobin?

Back 657

Haemoglobin has less affinity for O2 than myoglobin

Front 658

what partial pressure of O2 does haemoglobin require to bind?

Back 658

P50 = 26 torr (26mmHg)

Front 659

what partial pressure of )2 is required for the binding of myoglobin?

Back 659

P1/2 = 2 torr (2mmHg)

Front 660

what does the pressure difference mean for haemoglobin and myoglobin?

Back 660

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

Front 661

haemoglobin binds to O2 in what manner?

Back 661

in a co-operative manner

Front 662

what does haemoglobins co-operative binding/releasing manner mean?

Back 662

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

Front 663

what is the physiological significance of the Binding Curve for hemoglobin's "Sigmoid Curve"?

Back 663

the Sigmoid curve allows more O2 to be released at the tissues (as seen in the steep part of the curve)

Front 664

what is the pressure of O2 in the tissues?

Back 664

20 torr (20mmHg)

Front 665

what is the pressure of O2 in the lungs?

Back 665

100 Torr (100mmHg)

Front 666

what percent of partial pressure does Haemoglobin release when binding oxygen?

Back 666

66%

Front 667

what percent of partial pressure does myoglobin release in order to bind oxygen?

Back 667

7%

Front 668

Haemoglobins co-operative process allows it to

Back 668

deliver 10 times more Oxygen (O2) than myglobin

Front 669

haemoglobin delivers 1.7 times more oxygen than a

Back 669

noncoperative protein (a noncooperative protein releases 38% partial pressure to bind to O2)

Front 670

what protein is efficient at delivering Oxygen at rest and during exercise?

Back 670

haemoglobin

Front 671

imagining at oxygen binding curve, how is haemoglobin efficient at O2 delivery at rest and during exercise?

Back 671

haemoglobin delivers 45% more Oxygen during Exercise due to its Sigmoid curve being steeper from 40 to 20 too (mmHg)

Front 672

what does the steep curve from 40 to 20 Torr (mmHg) for haemoglobin tell about its ability?

Back 672

haemoglobin delivers 45% more oxygen during exercise than myoglobin

Front 673

what happens to the haemoglobin structure after it binds to oxygen?

Back 673

the binding of O2 on haemoglobin affects the structure of tetramer

Front 674

to what degree does deoxyhemoglobin twist when it becomes oxyhemoglobin?

Back 674

it twists 15 degrees to the right

Front 675

what does haemoglobin rotate by 15 degrees?

Back 675

it rotates its dimers (a1, B1 and a2, B2)

Front 676

when is a haemoglobin in a T (tense) state?

Back 676

when it is deoxyhemoglobin

Front 677

when is haemoglobin in a R (relaxed) state?

Back 677

when it is Oxyhemoglobin

Front 678

in which state does haemoglobin have a low affinity for O2?

Back 678

in its T state

Front 679

in which state does haemoglobin have a high affinity for O2 (more likely to bind O2)?

Back 679

in R state

Front 680

how are T and R states in equilibrium?

Back 680

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

Front 681

the sigmoid curve is a mixture of the

Back 681

R state and T state binding curves being in equilibrium

Front 682

how does the overall haemoglobin structure change during the binding of O2 at the haem group?

Back 682

-movement of Fe2+ move Histidine which moves the alpha helix and
-C terminal of alpha helix at junction of the 2 subunits also move

Front 683

which amino acids are charged?

Back 683

Charged:
• Arginine - Arg - R
• Lysine - Lys - K
• Aspartic acid - Asp - D
• Glutamic acid - Glu - E

Front 684

which amino acids are polar (Hydrophilic)?

Back 684

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

Front 685

which amino acids are non polar (Hydrophobic)?

Back 685

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

Front 686

the structure of a normal adult hemoglobin can be described as

Back 686

a tetramer composed of two alphaBeta dumers

Front 687

chemical cofactors that alter haemoglobin

Back 687

binding curves

Front 688

haemoglobins Relaxed and Tense states are in

Back 688

equilibrium

Front 689

what does the equilibrium lie towards, R or T state?

Back 689

R state

Front 690

in order for the T state to become stabilised it its shifts the equilibrium towards

Back 690

T state

Front 691

which state (R or T) forms less affinity for O2?

Back 691

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

Front 692

the presence of 2,3-BPG (2,3-Bisphoglycerate) dramatically

Back 692

decreases haemoglobins O2 affinity

Front 693

when the T state is unstable and the equilibrium lies to the R state side, what is needed to stabilise with the T state?

Back 693

2,3-BPG

Front 694

without 2,3-BPG, the R state would

Back 694

the R state would predominate and little O2 would be released

Front 695

where does 2,3-BPG bind on the haemoglobin molecule?

Back 695

2,3-BPG binds to a pocket between the dimers only in its T form

Front 696

what is the only form that 2,3-BPG can bind to the centre circle pocket in haemoglobin:

Back 696

in its T form (tense)

Front 697

when 2,3-BPG is bound to haemoglobins centre pocket, what happens when O2 binds?

Back 697

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

Front 698

2,3-BPG is an allosteric effector, what does this mean?

Back 698

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.

Front 699

how does 2,3-BPG have characteristics of an allosteric effector?

Back 699

-it is a different compound than O2 the normal binding molecule to haemoglobin
-it binds to the site distinct from O2

Front 700

llama's have low 2,3-DPG sensitivity, they have a mutation in their

Back 700

'B2 chain' where histidine becomes Asparagine

Front 701

why do llamas have low 2,3-BPG sensitivity?

Back 701

the histidine in their Beta chain becomes mutated to asparagine to increase the O2 capacity, to adapt in high climates and survival

Front 702

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?

Back 702

2,3-Bisphosphaoglycerate

Front 703

how does 2,3-Bisphosphoglycerate reduce the oxygen affinity of haemoglobin?

Back 703

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

Front 704

what does the Bohr effect, H+ and CO2 all do to the oxygen affinity of haemoglobin?

Back 704

they all decrease haemoglobins O2 binding affinity

Front 705

where is H+ and CO2 produced?

Back 705

at the tissues where O2 is needed most

Front 706

what does a decrease in O2 affinity help do?

Back 706

load off more O2 from haemoglobins binding sites

Front 707

explain the biochemical mechanisms which cause haemoglobin to reduce its oxygen affinity in the presence of CO2?

Back 707

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

Front 708

explain the biochemical mechanisms which cause haemoglobin to reduce its oxygen affinity in the presence of H+?

Back 708

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

Front 709

what is a salt bridge?

Back 709

also knwn as charge charge interactions, which is a noncovalent electrostatic interaction between two charged particles

Front 710

in deoxyhaemoglobin, Carboxyl group can form salt bridge with

Back 710

Lys 40

Front 711

Protonated his (histidine) can form a salt bridge with

Back 711

Asp 94

Front 712

what locks in the amino acid chain and staboloses T form?

Back 712

protonates histidine that forms a salt bridge with Asp (asparagine)94

Front 713

when the amino acid chain is locked in and the T state is stabilized, what does this do for O2?

Back 713

more O2 can be released

Front 714

at high pH (basic) Histidine is not

Back 714

protonated

Front 715

when Histidine is not protonated at high pH (basic) a salt bridge...

Back 715

cannot form

Front 716

when a salt bridge cannot form, a T state..

Back 716

cannot be locked in, and lower O2 binding affinity to release more O2

Front 717

in a salt bridge, positive histidine is attracted to

Back 717

negatrively charged Asp (asparagine)

Front 718

CO2 alone can decrease the

Back 718

O2 affinity of Hb

Front 719

with CO2 present, it can lower the pH to

Back 719

pH7.2 (40 Torr (40mmHg))

Front 720

how is carbamate formed?

Back 720

CO2 reacts with amino groups at the end of N terminus to form cabamate

Front 721

carbamate has a negative charge and so can participate in

Back 721

salt bridges

Front 722

when carbamate participates in salt bridges it can stabilise the T state to reduce

Back 722

haemoglobins oxygen binding affinity

Front 723

what is the bohr effect?

Back 723

the regulation of hemoglobin-binding by hydrogen ions and carbon dioxide

Front 724

what does CO2 do to the oxygen binding affinity of haemoglobin?

Back 724

decreases it

Front 725

in sickle cell anaemia haemoglobin forms

Back 725

fibers that distort the blood cell shape and clog capillaries and disrupt blood flow

Front 726

what happens in sickle cell anaemia when the abnormal blood cells are removed?

Back 726

the person becomes anaemic

Front 727

what causese sickle cell anaemia?

Back 727

a one amino acid mutation

Front 728

which amino acid and chain is mutated in haemoglobin that causes sickle cell anaemia?

Back 728

a mutation in the Beta (B) chain,
Glu 6 becomes Val 6

Front 729

what does the beta chain and amino acid (Glu 6 --> Val6) mutation in haemoglobin do to the molecule?

Back 729

it creates a hydrophoic patch on surface

Front 730

in sickle cell, what two molecules interact that causes the sickle cell shape?

Back 730

Val 6 interacts with Phe 85 and Val 88 on another Beta chain

Front 731

when Val 6 interacts with Phe 85 and Val 88 on another beta chain in haemoglobin, what does it caues?

Back 731

haemoglobin chains to form, which causes the sickle cell shape

Front 732

haemoglobin chains only form in

Back 732

deoxyhaemoglobin, not in oxyhaemoglobin

Front 733

why does sickle cell shape only occur in deoxyhaemoglobin and not oxyhaemoglobion

Back 733

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

Front 734

in malaria, which is more prone to survival of malaria?

Back 734

Heterozygotes survive more than homozygotes in malaria heterozygotes

Front 735

is heterozygote or homozygote malaria resistant?who is more prone to getting sickle cell?

Back 735

homozygotes

(heterozygote advantage)

Front 736

natural selection maintains how many phenotypes for heterozygotes?

Back 736

2 phenotypes

Front 737

sickle cell is a what sort of genetic disease

Back 737

recessive

Front 738

sickle cell anemia is caused by

Back 738

a substitution of a Val residue for a Glu residue at the B6 position

Front 739

the humoral immune system produces antibodies called

Back 739

Immunoglobins (Ig)

Front 740

immunoglobins bind to

Back 740

bacteria and viruses (targets them for distruction), Ig also bind to molecules called antigens

Front 741

immunoglobins (Ig) are produced by

Back 741

B lymphocytes or B cells which are produced in bone marrow

Front 742

what is a molecule that elicits an immune response?

Back 742

Antigen

Front 743

what is part of a molecule that binds to the antibody?

Back 743

Epitome

Front 744

the Cellular immune system includes

Back 744

T lymphocytes, that recognise cells infected with viruses and parasites

Front 745

Helper T cells produce

Back 745

signalling molecules

Front 746

how many chains do immunoglobulins have?

Back 746

4 chains

Front 747

describe the four chains of Immunoglobins (Ig)

Back 747

2 are light and 2 are heavy

Front 748

what is the MW of the 4 chains of an immunoglobin?

Back 748

150 KDa

Front 749

where is the light chains located?

Back 749

the top

Front 750

where is the heavy chains located

Back 750

the bottom

Front 751

in the heavy chains, how many constant regions are there, and how many variable regions?

Back 751

there are 3 constant and 1 variable

Front 752

what happens to the hinges that hold the four chains together in the immunoglobulin?

Back 752

the hinges can be cleaved with proteases producing two fragments

Front 753

what are the two fragments released once proteases cleave the immunoglobulins hinges?

Back 753

Fc-Crystallises fragment and
Fab - antigen binding fragment

Front 754

how many constant and how many variable regions are theire in a light chain?

Back 754

there is 1 constant and 1 variable

Front 755

why are all theoretical combinations of phi and psi not possible?

Back 755

because of steric hinderence

Front 756

what do Phi and psi represent?

Back 756

they represent rotation/angle of peptide bond (joins amino acid toegether)

Front 757

why cant a peptide bonmd roptate?

Back 757

steric hinderence, because the double bond character (limits rotation)

Front 758

when asked to identify a phi and psi bond, what are the only bonds that can rotate?

Back 758

single bonds

Front 759

how does carbon dioxide mainly travel in the blood?

Back 759

HCO3- (as the bicarbonate ion) it can also travel on carbomate, however that is only 20% of its travel preference

Front 760

when is the haemoglobin pocket hole open?

Back 760

in the T state when there is low oxygen binding affinity

Front 761

when is the pocket hole in haemoglobin closed?

Back 761

in the R state when oxygen affinity is high

Front 762

how is the T state represented on a Hb O2 binding curve?

Back 762

it is draw in a straight line underneath the main curve

Front 763

how is a R state represented on a O2 binding curve?

Back 763

it is above the initial curve, and has the same shape as the initial, it is not in a straight line

Front 764

when pH is 7.4 what does it change to when CO2 is produced in the blood?

Back 764

it changes to pH 7.2

Front 765

the reversible binding of oxygen is called

Back 765

oxygenation

Front 766

oxygen free myoglobin is called

Back 766

deoxymyoglobin

Front 767

oxygen bearing myoglobin molecule is called

Back 767

oxymyoglobin

Front 768

the two forms of hemoglobin are called

Back 768

-deoxyhemoglobin and
-oxyhaemoglobin

Front 769

some substituents of the heme prothetic group are

Back 769

hydrophobic

Front 770

what does the hydrophobic region of heme prosthetic group allow?

Back 770

allows prosthetic group to be partially buried in the hydrophobic interior of the myoglobin molecule

Front 771

what are the two polar residues located near the heme group?

Back 771

His-64 and
His-93

Front 772

his 93 is the

Back 772

proximal histidine

Front 773

His 64 is the

Back 773

distal histidine

Front 774

in oxymyoglobin, how many ligands are coordinated to the ferrous iron with the ligands in an octahedral geometry around the metal cation

Back 774

six

Front 775

describe the 6 ligands around Iron (Fe) in Hb

Back 775

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)

Front 776

in deoxymyoglobin, the iron is coordinated to how many ligands

Back 776

only 5 ligands because oxygen is not present

Front 777

the nonpolar side chains of Val 68 and Phe 43, contribute to the

Back 777

hydrophobicity of the oxygen binding pocket and help hold the heme group in place

Front 778

what blocks the entrance to the heme containing pocket in both oxymyoglobin and deoxymyoglobin?

Back 778

several side chains

Front 779

what must happen to allow oxygen to bind and dissociate in the blocked pocket of oxy and deoxy Hb

Back 779

must vibrate, breathe rapidly to allow O2 to bind

Front 780

the structure of myoglobin and hemoglobin prevents the permanent transfer of an

Back 780

electron or irreversible oxidation and thereby ensuring the reversible binding of molecule oxygen for transport

Front 781

the ferrous iron atom of heme in hemoglobin is partially oxidized when

Back 781

O2 is bound

Front 782

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

Back 782

Fe+3 --O2- (a superoxide anion attached to ferric iron)

Front 783

the globin crevice prevents

Back 783

complete electron transfer and enforces return of the electron to the iron atom when OP2 dissociates

Front 784

oxygen binds reversible to

Back 784

myoglobin and hemoglobin

Front 785

the extent of O2 binding at equilibrium depends on the

Back 785

concentration of the protein and the concetration of oxygen

Front 786

the oxygen binding curve of myoglobin is hyperbolic indicating that there is a

Back 786

single equilibrium constant for the binding of O2 to the macromolecule

Front 787

the O2 binding curve depicts the relationship between oxygen concentrations and binding to hemoglobin is

Back 787

sigmoidal

Front 788

signoidal (S shaped) binding curves indicate that

Back 788

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)

Front 789

the shape of the S curve indicates that the oxygen binding sites of hemoglobin interact such that the

Back 789

binding of one molecule of oxygen to one heme group facilitates the binding of oxygen molecules to other hemes

Front 790

the oxygen affinity of hemoglobin increases as each oxygen molecule is bound, this interactive binding phenomenon is termed

Back 790

positive cooperativity of binding

Front 791

the partial pressure of half saturation (P50) is a measure of

Back 791

the affinity of the protein for O2.

Front 792

A low P50 indicates a

Back 792

high affinity for oxygen since the protein is half saturated with oxygen at a low oxygen concetration

Front 793

a high p50 indiactes a

Back 793

low affinity

Front 794

myoglobin molecules are half saturated at a pO2 of 2.8 torr

Back 794

the p50 of hemogloin is much higher at (26 torr) reflecting its lower affinity for oxygen

Front 795

the heme prosthetic groups of myoglobin and hemoglobin are identical but the affinities of these groups for oxygen differ because

Back 795

the microenvironments provided by the proteins are slighly different

Front 796

the cooperative binding of oxygen by hemoglobin can be related to changes in the protein conformation that occur on

Back 796

oxygenation

Front 797

deoxyhemoglobin is stabilized by

Back 797

several intra-and intersubunit ion pairs

Front 798

which amino acid has the one letter key word G

Back 798

Glycine

Front 799

which amino acid has the one letter key word A

Back 799

Alanine

Front 800

which amino acid has the one letter key word V

Back 800

Valine

Front 801

which amino acid has the one letter key word L

Back 801

Leucine

Front 802

which amino acid has the one letter key word I

Back 802

Isoleucine

Front 803

which amino acid has the one letter key word F

Back 803

Phenylalanine

Front 804

which amino acid has the one letter key word Y

Back 804

Tyrosine

Front 805

which amino acid has the one letter key word W

Back 805

Tryptophan

Front 806

which amino acid has the one letter key word M

Back 806

Methionine

Front 807

which amino acid has the one letter key word C

Back 807

Cysteine

Front 808

which amino acid has the one letter key word

Back 808

Serine

Front 809

which amino acid has the one letter key word T

Back 809

Threonine

Front 810

which amino acid has the one letter key word K

Back 810

lysine

Front 811

which amino acid has the one letter key word R

Back 811

Arginine

Front 812

which amino acid has the one letter key word H

Back 812

Histidine

Front 813

which amino acid has the one letter key word P

Back 813

Proline

Front 814

which amino acid has the one letter key word D

Back 814

Aspartate

Front 815

which amino acid has the one letter key word E

Back 815

Glutamate

Front 816

which amino acid has the one letter key word N

Back 816

Asparagine

Front 817

which amino acid has the one letter key word Q

Back 817

Glutamine

Front 818

name the hydrophobic amino acids

Back 818

G
A
V
L
I
F
Y
M
P

Front 819

name the hydrophilic amino acids

Back 819

W
C
S
T
K
R
H
D
E
N
Q

Front 820

name the aliphatic amino acids

Back 820

G
A
V
L
I

Front 821

name the aromatic amino acids

Back 821

F
Y
W

Front 822

name the sulphur containing amino acids

Back 822

M
C

Front 823

name the alcahole amino acids

Back 823

S
T

Front 824

name the basic amino acids

Back 824

K
R

Front 825

name the neutral amino acids

Back 825

H
P

Front 826

name the acidic amino acids

Back 826

D
E
N
Q

Front 827

which amino acids have a pKa value of 2.4 for their Carboxyl group?

Back 827

Glycine
Alanine

Front 828

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

Back 828

False

Front 829

Amino acids are neutral at the isoelectric pH.
Question 2 options:
True
False

Back 829

True

Front 830

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.

Back 830

is an amino derivative of a carboxylic acid.

Front 831

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.

Back 831

L amino acids.

Front 832

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

Back 832

at physiological pH, pH = 7.4

Front 833

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

Back 833

All of the above

Front 834

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

Back 834

All of the above

Front 835

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.

Back 835

the nitrogen of the amino group is in a ring.

Front 836

Which structure below is appropriate for glycine at neutral pH?
Question 9 options:

+H3NCH2COO-

H2NCH2COO-

H2NCH2COOH

+H3NCH2COOH

Back 836

+H3NCH2COO-

Front 837

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.

Back 837

1000:1

Front 838

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.

Back 838

pH = pKa.

Front 839

For the amino acid lysine, the Henderson-Hasselbalch equation can be applied to ________ ionization group(s).
Question 12 options:

one

three

four

two

Back 839

three (because it has three ionizable groups)

Front 840

All 20 common amino acids have an amino group and a carboxyl group bonded to the same carbon atom.
Question 13 options:
True
False

Back 840

True

Front 841

All 20 common amino acids exist in nature equally as both the D and L stereoisomers.
Question 14 options:
True
False

Back 841

False

Front 842

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

Back 842

True

Front 843

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.

Back 843

cysteine and methionine.

Front 844

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

Back 844

positive; negative

Front 845

An amino acid named for a plant from which it was first isolated is
Question 18 options:

methionine.

threonine.

proline.

asparagine.

Back 845

asparagine.

Front 846

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.

Back 846

hydrophobic.

Front 847

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.

Back 847

0

Front 848

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.

Back 848

neutral (uncharged).

Front 849

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

Back 849

Histidine

Front 850

The ________ is the single shape a protein adopts under physiological conditions.
Question 1 options:

primary structure

most stable enantiomer

native conformation

minimal configuration

Back 850

native conformation

Front 851

To what level of structure do α-helices belong?
Question 2 options:

primary

secondary

quaternary

tertiary

Back 851

secondary

Front 852

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.

Back 852

The active protein involves the association of two or more polypeptide chains.

Front 853

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.

Back 853

The peptide bond is longer than the typical carbon-nitrogen bond.

Front 854

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

Back 854

motifs

Front 855

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.

Back 855

They extend radially outward from the helix axis.

Front 856

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

Back 856

steric hindrance

Front 857

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.

Back 857

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

Front 858

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

Back 858

Proteins refold when the amino acid sequence is the same as in the native conformation

Front 859

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

Back 859

other proteins.

Front 860

All proteins possess primary, secondary, tertiary and quaternary structure.
Question 12 options:
True
False

Back 860

False

Front 861

β-strands are a type of secondary structure.
Question 13 options:
True
False

Back 861

True

Front 862

Proline exists in the cis configuration more frequently than any other amino acid.
Question 14 options:
True
False

Back 862

True

Front 863

In oligomeric proteins all the subunits are always identical.
Question 15 options:
True
False

Back 863

False

Front 864

Chaperones are proteins which prevent incorrect folding of proteins as well as preventing some proteins from aggregating.
Question 16 options:
True
False

Back 864

True

Front 865

The principle forces holding subunits of an oligomeric protein to each other are ________.
Question 1 options:

covalent bonds

disulfide bonds

peptide bonds

hydrophobic interactions

Back 865

hydrophobic interactions

Front 866

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

Back 866

A or B only

Front 867

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

Back 867

the folding of the polypeptide chain.

Front 868

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

Back 868

different binding affinities for oxygen

Front 869

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.

Back 869

is induced by oxygenation.

Front 870

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.

Back 870

When oxygen binds to heme, the iron ion is oxidized from Fe2+ to Fe3+.

Front 871

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

Back 871

All of the above

Front 872

Antibodies bind antigens at
Question 8 options:

light chains.

heavy chains.

glycoprotein regions.

hypervariable regions.

All of the above

Back 872

hypervariable regions.

Front 873

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.

Back 873

they bind very specifically to antigens.

Front 874

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

Back 874

False

Front 875

Myoglobin has a greater affinity for oxygen than hemoglobin.
Question 11 options:
True
False

Back 875

True

Front 876

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

Back 876

True

Front 877

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

Back 877

False

Front 878

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

Back 878

True