Option B: Biochemistry Flashcards
paper 3
why does a change in the pH affect the active site of the enzyme
changes in pH affect the equilibrium of ionization reactions of some R group chains of amino acids in the enzyme structure. For example, at low pH some R groups may gain protons and at high pH some R groups may lose protons. Changes in the ionic charges of the R groups alters the attractive forces that stabilize the molecule and hence alter its tertiary shape and ability to bind to substrates
mechanism of enzyme activity
R groups of active site of the enzyme bind with the substrate which places a strain on the molecule, breaking the substrate apart and forming a new molecule which no is no longer complementary to the active site and no longer fits
why are amino acids in the zwitterion form
they undergo an internal transfer of H+ to make the amino acid more ionically stable
buffer
a solution that is able to resist changes in pH when small amounts of acids or bases are added to it
how does an amino acid act as a buffer when H+ ions are added to it
H+ + A- –> HA
NH3+CH2COO- + H+ –> NH3+CH2COOH
how does an amino acid act as a buffer when OH- ions are added to it
HA + OH- –> H2O + A-
NH3+CH2COOH + OH- –> NH3+CH2COO- + H2O
Vmax
maximum rate of reaction (units of rate moldm^-3s^-1) and changes with temperature (i.e. maximum frequency of successful collisions between active sites and substrates)
Km
substrate concentration @ 1/2 the maximum rate
what is the significance of Km
suggests the affinity of a substrate for the active site of the enzyme, there is an inverse relationship between Km and enzyme affinity. Low Km means a higher affinity of enzyme for the substrate, and a higher affinity suggests a lower affinity of enzyme for the substrate
allosteric site
the site on the enzyme that a non-competitive inhibitor binds to, changing the shape of the active site
what happens to Km and Vmax in non-competitive inhibition and competitive inhibition versus normally
For competitive inhibition: Vmax stays the same, but Km value increases
For noncompetitive inhibition: Vmax is decreased, but the Km value is the same
when is an amino acid in its anionic form
when it is placed in a solution with a pH higher than its isoelectric point (i.e. more basic)
when is an amino acid in its cationic form
when it is placed in a solution with a pH lower than its isoelectric point (i.e. more acidic)
what occurs to enzymes at low temperatures
deactivation NOT denaturation
how do heavy metal ions interfere with enzyme activity
metals like lead, mercury, and silver are poisonous and react with sulfhydryl (-SH) groups in the R groups of cysteine residues in the protein, forming a covalent bond with the sulfur and displacing the hydrogen. This disrupts the folding of the protein (i.e. tertiary structure), and acts as a form of non-competitive inhibition, the amino acid can no longer form disulfide bridges
what are the two ways of determining the concentration of a protein solution after using protein assays
- calibration curve (using known concentrations of proteins)
- beer-lambert law - relates amount of light asborbed with concentration and path length
i.e. A = ϵcl
where
A = Io/I (intensity of light before and after passing through the sample i.e. absorbance
ϵ = molar absorptivity (nm)
c = concentration of solution (mol/dm^3)
l = path length (cm)
which nitrogenous bases are purines (2- ring)
adenine and guanine
which nitrogenous bases are pyrimidines (one-ring)
thymine, uracil, cytosine
why is DNA stable in aqueous solutions
sugar phosphate backbone is hydrophilic due to the polar sugars with lots of -OH groups and the negative charge of the phosphate group. there are also strong hydrophobic interactions between nitrogenous bases that are mainly nonpolar and add further stability
how many H bonds are there between C and G and A and T
AT is 2 H bonds
CG 2 H bonds
why do histone proteins have a positive charge
histone proteins contain many amino acids with R groups that are basic (have an NH2) and as such, at cellular pH (7-7.4), they are protonated and have a positive charge (cationic form)
why is a codon 3 bases long?
because it can produce 64 combinations for amino acids and there are 20, versus 2 bases which would only produce 16 amino acids, and 4 which would produce 256 combinations (a huge waste of energy)
describe how DNA determines the primary structure of a protein
A codon, composed of a triplet of bases, corresponds to a specific amino acid
explain how the double-helical structure of DNA is stabilized once formed
the sugar phosphate backbone is negatively charged and faces the exterior (the aqueous solution) because it is hydrophilic. the nitrogenous bases face away from the aqueous surroundings because they are hydrophobic and are stabilized by the London forces with each other
what is the type of interaction between the DNA and histone protein
ionic
what is the type of interaction between water and DNA
hydrogen bonding
name the 7 lipid functions
- energy storage
- thermal insulation and protection of organs (adipose tissue)
- electrical insulation (myelination)
- steroid hormones
- structural components of cell membranes (e.g. phospholipids)
- transporters of lipid-soluble vitamins
- lowering of LDL and reducing risk of heart disease by consuming the right types of lipids
because lipids have a higher hydrogen to oxygen ratio compared to hydrogens…
they are less oxidized and have more potential for oxidation and can therefore produce more energy per gram (9cal/g vs 4cal/g), but because of their insolubility, the energy is not as readily available compared to carbohydrates
iodine number
mass of iodine in grams that reacts with 100g of fat
distinguish between HDL and LDL
HDL - smaller and lighter, higher proportion of protein, and carries cholesterol away from arteries
to the liver
LDL - carries cholesterol to arteries, lower proportion of protein
conjugation
a system of overlapping p-orbitals that delocalized electrons can move between
why is a molecule with extensive conjugation (i.e. 8 pi bonds or more) colored
if a molecule is conjugated, there is less of an energy difference between the lower and higher energy levels, and as such, longer wavelengths of light are absorbed (the wavelengths are within the visible light region of the EM spectrum) rather than UV
why would a molecule appear colorless
pi bonds absorb UV light, which causes an electron to be promoted from a lower energy level to a higher energy level. if the molecule is not conjugated enough (i.e. less than 8 pi bonds), then it will not absorb light in the lower energy UV region
what is the chromophore
the conjugated part of a molecule that is responsible for absorbing visible light
the longer a conjugated chain (delocalized system)…
the longer the wavelengths absorbed are (and lower energy)
why are porphyrins (biological pigment) colored
they have an extensive conjugated system of pi bonds
what are porphyrin rings also called and why
macrocyclic ligands; because they donate a lone pair of electrons to form a dative covalent bond with a central metal ion
how do you determine the coordination number of a chelate
number of coordinate (dative) bonds
what is a chelate complex composed of
macrocyclic ligand and central metal ion
why is chlorophyll highly unstable in acidic solutions (pH 3)
the Mg2+ (central metal ion) is displaced by 2 H+ at low pH, forming a brown complex
what do hemoglobin and myoglobin have in common
heme groups (which is a type of porphyrin ring)
what is the heme group composed of
porphyrin ring with Fe2+ at the center
function of hemoglobin vs myoglobin
myoglobin stores oxygen in the muscles and contains 1 heme group (one polypeptide chain so it is tertiary structure only), hemoglobin carries oxygen in the blood and contains 4 heme groups
describe the structure of hemoglobin
4 heme groups each group bound to a polypeptide chain, so the entire molecule is made up of 4 polypeptide chains (quaternary structure) and is a globular protein
how does oxygen bind to heme groups
O2 acts as a ligand and forms an additional dative covalent bond with the Fe2+ at the center, which changes the coordination number to 5
what does it mean when it is stated that the binding of oxygen to hemoglobin is cooperative
the ability to bind oxygen is increased by the initial binding of oxygen to a heme group which leads to a conformational change in the polypeptide, which has an allosteric effect on the other heme groups which makes it easier for subsequent oxygens to bind (shown by the sigmoidal shape).
what does the sigmoidal shape reveal about oxygen and hemoglobin affinity
at low ppO2, the hemoglobin has a low affinity for O2 and at higher ppO2 the hemoglobin has a high affinity for oxygen
how does temperature affect the oxygen saturation of hemoglobin
Hb + 4 (O2) <–> Hb-(O2)4 (delta H <0)
at lower temperatures, the forward reaction (exothermic) will be favored and the Hb affinity for O2 will increase
at higher temperatures, the reverse reaction (endothermic) will be favored and the Hb affinity for O2 will decrease
how does the pH affect the oxygen saturation of Hb
Hb affinity for O2 decreases because:
when pH is decreased: the H+ ions protonate the basic R groups of amino acids, which alters the ionic bonding that holds the tertiary structure together causing the protein shape to change, reducing the Hb affinity for O2.
Additionally, at very low pHs, the H+ can replace the Fe2+ central metal ion, preventing O2 from binding
how does carbon dioxide affect the oxygen saturation of Hb
has the same effect as a decrease in the pH because CO2 dissolves to form carbonic acid, which lowers the pH (i.e. oxygen saturation decreases)
how does carbon monoxide affect the oxygen saturation of Hb
CO acts as a competitive inhibitor (i.e. it is also a ligand) of oxygen binding because its Hb affinity is 200x that of oxygen, so it will bind to Hb more readily instead of O2. This effectively makes Hb unable to carry oxygen, which means cells cannot receive oxygen and therefore cannot respire and will soon die. Carbon monoxide binding forms a complex called carboxyhemoglobin which does not readily dissociate.
How is fetal hemoglobin different to adult hemoglobin (and how would its oxygen saturation curve compare)
fetal hemoglobin has a higher oxygen affinity because it must be able to bind oxygen in low ppO2 from the mother’s blood, and it is also less sensitive to inhibitors because of its high O2 affinity. the curve would be shifted left
what does the iron in the heme group of the cytochrome do
interconverts between +2 and +3 when it gets oxidized or reduced because it is a transition metal with variable oxidation states
what are cytochromes
redox-active protein containing a heme group and are classed as chelates; they are involved in the electron transport chain
what are carotenoids
lipid-soluble pigments that harvest light (accessory pigments) for photosynthesis
why are carotenoids lipid soluble
long non-polar hydrocarbon chain; hydrophobic and lipophilic (because lipids are also nonpolar)
why are carotenoids susceptible to oxidation
large number of C=C bonds, which is catalyzed by light; they can act as antioxidants because of their reactions with oxygen
what are anthocyanins
aromatic, water-soluble pigments widely distributed in plants; Their specific colour depends on metal ions and pH (so they can be used as indicators)
why are anthocyanins water soluble
they have several OH groups that can hydrogen bond with water
atom economy
gives indication of proportion of atoms in reactants that end up in the desired product. other compounds produced are considered waste and are disposed of. the higher the percentage atom economy, the greener
percentage atom economy formula
(total Mr of desired product/ total Mr of reactants) x100
green chemistry/sustainable chemistry aim
minimize the production and release to the environment of hazardous substances
xenobiotics
harmful substances found in an organism that are not normally there
why are most polymers non degradable
they are inert because they have lots of strong C-C bonds, makes them difficult to dispose of and they pile up in landfills
benefits and drawbacks to using starch as an alternative for plastics
biodegradable (degrades at same rate as nutrient food products), compostable which minimizes environmental damage, linkages can be hydrolyzed by other living organisms e.g. bacteria,
drawbacks: bad mechanical properties, land used for growing corn for bioplastics cannot be used for food production; anaerobic resp of bioplastics releases methane
biomagnification
increase in concentration of a substance in a food chain (i.e. increases going up the food chain)
when would biomagnification occur
if the substance cannot be metabolized or if it is insoluble and stored in lipid/fatty tissue
state two properties of DDT that explain why it is able to accumulate in fatty tissue
non-polar and dissolves and accumulates in lipids, it is not metabolized or excreted
host-guest chemistry
creation of synthetic host molecules that mimic some of the actions performed by enzymes in cells, by selectively binding to specific guest species, such as toxic materials in the environment (xenobiotics)
what kinds of interactions are formed between the host and guest in host guest chemistry
ionic bonds, hydrogen bonds, London forces, BUT NOT COVALENT BONDS!!!! THUS the interactions are weaker and the 3D structure is therefore only maintained temporarily
explain how enzymes can be used for bioremediation
Enzymes have been developed to help in the breakdown of oil spills and other industrial wastes.
Enzymes in biological detergents can improve energy efficiency by enabling effective cleaning at lower temperatures.
outline retinol’s (vitamin A) structure, solubility and function
long non polar hydrocarbon chain, therefore it is lipid soluble, its function is in the visual cycle in the eye particularly at low light intensities
outline vitamin D’s solubility and function
lipid soluble because it cannot form hydrogen bonds and is not soluble in water but instead has London forces, stimulates uptake of Ca2+ by cells so it is important for teeth and bone health
outline vitamin C’s solubility and function
water soluble because of its many OH groups, important in tissue regeneration
effect of heat on vitamins
C=O and OH groups are susceptible to oxidation and are easily oxidized and break down on heating, so it is important to obtain vitamin C through fresh foods
why should water soluble vitamins be consumed daily compared to fat soluble vitamins
water soluble vitamins are transported directly in the blood and filtered by the kidneys and excreted; lipid soluble vitamins are transported to fat stores
causes of vitamin deficiencies
geography, genetics (e.g. more melanin makes it harder to absorb vitamin D), income (e.g. access to vitamin C from fresh fruit), diet and lifestyle (e.g. malnourishment can cause vitamin A deficiency)
solutions to overcome vitamin deficiencies
solve poverty, education, food fortification (adding nutrients commonly missed in foods), genetic modification of food, providing food rations of vitamin rich foods
haworth projection vs fischer projection
cyclical projection is haworth
fischer is linear
what is the functional group of a glycosidic linkage
ether
how do ring structures make isomerism possible
rotation is restricted around carbon atoms in the ring
why is the extensive branching of glycogen important
it increases the surface area, which increases the frequency of collisions with water and enzymes, so there is more hydrolysis
explain how the structure of vitamin A is important to vision
vitamin A is oxidized to the aldehyde, cis-retinal; which has a highly conjugated delocalized pi bond system enabling it to absorb light in the visible region, the absorption of light converts the cis-retinal to 11-trans-retinal
which configurations are found in carbs versus proteins
L is found in proteins
D is found in carbohydrates
all proteins besides glycine are chiral and therefore have
enantiomers
ketose vs aldose
ketose is fructose because it has a ketone functional group
aldose is glucose because it has an aldehyde functional group
similarity and difference between host guest chemistry and porphyrin rings
similarity: large molecule interacting with an ion
difference: dative covalent bonds are formed between ligands and central metal ion, but there are only non-covalent interactions in host-guest chemistry
explain the initial shape of the oxygen dissociation curve at low ppO2 to 5kPa(middle of the graph)
binding of one O2 affects the active sites and binding of other Hb active sites, this leads to the cooperative binding effect in which there is enhanced binding of further O2 molecules
outline the action of non-competitive inhibitors on enzyme catalyzed reactions
bind to enzymes at an allosteric site, leading to a conformational change in the shape of the enzyme active site, lowers the Vmax, and does not compete for the active site
what does the reaction of a strong base with a triglyceride form
soluble products; the glycerol and 3x the salt of the fatty acid
explain why a molecule of C18H32O2 (linoleic acid) would be a more efficient energy storage than a molecule of C18H32O16 (raffinose)
linoleic acid has a lower proportion of oxygen and is less oxidized than raffinose AND its combustion is more exothermic
outline how the formation of 11-trans-retinal results in the generation of nerve signals to the brain
11-trans-retinal no longer fits into the rhodopsin protein and is ejected; this leads to a conformational change in rhodopsin and to opsin generating signals
explain why biodegradable polymers can be degraded naturally compared to a non-biodegradable polymer
the ester bonds that hold the biodegradable polymers together are susceptible to hydrolysis by living organisms and bacteria, because they are polar bonds they can also dissolve also in water. by contrast, non-biodegradable polymers contain long hydrocarbon chains which are nonpolar and do not biodegrade easily
benefits and concerns of using genetically modified products
benefits:
higher yield
can withstand extreme weather better (e.g. drought resistance)
resistance to pests and disease which reduces need for pesticides
can increase shelf life
increase concentration of vitamins
improve, taste, color size, nutritional value
concerns:
lack of information about longterm effects
changes to natural ecosystem through cross pollination
possible links to increased allergies
risk of altering natural composition of food
lack of information through food labelling
concerns of breeding species that are resistant to control
outline hydrolytic rancidity
- affects the ester group of saturated fatty acids
- broken down into glycerol and fatty acids
- conditions: low pH, lipases, high pH conditions, increased temperatures
outline oxidative rancidity
- occurs when oxygens are added across C=C bonds in unsaturated fatty acids
- fatty acids break down into some forms aldehydes, ketones and alcohols
- conditions: occurs via free radical mechanism, so is catalyzed by light and enzymes
products of hydrolysis of phospholipids in conc. acid
broken down into all of its components
products of hydrolysis of phospholipids in dilute acid and less heat
breaking of two ester linkages to form two fatty acid molecules and phosphodiester
