Option B: Biochemistry Flashcards
metabolism
sum of all chemical reactions in an organism (necessary to sustain life)
metabolic pathways
sequences and cycles that metabolic reactions go through
metabolites
compounds taking part in metabolism
anabolism
- metabolic reactions involved in building up (i.e. synthesis)
- requires energy to carry out
- reactants are small molecules (called precursors)
- products are large, complex molecules of higher energy
e.g. nucleotides –> nucleic acids, amino acids –> proteins, photosynthesis
catabolism
- metabolic reactions involved in breaking down
- releases energy
- reactants are larger molecules
- products are smaller and energy-poor
e.g. breakdown of glucose during cell respiration
biomolecules
all molecules present in a living organism
macromolecules
- compounds with relative molecular masses numbering in the thousands
e. g. polysaccharides, proteins, nucleic acids - they can be described by their constituents (monomers) which are covalently bonded
biopolymers
- biodegradable polymers
- produced by organisms
- substances bonded together with a covalent bond after a condensation reaction
concept of energy coupling
- energy obtained from catabolism is used to fuel anabolic reactions
- through the use of ATP (adenosine triphosphate) as the intermediary energy carrier
concept of futile cycles
- the metabolic pathways for anabolism and catabolism of a specific substance differ from each other and also involve different enzymes
- if they were the same, futile cycles would occur
- i.e. stable complex structures would not exist in cells as they would be broken down immediately after synthesis
condensation reactions
- all biopolymers are condensation polymers
- i.e. they are synthesized through condensation reactions
- to undergo a condensation reaction, both monomers involved must have 2 functional groups
- these reactions are catalysed by polymerases
hydrolysis reactions
- reverse of condensation reaction
- involves the addition of a H2O unit for every covalent bond broken
photosynthesis
- anabolic process used by plants to synthesize energy-rich biomolecules
- uses solar energy absorbed using photosynthetic pigments (chlorophyll)
- all organisms on Earth are dependent on this process for food, directly or indirectly
overview of photosynthetic reactions
- series of redox reactions
- water is split into H2 and O (O is the waste product)
- H2 is used to reduce CO2 to form glucose
- essentially transforms energy-poor CO2 and H2O into glucose
respiration
- catabolic process used by all organisms to release energy from energy-rich molecules
- essential to life and occurs continuously in every cell
- glycolysis –> link reaction –> krebs cycle –> electron transport chain
- in anaerobic conditions only glycolysis takes place
- in the electron transport chain, cytochromes are reduced and oxidized in succession
- the last step of the electron tranport chain involves the reduction of the final electron acceptor, oxygen, to H2O
cycle of photosynthesis and respiration
- photosynthesis: carbon sink, removes carbon from atmosphere
- respiration: carbon source, releases carbon to atmosphere
types of proteins
- fibrous proteins
- globular proteins
fibrous proteins
- supports structure/movement
- elongated molecules with a dominant secondary structure
- insoluble in water
globular proteins
- operate on the molecular level (e.g. enzymes, receptors)
- compact spherical molecules with a dominant tertiary structure
- soluble in water
examples of fibrous proteins
- keratin: the protective covering in claws/hair/wool
- collagen: connective tissue in skin and tendons
examples of globular proteins
- polymerase: catalyses anabolic reactions
- insulin: hormone that controls + maintains blood glucose levels
- haemoglobin: carries oxygen in the blood
amino acids
- building blocks of proteins
- contains an amino group (NH2) and a carboxyl group (COOH)
- called 2-amino acids
- all amino acids differ by their variable R group
types of amino acids
- non-polar
- polar
- basic
- acidic
this is because they can exist as cations, anions, or zwitterions
zwitterions
- molecules containing both positive and negative charges
- they are neutral as a whole
types of amino acids: non-polar
- R group: hydrocarbon
e. g. alanine
types of amino acids: uncharged polar
- R group: hydroxyl (OH), sulfhydryl (SH), or amide (CONH2)
e. g. serine
types of amino acids: basic
- R group: amino (NH2)
e. g. lysine
types of amino acids: acidic
- R group: carboxyl (COOH)
e. g. aspartic acid
properties of amino acids
- crystalline compounds with high m.pt (usually > 200 C)
- much greater solubility in polar solvents (e.g. water)
- usually move in an electric field
- i.e. similar properties to ionic compounds
- commonly exist as zwitterions (due to internal salts – a proton is transferred from the carboxyl to the amino group)
- amphoteric in zwitterion state (due to carrying both an acidic and a basic group)
- can act as pH buffers
internal salts
zwitterions that formed charges due to acid-base reactions
relationship between charge of amino acid and pH
- high pH = low [H+] = acts like acid (proton donor) = forms anion
- low pH = high [H+] = acts like base (proton acceptor) = forms cation
isoelectric point
- intermediate point at which the amino acid is electrically neutral
- no net charge at this pH = amino acid won’t move in electric field
- least soluble at this point as mutual repulsion is at its minimum
bond between amino acids
peptide bond (in biochem we do NOT call them amide linkages)
how do amino acids switch between zwitterion - anion - cation states?
- the zwitterion can lose or accept hydrogen
- at high pH, the zwitterion will lose one H+
from its amino group and form an anion molecule - at low pH, the zwitterion will gain one H+ to its carboxyl group and form a cation molecule
- the pH at which the zwitterion is neutral is called isoelectric point
- the isoelectric point is dependent on the character of the R group
proteins: primary structure
- number and sequence of amino acids in the polypeptide chain
- they are bonded covalently
proteins: secondary structure
folding of the polypeptide chain due to H bonds between peptide bonds (between C=O and N-H)
proteins: types of secondary structures
- alpha helix
- beta pleated sheet
proteins: alpha helix
- secondary structure
- regular coiled configuration
- results from H bonds between peptide bonds that are 4 amino acids apart
- results in a tightly-coiled helix with 3.6 amino acids per turn
- flexible and elastic due to the intra-chain H bonds easily breaking and reforming as the molecule is stretched
e.g. keratin (protein forming support structure in hair)
proteins: beta pleated sheet
- secondary structure
- peptides are placed side by side in extended form (NOT tightly coiled)
- arranged in pleated sheets that are cross-linked by inter-chain H bonds
- flexible but inelastic
e.g. fibroin (protein forming support structure in spider silk)
differences in secondary structure between fibrous and globular proteins
- fibrous proteins have a more well-defined secondary structure
- as they rely on characteristics bestowed by their secondary structure to carry out their functions
- well defined secondary structure = tougher and less water-soluble
proteins: tertiary structure
- further twisting, folding, and coiling of the polypeptide chain due to interactions between R groups in the polypeptide chain
- results in a very specific compact 3-D structure (the protein’s conformation)
- this is the most stable arrangement of the protein
- all interactions are intra-molecular only
- all hydrophilic molecules are placed along the outer surface while all hydrophobic molecules are placed on the inner side
interactions that stabilize protein conformation
- hydrophobic interactions
- hydrogen bonding
- ionic bonding
- disulfide bridges
tertiary structure interactions: hydrophobic interactions
occurs between non-polar side chains
e.g. between two alkyl side chains
tertiary structure interactions: hydrogen bonding
occurs between polar side chains
e.g. between serine’s CH2OH and aspartic acid’s CH2COOH
tertiary structure interactions: ionic bonding
occurs between charged side chains
e.g. between lysine’s (CH2)4NH3+ and aspartic acid’s CH2COO+
tertiary structure interactions: disulfide bridges
- between sulfur-containing amino acid cysteine
- these are covalent bonds so they’re the strongest of these interactions
factors affecting tertiary structure interactions
- temperature
- pH
- presence of metal ions
proteins: quaternary structure
- occurs in proteins with more than 1 polypeptide chain
- based on inter-molecular interactions between polypeptide chains (similar interactions to those found in the tertiary structure)
co-factors
- non-protein molecules that enzymes may require to function
- they are called co-enzymes when organic, but there are also inorganic co-factors (e.g. metal ions)
enzyme-substrate complex
- temporary complex formed when the enzyme binds to the substrate at the active site
- due to the substrate typically being much smaller than the enzyme
- the formation of the complex depends on a chemical fit (i.e. compatibility between the enzyme and substrate)
- the binding of the complex puts a strain on the substrate molecule, causing bonds to break/form
enzymes: induced-fit mechanism
- theorizes that an enzyme’s active site undergoes conformational changes in the presence of a substrate
- it reshapes itself to allow a better fit
enzymes: Vmax
- maximum velocity of enzyme under the experimental conditions
- varies greatly between enzymes
- affected by pH and temp
- also expressed as turnover rate
turnover rate
(no of molecules of substrate processed into products) per (enzyme molecule) per (unit of time)
enzymes: Km
- Michaelis constant
- [S] = Km when the rate is Vmax / 2
- the lower the Km value, the better the enzyme’s affinity for its substrate
- the lower the Km value, the less sensitive the enzyme is to changes in [S]
factors affecting enzyme activity
- pH
- temperature
- presence of inhibitors (e.g. heavy metal ions)
factors affecting enzyme activity: heavy metal ions
- positive metal ions will react with sulfhydryl groups (SH) and displace H+ to form a covalent bond with S
- this disrupts the folding (secondary structure) and may change the shape of the active site and its ability to bind substrates
factors affecting enzyme activity: pH
- changes in pH will react with the polypeptide to change its conformation
- may cause denaturation
factors affecting enzyme activity: temperature
- too high temps may break secondary, tertiary, and quaternary bonds
- this causes denaturation
competitive inhibitors
- inhibitors that “compete” with the substrate to bind at the active site
- usually have similar chemical structure to the substrate
- once bound they don’t react to form products (so they just block the active site)
- Vmax remains unchanged but Km is increased
- their effect can be minimized by increasing [S]
non-competitive inhibitors
- inhibitors that bind away from the active site (the site they bind to is called the “allosteric site”)
- they cause a conformational change to the protein on binding, thus altering the active site
- increasing [S] has no effect on non-com inhibitors
- Vmax is decreased but Km remains unchanged
coenzymes
organic molecules that aids enzyme function
cofactors
inorganic molecules that aids enzyme function (e.g. metal ions)
induced-fit model
- an enzyme binds to its substrate by intermolecular bonds at a particular reactive site
- its conformation of enzyme changes when it binds to substrate, and changes back when product is released
product inhibition
- enzyme inhibition can be used to control metabolic activity
- product inhibition occurs when the product of a reaction acts as an inhibitor for the enzyme in the first step of the reaction
irreversible inhibitors
inhibitor effects are permanent when the inhibitor’s binding to the enzyme is permanent
e.g. cyanide is an irreversible inhibitor of cytochrome oxidase
methods of analysing protein composition
- chromatography
- gel electrophoresis
chromatography
- used to separate and identify components of a mixture
- chromatography techniques take advantage of differing affinities that components have for two phases (stationary and mobile)
- in paper chromatography the components are separated on the basis of different solubilities in the two phases
- used mainly for qualitative analysis
- stationary phase: the paper contains about 10% water, which is adsorbed by forming H bonds with the hydroxyl groups in the cellulose of the paper
- mobile phase: the solvent rises up the paper by capillary action, dissolving the components of the mixture to different extents, and carrying them at different rates
- amino acids are colourless in solution they are usually treated with a locating reagent (e.g. ninhydrin) at the end of the process to color them
calculating Rf
distance traveled by solute / distance traveled by solvent
gel electrophoresis
- used to analyse and separate components of a mixture based on the movement of charged particles in an electric field
- exploits the fact that amino acids carry different charges depending on the pH by placing the mixture in a buffered solution at a particular pH
- can also be used to separate and identify intact proteins according to different rates of movement
- extent of movement depends on the ion’s charge and mass, and pH
- pH = isoelectric point, amino acids will not move
- pH > isoelectric point, amino acid exists as anions and move to the anode
- pH < their isoelectric point, amino acid exists as cations and moves to the cathode
factors affecting rate of movement of ions in gel electrophoresis
- charge
- mass
- voltage used
- temperature
- pH of the solution
factors affecting rate of movement of ions in gel electrophoresis: charge
higher charge = more movement
factors affecting rate of movement of ions in gel electrophoresis: mass
lower mass = more movement
protein assays
investigation procedures used to measure the concentration of protein in a sample
UV-visible spectroscopy
- a protein assay procedure
- relies on the fact that molecules interact with different parts of the electromagnetic spectrum based on their chemical composition
- produces an absorption spectrum showing wavelength on x-axis and intensity of absorption on y-axis
spectrophotometer
used as a logging device to obtain absorption spectra
analyzing results of UV visible spectroscopy
- wavelength of maximum absorption is taken
- A = log (I0 / I), wherein A = intensity of absorption, I0 = intensity of light before being passed through, and I = intensity of light after being passed through
- other factors are considered: molar absorptivity, concentration of solution, and path length
- this can be expressed in an equation (Beer-Lambert Law), seen in Table 1 of the data booklet
molar absorptivity
absorbance of a 1 mol/dm3 solution in a 1 cm cell at a specific wavelength
relationship between absorbance and concentration of solution
directly proportional
lipids
- biomolecules containing CHO
- hydrophobic and only soluble in non-polar solvents
functions of lipids
- stores energy
- stored fat (in adipose tissue/blubber) helps protect internal organs and acts as a thermal insulator
- they can also act as electrical insulators (they are the myelin sheaths in nerve cells)
- some hormones (e.g. the sex hormones) are steroids, which are also lipids
- cholesterol is another lipid that is important in the plasma membrane
efficiency of lipids vs carbohydrates as fat stores
- lipids are more reduced so they release more energy in respiration (almost 2x of carbs)
- but lipids are harder to break down
- due to their insolubility in water, they are difficult to transport in lipoproteins
drawbacks of excess lipids in the diet
atherosclerosis
- their low solubility that causes some lipids to be deposited in the walls of the main blood vessels
- this restrict blood flow
- associated with high blood pressure and can lead to heart disease
- primarily caused by high LDL cholesterol
- cholesterol is insoluble in blood so it is transported with lipoproteins
- 2 types of lipoproteins: LDL (low-density lipoprotein, ‘bad’) and HDL (high-density lipoprotein, ‘good’)
- high LDL cholesterol levels are associated with atherosclerosis while high HDL cholesterol levels seem to protect against heart attack
- it’s believed that HDL cholesterol actually slow LDL buildup
sources of LDL: saturated fats and trans fats
obesity
- the body tends to convert excess fat into adipose tissue
- obesity occurs in a diet with excess fat
- it’s linked to other health issues like diabetes and cancer
uses of steroids
- female steroid hormones are used in contraceptive pill formulations and in HRT (hormone
replacement therapy) which is sometimes prescribed during menopause - male steroid hormones (AKA androgens): testosterone is used to treat testes disorders and breast cancer
- androgens are also known as anabolic steroids because they promote tissue growth
- synthetic anabolic steroids are used medically to help gain weight after debilitating diseases
- they can also be used as performance-enhancing drugs, so their use is banned by sporting authorities for medical and ethical reasons
triglycerides
- produced by condensation of glycerol and three fatty acids
- forms ester links (ester link is C-O-C=O)
- glycerol is a 3C molecule with hydroxyl groups on each carbon
- fatty acids are long-chain carboxylic acids and can be saturated, mono-unsaturated, or poly-unsaturated
- hydroxyl (OH) from glycerol and carboxyl (COOH) from fatty acids reacts to form three water and one triglyceride
phospholipids
- derivation of triglycerides
- but one fatty acid was replaced by a phosphate group
- so we naturally have a hydrophilic part and a hydrophobic part
- phospholipids will naturally form a bilayer in water
hydrolysis of triglycerides/phospholipids
occurs at most pHs with the enzyme lipase
saponification
- hydrolysis of triglycerides in an alkali solution
- they make salts of fatty acids which can be used to make soap
functions of cholesterol
- integral part of phospholipid bilayer, provides fluidity and permeability
- their OH group interacts with the polar heads of phospholipids while the non-polar rings and hydrocarbon chain interact with the hydrophobic tails
- precursor to many vitamins and hormones (e.g. Vit D, sex hormones, bile acids)
predicting relative melting points of fats and oils
higher unsaturation = more bent shape = less intermolecular bonds = lower melting point
EXCEPTION: trans fats are straight (that sounded peculiar) although they are unsaturated
difference between saturated and unsaturated fatty acids
- saturated fatty acid are FATS while unsaturated fatty acids are OILS
- due to high intermolecular bonds, saturated fatty acids are solid in room temperature
- unsaturated fatty acids cannot form a straight structure so intermolecular bonds are reduced, making them liquid in room temperature
hydrolytic rancidity
- fats undergo hydrolysis
- so we get glycerol and three fatty acids
- fatty acids smell!
- can partially be prevented in by placing them in cooler areas
determining degree of unsaturation in fats
refresher: alkenes undergo addition reactions, and I2 can react with unsaturated fats in this way
- 1 mol of I2 reacts with each mol of double bonds in the fat (1:1 ratio of I2:double bond)
- so a fat’s unsaturation is measured by its iodine number
iodine number
number of grams of iodine which reacts with 100 grams of fat
hydrogenation
- addition reaction of fats + H2
- carried out by food industry to increase saturation of oils
- partial hydrogenation produces trans fats, which poses health risks
define rancidity of fats
- fats in the food industry may be stored for long periods of time
- this may cause chemical changes, causing rancidity
causes of rancidity of fats
- oxidative rancidity
- hydrolytic rancidity
hydrolytic rancidity
- hydrolysis: addition of H2O (from the food) to cause breakdown of fats
- occurs in the ester linkages (-COOC-)
- may be catalysed by lipase
- remember that hydrolysis is the reverse of condensation, which is how triglycerides form
- so instead of 1 triglyceride we now have 1 glycerol and 3 fatty acids
- cause of rancidity: fatty acids stink!
- favored by high temps, so it can be minimized by refrigeration
NOTE: not all hydrolysis reactions result in rancidity! look at saponification :)
oxidative rancidity
AKA auto-oxidation
- oxidation: unsaturated fats react with atmospheric oxygen
- occurs in the C=C bonds in unsaturated triglycerides
- cause of rancidity: volatile aldehydes and ketones that result from the oxidation
- favored by light and the presence of certain enzymes/metal ions
- proceeds via a free-radical mechanism, so yields a mixture of products
- occurs in fats and oils with a high proportion of C=C bonds
- can be minimized by the addition of antioxidants
- saturated fats CANNOT undergo oxidative rancidity
steroids
- lipids with a structure containing 4 fused rings (the steroidal backbone)
- cholesterol is a steroid
carbohydrates
as the name suggests, they are carbons with water
formula: Cx(H2O)y
functions of carbohydrates
- energy store
- structural support (plants only, with cellulose)
bonding in monosaccharides
- all have 1 carbonyl group (C=O)
- all have at least 2 hydroxyl (OH) groups, which are polar, they are all soluble in water
- can contain either an aldose/aldehyde group (CHO) or a ketose/ketone group (basically carbonyl but it’s placed like an ester linkage)
characteristics of monosaccharides
- simple sugars
- soluble in water (due to the polar hydroxyl/OH groups)
structure of monosaccharides
- they exist as straight sugars but will “cyclize” (form a ring) in aqueous conditions
- this is because rings are energetically more stable
- the aldose/ketose reacts with a hydroxyl group to form an ether bond
forming disaccharides
- monosaccharides can react together through a condensation reaction between C1 and C4 to form a disaccharide
- the linkage is called a 1,4-glycosidic bond
- in reality, the glycosidic bonds can be situated on different carbons depending on whether it is lactose (1,4), sucrose (1,2) and amylopectin (1,4 and 1,6)
- what’s important is that the OH groups are the ones that react
forming polysaccharides
- polysaccharides form by repetitions of condensation reactions
- this results in a long chain of monosaccharide units held together by glycosidic bonds
polysaccharides
- sugar polymers
- due to their large size, polysaccharides are all insoluble molecules
- this also makes them ideal to store energy
examples of polysaccharides
- starch – carbohydrate store in plants
- glycogen – carbohydrate store in animals
- cellulose – structural material in plants.
they are all polymers of glucose, but they differ in terms of the isomer of glucose used and/or the amount of cross-linking in the chain
micronutrients
- required diet nutrients that are only needed in extremely small amounts
- still needed bc we can’t synthesize most of them ourselves
e. g. vitamins, trace minerals (e.g. Fe, Cu, Zn…)
water-soluble vitamins
- have polar bonds
- can form H bonds with water
- directly transported via bloodstream and filtered out with the kidneys
- heat-sensitive
- Vit B, C
lipid-soluble vitamins
- non-polar
- have long hydrocarbon chains/rings
- slower absorption
- excess are not filtered out in the kidneys but stored in adipose tissue
- excess intake may have serious side effects
- heat-sensitive but to a lesser extent compared to water-soluble vitamins
- vit A, D, E, K
vit A
- involved in the visual cycle in the eye
- important for vision in low light intensity
- has one hydroxyl group but the hydrocarbon chain and ring are non-polar, which influences its solubility (it is fat-soluble only)
vit C
- has multiple OH groups, making it polar and water-soluble
- also allows it to form H bonds w water
- acts as cofactor in some enzymic reactions
- important in tissue regeneration (e.g. after injury)
- aids resistance to certain diseases
- has many easily oxidized groups (e.g. OH, C=C) so it is easily destroyed by food processing and storage
vit D
- has one hydroxyl group but the hydrocarbon chain and ring are non-polar, which influences its solubility (it is fat-soluble only)
- chemically similar to cholesterol
- stimulates the uptake of Ca ions in cells
- important for the health of bones and teeth
why are vitamins heat-sensitive?
- heat and oxidation are related
- the oxidation reactions that vitamins undergo are endothermic, so are favored by higher temperatures
causes of vitamin deficiency in some countries
- poverty as a country.
- poor distribution of food
- over-processed food (vits are heat-sensitive)
- Lack of education.
- Climate change.
consequences of vitamin deficiency
Vitamin A = night blindness
Vitamin B = anemia, fatigue, weight loss
Vitamin C = bleeding in gum (scurvy)
Vitamin D = rickets
solutions to vitamin deficiency
- vitamin fortification (adding vitamin to a processed product)
- more vitamin tablets
- making improvements to nutrient content of food through genetic modification (GM foods)
- educate the masses!
determine the concentration of a protein in solution from a calibration curve (NOTES)
- plot absorption to concentration of protein
- calculate protein concentration value by c1v1 = c2v2
- for the given sample of protein, look at where the absorption is on the graph and deduce the concentration of protein
DNA
deoxyribonucleic acid
- nucleic acid
- responsible for storing info on genetic characteristics
RNA
ribonucleic acid
- nucleic acid
- enables info stored in DNA to be expressed by controlling the primary structures of synthesized proteins
adaptations of DNA to its function
- very stable molecule, can retain its precise chemical structure in cell conditions
- contains a ‘code’ storing genetic information
- can replicate (produce an exact copy of itself)
nucleotides
monomers of nucleic acids
components of a nucleotide
- a pentose sugar
- a phosphate group
- a nitrogen base
components of a nucleotide: pentose sugar
DNA: deoxyribose
RNA: ribose
difference – at C2, Ribose has a H and OH attached but deoxyribose has 2 Hs
components of a nucleotide: nitrogen base
- purines: (A/G bases) larger and contain 2 fused rings
- pyramidines: (C/T/U bases) smaller and only has 1 ring
structure of a nucleotide
- the nitrogen base always attaches to C1
- the phosphate group always attaches to C5 (the 5’ position)
structure of polynucleotides
- the phosphate group of one nucleotide attaches to the OH group at the C3 (3’) of the other nucleotide (so the direction is 5’ to 3’)
- via condensation reaction
- the phosphate to OH bonds are called phosphodiester links
geometry of DNA
- 2 polynucleotide strands run antiparallel to each other in the form of a double helix
- nitrogen bases pair with their complementary pair (A-T and C-G)
- A-T form 2 H bonds
- C-G form 3 H bonds
structural differences between DNA and RNA
- RNA has ribose instead of deoxyribose
- RNA has uracil instead of thymine
- RNA is single-stranded instead of double-stranded – because it is less stable than DNA and anyway it will need to be single-stranded for its function
how can DNA associate with histones
- DNA is negatively charged due to phosphate groups
- this causes an attraction to histones
- histones have a high proportion of basic amino acids, so carry positive charges at cell pH
function of histones in DNA
they add to stability by supercoiling DNA
how does DNA lead to protein synthesis?
- section of DNA gets unzipped and the antisense strand gets transcribed into mRNA (making mRNA a copy of the sense strand)
- mRNA gets matured in the nucleus by removing introns
- mature mRNA goes to ribosome and translated into
protein through tRNA and its anticodons
how can DNA get transferred between species?
- codons in all living organisms code for the same representing amino acid
- basically, genetics is a universal language!
- this enables scientists to add a certain codon into another species so that species can translate the targeted amino acid
stability of the DNA structure
- stable
- because the nitrogen bases become hydrophobic when they have H bonding with their complementary base pair
- this makes them hydrophobic in the inside (no water can disturb the bonds) and polar on the outside with the phosphate group
pros of GMO foods
- it stays fresh for longer
- improved flavor and texture
- resistance to pests
- better climate tolerance
- can alter nutrient content, and add vitamins and vaccines!
cons of GMO foods
- long-term effects unknown
- changes to the natural ecosystem through cross-pollination
- ecosystem may be disturbed
- pests may build up resistance
- unknown allergies may manifest
biological pigments
coloured compounds produced by metabolism
highly conjugated structures
- molecules with delocalized p orbital e-s
- due to resonance structure
- so they can alternate between single and double bonds and through benzene ring structures
why are pigments colored?
- they have chromophores (light-absorbing structures) that can absorb a certain wavelength
- the colors that are not absorbed (instead reflected) are the ones seen on the pigment
- the color they absorb is the complementary color of the observed color (on the color wheel)
- because pigments are also highly conjugated structures, their p orbital e-s can become excited when absorbing wavelengths
types of pigments
- porphyrins
- carotenoids
- anthocyanins
porphyrins
- has a planar ring structure
- made up of 4 heterocyclic rings of C and N, linked by bridging C atoms
- the ring acts as a ligand and forms a chelate with a metal ion involving coordinate bonds (the metal ion will be placed in the centre of the compound)
- porphyrins differ in the substituent group attached to their 8 outer points
common porphyrins
- hemoglobin
- chlorophyll
- myoglobin
- cytochromes
how chlorophyll works, chemically
- central metal ion: Mg2+
- light → several accessory pigments pass on the energy → chlorophyll gets oxidized and its electrons go to electron transport chain → chlorophyll regains is electrons by oxidizing water
difference between hemoglobin and myoglobin
- centra metal ion: Fe2+
- hemoglobin transports oxygen in blood while myoglobin does it in muscle cells
- hemoglobin has 4 different polypeptides while myoglobin only has 1
- hemoglobin has 1 Fe2+ per polypeptide so it can bind to 4 oxygen molecules, but myoglobin only has 1 Fe2+ ion and can only bind to 1 oxygen
how does oxygen bind to hemoglobin/myoglobin?
- it forms a weak bond with the iron
- since it does not change any oxidation state, we say hemoglobin/myoglobin is oxygenated, NOT oxidized
- when oxidized their names are oxyhemoglobin and oxymyoglobin
- the binding of hemoglobin to oxygen is cooperative (gets easier to bind oxygen after the first binding of oxygen)
- the cooperative nature is caused by a conformational shift in the tertiary structure of hemoglobin after the first binding (allosteric effect that ENHANCES function!!)
- this is why the shape of the binding graph of hemoglobin and oxygen is sigmoidal
how do cytochromes work, chemically?
- central metal ion: iron (can shift between Fe2+/3+)
- work as e- carriers in mitochondria and chloroplasts
- successively reduced and oxidized as they in turn accept and then pass on electrons
- organized according to electrode potentials (e-s basically go down an electrochemical gradient)
- their structures are similar to hemoglobin, but their carrier mechanism differs
- in cytochromes the Fe ion converts oxidation state between +2 and +3 as the cytochrome undergoes redox change
- the final cytochrome in aerobic respiration passes its e-s to the terminal acceptor oxygen to form water
NOTE: the final cytochrome is where the poison cyanide attaches to: by blocking the chain, it prevents aerobic respiration from occurring.
factors influencing oxygenation of hemoglobin
- temperature
- pH
- location
factors influencing oxygenation of hemoglobin: temperature
↑ temp = ↓ affinity of hemoglobin for O2
- oxyhemoglobin releases oxygen more readily in higher temps (e.g. during high metabolic activity in cells)
factors influencing oxygenation of hemoglobin: pH
↓ pH = ↓ affinity of hemoglobin for O2
- oxyhemoglobin releases oxygen more readily in acidic conditions
NOTE: increases in the concentration of CO2 have this effect, as CO2 dissolves to form carbonic acid, increasing the acidity of the blood
factors influencing oxygenation of hemoglobin: location
- foetal hemoglobin and myoglobin have higher base affinity for oxygen than adult hemoglobin
- so they can remove oxygen from adult hemoglobin
- thus hemoglobin is likely to release oxygen in muscle cells and in the placenta
competitive inhibition of hemoglobin
- CO has higher affinity to hemoglobin than oxygen
- thus it prevents oxygen from binding
carotenoids
- group of pigments
- contains long hydrocarbon chains with many double bonds
- fat soluble (due to the long non-polar hydrocarbon chain)
- color range: yellow to red
significance of carotenoids
- alpha- and beta-carotene are vitamin A precursors (so they play an important role in vision)
- carotenoids in plant leaves help ‘harvest’ light for photosynthesis as accessory pigments (i.e. they help to pass light energy to chlorophyll)
stability of carotenoids
- double bonds can be oxidized by oxygen (oxidation is favored by light)
- this is significant as the double bonds are what give carotenoids their color
- oxidation causes a change from trans-isomer to cis-isomer
- oxidation of carotenoids can be reduced by preventing exposure to air and light, and decreasing storage time
stability of chlorophyll
- in acidic solutions, Mg2+ is replaced by 2H+
- thus chlorophyll loses its colour and can’t function
- this is why NaHCO3 is often added to water during cooking – it provides an alkaline environment to stabilize chlorophyll
- temperature also deteriorates the cell membrane
anthocyanin
- type of pigment
- strongly absorb blue and green parts of the spectrum
- so they appear as pink/red/blue colors (responsible for this coloration in plants)
- aromatic compounds with a three-ring C6C3C6 structure (one of the rings is an arene, hence the compound is aromatic)
- contains conjugated carbon–carbon double bonds
- their color depends on the central metal ion and the pH
solubility of anthocyanins
- contains multiple OH groups (which are polar), allowing them to form H bonds and be water-soluble
- this is why they are mostly found dissolved in the aqueous cell sap rather than in the lipid-rich membranes
forming anthocyanins
- reaction between sugars and proteins
- light-dependent
- this is why fruit often changes colour as its sugar concentration increases (i.e. when it ripens)
factors affecting anthocyanin color
- pH
- the central metal ion
factors affecting anthocyanin color: pH
- colour of anthocyanins changes as pH of cell sap changes
- pink in acidic solution, purple in neutral solution, greenish-yellow in alkaline solution
- caused by removal of H+ from the OH groups in anthocyanin in basic conditions, and vice versa
- this alters the conjugation and therefore the absorbance at the chromophore
factors affecting anthocyanin color: central metal ion
- anthocyanins can take Fe3+ or Al3+ as their central metal ion, forming deeply coloured coordination complexes
- this is why there is sometimes discolouration in canned fruit
techniques used in analysis of pigments
- paper chromatography
- thin-layer chromatography
thin-layer chromatography
- follows the same basic principles as paper chromatography, but finishes faster
- the stationary phase is a thin layer (around 0.2 mm thick) of adsorbent particles of alumina/silica which is supported on glass or a thin plastic plate
- mobile phase is the solvent, which is chosen according to the chemical nature of the pigments
- small spots of the pigment extract are placed on the origin
- capillary action causes different compounds to separate, leading to identification from their Rf values
stereoisomers
molecules with the same chemical formula but with different spatial arrangements of the atoms
significance of stereochemistry in biochemistry
- many biopolymers can exist as stereoisomers
- metabolic reactions are usually stereospecific
stereochemistry in amino acids
- they are all chiral, so they all have 2 enantiomers (mirror reflections)
- proteins are made up of amino acids, so all proteins are chiral as well
exceptions: glycine - the enantiomers are classified into D-amino acid and L-amino acid
D-amino acid
D = dextrorotation
i. e. rotation to right in polarized light
- often noted as +
L-amino acid
L = levorotation
i. e. rotation to the left in polarized light
- often noted as -
- biological systems only use L-amino acids
differences between D- and L-amino acids
- identical chemical and physical properties
- only difference: D-amino acids rotate polarized light to the right, while L-amino acids rotate them to the left
stereochemistry in lipids
- unsaturated fatty acids contain C=C bonds
- thus they can exist as cis–trans isomers due to the restriction on rotation around the double bond
- most natural unsaturated fatty acids are cis
difference between cis and trans fats
- cis fats can’t easily arrange themselves side by side to solidify
- so they generally have lower melting points than their trans isomer
hydrogenation of fats
addition rxn between H2 and an unsaturated fat
catalyst: finely divided Ni
- used in the food industry (e.g. production of margarine)
pros and cons of hydrogenation of fats
- hydrogenation causes saturation in fats, making their melting points higher
- this makes it more convenient to store them
- saturated fats are also less heat-sensitive and have a longer shelf-life than liquid oils
- however, if partial hydrogenation occurs (where H2 is limited), not all = bonds will be broken and those that remain will be modified from cis to trans
health risks of trans fats
- raises LDL cholesterol levels in blood
- reduces HDL cholesterol levels in blood
- basically, is related to cardiovascular diseases
stereochemistry in carbohydrates
- like amino acids, carbs are chiral and are divided into D- and L-carbs
- as carbs may contain more than 1 chiral C, whether a carb is D- or L- is defined by the C furthest away from the aldose/ketose group (for straight carbs only)
- if that C’s OH is on the left, the carb is an L-carb, and vice versa
- D-carbs are most abundant in nature
- for aromatic carbs (e.g. monosaccharides in aqueous solutions), there are also alpha- and beta- isomers
- in alpha isomers the H bonded to the important C directs up
- in pentose sugars the important C is C2
- in hexose sugars the important C is C1
alpha- carbohydrates
e. g. starch (includes amylose and amylopectin) and glycogen
- very branched and compact spiral structure
- good for energy storage
- α-glycosidic link
beta- carbohydrates
e. g. cellulose
- unbranched, forms a long and strong straight cable
- β-glycosidic link (1-4 glycosidic links)
- cellulose forms microfibrils (cables) of parallel chains that give it a rigid structure
- this makes cellulose an important building component and is why wood is a useful building material
importance of cellulose
- humans cannot digest cellulose’s β-glycosidic link
- so cellulose passes through our digestive system and straight to feces
- cellulose is a dietary fibre that helps stimulate mucous production in intestine
- this leads to better movement and digestion and reduced conditions like constipation, haemorrhoids, and possibly colorectal cancer
stereochemistry in vitamins
- Vit A (AKA retinal) is involved with the visual cycle (photochemical changes associated with our ability to detect light)
- rhodopsin is the major photoreceptor pigment in rods
- it is a large conjugated protein molecule consisting of the protein opsin which is tightly bound to 11-cis-retinal (derived from vitamin A)
exposure to light → causes 11-cis-retinal to change to all-trans retinal → all-trans isomer dissociates from the opsin → nerve impulse triggered → all-trans form isomerizes back to the 11-cis form (enzyme-catalysed) → rhodopsin is regenerated from opsin and 11-cis-retinal after the
xenobiotics
- foreign chemicals (usually non-polar) that are found in
an organism - can refer to substances that are simply present in abnormally high concentrations, or synthetic substances that are not supposed to be there at all
examples of xenobiotics
- antibiotics
- MSG
- pollutants
- plastic
- certain hormones (e.g. oestrogen in fish!!)
effect of xenobiotics in organisms
- non-polar molecules (e.g. drugs) pass relatively easily across the cell membranes (which are hydrophobic and therefore non-polar as well)
- in the cells they may be modified and detoxified
- however, if the xenobiotic cannot be modified it may build up (bioaccumulation)
e. g. methylmercury build-ups in the brain, causing mercury poisoning - in agriculture, pesticides may be metabolized by similar processes
- this sometimes leads to resistance to the effect of the chemical
reducing xenobiotics using sewage treatment plants
- in urine there are many different xenobiotics (e.g. estrogen)
- hospitals may flush antibiotics/painkillers/etc
- sewage plants may not completely break down all xenobiotics before dumping into lakes
- male fish may consume enough oestrogen to be ‘feminized’, reducing their ability to breed
biomagnification
the increase in concentration of a xenobiotic substance in a food web
why does biomagnification occur?
- natural toxins (e.g. snake venom) do not build up in the environment as they are broken down by enzymes
- however, some synthetic chemicals cannot be naturally broken down as there are no enzymes for them
- so they build up in the environment
- in some cases their concentration can increase in food webs to potentially harmful levels
- when a xenobiotic cannot be metabolized, it is taken up directly when one organism feeds on another
- it has the greatest effect on apex predators
example of biomagnification
- the insecticide DDT
- a complex aromatic molecule used during WWII to control the mosquitoes responsible for the spread of diseases (e.g. malaria, typhus)
- DDT is readily soluble in fat and there is no enzyme that can metabolize it
- so it bioaccumulates in tissues and passes unchanged through food chains
- apex predators accumulate elevated concentrations of DDT, as much as 10 million times the original concentration
- it was found that high levels of DDT in the tissues of birds of prey (e.g. ospreys) caused the eggshells they produced to be thinner than usual
- the result: eggs broke under their parent’s weight
amelioration
- means ‘making things better’
- in this context it refers to reducing problems related to xenobiotics
forms of amelioration for xenobiotics
- using biodegradable substances
- host-guest chemistry
- bioremediation
amelioration: host-guest chemistry
- basically “arrests” the xenobiotic with a similar mechanism to enzymes, except the “enzyme” just latches onto the “substrate” instead of breaking it down
- the “host” molecule binds to the xenobiotic to form a “supermolecule” (like an enzyme-substrate complex)
- involves all forms of bonding except covalent and metallic (obviously)
- covalent bonding would produce a new molecule: something we DON’T want
- all we need to do is immobilize it so it cannot enter any other organisms
- many host molecules have a cage-like or tube-like structure which traps the guest molecule
amelioration: using biodegradable substances
- basically, not making xenobiotics in the first place
- biodegradable substances are substances that can be naturally broken down by organisms
- there are two main forms of biodegradable plastics: plant-based and petroleum-based
- plant-based plastic can be broken down with hydrolysis and is mainly made of starch
- produces carbon dioxide and water when hydrolysed
- petroleum-based plastic can be broken down with bacteria (thus they are “compostable”) and is made of wastes from oil industries
amelioration: bioremediation
- using natural organisms to break down the pollutants
- many bacteria and fungi oxidize hydrocarbons as part of their respiration, so they’re used when cleaning up oil spills and other industrial waste
- target bacteria/fungi may be grown in a lab and released onto the affected area
- issue: we disturb the ecosystem by dumping organisms
green chemistry
- form of regulation to stop environmental degradation
- aims to minimize production of hazardous
substances - has helped in terms of food and drinks, bioplastics, cosmetics, clothing, etc
assessing the “greenness” of a substance used in biochemical research
- effective mass yield
- atom economy
- environmental (E) factor
- EcoScale
assessing the “greenness” of a substance used in biochemical research: effective mass yield
% of mass of wanted products over mass of unwanted products
Problems:
- ‘unwanted’ is subjective
- method fails to assess toxicity of products
assessing the “greenness” of a substance used in biochemical research: atom economy
% of product over all reactants
Problems:
- inorganic compounds are ignored because they are not in the final product (??? wut)
- solvents used are ignored (they may be dangerous!)
assessing the “greenness” of a substance used in biochemical research: E factor
measured as total waste divided by product (the lower the value, the better)
Problem: ignores actual amounts
e.g. oil industries have much lower E than pharmaceuticals but they produce much more in absolute terms
assessing the “greenness” of a substance used in biochemical research: EcoScale
takes into account the cost, safety, technical set-up,
energy and purification aspects
