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Chemistry IB HL (2016+) > Option B: Biochemistry > Flashcards

Option B: Biochemistry Flashcards

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1
Q

metabolism

A

sum of all chemical reactions in an organism (necessary to sustain life)

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2
Q

metabolic pathways

A

sequences and cycles that metabolic reactions go through

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3
Q

metabolites

A

compounds taking part in metabolism

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4
Q

anabolism

A
  • 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

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5
Q

catabolism

A
  • 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

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6
Q

biomolecules

A

all molecules present in a living organism

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7
Q

macromolecules

A
  • 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
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8
Q

biopolymers

A
  • biodegradable polymers
  • produced by organisms
  • substances bonded together with a covalent bond after a condensation reaction
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9
Q

concept of energy coupling

A
  • energy obtained from catabolism is used to fuel anabolic reactions
  • through the use of ATP (adenosine triphosphate) as the intermediary energy carrier
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10
Q

concept of futile cycles

A
  • 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
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11
Q

condensation reactions

A
  • 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
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12
Q

hydrolysis reactions

A
  • reverse of condensation reaction

- involves the addition of a H2O unit for every covalent bond broken

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13
Q

photosynthesis

A
  • 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
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14
Q

overview of photosynthetic reactions

A
  • 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
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15
Q

respiration

A
  • 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
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16
Q

cycle of photosynthesis and respiration

A
  • photosynthesis: carbon sink, removes carbon from atmosphere
  • respiration: carbon source, releases carbon to atmosphere
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17
Q

types of proteins

A
  • fibrous proteins

- globular proteins

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18
Q

fibrous proteins

A
  • supports structure/movement
  • elongated molecules with a dominant secondary structure
  • insoluble in water
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19
Q

globular proteins

A
  • operate on the molecular level (e.g. enzymes, receptors)
  • compact spherical molecules with a dominant tertiary structure
  • soluble in water
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20
Q

examples of fibrous proteins

A
  • keratin: the protective covering in claws/hair/wool

- collagen: connective tissue in skin and tendons

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21
Q

examples of globular proteins

A
  • polymerase: catalyses anabolic reactions
  • insulin: hormone that controls + maintains blood glucose levels
  • haemoglobin: carries oxygen in the blood
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22
Q

amino acids

A
  • 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
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23
Q

types of amino acids

A
  • non-polar
  • polar
  • basic
  • acidic
    this is because they can exist as cations, anions, or zwitterions
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24
Q

zwitterions

A
  • molecules containing both positive and negative charges

- they are neutral as a whole

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25
Q

types of amino acids: non-polar

A
  • R group: hydrocarbon

e. g. alanine

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26
Q

types of amino acids: uncharged polar

A
  • R group: hydroxyl (OH), sulfhydryl (SH), or amide (CONH2)

e. g. serine

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27
Q

types of amino acids: basic

A
  • R group: amino (NH2)

e. g. lysine

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28
Q

types of amino acids: acidic

A
  • R group: carboxyl (COOH)

e. g. aspartic acid

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29
Q

properties of amino acids

A
  • 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
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30
Q

internal salts

A

zwitterions that formed charges due to acid-base reactions

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31
Q

relationship between charge of amino acid and pH

A
  • high pH = low [H+] = acts like acid (proton donor) = forms anion
  • low pH = high [H+] = acts like base (proton acceptor) = forms cation
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32
Q

isoelectric point

A
  • 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
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33
Q

bond between amino acids

A

peptide bond (in biochem we do NOT call them amide linkages)

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34
Q

how do amino acids switch between zwitterion - anion - cation states?

A
  • 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
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35
Q

proteins: primary structure

A
  • number and sequence of amino acids in the polypeptide chain
  • they are bonded covalently
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36
Q

proteins: secondary structure

A

folding of the polypeptide chain due to H bonds between peptide bonds (between C=O and N-H)

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37
Q

proteins: types of secondary structures

A
  • alpha helix

- beta pleated sheet

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38
Q

proteins: alpha helix

A
  • 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)

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39
Q

proteins: beta pleated sheet

A
  • 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)

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40
Q

differences in secondary structure between fibrous and globular proteins

A
  • 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
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41
Q

proteins: tertiary structure

A
  • 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
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42
Q

interactions that stabilize protein conformation

A
  • hydrophobic interactions
  • hydrogen bonding
  • ionic bonding
  • disulfide bridges
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43
Q

tertiary structure interactions: hydrophobic interactions

A

occurs between non-polar side chains

e.g. between two alkyl side chains

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44
Q

tertiary structure interactions: hydrogen bonding

A

occurs between polar side chains

e.g. between serine’s CH2OH and aspartic acid’s CH2COOH

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45
Q

tertiary structure interactions: ionic bonding

A

occurs between charged side chains

e.g. between lysine’s (CH2)4NH3+ and aspartic acid’s CH2COO+

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46
Q

tertiary structure interactions: disulfide bridges

A
  • between sulfur-containing amino acid cysteine

- these are covalent bonds so they’re the strongest of these interactions

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47
Q

factors affecting tertiary structure interactions

A
  • temperature
  • pH
  • presence of metal ions
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48
Q

proteins: quaternary structure

A
  • 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)
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49
Q

co-factors

A
  • 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)

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50
Q

enzyme-substrate complex

A
  • 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
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51
Q

enzymes: induced-fit mechanism

A
  • theorizes that an enzyme’s active site undergoes conformational changes in the presence of a substrate
  • it reshapes itself to allow a better fit
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52
Q

enzymes: Vmax

A
  • maximum velocity of enzyme under the experimental conditions
  • varies greatly between enzymes
  • affected by pH and temp
  • also expressed as turnover rate
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53
Q

turnover rate

A

(no of molecules of substrate processed into products) per (enzyme molecule) per (unit of time)

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54
Q

enzymes: Km

A
  • 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]
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55
Q

factors affecting enzyme activity

A
  • pH
  • temperature
  • presence of inhibitors (e.g. heavy metal ions)
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56
Q

factors affecting enzyme activity: heavy metal ions

A
  • 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
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57
Q

factors affecting enzyme activity: pH

A
  • changes in pH will react with the polypeptide to change its conformation
  • may cause denaturation
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58
Q

factors affecting enzyme activity: temperature

A
  • too high temps may break secondary, tertiary, and quaternary bonds
  • this causes denaturation
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59
Q

competitive inhibitors

A
  • 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]
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60
Q

non-competitive inhibitors

A
  • 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
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61
Q

coenzymes

A

organic molecules that aids enzyme function

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62
Q

cofactors

A

inorganic molecules that aids enzyme function (e.g. metal ions)

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63
Q

induced-fit model

A
  • 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
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64
Q

product inhibition

A
  • 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
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65
Q

irreversible inhibitors

A

inhibitor effects are permanent when the inhibitor’s binding to the enzyme is permanent
e.g. cyanide is an irreversible inhibitor of cytochrome oxidase

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66
Q

methods of analysing protein composition

A
  • chromatography

- gel electrophoresis

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67
Q

chromatography

A
  • 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
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68
Q

calculating Rf

A

distance traveled by solute / distance traveled by solvent

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69
Q

gel electrophoresis

A
  • 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
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70
Q

factors affecting rate of movement of ions in gel electrophoresis

A
  • charge
  • mass
  • voltage used
  • temperature
  • pH of the solution
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71
Q

factors affecting rate of movement of ions in gel electrophoresis: charge

A

higher charge = more movement

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72
Q

factors affecting rate of movement of ions in gel electrophoresis: mass

A

lower mass = more movement

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73
Q

protein assays

A

investigation procedures used to measure the concentration of protein in a sample

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74
Q

UV-visible spectroscopy

A
  • 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
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75
Q

spectrophotometer

A

used as a logging device to obtain absorption spectra

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76
Q

analyzing results of UV visible spectroscopy

A
  • 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
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77
Q

molar absorptivity

A

absorbance of a 1 mol/dm3 solution in a 1 cm cell at a specific wavelength

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78
Q

relationship between absorbance and concentration of solution

A

directly proportional

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79
Q

lipids

A
  • biomolecules containing CHO

- hydrophobic and only soluble in non-polar solvents

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80
Q

functions of lipids

A
  • 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
81
Q

efficiency of lipids vs carbohydrates as fat stores

A
  • 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
82
Q

drawbacks of excess lipids in the diet

A

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
83
Q

uses of steroids

A
  • 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
84
Q

triglycerides

A
  • 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
85
Q

phospholipids

A
  • 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
86
Q

hydrolysis of triglycerides/phospholipids

A

occurs at most pHs with the enzyme lipase

87
Q

saponification

A
  • hydrolysis of triglycerides in an alkali solution

- they make salts of fatty acids which can be used to make soap

88
Q

functions of cholesterol

A
  • 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)
89
Q

predicting relative melting points of fats and oils

A

higher unsaturation = more bent shape = less intermolecular bonds = lower melting point
EXCEPTION: trans fats are straight (that sounded peculiar) although they are unsaturated

90
Q

difference between saturated and unsaturated fatty acids

A
  • 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
91
Q

hydrolytic rancidity

A
  • 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
92
Q

determining degree of unsaturation in fats

A

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

93
Q

iodine number

A

number of grams of iodine which reacts with 100 grams of fat

94
Q

hydrogenation

A
  • addition reaction of fats + H2
  • carried out by food industry to increase saturation of oils
  • partial hydrogenation produces trans fats, which poses health risks
95
Q

define rancidity of fats

A
  • fats in the food industry may be stored for long periods of time
  • this may cause chemical changes, causing rancidity
96
Q

causes of rancidity of fats

A
  • oxidative rancidity

- hydrolytic rancidity

97
Q

hydrolytic rancidity

A
  • 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 :)
98
Q

oxidative rancidity

A

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
99
Q

steroids

A
  • lipids with a structure containing 4 fused rings (the steroidal backbone)
  • cholesterol is a steroid
100
Q

carbohydrates

A

as the name suggests, they are carbons with water

formula: Cx(H2O)y

101
Q

functions of carbohydrates

A
  • energy store

- structural support (plants only, with cellulose)

102
Q

bonding in monosaccharides

A
  • 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)
103
Q

characteristics of monosaccharides

A
  • simple sugars

- soluble in water (due to the polar hydroxyl/OH groups)

104
Q

structure of monosaccharides

A
  • 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
105
Q

forming disaccharides

A
  • 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
106
Q

forming polysaccharides

A
  • polysaccharides form by repetitions of condensation reactions
  • this results in a long chain of monosaccharide units held together by glycosidic bonds
107
Q

polysaccharides

A
  • sugar polymers
  • due to their large size, polysaccharides are all insoluble molecules
  • this also makes them ideal to store energy
108
Q

examples of polysaccharides

A
  • 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
109
Q

micronutrients

A
  • 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…)
110
Q

water-soluble vitamins

A
  • have polar bonds
  • can form H bonds with water
  • directly transported via bloodstream and filtered out with the kidneys
  • heat-sensitive
  • Vit B, C
111
Q

lipid-soluble vitamins

A
  • 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
112
Q

vit A

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)
113
Q

vit C

A
  • 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
114
Q

vit D

A
  • 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
115
Q

why are vitamins heat-sensitive?

A
  • heat and oxidation are related

- the oxidation reactions that vitamins undergo are endothermic, so are favored by higher temperatures

116
Q

causes of vitamin deficiency in some countries

A
  • poverty as a country.
  • poor distribution of food
  • over-processed food (vits are heat-sensitive)
  • Lack of education.
  • Climate change.
117
Q

consequences of vitamin deficiency

A

Vitamin A = night blindness
Vitamin B = anemia, fatigue, weight loss
Vitamin C = bleeding in gum (scurvy)
Vitamin D = rickets

118
Q

solutions to vitamin deficiency

A
  • 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!
119
Q

determine the concentration of a protein in solution from a calibration curve (NOTES)

A
  • 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
120
Q

DNA

A

deoxyribonucleic acid

  • nucleic acid
  • responsible for storing info on genetic characteristics
121
Q

RNA

A

ribonucleic acid

  • nucleic acid
  • enables info stored in DNA to be expressed by controlling the primary structures of synthesized proteins
122
Q

adaptations of DNA to its function

A
  • 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)
123
Q

nucleotides

A

monomers of nucleic acids

124
Q

components of a nucleotide

A
  • a pentose sugar
  • a phosphate group
  • a nitrogen base
125
Q

components of a nucleotide: pentose sugar

A

DNA: deoxyribose
RNA: ribose
difference – at C2, Ribose has a H and OH attached but deoxyribose has 2 Hs

126
Q

components of a nucleotide: nitrogen base

A
  • purines: (A/G bases) larger and contain 2 fused rings

- pyramidines: (C/T/U bases) smaller and only has 1 ring

127
Q

structure of a nucleotide

A
  • the nitrogen base always attaches to C1

- the phosphate group always attaches to C5 (the 5’ position)

128
Q

structure of polynucleotides

A
  • 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
129
Q

geometry of DNA

A
  • 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
130
Q

structural differences between DNA and RNA

A
  • 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
131
Q

how can DNA associate with histones

A
  • 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
132
Q

function of histones in DNA

A

they add to stability by supercoiling DNA

133
Q

how does DNA lead to protein synthesis?

A
  • 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
134
Q

how can DNA get transferred between species?

A
  • 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
135
Q

stability of the DNA structure

A
  • 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
136
Q

pros of GMO foods

A
  • it stays fresh for longer
  • improved flavor and texture
  • resistance to pests
  • better climate tolerance
  • can alter nutrient content, and add vitamins and vaccines!
137
Q

cons of GMO foods

A
  • 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
138
Q

biological pigments

A

coloured compounds produced by metabolism

139
Q

highly conjugated structures

A
  • 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
140
Q

why are pigments colored?

A
  • 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
141
Q

types of pigments

A
  • porphyrins
  • carotenoids
  • anthocyanins
142
Q

porphyrins

A
  • 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
143
Q

common porphyrins

A
  • hemoglobin
  • chlorophyll
  • myoglobin
  • cytochromes
144
Q

how chlorophyll works, chemically

A
  • 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
145
Q

difference between hemoglobin and myoglobin

A
  • 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
146
Q

how does oxygen bind to hemoglobin/myoglobin?

A
  • 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
147
Q

how do cytochromes work, chemically?

A
  • 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.
148
Q

factors influencing oxygenation of hemoglobin

A
  • temperature
  • pH
  • location
149
Q

factors influencing oxygenation of hemoglobin: temperature

A

↑ temp = ↓ affinity of hemoglobin for O2

- oxyhemoglobin releases oxygen more readily in higher temps (e.g. during high metabolic activity in cells)

150
Q

factors influencing oxygenation of hemoglobin: pH

A

↓ 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

151
Q

factors influencing oxygenation of hemoglobin: location

A
  • 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
152
Q

competitive inhibition of hemoglobin

A
  • CO has higher affinity to hemoglobin than oxygen

- thus it prevents oxygen from binding

153
Q

carotenoids

A
  • 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
154
Q

significance of carotenoids

A
  • 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)
155
Q

stability of carotenoids

A
  • 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
156
Q

stability of chlorophyll

A
  • 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
157
Q

anthocyanin

A
  • 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
158
Q

solubility of anthocyanins

A
  • 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
159
Q

forming anthocyanins

A
  • reaction between sugars and proteins
  • light-dependent
  • this is why fruit often changes colour as its sugar concentration increases (i.e. when it ripens)
160
Q

factors affecting anthocyanin color

A
  • pH

- the central metal ion

161
Q

factors affecting anthocyanin color: pH

A
  • 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
162
Q

factors affecting anthocyanin color: central metal ion

A
  • 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
163
Q

techniques used in analysis of pigments

A
  • paper chromatography

- thin-layer chromatography

164
Q

thin-layer chromatography

A
  • 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
165
Q

stereoisomers

A

molecules with the same chemical formula but with different spatial arrangements of the atoms

166
Q

significance of stereochemistry in biochemistry

A
  • many biopolymers can exist as stereoisomers

- metabolic reactions are usually stereospecific

167
Q

stereochemistry in amino acids

A
  • 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
168
Q

D-amino acid

A

D = dextrorotation

i. e. rotation to right in polarized light
- often noted as +

169
Q

L-amino acid

A

L = levorotation

i. e. rotation to the left in polarized light
- often noted as -
- biological systems only use L-amino acids

170
Q

differences between D- and L-amino acids

A
  • 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

171
Q

stereochemistry in lipids

A
  • 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
172
Q

difference between cis and trans fats

A
  • cis fats can’t easily arrange themselves side by side to solidify
  • so they generally have lower melting points than their trans isomer
173
Q

hydrogenation of fats

A

addition rxn between H2 and an unsaturated fat

catalyst: finely divided Ni
- used in the food industry (e.g. production of margarine)

174
Q

pros and cons of hydrogenation of fats

A
  • 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
175
Q

health risks of trans fats

A
  • raises LDL cholesterol levels in blood
  • reduces HDL cholesterol levels in blood
  • basically, is related to cardiovascular diseases
176
Q

stereochemistry in carbohydrates

A
  • 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
177
Q

alpha- carbohydrates

A

e. g. starch (includes amylose and amylopectin) and glycogen
- very branched and compact spiral structure
- good for energy storage
- α-glycosidic link

178
Q

beta- carbohydrates

A

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

179
Q

importance of cellulose

A
  • 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
180
Q

stereochemistry in vitamins

A
  • 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
181
Q

xenobiotics

A
  • 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
182
Q

examples of xenobiotics

A
  • antibiotics
  • MSG
  • pollutants
  • plastic
  • certain hormones (e.g. oestrogen in fish!!)
183
Q

effect of xenobiotics in organisms

A
  • 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
184
Q

reducing xenobiotics using sewage treatment plants

A
  • 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
185
Q

biomagnification

A

the increase in concentration of a xenobiotic substance in a food web

186
Q

why does biomagnification occur?

A
  • 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
187
Q

example of biomagnification

A
  • 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
188
Q

amelioration

A
  • means ‘making things better’

- in this context it refers to reducing problems related to xenobiotics

189
Q

forms of amelioration for xenobiotics

A
  • using biodegradable substances
  • host-guest chemistry
  • bioremediation
190
Q

amelioration: host-guest chemistry

A
  • 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
191
Q

amelioration: using biodegradable substances

A
  • 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
192
Q

amelioration: bioremediation

A
  • 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
193
Q

green chemistry

A
  • 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
194
Q

assessing the “greenness” of a substance used in biochemical research

A
  • effective mass yield
  • atom economy
  • environmental (E) factor
  • EcoScale
195
Q

assessing the “greenness” of a substance used in biochemical research: effective mass yield

A

% of mass of wanted products over mass of unwanted products

Problems:

  • ‘unwanted’ is subjective
  • method fails to assess toxicity of products
196
Q

assessing the “greenness” of a substance used in biochemical research: atom economy

A

% 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!)
197
Q

assessing the “greenness” of a substance used in biochemical research: E factor

A

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

198
Q

assessing the “greenness” of a substance used in biochemical research: EcoScale

A

takes into account the cost, safety, technical set-up,

energy and purification aspects

Chemistry IB HL (2016+) (13 decks)

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