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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

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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7
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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8
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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9
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 enzymes (polymerases)
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10
Q

hydrolysis reactions

A
  • reverse of condensation reaction

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

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11
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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12
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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13
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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14
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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15
Q

types of proteins

A
  • fibrous proteins

- globular proteins

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16
Q

fibrous proteins

A
  • supports structure/movement
  • elongated molecules with a dominant secondary structure
  • insoluble in water
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17
Q

globular proteins

A
  • tools operating on the molecular level (e.g. enzymes, receptors)
  • compact spherical molecules with a dominant tertiary structure
  • soluble in water
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18
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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19
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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20
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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21
Q

types of amino acids: non-polar

A
  • R group: hydrocarbon

e. g. alanine

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22
Q

types of amino acids: uncharged polar

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

e. g. serine

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23
Q

types of amino acids: basic

A
  • R group: amino (NH2)

e. g. lysine

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24
Q

types of amino acids: acidic

A
  • R group: carboxyl (COOH)

e. g. aspartic acid

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25
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 (due to carrying both an acidic and a basic group)
  • can act as pH buffers
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26
Q

zwitterions

A

molecules containing both positive and negative charges

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27
Q

internal salts

A

zwitterions that formed charges due to acid-base reactions

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28
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
29
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
30
Q

bond between amino acids

A

peptide bond

31
Q

proteins: primary structure

A

number and sequence of amino acids in the polypeptide chain

32
Q

proteins: secondary structure

A

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

33
Q

proteins: types of secondary structures

A
  • alpha helix

- beta pleated sheet

34
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)

35
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)

36
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
37
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
38
Q

interactions that stabilize protein conformation

A
  • hydrophobic interactions
  • hydrogen bonding
  • ionic bonding
  • disulfide bridges
39
Q

tertiary structure interactions: hydrophobic interactions

A

occurs between non-polar side chains

e.g. between two alkyl side chains

40
Q

tertiary structure interactions: hydrogen bonding

A

occurs between polar side chains

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

41
Q

tertiary structure interactions: ionic bonding

A

occurs between charged side chains

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

42
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

43
Q

factors affecting tertiary structure interactions

A
  • temperature
  • pH
  • presence of metal ions
44
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)
45
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)

46
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
47
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
48
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
49
Q

turnover rate

A

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

50
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]
51
Q

factors affecting enzyme activity

A
  • pH
  • temperature
  • presence of inhibitors (e.g. heavy metal ions)
52
Q

factors affecting enzyme activity: heavy metal ions

A
  • positive metal ions will react with sulfhydryl groups (SH), displacing the H ion to form a covalent bond with the S
  • this disrupts the folding (secondary structure) and may change the shape of the active site and its ability to bind substrates
53
Q

competitive inhibitors

A
  • inhibitors that “compete” with the substrate to bind at the active site
  • they usually have a 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]
54
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
55
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
56
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

57
Q

methods of analysing protein composition

A
  • chromatography

- gel electrophoresis

58
Q

chromatography

A

(fill in)

59
Q

chromatography: process

A

(fill in)

60
Q

gel electrophoresis

A

(fill in)

61
Q

gel electrophoresis: process

A

(fill in)

62
Q

composition of generic pH buffers

A
  • weak acid/base and its conjugate

- weak base + salt of weak base & strong acid (or vice versa for acidic buffers)

63
Q

determining the pH of buffer solutions

A 
HA = weak acid
MA = salt of weak acid + strong base

Assumptions made:

  • weak acids’ dissociation is considered negligible, so HA = HA
  • the salt is considered to be fully dissociated, so MA = A-

Ka = [H+][A-]/[HA], so [H+] = Ka [HA]/[A-]
Using the assumptions, we can say [H+] = Ka HA/MA
Using the Henderson-Hasselbalch equation,
pH = pKa + log([salt]/[acid])

64
Q

protein assays

A

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

65
Q

UV-visible spectroscopy

A
  • technique used in protein assays
  • 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
66
Q

spectrophotometer

A

used as a logging device to obtain absorption spectra

67
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
68
Q

molar absorptivity

A

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

69
Q

relationship between absorbance and concentration of solution

A

directly proportional

Chemistry IB HL (2016+) (13 decks)

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