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IB Chemistry HL > B: Proteins > Flashcards

B: Proteins Flashcards

1
Q

Catabolic Reactions

A

Breakdown reactions

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2
Q

Anabolic reactions

A

Synthesis reactions

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3
Q

Hydrolysis

A

Where molecules are broken down by the reaction of dilute acid/ alkali in high temps (reflux)

  • enzyme reactions 37C
  • Proteins –> amino acids
  • Starch –> simple sugars
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4
Q

Condensation Polymerization

A

Anabolism

monomers combine together to form polymers and water is eliminated

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5
Q

Functions of Proteins

A
  • Enzymes - biological catalysts
  • Transport proteins - haemoglobin
  • Immunoproteins - antibodies
  • Hormones - chemical messengers
  • structural proteins - collagen
  • Energy source - when fats and carbohydrates become scarce
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6
Q

Amino Acids

Functional Groups and chemical properties

A
  • COOH carboxy
    • can be considered as weak acids as they are partially dissociated aqueous solution
  • NH2 Amine
    • behaves as base because they accept protons
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7
Q

Amino Acids

Zwitterions

A
  • Amino acids exist as zwitterions in solid or aqueous solution
  • Isoelectric point - pH wehre Amino acid becomes zwitterion
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8
Q

Dipeptide

A

2-Aminoacids will combine together in a condensation reaction to form a dipeptide –> anabolic reaction, energy required

compounds will have an amide/ peptide link

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9
Q

Thin Layer Chromatography

A

Alumina Al2O3 + Silica SiO2

Retardation factor x/y –> used to identitfy the components as long as external conditions remain the same

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10
Q

Gel Electrophoresis

A

Buffer solution - zwitter ion used to control the degree of ionization

  • Polyacylamide gel (PAGE)
  • locating agent: Ninhydrin
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11
Q

Gel electrophoresis - Amino Acid separation

A

Amino Acids will separate according to

  • their Mr
  • The overall charge on the molecule
  • potential difference applied
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12
Q

Primary Structure

A
  • Sequence of Amino Acids in the polypeptide chain
  • bond responsible: peptide bond/ amide link
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13
Q

Secondary Structure

A

The folding of the polypeptide chain as a result of hydrogen bonding

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14
Q

Proteins

A

Polymers composed of amino acids (monomers)

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15
Q

Secondary Structure

alpha-helix

A

alpha-helix

H bond between the C=O of 1 peptide bond and the NH of the peptide bond 4 amino acids down

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16
Q

Secondary Structure

Beta-pleated Sheets

A

ß-pleated sheet

consists of 2 or more stretches of amino acids in which the polypeptide chain is almost fully extended

H bonds form between a C=O on one strand and an NH on an adjacent strand

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17
Q

Tertiary Structure

A

The twisting and folding of the Secondary structure to form a specific 3D shape

Bonds involved

  • LDF - between nonpolar side chains
  • Hydrogen - between polar side chains
  • Ionic - between polar side chains
  • Disulfide bridges (covalent) - between the side chains of cysteine which contain CH2-SH
18
Q

Quaternary Structure

A
  • Interactions between polypeptide chains (sub-units)
  • sub-units held together by various intermolecular forces
    • Dimers - 2 sub-units
    • Trimers - 3 sub-units
    • Tetramers - 4 sub-units
    • (sub units may be identical or different)
19
Q

Biological catalysts - Enzymes

A
  • increases rate of reaction by lowering the activation energy of the forward and backward reactions equally
  • remains unchanged in mass and composition
20
Q

Enzymes

A

E + S <—> ES —> E + P

  1. Enzyme binds to substrate @ active side
    1. hydrophobic pocket, nonpolar
  2. Active complex
  3. E –> unchanged in mass and composition ; P –> products
21
Q

Induced Fit theory

A
22
Q

Lock and Key theory

A
23
Q

Enzyme Kinetics

A
  • Molecules must have Ea and a certain orientation to react successfully
  • As conc. of substrate increases, rate of reaction increases proportionally
    • because of sufficient active sites to bind to
  • As the reaction progresses, the active sites are becoming occupied –> fewer are available and rate of reaction decreases
  • Eventually, a maximum value is reached, after which the rate no longer increases
24
Q

Enzymes - Effect of Temperature

A
  1. collisions with E > Ea, orientation allows for the ES activated complex to form, frequency of collisions is high
  2. optimum temperature at which the rate is a maximum
  3. due to increased vibration of the molecule, the active site’s shape changes and hence fewer substrate molecules can bind –> denature
25
Q

Enzymes - Effect of pH

A

Low pH - Protonation of NH2

  • changes the shape of the active site –> prevents formation of ES complex

High pH - Denaturisation

  • the charge on the R group changes –> responsible for the formation of attractions between the enzyme and substrate –> denaturisation
26
Q

Enzymes and Heavy Metal Ions

A
  • Pb, Ag, Hg
  • Have a strong affinity for the S-H groups in enzymes. These groups form the quaternery structure of the enzyme
    • the shape is altered and the enzyme can no longer function effectively
27
Q

Fibrous Proteins

A
  • Shape: long and narrow (secondary structures)
  • Role: structural (strength and support)
  • Solubility: mostly insoluble
  • Sequence: repetative amino acid sequence
  • Stability: less sensative to changes in pH / temp
  • Examples: Collagen, Keratin
28
Q

Globular Proteins

A
  • Shape: rounded / spherical
  • Role: functional (catalyst and transport)
  • Solubility: mostly soluble
  • Sequence: irregular amino acid sequence
  • Stability: more sensative
  • Examples: hemoglobin, insulin, catalase
29
Q

Michaelis-Menten Curve - Vmax

A

Vmax - the point where all the active sites are bound to substrate (enzyme is saturated)

  • High Vmax = fast conversion of substrate per unit tiem
30
Q

Michaelis-Menten Curve - Km

A

Km Michaelic Constant - concentration of substrate when the rate of the reaction has 0.5Vmax

  • gives indication of how strongly the enzyme is bound to the substrate
    • the lower Km the stronger the bonding between the enzyme and substrate
  • Km does not depend on substrate concentration
31
Q

Inhibitors - Temperature

A
  • Low temp - molecules of enzyme will have low values of Kinetic E.
  • High temp - denaturing happens, enzymes lose its tertiary / quaternary structure and will no longer function
32
Q

Inhibitors - pH

A
  • Low pH - protonation of NH2 –> NH3+
  • High pH - becomes anion –> ionic bonds in the quaternary structure are disrupted
33
Q

Inhibitors - Chemical

A
  • React with the S-H bonds preventing the formation of S-S links
    • can be removed from H2O supply by host-guest chemistry
34
Q

Competitive Inhibitors

A
  • reduces enzyme activity
  • these substances bind directly and reversibly to the active site without producing products
  • they compete with the substrate for the active sites –> reduces the numbre of enzyme molecules available to bind with the substrates
35
Q

Noncompetitive Inhibitors

A
  • Inhibitor binds reversibly to the enzyme away from the active site at the allosteric site –> changes the shape of the active site
    • The enzyme loses its tertiary structure
36
Q

UV Visible Spectrophotometry - π e-

A
  • Chromophores
    • molecules with π electrons ( C=C, C=O, C=-N)
  • π e- absorbs energy to excited state; releases energy to return to ground state
    • wavelength corresponds to wavelength of UV light
37
Q

Beer-Lambert Law

A

A = log10( I0/I ) = Σlc

A = absorbance

l = pathlength (1cm)

c = concentration moldm-3

Σ = molar absorptivity constant

38
Q

UV spectrophotometry - process

A
  1. scan sample to determine the wavelength at which the chromophore absorbs UV
  2. make a range of standard solutions of known concentration and measure absorbance at the wavelength above
  3. plot the standard curve
  4. measure the absorbance of the sample and extrapolate
39
Q

Buffer Solutions - Acid buffer

A

weak acid + salt of weak acid

CH3COOH CH3COO-Na+

ethanoic acid sodium ethanoate

CH3COOH <—> CH3COO- + H+

CH3COO-Na+ —-> CH3COO- + Na+

  • adding acid: H+ reacts with conjugate base reservoir –> equilibrium shifts to the left
  • adding base: OH- reacts with H+ to give H2O –> equilibrium shifts to the right, using up acid
40
Q

Buffer Solutions - Base buffer

A

weak base + its salt

NH3 NH4Cl

ammonia ammonium chloride

NH3 + H2O <—> NH4+ + OH-

NH4Cl —> NH4+ + Cl-

  • adding acid: H+ reacts with NH3, moves equilibrium right
  • adding base: OH- reacts with NH4+, shifts equilibrium left
41
Q

Henderson-Hasselboch Equation

A

pH = pKa + log([A-]/[HA])

Ka = [H+][A-] / [HA]

[H+] = Ka[acid] / [salt]

IB Chemistry HL (19 decks)

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