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Biology pt2 > 1.4 Proteins > Flashcards

1.4 Proteins Flashcards

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1
Q

General structure of an amino acid

A
  • COOH carboxyl group
  • R variable side group consists of carbon chain and may include other functional groups e.g. benzene ring
  • NH2 amine group
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2
Q

What does Biuret test do?

A

Confirms presence of peptide bond

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3
Q

Describe how to test for proteins in a sample

A
  • Add 2cm3 food sample to test tube
  • Add equal volume of sodium hydroxide to sample at room temp
  • Add two drops of dilute copper (II) sulfate solution. Mix
  • Positive result: colour changes from blue to purple
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4
Q

How many amino acids are there and how do they differ from one another?

A
  • 20
  • Differ only by side ‘R’ group
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5
Q

How do dipeptides and polypeptides form?

A
  • Condensation reaction forms peptide bond (-CONH-) and eliminates molecule of water
  • Dipeptide: two amino acids
  • Polypeptide: 3 or more amino acids
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6
Q

How many levels of protein structure are there?

A

4

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7
Q

Define ‘primary structure’ of a protein

A
  • Sequence, number and type of amino acids in the polypeptide
  • Determined by sequence of codons on mRNA
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8
Q

Define ‘secondary structure’ of a protein

A

hydrogen bonds form between O delta-negative (slightly negative) attached to -C=O and H delta-positive (slightly positive) attached to -NH

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9
Q

Describe the 2 types of secondary protein structure

A

Alpha helix
- All N-H bonds on the same side of protein chain
- Spiral shape
- H-bonds parallel to helical axis
Beta pleated sheet
- N-H and C=O groups alternate from one side to the other

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10
Q

Define tertiary structure of a protein.

A

3D structure formed by further folding of polypeptide

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11
Q

Name the bonds present in the tertiary structure of a protein

A
  • Disulfide bridges
  • Ionic bonds
  • Hydrogen bonds
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12
Q

Describe disulfide bonds in tertiary structure of proteins

A

Strong covalent S-S bonds between molecules of the amino acid cysteine

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13
Q

Describe ionic bonds in the tertiary structure of proteins

A

Relatively strong bonds between charged R groups (pH changes causes these bonds to break)

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14
Q

Describe hydrogen bonds in tertiary structure of proteins

A

Numerous and easily broken

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15
Q

Define quaternary structure of a protein

A
  • Functional proteins may consist of more than one polypeptide
  • Precise 3D structure held together by the same types of bond as tertiary structure
  • May involve addition of prosthetic groups e.g. metal ions or phosphate groups
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16
Q

Describe structure and function of globular proteins

A
  • Spherical and compact
  • Hydrophilic R groups face outwards and hydrophobic R groups face inwards = usually water-soluble
  • Involved in metabolic processes e.g. enzymes and haemoglobin
17
Q

Describe structure and function of fibrous proteisn

A
  • Can form long chains or fibres
  • Insoluble in water
  • Useful for structure and support e.g. collagen in skin
18
Q

Outline how chromatography could be used to identify amino acids in a mixture

A
  • Use capillary tube to spot mixture onto pencil origin line and place chromatography paper in solvent
  • Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper and solubility in solvent
  • Use revealing agent or UV light to see spots
  • Calculate Rf values and match to database
19
Q

What are enzymes

A
  • Biological catalysts for intra and extracellular reactions
  • Specific tertiary structure determine shape of active site, complementary to a specific substrate
  • Formation of enzyme-substrate complexes lowers activation energy of metabolic reactions
20
Q

Explain induced fit model of enzyme action

A
  • Shape of active site not complementary to substrate and is flexible
  • conformational changes enables ES complexes to form
  • Puts a strain on substrate bonds, lowering activation energy
21
Q

How have models of enzyme action changed?

A
  • Initially lock and key model: rigid shape of active site complementary to only 1 substrate
  • Currently induced fit model: also explains why binding at allosteric sites can change the shape of active site
22
Q

How could a student identify the activation energy of a metabolic reaction from an energy level graph?

A

Difference between free energy of substrate and peak of curve

23
Q

Name 5 factors that affect the rate of enzyme controlled reactions

A
  • Enzyme concentration
  • Substrate concentration
  • Concentration of inhibitors
  • pH
  • Temperature
24
Q

How does substrate concentration affect rate of reaction?

A
  • Given that enzyme concentration is fixed, rate increases proportionally to substrate concentration
  • Rate levels off when maximum number of ES complexes form at any given time
25
Q

How does enzyme concentration affect rate of reaction

A
  • Given that substrate is in excess, rate increases proportionally to enzyme concentration
  • Rate levels off when maximum number of ES complexes form at any given time
26
Q

How does temperature affect rate of reaction?

A
  • Rate increases as kinetic energy increases and peaks at optimum temperature
  • Above optimum, ionic and H-bonds in tertiary structure break = active site no longer complementary to substrate (denaturation)
27
Q

How does pH affect rate of reaction?

A
  • Enzymes have a narrow optimum pH range
  • Outside range, H+/OH- ions interact with H-bonds and ionic bonds in tertiary structure = denaturation
28
Q

Contrast competitive and non-competitive inhibitors

A
  • Competitive: similar shape to substrate=bind to active site, non-competitive: bind at allosteric binding site
  • Competitive: do not stop reaction - ES complex forms when inhibitor is released, non-competitive: may permanently stop reaction - triggers active site to change shape
  • Competitive: increasing substrate concentration decreases their effect, non-competitive: increasing substrate concentration has no impact on their effect
29
Q

Outline how to calculate rate of reaction from a graph

A
  • Calculate gradient of line or gradient of tangent to a point
  • Initial rate: draw tangent at t=0
30
Q

Outline how to calculate rate of reaction from raw data

A

Change in concentration of product or reactant/time

31
Q

Why is it advantageous to calculate initial rate?

A

Represents maximum rate of reaction before concentration of reactants decreases and ‘end product inhibition’

32
Q

State formula for pH

A

pH=-log10[H+]

Biology pt2 (33 decks)

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