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Biology Year 12 > Proteins (1) > Flashcards

Proteins (1) Flashcards

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1
Q

Draw the structure of an amino acid.

A

Look at notes

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2
Q

What is the COOH group?

A

carboxyl/carboxylic group

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3
Q

What is the NH2 group?

A

amine/amino group

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4
Q

What is the R group?

A

variable side group which consists of a carbon chain and may include other functional groups e.g. benzene ring or -OH (alcohol)

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5
Q

How many amino acids are there?

A

20

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6
Q

How do different amino acids differ?

A

differ only by the side ‘R’ group

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7
Q

What bond forms between 2 amino acids?

A

peptide bond

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8
Q

Where is the peptide bond between 2 amino acids?

A

H of one and OH of another

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9
Q

What is used to test for proteins?

A

biuret reagent

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10
Q

What does biuret reagent do?

A

confirms presence of peptide bonds, which shows proteins are present

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11
Q

How do you test for proteins?

A

1) add an equal volume of sodium hydroxide to sample at room temperature
2) add drops of dilute copper (II) sulfate solution and swirl to mix
3) positive result = change from blue to purple

(first 2 steps make biuret reagent)

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12
Q

What is a dipeptide?

A

2 amino acids

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13
Q

What is a polypeptide?

A

3 or more amino acids

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14
Q

How do dipeptides and polypeptides form?

A

When a condensation reaction forms a peptide bond between 2 amino acids

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15
Q

What is the primary structure of a protein?

A

sequence, number and type of amino acids in the polypeptide

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16
Q

What determines the primary structure of a protein?

A

the sequence of codons on mRNA

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17
Q

What is the secondary structure of a protein?

A
  • where H bonds form between partially negative O and partially positive Nitrogen
  • 2 types: alpha-helix and beta-pleated sheets
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18
Q

What is the tertiary structure of a protein?

A
  • 3D structure formed by further folding of polypeptide
  • has disulfide bridges, ionic bonds and hydrogen bonds
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19
Q

What is the structure of the alpha-helix?

A
  • all nitrogen-hydrogen bonds on same side of protein chain
  • spiral shape
  • H-bonds parallel to helical axis
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20
Q

What is the structure of the beta-pleated sheets?

A

nitrogen-hydrogen and carbon monoxide groups alternate from one side to the other

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21
Q

What is the structure of disulfide bridges?

A

strong covalent S-S bonds between molecules of cysteine (an amino acid)

22
Q

What is the structure of ionic bonds?

A

relatively strong bonds between charged R groups

23
Q

What causes ionic bonds to break?

A

pH changes

24
Q

What are hydrogen bonds?

A

numerous + easily broken

25
Q

What is the quaternary structure of a protein?

A
  • precise 3D structure held together by disulfide bridges, ionic bonds and hydrogen bonds
  • made up of polypeptides
  • functional proteins may have more than 1 polypeptide
  • may involve addition of prosthetic group e.g. metal ions or phosphate groups
26
Q

What is the structure of globular proteins?

A
  • spherical + compact
  • hydrophilic R groups face outwards and hydrophobic R groups face inwards, therefore they are usually water soluble
27
Q

What is the role of globular proteins?

A

involved in metabolic processes e.g. enzymes and haemoglobin

28
Q

What is the role of fibrous proteins?

A
  • can form long chains or fibres
  • insoluble in water
  • useful for structure and support e.g. collagen in skin
29
Q

What are enzymes?

A

biological catalysts for intra and extracellular reactions

30
Q

What determines the shape of an enzymes active site?

A

specific tertiary structure

31
Q

What is the role of an active site?

A

complementary to a specific substrate

32
Q

What lowers activation energy for metabolic reactions?

A

formation of enzyme-substrate complexes

33
Q

What does the formation of enzyme-substrate complexes do?

A

lowers activation energy for metabolic reactions

34
Q

How can chromatography be used to identify amino acids in a mixture?

(5 points)

A

1) use a capillary tube to spot mixture onto pencil origin line
2) place chromatography paper in solvent
3) allow solvent to run until almost touches other end of paper
4) use revealing agent or UV light to see spots
5) calculate Rf values and match to data base

35
Q

How are amino acids able to be separated using chromatography?

A

amino acids move different distances based on relative attraction to paper and solubility in solvent

36
Q

What does the induced fit model suggest?

A
  • shape of active site is not directly complementary to substrate and is flexible
  • conformational change enables enzyme-substrate complexes to form
  • this puts strain on substrate bonds, lowering activation energy
37
Q

How have models of enzyme action changed?

A
  • initially lock & key model
  • currently induced fit model
38
Q

What did the lock & key model suggest?

A

rigid shape of active site complementary to only 1 substrate

39
Q

What does the induced fit model explain?

A

explains why binding at allosteric sites can change the shape of an active site

40
Q

How can the activation energy of a metabolic reaction be identified from an energy level diagram?

A

difference between free energy of substrate and peak of curve

41
Q

What are 5 factors that affect rate of enzyme-controlled reactions?

A

1) enzyme concentration
2) substrate concentration
3) concentration of inhibitors
4) pH
5) temperature

42
Q

How does substrate concentration affect rate of reaction?

A
  • if enzyme concentration is fixed, rate increases proportionally to substrate concentration
  • rate levels off when max number of enzyme-substrate complexes form at any given time
43
Q

How does enzyme concentration affect rate of reaction?

A
  • if substrate is in excess, rate increases proportionally to enzyme concentration
  • rate levels off when max number of enzyme-substrate complexes form at any given time
44
Q

How does temperature affect rate of reaction?

A
  • rate increases as kinetic energy increases, and peaks at optimum temperature
  • above optimum, ionic and hydrogen bonds break so active site is no longer complementary to substrate (denaturation)
45
Q

How does pH affect rate of reaction?

A
  • enzymes have a narrow optimum pH range
  • outside range, Hydrogen ions and hydroxide ions interact with H-bonds and ionic bonds in 3D structure (denaturation)
46
Q

How do you calculate rate of reaction from a graph?

A
  • calculate gradient of line or gradient of tangent to a point
  • for initial rate - draw tangent at t=0
47
Q

How do you calculate rate of reaction from raw data?

A

change in concentration of product/reactant
____________________________
time

48
Q

What is the equation to work out pH?

A

-log10 [H+]

49
Q

Describe competitive inhibitors.

A
  • similar shape to substrate so bind to active site
  • do not stop reaction as E-S complex forms when inhibitor is released
  • increasing substrate concentration decreases their effect
50
Q

Describe non-competitive inhibitors.

A
  • bind at allosteric binding site
  • may permanently stop reaction as they trigger active site to change shape
  • increasing substrate concentration has no impact on their effect
51
Q

Why is it advantageous to calculate initial rate?

A

represents max rate of reaction before concentration of reactants decreases and ‘ends product inhibition’

Biology Year 12 (22 decks)

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