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B = Biological Molecules & Cells = > Proteins > Flashcards

Proteins Flashcards

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Organic Chemistry 101 flashcards
1
Q

How many different types of amino acids are there and how do they differ?

A

20

Differ only by side ‘R’ group.

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2
Q

Draw the general structure of amino acids.

A

Central carbon
Hydrogen bonded to carbon
Amine group (NH₂)
Carboxyl group (-COOH)
R group (different for every amino acid)

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3
Q

Name the elements present in a protein.

A

Carbon
Hydrogen
Oxygen
Nitrogen

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4
Q

How do you test for proteins in a food sample?

A

Biuret test confirms presence of peptide bonds,

1~ Add equal volume of NaOH to sample at room temp.
2~ Add drops of dilute copper (II) sulfate solution.
Swirl to mix.
Positive result: colour change - blue to purple.
Negative result: solution remains blue.

Steps 1 & 2 make Biuret reagent.

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5
Q

What is a dipeptide?

A

When 2 amino acids form a peptide bond during a condensation reaction & eliminates water molecules.

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6
Q

What is a polypeptide?

A

When 3 or more amino acids form peptide bonds during a condensation reaction.

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7
Q

What is a peptide bond?

A

A bond formed when amino acids join together.

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8
Q

What is the functional group of a peptide bond?

A

(-CONH-)

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9
Q

What are the 4 levels of protein structures?

A

Primary
Secondary
Tertiary
Quaternary

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10
Q

Where do amino acids bond together?

A

In ribosomes.

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11
Q

What enzyme breaks peptide bonds during a hydrolysis reaction?

A

Protease.

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12
Q

What’s the difference between a polypeptide and a protein?

A

A polypeptide has to fold into a complex, 3D shape in order to be a protein and carry out its function.

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13
Q

What is the primary structure of a protein?

A

The sequence of amino acids linked together to form a polypeptide chain.

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14
Q

Why is the primary structure of a protein important?

A

Helps determine the final 3D shape of a protein.

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15
Q

Why is the shape of a protein important?

A

It’s important for its function.
Changing a single amino acid in the primary structure can prevent the protein carrying out its function effectively.

E.G. if the active site of an enzyme changes, it cannot break down molecules effectively as the substrate no longer fits in the enzyme.

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16
Q

What is the secondary structure of a protein?

A

The REAL answer:
The H bonds cause the polypeptide to fold into ALPHA-HELIX or BETA-PLEATED SHEETS.

HOW is it formed?
When hydrogen bonds form since the partially negative oxygen ion (Oδ-) is attracted to the partially positive hydrogen ion (δ+).

The NH in 1 amino acid bonds to the C=O in another amino acid.

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17
Q

Where is the Oδ- and the Hδ+ found in the polypeptide chain?

A

The partially negative oxygen is attached to…
C=O

The partially positive hydrogen is attached to…
NH

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18
Q

What are the 2 types of secondary protein structures?

A

Alpha helix (α-helix)

Beta-pleated sheet (β-pleated sheet)

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19
Q

Describe the alpha helix secondary protein structure.

A

Spiral shape
Weak H-bonds hold the structure in place
All N-H bonds on same side of protein chain.

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20
Q

Describe the beta-pleated sheet secondary protein structure.

A

Sheet-like structure.
Weak H-bonds between amino acids hold shape in place.
N-H & C=O groups alternate from one side to the other.

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21
Q

How is the type of secondary structure determined?

A

By the primary structure in that region.

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22
Q

What is the tertiary structure of a protein?

A

The 3D structure formed by further folding of polypeptide.

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23
Q

Name the bonds present in the tertiary structure.

A

Disulfide bridges
Ionic bonds
Hydrogen bonds

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24
Q

Why is the tertiary structure critical for how a protein functions?

A

Active site of an enzyme depends on the protein forming a very specific tertiary structure.

If change tertiary structure of enzyme by heating it, shape of active site changes and becomes DENATURED.

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25
Q

Describe each type of bond in the tertiary structure of proteins.

A

= Disulfide bridges =
Strong covalent S-S bonds.

= Ionic bonds =
Strong bonds between charged R groups.

= Hydrogen bonds =
Many of them - easily broken (weak)

26
Q

What is the quaternary structure of a protein?

A

Shows how the individual subunits (polypeptides) are arranged to form a larger 3D structure.

Basically a group of polypeptides.

Only applies to proteins with AT LEAST 2 subunits.

27
Q

What are the features of a quaternary protein structure?

A

Contain non-proteins molecules called “prosthetic groups” (e.g metal ions & phosphate groups) which help proteins carry out their role.

Contains more than 1 subunits.

28
Q

What are the 2 types of proteins?

A

Globular proteins

Fibrous proteins

29
Q

Describe the structure and function of globular proteins.

A

Spherical & compact.
Involved in metabolic processes
Globular proteins include enzymes & haemoglobin

Hydrophilic R groups face outwards
Hydrophobic R groups face inwards…

so they’re SOLUBLE in water.

30
Q

Describe the structure and function of fibrous proteins.

A

Can form long chains or fibres.
INSOLUBLE in water.
Useful for structure & support (e.g collagen in skin)

31
Q

Give examples of globular and fibrous proteins.

A

= Globular =
enzymes & haemoglobin

= Fibrous =
collagen & keratin

32
Q

What are enzymes?

A

Biological catalysts that increase the rate of reaction (doesn’t get used up)

They are globular proteins with a specific tertiary structure.

33
Q

What are some examples of enzymes?

A

Catalase =
hydrogen peroxide –> water + oxygen

Amylase =
starch –> maltose

Trypsin =
proteins –> peptides

34
Q

What is a substrate?

A

Substance on which an enzyme acts.

It forms the enzymes-substrate complex structure.

35
Q

What is the structure of an enzyme?

A

Enzymes are globular proteins.
Hydrophilic on the surface (hydrophobic parts deep within them) - so they’re soluble.

Enzymes have an active site they attach to the substrate to form the enzyme-substrate complex.

36
Q

What is the induced fit model of enzyme action?

A
  1. Enzyme binds onto substrate.
  2. Tertiary structure of the active site changes and becomes complementary
    It moulds itself tightly around the substrate - ensures the active sight fits perfectly
  3. Temporary bonds are formed - helps catalyse reaction
  4. Bonds are stressed and products are formed.
37
Q

What is the enzyme-substrate complex?

A

When active site attaches to substrate and becomes complementary.

38
Q

How do enzymes increase the rate of reaction?

A

Lowers the activation energy by providing an alternative energy pathway.

Enzymes allow reactions to take place at lower temperatures than normal.

39
Q

What is the activation energy?

A

Minimum amount of energy required for a chemical reaction to take place.

40
Q

Compare the lock & key theory with the induced-fit model.

A

Lock & key theory =
Active site doesn’t change shape when substrate binds.

Induced-fit model =
Tertiary structure of enzyme changes as substrate approaches so active site moulds around substrate.

41
Q

How do products form in an enzymatic reaction?

A

The substrate molecule collides with the active site.

42
Q

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

A

pH
Temperature
Enzyme concentration
Substrate concentration
Inhibitors concentration

43
Q

Describe the effect of pH on the rate of reaction.

A

As the pH moves away from the optimum, the rate decreases.
Bc change in pH changes the CHARGES on the R groups of amino acids. Since H+ ions are donated.
So it changes the IONIC and HYDROGEN bonding between R groups.
Tertiary structure of active site changes, and enzyme has DENATURES.
Active site can no longer become complementary to substrate.
Fewer ES complexes formed.

44
Q

Explain the effect of temperature on the rate of reaction.

A

Increase in temperature increases kinetic energy of molecules - move around more quickly and collide more frequently - more ES - complexes formed - rate of reaction increases.

At higher temperatures, hydrogen / other bonds in enzyme begin to break - changes tertiary structure to change - active site changes - substrate no longer fits in site - enzyme denatured - doesn’t function again.

OPTIMUM temp usually 40 degrees.

45
Q

Describe the effect of enzyme concentration on the rate of reaction.

A

Given that substrate is in excess, rate increases proportionally to enzyme concentration.

Higher enzyme concentration means that more enzymes are available for ES complexes to form, more frequent successful collisions, increasing the rate.

Rate levels off when the maximum number of ES complexes form - when substrate is limiting.

46
Q

Describe the effect of substrate concentration on the rate of reaction.

A

Given that enzyme concentration is fixed, rate increases proportionally to substrate concentration.

Higher substrate concentration means that more substrates are available for ES complexes to form, more frequent successful collisions, increasing the rate.

Rate levels off when the maximum number of ES complexes form - when enzymes are limiting.

47
Q

What conditions are needed for a reaction to take place?

A

The reactants must collide with sufficient energy to break bonds and form the products.

The higher the rate, the more frequent collisions.

The activation energy must be met for the reaction to occur.

48
Q

How is the pH of a solution calculated?

A

Using the formula…

pH = -log₁₀[H⁺]

Substitute the H+ ion concentration into the formula.
A hydrogen ion [H⁺] concentration of 1 x 10⁻⁹ has a pH of 9.

49
Q

Describe competitive inhibitors.

A

Similar shape to substrate = binds to active site.

Doesn’t stop reaction - ES 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 - triggers active site to change shape.

Increasing substrate concentration has no impact on their effect.

51
Q

How do you calculate the rate of reaction from at a single time point?

A

Draw tangent on point.

Calculate gradient of line.

52
Q

What is the initial rate?

A

The rate of reaction at t=0

53
Q

How do you calculate the overall rate of reaction?

A

Change in concentration of product or reaction / time.

Reactants used / Products formed.

54
Q

Why is it advantageous to calculate the initial rate?

A

Represents the maximum rate of reaction before the changes in concentration of reactants or products.

55
Q

Draw a graph showing the effect of temperature and pH on the rate of reaction.

A

= Temperature =
x-axis –> Temperature (°C)
y-axis –> Rate of reaction

Bell-curve shape - the beginning is more slanted.

= pH =
x-axis –> pH
y-axis –> Rate of reaction

A SLIM bell-curve shape.

56
Q

Draw a graph showing the effect of enzyme and substrate concentration on the rate of reaction.

A

= Enzyme & Substrate =
x-axis –> Enzyme/substrate concentration
y-axis –> Rate of reaction

Line increases proportionally, and then stops increasing eventually.
It looks like a hill.

57
Q

Draw an energy level diagram of a metabolic reaction.

A

= Enzymes =
x-axis –> Reaction progress
y-axis –> Free energy

Substrate (reactant) has more free energy than the Products.

The activation energy is the difference between the peak of the curve and the free energy of the substrate.

58
Q

Two proteins have the same number and types of amino acids but different tertiary structures.
Explain why. [2 marks]

A

Different sequence of amino acids OR different primary structure

forms ionic/ hydrogen/ disulphide bonds in different places

creates variation / change in the final 3D shape / tertiary structure.

59
Q

Two proteins have the same number and type of amino acids but different tertiary structures.

Explain why. [2 marks]

A

Different sequence of amino acids / primary structure.

Forms ionic / hydrogen / disulfide bridges in different places, changing the overall shape of the tertiary structure.

60
Q

Describe the structure of proteins [6 marks]

A

> Polymer of amino acids
Joined by peptide bonds
That are formed by condensation

> Primary structure is the sequence/order of amino acids

> Secondary structure is folding of polypeptide chain due to hydrogen bonding - forms alpha helixes / beta pleated sheets.

> Tertiary is 3D folding due to hydrogen, ionic and disulfide bonds.

> Quaternary structure is 2 or more polypeptide chains.

B = Biological Molecules & Cells = (26 decks)

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