Proteins Flashcards

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1
Q

What are amino acids

A

The monomers from which proteins are made

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2
Q

What elements are in ALL proteins and amino acids

A

Carbon hydrogen oxygen and nitrogen

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3
Q

What element is in SOME proteins

A

Sulphur

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4
Q

What is the general structure of an amino acid

A

H2N——-C——-COOH
I
H
(Above is R)

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5
Q

What is in the amino acid structure

A

Amine group
Carboxylate group
R group (represents a carbon containing side chain)

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6
Q

What do the 20 amino acids differ only in

A

Their R group

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7
Q

What is a peptide bond

A

Formed by the condensation between 2 amino acids

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8
Q

What are di peptides

A

Formed by the condensation of 2 amino acids
The hydroxyl group from 1 amino acid reacts with a hydrogen from the amine group in the second amino acid to form water
A water is removed in the formation of a peptide bond. A di peptide and a molecule of water is formed

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9
Q

How does a peptide bond form

A

OH. H |
|Condensation
¥. Reaction + H2O

       C———-N
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10
Q

How are polypeptides formed

A

By the condensation of many amino acids

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11
Q

What are the 4 organisations of proteins

A

Primary
Secondary
Tertiary
Quaternary

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12
Q

What is the primary structure of a protein

A

The sequence of amino acids in the protein. This is important as it determines the rest of the structure
Proteins differ from eacjother as their primary structure is different

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13
Q

What is the secondary protein structure

A

The folding of the polypeptide chain into an alpha helix or beta pleated sheet because of hydrogen bonding between the carbonyl and amine amino acids

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14
Q

What is an alpha helix

A

The polypeptide chain is wound round to form a helix. It’s held together by hydrogen bonds

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15
Q

What is a beta pleated sheet

A

The polypeptide chain zig zags back and forward forming a sheet of antiparallel strands. Held by many hydrogen bonds

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16
Q

What is tertiary structure

A

The further folding of the polypeptide chain into a specific 3D shape
The R groups on the amino acids in the polypeptide chains determines how the polypeptide chain folds into the specific 3D shape
Held by hydrogen ionic bonds and disulphide bridges

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17
Q

What is the quaternary structure

A

More than one polypeptide chain
If a protein contains 1 polypeptide chain it doesn’t have a quaternary structure

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18
Q

What is the Biochemical test for proteins

A

Biuret test

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19
Q

What do you do in the biuret test

A

Mix biuret solution which is blue with a sample
If proteins are present then the solution will turn to violet

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20
Q

What are enzymes

A

Biological catalysts

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21
Q

How do they speed up the rate of reaction

A

By lowering the activation energy needed for the chemical reaction
Induced fir causes the active site for f an enzyme to change shape
They do this by helping to align the reactants through the formation of enzyme substrate complexes
Allows reactions that would normally need high temperatures to work at lower temperatures

22
Q

What do enzymes only combine wirh

A

One particular substrate because the enzyme has a specific tertiary structure and so the active site has a specific shape which is only complementary to one type of substrate
Fits into active site to form eS complex

23
Q

What is the difference between the induced fit model and the lock and key model

A

The active site isn’t fully fixed and is flexible in the induced fit model and the substrate induces a change int he shape of the active site making it complimentary. Lock and key model proposes thag enzymes only bind to one specific substrate and rigid shape

24
Q

What are the steps of the induced fit model

A

1) The substrate enters the enzymes active site forming an enzyme substrate complex
2)the binding of the substrate molecule alters the 3D tertiary structure of the active site so it becomes complimentary to the substrate
3)an enzymes substrate complex forms, stressing and bending the bonds causing them to break more easily. This reduces the activation energy
4) When the substrate leaves the active site then returns to its previous shape allowing it to bind to other substrates
It acts as a catalyst by lowering the activation energy

25
Q

What are the factors that affect enzymes

A

Temperature,pH, substrate concentration and enzyme concentration

26
Q

What is the effect of temperature in enzymes

A

As the temperature increases the substrate and enzyme molecules gain kinetic energy causing it to move faster increasing the number of successful collisions forming more enzyme substrate complexes between the substrate and active site increasing the rate of reaction

27
Q

What happens in the effect of temperature as it reaches the optimum

A

As it goes beyond the optimum temperature the enzyme denatures as the hydrogen bonds breaks which alters the specific 3D tertiary structure of the active site so it’s no longer complimentary to the substrate. This means that less enzyme substrate complexes form

28
Q

Why is the rate of reaction not 0 at a temperature of 0•C

A

Because the temperature can still fall below 0 the enzyme will still have some kinetic energy at 0 decrees Celsius

29
Q

What is ph

A

The measure of hydrogen ion concentration

30
Q

What is the effect of pH

A

Above and below the optimum pH the concentration of hydrogen ions starts to decrease. The charge on the R groups of amino acids are altered and hydrogen and ionic bonds in the 3D tertiary structure are broken so it changes. The active site changes shape so it no longer complimentary to the substrate and cant fit. No enzyme substrate complexes form and the rate of reaction decreases either side of the optimum. The enzyme is denatured

31
Q

what is the description of the effect of substrate concentration

A

As the substrate concentration increases the rate of reaction increases then plateaus

32
Q

What is the explanation for substrate concentration

A

The rate of reaction is low at low substrate concentrations as not all of the active site are saturated. The substrate is the limiting factor. As the substrate concentration increases the active sites are filled and the rate of reaction increases due to more successful collisions between enzymes active sites and the substrate. So more enzyme substrate complexes form per second. The substrate is no longer a limiting factor. At high substrate concentrations there is no further rise in the rate of reaction since the enzyme cannot form anymore enzyme substrate complexes as all the active sites are filled. The concentration of enzymes are the limiting factor

33
Q

What is the effect of enzyme concentration

A

Adding more enzyme increases the rate of reaction as more enzyme substrate complexes form. The concentration of enzymes is the limiting factor. At high enzyme concentration there are no free substrate molecules. and the max number of enzyme substrate complexes are formed. The substrate concentration is the limiting factor

34
Q

What are the features of competitive inhibitors

A

Similar in shape to the real substrate
Enter the enzymes active site and prevent the substrate from binding
Not permanently bound

35
Q

Explain why the inhibitor reduces the rate of reaction

A

The inhibitor is similar in shape to the substrate
Enters the active site of the enzyme its a competitive inhibitor
The substrate cannot bind to the active site
Less ES complexes form

36
Q

Explain why a max rate of reaction can be reached with a high conc of substrate in the presence of a competitive inhibitor

A

At high substrate concentrations the chance of an inhibitor molecule entering the active site is very low so the max number of enzyme substrate complexes can still be reached

37
Q

What are the features of a non competitive inhibitor

A

These bind to the enzyme away from the active site
They change the specific tertiary structure and shape of the active site
The enzyme is no longer complimentary so ES complexes cant form

38
Q

Explain how a non competitive inhibitor reduces the rate of reaction of an enzyme

A

The non competitive inhibitor binds to the enzyme NOT tot the active site so they change the tertiary structure and shape of the active site
the active site is no longer complimentary to the substrate so less enzyme substrate complexes form reducing the rate of reaction

39
Q

Explain why by adding substrate you cant reduce the effect of a non competitive inhibitor

A

The active site has been changed on some enzymes permanently reducing the concentration of functioning enzymes
You cant reach the max number of enzyme substrate complexes as without the inhibitor

40
Q

When should you describe how a competitive inhibitor works

A

Mentions a reaction involving an enzyme
Are the molecules a similar shape
Shoe picture of substrate enxt to another molecule

41
Q

What is the effect of pH

A

Above and below the optimum pH the concentration of hydrogen ions start to decrease. The charges on the R groups of amino acids

42
Q

How do you calculate the pH

A

-log [H+]
10

43
Q

What is the contrast between competitive and non competitive inhibitors

A

Competitive inhibitors are a similar shape to the substrate so bind to the active site whereas non competitive inhibitors bind at allosteric binding sites
Competitive inhibitors don’t stop reaction so ES complexes form when inhibitors released where as non competitive inhibitors may permenantly stop the reaction triggering AS to change shape

44
Q

How do you calculate rate of reaction from a graph

A

Calculate gradient of a line of gradient of a tangent to a point

45
Q

How do you calculate rate of reaction from raw data

A

Change in concentration of product/ reactant over time

46
Q

Why is it advantageous to calculate initial rate

A

Represents maximum rate of reaction before concentration of reactants decreases and “end product inhibition”

47
Q

Describe how the structure of a protein depends on the amino acids it contain

A

Determined by the position of R groups.
Primary structure is the sequence of amino acids
Secondary structure def.
Tertiary structure def.
Quaternary structure def.

48
Q

If 2 proteins have the same number and type of AA but diff tertiary structure why?

A

Diff sequence of amino acids which form ionic, hydrogen bonds and disulphide bridges in different places

49
Q

Explain why pepsin can only be an endopeptidass

A

Proteins are polymer that are made up of amino acid monomers which are connected by peptide bonds
The ends of the protein do not have a peptide bond but instead have an amine group on one end and a carboxyl group on the other
The active sit of pepsin has a specific shape. The tertiary structure of the enzyme is complimentary to a peptide bond between amino acids
This means that the ends of the protein can’t fit into the active site
Only the middle of the protein can bind to the enzyme and form an enzyme substrate complex

50
Q

Why are patients given insulin via injections instead of taking a pill

A

If insulin were eaten as a pill it’ll be broken down by protease enzymes in the stomach or the intestine
If some insulin managed to escape digestion it would likely be denatured due to the low pH in the stomach
If insulin survived both these things it wouldnt be small enough to be absorbed in the small intestine into the bloodstream therefore it wouldnt reach body tissues

51
Q
A