Proteins

Question 1

What are amino acids

Answer 1

The monomers from which proteins are made

Question 2

What elements are in ALL proteins and amino acids

Answer 2

Carbon hydrogen oxygen and nitrogen

Question 3

What element is in SOME proteins

Answer 3

Sulphur

Question 4

What is the general structure of an amino acid

Answer 4

H2N——-C——-COOH
I
H
(Above is R)

Question 5

What is in the amino acid structure

Answer 5

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

Question 6

What do the 20 amino acids differ only in

Answer 6

Their R group

Question 7

What is a peptide bond

Answer 7

Formed by the condensation between 2 amino acids

Question 8

What are di peptides

Answer 8

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

Question 9

How does a peptide bond form

Answer 9

OH. H |
|Condensation
¥. Reaction + H2O

       C———-N

Question 10

How are polypeptides formed

Answer 10

By the condensation of many amino acids

Question 11

What are the 4 organisations of proteins

Answer 11

Primary
Secondary
Tertiary
Quaternary

Question 12

What is the primary structure of a protein

Answer 12

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

Question 13

What is the secondary protein structure

Answer 13

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

Question 14

What is an alpha helix

Answer 14

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

Question 15

What is a beta pleated sheet

Answer 15

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

Question 16

What is tertiary structure

Answer 16

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

Question 17

What is the quaternary structure

Answer 17

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

Question 18

What is the Biochemical test for proteins

Answer 18

Biuret test

Question 19

What do you do in the biuret test

Answer 19

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

Question 20

What are enzymes

Answer 20

Biological catalysts

Question 21

How do they speed up the rate of reaction

Answer 21

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

Question 22

What do enzymes only combine wirh

Answer 22

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

Question 23

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

Answer 23

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

Question 24

What are the steps of the induced fit model

Answer 24

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

Question 25

What are the factors that affect enzymes

Answer 25

Temperature,pH, substrate concentration and enzyme concentration

Question 26

What is the effect of temperature in enzymes

Answer 26

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

Question 27

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

Answer 27

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

Question 28

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

Answer 28

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

Question 29

What is ph

Answer 29

The measure of hydrogen ion concentration

Question 30

What is the effect of pH

Answer 30

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

Question 31

what is the description of the effect of substrate concentration

Answer 31

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

Question 32

What is the explanation for substrate concentration

Answer 32

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

Question 33

What is the effect of enzyme concentration

Answer 33

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

Question 34

What are the features of competitive inhibitors

Answer 34

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

Question 35

Explain why the inhibitor reduces the rate of reaction

Answer 35

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

Question 36

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

Answer 36

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

Question 37

What are the features of a non competitive inhibitor

Answer 37

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

Question 38

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

Answer 38

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

Question 39

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

Answer 39

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

Question 40

When should you describe how a competitive inhibitor works

Answer 40

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

Question 41

What is the effect of pH

Answer 41

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

Question 42

How do you calculate the pH

Answer 42

-log [H+] 10

Question 43

What is the contrast between competitive and non competitive inhibitors

Answer 43

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

Question 44

How do you calculate rate of reaction from a graph

Answer 44

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

Question 45

How do you calculate rate of reaction from raw data

Answer 45

Change in concentration of product/ reactant over time

Question 46

Why is it advantageous to calculate initial rate

Answer 46

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

Question 47

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

Answer 47

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

Question 48

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

Answer 48

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

Question 49

Explain why pepsin can only be an endopeptidass

Answer 49

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

Question 50

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

Answer 50

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