AS Booklet 2- Biological Molecules 2

Question 1

What is a protein?

Answer 1

A protein contains the elements carbon, hydrogen, oxygen and nitrogen and occasionally sulphur formed from monomers (amino acids).
Proteins can contain one or more polypeptide chains.

Question 2

What is an amino acid?

Answer 2

An amino acid is a monomer/sub-unit used to make polypeptides such as proteins.
They all contain an amine group (NH2) and carboxylic acid group (COOH) but their R group is different.

Question 3

What is the generalised structure of an amino acid?

Answer 3

R
            |
H2N—C—COOH
            |
           H

Question 4

How many common amino acids are there?

Answer 4

20 different, commonly occurring amino acids.

Question 5

How do you hydrolyse a protein?

Answer 5

• Heat with an acid (e.g. dilute HCl)

* With the specific enzyme (a protease) at its optimum pH and temperature.

Question 6

What are the four structures of proteins?

Answer 6

• Primary Structure:
The sequence of amino acids.

• Secondary Structure:
Alpha double helix or beta-pleated sheets.

• Tertiary Structure:
Folding and coiling of secondary structure. Disulphide bridges, ionic bonds and H bonds allow this to happen.

• Quaternary Structure:
More than one polypeptide chain and sometimes an inorganic/synthetic group (e.g. haemoglobin have a haem group, 2 beta-pleated sheets and 2 alpha double helices).

Question 7

What is a globular protein?

Answer 7

A protein that is soluble and has highly folded and coiled polypeptide chain(s) with a complex tertiary structure.
Enzymes and antibodies are two examples of globular proteins.

Question 8

How can a protein be denatured?

Answer 8

Hydrogen and ionic bonds are broken down by something, such as:
• Temperature above optimum.
• Extreme pH changes.
• Heavy metals
Disulphide bridges are not broken at the temperatures which break H and ionic bonds.

Question 9

Why is it bad for a protein to become denatured?

Answer 9

Because proteins have specific tertiary structures that are suited to their function, and if this tertiary structure changes it can cause the protein to become useless.
For example, when enzymes become denatured, the active site changes shape due to some bonds in the tertiary structure breaking, meaning it cannot catalyse the reactions it is meant to.

Question 10

What is the Biuret test for proteins?

Answer 10

• Add Biuret agent.
• Purple indicates protein is present.
• If solution remains blue, no protein is present.

Question 11

What is an enzyme?

What are the functions of an enzyme?

Answer 11

An enzyme is a protein and biological catalyst.

Regulates biological processes in living organisms.

Question 12

Why and how do enzymes lower activation energy?

How is it beneficial?

Answer 12

Lowering the activation energy means rate of reaction is increased because less energy is required for molecules to react when there is a successful collision.
The energy is lowered due to the enzymes holding the reactants in a way that makes the reaction more likely to happen.

Question 13

What is meant by enzyme specificity?

Answer 13

Enzymes are specific to substrates of complementary shape(or other things) due to the tertiary structure being folded and coiled in a certain way to create a specific active site.
For example, amylase act on a single substrate whereas lipases are specific to chemical bonds.

Question 14

What are the two models of enzyme-substrate complexes?

Answer 14

Lock and Key model:
• Complementary substrate enters active site to creat enzyme-substrate complex.
• Enzyme-product complex as reaction has been catalysed.
• Products leave active site.

Induced Fit model:
• Complementary substrate enters active site.
• This induces the active site to change shape slightly and mould itself around the substrate (forming e-s complex).
• Reaction is catalysed forming an e-p complex.
• Products leave active site.

Question 15

What factors affect the rate of enzyme-catalysed reactions?

Answer 15

• Substrate concentration
• Enzyme concentration
• Temperature
• pH
• Inhibitors

Question 16

How does substrate concentration affect enzyme-catalysed reactions?

Answer 16

An increase in substrate concentration increases rate of reaction (ROR) until constant maximum rate reached (Vmax).

• ROR increases as collisions between substrate and enzyme molecules are more likely.
• ROR levels out as all enzyme active sites are taken up (saturation and Vmax).
• ROR is now limited by concentration of enzymes.
• Only was to increase ROR is to add more enzyme.

Question 17

How does enzyme concentration affect enzyme-catalysed reactions?

Answer 17

• When concentration of substrate is in excess, an increase in enzyme concentration increases ROR.
• More enzyme molecules = more available active sites.
• Increases number of successful collisions between active sites and substrates, forming e-s complexes.
• Directly proportional and line on graph continues at a constant rate (diagonal).

Question 18

How does temperature affect enzyme-catalysed reactions?

Answer 18

• An increase of temperature up to the optimum gives the molecules of both enzymes and substrates more KE and therefore there are more successful collisions forming e-s complexes.
• Increases ROR.
• Optimum temperature
• Past optimum temperature, enzymes denature because their ionic and H bonds in their tertiary structure get broken, meaning active site shape changes and e-s complexes can no longer be formed (as substrate cannot bind to active site).

Question 19

How does pH affect enzyme-catalysed reactions?

Answer 19

Most enzymes have narrow pH range in which they can function.
• Change in pH alters ionic charges on acidic and basic groups.
• H and ionic bonds are broken, tertiary structure changes, active site change so substrate can’t bind and e-s complexes can’t be formed.

Question 20

What are the two types of enzyme inhibitors and how do they affect enzyme-catalysed reactions?

Answer 20

Competitive and non-competitive inhibitors.

Competitive inhibitors compete for the active site as they are complementary in structure to the enzyme and similar in structure to the substrate. This lowers the ROR and it takes longer to reach Vmax.

Non-competitive inhibitors bind elsewhere on the enzyme, not at the active site. This changes the tertiary structure of the enzyme meaning the active site changes and the substrate cannot bind to form e-s complexes. ROR is lowered more than with competitive inhibitors and does not reach Vmax.

Question 21

What are independent, dependent and controlled variables?
What is a control?
Give an example of each from one experiment.

Answer 21

The independent variable is the variable being changed.
The dependent variable is the variable being tested/measured.
Controlled variables are other factors that must remain constant to ensure a fair test.
Any change to the independent variable directly effects the dependent variable.
A control is separate experiment used for comparing the effects of the independent variable on the dependent. The control does not receive treatment/change.

Question 22

What are the two named nucleic acids?

How do they differ from one another?

Answer 22

DNA and RNA.
Deoxyribose nucleic acid and ribose nucleic acid.

Their structure is different. Both have pentose sugars but DNA has Deoxyribose and RNA has Ribose.
DNA has C, T, A and G but RNA has C, U, A and G.
DNA has a phosphate group.

Question 23

What is the structure of DNA?

Answer 23

DNA is a polymer made of polynucleotides.
One polynucleotide is made up of 4 nucleotides.
One nucleotide is made up of a phosphate group, a deoxyribose sugar and a nitrogenous base.

The nucleotides of each strand are joined by phosphodiester bonds, formed in condensation reactions.
The sugar and phosphate form the sugar-phosphate backbone.
The organic nitrogenous based face inwards and are joined to the complementary base on the other strand by weak H bonds (complementary base pairings: A and T, C and G).

Question 24

How is the structure of DNA adapted to its function?

Answer 24

The sugar phosphate backbone gives strength to the alpha double helix, which protects the genetic code (sequence of bases, which codes for proteins).
Each strand of alpha double helix serves as a template for replication and makes the molecule more stable.
The coiling of DNA means compact shape so more information can be stored in smaller spaces. Large molecule = lots of info.
Complementary base-pairing allows info to be replicated accurately.
Weak H bonds give stability and ease for unzipping during replication.

Question 25

How do you do base calculations?

Answer 25

Use complementary base pairs. 
Examples:
28% of organic bases are thymine, what is % of cytosine present?
28% of T means 28% of A.
28 + 28 = 56 
100-56 = 44
44% of DNA is C + G. So 22% = C

Question 26

What is the semi-conservative mechanism of DNA replication?

Answer 26

During replication:
• DNA helipads unwinds alpha double helix, breaks weak H bonds between complementary bases of the two strands.
• Each strand acts as template.
• Free DNA bases align next to exposed bases of each strand.
• DNA nucleotides of each new strand are joined by phosphodiester bonds, formed by condensation reactions catalysed by DNA polymerase to form complementary strands to original strands.
• The one original and one new strand are joined by weak H bonds.
• These two DNA molecules are identical to each other and original DNA strands.
• Each new DNA molecule contains one original strand and one new strand, so replication is semi-conservative.

Question 27

What is the structure of RNA?

Answer 27

A pentose sugar (ribose).
Uracil replaces Thymine to pair with adenine.
mRNA and tRNA are single-stranded.

Question 28

What is the function and structure of mRNA? Where is it found?

Answer 28

Formed in- and therefore found in- the nucleus during transcription and later moves to cytoplasm to ribosomes.
Linear structure with codons (mRNA base triplets).

Involved in protein synthesis. mRNA is the copy of the DNA code, formed as a strand when free RNA nucleotides align with complementary bade pairs on the original DNA strand. Once enough (pre)mRNA has been formed, the mRNA molecule enters the cytoplasm.

Question 29

What is the function and structure of tRNA? Where is it found?

Answer 29

20 different types can be found in the cytoplasm.
It’s got a “clover” shape due to H bonding.
||

Question 30

What is ribosomal RNA? Where is it found?

Answer 30

It is the RNA component that is joined with proteins to form ribosomes.
There are two major rRNAs and lots of proteins combined to make a ribosome.
Found in cytoplasm.

Question 31

What is the structure and function of ATP and ADP?

Answer 31

ATP has an adenine, ribose sugar and three phosphate groups.
ADP has an adenine, ribose sugar and two phosphate groups.

The function of ATP is to give energy to metabolic reactions. It is the main source of energy for metabolic reactions and aids energy transfer in cells

Question 32

How is ATP synthesised?

Answer 32

ATP🔁ADP + Pi

(Pi is inorganic phosphate).
ATP is resynthesised by the condensation of ADP and Pi, using energy from respiration and catalysed by ATP synthase.
ATP is hydrolysed to produce ADP and Pi.

The energy released by the hydrolysis ATP can be coupled/linked to other energy-requiring reactions in cells.
The Pi released during hydrolysis of ATP can be used to phosphorylate other compounds, usually making them more reactive.

Question 33

What are the uses of ATP?

Answer 33

ATP is used to give immediate energy to metabolic reactions.

Question 34

How are amino acids joined together?

Answer 34

By a peptide bond (-CONH-) formed in a condensation reaction. Two amino acids joined together are called a dipeptide.

Question 35

What are the differences between the structure of tRNA and mRNA?

Answer 35

tRNA is clover-shaped and mRNA is linear
mRNA has codons, tRNA has anticodons.
mRNA is single-stranded but tRNA is double-stranded